Publications - Englander Institute for Precision Medicine

2023

May

Apoptotic cell death in disease-Current understanding of the NCCD 2023. Vitale I, Pietrocola F, Guilbaud E, Aaronson SA, Abrams JM, Adam D, Agostini M, Agostinis P, Alnemri ES, Altucci L, Amelio I, Andrews DW, Aqeilan RI, Arama E, Baehrecke EH, Balachandran S, Bano D, Barlev NA, Bartek J, Bazan NG, Becker C, Bernassola F, Bertrand MJM, Bianchi ME, Blagosklonny MV, Blander JM, Blandino G, Blomgren K, Borner C, Bortner CD, Bove P, Boya P, Brenner C, Broz P, Brunner T, Damgaard RB, Calin GA, Campanella M, Candi E, Carbone M, Carmona-Gutierrez D, Cecconi F, Chan FK, Chen GQ, Chen Q, Chen YH, Cheng EH, Chipuk JE, Cidlowski JA, Ciechanover A, Ciliberto G, Conrad M, Cubillos-Ruiz JR, Czabotar PE, D’Angiolella V, Daugaard M, Dawson TM, Dawson VL, De Maria R, De Strooper B, Debatin KM, Deberardinis RJ, Degterev A, Del Sal G, Deshmukh M, Di Virgilio F, Diederich M, Dixon SJ, Dynlacht BD, El-Deiry WS, Elrod JW, Engeland K, Fimia GM, Galassi C, Ganini C, Garcia-Saez AJ, Garg AD, Garrido C, Gavathiotis E, Gerlic M, Ghosh S, Green DR, Greene LA, Gronemeyer H, Häcker G, Hajnóczky G, Hardwick JM, Haupt Y, He S, Heery DM, Hengartner MO, Hetz C, Hildeman DA, Ichijo H, Inoue S, Jäättelä M, Janic A, Joseph B, Jost PJ, Kanneganti TD, Karin M, Kashkar H, Kaufmann T, Kelly …See abstract for full author list ➔Cell Death Differ. 2023 May;30(5):1097-1154. doi: 10.1038/s41418-023-01153-w. Epub 2023 Apr 26. PMID: 37100955
Radiation therapy improves CAR T cell activity in acute lymphoblastic leukemia. Sugita M, Yamazaki T, Alhomoud M, Martinet J, Latouche JB, Golden E, Boyer O, Van Besien K, Formenti SC, Galluzzi L, Guzman ML.Cell Death Dis. 2023 May 4;14(5):305. doi: 10.1038/s41419-023-05829-6. PMID: 37142568
Distinct cAMP signaling microdomains differentially regulate melanosomal pH and pigmentation. Yusupova M, Zhou D, You J, Gonzalez-Guzman J, Ghanta MB, Pu H, Abdel-Malek Z, Chen Q, Gross SS, D’Orazio J, Ito S, Wakamatsu K, Harris ML, Zippin JH.J Invest Dermatol. 2023 May 2:S0022-202X(23)02044-4. doi: 10.1016/j.jid.2023.04.011. Online ahead of print. PMID: 37142186

April

Soluble adenylyl cyclase contributes to imiquimod-mediated inflammation and is a potential therapeutic target in psoriasis. You J, Reilly MD, Eljalby M, Bareja R, Yusupova M, Vyas NS, Bang J, Ding W, Desman G, Miller LS, Elemento O, Granstein RD, Zippin JH.Exp Dermatol. 2023 Apr 11. doi: 10.1111/exd.14811. Online ahead of print. PMID: 37039485
External Validation of a Prognostic Model of Overall Survival in Men With Chemotherapy-Naïve Metastatic Castration-Resistant Prostate Cancer. Halabi S, Yang Q, Roy A, Luo B, Araujo JC, Logothetis C, Sternberg CN, Armstrong AJ, Carducci MA, Chi KN, de Bono JS, Petrylak DP, Fizazi K, Higano CS, Morris MJ, Rathkopf DE, Saad F, Ryan CJ, Small EJ, Kelly WK.J Clin Oncol. 2023 Apr 11:JCO2202661. doi: 10.1200/JCO.22.02661. Online ahead of print. PMID: 37040594
Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Weinstock JS, Gopakumar J, Burugula BB, Uddin MM, Jahn N, Belk JA, Bouzid H, Daniel B, Miao Z, Ly N, Mack TM, Luna SE, Prothro KP, Mitchell SR, Laurie CA, Broome JG, Taylor KD, Guo X, Sinner MF, von Falkenhausen AS, Kääb S, Shuldiner AR, O’Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Hou L, Lloyd-Jones DM, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Palmer ND, Freedman BI, Bowden DW, Cho MH, DeMeo DL, Vasan RS, Yanek LR, Becker LC, Kardia SLR, Peyser PA, He J, Rienstra M, Van der Harst P, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Cutler MJ, Knight S, Muhlestein JB, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Tracy RP, Konkle BA, Johnsen JM, Wheeler MM, Smith JG, Melander O, Nilsson PM, Custer BS, Duggirala R, Curran JE, Blangero J, McGarvey S, Williams LK, Xiao S, Yang M, Gu CC, Chen YI, Lee WJ, Marcus GM, Kane JP, Pullinger CR, Shoemaker MB, Darbar D, Roden DM, Albert C, Kooperberg C, Zhou Y, Manson JE, Desai P, Johnson AD, Mathias RA; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Blackwell TW, Abecasis GR, Smith AV, Kang HM, Satpathy A…See abstract for full author list ➔Nature. 2023 Apr;616(7958):755-763. doi: 10.1038/s41586-023-05806-1. Epub 2023 Apr 12. PMID: 37046083
Epigenetic escape of immunosurveillance by malignant cell precursors. Galassi C, Galluzzi L.EMBO J. 2023 Apr 13:e114050. doi: 10.15252/embj.2023114050. Online ahead of print. PMID: 37051718
Multi-omic molecular profiling and network biology for precision anaesthesiology: a narrative review. Scarpa JR, Elemento O.Br J Anaesth. 2023 Apr 11:S0007-0912(23)00125-3. doi: 10.1016/j.bja.2023.03.006. Online ahead of print. PMID: 37055274
Bladder cancer organoids as a functional system to model different disease stages and therapy response. Minoli M, Cantore T, Hanhart D, Kiener M, Fedrizzi T, La Manna F, Karkampouna S, Chouvardas P, Genitsch V, Rodriguez-Calero A, Compérat E, Klima I, Gasperini P, Kiss B, Seiler R, Demichelis F, Thalmann GN, Kruithof-de Julio M.Nat Commun. 2023 Apr 18;14(1):2214. doi: 10.1038/s41467-023-37696-2. PMID: 37072390
Interplay of Metabolome and Gut Microbiome in Individuals With Major Depressive Disorder vs Control Individuals. Amin N, Liu J, Bonnechere B, MahmoudianDehkordi S, Arnold M, Batra R, Chiou YJ, Fernandes M, Ikram MA, Kraaij R, Krumsiek J, Newby D, Nho K, Radjabzadeh D, Saykin AJ, Shi L, Sproviero W, Winchester L, Yang Y, Nevado-Holgado AJ, Kastenmüller G, Kaddurah-Daouk R, van Duijn CM.JAMA Psychiatry. 2023 Apr 19:e230685. doi: 10.1001/jamapsychiatry.2023.0685. Online ahead of print. PMID: 37074710
Avelumab First-line Maintenance Therapy for Advanced Urothelial Carcinoma: Comprehensive Clinical Subgroup Analyses from the JAVELIN Bladder 100 Phase 3 Trial. Grivas P, Park SH, Voog E, Caserta C, Gurney H, Bellmunt J, Kalofonos H, Ullén A, Loriot Y, Sridhar SS, Yamamoto Y, Petrylak DP, Sternberg CN, Gupta S, Huang B, Costa N, Laliberte RJ, di Pietro A, Valderrama BP, Powles T.Eur Urol. 2023 Apr 28:S0302-2838(23)02708-2. doi: 10.1016/j.eururo.2023.03.030. Online ahead of print. PMID: 37121850
The genetic determinants of recurrent somatic mutations in 43,693 blood genomes. Weinstock JS, Laurie CA, Broome JG, Taylor KD, Guo X, Shuldiner AR, O’Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Redline S, Cade BE, Gilliland FD, Chen Z, Gauderman WJ, Kumar R, Grammer L, Schleimer RP, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Weiss ST, Lasky-Su J, DeMeo DL, Palmer ND, Freedman BI, Bowden DW, Cho MH, Vasan RS, Johnson AD, Yanek LR, Becker LC, Kardia S, He J, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Manichaikul AW, Konkle BA, Johnsen JM, Wheeler MM, Custer BS, Duggirala R, Curran JE, Blangero J, Gui H, Xiao S, Williams LK, Meyers DA, Li X, Ortega V, McGarvey S, Gu CC, Chen YI, Lee WJ, Shoemaker MB, Darbar D, Roden D, Albert C, Kooperberg C, Desai P, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Mathias R, Natarajan P, Jaiswal S, Reiner AP, Bick AG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium.Sci Adv. 2023 Apr 28;9(17):eabm4945. doi: 10.1126/sciadv.abm4945. Epub 2023 Apr 26. PMID: 37126548
The DNA Damage Response and Inflammation in Cancer. Klapp V, Álvarez-Abril B, Leuzzi G, Kroemer G, Ciccia A, Galluzzi L.Cancer Discov. 2023 Apr 7:OF1-OF25. doi: 10.1158/2159-8290.CD-22-1220. Online ahead of print. PMID: 37026695
ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer. Li D, Zhan Y, Wang N, Tang F, Lee CJ, Bayshtok G, Moore AR, Wong EWP, Pachai MR, Xie Y, Sher J, Zhao JL, Khudoynazarova M, Gopalan A, Chan J, Khurana E, Shepherd P, Navone NM, Chi P, Chen Y.Sci Adv. 2023 Apr 5;9(14):eadc9446. doi: 10.1126/sciadv.adc9446. Epub 2023 Apr 5. PMID: 37018402
Metasurface-enhanced infrared spectroscopy in multiwell format for real-time assaying of live cells. Huang SH, Sartorello G, Shen PT, Xu C, Elemento O, Shvets G.Lab Chip. 2023 Apr 3. doi: 10.1039/d3lc00017f. Online ahead of print. PMID: 37010356
Author Correction: T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Steele MM, Jaiswal A, Delclaux I, Dryg ID, Murugan D, Femel J, Son S, du Bois H, Hill C, Leachman SA, Chang YH, Coussens LM, Anandasabapathy N, Lund AW.Nat Immunol. 2023 Apr;24(4):729. doi: 10.1038/s41590-023-01491-4. PMID: 36932125
Combinatorial treatment rescues tumour-microenvironment-mediated attenuation of MALT1 inhibitors in B-cell lymphomas. Shah SB, Carlson CR, Lai K, Zhong Z, Marsico G, Lee KM, Félix Vélez NE, Abeles EB, Allam M, Hu T, Walter LD, Martin KE, Gandhi K, Butler SD, Puri R, McCleary-Wheeler AL, Tam W, Elemento O, Takata K, Steidl C, Scott DW, Fontan L, Ueno H, Cosgrove BD, Inghirami G, García AJ, Coskun AF, Koff JL, Melnick A, Singh A.Nat Mater. 2023 Apr;22(4):511-523. doi: 10.1038/s41563-023-01495-3. Epub 2023 Mar 16. PMID: 36928381
T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Steele MM, Jaiswal A, Delclaux I, Dryg ID, Murugan D, Femel J, Son S, du Bois H, Hill C, Leachman SA, Chang YH, Coussens LM, Anandasabapathy N, Lund AW.Nat Immunol. 2023 Apr;24(4):664-675. doi: 10.1038/s41590-023-01443-y. Epub 2023 Feb 27. PMID: 36849745
Types of Liquid Biopsies: Understanding the Different Lenses Through Which They Can Detect Cancer. Kasi PM.Oncologist. 2023 Apr 6;28(4):281-282. doi: 10.1093/oncolo/oyad006. PMID: 36848223
Safety Profile of Ipatasertib Plus Abiraterone vs Placebo Plus Abiraterone in Metastatic Castration-resistant Prostate Cancer. Matsubara N, de Bono J, Sweeney C, Chi KN, Olmos D, Sandhu S, Massard C, Garcia J, Chen G, Harris A, Schenkel F, Sane R, Hinton H, Bracarda S, Sternberg CN.Clin Genitourin Cancer. 2023 Apr;21(2):230-237.e1. doi: 10.1016/j.clgc.2023.01.001. Epub 2023 Jan 7. PMID: 36697317
Landscape of prostate-specific membrane antigen heterogeneity and regulation in AR-positive and AR-negative metastatic prostate cancer. Bakht MK, Yamada Y, Ku SY, Venkadakrishnan VB, Korsen JA, Kalidindi TM, Mizuno K, Ahn SH, Seo JH, Garcia MM, Khani F, Elemento O, Long HW, Chaglassian A, Pillarsetty N, Lewis JS, Freedman M, Belanger AP, Nguyen QD, Beltran H.Nat Cancer. 2023 Apr 10. doi: 10.1038/s43018-023-00539-6. Online ahead of print. PMID: 37038004

March

Long-term tolerance to skin commensals is established neonatally through a specialized dendritic cell subgroup. Weckel A, Dhariwala MO, Ly K, Tran VM, Ojewumi OT, Riggs JB, Gonzalez JR, Dwyer LR, Okoro JN, Leech JM, Bacino MS, Cho GD, Merana G, Anandasabapathy N, Kumamoto Y, Scharschmidt TC.Immunity. 2023 Mar 29:S1074-7613(23)00128-0. doi: 10.1016/j.immuni.2023.03.008. Online ahead of print. PMID: 37028427
Management of patients with advanced prostate cancer-metastatic and/or castration-resistant prostate cancer: report of the Advanced Prostate Cancer Consensus Conference (APCCC) 2022. Gillessen S, Bossi A, Davis ID, de Bono J, Fizazi K, James ND, Mottet N, Shore N, Small E, Smith M, Sweeney CJ, Tombal B, Antonarakis ES, Aparicio AM, Armstrong AJ, Attard G, Beer TM, Beltran H, Bjartell A, Blanchard P, Briganti A, Bristow RG, Bulbul M, Caffo O, Castellano D, Castro E, Cheng HH, Chi KN, Chowdhury S, Clarke CS, Clarke N, Daugaard G, De Santis M, Duran I, Eeles R, Efstathiou E, Efstathiou J, Ekeke ON, Evans CP, Fanti S, Feng FY, Fonteyne V, Fossati N, Frydenberg M, George D, Gleave M, Gravis G, Halabi S, Heinrich D, Herrmann K, Higano C, Hofman MS, Horvath LG, Hussain M, Jereczek-Fossa BA, Jones R, Kanesvaran R, Kellokumpu-Lehtinen PL, Khauli RB, Klotz L, Kramer G, Leibowitz R, Logothetis C, Mahal B, Maluf F, Mateo J, Matheson D, Mehra N, Merseburger A, Morgans AK, Morris MJ, Mrabti H, Mukherji D, Murphy DG, Murthy V, Nguyen PL, Oh WK, Ost P, O’Sullivan JM, Padhani AR, Pezaro CJ, Poon DMC, Pritchard CC, Rabah DM, Rathkopf D, Reiter RE, Rubin MA, Ryan CJ, Saad F, Sade JP, Sartor O, Scher HI, Sharifi N, Skoneczna I, Soule H, Spratt DE, Srinivas S, Sternberg CN, Steuber T, Suzuki H, Sydes MR, Taplin ME, Tilki D, Türkeri L, Turco F, Uemura H, Uemura H, Ürün Y, Vale CL, …See abstract for full author list ➔Eur J Cancer. 2023 Mar 3;185:178-215. doi: 10.1016/j.ejca.2023.02.018. Online ahead of print. PMID: 37003085
Back in 3D-a report on Genome Informatics 2022. Hajirasouliha I, Semrau S.Genome Biol. 2023 Mar 28;24(1):57. doi: 10.1186/s13059-023-02870-8. PMID: 36978161
Type I interferon signaling in malignant blasts contributes to treatment efficacy in AML patients. Holicek P, Truxova I, Rakova J, Salek C, Hensler M, Kovar M, Reinis M, Mikyskova R, Pasulka J, Vosahlikova S, Remesova H, Valentova I, Lysak D, Holubova M, Kaspar P, Prochazka J, Kasikova L, Spisek R, Galluzzi L, Fucikova J.Cell Death Dis. 2023 Mar 24;14(3):209. doi: 10.1038/s41419-023-05728-w. PMID: 36964168
Cue: a deep-learning framework for structural variant discovery and genotyping. Popic V, Rohlicek C, Cunial F, Hajirasouliha I, Meleshko D, Garimella K, Maheshwari A.Nat Methods. 2023 Mar 23. doi: 10.1038/s41592-023-01799-x. Online ahead of print. PMID: 36959322
RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Jbara A, Lin KT, Stossel C, Siegfried Z, Shqerat H, Amar-Schwartz A, Elyada E, Mogilevsky M, Raitses-Gurevich M, Johnson JL, Yaron TM, Ovadia O, Jang GH, Danan-Gotthold M, Cantley LC, Levanon EY, Gallinger S, Krainer AR, Golan T, Karni R.Nature. 2023 Mar 22. doi: 10.1038/s41586-023-05820-3. Online ahead of print. PMID: 36949200
p53 regulates the mitochondrial immune checkpoint. Vanpouille-Box C, Galluzzi L.Trends Immunol. 2023 Apr;44(4):245-247. doi: 10.1016/j.it.2023.03.001. Epub 2023 Mar 16. PMID: 36933950
Identification of Novel Genetic Markers for the Risk of Spinal Pathologies: A Genome-Wide Association Study of 2 Biobanks. Bovonratwet P, Kulm S, Kolin DA, Song J, Morse KW, Cunningham ME, Albert TJ, Sandhu HS, Kim HJ, Iyer S, Elemento O, Qureshi SA.J Bone Joint Surg Am. 2023 Mar 16. doi: 10.2106/JBJS.22.00872. Online ahead of print. PMID: 36927824
Autoimmunity to the modified self. Santambrogio L.Science. 2023 Mar 17;379(6637):1092-1093. doi: 10.1126/science.adg3925. Epub 2023 Mar 16. PMID: 36927028
GA4GH Phenopackets: A Practical Introduction. Ladewig MS, Jacobsen JOB, Wagner AH, Danis D, El Kassaby B, Gargano M, Groza T, Baudis M, Steinhaus R, Seelow D, Bechrakis NE, Mungall CJ, Schofield PN, Elemento O, Smith L, McMurry JA, Munoz-Torres M, Haendel MA, Robinson PN.Adv Genet (Hoboken). 2022 Aug 25;4(1):2200016. doi: 10.1002/ggn2.202200016. eCollection 2023 Mar. PMID: 36910590
Immunogenic cell death in cancer: concept and therapeutic implications. Galluzzi L, Kepp O, Hett E, Kroemer G, Marincola FM.J Transl Med. 2023 Mar 2;21(1):162. doi: 10.1186/s12967-023-04017-6. PMID: 36864446
Nadir Prostate-specific Antigen as an Independent Predictor of Survival Outcomes: A Post Hoc Analysis of the PROSPER Randomized Clinical Trial. Hussain M, Sternberg CN, Efstathiou E, Fizazi K, Shen Q, Lin X, Sugg J, Steinberg J, Noerby B, De Giorgi U, Shore ND, Saad F.J Urol. 2023 Mar;209(3):532-539. doi: 10.1097/JU.0000000000003084. Epub 2023 Feb 9. PMID: 36756959

February

Prognostic Value of the Lung Immune Prognosis Index Score for Patients Treated with Immune Checkpoint Inhibitors for Advanced or Metastatic Urinary Tract Carcinoma. Parent P, Auclin E, Patrikidou A, Mezquita L, Martínez Chanzá N, Dumont C, Rodriguez-Vida A, Llacer C, Lozano R, Ratta R, Merseburger AS, Sternberg CN, Baciarello G, Colomba E, Fuerea A, Besse B, Loriot Y, Lavaud P.Cancers (Basel). 2023 Feb 7;15(4):1066. doi: 10.3390/cancers15041066. PMID: 36831409
Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor. Darabedian N, Ji W, Fan M, Lin S, Seo HS, Vinogradova EV, Yaron TM, Mills EL, Xiao H, Senkane K, Huntsman EM, Johnson JL, Che J, Cantley LC, Cravatt BF, Dhe-Paganon S, Stegmaier K, Zhang T, Gray NS, Chouchani ET.Nat Chem Biol. 2023 Feb 23. doi: 10.1038/s41589-023-01273-x. Online ahead of print. PMID: 36823351
A systematic review and meta-analysis of germline BRCA mutations in pancreatic cancer patients identifies global and racial disparities in access to genetic testing. Paiella S, Azzolina D, Gregori D, Malleo G, Golan T, Simeone DM, Davis MB, Vacca PG, Crovetto A, Bassi C, Salvia R, Biankin AV, Casolino R.ESMO Open. 2023 Feb 21;8(2):100881. doi: 10.1016/j.esmoop.2023.100881. Online ahead of print. PMID: 36822114
Obesity promotes breast epithelium DNA damage in women carrying a germline mutation in BRCA1 or BRCA2. Bhardwaj P, Iyengar NM, Zahid H, Carter KM, Byun DJ, Choi MH, Sun Q, Savenkov O, Louka C, Liu C, Piloco P, Acosta M, Bareja R, Elemento O, Foronda M, Dow LE, Oshchepkova S, Giri DD, Pollak M, Zhou XK, Hopkins BD, Laughney AM, Frey MK, Ellenson LH, Morrow M, Spector JA, Cantley LC, Brown KA.Sci Transl Med. 2023 Feb 22;15(684):eade1857. doi: 10.1126/scitranslmed.ade1857. Epub 2023 Feb 22. PMID: 36812344
Darolutamide Plus Androgen-Deprivation Therapy and Docetaxel in Metastatic Hormone-Sensitive Prostate Cancer by Disease Volume and Risk Subgroups in the Phase III ARASENS Trial. Hussain M, Tombal B, Saad F, Fizazi K, Sternberg CN, Crawford ED, Shore N, Kopyltsov E, Kalebasty AR, Bögemann M, Ye D, Cruz F, Suzuki H, Kapur S, Srinivasan S, Verholen F, Kuss I, Joensuu H, Smith MR.J Clin Oncol. 2023 Feb 16:JCO2300041. doi: 10.1200/JCO.23.00041. Online ahead of print. PMID: 36795843
Harnessing transcriptionally driven chromosomal instability adaptation to target therapy-refractory lethal prostate cancer. Dhital B, Santasusagna S, Kirthika P, Xu M, Li P, Carceles-Cordon M, Soni RK, Li Z, Hendrickson RC, Schiewer MJ, Kelly WK, Sternberg CN, Luo J, Lujambio A, Cordon-Cardo C, Alvarez-Fernandez M, Malumbres M, Huang H, Ertel A, Domingo-Domenech J, Rodriguez-Bravo V.Cell Rep Med. 2023 Feb 21;4(2):100937. doi: 10.1016/j.xcrm.2023.100937. Epub 2023 Feb 13. PMID: 36787737
Cellular senescence in the response of HR⁺ breast cancer to radiotherapy and CDK4/6 inhibitors. Klapp V, Buqué A, Bloy N, Sato A, Yamazaki T, Zhou XK, Formenti SC, Galluzzi L, Petroni G.J Transl Med. 2023 Feb 10;21(1):110. doi: 10.1186/s12967-023-03964-4. PMID: 36765430
Nadir Prostate-specific Antigen as an Independent Predictor of Survival Outcomes: A Post Hoc Analysis of the PROSPER Randomized Clinical Trial. Hussain M, Sternberg CN, Efstathiou E, Fizazi K, Shen Q, Lin X, Sugg J, Steinberg J, Noerby B, De Giorgi U, Shore ND, Saad F.J Urol. 2023 Mar;209(3):532-539. doi: 10.1097/JU.0000000000003084. Epub 2023 Feb 9. PMID: 36756959
Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group; Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium.Nature. 2023 Feb;614(7948):E40. doi: 10.1038/s41586-022-05599-9. PMID: 36697832

January

Urine-based multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS. Batra R, Uni R, Akchurin OM, Alvarez-Mulett S, Gómez-Escobar LG, Patino E, Hoffman KL, Simmons W, Whalen W, Chetnik K, Buyukozkan M, Benedetti E, Suhre K, Schenck E, Cho SJ, Choi AMK, Schmidt F, Choi ME, Krumsiek J.Mol Med. 2023 Jan 26;29(1):13. doi: 10.1186/s10020-023-00609-6. PMID: 36703108.
Safety Profile of Ipatasertib Plus Abiraterone vs Placebo Plus Abiraterone in Metastatic Castration-resistant Prostate Cancer. Matsubara N, de Bono J, Sweeney C, Chi KN, Olmos D, Sandhu S, Massard C, Garcia J, Chen G, Harris A, Schenkel F, Sane R, Hinton H, Bracarda S, Sternberg CN.Clin Genitourin Cancer. 2023 Jan 7:S1558-7673(23)00001-0. doi: 10.1016/j.clgc.2023.01.001. Online ahead of print. PMID: 36697317
Population-Level Prevalence of Rare Variants Associated With Atrial Fibrillation and its Impact on Patient Outcomes. Kandola MS, Kulm S, Kim LK, Markowitz SM, Liu CF, Thomas G, Ip JE, Lerman BB, Elemento O, Cheung JW.JACC Clin Electrophysiol. 2023 Jan 11:S2405-500X(22)01054-4. doi: 10.1016/j.jacep.2022.11.022. Online ahead of print. PMID: 36669898
BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A.Science. 2023 Jan 20;379(6629):eabj7412. doi: 10.1126/science.abj7412. Epub 2023 Jan 20. PMID: 36656933
An atlas of substrate specificities for the human serine/threonine kinome. Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC.Nature. 2023 Jan;613(7945):759-766. doi: 10.1038/s41586-022-05575-3. Epub 2023 Jan 11. PMID: 36631611
New prognostic model in patients with advanced urothelial carcinoma treated with second-line immune checkpoint inhibitors. Bamias A, Merseburger A, Loriot Y, James N, Choy E, Castellano D, Lopez-Rios F, Calabrò F, Kramer M, de Velasco G, Zakopoulou R, Tzannis K, Sternberg CN.J Immunother Cancer. 2023 Jan;11(1):e005977. doi: 10.1136/jitc-2022-005977. PMID: 36627145
Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer. Crowley MJP, Bhinder B, Markowitz GJ, Martin M, Verma A, Sandoval TA, Chae CS, Yomtoubian S, Hu Y, Chopra S, Tavarez DA, Giovanelli P, Gao D, McGraw TE, Altorki NK, Elemento O, Cubillos-Ruiz JR, Mittal V.Nat Commun. 2023 Jan 9;14(1):120. doi: 10.1038/s41467-022-35584-9. PMID: 36624093
Meta-hallmarks of aging and cancer. López-Otín C, Pietrocola F, Roiz-Valle D, Galluzzi L, Kroemer G.Cell Metab. 2023 Jan 3;35(1):12-35. doi: 10.1016/j.cmet.2022.11.001. PMID: 36599298
A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study. Barnes J, Brendel M, Gao VR, Rajendran S, Kim J, Li Q, Malmsten JE, Sierra JT, Zisimopoulos P, Sigaras A, Khosravi P, Meseguer M, Zhan Q, Rosenwaks Z, Elemento O, Zaninovic N, Hajirasouliha I.Lancet Digit Health. 2023 Jan;5(1):e28-e40. doi: 10.1016/S2589-7500(22)00213-8. PMID: 36543475

2022

December

A novel immunotherapy prognostic score for patients with pretreated advanced urInary TrAct CArcinoma from the subgroup analysis of the SAUL study: the ITACA Score. Fornarini G, Rebuzzi SE, Buti S, Rescigno P, Merseburger A, Sternberg CN, de Giorgi U, Basso U, Maruzzo M, Giannatempo P, Ponzano M, Giunta EF, Catalano F, Murianni V, Damassi A, Cremante M, Gandini A, Puglisi S, Llaja Obispo MA, Signori A, Banna GL.Minerva Urol Nephrol. 2022 Dec 13. doi: 10.23736/S2724-6051.22.05135-7. Online ahead of print. PMID: 36511379
Spatial omics technologies at multimodal and single cell/subcellular level. Park J, Kim J, Lewy T, Rice CM, Elemento O, Rendeiro AF, Mason CE.Genome Biol. 2022 Dec 13;23(1):256. doi: 10.1186/s13059-022-02824-6. PMID: 36514162
Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review. Brendel M, Su C, Bai Z, Zhang H, Elemento O, Wang F.Genomics Proteomics Bioinformatics. 2022 Dec 14:S1672-0229(22)00166-8. doi: 10.1016/j.gpb.2022.11.011. Online ahead of print. PMID: 36528240
T cell-independent abscopal responses to radiotherapy. Guilbaud E, Yamazaki T, Galluzzi L.Trends Cancer. 2022 Dec 20:S2405-8033(22)00266-7. doi: 10.1016/j.trecan.2022.12.005. Online ahead of print. PMID: 36543690
Whole-genome characterization of myoepithelial carcinomas of the soft tissue. Cyrta J, Rosiene J, Bareja R, Kudman S, Al Zoughbi W, Motanagh S, Wilkes DC, Eng K, Zhang T, Sticca E, Mathew S, Rubin MA, Sboner A, Elemento O, Rubin BP, Imielinski M, Mosquera JM.Cold Spring Harb Mol Case Stud. 2022 Dec 28;8(7):a006227. doi: 10.1101/mcs.a006227. Print 2022 Dec. PMID: 36577525
Modeling development of genitourinary birth defects to understand disruption due to changes in gene dosage. Ruthig VA, Lamb DJ.Am J Clin Exp Urol. 2022 Dec 25;10(6):412-424. eCollection 2022. PMID: 36636694
Management of Patients with Advanced Prostate Cancer. Part I: Intermediate-/High-risk and Locally Advanced Disease, Biochemical Relapse, and Side Effects of Hormonal Treatment: Report of the Advanced Prostate Cancer Consensus Conference 2022. Gillessen S, Bossi A, Davis ID, de Bono J, Fizazi K, James ND, Mottet N, Shore N, Small E, Smith M, Sweeney C, Tombal B, Antonarakis ES, Aparicio AM, Armstrong AJ, Attard G, Beer TM, Beltran H, Bjartell A, Blanchard P, Briganti A, Bristow RG, Bulbul M, Caffo O, Castellano D, Castro E, Cheng HH, Chi KN, Chowdhury S, Clarke CS, Clarke N, Daugaard G, De Santis M, Duran I, Eeles R, Efstathiou E, Efstathiou J, Ngozi Ekeke O, Evans CP, Fanti S, Feng FY, Fonteyne V, Fossati N, Frydenberg M, George D, Gleave M, Gravis G, Halabi S, Heinrich D, Herrmann K, Higano C, Hofman MS, Horvath LG, Hussain M, Alicja Jereczek-Fossa B, Jones R, Kanesvaran R, Kellokumpu-Lehtinen PL, Khauli RB, Klotz L, Kramer G, Leibowitz R, Logothetis CJ, Mahal BA, Maluf F, Mateo J, Matheson D, Mehra N, Merseburger A, Morgans AK, Morris MJ, Mrabti H, Mukherji D, Murphy DG, Murthy V, Nguyen PL, Oh WK, Ost P, O’Sullivan JM, Padhani AR, Pezaro C, Poon DMC, Pritchard CC, Rabah DM, Rathkopf D, Reiter RE, Rubin MA, Ryan CJ, Saad F, Pablo Sade J, Sartor OA, Scher HI, Sharifi N, Skoneczna I, Soule H, Spratt DE, Srinivas S, Sternberg CN, Steuber T, Suzuki H, Sydes MR, Taplin ME, Tilki D, Türkeri L, Turco F, Uemura H, Uemura H, Ürün Y, Vale CL, van Oort I, Vapiwala N, Walz J, Yamoah K, Ye D, Yu EY, Zapatero A, Zilli T, Omlin A.Eur Urol. 2022 Dec 6:S0302-2838(22)02789-0. doi: 10.1016/j.eururo.2022.11.002. Online ahead of print. PMID: 36494221
Analysis of Circulating Tumor DNA to Predict Risk of Recurrence in Patients With Esophageal and Gastric Cancers. Huffman BM, Aushev VN, Budde GL, Chao J, Dayyani F, Hanna D, Botta GP, Catenacci DVT, Maron SB, Krinshpun S, Sharma S, George GV, Malhotra M, Jurdi A, Moshkevich S, Aleshin A, Kasi PM, Klempner SJ.JCO Precis Oncol. 2022 Dec;6:e2200420. doi: 10.1200/PO.22.00420. PMID: 36480779.
Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care. Cuppen E, Elemento O, Rosenquist R, Nikic S, IJzerman M, Zaleski ID, Frederix G, Levin LÅ, Mullighan CG, Buettner R, Pugh TJ, Grimmond S, Caldas C, Andre F, Custers I, Campo E, van Snellenberg H, Schuh A, Nakagawa H, von Kalle C, Haferlach T, Fröhling S, Jobanputra V.JCO Precis Oncol. 2022 Dec;6:e2200245. doi: 10.1200/PO.22.00245. PMID: 36480778
Genetic features and therapeutic relevance of emergent circulating tumor DNA alterations in refractory non-colorectal gastrointestinal cancers. Hsiehchen D, Bucheit L, Yang D, Beg MS, Lim M, Lee SS, Kasi PM, Kaseb AO, Zhu H.Nat Commun. 2022 Dec 3;13(1):7477. doi: 10.1038/s41467-022-35144-1. PMID: 36463294
Author Correction: Unsupervised discovery of tissue architecture in multiplexed imaging. Kim J, Rustam S, Mosquera JM, Randell SH, Shaykhiev R, Rendeiro AF, Elemento O.Nat Methods. 2022 Dec;19(12):1662. doi: 10.1038/s41592-022-01717-7. PMID: 36414761
Unsupervised discovery of tissue architecture in multiplexed imaging. Kim J, Rustam S, Mosquera JM, Randell SH, Shaykhiev R, Rendeiro AF, Elemento O.Nat Methods. 2022 Dec;19(12):1653-1661. doi: 10.1038/s41592-022-01657-2. Epub 2022 Oct 31. PMID: 36316562
Calreticulin surface presentation can promote quality control of hematopoietic stem cells. Galluzzi L, Kroemer G.Trends Immunol. 2022 Dec;43(12):950-952. doi: 10.1016/j.it.2022.10.008. Epub 2022 Oct 25. PMID: 36307308
Metastatic pancreatic neuroendocrine tumors feature elevated T cell infiltration. Greenberg J, Limberg J, Verma A, Kim D, Chen X, Lee YJ, Moore MD, Ullmann TM, Thiesmeyer JW, Loewenstein Z, Chen KJ, Egan CE, Stefanova D, Bareja R, Zarnegar R, Finnerty BM, Scognamiglio T, Du YN, Elemento O, Fahey TJ 3rd, Min IM.JCI Insight. 2022 Dec 8;7(23):e160130. doi: 10.1172/jci.insight.160130. PMID: 36301668

November

The broad spectrum of pathogenic autoreactivity. Santambrogio L, Marrack P.Nat Rev Immunol. 2022 Nov 23:1-2. doi: 10.1038/s41577-022-00812-2. Online ahead of print. PMID: 36418434
The yin/yang balance of the MHC-self–immunopeptidome. Santambrogio L, Franco A.Front Immunol. 2022 Nov 2;13:1035363. doi: 10.3389/fimmu.2022.1035363. eCollection 2022. PMID: 36405763
NK cells and solid tumors: therapeutic potential and persisting obstacles. Tong L, Jiménez-Cortegana C, Tay AHM, Wickström S, Galluzzi L, Lundqvist A.Mol Cancer. 2022 Nov 1;21(1):206. doi: 10.1186/s12943-022-01672-z. PMID: 36319998

October

Exploring anti-androgen therapies in hormone dependent prostate cancer and new therapeutic routes for castration resistant prostate cancer. Harris AE, Metzler VM, Lothion-Roy J, Varun D, Woodcock CL, Haigh DB, Endeley C, Haque M, Toss MS, Alsaleem M, Persson JL, Gudas LJ, Rakha E, Robinson BD, Khani F, Martin LM, Moyer JE, Brownlie J, Madhusudan S, Allegrucci C, James VH, Rutland CS, Fray RG, Ntekim A, de Brot S, Mongan NP, Jeyapalan JN.Front Endocrinol (Lausanne). 2022 Oct 3;13:1006101. doi: 10.3389/fendo.2022.1006101. eCollection 2022. PMID: 36263323
Predicting Inpatient Mortality in Patients with Inflammatory Bowel Disease: a Machine Learning Approach. Charilaou P, Mohapatra S, Doukas S, Kohli M, Radadiya D, Devani K, Broder A, Elemento O, Lukin DJ, Battat R.J Gastroenterol Hepatol. 2022 Oct 18. doi: 10.1111/jgh.16029. Online ahead of print. PMID: 36258306
FORT-1: Phase II/III Study of Rogaratinib Versus Chemotherapy in Patients With Locally Advanced or Metastatic Urothelial Carcinoma Selected Based on FGFR1/3 mRNA Expression. Sternberg CN, Petrylak DP, Bellmunt J, Nishiyama H, Necchi A, Gurney H, Lee JL, van der Heijden MS, Rosenbaum E, Penel N, Pang ST, Li JR, García Del Muro X, Joly F, Pápai Z, Bao W, Ellinghaus P, Lu C, Sierecki M, Coppieters S, Nakajima K, Ishida TC, Quinn DI.J Clin Oncol. 2022 Oct 14:JCO2102303. doi: 10.1200/JCO.21.02303. Online ahead of print. PMID: 36240478
Which traits affect how long patients with advanced prostate cancer live when treated with enzalutamide? De Giorgi U, Hussain M, Shore N, Fizazi K, Tombal B, Penson D, Saad F, Efstathiou E, Madziarska K, Steinberg J, Sugg J, Lin X, Shen Q, Sternberg CN.Future Oncol. 2022 Oct 13. doi: 10.2217/fon-2022-0661. Online ahead of print. PMID: 36226865
Peptide Receptor Radionuclide Therapy in Merkel Cell Carcinoma: A Comprehensive Review. Askari E, Moghadam SZ, Wild D, Delpassand E, Baldari S, Nilica B, Hartrampf PE, Kong G, Grana CM, Walter MA, Capoccetti F, Kasi PM, Strosberg J.J Nucl Med Technol. 2022 Oct 4:jnmt.122.264904. doi: 10.2967/jnmt.122.264904. Online ahead of print. PMID: 36195446
Unsupervised discovery of tissue architecture in multiplexed imaging.
Kim J, Rustam S, Mosquera JM, Randell SH, Shaykhiev R, Rendeiro AF, Elemento O.Nat Methods. 2022 Oct 31. doi: 10.1038/s41592-022-01657-2. Online ahead of print. PMID: 36316562
Editorial: Computational systems biomedicine. Batra R, Baloni P, Alcaraz N, Hauschild AC, Cervera A.Front Genet. 2022 Oct 12;13:1047760. doi: 10.3389/fgene.2022.1047760. eCollection 2022. PMID: 36313421
Calreticulin surface presentation can promote quality control of hematopoietic stem cells.
Galluzzi L, Kroemer G.Trends Immunol. 2022 Oct 25:S1471-4906(22)00229-0. doi: 10.1016/j.it.2022.10.008. Online ahead of print.PMID: 36307308
Metastatic pancreatic neuroendocrine tumors manifest elevated T cell infiltration. Greenberg J, Limberg J, Verma A, Kim D, Chen X, Lee YJ, Moore MD, Ullmann TM, Thiesmeyer JW, Loewenstein Z, Chen KJ, Egan CE, Stefanova D, Bareja R, Zarnegar R, Finnerty BM, Scognamiglio T, Du YN, Elemento O, Fahey Iii TJ, Min IM.JCI Insight. 2022 Oct 27:e160130. doi: 10.1172/jci.insight.160130. Online ahead of print. PMID: 36301668
Emergent impact of lifestyle on tumor progression and response to therapy. Buqué A, Montrose DC, Galluzzi L.Int Rev Cell Mol Biol. 2022;373:ix-xvii. doi: 10.1016/S1937-6448(22)00132-0. PMID: 36283769
Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication. Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, Cohen BM, Kerelsky A, Lin TY, Liberatore KM, Bulaon DK, Van Nest SJ, Koundouros N, Kastenhuber ER, Mercadante MN, Shobana-Ganesh K, He L, Schwartz RE, Chen S, Weinstein H, Elemento O, Piskounova E, Nilsson-Payant BE, Lee G, Trimarco JD, Burke KN, Hamele CE, Chaparian RR, Harding AT, Tata A, Zhu X, Tata PR, Smith CM, Possemato AP, Tkachev SL, Hornbeck PV, Beausoleil SA, Anand SK, Aguet F, Getz G, Davidson AD, Heesom K, Kavanagh-Williamson M, Matthews DA, tenOever BR, Cantley LC, Blenis J, Heaton NS.Sci Signal. 2022 Oct 25;15(757):eabm0808. doi: 10.1126/scisignal.abm0808. Epub 2022 Oct 25. PMID: 36282911
A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. Jang JY, Hwang I, Pan H, Yao J, Alinari L, Imada E, Zanettini C, Kluk M, Wang Y, Lee YK, Lin HV, Huang X, Di Liberto M, Chen Z, Ballman KV, Cantley LC, Marchionni L, Inghirami G, Elemento O, Baiocchi R, Chen-Kiang S, Belvedere S, Zheng H, Paik J.J Clin Invest. 2022 Oct 25:e160767. doi: 10.1172/JCI160767. Online ahead of print. PMID: 36282572
Case report: Metastatic urothelial cancer with an exceptional response to immunotherapy and comprehensive understanding of the tumor and the tumor microenvironment. Sternberg CN, Shin N, Chernyshov K, Calabro F, Cerbone L, Procopio G, Miheecheva N, Sagaradze G, Zaichikova A, Samarina N, Boyko A, Brown JH, Yunusova L, Guevara D, Manohar J, Sigouros M, Al Assaad M, Elemento O, Mosquera JM.Front Oncol. 2022 Oct 31;12:1006017. doi: 10.3389/fonc.2022.1006017. eCollection 2022. PMID: 36387205

September

JAK inhibition shows two faces in prostate cancer. Brady NJ, Barbieri CE.Nat Cancer. 2022 Sep;3(9):1021-1023. doi: 10.1038/s43018-022-00437-3. PMID: 36138136
Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers. Martinez-Fundichely A, Dixon A, Khurana E.Nat Commun. 2022 Sep 26;13(1):5640. doi: 10.1038/s41467-022-32945-2. PMID: 36163358
A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation. Drozdz MM, Doane AS, Alkallas R, Desman G, Bareja R, Reilly M, Bang J, Yusupova M, You J, Eraslan Z, Wang JZ, Verma A, Aguirre K, Kane E, Watson IR, Elemento O, Piskounova E, Merghoub T, Zippin JH.Cell Rep. 2022 Sep 27;40(13):111412. doi: 10.1016/j.celrep.2022.111412. PMID: 36170819
Improved Macro- and Micronutrient Supply for Favorable Growth and Metabolomic Profile with Standardized Parenteral Nutrition Solutions for Very Preterm Infants. Kindt A, Kraus Y, Rasp D, Foerster KM, Ahmidi N, Flemmer AW, Herber-Jonat S, Heinen F, Weigand H, Hankemeier T, Koletzko B, Krumsiek J, Babl J, Hilgendorff A.Nutrients. 2022 Sep 21;14(19):3912. doi: 10.3390/nu14193912. PMID: 36235563
Genetic Implications of Male-Reproductive-Health-Associated Comorbidities. Punjani N, Kang C, Lamb DJ.Turk J Urol. 2022 Sep;48(5):363-374. doi: 10.5152/tud.2022.20463. PMID: 36197143
Liquid biopsies and tumor mutational burden: the cutoff conundrum. Kasi PM.Nat Med. 2022 Sep 12. doi: 10.1038/s41591-022-01999-6. Online ahead of print. PMID: 36097224
Sensing of SARS-CoV-2 by pDCs and their subsequent production of IFN-I contribute to macrophage-induced cytokine storm during COVID-19. Laurent P, Yang C, Rendeiro AF, Nilsson-Payant BE, Carrau L, Chandar V, Bram Y, tenOever BR, Elemento O, Ivashkiv LB, Schwartz RE, Barrat FJ.Sci Immunol. 2022 Sep 9;7(75):eadd4906. doi: 10.1126/sciimmunol.add4906. Epub 2022 Sep 9. PMID: 36083891
Radiation therapy: An old dog learning new tricks. Sato A, Kraynak J, Marciscano AE, Galluzzi L.Methods Cell Biol. 2022;172:xiii-xxiii. doi: 10.1016/S0091-679X(22)00139-X. PMID: 36064230
Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis. Xu X, Wang K, Vera O, Verma A, Jasani N, Bok I, Elemento O, Du D, Yu X, Karreth FA.Cancer Res. 2022 Sep 2;82(17):3016-3031. doi: 10.1158/0008-5472.CAN-22-0283. PMID: 36052492
Immuno-epigenetic escape of cancer stem cells. Galluzzi L, Kroemer G.Nat Immunol. 2022 Sep;23(9):1300-1302. doi: 10.1038/s41590-022-01293-0. PMID: 36002649
Triplet therapy with androgen deprivation, docetaxel, and androgen receptor signalling inhibitors in metastatic castration-sensitive prostate cancer: A meta-analysis. Ciccarese C, Iacovelli R, Sternberg CN, Gillessen S, Tortora G, Fizazi K.Eur J Cancer. 2022 Sep;173:276-284. doi: 10.1016/j.ejca.2022.07.011. Epub 2022 Aug 11. PMID: 35964470
In vivo intervertebral disc mechanical deformation following a treadmill walking “stress test” is inversely related to T1rho relaxation time. Coppock JA, Zimmer NE, Englander ZA, Danyluk ST, Kosinski AS, Spritzer CE, Goode AP, DeFrate LE.Osteoarthritis Cartilage. 2022 Sep 30:S1063-4584(22)00860-3. doi: 10.1016/j.joca.2022.09.008. Online ahead of print. PMID: 36191831
Adaptation to MOMP drives cancer persistence. Guilbaud E, Galluzzi L.Cell Res. 2022 Sep 26. doi: 10.1038/s41422-022-00729-4. Online ahead of print. PMID: 36163426
Cell-intrinsic melanin fails to protect melanocytes from ultraviolet-mutagenesis in the absence of epidermal melanin. Weiss TJ, Crawford ER, Posada V, Rahman H, Liu T, Murphy BM, Arnold TE, Gray S, Hu Z, Hennessey RC, Yu L, D’Orazio JA, Burd CJ, Zippin JH, Grossman D, Burd CE.Pigment Cell Melanoma Res. 2022 Sep 23. doi: 10.1111/pcmr.13070. Online ahead of print. PMID: 36148789
Multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS. Batra R, Whalen W, Alvarez-Mulett S, Gomez-Escobar LG, Hoffman KL, Simmons W, Harrington J, Chetnik K, Buyukozkan M, Benedetti E, Choi ME, Suhre K, Schenck E, Choi AMK, Schmidt F, Cho SJ, Krumsiek J.PLoS Pathog. 2022 Sep 19;18(9):e1010819. doi: 10.1371/journal.ppat.1010819. eCollection 2022 Sep. PMID: 36121875
Standards in semen examination: publishing reproducible and reliable data based on high-quality methodology. Björndahl L, Barratt CLR, Mortimer D, Agarwal A, Aitken RJ, Alvarez JG, Aneck-Hahn N, Arver S, Baldi E, Bassas L, Boitrelle F, Bornman R, Carrell DT, Castilla JA, Cerezo Parra G, Check JH, Cuasnicu PS, Darney SP, de Jager C, De Jonge CJ, Drevet JR, Drobnis EZ, Du Plessis SS, Eisenberg ML, Esteves SC, Evgeni EA, Ferlin A, Garrido N, Giwercman A, Goovaerts IGF, Haugen TB, Henkel R, Henningsohn L, Hofmann MC, Hotaling JM, Jedrzejczak P, Jouannet P, Jørgensen N, Kirkman Brown JC, Krausz C, Kurpisz M, Kvist U, Lamb DJ, Levine H, Loveland KL, McLachlan RI, Mahran A, Maree L, Martins da Silva S, Mbizvo MT, Meinhardt A, Menkveld R, Mortimer ST, Moskovtsev S, Muller CH, Munuce MJ, Muratori M, Niederberger C, O’Flaherty C, Oliva R, Ombelet W, Pacey AA, Palladino MA, Ramasamy R, Ramos L, Rives N, Roldan ER, Rothmann S, Sakkas D, Salonia A, Sánchez-Pozo MC, Sapiro R, Schlatt S, Schlegel PN, Schuppe HC, Shah R, Skakkebæk NE, Teerds K, Toskin I, Tournaye H, Turek PJ, van der Horst G, Vazquez-Levin M, Wang C, Wetzels A, Zeginiadou T, Zini A.Hum Reprod. 2022 Sep 16:deac189. doi: 10.1093/humrep/deac189. Online ahead of print. PMID: 36112046

August

Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations. Ashley S. Doane and Olivier Elemento. August 2022. PMID: 35609422
A Knock-in Mouse Model of Thymoma with the GTF2I L424H Mutation. He Y, Kim IK, Bian J, Polyzos A, Di Giammartino DC, Zhang Y, Luo J, Hernandez MO, Kedei N, Cam M, Borczuk AC, Lee T, Han Y, Conner EA, Wong MMF, Tillo DC, Umemura S, Chen V, Ruan L, White JB, Miranda IC, Awasthi PP, Altorki NK, Divakar P, Elemento O, Apostolou E, Giaccone G.J Thorac Oncol. 2022 Aug 29:S1556-0864(22)01550-7. doi: 10.1016/j.jtho.2022.08.008. Online ahead of print. PMID: 36049655
Acid Sphingomyelinase-Ceramide Induced Vascular Injury Determines Colorectal Cancer Stem Cell Fate. Li C, Klingler S, Bodo S, Cheng J, Pan Y, Adileh M, Martin ML, Fuller J, Feldman R, Michel A, Zhang Z, Fuks Z, Kolesnick R.Cell Physiol Biochem. 2022 Aug 31;56(4):436-448. doi: 10.33594/000000562. PMID: 36037065
Characterization of Genetic Risk of End-Stage Knee Osteoarthritis Treated with Total Knee Arthroplasty: A Genome-Wide Association Study. Kulm S, Kolin DA, Langhans MT, Kaidi AC, Elemento O, Bostrom MP, Shen TS.J Bone Joint Surg Am. 2022 Aug 23. doi: 10.2106/JBJS.22.00364. Online ahead of print. PMID: 36000784
PDIA3 epitope-driven immune autoreactivity contributes to hepatic damage in type 2 diabetes. Clement CC, Osan J, Buque A, Nanaware PP, Chang YC, Perino G, Shetty M, Yamazaki T, Tsai WL, Urbanska AM, Calvo-Calle JM, Ramsamooj S, Ramsamooj S, Vergani D, Mieli-Vergani G, Terziroli Beretta-Piccoli B, Gadina M, Montagna C, Goncalves MD, Sallusto F, Galluzzi L, Soni RK, Stern LJ, Santambrogio L.Sci Immunol. 2022 Aug 12;7(74):eabl3795. doi: 10.1126/sciimmunol.abl3795. Epub 2022 Aug 19. PMID: 35984892
Endothelial-leukemia interactions remodel drug responses uncovering T-ALL vulnerabilities. Cappelli LV, Fiore D, Phillip JM, Yoffe L, Di Giacomo F, Chiu W, Hu Y, Kayembe C, Ginsberg M, Consolino L, Barcia Durán JG, Zamponi N, Melnick AM, Boccalatte F, Tam W, Elemento O, Chiaretti S, Guarini AR, Foà R, Cerchietti L, Rafii S, Inghirami GG.Blood. 2022 Aug 18:blood.2022015414. doi: 10.1182/blood.2022015414. Online ahead of print. PMID: 35981563
GLI1-Rearranged Enteric Tumor: Expanding the Spectrum of Gastrointestinal Neoplasms with GLI1 gene fusions. Jessurun J, Orr C, McNulty SN, Hagen CE, Alnajar H, Wilkes D, Kudman S, Al Assaad M, Dorsaint P, Ohara K, He F, Chu K, Yin YM, Xiang JZ, Qin L, Sboner A, Elemento O, Yantiss RK, Graham RP, Poizat F, Mosquera JM.Am J Surg Pathol. 2022 Aug 15. doi: 10.1097/PAS.0000000000001950. Online ahead of print. PMID: 35968961
Next generation patient derived tumor organoids. Podaza E, Kuo HH, Nguyen J, Elemento O, Martin ML.Transl Res. 2022 Aug 12:S1931-5244(22)00176-1. doi: 10.1016/j.trsl.2022.08.003. Online ahead of print. PMID: 35964899
Publisher Correction: Recurrent somatic mutations as predictors of immunotherapy response. Gajic ZZ, Deshpande A, Legut M, Imieliński M, Sanjana NE.Nat Commun. 2022 Aug 5;13(1):4558. doi: 10.1038/s41467-022-32460-4. PMID: 35931739
Efficient detection and assembly of non-reference DNA sequences with synthetic long reads. Meleshko D, Yang R, Marks P, Williams S, Hajirasouliha I.Nucleic Acids Res. 2022 Aug 4:gkac653. doi: 10.1093/nar/gkac653. Online ahead of print. PMID: 35924489

July

Using Circulating Tumor DNA in Colorectal Cancer: Current and Evolving Practices. Malla M, Loree JM, Kasi PM, Parikh AR.J Clin Oncol. 2022 Jul 15:JCO2102615. doi: 10.1200/JCO.21.02615. Online ahead of print. PMID: 35839443
Reply to F. Dayyani et al. Kasi PM, Fehringer G, Aleshin A, Kopetz S.JCO Precis Oncol. 2022 Jul;6:e2200275. doi: 10.1200/PO.22.00275. PMID: 35834757
The landscape of metabolic brain alterations in Alzheimer’s disease. Batra R, Arnold M, Wörheide MA, Allen M, Wang X, Blach C, Levey AI, Seyfried NT, Ertekin-Taner N, Bennett DA, Kastenmüller G, Kaddurah-Daouk RF, Krumsiek J; Alzheimer’s Disease Metabolomics Consortium (ADMC).Alzheimers Dement. 2022 Jul 13. doi: 10.1002/alz.12714. Online ahead of print. PMID: 35829654
Recurrent somatic mutations as predictors of immunotherapy response. Gajic ZZ, Deshpande A, Legut M, Imieliński M, Sanjana NE.Nat Commun. 2022 Jul 8;13(1):3938. doi: 10.1038/s41467-022-31055-3. PMID: 35803911
Integrative metabolomic and proteomic signatures define clinical outcomes in severe COVID-19. Buyukozkan M, Alvarez-Mulett S, Racanelli AC, Schmidt F, Batra R, Hoffman KL, Sarwath H, Engelke R, Gomez-Escobar L, Simmons W, Benedetti E, Chetnik K, Zhang G, Schenck E, Suhre K, Choi JJ, Zhao Z, Racine-Brzostek S, Yang HS, Choi ME, Choi AMK, Cho SJ, Krumsiek J.iScience. 2022 Jul 15;25(7):104612. doi: 10.1016/j.isci.2022.104612. Epub 2022 Jun 17. PMID: 35756895
Darolutamide and survival in metastatic, hormone-sensitive prostate cancer: a patient and caregiver perspective and plain language summary of the ARASENS trial. Smith MR, Hussain M, Saad F, Fizazi K, Sternberg CN, Crawford D, Manarite J, Muslin D, Farrington T, Tombal B.Future Oncol. 2022 Jul;18(21):2585-2597. doi: 10.2217/fon-2022-0433. Epub 2022 Jun 3. PMID: 35656777
Statin and metformin use and outcomes in patients with castration-resistant prostate cancer treated with enzalutamide: A meta-analysis of AFFIRM, PREVAIL and PROSPER. Joshua AM, Armstrong A, Crumbaker M, Scher HI, de Bono J, Tombal B, Hussain M, Sternberg CN, Gillessen S, Carles J, Fizazi K, Lin P, Duggan W, Sugg J, Russell D, Beer TM.Eur J Cancer. 2022 Jul;170:285-295. doi: 10.1016/j.ejca.2022.04.005. Epub 2022 May 26. PMID: 35643841
The regulation of CD73 in non-small cell lung cancer. Han Y, Lee T, He Y, Raman R, Irizarry A, Martin ML, Giaccone G.Eur J Cancer. 2022 Jul;170:91-102. doi: 10.1016/j.ejca.2022.04.025. Epub 2022 May 19. PMID: 35598361
Effects of metformin and statins on outcomes in men with castration-resistant metastatic prostate cancer: Secondary analysis of COU-AA-301 and COU-AA-302. Wilson BE, Armstrong AJ, de Bono J, Sternberg CN, Ryan CJ, Scher HI, Smith MR, Rathkopf D, Logothetis CJ, Chi KN, Jones RJ, Saad F, De Porre P, Tran N, Hu P, Gillessen S, Carles J, Fizazi K, Joshua AM.Eur J Cancer. 2022 Jul;170:296-304. doi: 10.1016/j.ejca.2022.03.042. Epub 2022 May 11. PMID: 35568679
An Autologous Dendritic Cell Vaccine Promotes Anticancer Immunity in Patients with Ovarian Cancer with Low Mutational Burden and Cold Tumors. Fucikova J, Hensler M, Kasikova L, Lanickova T, Pasulka J, Rakova J, Drozenova J, Fredriksen T, Hraska M, Hrnciarova T, Sochorova K, Rozkova D, Sojka L, Dundr P, Laco J, Brtnicky T, Praznovec I, Halaska MJ, Rob L, Ryska A, Coosemans A, Vergote I, Cibula D, Bartunkova J, Galon J, Galluzzi L, Spisek R.Clin Cancer Res. 2022 Jul 15;28(14):3053-3065. doi: 10.1158/1078-0432.CCR-21-4413. PMID: 35536547
Mitochondrial control of inflammation. Marchi S, Guilbaud E, Tait SWG, Yamazaki T, Galluzzi L.Nat Rev Immunol. 2022 Jul 25:1-15. doi: 10.1038/s41577-022-00760-x. Online ahead of print. PMID: 35879417

June

A multidisciplinary approach to optimize primary prostate cancer biobanking. Cai PY, Asad M, Augello MA, Martin L, Louie C, Basourakos SP, Gaffney CD, Shoag J, Tu JJ, Khani F, Mosquera JM, Loda M, Scherr DS, Barbieri CE, Robinson BD.Urol Oncol. 2022 Jun;40(6):271.e1-271.e7. doi: 10.1016/j.urolonc.2022.03.015. Epub 2022 Apr 28. PMID: 35490048
Plain language summary of results from the JAVELIN Bladder 100 study: avelumab maintenance treatment for advanced urothelial cancer. Powles T, Park SH, Voog E, Caserta C, Valderrama BP, Gurney H, Kalofonos H, Radulovic S, Demey W, Ullén A, Loriot Y, Sridhar SS, Tsuchiya N, Kopyltsov E, Sternberg CN, Bellmunt J, Aragon-Ching JB, Petrylak DP, Laliberte RJ, Huang B, Costa N, Blake-Haskins JA, Grivas P.Future Oncol. 2022 Jun;18(19):2361-2371. doi: 10.2217/fon-2021-1631. Epub 2022 Apr 13. PMID: 35416053
Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer. Raman R, Villefranc JA, Ullmann TM, Thiesmeyer J, Anelli V, Yao J, Hurley JR, Pauli C, Bareja R, Wha Eng K, Dorsaint P, Wilkes DC, Beg S, Kudman S, Shaw R, Churchill M, Ahmed A, Keefer L, Misner I, Nichol D, Gumpeni N, Scognamiglio T, Rubin MA, Grandori C, Solomon JP, Song W, Mosquera JM, Dephoure N, Sboner A, Elemento O, Houvras Y.J Exp Med. 2022 Jun 6;219(6):e20210390. doi: 10.1084/jem.20210390. Epub 2022 May 5. PMID: 35510953
Circulating Tumor DNA in Identifying Resistant Sub-Clones Post EGFR Blockade: Implications for EGFR Rechallenge.
Chennamadhavuni A, Kasi PM.Front Oncol. 2022 Jun 28;12:847299. doi: 10.3389/fonc.2022.847299. eCollection 2022. PMID: 35837097
Variational autoencoders learn transferrable representations of metabolomics data. Gomari DP, Schweickart A, Cerchietti L, Paietta E, Fernandez H, Al-Amin H, Suhre K, Krumsiek J.Commun Biol. 2022 Jun 30;5(1):645. doi: 10.1038/s42003-022-03579-3. PMID: 35773471
Mitonuclear genotype remodels the metabolic and microenvironmental landscape of Hürthle cell carcinoma. Ganly I, Liu EM, Kuo F, Makarov V, Dong Y, Park J, Gong Y, Gorelick AN, Knauf JA, Benedetti E, Tait-Mulder J, Morris LGT, Fagin JA, Intlekofer AM, Krumsiek J, Gammage PA, Ghossein R, Xu B, Chan TA, Reznik E.Sci Adv. 2022 Jun 24;8(25):eabn9699. doi: 10.1126/sciadv.abn9699. Epub 2022 Jun 22. PMID: 35731870
Unmet Needs in Oncology Clinical Research and Treatment in Africa: Focus on Ghana. Roberts LR, Rivers BM, Yates CC, Newman LA, Sarkodie BD, Davis MB, Asare-Aboagye Y, Adjei AA, Harris AE, Awuah B.Oncologist. 2022 Jun 21:oyac109. doi: 10.1093/oncolo/oyac109. Online ahead of print. PMID: 35726905
Transcriptional and metabolic remodeling in clear cell renal cell carcinoma caused by ATF4 activation and the integrated stress response (ISR). van der Mijn JC, Chen Q, Laursen KB, Khani F, Wang X, Dorsaint P, Sboner A, Gross SS, Nanus DM, Gudas LJ.Mol Carcinog. 2022 Jun 21. doi: 10.1002/mc.23437. Online ahead of print. PMID: 35726553
Matching-adjusted indirect treatment comparison of the efficacy of enzalutamide versus apalutamide for the treatment of nonmetastatic castration-resistant prostate cancer. Tombal B, Sternberg CN, Hussain M, Ganguli A, Li Y, Sandin R, Bhadauria H, Oh M, Saad F.ESMO Open. 2022 Jun;7(3):100510. doi: 10.1016/j.esmoop.2022.100510. Epub 2022 Jun 15. PMID: 35714477
The GA4GH Phenopacket schema defines a computable representation of clinical data. Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C; GAGH Phenopacket Modeling Consortium, Haendel MA, Robinson PN.Nat Biotechnol. 2022 Jun;40(6):817-820. doi: 10.1038/s41587-022-01357-4. PMID: 35705716
Nicotinamide drives T cell activation in the mammary tumor microenvironment. Hu Y, Bloy N, Elemento O, Buqué A.J Transl Med. 2022 Jun 3;20(1):251. doi: 10.1186/s12967-022-03454-z. PMID: 35659314
Weakly-supervised tumor purity prediction from frozen H&E stained slides. Brendel M, Getseva V, Assaad MA, Sigouros M, Sigaras A, Kane T, Khosravi P, Mosquera JM, Elemento O, Hajirasouliha I.EBioMedicine. 2022 Jun;80:104067. doi: 10.1016/j.ebiom.2022.104067. Epub 2022 May 26. PMID: 35644123
Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. Schad SE, Chow A, Mangarin L, Pan H, Zhang J, Ceglia N, Caushi JX, Malandro N, Zappasodi R, Gigoux M, Hirschhorn D, Budhu S, Amisaki M, Arniella M, Redmond D, Chaft J, Forde PM, Gainor JF, Hellmann MD, Balachandran V, Shah S, Smith KN, Pardoll D, Elemento O, Wolchok JD, Merghoub T.J Exp Med. 2022 Jun 6;219(6):e20212169. doi: 10.1084/jem.20212169. Epub 2022 May 23. PMID: 35604411

May

Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets. Tang F, Xu D, Wang S, Wong CK, Martinez-Fundichely A, Lee CJ, Cohen S, Park J, Hill CE, Eng K, Bareja R, Han T, Liu EM, Palladino A, Di W, Gao D, Abida W, Beg S, Puca L, Meneses M, de Stanchina E, Berger MF, Gopalan A, Dow LE, Mosquera JM, Beltran H, Sternberg CN, Chi P, Scher HI, Sboner A, Chen Y, Khurana E.Science. 2022 May 27;376(6596):eabe1505. doi: 10.1126/science.abe1505. Epub 2022 May 27. PMID: 35617398
Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. Schad SE, Chow A, Mangarin L, Pan H, Zhang J, Ceglia N, Caushi JX, Malandro N, Zappasodi R, Gigoux M, Hirschhorn D, Budhu S, Amisaki M, Arniella M, Redmond D, Chaft J, Forde PM, Gainor JF, Hellmann MD, Balachandran V, Shah S, Smith KN, Pardoll D, Elemento O, Wolchok JD, Merghoub T.J Exp Med. 2022 Jun 6;219(6):e20212169. doi: 10.1084/jem.20212169. Epub 2022 May 23. PMID: 35604411
The regulation of CD73 in non-small cell lung cancer. Han Y, Lee T, He Y, Raman R, Irizarry A, Martin ML, Giaccone G.Eur J Cancer. 2022 May 19;170:91-102. doi: 10.1016/j.ejca.2022.04.025. Online ahead of print. PMID: 35598361
The WHO 2022 landscape of papillary and chromophobe renal cell carcinoma. Lobo J, Ohashi R, Amin MB, Berney DM, Compérat EM, Cree IA, Gill AJ, Hartmann A, Menon S, Netto GJ, Raspollini MR, Rubin MA, Tan PH, Tickoo SK, Tsuzuki T, Turajlic S, Zhou M, Srigley JR, Moch H.Histopathology. 2022 May 21. doi: 10.1111/his.14700. Online ahead of print. PMID: 35596618
Effects of metformin and statins on outcomes in men with castration-resistant metastatic prostate cancer: Secondary analysis of COU-AA-301 and COU-AA-302. Wilson BE, Armstrong AJ, de Bono J, Sternberg CN, Ryan CJ, Scher HI, Smith MR, Rathkopf D, Logothetis CJ, Chi KN, Jones RJ, Saad F, De Porre P, Tran N, Hu P, Gillessen S, Carles J, Fizazi K, Joshua AM.Eur J Cancer. 2022 May 11:S0959-8049(22)00205-2. doi: 10.1016/j.ejca.2022.03.042. Online ahead of print. PMID: 35568679
The lactate-NAD⁺ axis activates cancer-associated fibroblasts by downregulating p62. Linares JF, Cid-Diaz T, Duran A, Osrodek M, Martinez-Ordoñez A, Reina-Campos M, Kuo HH, Elemento O, Martin ML, Cordes T, Thompson TC, Metallo CM, Moscat J, Diaz-Meco MT.Cell Rep. 2022 May 10;39(6):110792. doi: 10.1016/j.celrep.2022.110792. PMID: 35545049
An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes. Jaiswal A, Verma A, Dannenfelser R, Melssen M, Tirosh I, Izar B, Kim TG, Nirschl CJ, Devi KSP, Olson WC Jr, Slingluff CL Jr, Engelhard VH, Garraway L, Regev A, Minkis K, Yoon CH, Troyanskaya O, Elemento O, Suárez-Fariñas M, Anandasabapathy N.Cancer Cell. 2022 May 9;40(5):524-544.e5. doi: 10.1016/j.ccell.2022.04.005. Epub 2022 May 9. PMID: 35537413
Inflammatory responses in the placenta upon SARS-CoV-2 infection late in pregnancy. Argueta LB, Lacko LA, Bram Y, Tada T, Carrau L, Rendeiro AF, Zhang T, Uhl S, Lubor BC, Chandar V, Gil C, Zhang W, Dodson BJ, Bastiaans J, Prabhu M, Houghton S, Redmond D, Salvatore CM, Yang YJ, Elemento O, Baergen RN, tenOever BR, Landau NR, Chen S, Schwartz RE, Stuhlmann H.iScience. 2022 May 20;25(5):104223. doi: 10.1016/j.isci.2022.104223. Epub 2022 Apr 11. PMID: 35434541
Myeloid-Derived Suppressor Cells and Radiotherapy. Jiménez-Cortegana C, Galassi C, Klapp V, Gabrilovich DI, Galluzzi L.Cancer Immunol Res. 2022 May 3;10(5):545-557. doi: 10.1158/2326-6066.CIR-21-1105. PMID: 35426936
Call for Adoption of Synchronized Biweekly Dosing of Anti-EGFR Agent Cetuximab: Implications for Patients with Metastatic Colorectal Cancer, and Squamous Cell Carcinoma of the Head and Neck. Kasi PM.Oncologist. 2022 May 6;27(5):336-337. doi: 10.1093/oncolo/oyac070. PMID: 35403691
Loss of function mutations in CDKN1A are permissive for APOBEC3-induced mutagenesis in urothelial carcinoma. Liu W, Faltas BM.Am J Cancer Res. 2022 May 15;12(5):2419-2421. eCollection 2022. PMID: 35693069
Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay. Orlando F, Romanel A, Trujillo B, Sigouros M, Wetterskog D, Quaini O, Leone G, Xiang JZ, Wingate A, Tagawa S, Jayaram A, Linch M; PEACE Consortium, Jamal-Hanjani M, Swanton C, Rubin MA, Wyatt AW, Beltran H, Attard G, Demichelis F.NAR Cancer. 2022 May 27;4(2):zcac016. doi: 10.1093/narcan/zcac016. eCollection 2022 Jun. PMID: 35664542
Molecular Determinants Regulating the Plasticity of the MHC Class II Immunopeptidome. Santambrogio L.Front Immunol. 2022 May 16;13:878271. doi: 10.3389/fimmu.2022.878271. eCollection 2022. PMID: 35651601
Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing. Deshpande AS, Ulahannan N, Pendleton M, Dai X, Ly L, Behr JM, Schwenk S, Liao W, Augello MA, Tyer C, Rughani P, Kudman S, Tian H, Otis HG, Adney E, Wilkes D, Mosquera JM, Barbieri CE, Melnick A, Stoddart D, Turner DJ, Juul S, Harrington E, Imieliński M.Nat Biotechnol. 2022 May 30. doi: 10.1038/s41587-022-01289-z. Online ahead of print. PMID: 35637420
Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations. Doane AS, Elemento O.Curr Opin Genet Dev. 2022 May 21;75:101919. doi: 10.1016/j.gde.2022.101919. Online ahead of print. PMID: 35609422
WHO 2022 landscape of papillary and chromophobe renal cell carcinoma. Lobo J, Ohashi R, Amin MB, Berney DM, Compérat EM, Cree IA, Gill AJ, Hartmann A, Menon S, Netto GJ, Raspollini MR, Rubin MA, Tan PH, Tickoo SK, Tsuzuki T, Turajlic S, Zhou M, Srigley JR, Moch H.Histopathology. 2022 May 21. doi: 10.1111/his.14700. Online ahead of print. PMID: 35596618

April

Plain language summary of results from the JAVELIN Bladder 100 study: avelumab maintenance treatment for advanced urothelial cancer. Powles T, Park SH, Voog E, Caserta C, Valderrama BP, Gurney H, Kalofonos H, Radulovic S, Demey W, Ullén A, Loriot Y, Sridhar SS, Tsuchiya N, Kopyltsov E, Sternberg CN, Bellmunt J, Aragon-Ching JB, Petrylak DP, Laliberte RJ, Huang B, Costa N, Blake-Haskins JA, Grivas P.Future Oncol. 2022 Apr 13. doi: 10.2217/fon-2021-1631. Online ahead of print. PMID: 35416053
Call for Adoption of Synchronized Biweekly Dosing of Anti-EGFR Agent Cetuximab: Implications for Patients with Metastatic Colorectal Cancer, and Squamous Cell Carcinoma of the Head and Neck. Kasi PM.Oncologist. 2022 Apr 11:oyac070. doi: 10.1093/oncolo/oyac070. Online ahead of print. PMID: 35403691
Molecular and Pharmacological Bladder Cancer Therapy Screening: Discovery of Clofarabine as a Highly Active Compound. Ertl IE, Lemberger U, Ilijazi D, Hassler MR, Bruchbacher A, Brettner R, Kronabitter H, Gutmann M, Vician P, Zeitler G, Koren A, Lardeau CH, Mohr T, Haitel A, Compérat E, Oszwald A, Wasinger G, Clozel T, Elemento O, Kubicek S, Berger W, Shariat SF.Eur Urol. 2022 Apr 4:S0302-2838(22)01678-5. doi: 10.1016/j.eururo.2022.03.009. Online ahead of print. PMID: 35393162
Predictive biomarkers for survival benefit with ramucirumab in urothelial cancer in the RANGE trial. van der Heijden MS, Powles T, Petrylak D, de Wit R, Necchi A, Sternberg CN, Matsubara N, Nishiyama H, Castellano D, Hussain SA, Bamias A, Gakis G, Lee JL, Tagawa ST, Vaishampayan U, Aragon-Ching JB, Eigl BJ, Hozak RR, Rasmussen ER, Xia MS, Rhodes R, Wijayawardana S, Bell-McGuinn KM, Aggarwal A, Drakaki A.Nat Commun. 2022 Apr 6;13(1):1878.doi: 10.1038/s41467-022-29441-y. PMID: 35388003
Global evolution of the tumor microenvironment associated with progression from preinvasive invasive to invasive human lung adenocarcinoma. Altorki NK, Borczuk AC, Harrison S, Groner LK, Bhinder B, Mittal V, Elemento O, McGraw TE.Cell Rep. 2022 Apr 5;39(1):110639.doi: 10.1016/j.celrep.2022.110639. PMID: 35385730
ASO Visual Abstract: RET Fusion-Positive Papillary Thyroid Cancers are Associated with a More Aggressive Phenotype. Ullmann TM, Thiesmeyer JW, Lee YJ, Beg S, Mosquera JM, Elemento O, Fahey TJ 3rd, Scognamiglio T, Houvras Y.Ann Surg Oncol. 2022 Apr 30. doi: 10.1245/s10434-022-11450-2. Online ahead of print. PMID: 35499785
Catastrophic DNA replication in unscheduled tetraploid cells. Manic G, Galluzzi L, Vitale I.Trends Genet. 2022 Apr 27:S0168-9525(22)00085-3. doi: 10.1016/j.tig.2022.04.005. Online ahead of print. PMID: 35490031
Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression. Paulson TG, Galipeau PC, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Hadi K, Shah M, Arora K, Shelton J, Johnson M, Corvelo A, Maley CC, Yao X, Sanghvi R, Venturini E, Emde AK, Hubert B, Imielinski M, Robine N, Reid BJ, Li X.Nat Commun. 2022 Apr 28;13(1):2300. doi: 10.1038/s41467-022-29767-7. PMID: 35484108
Tumor-immune microenvironment revealed by Imaging Mass Cytometry in a metastatic sarcomatoid urothelial carcinoma with a prolonged response to pembrolizumab. Alnajar H, Ravichandran H, Figueiredo Rendeiro A, Ohara K, Al Zoughbi W, Manohar J, Greco N, Sigouros M, Fox J, Muth E, Angiuoli S, Faltas B, Shusterman M, Sternberg CN, Elemento O, Mosquera JM.Cold Spring Harb Mol Case Stud. 2022 Apr 28;8(3):a006151. doi: 10.1101/mcs.a006151. Print 2022 Apr. PMID: 35483877
A loss-of-function polymorphism in ATG16L1 compromises therapeutic outcome in head and neck carcinoma patients. Le Naour J, Sztupinszki Z, Carbonnier V, Casiraghi O, Marty V, Galluzzi L, Szallasi Z, Kroemer G, Vacchelli E.Oncoimmunology. 2022 Apr 17;11(1):2059878. doi: 10.1080/2162402X.2022.2059878. eCollection 2022. PMID: 35481288
Management of Patients with Advanced Prostate Cancer: Report from the Advanced Prostate Cancer Consensus Conference 2021. Gillessen S, Armstrong A, Attard G, Beer TM, Beltran H, Bjartell A, Bossi A, Briganti A, Bristow RG, Bulbul M, Caffo O, Chi KN, Clarke CS, Clarke N, Davis ID, de Bono JS, Duran I, Eeles R, Efstathiou E, Efstathiou J, Ekeke ON, Evans CP, Fanti S, Feng FY, Fizazi K, Frydenberg M, George D, Gleave M, Halabi S, Heinrich D, Higano C, Hofman MS, Hussain M, James N, Jones R, Kanesvaran R, Khauli RB, Klotz L, Leibowitz R, Logothetis C, Maluf F, Millman R, Morgans AK, Morris MJ, Mottet N, Mrabti H, Murphy DG, Murthy V, Oh WK, Ost P, O’Sullivan JM, Padhani AR, Parker C, Poon DMC, Pritchard CC, Rabah DM, Rathkopf D, Reiter RE, Rubin M, Ryan CJ, Saad F, Sade JP, Sartor O, Scher HI, Shore N, Skoneczna I, Small E, Smith M, Soule H, Spratt DE, Sternberg CN, Suzuki H, Sweeney C, Sydes MR, Taplin ME, Tilki D, Tombal B, Türkeri L, Uemura H, Uemura H, van Oort I, Yamoah K, Ye D, Zapatero A, Omlin A.Eur Urol. 2022 Apr 18:S0302-2838(22)01807-3. doi: 10.1016/j.eururo.2022.04.002. Online ahead of print. PMID: 35450732
Management of Patients with Advanced Prostate Cancer: Report from the Advanced Prostate Cancer Consensus Conference 2021. Gillessen S, Armstrong A, Attard G, Beer TM, Beltran H, Bjartell A, Bossi A, Briganti A, Bristow RG, Bulbul M, Caffo O, Chi KN, Clarke CS, Clarke N, Davis ID, de Bono JS, Duran I, Eeles R, Efstathiou E, Efstathiou J, Ekeke ON, Evans CP, Fanti S, Feng FY, Fizazi K, Frydenberg M, George D, Gleave M, Halabi S, Heinrich D, Higano C, Hofman MS, Hussain M, James N, Jones R, Kanesvaran R, Khauli RB, Klotz L, Leibowitz R, Logothetis C, Maluf F, Millman R, Morgans AK, Morris MJ, Mottet N, Mrabti H, Murphy DG, Murthy V, Oh WK, Ost P, O’Sullivan JM, Padhani AR, Parker C, Poon DMC, Pritchard CC, Rabah DM, Rathkopf D, Reiter RE, Rubin M, Ryan CJ, Saad F, Sade JP, Sartor O, Scher HI, Shore N, Skoneczna I, Small E, Smith M, Soule H, Spratt DE, Sternberg CN, Suzuki H, Sweeney C, Sydes MR, Taplin ME, Tilki D, Tombal B, Türkeri L, Uemura H, Uemura H, van Oort I, Yamoah K, Ye D, Zapatero A, Omlin A.Eur Urol. 2022 Apr 18:S0302-2838(22)01807-3. doi: 10.1016/j.eururo.2022.04.002. Online ahead of print. PMID: 35450732
An Update of Cutaneous Melanoma Patients Treated in Adjuvancy With the Allogeneic Melanoma Vaccine VACCIMEL and Presentation of a Selected Case Report With In-Transit Metastases. Mordoh A, Aris M, Carri I, Bravo AI, Podaza E, Pardo JCT, Cueto GR, Barrio MM, Mordoh J.Front Immunol. 2022 Apr 1;13:842555. doi: 10.3389/fimmu.2022.842555. eCollection 2022. PMID: 35432383
Restored Ketosis Drives Anticancer Immunity in Colorectal Cancer. Montrose DC, Galluzzi L.Cancer Res. 2022 Apr 15;82(8):1464-1466. doi: 10.1158/0008-5472.CAN-22-0686. PMID: 35425965

March

Primary results of STRONG: An open-label, multicenter, phase 3b study of fixed-dose durvalumab monotherapy in previously treated patients with urinary tract carcinoma. Sonpavde GP, Sternberg CN, Loriot Y, Marabelle A, Lee JL, Fléchon A, Roubaud G, Pouessel D, Zagonel V, Calabro F, Banna GL, Shin SJ, Vera-Badillo FE, Powles T, Hellmis E, Miranda PAP, Lima AR, Emeribe U, Oh SM, Hotte SJ.Eur J Cancer. 2022 Mar;163:55-65. doi: 10.1016/j.ejca.2021.12.012. Epub 2022 Jan 15. PMID: 35042068
BAX and BAK dynamics control mitochondrial DNA release during apoptosis. Yamazaki T, Galluzzi L.Cell Death Differ. 2022 Mar 26. doi: 10.1038/s41418-022-00985-2. Online ahead of print. PMID: 35347233
Lung lymphatic thrombosis and dysfunction caused by cigarette smoke exposure precedes emphysema in mice. Summers BD, Kim K, Clement CC, Khan Z, Thangaswamy S, McCright J, Maisel K, Zamora S, Quintero S, Racanelli AC, Redmond D, D’Armiento J, Yang J, Kuang A, Monticelli L, Kahn ML, Choi AMK, Santambrogio L, Reed HO.Sci Rep. 2022 Mar 23;12(1):5012. doi: 10.1038/s41598-022-08617-y. PMID: 35322079
Platinum-based chemotherapy inflames the ovarian carcinoma microenvironment through cellular senescence. Álvarez-Abril B, García-Martínez E, Galluzzi L.Oncoimmunology. 2022 Mar 17;11(1):2052411. doi: 10.1080/2162402X.2022.2052411. eCollection 2022. PMID: 35309729
Targeting oncogene and non-oncogene addiction to inflame the tumour microenvironment. Petroni G, Buqué A, Coussens LM, Galluzzi L.Nat Rev Drug Discov. 2022 Mar 15. doi: 10.1038/s41573-022-00415-5. Online ahead of print. PMID: 35292771
Leptin secreted from testicular microenvironment modulates hedgehog signaling to augment the endogenous function of Leydig cells. Arora H, Qureshi R, Khodamoradi K, Seetharam D, Parmar M, Van Booven DJ, Issa IC, Sackstein R, Lamb D, Hare JM, Ramasamy R.Cell Death Dis. 2022 Mar 4;13(3):208. doi: 10.1038/s41419-022-04658-3. PMID: 35246515
The genomic landscape of metastatic clear cell renal cell carcinoma after systemic therapy. van der Mijn JC, Eng KW, Chandra P, Fernandez E, Ramazanoglu S, Sigaras A, Oromendia C, Gudas LJ, Tagawa ST, Nanus DM, Faltas BF, Beltran H, Sternberg CN, Elemento O, Sboner A, Mosquera JM, Molina AM.Mol Oncol. 2022 Mar 1. doi: 10.1002/1878-0261.13204. Online ahead of print. PMID: 35231161
RET Fusion-Positive Papillary Thyroid Cancers are Associated with a More Aggressive Phenotype. Ullmann TM, Thiesmeyer JW, Lee YJ, Beg S, Mosquera JM, Elemento O, Fahey TJ 3rd, Scognamiglio T, Houvras Y.Ann Surg Oncol. 2022 Mar 1. doi: 10.1245/s10434-022-11418-2. Online ahead of print. PMID: 35230579
Utility of multimodality molecular profiling for pediatric patients with central nervous system tumors. Rajappa P, Eng KW, Bareja R, Bander ED, Yuan M, Dua A, Bhanu Maachani U, Snuderl M, Pan H, Zhang T, Tosi U, Ivasyk I, Souweidane MM, Elemento O, Sboner A, Greenfield JP, Pisapia DJ.Neurooncol Adv. 2022 Mar 10;4(1):vdac031. doi: 10.1093/noajnl/vdac031. eCollection 2022 Jan-Dec. PMID: 35475276

February

Comparative genomics of primary prostate cancer and paired metastases: insights from 12 molecular case studies. Cyrta J, Prandi D, Arora A, Hovelson DH, Sboner A, Rodriguez A, Fedrizzi T, Beltran H, Robinson DR, Gopalan A, True L, Nelson PS, Robinson BD, Mosquera JM, Tomlins SA, Shen R, Demichelis F, Rubin MA.J Pathol. 2022 Feb 26. doi: 10.1002/path.5887. Online ahead of print. PMID: 35220606
Real-world patient characteristics associated with survival of 2 years or more after radium-223 treatment for metastatic castration-resistant prostate cancer (EPIX study). George DJ, Agarwal N, Sartor O, Sternberg CN, Tombal B, Saad F, Miller K, Constantinovici N, Guo H, Reeves J, Jiao X, Sandström P, Verholen F, Higano CS, Shore N.Prostate Cancer Prostatic Dis. 2022 Feb 21. doi: 10.1038/s41391-021-00488-0. Online ahead of print. PMID: 35190653
Immunostimulatory effects of radioimmunotherapy. Constanzo J, Galluzzi L, Pouget JP.J Immunother Cancer. 2022 Feb;10(2):e004403. doi: 10.1136/jitc-2021-004403. PMID: 35190377
Containers in Bioinformatics: Applications, Practical Considerations, and Best Practices in Molecular Pathology. Kadri S, Sboner A, Sigaras A, Roy S.J Mol Diagn. 2022 Feb 18:S1525-1578(22)00038-1. doi: 10.1016/j.jmoldx.2022.01.006. Online ahead of print. PMID: 35189355
Author Correction: Radiotherapy as a tool to elicit clinically actionable signalling pathways in cancer. Petroni G, Cantley LC, Santambrogio L, Formenti SC, Galluzzi L.Nat Rev Clin Oncol. 2022 Feb 18. doi: 10.1038/s41571-022-00611-7. Online ahead of print. PMID: 35181748
Immunological control of ovarian carcinoma by chemotherapy and targeted anticancer agents. Fucikova J, Palova-Jelinkova L, Klapp V, Holicek P, Lanickova T, Kasikova L, Drozenova J, Cibula D, Álvarez-Abril B, García-Martínez E, Spisek R, Galluzzi L.Trends Cancer. 2022 Feb 15:S2405-8033(22)00017-6. doi: 10.1016/j.trecan.2022.01.010. Online ahead of print. PMID: 35181272
Darolutamide and Survival in Metastatic, Hormone-Sensitive Prostate Cancer. Smith MR, Hussain M, Saad F, Fizazi K, Sternberg CN, Crawford ED, Kopyltsov E, Park CH, Alekseev B, Montesa-Pino Á, Ye D, Parnis F, Cruz F, Tammela TLJ, Suzuki H, Utriainen T, Fu C, Uemura M, Méndez-Vidal MJ, Maughan BL, Joensuu H, Thiele S, Li R, Kuss I, Tombal B; ARASENS Trial Investigators.N Engl J Med. 2022 Feb 17. doi: 10.1056/NEJMoa2119115. Online ahead of print. PMID: 35179323
Dihydroceramide- and ceramide-profiling provides insights into human cardiometabolic disease etiology. Wittenbecher C, Cuadrat R, Johnston L, Eichelmann F, Jäger S, Kuxhaus O, Prada M, Del Greco M F, Hicks AA, Hoffman P, Krumsiek J, Hu FB, Schulze MB.Nat Commun. 2022 Feb 17;13(1):936. doi: 10.1038/s41467-022-28496-1. PMID: 35177612
Philadelphia-negative myeloproliferative neoplasms: From origins to new perspectives.
Bartalucci N, Galluzzi L.Int Rev Cell Mol Biol. 2022;366:ix-xx. doi: 10.1016/S1937-6448(22)00019-3. PMID: 35153008
Immunogenic cell stress and death. Kroemer G, Galassi C, Zitvogel L, Galluzzi L.Nat Immunol. 2022 Feb 10. doi: 10.1038/s41590-022-01132-2. Online ahead of print. PMID: 35145297
What advances may the future bring to the diagnosis, treatment, and care of male sexual and reproductive health? Barratt CLR, Wang C, Baldi E, Toskin I, Kiarie J, Lamb DJ; other Editorial Board Members of the WHO Laboratory Manual for the Examination and Processing of Human Semen.Fertil Steril. 2022 Feb;117(2):258-267. doi: 10.1016/j.fertnstert.2021.12.013. PMID: 35125173
Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci. Fontugne J, Cai PY, Alnajar H, Bhinder B, Park K, Ye H, Beg S, Sailer V, Siddiqui J, Blattner-Johnson M, Croyle JA, Noorzad Z, Calagua C, MacDonald TY, Axcrona U, Bogaard M, Axcrona K, Scherr DS, Sanda MG, Johannessen B, Chinnaiyan AM, Elemento O, Skotheim RI, Rubin MA, Barbieri CE, Mosquera JM.JCI Insight. 2022 Feb 22;7(4):e155309. doi: 10.1172/jci.insight.155309. PMID: 35050902
What Experts Think About Prostate Cancer Management During the COVID-19 Pandemic: Report from the Advanced Prostate Cancer Consensus Conference 2021. Turco F, Armstrong A, Attard G, Beer TM, Beltran H, Bjartell A, Bossi A, Briganti A, Bristow RG, Bulbul M, Caffo O, Chi KN, Clarke CS, Clarke N, Davis ID, de Bono J, Duran I, Eeles R, Efstathiou E, Efstathiou J, Evans CP, Fanti S, Feng FY, Fizazi K, Frydenberg M, George D, Gleave M, Halabi S, Heinrich D, Higano C, Hofman MS, Hussain M, James N, Jones R, Kanesvaran R, Khauli RB, Klotz L, Leibowitz R, Logothetis C, Maluf F, Millman R, Morgans AK, Morris MJ, Mottet N, Mrabti H, Murphy DG, Murthy V, Oh WK, Ekeke ON, Ost P, O’Sullivan JM, Padhani AR, Parker C, Poon DMC, Pritchard CC, Rabah DM, Rathkopf D, Reiter RE, Rubin M, Ryan CJ, Saad F, Sade JP, Sartor O, Scher HI, Shore N, Skoneczna I, Small E, Smith M, Soule H, Spratt DE, Sternberg CN, Suzuki H, Sweeney C, Sydes MR, Taplin ME, Tilki D, Tombal B, Türkeri L, Uemura H, Uemura H, van Oort I, Yamoah K, Ye D, Zapatero A, Gillessen S, Omlin A.Eur Urol. 2022 Feb 17:S0302-2838(22)01650-5. doi: 10.1016/j.eururo.2022.02.010. Online ahead of print. PMID: 35393158
Serial ctDNA analysis predicts clinical progression in patients with advanced urothelial carcinoma. Shohdy KS, Villamar DM, Cao Y, Trieu J, Price KS, Nagy R, Tagawa ST, Molina AM, Sternberg CN, Nanus DM, Mosquera JM, Elemento O, Sonpavde GP, Grivas P, Vogelzang NJ, Faltas BM.Br J Cancer. 2022 Feb;126(3):430-439. doi: 10.1038/s41416-021-01648-8. Epub 2022 Jan 19. PMID: 35046520
Simple Linear Cancer Risk Prediction Models With Novel Features Outperform Complex Approaches. Kulm S, Kofman L, Mezey J, Elemento O.JCO Clin Cancer Inform. 2022 Feb;6:e2100166. doi: 10.1200/CCI.21.00166. PMID: 35239414

January

Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci. Fontugne J, Cai PY, Alnajar H, Bhinder B, Park K, Ye H, Beg S, Sailer V, Siddiqui J, Blattner-Johnson M, Croyle JA, Noorzad Z, Calagua C, MacDonald TY, Axcrona U, Bogaard M, Axcrona K, Scherr DS, Sanda MG, Johannessen B, Chinnaiyan AM, Elemento O, Skotheim RI, Rubin MA, Barbieri CE, Mosquera JM.JCI Insight. 2022 Jan 20:e155309. doi: 10.1172/jci.insight.155309. Online ahead of print. PMID: 35050902
Serial ctDNA analysis predicts clinical progression in patients with advanced urothelial carcinoma. Shohdy KS, Villamar DM, Cao Y, Trieu J, Price KS, Nagy R, Tagawa ST, Molina AM, Sternberg CN, Nanus DM, Mosquera JM, Elemento O, Sonpavde GP, Grivas P, Vogelzang NJ, Faltas BM.Br J Cancer. 2022 Jan 19. doi: 10.1038/s41416-021-01648-8. Online ahead of print. PMID: 35046520
Primary results of STRONG: An open-label, multicenter, phase 3b study of fixed-dose durvalumab monotherapy in previously treated patients with urinary tract carcinoma. Sonpavde GP, Sternberg CN, Loriot Y, Marabelle A, Lee JL, Fléchon A, Roubaud G, Pouessel D, Zagonel V, Calabro F, Banna GL, Shin SJ, Vera-Badillo FE, Powles T, Hellmis E, Miranda PAP, Lima AR, Emeribe U, Oh SM, Hotte SJ.Eur J Cancer. 2022 Jan 15;163:55-65. doi: 10.1016/j.ejca.2021.12.012. Online ahead of print. PMID: 35042068
Exposure-response relationship of ramucirumab in RANGE, a randomized phase III trial in advanced urothelial carcinoma refractory to platinum therapy. de Wit R, Powles T, Castellano D, Necchi A, Lee JL, van der Heijden MS, Matsubara N, Bamias A, Fléchon A, Sternberg CN, Drakaki A, Yu EY, Zimmermann AH, Long A, Walgren RA, Gao L, Bell-McGuinn KM, Petrylak DP.Br J Clin Pharmacol. 2022 Jan 13. doi: 10.1111/bcp.15233. Online ahead of print. PMID: 35029306
Understanding how genetic ancestry may influence cancer development. Lord BD, Martini RN, Davis MB.Trends Cancer. 2022 Jan 10:S2405-8033(21)00259-4. doi: 10.1016/j.trecan.2021.12.006. Online ahead of print. PMID: 35027335
Advances in understanding and examining lymphatic function: relevance for understanding autoimmunity. Ambler W, Santambrogio L, Lu TT.Curr Opin Rheumatol. 2022 Mar 1;34(2):133-138. doi: 10.1097/BOR.0000000000000864. PMID: 34954700
Identification of Robust Protein Associations With COVID-19 Disease Based on Five Clinical Studies. Suhre K, Sarwath H, Engelke R, Sohail MU, Cho SJ, Whalen W, Alvarez-Mulett S, Krumsiek J, Choi AMK, Schmidt F.Front Immunol.2022 Jan 25;12:781100. doi: 10.3389/fimmu.2021.781100. eCollection 2021. PMID: 35145507
Metabolic and Immune Markers for Precise Monitoring of COVID-19 Severity and Treatment. Rendeiro AF, Vorkas CK, Krumsiek J, Singh HK, Kapadia SN, Cappelli LV, Cacciapuoti MT, Inghirami G, Elemento O, Salvatore M.Front Immunol. 2022 Jan 12;12:809937. doi: 10.3389/fimmu.2021.809937. eCollection 2021. PMID: 35095900

2021

December

Advances in understanding and examining lymphatic function: relevance for understanding autoimmunity. Ambler W, Santambrogio L, Lu TT.Curr Opin Rheumatol. 2021 Dec 24. doi: 10.1097/BOR.000000000000086 Online ahead of print. PMID: 34954700
GCN2 kinase activation by ATP-competitive kinase inhibitors. Tang CP, Clark O, Ferrarone JR, Campos C, Lalani AS, Chodera JD, Intlekofer AM, Elemento O, Mellinghoff IK.Nat Chem Biol. 2021 Dec 23. doi: 10.1038/s41589-021-00947-8. Online ahead of print. PMID: 34949839
Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Aguiar-Pulido V, Wolujewicz P, Martinez-Fundichely A, Elhaik E, Thareja G, Abdel Aleem A, Chalhoub N, Cuykendall T, Al-Zamer J, Lei Y, El-Bashir H, Musser JM, Al-Kaabi A, Shaw GM, Khurana E, Suhre K, Mason CE, Elemento O, Finnell RH, Ross ME.Proc Natl Acad Sci U S A. 2021 Dec 21;118(51):e2106844118. doi: 10.1073/pnas.2106844118. PMID: 34916285
Detecting neuroendocrine prostate cancer through tissue-informed cell-free DNA methylation analysis. Berchuck JE, Baca SC, McClure HM, Korthauer K, Tsai HK, Vitale Nuzzo P, Kelleher KM, He M, Steinharter JA, Zacharia S, Spisak S, Seo JH, Conteduca V, Elemento O, Auh J, Sigouros M, Corey E, Hirsch MS, Taplin ME, Choueiri TK, Pomerantz MM, Beltran H, Freedman ML.Clin Cancer Res. 2021 Dec 14:clincanres.CCR-21-3762-E.2021. doi: 10.1158/1078-0432.CCR-21-3762. Online ahead of print. PMID: 34907080
Using epigenetic modifiers to target cancer stem cell immunoevasion. Galassi C, Vitale I, Galluzzi L.Cancer Cell. 2021 Dec 13;39(12):1573-1575. doi: 10.1016/j.ccell.2021.11.003. PMID: 34906316
Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial.
Powles T, Sridhar SS, Loriot Y, Bellmunt J, Mu XJ, Ching KA, Pu J, Sternberg CN, Petrylak DP, Tambaro R, Dourthe LM, Alvarez-Fernandez C, Aarts M, di Pietro A, Grivas P, Davis CB.Nat Med. 2021 Dec;27(12):2200-2211. doi: 10.1038/s41591-021-01579-0. Epub 2021 Dec 10. PMID: 34893775
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. Sheffield NC, Stolarczyk M, Reuter VP, Rendeiro AF.Gigascience. 2021 Dec 6;10(12):giab077. doi: 10.1093/gigascience/giab077.PMID: 34890448
The Impact of Enzalutamide on the Prostate Cancer Patient Experience: A Summary Review of Health-Related Quality of Life across Pivotal Clinical Trials.Tombal B, Stenzl A, Cella D, Loriot Y, Armstrong AJ, Fizazi K, Beer T, Sternberg CN, Hussain M, Ivanescu C, Ganguli A, Ramaswamy K, Saad F.Cancers (Basel). 2021 Nov 23;13(23):5872. doi: 10.3390/cancers13235872. PMID: 34884981
Pan-cancer analysis reveals molecular patterns associated with age.Shah Y, Verma A, Marderstein AR, White J, Bhinder B, Garcia Medina JS, Elemento O.Cell Rep. 2021 Dec 7;37(10):110100. doi: 10.1016/j.celrep.2021.110100. PMID: 34879281
Stage-specific regulation of DNA methylation by TET enzymes during human cardiac differentiation.
Lan Y, Banks KM, Pan H, Verma N, Dixon GR, Zhou T, Ding B, Elemento O, Chen S, Huangfu D, Evans T.Cell Rep. 2021 Dec 7;37(10):110095. doi: 10.1016/j.celrep.2021.110095. PMID: 34879277
MDSCs sneak CSCs out of (immuno)surveillance. Jiménez-Cortegana C, Galassi C, Galluzzi L.Trends Immunol. 2021 Dec 2:S1471-4906(21)00257-X. doi: 10.1016/j.it.2021.11.008. PMID: 34863632
Are worldwide sperm counts declining? Jørgensen N, Lamb DJ, Levine H, Pastuszak AW, Sigalos JT, Swan SH, Eisenberg ML.Fertil Steril. 2021 Dec;116(6):1457-1463. doi: 10.1016/j.fertnstert.2021.10.020. PMID: 34836581

November

Application of Artificial Intelligence to Overcome Clinical Information Overload in Urologic Cancer. Stenzl A, Sternberg CN, Ghith J, Serfass L, Schijvenaars BJA, Sboner A.BJU Int. 2021 Nov 30. doi: 10.1111/bju.15662. Online ahead of print. PMID: 34846775
Publisher Correction: Prediction of primary venous thromboembolism based on clinical and genetic factors within the U.K. Biobank.
Kolin DA, Kulm S, Elemento O.Sci Rep. 2021 Nov 29;11(1):23364. doi: 10.1038/s41598-021-02115-3. PMID: 34845243
Immune Checkpoint Blockade and Skin Toxicity Pathogenesis. Ma B, Anandasabapathy N.J Invest Dermatol. 2021 Nov 26:S0022-202X(21)02308-3. doi: 10.1016/j.jid.2021.06.040. Online ahead of print. PMID: 34844731
Multimodal immunostimulation to control BRCA1-defective ovarian carcinoma. Klapp V, Galluzzi L.Trends Cancer. 2021 Nov 25:S2405-8033(21)00232-6. doi: 10.1016/j.trecan.2021.11.006. PMID: 34840109
Radiotherapy as a tool to elicit clinically actionable signalling pathways in cancer.

Petroni G, Cantley LC, Santambrogio L, Formenti SC, Galluzzi L.Nat Rev Clin Oncol. 2021 Nov 24. doi: 10.1038/s41571-021-00579-w. PMID: 34819622
Are we there yet? A machine learning architecture to predict organotropic metastases.
Skaro M, Hill M, Zhou Y, Quinn S, Davis MB, Sboner A, Murph M, Arnold J.BMC Med Genomics. 2021 Nov 24;14(1):281.doi: 10.1186/s12920-021-01122-7. PMID: 34819069
G3BP1 inhibits Cul3^SPOP to amplify AR signaling and promote prostate cancer.
Mukhopadhyay C, Yang C, Xu L, Liu D, Wang Y, Huang D, Deonarine LD, Cyrta J, Davicioni E, Sboner A, Robinson BD, Chinnaiyan AM, Rubin MA, Barbieri CE, Zhou P.Nat Commun. 2021 Nov 18;12(1):6662. doi: 10.1038/s41467-021-27024-x. PMID: 34795264
Consistent survival benefit of enzalutamide plus androgen deprivation therapy in men with nonmetastatic castration-resistant prostate cancer: PROSPER subgroup analysis by age and region.
De Giorgi U, Hussain M, Shore N, Fizazi K, Tombal B, Penson D, Saad F, Efstathiou E, Madziarska K, Steinberg J, Sugg J, Lin X, Shen Q, Sternberg CN.Eur J Cancer. 2021 Nov 13;159:237-246. doi: 10.1016/j.ejca.2021.10.015. Online ahead of print. PMID: 34784577
Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer’s disease.
Horgusluoglu E, Neff R, Song WM, Wang M, Wang Q, Arnold M, Krumsiek J, Galindo-Prieto B, Ming C, Nho K, Kastenmüller G, Han X, Baillie R, Zeng Q, Andrews S, Cheng H, Hao K, Goate A, Bennett DA, Saykin AJ, Kaddurah-Daouk R, Zhang B; Alzheimer’s Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Metabolomics Consortium.Alzheimers Dement. 2021Nov 10. doi: 10.1002/alz.12468. Online ahead of print. PMID: 34757660
Opposing transcriptional programs of KLF5 and AR emerge during therapy for advanced prostate cancer.
Che M, Chaturvedi A, Munro SA, Pitzen SP, Ling A, Zhang W, Mentzer J, Ku SY, Puca L, Zhu Y, Bergman AM, Severson TM, Forster C, Liu Y, Hildebrand J, Daniel M, Wang TY, Selth LA, Hickey T, Zoubeidi A, Gleave M, Bareja R, Sboner A, Tilley W, Carroll JS, Tan W, Kohli M, Yang R, Hsieh AC, Murugan P, Zwart W, Beltran H, Huang RS, Dehm SM.NatCommun. 2021 Nov 4;12(1):6377. doi: 10.1038/s41467-021-26612-1. PMID: 34737261
A Functional Precision Oncology Approach to Identify Treatment Strategies for Myxofibrosarcoma Patients.
Pauli C, De Boni L, Pauwels JE, Chen Y, Planas-Paz L, Shaw R, Emerling BM, Grandori C, Hopkins BD, Rubin MA.Mol Cancer Res. 2021Nov 2. doi: 10.1158/1541-7786.MCR-21-0255. Online ahead of print. PMID: 34728552
Prediction of primary venous thromboembolism based on clinical and genetic factors within the U.K. Biobank. Kolin DA, Kulm S, Elemento O.Sci Rep. 2021 Nov 1;11(1):21340. doi: 10.1038/s41598-021-00796-4. PMID: 34725413

October

Trial watch: intratumoral immunotherapy. Humeau J, Le Naour J, Galluzzi L, Kroemer G, Pol JG.Oncoimmunology. 2021 Oct 15;10(1):1984677. doi: 10.1080/2162402X.2021.1984677. eCollection 2021. PMID: 34676147
Extracellular Matrix in Synthetic Hydrogel-based Prostate Cancer Organoids Regulate Therapeutic Response to EZH2 and DRD2 inhibitors. Mosquera MJ, Kim S, Bareja R, Fang Z, Cai S, Pan H, Asad M, Martin ML, Sigouros M, Rowdo FM, Ackermann S, Capuano J, Bernheim J, Cheung C, Doane A, Brady N, Singh R, Rickman DS, Prabhu V, Allen JE, Puca L, Coskun A, Rubin M, Beltran H, Mosquera JM, Elemento O, Singh A.Adv Mater. 2021 Oct 22:e2100096. doi: 10.1002/adma.202100096. Online ahead of print. PMID: 34676924
RNA-Sequencing-Based Transcriptomic Score with Prognostic and Theranostic Values in Multiple Myeloma.
Alaterre E, Vikova V, Kassambara A, Bruyer A, Robert N, Requirand G, Bret C, Herbaux C, Vincent L, Cartron G, Elemento O, Moreaux J.J Pers Med. 2021 Sep 30;11(10):988. doi: 10.3390/jpm11100988. PMID: 34683129
maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines. Chetnik K, Benedetti E, Gomari DP, Schweickart A, Batra R, Buyukozkan M, Wang Z, Arnold M, Zierer J, Suhre K, Krumsiek J.
Bioinformatics. 2021 Oct 25:btab741. doi: 10.1093/bioinformatics/btab741. Online ahead of print. PMID: 34694386
Control of host mitochondria by bacterial pathogens. Marchi S, Morroni G, Pinton P, Galluzzi L.Trends Microbiol. 2021 Oct 13:S0966-842X(21)00237-7. doi: 10.1016/j.tim.2021.09.010. Online ahead of print. PMID: 34656395
Immunological configuration of ovarian carcinoma: features and impact on disease outcome. Fucikova J, Coosemans A, Orsulic S, Cibula D, Vergote I, Galluzzi L, Spisek R.J Immunother Cancer. 2021 Oct;9(10):e002873. doi: 10.1136/jitc-2021-002873. PMID: 34645669
Real-world outcomes of second novel hormonal therapy or radium-223 following first novel hormonal therapy for mCRPC. Sartor O, George D, Tombal B, Agarwal N, Higano CS, Sternberg CN, Miller K, Jiao X, Guo H, Sandström P, Bruno A, Verholen F, Saad F, Shore N.Future Oncol. 2021 Oct 12. doi: 10.2217/fon-2021-0886. Online ahead of print. PMID: 34636627
Author Correction: A molecular single-cell lung atlas of lethal COVID-19. Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Tsai EJ, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B.Nature. 2021 Oct 8:1. doi: 10.1038/s41586-021-03921-5. Online ahead of print. PMID: 34625743
Dissecting bulk transcriptomes of diffuse large B cell lymphoma. McNally DR, Elemento O, Melnick A.Cancer Cell. 2021 Oct 11;39(10):1305-1307. doi: 10.1016/j.ccell.2021.09.006. Epub 2021 Sep 30. PMID: 34597590
OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Doane AS, Chu CS, Di Giammartino DC, Rivas MA, Hellmuth JC, Jiang Y, Yusufova N, Alonso A, Roeder RG, Apostolou E, Melnick AM, Elemento O.Nat Immunol. 2021 Oct;22(10):1327-1340. doi: 10.1038/s41590-021-01025-w. Epub 2021 Sep 23. PMID: 34556886
Deploying an artificial intelligence-based online search tool to increase patients’ access to and understanding of solid tumor gastrointestinal clinical trials.
Jordan ER, Jahreiss L, Kasi PM.J Gastrointest Oncol. 2021 Oct;12(5):2045-2051. doi: 10.21037/jgo-21-175. PMID: 34790372
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer.
Ciani Y, Fedrizzi T, Prandi D, Lorenzin F, Locallo A, Gasperini P, Franceschini GM, Benelli M, Elemento O, Fava LL, Inga A,Demichelis F.Cell Syst. 2021 Oct 26:S2405-4712(21)00383-5. doi: 10.1016/j.cels.2021.10.001. Online ahead of print. PMID: 34731645

September

OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Doane AS, Chu CS, Di Giammartino DC, Rivas MA, Hellmuth JC, Jiang Y, Yusufova N, Alonso A, Roeder RG, Apostolou E, Melnick AM, Elemento O.Nat Immunol. 2021 Sep 23. doi: 10.1038/s41590-021-01025-w. Online ahead of print. PMID: 34556886.
Artificial intelligence in cancer research, diagnosis and therapy. Elemento O, Leslie C, Lundin J, Tourassi G.Nat Rev Cancer. 2021 Sep 17. doi: 10.1038/s41568-021-00399-1. Online ahead of print. PMID: 34535775
SGI: Automatic clinical subgroup identification in omics datasets.
Buyukozkan M, Suhre K, Krumsiek J.Bioinformatics. 2021 Sep 16:btab656. doi: 10.1093/bioinformatics/btab656. Online ahead of print. PMID: 34529048
The NF-κB transcriptional footprint is essential for SARS-CoV-2 replication.
Nilsson-Payant BE, Uhl S, Grimont A, Doane AS, Cohen P, Patel RS, Higgins CA, Acklin JA, Bram Y, Chandar V, Blanco-Melo D, Panis M, Lim JK, Elemento O, Schwartz RE, Rosenberg BR, Chandwani R, tenOever BR.J Virol. 2021 Sep 15:JVI0125721. doi: 10.1128/JVI.01257-21. Online ahead of print. PMID: 34523966
Impact of enzalutamide on patient-reported fatigue in patients with prostate cancer: data from the pivotal clinical trials.
Tombal BF, Freedland SJ, Armstrong AJ, Beer TM, Stenzl A, Sternberg CN, Hussain M, Ganguli A, Ramaswamy K, Bhadauria H, Ivanescu C, Turnbull J, Holmstrom S, Saad F.Prostate Cancer Prostatic Dis. 2021 Sep 13. doi: 10.1038/s41391-021-00447-9. Online ahead of print. PMID: 34518652
Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia.
Bloehdorn J, Braun A, Taylor-Weiner A, Jebaraj BMC, Robrecht S, Krzykalla J, Pan H, Giza A, Akylzhanova G, Holzmann K, Scheffold A, Johnston HE, Yeh RF, Klymenko T, Tausch E, Eichhorst B, Bullinger L, Fischer K, Weisser M, Robak T, Schneider C, Gribben J, Dahal LN, Carter MJ, Elemento O, Landau DA, Neuberg DS, Cragg MS, Benner A, Hallek M, Wu CJ, Döhner H, Stilgenbauer S, Mertens D.Nat Commun. 2021 Sep 13;12(1):5395. doi: 10.1038/s41467-021-25403-y. PMID: 34518531
Developmental chromatin programs determine oncogenic competence in melanoma.
Baggiolini A, Callahan SJ, Montal E, Weiss JM, Trieu T, Tagore MM, Tischfield SE, Walsh RM, Suresh S, Fan Y, Campbell NR, Perlee SC, Saurat N, Hunter MV, Simon-Vermot T, Huang TH, Ma Y, Hollmann T, Tickoo SK, Taylor BS, Khurana E, Koche RP, Studer L, White RM.Science. 2021 Sep 3;373(6559):eabc1048. doi: 10.1126/science.abc1048. Epub 2021 Sep 3. PMID: 34516843
Chromatin and genomic instability in cancer. Weyemi U, Galluzzi L.Int Rev Cell Mol Biol. 2021;364:ix-xvii. doi: 10.1016/S1937-6448(21)00116-7. PMID: 34507786
Reshaping of the androgen-driven chromatin landscape in normal prostate cells by early cancer drivers and effect on therapeutic sensitivity.
Grbesa I, Augello MA, Liu D, McNally DR, Gaffney CD, Huang D, Lin K, Ivenitsky D, Goueli R, Robinson BD, Khani F, Deonarine LD, Blattner M, Elemento O, Davicioni E, Sboner A, Barbieri CE.Cell Rep. 2021 Sep 7;36(10):109625. doi: 10.1016/j.celrep.2021.109625. PMID: 34496233
Correction to: The role of machine learning in clinical research: transforming the future of evidence generation.
Weissler EH, Naumann T, Andersson T, Ranganath R, Elemento O, Luo Y, Freitag DF, Benoit J, Hughes MC, Khan F, Slater P, Shameer K, Roe M, Hutchison E, Kollins SH, Broedl U, Meng Z, Wong JL, Curtis L, Huang E, Ghassemi M.Trials. 2021 Sep 6;22(1):593. doi: 10.1186/s13063-021-05571-4. PMID: 34488840
Molecular Evaluation of Low-grade Low-stage Endometrial Cancer With and Without Recurrence.
Matrai CE, Ohara K, Eng KW, Glynn SM, Chandra P, Chatterjee-Paer S, Motanagh S, Mirabelli S, Kurtis B, He B, Sigaras A, Gupta D, Chapman-Davis E, Holcomb K, Sboner A, Elemento O, Ellenson LH, Mosquera JM.Int J Gynecol Pathol. 2021 Sep 6. doi: 10.1097/PGP.0000000000000798. Online ahead of print. PMID: 34483300
A polygenic-score-based approach for identification of gene-drug interactions stratifying breast cancer risk. Marderstein AR, Kulm S, Peng C, Tamimi R, Clark AG, Elemento O.Am J Hum Genet. 2021 Sep 2;108(9):1752-1764. doi: 10.1016/j.ajhg.2021.07.008. Epub 2021 Aug 6. PMID: 34363748
Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes.
Rivas MA, Durmaz C, Kloetgen A, Chin CR, Chen Z, Bhinder B, Koren A, Viny AD, Scharer CD, Boss JM, Elemento O, Mason CE, Melnick AM.Front Immunol. 2021 Sep 21;12:688493. doi: 10.3389/fimmu.2021.688493. eCollection 2021. PMID: 34621263

August

Targeting Serine in Cancer: Is Two Better Than One? Buqué A, Galluzzi L, Montrose DC.Trends Cancer. 2021 Aug;7(8):668-670. doi: 10.1016/j.trecan.2021.06.004. Epub 2021 Jul 1. PMID: 34219053
Autophagy in major human diseases. Klionsky DJ, Petroni G, Amaravadi RK, Baehrecke EH, Ballabio A, Boya P, Bravo-San Pedro JM, Cadwell K, Cecconi F, Choi AMK, Choi ME, Chu CT, Codogno P, Colombo MI, Cuervo AM, Deretic V, Dikic I, Elazar Z, Eskelinen EL, Fimia GM, Gewirtz DA, Green DR, Hansen M, Jäättelä M, Johansen T, Juhász G, Karantza V, Kraft C, Kroemer G, Ktistakis NT, Kumar S, Lopez-Otin C, Macleod KF, Madeo F, Martinez J, Meléndez A, Mizushima N, Münz C, Penninger JM, Perera RM, Piacentini M, Reggiori F, Rubinsztein DC, Ryan KM, Sadoshima J, Santambrogio L, Scorrano L, Simon HU, Simon AK, Simonsen A, Stolz A, Tavernarakis N, Tooze SA, Yoshimori T, Yuan J, Yue Z, Zhong Q, Galluzzi L, Pietrocola F.EMBO J. 2021 Aug 30:e108863. doi: 10.15252/embj.2021108863. Online ahead of print. PMID: 34459017
Baseline neutrophil-to-lymphocyte ratio as a predictive and prognostic biomarker in patients with metastatic castration-resistant prostate cancer treated with cabazitaxel versus abiraterone or enzalutamide in the CARD study.
de Wit R, Wülfing C, Castellano D, Kramer G, Eymard JC, Sternberg CN, Fizazi K, Tombal B, Bamias A, Carles J, Iacovelli R, Melichar B, Sverrisdóttir Á, Theodore C, Feyerabend S, Helissey C, Foster MC, Ozatilgan A, Geffriaud-Ricouard C, de Bono J.ESMO Open. 2021 Aug 24;6(5):100241. doi: 10.1016/j.esmoop.2021.100241. Online ahead of print. PMID: 34450475
Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations.
Fedrizzi T, Ciani Y, Lorenzin F, Cantore T, Gasperini P, Demichelis F.Comput Struct Biotechnol J. 2021 Aug 5;19:4394-4403. doi: 10.1016/j.csbj.2021.08.001. eCollection 2021. PMID: 34429855
LTX-315-enabled, radiotherapy-boosted immunotherapeutic control of breast cancer by NK cells.
Yamazaki T, Wennerberg E, Hensler M, Buqué A, Kraynak J, Fucikova J, Zhou XK, Sveinbjørnsson B, Rekdal Ø, Demaria S, Galluzzi L. Oncoimmunology. 2021 Aug 10;10(1):1962592. doi: 10.1080/2162402X.2021.1962592. eCollection 2021. PMID: 34408925
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies.
Meleshko D, Hajirasouliha I, Korobeynikov A.Bioinformatics. 2021 Aug 18:btab597. doi: 10.1093/bioinformatics/btab597. Online ahead of print. PMID: 34406356
The role of machine learning in clinical research: transforming the future of evidence generation.
Weissler EH, Naumann T, Andersson T, Ranganath R, Elemento O, Luo Y, Freitag DF, Benoit J, Hughes MC, Khan F, Slater P, Shameer K, Roe M, Hutchison E, Kollins SH, Broedl U, Meng Z, Wong JL, Curtis L, Huang E, Ghassemi M.Trials. 2021 Aug 16;22(1):537. doi: 10.1186/s13063-021-05489-x. PMID: 34399832
Ca(2+) in health and disease. Marchi S, Galluzzi L.Int Rev Cell Mol Biol. 2021;363:ix-xv. doi: 10.1016/S1937-6448(21)00101-5. PMID: 34392933
Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors.
Shohdy KS, Bareja R, Sigouros M, Wilkes DC, Dorsaint P, Manohar J, Bockelman D, Xiang JZ, Kim R, Ohara K, Eng K, Mosquera JM, Elemento O, Sboner A, Alonso A, Faltas BM.NPJ Genom Med. 2021 Aug 12;6(1):66. doi: 10.1038/s41525-021-00231-7. PMID: 34385467
The pediatric precision oncology INFORM registry: clinical outcome and benefit for patients with very high-evidence targets.
van Tilburg CM, Pfaff E, Pajtler KW, Langenberg KPS, Fiesel P, Jones BC, Balasubramanian GP, Stark S, Johann PD, Blattner-Johnson M, Schramm K, Dikow N, Hirsch S, Sutter C, Grund K, von Stackelberg A, Kulozik AE, Lissat A, Borkhardt A, Meisel R, Reinhardt D, Klusmann JH, Fleischhack G, Tippelt S, von Schweinitz D, Schmid I, Kramm CM, von Bueren AO, Calaminus G, Vorwerk P, Graf N, Westermann F, Fischer M, Eggert A, Burkhardt B, Wossmann W, Nathrath M, Hecker-Nolting S, Fruhwald MC, Schneider DT, Brecht IB, Ketteler P, Fulda S, Koscielniak E, Meister MT, Scheer M, Hettmer S, Schwab M, Tremmel R, Ora I, Hutter C, Gerber NU, Lohi O, Kazanowska B, Kattamis A, Filippidou M, Goemans B, Zwaan CM, Milde T, Jager N, Wolf S, Reuss D, Sahm F, von Deimling A, Dirksen U, Freitag A, Witt R, Lichter P, Kopp-Schneider A, Jones DTW, Molenaar JJ, Capper D, Pfister SM, Witt O.Cancer Discov. 2021 Aug 9:candisc.0094.2021. doi: 10.1158/2159-8290.CD-21-0094. Online ahead of print. PMID: 34373263
Efficacy of Platinum Rechallenge in Metastatic Urothelial Carcinoma After Previous Platinum-Based Chemotherapy for Metastatic Disease.
Wong RL, Ferris LA, Do OA, Holt SK, Ramos JD, Crabb SJ, Sternberg CN, Bellmunt J, Ladoire S, De Giorgi U, Harshman LC, Vaishampayan UN, Necchi A, Srinivas S, Pal SK, Niegisch G, Dorff TB, Galsky MD, Yu EY.Oncologist. 2021 Aug 6. doi: 10.1002/onco.13925. Online ahead of print. PMID: 34355457

July

Blood Biomarkers Reflect the Effects of Obesity and Inflammation on the Human Breast Transcriptome. Cho BA, Iyengar NM, Zhou XK, Morrow M, Giri DD, Verma A, Elemento O, Pollak M, Dannenberg AJ.Carcinogenesis. 2021 Jul 27:bgab066. doi: 10.1093/carcin/bgab066. Online ahead of print. PMID: 34314488
Dendritic cell-based immunotherapy (DCVAC/OvCa) combined with second-line chemotherapy in platinum-sensitive ovarian cancer (SOV02): A randomized, open-label, phase 2 trial.
Cibula D, Rob L, Mallmann P, Knapp P, Klat J, Chovanec J, Minar L, Melichar B, Hein A, Kieszko D, Pluta M, Spacek J, Bartos P, Wimberger P, Madry R, Markowska J, Streb J, Valha P, Hassan HIB, Pecen L, Galluzzi L, Fucikova J, Hrnciarova T, Hraska M, Bartunkova J, Spisek R.Gynecol Oncol. 2021 Jul 19:S0090-8258(21)00533-3. doi: 10.1016/j.ygyno.2021.07.003. Online ahead of print. PMID: 34294416
3-hydroxy-L-kynurenamine is an immunomodulatory biogenic amine.
Clement CC, D’Alessandro A, Thangaswamy S, Chalmers S, Furtado R, Spada S, Mondanelli G, Ianni F, Gehrke S, Gargaro M, Manni G, Cara LCL, Runge P, Tsai WL, Karaman S, Arasa J, Fernandez-Rodriguez R, Beck A, Macchiarulo A, Gadina M, Halin C, Fallarino F, Skobe M, Veldhoen M, Moretti S, Formenti S, Demaria S, Soni RK, Galarini R, Sardella R, Lauvau G, Putterman C, Alitalo K, Grohmann U, Santambrogio L.Nat Commun. 2021 Jul 21;12(1):4447. doi: 10.1038/s41467-021-24785-3. PMID: 34290243
Validation of a ctDNA-based next-generation sequencing assay in a cohort of solid tumor patients: a proposed solution for decentralized plasma testing.
Zoughbi WA, Fox J, Beg S, Papp E, Hissong E, Ohara K, Keefer L, Sigouros M, Kane T, Bockelman D, Nichol D, Patchell E, Bareja R, Karandikar A, Alnajar H, Cerqueira G, Guthrie VB, Verner E, Manohar J, Greco N, Wilkes D, Tagawa S, Malbari MS, Holcomb K, Eng KW, Shah M, Altorki NK, Sboner A, Nanus D, Faltas B, Sternberg CN, Simmons J, Houvras Y, Molina AM, Angiuoli S,Elemento O, Mosquera JM.Oncologist. 2021 Jul 19. doi: 10.1002/onco.13905. Online ahead of print. PMID: 34286887
Efficacy and Safety of Cabazitaxel Versus Abiraterone or Enzalutamide in Older Patients with Metastatic Castration-resistant Prostate Cancer in the CARD Study. Sternberg CN, Castellano D, de Bono J, Fizazi K, Tombal B, Wülfing C, Kramer G, Eymard JC, Beams A, Carles J, Iacovelli R, Melichar B, Sverrisdóttir Á, Theodore C, Feyerabend S, Helissey C, Poole EM, Ozatilgan A, Geffriaud-Ricouard C, de Wit R. Eur Urol. 2021 Jul 14:S0302-2838(21)01862-5. doi: 10.1016/j.eururo.2021.06.021. Online ahead of print. PMID: 34274136
Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology.
Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O.Semin Cancer Biol. 2021 Jul 10:S1044-579X(21)00197-8. doi: 10.1016/j.semcancer.2021.07.003. Online ahead of print. PMID: 34256129
Preface: Ca(2+) in health and disease.
Marchi S, Galluzzi L.Int Rev Cell Mol Biol. 2021;362:xi-xvii. doi: 10.1016/S1937-6448(21)00088-5. PMID: 34253299
Ipatasertib plus abiraterone and prednisolone in metastatic castration-resistant prostate cancer (IPATential150): a multicentre, randomised, double-blind, phase 3 trial.
Sweeney C, Bracarda S, Sternberg CN, Chi KN, Olmos D, Sandhu S, Massard C, Matsubara N, Alekseev B, Parnis F, Atduev V, Buchschacher GL Jr, Gafanov R, Corrales L, Borre M, Stroyakovskiy D, Alves GV, Bournakis E, Puente J, Harle-Yge ML, Gallo J, Chen G, Hanover J, Wongchenko MJ, Garcia J, de Bono JS.Lancet. 2021 Jul 10;398(10295):131-142. doi: 10.1016/S0140-6736(21)00580-8. PMID: 34246347
Vesicular trafficking in cellular responses to stress. Kepp O, Galluzzi L.Methods Cell Biol. 2021;164:xvii-xxi. doi: 10.1016/S0091-679X(21)00069-8. PMID: 34225922
Targeting Serine in Cancer: Is Two Better Than One? Buqué A, Galluzzi L, Montrose DC.Trends Cancer. 2021 Jul 1:S2405-8033(21)00134-5. doi: 10.1016/j.trecan.2021.06.004. Online ahead of print. PMID: 34219053
Diet-regulated production of PDGFcc by macrophages controls energy storage. Cox N, Crozet L, Holtman IR, Loyher PL, Lazarov T, White JB, Mass E, Stanley ER, Elemento O, Glass CK,Geissmann F.Science. 2021 Jul 2;373(6550):eabe9383. doi: 10.1126/science.abe9383. PMID: 34210853
A protocol for qualitative and quantitative measurement of endosomal processing using hot spot analysis.
Clement CC, Nanaware PP, Stern LJ, Santambrogio L.STAR Protoc. 2021 Jul 6;2(3):100648. doi: 10.1016/j.xpro.2021.100648. eCollection2021 Sep 17. PMID: 34278334
Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology.
Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O.Semin Cancer Biol. 2021 Jul 10:S1044-579X(21)00197-8. doi: 10.1016/j.semcancer.2021.07.003. Online ahead of print. PMID: 34256129
Current updates and future perspectives in the evaluation of azoospermia: A systematic review.
Punjani N, Kang C, Lamb DJ, Schlegel PN.Arab J Urol. 2021 Jul 22;19(3):206-214. doi: 10.1080/2090598X.2021.1954415. eCollection 2021. PMID: 34552771
MicroRNA-1205 Regulation of FRYL in Prostate Cancer. Naidoo M, Levine F, Gillot T, Orunmuyi AT, Olapade-Olaopa EO, Ali T, Krampis K, Pan C, Dorsaint P, Sboner A, Ogunwobi OO.Front Cell Dev Biol. 2021 Jul 27;9:647485. doi: 10.3389/fcell.2021.647485. eCollection 2021. PMID: 34386489

June

Temporal evolution of cellular heterogeneity during the progression to advanced AR-negative prostate cancer. Brady NJ, Bagadion AM, Singh R, Conteduca V, Van Emmenis L, Arceci E, Pakula H, Carelli R, Khani F, Bakht M, Sigouros M, Bareja R, Sboner A, Elemento O, Tagawa S, Nanus DM, Loda M, Beltran H, Robinson B, Rickman DS.Nat Commun. 2021 Jun 7;12(1):3372. doi: 10.1038/s41467-021-23780-y. PMID: 34099734
A metabolome-wide association study in the general population reveals decreased levels of serum laurylcarnitine in people with depression. Zacharias HU, Hertel J, Johar H, Pietzner M, Lukaschek K, Atasoy S, Kunze S, Völzke H, Nauck M, Friedrich N, Kastenmüller G, Grabe HJ, Gieger C, Krumsiek J, Ladwig KH.Mol Psychiatry. 2021 Jun 4. doi: 10.1038/s41380-021-01176-0. Online ahead of print. PMID: 34088979
Comparison of genetic risk prediction models to improve prediction of coronary heart disease in two large cohorts of the MONICA/KORA study. Bauer A, Zierer A, Gieger C, Büyüközkan M, Müller-Nurasyid M, Grallert H, Meisinger C, Strauch K, Prokisch H, Roden M, Peters A, Krumsiek J, Herder C, Koenig W, Thorand B, Huth C. Genet Epidemiol. 2021 Jun 3. doi: 10.1002/gepi.22389. Online ahead of print. PMID: 34082474
Immunofluorescence microscopy-based assessment of cytosolic DNA accumulation in mammalian cells. Sato A, Buque A, Yamazaki T, Bloy N, Petroni G, Galluzzi L.STAR Protoc. 2021 May 18;2(2):100488. doi: 10.1016/j.xpro.2021.100488. eCollection 2021 Jun 18. PMID: 34041502
Could Protons Promote Tumor Control by Avoiding Lymphopenia? Deutsch E, Cengel KA, Galluzzi L, Levy A.J Thorac Oncol. 2021 Jun;16(6):e39-e41. doi: 10.1016/j.jtho.2021.01.1614. PMID: 34034888
Clinical utility of whole-genome sequencing in precision oncology. Rosenquist R, Cuppen E, Buettner R, Caldas C, Dreau H, Elemento O, Frederix G, Grimmond S, Haferlach T, Jobanputra V, Meggendorfer M, Mullighan CG, Wordsworth S, Schuh A.Semin Cancer Biol. 2021 Jun 25:S1044-579X(21)00189-9. doi: 10.1016/j.semcancer.2021.06.018. Online ahead of print. PMID: 34175442
Androgen receptor variant shows heterogeneous expression in prostate cancer according to differentiation stage. Gjyrezi A, Galletti G, Zhang J, Worroll D, Sigouros M, Kim S, Cooley V, Ballman KV, Ocean AJ, Shah MA, Scandura JM, Sboner A, Nanus DM, Beltran H, Tagawa S, Giannakakou P.Commun Biol. 2021 Jun 24;4(1):785. doi: 10.1038/s42003-021-02321-9. PMID: 34168263

May

Seasonal Regulation of Metabolism: The Effect of Wintertime Fasting and Autumnal Fattening on Key Central Regulators of Metabolism and the Metabolic Profile of the Raccoon Dog ( Nyctereutes Procyonoides). Niiranen L, Mäkelä KA, Dona A, Krumsiek J, Karhu T, Mäkinen MJ, Thalmann O, Saarela S, Herzig KH.Int J Mol Sci. 2021 May 7;22(9):4965. doi: 10.3390/ijms22094965. PMID: 34067001
Immunology of Cell Death in Cancer Immunotherapy. Galluzzi L, Garg AD.Cells. 2021 May 15;10(5):1208. doi: 10.3390/cells10051208. PMID: 34063358
Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia. Sugita M, Wilkes DC, Bareja R, Eng KW, Nataraj S, Jimenez-Flores RA, Yan L, De Leon JP, Croyle JA, Kaner J, Merugu S, Sharma S, MacDonald TY, Noorzad Z, Panchal P, Pancirer D, Cheng S, Xiang JZ, Olson L, Van Besien K, Rickman DS, Mathew S, Tam W, Rubin MA, Beltran H, Sboner A, Chiosis G, Elemento O, Roboz GJ, Mosquera JM, Guzman ML.NPJ Precis Oncol. 2021 May 26;5(1):44. doi: 10.1038/s41698-021-00183-2. PMID: 34040147
Towards artificial intelligence-driven pathology assessment for hematological malignancies. Elemento O.Blood Cancer Discov. 2021 May;2(3):195-197. doi: 10.1158/2643-3230.bcd-21-0048. Epub 2021 Mar 22. PMID: 34027414
The role of dendritic cells in cancer and anti-tumor immunity. Marciscano AE, Anandasabapathy N.Semin Immunol. 2021 May 19:101481. doi: 10.1016/j.smim.2021.101481. Online ahead of print. PMID: 34023170
Tumor subtype defines distinct pathways of molecular and clinical progression in primary prostate cancer. Liu D, Augello MA, Grbesa I, Prandi D, Liu Y, Shoag JE, Karnes RJ, Trock BJ, Klein EA, Den RB, Demichelis F, Davicioni E, Sboner A, Barbieri CE.J Clin Invest. 2021 May 17;131(10):e147878. doi: 10.1172/JCI147878. PMID: 33998599
Deep learning predicts chromosomal instability from histopathology images. Xu Z, Verma A, Naveed U, Bakhoum SF, Khosravi P, Elemento O.iScience. 2021 Apr 3;24(5):102394. doi: 10.1016/j.isci.2021.102394. eCollection 2021 May 21. PMID: 33997679
Immune-inflammatory biomarkers as prognostic factors for immunotherapy in pretreated advanced urinary tract cancer patients: an analysis of the Italian SAUL cohort. Fornarini G, Rebuzzi SE, Banna GL, Calabrò F, Scandurra G, De Giorgi U, Masini C, Baldessari C, Naglieri E, Caserta C, Manacorda S, Maruzzo M, Milella M, Buttigliero C, Tambaro R, Ermacora P, Morelli F, Nolè F, Astolfi C, Sternberg CN.ESMO Open. 2021 May 10;6(3):100118. doi: 10.1016/j.esmoop.2021.100118. Online ahead of print. PMID: 33984678
SAUL, a single-arm study of atezolizumab for chemotherapy-pretreated locally advanced or metastatic carcinoma of the urinary tract: outcomes by key baseline factors, PD-L1 expression and prior platinum therapy. Bamias A, Merseburger AS, Loriot Y, James N, Choy E, Castellano D, Lopez-Rios F, Calabrò F, Kramer M, de Velasco G, Zakopoulou R, Tzannis K, Sternberg CN.ESMO Open. 2021 May 10;6(3):100152. doi: 10.1016/j.esmoop.2021.100152. Online ahead of print. PMID: 33984672

April

Incorporating cytologic adequacy assessment into precision oncology workflow using telepathology: An institutional experience. Al Zoughbi W, Kim D, Alperstein SA, Ohara K, Manohar J, Greco N, Khani F, Robinson BD, Rao RA, Elemento O, Mosquera JM, Siddiqui MT. Cancer Cytopathol. 2021 Apr 30. doi: 10.1002/cncy.22441. Online ahead of print. PMID: 33929788.
A molecular single-cell lung atlas of lethal COVID-19. Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B.Nature. 2021 Apr 29. doi: 10.1038/s41586-021-03569-1. Online ahead of print. PMID: 33915568.
Artificial intelligence in oncology: From bench to clinic. Elkhader J, Elemento O.Semin Cancer Biol. 2021 Apr 26:S1044-579X(21)00114-0. doi: 10.1016/j.semcancer.2021.04.013. Online ahead of print. PMID: 33915289.
Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome. Bourdenx M, Martín-Segura A, Scrivo A, Rodriguez-Navarro JA, Kaushik S, Tasset I, Diaz A, Storm NJ, Xin Q, Juste YR, Stevenson E, Luengo E, Clement CC, Choi SJ, Krogan NJ, Mosharov EV, Santambrogio L, Grueninger F, Collin L, Swaney DL, Sulzer D, Gavathiotis E, Cuervo AM.Cell. 2021 Apr 14:S0092-8674(21)00379-2. doi: 10.1016/j.cell.2021.03.048. Online ahead of print. PMID: 33891876.
A naturally occurring mutation in ATP synthase subunit c is associated with increased damage following hypoxia/reoxygenation in STEMI patients. Morciano G, Pedriali G, Bonora M, Pavasini R, Mikus E, Calvi S, Bovolenta M, Lebiedzinska-Arciszewska M, Pinotti M, Albertini A, Wieckowski MR, Giorgi C, Ferrari R, Galluzzi L, Campo G, Pinton P.Cell Rep. 2021 Apr 13;35(2):108983. doi: 10.1016/j.celrep.2021.108983. PMID: 33852870.
Safety and Efficacy of Atezolizumab in Understudied Populations with Pretreated Urinary Tract Carcinoma: Subgroup Analyses of the SAUL Study in Real-World Practice. Merseburger AS, Castellano D, Powles T, Loriot Y, Retz M, Voortman J, Huddart RA, Gedye C, Van Der Heijden MS, Gurney H, Ong M, de Ducla S, Pavlova J, Fear S, Sternberg CN.J Urol. 2021 Apr 9:101097JU0000000000001768. doi: 10.1097/JU.0000000000001768. Online ahead of print. PMID: 33835866.
QSER1 protects DNA methylation valleys from de novo methylation. Dixon G, Pan H, Yang D, Rosen BP, Jashari T, Verma N, Pulecio J, Caspi I, Lee K, Stransky S, Glezer A, Liu C, Rivas M, Kumar R, Lan Y, Torregroza I, He C, Sidoli S, Evans T, Elemento O, Huangfu D.Science. 2021 Apr 9;372(6538):eabd0875. doi: 10.1126/science.abd0875. PMID: 33833093.
Structural variant evolution after telomere crisis. Dewhurst SM, Yao X, Rosiene J, Tian H, Behr J, Bosco N, Takai KK, de Lange T, Imieliński M.Nat Commun. 2021 Apr 7;12(1):2093. doi: 10.1038/s41467-021-21933-7. PMID: 33828097.
RNA-sequencing data-driven dissection of human plasma cell differentiation reveals new potential transcription regulators. Kassambara A, Herviou L, Ovejero S, Jourdan M, Thibaut C, Vikova V, Pasero P, Elemento O, Moreaux J.Leukemia. 2021 Apr 6. doi: 10.1038/s41375-021-01234-0. Online ahead of print. PMID: 33824465.
Predicting Outcomes in Men With Metastatic Nonseminomatous Germ Cell Tumors (NSGCT): Results From the IGCCCG Update Consortium. Gillessen S, Sauvé N, Collette L, Daugaard G, de Wit R, Albany C, Tryakin A, Fizazi K, Stahl O, Gietema JA, De Giorgi U, Cafferty FH, Hansen AR, Tandstad T, Huddart RA, Necchi A, Sweeney CJ, Garcia-Del-Muro X, Heng DYC, Lorch A, Chovanec M, Winquist E, Grimison P, Feldman DR, Terbuch A, Hentrich M, Bokemeyer C, Negaard H, Fankhauser C, Shamash J, Vaughn DJ, Sternberg CN, Heidenreich A, Beyer J; International Germ Cell Cancer Classification Update Consortium. J Clin Oncol. 2021 Apr 6:JCO2003296. doi: 10.1200/JCO.20.03296. Online ahead of print. PMID: 33822655.
Artificial Intelligence in Cancer Research and Precision Medicine. Bhinder B, Gilvary C, Madhukar NS, Elemento O.Cancer Discov. 2021 Apr;11(4):900-915. doi: 10.1158/2159-8290.CD-21-0090. PMID: 33811123.
Genomics and Cancer Disparities: The Justice and Power of Inclusion. Davis MB.Cancer Discov. 2021 Apr;11(4):805-809. doi: 10.1158/2159-8290.CD-21-0225. PMID: 33811116.
Plasma tumor gene conversions after one cycle abiraterone acetate for metastatic castration-resistant prostate cancer: a biomarker analysis of a multicenter international trial. Jayaram A, Wingate A, Wetterskog D, Wheeler G, Sternberg CN, Jones R, Berruti A, Lefresne F, Lahaye M, Thomas S, Gormley M, Meacham F, Garg K, Lim LP, Merseburger AS, Tombal B, Ricci D, Attard G.Ann Oncol. 2021 Mar 29:S0923-7534(21)01074-7. doi: 10.1016/j.annonc.2021.03.196. Online ahead of print. PMID: 33794293.
Preface: Chemical carcinogenesis in mice as a model of human cancer: Pros and cons. Buqué A, Galluzzi L.Methods Cell Biol. 2021;163:xvii-xxv. doi: 10.1016/S0091-679X(21)00040-6. PMID: 33785172.

March

Cabazitaxel versus abiraterone or enzalutamide in metastatic castration-resistant prostate cancer: post hoc analysis of the CARD study excluding chemohormonal therapy for castrate-naive disease.
Suzuki H, Castellano D, de Bono J, Sternberg CN, Fizazi K, Tombal B, Wülfing C, Foster MC, Ozatilgan A, Geffriaud-Ricouard C, deWit R.Jpn J Clin Oncol. 2021 Mar 19:hyab028. doi: 10.1093/jjco/hyab028. Online ahead of print. PMID: 33738495
TIM-3 levels correlate with enhanced NK cell cytotoxicity and improved clinical outcome in AML patients.
Rakova J, Truxova I, Holicek P, Salek C, Hensler M, Kasikova L, Pasulka J, Holubova M, Kovar M, Lysak D, Kline JP, Racil Z, Galluzzi L, Spisek R, Fucikova J.Oncoimmunology. 2021 Mar 8;10(1):1889822. doi: 10.1080/2162402X.2021.1889822. PMID: 33758676
Targeting replication stress to tackle cancer stem cells. Galluzzi L.Cell Death Dis. 2021 Mar 24;12(4):315. doi: 10.1038/s41419-021-03609-8. PMID: 33762581
The spatial landscape of lung pathology during COVID-19 progression. Rendeiro AF, Ravichandran H, Bram Y, Chandar V, Kim J, Meydan C, Park J, Foox J, Hether T, Warren S, Kim Y, Reeves J, Salvatore S, Mason CE, Swanson EC, Borczuk AC, Elemento O, Schwartz RE.Nature. 2021 Mar 29. doi: 10.1038/s41586-021-03475-6. Online ahead of print. PMID: 33780969
MPA/DMBA-driven mammary carcinomas. Buqué A, Perez-Lanzón M, Petroni G, Humeau J, Bloy N, Yamazaki T, Sato A, Kroemer G, Galluzzi L.Methods Cell Biol. 2021;163:1-19. doi: 10.1016/bs.mcb.2020.08.003. Epub 2020 Oct 1. PMID: 33785159
Plasma tumor gene conversions after one cycle abiraterone acetate for metastatic castration-resistant prostate cancer: a biomarker analysis of a multi-center international trial.
Jayaram A, Wingate A, Wetterskog D, Wheeler G, Sternberg CN, Jones R, Berruti A, Lefresne F, Lahaye M, Thomas S, Gormley M, Meacham F, Garg K, Lim LP, Merseburger AS, Tombal B, Ricci D, Attard G.Ann Oncol. 2021 Mar 29:S0923-7534(21)01074-7. doi: 10.1016/j.annonc.2021.03.196. Online ahead of print. PMID: 33794293
Preface: Chemical carcinogenesis in mice as a model of human cancer: Pros and cons.

Buqué A, Galluzzi L.Methods Cell Biol. 2021;163:xvii-xxv. doi: 10.1016/S0091-679X(21)00040-6. PMID: 33785172
Towards artificial intelligence-driven pathology assessment for hematological malignancies, EIPM Director Olivier Elemento, Ph.D., Blood Cancer Discovery, March 22.
Immune checkpoint inhibitor-associated myocarditis: manifestations and mechanisms, Moslehi J, Lichtman AH, Sharpe AH, Galluzzi L, Kitsis RN.J Clin Invest. 2021 Mar 1;131(5):e145186. doi: 10.1172/JCI145186. PMID: 33645548
Immunogenic Therapies Drive CAR T Cells towards Superior Efficacy. Petroni G, Kroemer G, Galluzzi L.Trends Cancer. 2021 Mar;7(3):179-181. doi: 10.1016/j.trecan.2021.01.005. Epub 2021 Jan 29. PMID: 33518493
Chemical systems biology reveals mechanisms of glucocorticoid receptor signaling. Bruno NE, Nwachukwu JC, Srinivasan S, Nettles CC, Izard T, Jin Z, Nowak J, Cameron MD, Boregowda SV, Phinney DG, Elemento O, Liu X, Ortlund EA, Houtman R, Stavreva DA, Hager GL, Kamenecka TM, Kojetin DJ, Nettles KW.Nat Chem Biol. 2021 Mar;17(3):307-316. doi: 10.1038/s41589-020-00719-w. Epub 2021 Jan 28. PMID: 33510451
Radiotherapy-exposed CD8+ and CD4+ neoantigens enhance tumor control. Lhuillier C, Rudqvist NP, Yamazaki T, Zhang T, Charpentier M, Galluzzi L, Dephoure N, Clement CC, Santambrogio L, Zhou XK, Formenti SC, Demaria S.J Clin Invest. 2021 Mar 1;131(5):e138740. doi: 10.1172/JCI138740. PMID: 3347630
Adjuvant Pazopanib Versus Placebo After Nephrectomy in Patients With Localized or Locally Advanced Renal Cell Carcinoma: Final Overall Survival Analysis of the Phase 3 PROTECT Trial, Motzer RJ, Russo P, Haas N, Doehn C, Donskov F, Gross-Goupil M, Varlamov S, Kopyltsov E, Lee JL, Lim HY, Melichar B, Zemanova M, Rini B, Choueiri TK, Wood L, Reaume MN, Stenzl A, Chowdhury S, McDermott R, Michael A, Izquierdo M, Aimone P, Zhang H, Sternberg CN; PROTECT study investigators.Eur Urol. 2021 Mar;79(3):334-338. doi: 10.1016/j.eururo.2020.12.029. Epub 2021 Jan 15. PMID: 33461782Affiliations.
Survival and New Prognosticators in Metastatic Seminoma: Results From the IGCCCG-Update Consortium, Jörg Beyer, Laurence Collette, Nicolas Sauvé, Gedske Daugaard, Darren R Feldman, Torgrim Tandstad, Alexey Tryakin, Olof Stahl, Enrique Gonzalez-Billalabeitia, Ugo De Giorgi, Stéphane Culine, Ronald de Wit, Aaron R Hansen, Marko Bebek, Angelika Terbuch, Costantine Albany, Marcus Hentrich, Jourik A Gietema, Helene Negaard, Robert A Huddart, Anja Lorch, Fay H Cafferty, Daniel Y C Heng, Christopher J Sweeney, Eric Winquis, Michal Chovanec, Christian Fankhauser, Daniel Stark, Peter Grimison, Andrea Necchi, Ben Tran, Axel Heidenreich, Jonathan Shamash, Cora N Sternberg, David J Vaughn, Ignacio Duran, Carsten Bokemeyer, Anna Patrikidou, Richard Cathomas, Samson Assele, Silke Gillessen. International Germ Cell Cancer Classification Update Consorti2021 Mar 17;JCO2003292.PMID: 33729863
Cabazitaxel versus abiraterone or enzalutamide in metastatic castration-resistant prostate cancer: post hoc analysis of the CARD study excluding chemohormonal therapy for castrate-naive disease, Hiroyoshi Suzuki, Daniel Castellano, Johann de Bono, Cora N Sternberg, Karim Fizazi, Bertrand Tombal, Christian Wülfing, Meredith C Foster, Ayse Ozatilgan, Christine Geffriaud-Ricouard, Ronald de Wit. Jpn J Clin Oncolo. doi: 10.1093/jjco/hyab02. 2021 Mar 19;hyab028.
Adjuvant atezolizumab versus observation in muscle-invasive urothelial carcinoma (IMvigor010): a multicentre, open-label, randomised, phase 3 trial

Joaquim Bellmunt, Maha Hussain, Jürgen E Gschwend, Peter Albers, Stephane Oudard, Daniel Castellano, Siamak Daneshman, Hiroyuki

Nishiyama, Martin Majchrowicz, Viraj Degaonkar, Yi Shi, Sanjeev Mariathasan, Petros Grivas, Alexandra Drakaki, Peter H O’Donnell,

Jonathan E Rosenberg, Daniel M Geynisman, Daniel P Petrylak, Jean Hoffman-Censits, Jens Bedke, Arash Rezazadeh Kalebasty,

Yousef Zakharia, Michiel S van der Heijden, Cora N Sternberg, Nicole N Davarpanah, Thomas Powles, IMvigor010 Study Group

Affiliations. Lancet Oncology. PMID: 33721560
Avelumab first-line maintenance in locally advanced or metastatic urothelial carcinoma: Applying clinical trial findings to clinical practice. Grivas P, Agarwal N, Pal S, Kalebasty AR, Sridhar SS, Smith J, Devgan G, Sternberg CN, Bellmunt J.Cancer Treat Rev. 2021 Mar 22;97:102187. doi: 10.1016/j.ctrv.2021.102187. Online ahead of print. PMID: 33839438

February

Impact of treatment schedule on the efficacy of cytostatic and immunostimulatory agents. Petroni G, Galluzzi L. Oncoimmunology. 2021 Feb 19;10(1):1889101. doi: 10.1080/2162402X.2021.1889101. PMID: 33659100
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition), Galluzzi L. and colleagues, Autophagy. 2021, Feb 8:1-382. doi: 10.1080/15548627.2020.1797280. Online ahead of print. PMID: 33634751
Patient-derived xenografts and organoids model therapy response in prostate cancer, Karkampouna S, La Manna F, Benjak A, Kiener M, De Menna M, Zoni E, Grosjean J, Klima I, Garofoli A, Bolis M, Vallerga A, Theurillat JP, De Filippo MR, Genitsch V, Keller D, Booij TH, Stirnimann CU, Eng K, Sboner A, Ng CKY, Piscuoglio S, Gray PC, Spahn M, Rubin MA, Thalmann GN, Kruithof-de Julio M.Nat Commun. 2021 Feb 18;12(1):1117. doi: 10.1038/s41467-021-21300-6. PMID: 33602919
Intratumoral heterogeneity in cancer progression and response to immunotherapy, Vitale I, Shema E, Loi S, Galluzzi L.Nat Med. 2021. Feb;27(2):212-224. doi: 10.1038/s41591-021-01233-9. Epub 2021 Feb 11. PMID: 33574607
Oncosuppressive functions of PIDD1 in response to centrosome amplification, Vitale I, Manic G, Galluzzi L.Cell Death Dis. 2021 Feb 11;12(2):175. doi: 10.1038/s41419-021-03467-4. PMID: 33574219
Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer, Armstrong AJ, Li X, Tucker M, Li S, Mu XJ, Eng KW, Sboner A, Rubin M, Gerstein M.Prostate Cancer Prostatic Dis. 2021 Feb 10. doi: 10.1038/s41391-021-00324-5. Online ahead of print. PMID: 33568750
Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N; TCGA Research Network, Meyerson M, Govindan R, Imielinski M.Cell Rep. 2021 Feb 2;34(5):108707. doi: 10.1016/j.celrep.2021.108707. PMID: 33535033
First-line treatment of metastatic clear cell renal cell carcinoma: a decision-making analysis among experts. Aeppli S, Schmaus M, Eisen T, Escudier B, Grünwald V, Larkin J, McDermott D, Oldenburg J, Porta C, Rini BI, Schmidinger M, Sternberg CN, Rothermundt C, Putora PM.ESMO Open. 2021 Feb;6(1):100030. doi: 10.1016/j.esmoop.2020.100030. Epub 2021 Jan 15. PMID: 33460963
Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Rivas MA, Meydan C, Chin CR, Challman MF, Kim D, Bhinder B, Kloetgen A, Viny AD, Teater MR, McNally DR, Doane AS, Béguelin W, Fernández MTC, Shen H, Wang X, Levine RL, Chen Z, Tsirigos A, Elemento O, Mason CE, Melnick AM.Nat Immunol. 2021 Feb;22(2):240-253. doi: 10.1038/s41590-020-00827-8. Epub 2021 Jan 11. PMID: 33432228

January

Adjuvant Pazopanib Versus Placebo After Nephrectomy in Patients With Localized or Locally Advanced Renal Cell Carcinoma: Final Overall Survival Analysis of the Phase 3 PROTECT TrialRobert J Motzer, Paul Russo, Naomi Haas, Christian Doehn, Frede Donskov, Marine Gross-Goupil, Sergei Varlamov, Evgeny Kopyltsov, Jae Lyun Lee, Ho Yeong Lim, Bohuslav Melichar, Milada Zemanova, Brian Rini, Toni K Choueiri, Lori Wood, M Neil Reaume, Arnulf Stenzl, Simon Chowdhury, Ray McDermott, Agnieszka Michael, Miguel Izquierdo, Paola Aimone, Hong Zhang, Cora N Sternberg. 2021 Mar;79(3):334-338. doi: 10.1016/j.eururo.2020.12.029. Epub 2021 Jan 15.PMID: 33461782
Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology. Shaham Beg, Rohan Bareja, Kentaro Ohara, Kenneth Wha Eng, David C Wilkes, David J Pisapia, Wael Al Zoughbi, Sarah Kudman, Wei Zhang, Rema Rao, Jyothi Manohar, Troy Kane, Michael Sigouros, Jenny Zhaoying Xiang, Francesca Khani, Brian D Robinson, Bishoy M Faltas, Cora N Sternberg, Andrea Sboner, Himisha Beltran, Olivier Elemento, Juan Miguel Mosquera. 2021 Jan;14(1):100944. PMID: 33190043
Ketosis versus carbotoxicity – metabolism determines the outcome of cancer immunotherapy. Buqué A, Galluzzi L, Kroemer G.Mol Cell Oncol. 2021 Jan 15;8(1):1868266. doi: 10.1080/23723556.2020.1868266. eCollection 2021. PMID: 33553614
Radiotherapy Delivered before CDK4/6 Inhibitors Mediates Superior Therapeutic Effects in ER ⁺ Breast Cancer. Petroni G, Buqué A, Yamazaki T, Bloy N, Liberto MD, Chen-Kiang S, Formenti SC, Galluzzi L.Clin Cancer Res. 2021 Jan 25. doi: 10.1158/1078-0432.CCR-20-3871. Online ahead of print. PMID: 33495311
Genomic Testing in Patients with Metastatic Castration-resistant Prostate Cancer: A Pragmatic Guide for Clinicians. Merseburger AS, Waldron N, Ribal MJ, Heidenreich A, Perner S, Fizazi K, Sternberg CN, Mateo J, Wirth MP, Castro E, Olmos D, Petrylak DP, Chowdhury S.Eur Urol. 2021 Jan 22:S0302-2838(20)31025-3. doi: 10.1016/j.eururo.2020.12.039. Online ahead of print. PMID: 33494937
Targeting Cancer Heterogeneity with Immune Responses Driven by Oncolytic Peptides. Vitale I, Yamazaki T, Wennerberg E, Sveinbjørnsson B, Rekdal Ø, Demaria S, Galluzzi L.Trends Cancer. 2021 Jan 11:S2405-8033(20)30339-3. doi: 10.1016/j.trecan.2020.12.012. Online ahead of print. PMID: 33446447
E2F1 regulates testicular descent and controls spermatogenesis by influencing WNT4 signaling. Jorgez CJ, Seth A, Wilken N, Bournat JC, Chen CH, Lamb DJ.Development. 2021 Jan 13;148(1):dev191189. doi: 10.1242/dev.191189. PMID: 33441379

2020

December

A Panel of Six Biomarkers Significantly Improves the Prediction of Type 2 Diabetes in the MONICA/KORA Study Population. Thorand B, Zierer A, Büyüközkan M, Krumsiek J, Bauer A, Schederecker F, Sudduth-Klinger J, Meisinger C, Grallert H, Rathmann W, Roden M, Peters A, Koenig W, Herder C, Huth C.J Clin Endocrinol Metab. 2020 Dec 31:dgaa953. doi: 10.1210/clinem/dgaa953. Online ahead of print. PMID: 33382400
Metastasis and immune evasion from extracellular cGAMP hydrolysis. Li J, Duran MA, Dhanota N, Chatila WK, Bettigole SE, Kwon J, Sriram RK, Humphries MP, Salto-Tellez M, James JA, Hanna MG, Melms JC, Vallabhaneni S, Litchfield K, Usaite I, Biswas D, Bareja R, Li HW, Martin ML, Dorsaint P, Cavallo JA, Li P, Pauli C, Gottesdiener L, DiPardo BJ, Hollmann TJ, Merghoub T, Wen HY, Reis-Filho JS, Riaz N, Su SM, Kalbasi A, Vasan N, Powell SN, Wolchok JD, Elemento O, Swanton C, Shoushtari AN, Parkes EE, Izar B, Bakhoum SF.Cancer Discov. 2020 Dec 28:CD-20-0387. doi: 10.1158/2159-8290.CD-20-0387. Online ahead of print. PMID: 33372007
Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression. Rendeiro AF, Casano J, Vorkas CK, Singh H, Morales A, DeSimone RA, Ellsworth GB, Soave R, Kapadia SN, Saito K, Brown CD, Hsu J, Kyriakides C, Chiu S, Cappelli LV, Cacciapuoti MT, Tam W, Galluzzi L, Simonson PD, Elemento O, Salvatore M, Inghirami G.Life Sci Alliance. 2020 Dec 24;4(2):e202000955. doi: 10.26508/lsa.202000955. Print 2021 Feb. PMID: 33361110
Immunomodulation by targeted anticancer agents. Petroni G, Buqué A, Zitvogel L, Kroemer G, Galluzzi L.Cancer Cell. 2020 Dec 17:S1535-6108(20)30601-2. doi: 10.1016/j.ccell.2020.11.009. Online ahead of print. PMID: 33338426
Leveraging phenotypic variability to identify genetic interactions in human phenotypes. Marderstein AR, Davenport ER, Kulm S, Van Hout CV, Elemento O, Clark AG.Am J Hum Genet. 2021 Jan 7;108(1):49-67. doi: 10.1016/j.ajhg.2020.11.016. Epub 2020 Dec 15. PMID: 33326753
Publisher Correction: Mutation-selection balance and compensatory mechanisms in tumour evolution. Persi E, Wolf YI, Horn D, Ruppin E, Demichelis F, Gatenby RA, Gillies RJ, Koonin EV.Nat Rev Genet. 2020 Dec 14. doi: 10.1038/s41576-020-00313-9. Online ahead of print. PMID: 33318707
Autophagy in the cancer-immunity dialogue. Yamazaki T, Bravo-San Pedro JM, Galluzzi L, Kroemer G, Pietrocola F.Adv Drug Deliv Rev. 2021 Feb;169:40-50. doi: 10.1016/j.addr.2020.12.003. Epub 2020 Dec 8. PMID: 33301821
Common germline-somatic variant interactions in advanced urothelial cancer. Vosoughi A, Zhang T, Shohdy KS, Vlachostergios PJ, Wilkes DC, Bhinder B, Tagawa ST, Nanus DM, Molina AM, Beltran H, Sternberg CN, Motanagh S, Robinson BD, Xiang J, Fan X, Chung WK, Rubin MA, Elemento O, Sboner A, Mosquera JM, Faltas BM.Nat Commun. 2020 Dec 3;11(1):6195. doi: 10.1038/s41467-020-19971-8. PMID: 33273457
Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage. Chu CS, Hellmuth JC, Singh R, Ying HY, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG.Mol Cell. 2020 Dec 3;80(5):845-861.e10. doi: 10.1016/j.molcel.2020.10.036. Epub 2020 Nov 23. PMID: 33232656
Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome. Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W.Arch Pathol Lab Med. 2020 Dec 1;144(12):1535-1546. doi: 10.5858/arpa.2019-0162-OA. PMID: 32045275

November

Mutation-selection balance and compensatory mechanisms in tumour evolution. Persi E, Wolf YI, Horn D, Ruppin E, Demichelis F, Gatenby RA, Gillies RJ, Koonin EV.Nat Rev Genet. 2020 Nov 30. doi: 10.1038/s41576-020-00299-4. Online ahead of print. PMID: 33257848
A Workflow for Missing Values Imputation of Untargeted Metabolomics Data. Faquih T, van Smeden M, Luo J, le Cessie S, Kastenmüller G, Krumsiek J, Noordam R, van Heemst D, Rosendaal FR, van Hylckama Vlieg A, Willems van Dijk K, Mook-Kanamori DO.Metabolites. 2020 Nov 26;10(12):486. doi: 10.3390/metabo10120486. PMID: 33256233
Detection of immunogenic cell death and its relevance for cancer therapy. Fucikova J, Kepp O, Kasikova L, Petroni G, Yamazaki T, Liu P, Zhao L, Spisek R, Kroemer G, Galluzzi L.Cell Death Dis. 2020 Nov 26;11(11):1013. doi: 10.1038/s41419-020-03221-2. PMID: 33243969
Canary in the Coal Mine? Male Infertility as a Marker of Overall Health. Punjani N, Lamb DJ.Annu Rev Genet. 2020 Nov 23;54:465-486. doi: 10.1146/annurev-genet-022020-023434. PMID: 33228412
Clinical, regional, and genetic characteristics of Covid-19 patients from UK Biobank. Kolin DA, Kulm S, Christos PJ, Elemento O.PLoS One. 2020 Nov 17;15(11):e0241264. doi: 10.1371/journal.pone.0241264. eCollection 2020. PMID: 33201886
Mutations in long-lived epithelial stem cells and their clonal progeny in pre-malignant lesions and in oral squamous cell carcinoma. Melis M, Zhang T, Scognamiglio T, Gudas LJ.Carcinogenesis. 2020 Nov 13;41(11):1553-1564. doi: 10.1093/carcin/bgaa019. PMID: 32115621
Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology. Beg S, Bareja R, Ohara K, Eng KW, Wilkes DC, Pisapia DJ, Zoughbi WA, Kudman S, Zhang W, Rao R, Manohar J, Kane T, Sigouros M, Xiang JZ, Khani F, Robinson BD, Faltas BM, Sternberg CN, Sboner A, Beltran H, Elemento O, Mosquera JM.Transl Oncol. 2021 Jan;14(1):100944. doi: 10.1016/j.tranon.2020.100944. Epub 2020 Nov 12. PMID: 33190043
Class IA PI3Ks regulate subcellular and functional dynamics of IDO1. Iacono A, Pompa A, De Marchis F, Panfili E, Greco FA, Coletti A, Orabona C, Volpi C, Belladonna ML, Mondanelli G, Albini E, Vacca C, Gargaro M, Fallarino F, Bianchi R, De Marcos Lousa C, Mazza EM, Bicciato S, Proietti E, Milano F, Martelli MP, Iamandii IM, Graupera Garcia-Mila M, Llena Sopena J, Hawkins P, Suire S, Okkenhaug K, Stark AK, Grassi F, Bellucci M, Puccetti P, Santambrogio L, Macchiarulo A, Grohmann U, Pallotta MT.EMBO Rep. 2020 Nov 7;21(12):e49756. doi: 10.15252/embr.201949756. Online ahead of print. PMID: 33159421
Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity. Cyrta J, Augspach A, De Filippo MR, Prandi D, Thienger P, Benelli M, Cooley V, Bareja R, Wilkes D, Chae SS, Cavaliere P, Dephoure N, Uldry AC, Lagache SB, Roma L, Cohen S, Jaquet M, Brandt LP, Alshalalfa M, Puca L, Sboner A, Feng F, Wang S, Beltran H, Lotan T, Spahn M, Kruithof-de Julio M, Chen Y, Ballman KV, Demichelis F, Piscuoglio S, Rubin MA.Nat Commun. 2020 Nov 3;11(1):5549. doi: 10.1038/s41467-020-19328-1. PMID: 33144576
Predictive modeling in reproductive medicine: Where will the future of artificial intelligence research take us? Curchoe CL, Malmsten J, Bormann C, Shafiee H, Flores-Saiffe Farias A, Mendizabal G, Chavez-Badiola A, Sigaras A, Alshubbar H, Chambost J, Jacques C, Pena CA, Drakeley A, Freour T, Hajirasouliha I, Hickman CFL, Elemento O, Zaninovic N, Rosenwaks Z.Fertil Steril. 2020 Nov;114(5):934-940. doi: 10.1016/j.fertnstert.2020.10.040. PMID: 33160516
Precision medicine and artificial intelligence: overview and relevance to reproductive medicine. Fertil Steril. 2020 Nov;114(5):908-913. doi: 10.1016/j.fertnstert.2020.09.156. PMID: 33160512

October

Genetic implications of male-reproductive-health-associated comorbidities. Punjani N, Kang C, Lamb DJ.Turk J Urol. 2020 Oct 30. doi: 10.5152/tud.2020.20463. Online ahead of print. PMID: 33201798
Identification of SARS-CoV-2 inhibitors using lung and colonic organoids. Han Y, Duan X, Yang L, Nilsson-Payant BE, Wang P, Duan F, Tang X, Yaron TM, Zhang T, Uhl S, Bram Y, Richardson C, Zhu J, Zhao Z, Redmond D, Houghton S, Nguyen DT, Xu D, Wang X, Jessurun J, Borczuk A, Huang Y, Johnson JL, Liu Y, Xiang J, Wang H, Cantley LC, tenOever BR, Ho DD, Pan FC, Evans T, Chen HJ, Schwartz RE, Chen S.Nature. 2021 Jan;589(7841):270-275. doi: 10.1038/s41586-020-2901-9. Epub 2020 Oct 28. PMID: 33116299
Multi-omics integration in biomedical research – A metabolomics-centric review. Wörheide MA, Krumsiek J, Kastenmüller G, Arnold M. Anal Chim Acta. 2021 Jan 2;1141:144-162. doi: 10.1016/j.aca.2020.10.038. Epub 2020 Oct 22. PMID: 33248648
Converging focal radiation and immunotherapy in a preclinical model of triple negative breast cancer: contribution of VISTA blockade. Pilones KA, Hensler M, Daviaud C, Kraynak J, Fucikova J, Galluzzi L, Demaria S, Formenti SC.Oncoimmunology. 2020 Oct 20;9(1):1830524. doi: 10.1080/2162402X.2020.1830524. PMID: 33150045
Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription. Rimel JK, Poss ZC, Erickson B, Maas ZL, Ebmeier CC, Johnson JL, Decker TM, Yaron TM, Bradley MJ, Hamman KB, Hu S, Malojcic G, Marineau JJ, White PW, Brault M, Tao L, DeRoy P, Clavette C, Nayak S, Damon LJ, Kaltheuner IH, Bunch H, Cantley LC, Geyer M, Iwasa J, Dowell RD, Bentley DL, Old WM, Taatjes DJ.Genes Dev. 2020 Oct 15;34(21-22):1452-73. doi: 10.1101/gad.341545.120. Online ahead of print. PMID: 33060135
A strategy to incorporate prior knowledge into correlation network cutoff selection. Benedetti E, Pučić-Baković M, Keser T, Gerstner N, Büyüközkan M, Štambuk T, Selman MHJ, Rudan I, Polašek O, Hayward C, Al-Amin H, Suhre K, Kastenmüller G, Lauc G, Krumsiek J.Nat Commun. 2020 Oct 14;11(1):5153. doi: 10.1038/s41467-020-18675-3. PMID: 33056991
Two distinct immunopathological profiles in autopsy lungs of COVID-19. Nienhold R, Ciani Y, Koelzer VH, Tzankov A, Haslbauer JD, Menter T, Schwab N, Henkel M, Frank A, Zsikla V, Willi N, Kempf W, Hoyler T, Barbareschi M, Moch H, Tolnay M, Cathomas G, Demichelis F, Junt T, Mertz KD.Nat Commun. 2020 Oct 8;11(1):5086. doi: 10.1038/s41467-020-18854-2. PMID: 33033248.
Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M.Cell. 2020 Oct 1;183(1):197-210.e32. doi: 10.1016/j.cell.2020.08.006. PMID: 33007263

September

Short-Acting Testosterone: More Physiologic? Westfield G, Kaiser UB, Lamb DJ, Ramasamy R.Front Endocrinol (Lausanne). 2020 Sep 30;11:572465. doi: 10.3389/fendo.2020.572465. eCollection 2020. PMID: 33117287
Limitations of Detecting Genetic Variants from the RNA-Seq Data in Tissue and FNA Samples. Kaya C, Dorsaint P, Mercurio S, Campbell AM, Wha Eng K, Nikiforova MN, Elemento O, Nikiforov YE, Sboner A.Thyroid. 2020 Sep 18. doi: 10.1089/thy.2020.0307. Online ahead of print. PMID: 32948110
Publisher Correction: Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer. Buqué A, Bloy N, Perez-Lanzón M, Iribarren K, Humeau J, Pol JG, Levesque S, Mondragon L, Yamazaki T, Sato A, Aranda F, Durand S, Boissonnas A, Fucikova J, Senovilla L, Enot D, Hensler M, Kremer M, Stoll G, Hu Y, Massa C, Formenti SC, Seliger B, Elemento O, Spisek R, André F, Zitvogel L, Delaloge S, Kroemer G, Galluzzi L.Nat Commun. 2020 Sep 17;11(1):4787. doi: 10.1038/s41467-020-18719-8. PMID: 32943636
Quality of life in patients with metastatic prostate cancer following treatment with cabazitaxel versus abiraterone or enzalutamide (CARD): an analysis of a randomised, multicentre, open-label, phase 4 study. Fizazi K, Kramer G, Eymard JC, Sternberg CN, de Bono J, Castellano D, Tombal B, Wülfing C, Liontos M, Carles J, Iacovelli R, Melichar B, Sverrisdóttir Á, Theodore C, Feyerabend S, Helissey C, Oudard S, Facchini G, Poole EM, Ozatilgan A, Geffriaud-Ricouard C, Bensfia S, de Wit R.Lancet Oncol. 2020 Nov;21(11):1513-1525. doi: 10.1016/S1470-2045(20)30449-6. Epub 2020 Sep 11. PMID: 32926841
Caspase 2 and p53 Reunited in Tumor Control. Petroni G, Vitale I, Galluzzi L.Trends Cell Biol. 2020 Dec;30(12):917-918. doi: 10.1016/j.tcb.2020.09.001. Epub 2020 Sep 11. PMID: 32921524
The future of precision medicine: towards a more predictive personalized medicine. Elemento O.Emerg Top Life Sci. 2020 Sep 8;4(2):175-177. doi: 10.1042/ETLS20190197. PMID: 32856697
Systematic Assessment of Tumor Purity and Its Clinical Implications. Haider S, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W, Demichelis F, Loda M, Boutros PC; Cancer Genome Atlas Research Network.JCO Precis Oncol. 2020 Sep 4;4:PO.20.00016. doi: 10.1200/PO.20.00016. eCollection 2020. PMID: 33015524
In vivo T1 mapping for quantifying glymphatic system transport and cervical lymph node drainage. Xue Y, Liu X, Koundal S, Constantinou S, Dai F, Santambrogio L, Lee H, Benveniste H.Sci Rep. 2020 Sep 3;10(1):14592. doi: 10.1038/s41598-020-71582-x. PMID: 32884041
Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. Palikuqi B, Nguyen DT, Li G, Schreiner R, Pellegata AF, Liu Y, Redmond D, Geng F, Lin Y, Gómez-Salinero JM, Yokoyama M, Zumbo P, Zhang T, Kunar B, Witherspoon M, Han T, Tedeschi AM, Scottoni F, Lipkin SM, Dow L, Elemento O, Xiang JZ, Shido K, Spence JR, Zhou QJ, Schwartz RE, De Coppi P, Rabbany SY, Rafii S.Nature. 2020 Sep;585(7825):426-432. doi: 10.1038/s41586-020-2712-z. Epub 2020 Sep 9. PMID: 32908310
Author Correction: FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes. Adams EJ, Karthaus WR, Hoover E, Liu D, Gruet A, Zhang Z, Cho H, DiLoreto R, Chhangawala S, Liu Y, Watson PA, Davicioni E, Sboner A, Barbieri CE, Bose R, Leslie CS, Sawyers CL.Nature. 2020 Sep;585(7826):E20. doi: 10.1038/s41586-020-2678-x. PMID: 32895534.

August

NK cells beat T cells at early breast cancer control. Buque A, Bloy N, Petroni G, Kroemer G, Galluzzi L.Oncoimmunology. 2020
Aug 23;9(1):1806010. doi: 10.1080/2162402X.2020.1806010. PMID: 32923169
The transcription factor Maz is essential for normal eye development. Medina-Martinez O, Haller M, Rosenfeld JA, O’Neill MA, Lamb DJ,
Jamrich M.Dis Model Mech. 2020 Aug 18;13(8):dmm044412. doi: 10.1242/dmm.044412. PMID: 32571845
Inferring Cancer Progression from Single-Cell Sequencing while Allowing Mutation Losses. Ciccolella S, Ricketts C, Soto Gomez M, Patterson M, Silverbush D, Bonizzoni P, Hajirasouliha I, Della Vedova G.Bioinformatics. 2020 Aug 17:btaa722. doi: 10.1093/bioinformatics/btaa722. Online ahead of print. PMID: 32805010
Rucaparib in Men With Metastatic Castration-Resistant Prostate Cancer Harboring a BRCA1 or BRCA2 Gene Alteration. Abida W, Patnaik A, Campbell D, Shapiro J, Bryce AH, McDermott R, Sautois B, Vogelzang NJ, Bambury RM, Voog E, Zhang J, Piulats JM, Ryan CJ, Merseburger AS, Daugaard G, Heidenreich A, Fizazi K, Higano CS, Krieger LE, Sternberg CN, Watkins SP, Despain D, Simmons AD, Loehr A, Dowson M, Golsorkhi T, Chowdhury S; TRITON2 investigators.J Clin Oncol. 2020 Nov 10;38(32):3763-3772. doi: 10.1200/JCO.20.01035. Epub 2020 Aug 14. PMID: 32795228
A machine learning and network framework to discover new indications for small molecules. Gilvary C, Elkhader J, Madhukar N, Henchcliffe C, Goncalves MD, Elemento O.PLoS Comput Biol. 2020 Aug 7;16(8):e1008098. doi: 10.1371/journal.pcbi.1008098. eCollection 2020 Aug. PMID: 32764756
Immunostimulation with chemotherapy in the era of immune checkpoint inhibitors. Galluzzi L, Humeau J, Buqué A, Zitvogel L, Kroemer G. Nat Rev Clin Oncol. 2020 Dec;17(12):725-741. doi: 10.1038/s41571-020-0413-z. Epub 2020 Aug 5. PMID: 32760014
Selective dysregulation of ROCK2 activity promotes aberrant transcriptional networks in ABC diffuse large B-cell lymphoma. Ricker E, Verma A, Marullo R, Gupta S, Ye C, Pannellini T, Manni M, Tam W, Inghirami G, Elemento O, Cerchietti L, Pernis AB.Sci Rep. 2020 Aug 4;10(1):13094. doi: 10.1038/s41598-020-69884-1. PMID: 32753663
Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy. Yamazaki T, Kirchmair A, Sato A, Buqué A, Rybstein M, Petroni G, Bloy N, Finotello F, Stafford L, Navarro Manzano E, Ayala de la Peña F, García-Martínez E, Formenti SC, Trajanoski Z, Galluzzi L.Nat Immunol. 2020 Oct;21(10):1160-1171. doi: 10.1038/s41590-020-0751-0. Epub 2020 Aug 3. PMID: 32747819
M2-like macrophages dictate clinically relevant immunosuppression in metastatic ovarian cancer. Hensler M, Kasikova L, Fiser K, Rakova J, Skapa P, Laco J, Lanickova T, Pecen L, Truxova I, Vosahlikova S, Moserova I, Praznovec I, Drochytek V, Rehackova M, Brtnicky T, Rob L, Benes V, Pistolic J, Sojka L, Ryska A, Sautes-Fridman C, Fridman WH, Galluzzi L, Spisek R, Fucikova J.J
Immunother Cancer. 2020 Aug;8(2):e000979. doi: 10.1136/jitc-2020-000979. PMID: 32819974
Male infertility and genitourinary birth defects: there is more than meets the eye. Punjani N, Lamb DJ.Fertil Steril. 2020 Aug;114(2):209-218. doi: 10.1016/j.fertnstert.2020.06.042. PMID: 32741459
Molecular Profiles of Mixed Endometrial Carcinoma. Matrai C, Motanagh S, Mirabelli S, Ma L, He B, Chapman-Davis E, Kurtis B, Elemento O, Mosquera JM, Ellenson LH.Am J Surg Pathol. 2020 Aug;44(8):1104-1111. doi: 10.1097/PAS.0000000000001519. PMID: 32604171
Publisher Correction: Building an international consortium for tracking coronavirus health status. Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P.Nat Med. 2020 Aug;26(8):1309. doi: 10.1038/s41591-020-0983-4. PMID: 32591764
Building an international consortium for tracking coronavirus health status. Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P.Nat Med. 2020 Aug;26(8):1161-1165. doi: 10.1038/s41591-020-0929-x. PMID: 32488218

July

Calreticulin and cancer. Fucikova J, Spisek R, Kroemer G, Galluzzi L.Cell Res. 2021 Jan;31(1):5-16. doi: 10.1038/s41422-020-0383-9. Epub 2020 Jul 30. PMID: 32733014
Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer. Buqué A, Bloy N, Perez-Lanzón M, Iribarren K, Humeau J, Pol JG, Levesque S, Mondragon L, Yamazaki T, Sato A, Aranda F, Durand S, Boissonnas A, Fucikova J, Senovilla L, Enot D, Hensler M, Kremer M, Stoll G, Hu Y, Massa C, Formenti SC, Seliger B, Elemento O, Spisek R, André F, Zitvogel L, Delaloge S, Kroemer G, Galluzzi L.Nat Commun. 2020 Jul 30;11(1):3819. doi: 10.1038/s41467-020-17644-0. PMID: 32732875
Mitochondrial control of innate immune signaling by irradiated cancer cells. Yamazaki T, Galluzzi L.Oncoimmunology. 2020 Jul 22;9(1):1797292.doi: 10.1080/2162402X.2020.1797292. PMID: 32923160
Urinary Cell Transcriptome Profiling and Identification of ITM2A, SLAMF6, and IKZF3 as Biomarkers of Acute Rejection in Human Kidney Allografts. Dooley BJ, Verma A, Ding R, Yang H, Muthukumar T, Lubetzky M, Shankaranarayanan D, Elemento O, Suthanthiran M.Transplant Direct. 2020 Jul 22;6(8):e588. doi: 10.1097/TXD.0000000000001035. eCollection 2020 Aug. PMID: 32766436
Multicenter Phase II Study of Cabazitaxel in Advanced Gastroesophageal Cancer: Association of HER2 Expression and M2-Like Tumor-Associated Macrophages with Patient Outcome. Shah MA, Enzinger P, Ko AH, Ocean AJ, Philip PA, Thakkar PV, Cleveland K, Lu Y, Kortmansky J, Christos PJ, Zhang C, Kaur N, Elmonshed D, Galletti G, Sarkar S, Bhinder B, Pittman ME, Plotnikova OM, Kotlov N, Frenkel F, Bagaev A, Elemento O, Betel D, Giannakakou P, Lenz HJ.Clin Cancer Res. 2020 Sep 15;26(18):4756-4766. doi: 10.1158/1078-0432.CCR-19-3920. Epub 2020 Jul 8. PMID: 32641434
Impact of timing of adjuvant chemotherapy following radical cystectomy for bladder cancer on patient survival. Grunewald CM, Henn A, Galsky MD, Plimack ER, Harshman LC, Yu EY, Crabb SJ, Pal SK, Alva AS, Powles T, De Giorgi U, Agarwal N, Bamias A, Ladoire S, Necchi A, Vaishampayan UN, Sternberg CN, Bellmunt J, Baniel J, Niegisch G.Urol Oncol. 2020 Dec;38(12):934.e1-934.e9. doi: 10.1016/j.urolonc.2020.06.008. Epub 2020 Jul 10. PMID: 32660788
Trial Watch: experimental TLR7/TLR8 agonists for oncological indications. Frega G, Wu Q, Le Naour J, Vacchelli E, Galluzzi L, Kroemer G, Kepp O. Oncoimmunology. 2020 Jul 21;9(1):1796002. doi: 10.1080/2162402X.2020.1796002. PMID: 32934889
Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference. Benedetti E, Gerstner N, Pučić-Baković M, Keser T, Reiding KR, Ruhaak LR, Štambuk T, Selman MHJ, Rudan I, Polašek O, Hayward C, Beekman M, Slagboom E, Wuhrer M, Dunlop MG, Lauc G, Krumsiek J.Metabolites. 2020 Jul 2;10(7):E271. doi: 10.3390/metabo10070271. PMID: 32630764
A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. De Micheli AJ, Spector JA, Elemento O, Cosgrove BD.Skelet Muscle. 2020 Jul 6;10(1):19. doi: 10.1186/s13395-020-00236-3. PMID: 32624006
Preface-Autophagy: An old mechanism with new challenges ahead. Buqué Martinez A, Galluzzi L.Prog Mol Biol Transl Sci. 2020;172:xv-xix. doi: 10.1016/S1877-1173(20)30092-2.PMID: 32620253
TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Venturutti L, Teater M, Zhai A, Chadburn A, Babiker L, Kim D, Béguelin W, Lee TC, Kim Y, Chin CR, Yewdell WT, Raught B, Phillip JM, Jiang Y, Staudt LM, Green MR, Chaudhuri J, Elemento O, Farinha P, Weng AP, Nissen MD, Steidl C, Morin RD, Scott DW, Privé GG, Melnick AM. Cell. 2020 Jul 2:S0092-8674(20)30682-6. doi: 10.1016/j.cell.2020.05.049. Online ahead of print.PMID: 32619424
Molecular Profiles of Mixed Endometrial Carcinoma. Matrai C, Motanagh S, Mirabelli S, Ma L, He B, Chapman-Davis E, Kurtis B, Elemento O, Mosquera JM, Ellenson LH.Am J Surg Pathol. 2020 Jun 26. doi: 10.1097/PAS.0000000000001519. Online ahead of print. PMID: 32604171

June

Next-generation sequencing of residual cytologic fixative preserved DNA from pancreatic lesions: A pilot study. Fulmer CG, Park K, Dilcher T, Ho M, Mirabelli S, Alperstein S, Hissong EM, Pittman M, Siddiqui M, Heymann JJ, Yantiss RK, Borczuk AC, Fernandes H, Sigel C, Song W, Mosquera JM, Rao R. Cancer Cytopathol. 2020 Jun 29. doi: 10.1002/cncy.22315. Online ahead of print. PMID: 32598087
Publisher Correction: Building an international consortium for tracking coronavirus health status. Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Nat Med. 2020 Jun 26:1. doi: 10.1038/s41591-020-0983-4. Online ahead of print. PMID: 32591764
Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis. Auguste A, Blanc-Durand F, Deloger M, Le Formal A, Bareja R, Wilkes DC, Richon C, Brunn B, Caron O, Devouassoux-Shisheboran M, Gouy S, Morice P, Bentivegna E, Sboner A, Elemento O, Rubin MA, Pautier P, Genestie C, Cyrta J, Leary A. Cells. 2020 Jun 19;9(6):E1496. doi: 10.3390/cells9061496. PMID: 32575483
Immune-checkpoint inhibitors and metastatic prostate cancer therapy: Learning by making mistakes. Claps M, Mennitto A, Guadalupi V, Sepe P, Stellato M, Zattarin E, Gillessen SS, Sternberg CN, Berruti A, De Braud FGM, Verzoni E, Procopio G. Cancer Treat Rev. 2020 Jun 10;88:102057. doi: 10.1016/j.ctrv.2020.102057. Online ahead of print. PMID: 32574991
The transcription factor Maz is essential for normal eye development. Medina-Martinez O, Haller M, Rosenfeld JA, O’Neill MA, Lamb DJ, Jamrich M.Dis Model Mech. 2020 Jun 26:dmm.044412. doi: 10.1242/dmm.044412. Online ahead of print. PMID: 32571845
Molecular Characterization of Upper Tract Urothelial Carcinoma in the Era of Next-generation Sequencing: A Systematic Review of the Current Literature. Hassler MR, Bray F, Catto JWF, Grollman AP, Hartmann A, Margulis V, Matin SF, Roupret M, Sfakianos JP, Shariat SF, Faltas BM. Eur Urol. 2020 Jun 20:S0302-2838(20)30417-6. doi: 10.1016/j.eururo.2020.05.039. Online ahead of print. PMID: 32571725
Ca²⁺ Fluxes and Cancer. Marchi S, Giorgi C, Galluzzi L, Pinton P. Mol Cell. 2020 Jun 18;78(6):1055-1069. doi: 10.1016/j.molcel.2020.04.017. PMID: 32559424
Fusions involving BCOR and CREBBP are rare events in infiltrating glioma. Pisapia DJ, Ohara K, Bareja R, Wilkes DC, Hissong E, Croyle JA, Kim JH, Saab J, MacDonald TY, Beg S, O’Reilly C, Kudman S, Rubin MA, Elemento O, Sboner A, Greenfield J, Mosquera JM. Acta Neuropathol Commun. 2020 Jun 3;8(1):80. doi: 10.1186/s40478-020-00951-4. PMID: 32493417
Building an international consortium for tracking coronavirus health status. Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Nat Med. 2020 Jun 2. doi: 10.1038/s41591-020-0929-x. Online ahead of print.PMID: 32488218

May

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE.Version 5. bioRxiv. 2020 May 1:2020.04.20.048066. doi: 10.1101/2020.04.20.048066. Preprint. PMID: 32511352
Enzalutamide and Survival in Nonmetastatic, Castration-Resistant Prostate Cancer. Sternberg CN, Fizazi K, Saad F, Shore ND, De Giorgi U, Penson DF, Ferreira U, Efstathiou E, Madziarska K, Kolinsky MP, Cubero DIG, Noerby B, Zohren F, Lin X, Modelska K, Sugg J, Steinberg J, Hussain M; PROSPER Investigators.N Engl J Med. 2020 Jun 4;382(23):2197-2206. doi: 10.1056/ NEJMoa2003892. Epub 2020 May 29.PMID: 32469184
CDK12-Altered Prostate Cancer: Clinical Features and Therapeutic Outcomes to Standard Systemic Therapies, Poly (ADP-Ribose) Polymerase Inhibitors, and PD-1 Inhibitors.Antonarakis ES, Isaacsson Velho P, Fu W, Wang H, Agarwal N, Sacristan Santos V, Maughan BL, Pili R, Adra N, Sternberg CN, Vlachostergios PJ, Tagawa ST, Bryce AH, McNatty AL, Reichert ZR, Dreicer R, Sartor O, Lotan TL, Hussain M.JCO Precis Oncol. 2020;4:370-381. doi: 10.1200/po.19.00399. Epub 2020 Apr 21. PMID: 32462107
Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers. Sfakianos JP, Daza J, Hu Y, Anastos H, Bryant G, Bareja R, Badani KK, Galsky MD, Elemento O, Faltas BM, Mulholland DJ. Nat Commun. 2020 May 21;11(1):2540. doi: 10.1038/s41467-020-16162-3. PMID: 32439865
Identification of Distinct Heterogenic Subtypes and Molecular Signatures Associated with African Ancestry in Triple Negative Breast Cancer Using Quantified Genetic Ancestry Models in Admixed Race Populations. Davis M, Martini R, Newman L, Elemento O, White J, Verma A, Datta I, Adrianto I, Chen Y, Gardner K, Kim HG, Colomb WD, Eltoum IE, Frost AR, Grizzle WE, Sboner A, Manne U, Yates C. Cancers (Basel). 2020 May 13;12(5):1220. doi: 10.3390/cancers12051220. PMID: 32414099
Possible mechanisms of cancer prevention by nicotinamide. Buqué A, Bloy N, Kroemer G, Galluzzi L. Br J Pharmacol. 2020 May 7. doi: 10.1111/bph.15096. Online ahead of print. PMID: 32383227
Preface: Life through death-Key role of cellular suicide for colonial and organismal homeostasis. Spetz J, Galluzzi L. Int Rev Cell Mol Biol. 2020;353:ix-xiii. doi: 10.1016/S1937-6448(20)30058-7. PMID: 32381180
Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues. Marderstein AR, Uppal M, Verma A, Bhinder B, Tayyebi Z, Mezey J, Clark AG, Elemento O. Nat Commun. 2020 May 5;11(1):2213. doi: 10.1038/s41467-020-16097-9. PMID: 32371927

April

Adenomyoepithelial tumors of the breast: molecular underpinnings of a rare entity. Ginter PS, McIntire PJ, Kurtis B, Mirabelli S, Motanagh S, Hoda S, Elemento O, Shin SJ, Mosquera JM. Mod Pathol. 2020 Apr 30. doi: 10.1038/s41379-020-0552-x. Online ahead of print. PMID: 32355271
Cancer Immunotherapy with CDK7 Inhibitors. Petroni G, Galluzzi L. Trends Cancer. 2020 May;6(5):361-363. doi: 10.1016/j.trecan.2020.02.005. Epub 2020 Feb 28. PMID: 32348731
Immunomodulation by anticancer cell cycle inhibitors. Petroni G, Formenti SC, Chen-Kiang S, Galluzzi L. Nat Rev Immunol. 2020 Apr 28. doi: 10.1038/s41577-020-0300-y. Online ahead of print.PMID: 32346095
Preface: Life through death-Key role of cellular suicide for colonial and organismal homeostasis. Spetz J, Galluzzi L. Int Rev Cell Mol Biol. 2020;352:xi-xv. doi: 10.1016/S1937-6448(20)30047-2. No abstract available. PMID: 32334819
Integrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes. Liu D, Shoag JE, Poliak D, Goueli RS, Ravikumar V, Redmond D, Vosoughi A, Fontugne J, Pan H, Lee D, Thomas D, Salari K, Wang Z, Romanel A, Te A, Lee R, Chughtai B, Olumi AF, Mosquera JM, Demichelis F, Elemento O, Rubin MA, Sboner A, Barbieri CE. Nat Commun. 2020 Apr 24;11(1):1987. doi: 10.1038/s41467-020-15913-6. PMID: 32332823
Noncanonical Cell Fate Regulation by Bcl-2 Proteins. Chong SJF, Marchi S, Petroni G, Kroemer G, Galluzzi L, Pervaiz S. Trends Cell Biol. 2020 Apr 16. pii: S0962-8924(20)30070-2. doi: 10.1016/j.tcb.2020.03.004. [Epub ahead of print] Review. PMID: 32307222
Transient Autophagy Inhibition Precipitates Oncogenesis: A Red Flag For Pharmacological Autophagy Inhibitors? Galluzzi L, Kroemer G. Trends Cell Biol. 2020 May;30(5):339-340. doi: 10.1016/j.tcb.2020.02.004. Epub 2020 Feb 27. PMID: 32302546
Preanalytic variables in quality and quantity of nucleic acids extracted from FNA specimens of thyroid gland nodules collected in CytoLyt: Cellularity and storage time. Heymann JJ, Yoxtheimer LM, Park HJ, Fernandez EM, Facey KE, Alperstein SA, Tran HV, Baek I, Scognamiglio T, Rennert H, Siddiqui MT, Song W. Cancer Cytopathol. 2020 Apr 8. doi: 10.1002/cncy.22270. [Epub ahead of print] PMID: 32267620
Tumor microenvironment is critical for the maintenance of cellular states found in primary glioblastomas. Pine AR, Cirigliano SM, Nicholson JG, Hu Y, Linkous A, Miyaguchi K, Edwards L, Singhania R, Schwartz TH, Ramakrishna R, Pisapia DJ, Snuderl M, Elemento O, Fine HA. Cancer Discov. 2020 Apr 6. pii: CD-20-0057. doi: 10.1158/2159-8290.CD-20-0057. [Epub ahead of print] PMID: 32253265
Immunogenicity of cell death driven by immune effectors. Galluzzi L, Petroni G, Kroemer G. J Immunother Cancer. 2020 Apr;8(1). pii: e000802. doi: 10.1136/jitc-2020-000802. PMID: 32253221
Preface: Life through death-Key role of cellular suicide for colonial and organismal homeostasis. Spetz J, Galluzzi L. Int Rev Cell Mol Biol. 2020;351:xi-xv. doi: 10.1016/S1937-6448(20)30035-6. No abstract available. PMID: 32247583
Loss-of-function tolerance of enhancers in the human genome. Xu D, Gokcumen O, Khurana E. PLoS Genet. 2020 Apr 3;16(4):e1008663. doi: 10.1371/journal.pgen.1008663. eCollection 2020 Apr. PMID: 322434

March

DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure. Trieu T, Martinez-Fundichely A, Khurana E. Genome Biol. 2020 Mar 26;21(1):79. doi: 10.1186/s13059-020-01987-4. PMID: 32216817
Immunogenic Cell Death Driven by Radiation-Impact on the Tumor Microenvironment. Yamazaki T, Vanpouille-Box C, Demaria S, Galluzzi L. Cancer Treat Res. 2020;180:281-296. doi: 10.1007/978-3-030-38862-1_10. PMID: 32215874
Consensus guidelines for the definition, detection and interpretation of immunogenic cell death. Galluzzi L, Vitale I, Warren S, Adjemian S, Agostinis P, Martinez AB, Chan TA, Coukos G, Demaria S, Deutsch E, Draganov D, Edelson RL, Formenti SC, Fucikova J, Gabriele L, Gaipl US, Gameiro SR, Garg AD, Golden E, Han J, Harrington KJ, Hemminki A, Hodge JW, Hossain DMS, Illidge T, Karin M, Kaufman HL, Kepp O, Kroemer G, Lasarte JJ, Loi S, Lotze MT, Manic G, Merghoub T, Melcher AA, Mossman KL, Prosper F, Rekdal Ø, Rescigno M, Riganti C, Sistigu A, Smyth MJ, Spisek R, Stagg J, Strauss BE, Tang D, Tatsuno K, van Gool SW, Vandenabeele P, Yamazaki T, Zamarin D, Zitvogel L, Cesano A, Marincola FM. J Immunother Cancer. 2020 Mar;8(1). pii: e000337. doi: 10.1136/jitc-2019-000337. Review. PMID: 32209603
Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid. Lehmann GL, Hanke-Gogokhia C, Hu Y, Bareja R, Salfati Z, Ginsberg M, Nolan DJ, Mendez-Huergo SP, Dalotto-Moreno T, Wojcinski A, Ochoa F, Zeng S, Cerliani JP, Panagis L, Zager PJ, Mullins RF, Ogura S, Lutty GA, Bang J, Zippin JH, Romano C, Rabinovich GA, Elemento O, Joyner AL, Rafii S, Rodriguez-Boulan E, Benedicto I. J Exp Med. 2020 Jun 1;217(6). pii: e20190730. doi: 10.1084/jem.20190730. PMID: 32196081
VALOR2: characterization of large-scale structural variants using linked-reads. Karaoğlanoğlu F, Ricketts C, Ebren E, Rasekh ME, Hajirasouliha I, Alkan C. Genome Biol. 2020 Mar 19;21(1):72. doi: 10.1186/s13059-020-01975-8. PMID: 32192518
Preface: More than two decades of modern tumor immunology. Galluzzi L, Rudqvist NP. Methods Enzymol. 2020;636:xvii-xxxvi. doi: 10.1016/S0076-6879(20)30114-2. No abstract available. PMID: 32178830

February

Computational methods in tumor immunology. Bhinder B, Elemento O. Methods Enzymol. 2020;636:209-259. doi: 10.1016/bs.mie.2020.01.001. Epub 2020 Jan 25. PMID: 32178820
Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration. De Micheli AJ, Laurilliard EJ, Heinke CL, Ravichandran H, Fraczek P, Soueid-Baumgarten S, De Vlaminck I, Elemento O, Cosgrove BD. Cell Rep. 2020 Mar 10;30(10):3583-3595.e5. doi: 10.1016/j.celrep.2020.02.067. PMID: 32160558
Preface: Endoplasmic reticulum in health and disease. Kepp O, Galluzzi L. Int Rev Cell Mol Biol. 2020;350:xiii-xvii. doi: 10.1016/S1937-6448(20)30020-4. No abstract available. PMID: 32138905
An evaluation of the efficacy and safety of erdafitinib for the treatment of bladder cancer. Nauseef JT, Villamar DM, Lebenthal J, Vlachostergios PJ, Tagawa ST.
Expert Opin Pharmacother. 2020 Mar 3:1-8. doi: 10.1080/14656566.2020.1736036. [Epub ahead of print]. PMID: 32124650
The novel lncRNA BlackMamba controls the neoplastic phenotype of ALK^– anaplastic large cell lymphoma by regulating the DNA helicase HELLS. Fragliasso V, Verma A, Manzotti G, Tameni A, Bareja R, Heavican TB, Iqbal J, Wang R, Fiore D, Mularoni V, Chan WC, Lhoumaud P, Skok J, Zanetti E, Merli F, Ciarrocchi A, Elemento O, Inghirami G. Leukemia. 2020 Mar 2. doi: 10.1038/s41375-020-0754-8. [Epub ahead of print]PMID: 32123306
Sex and APOE ε4 genotype modify the Alzheimer’s disease serum metabolome. Arnold M, Nho K, Kueider-Paisley A, Massaro T, Huynh K, Brauner B, MahmoudianDehkordi S, Louie G, Moseley MA, Thompson JW, John-Williams LS, Tenenbaum JD, Blach C, Chang R, Brinton RD, Baillie R, Han X, Trojanowski JQ, Shaw LM, Martins R, Weiner MW, Trushina E, Toledo JB, Meikle PJ, Bennett DA, Krumsiek J, Doraiswamy PM, Saykin AJ, Kaddurah-Daouk R, Kastenmüller G.Nat Commun. 2020 Mar 2;11(1):1148. doi: 10.1038/s41467-020-14959-w. PMID: 32123170
Preface: More than two decades of modern tumor immunology. Galluzzi L, Rudqvist NP. Methods Enzymol. 2020;635:xix-xxxviii. doi: 10.1016/S0076-6879(20)30077-X. No abstract available. PMID: 32122557
PT-112 induces immunogenic cell death and synergizes with immune checkpoint blockers in mouse tumor models. Yamazaki T, Buqué A, Ames TD, Galluzzi L. Oncoimmunology. 2020 Feb 11;9(1):1721810. doi: 10.1080/2162402X.2020.1721810. eCollection 2020. PMID: 32117585
Mutations in long-lived epithelial stem cells and their clonal progeny in pre-malignant lesions and in oral squamous cell carcinoma. Marta M, Zhang T, Scognamiglio T, Gudas LJ. Carcinogenesis. 2020 Mar 2. pii: bgaa019. doi: 10.1093/carcin/bgaa019. [Epub ahead of print] PMID: 32115621
Urinary cell transcriptomics and acute rejection in human kidney allografts. Verma A, Muthukumar T, Yang H, Lubetzky M, Cassidy MF, Lee JR, Dadhania DM, Snopkowski C, Shankaranarayanan D, Salvatore SP, Sharma VK, Xiang JZ, De Vlaminck I, Seshan SV, Mueller FB, Suhre K, Elemento O, Suthanthiran M. JCI Insight. 2020 Feb 27;5(4). pii: 131552. doi: 10.1172/jci.insight.131552.PMID: 32102984
The aging skin microenvironment dictates stem cell behavior. Ge Y, Miao Y, Gur-Cohen S, Gomez N, Yang H, Nikolova M, Polak L, Hu Y, Verma A, Elemento O, Krueger JG, Fuchs E. Proc Natl Acad Sci U S A. 2020 Feb 24. pii: 201901720. doi: 10.1073/pnas.1901720117. [Epub ahead of print] PMID: 32094197
Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer. Beltran H, Romanel A, Conteduca V, Casiraghi N, Sigouros M, Franceschini GM, Orlando F, Fedrizzi T, Ku SY, Dann E, Alonso A, Mosquera JM, Sboner A, Xiang J, Elemento O, Nanus DM, Tagawa ST, Benelli M, Demichelis F. J Clin Invest. 2020 Feb 24. pii: 131041. doi: 10.1172/JCI131041. [Epub ahead of print] PMID: 32091413
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Kumar S, Warrell J, Li S, McGillivray PD, Meyerson W, Salichos L, Harmanci A, Martinez-Fundichely A, Chan CWY, Nielsen MM, Lochovsky L, Zhang Y, Li X, Lou S, Pedersen JS, Herrmann C, Getz G, Khurana E, Gerstein MB. Cell. 2020 Feb 14. pii: S0092-8674(20)30113-6. doi: 10.1016/j.cell.2020.01.032. [Epub ahead of print] PMID: 32084333
Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome. Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W. Arch Pathol Lab Med. 2020 Feb 11. doi: 10.5858/arpa.2019-0162-OA. [Epub ahead of print] PMID: 32045275
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium. Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5. PMID: 32025015
Positive allosteric modulation of indoleamine 2,3-dioxygenase 1 restrains neuroinflammation. Mondanelli G, Coletti A, Greco FA, Pallotta MT, Orabona C, Iacono A, Belladonna ML, Albini E, Panfili E, Fallarino F, Gargaro M, Manni G, Matino D, Carvalho A, Cunha C, Maciel P, Di Filippo M, Gaetani L, Bianchi R, Vacca C, Iamandii IM, Proietti E, Boscia F, Annunziato L, Peppelenbosch M, Puccetti P, Calabresi P, Macchiarulo A, Santambrogio L, Volpi C, Grohmann U. Proc Natl Acad Sci U S A. 2020 Feb 18;117(7):3848-3857. doi: 10.1073/pnas.1918215117. Epub 2020 Feb 5. PMID: 32024760

January

Trial watch: chemotherapy-induced immunogenic cell death in immuno-oncology. Vanmeerbeek I, Sprooten J, De Ruysscher D, Tejpar S, Vandenberghe P, Fucikova J, Spisek R, Zitvogel L, Kroemer G, Galluzzi L, Garg AD. Oncoimmunology. 2020 Jan 9;9(1):1703449. doi: 10.1080/2162402X.2019.1703449. eCollection 2020. Review. PMID: 32002302
Associations between adipose tissue volume and small molecules in plasma and urine among asymptomatic subjects from the general population. Otto L, Budde K, Kastenmüller G, Kaul A, Völker U, Völzke H, Adamski J, Kühn JP, Krumsiek J, Artati A, Nauck M, Friedrich N, Pietzner M. Sci Rep. 2020 Jan 30;10(1):1487. doi: 10.1038/s41598-020-58430-8. PMID: 32001750
Management of Patients with Advanced Prostate Cancer: Report of the Advanced Prostate Cancer Consensus Conference 2019. Gillessen S, Attard G, Beer TM, Beltran H, Bjartell A, Bossi A, Briganti A, Bristow RG, Chi KN, Clarke N, Davis ID, de Bono J, Drake CG, Duran I, Eeles R, Efstathiou E, Evans CP, Fanti S, Feng FY, Fizazi K, Frydenberg M, Gleave M, Halabi S, Heidenreich A, Heinrich D, Higano CTS, Hofman MS, Hussain M, James N, Kanesvaran R, Kantoff P, Khauli RB, Leibowitz R, Logothetis C, Maluf F, Millman R, Morgans AK, Morris MJ, Mottet N, Mrabti H, Murphy DG, Murthy V, Oh WK, Ost P, O’Sullivan JM, Padhani AR, Parker C, Poon DMC, Pritchard CC, Reiter RE, Roach M, Rubin M, Ryan CJ, Saad F, Sade JP, Sartor O, Scher HI, Shore N, Small E, Smith M, Soule H, Sternberg CN, Steuber T, Suzuki H, Sweeney C, Sydes MR, Taplin ME, Tombal B, Türkeri L, van Oort I, Zapatero A, Omlin A. Eur Urol. 2020 Jan 27. pii: S0302-2838(20)30048-8. doi: 10.1016/j.eururo.2020.01.012. [Epub ahead of print] PMID: 32001144
Preface: More than two decades of modern tumor immunology. Galluzzi L, Rudqvist NP. Methods Enzymol. 2020;632:xxiii-xlii. doi: 10.1016/S0076-6879(20)30043-4. No abstract available. PMID: 32000917
The emerging landscape of germline variants in urothelial carcinoma: Implications for genetic testing. Vlachostergios PJ, Faltas BM, Carlo MI, Nassar AH, Alaiwi SA, Sonpavde G. Cancer Treat Res Commun. 2020 Jan 7;23:100165. doi: 10.1016/j.ctarc.2020.100165. [Epub ahead of print] PMID: 31982787
A randomised phase II trial of three dosing regimens of radium-223 in patients with bone metastatic castration-resistant prostate cancer. Sternberg CN, Saad F, Graff JN, Peer A, Vaishampayan UN, Leung E, Rosenbaum E, Gurney H, Epstein RJ, Davis ID, Wu B, Trandafir L, Wagner VJ, Hussain M. Ann Oncol. 2020 Feb;31(2):257-265. doi: 10.1016/j.annonc.2019.10.025. Epub 2019 Dec 23.PMID: 31959342
Preface: More than two decades of modern tumor immunology. Galluzzi L, Rudqvist NP. Methods Enzymol. 2020;631:xxiii-xlii. doi: 10.1016/S0076-6879(20)30020-3. No abstract available. PMID: 31948570
ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA. Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A. Bioinformatics. 2020 Jan 10. pii: btaa016. doi: 10.1093/bioinformatics/btaa016. [Epub ahead of print] PMID: 31922552

2019

Cabazitaxel versus Abiraterone or Enzalutamide in Metastatic Prostate Cancer. de Wit R, de Bono J, Sternberg CN, Fizazi K, Tombal B, Wülfing C, Kramer G, Eymard JC, Bamias A, Carles J, Iacovelli R, Melichar B, Sverrisdóttir Á, Theodore C, Feyerabend S, Helissey C, Ozatilgan A, Geffriaud-Ricouard C, Castellano D; CARD Investigators. N Engl J Med. 2019 Dec 26;381(26):2506-2518. doi: 10.1056/NEJMoa1911206. Epub 2019 Sep 30. PMID: 31566937

Immunological impact of cell death signaling driven by radiation on the tumor microenvironment. Rodriguez-Ruiz ME, Vitale I, Harrington KJ, Melero I, Galluzzi L. Nat Immunol. 2019 Dec 23. doi: 10.1038/s41590-019-0561-4. [Epub ahead of print] Review. PMID: 31873291

Association Between New Unconfirmed Bone Lesions and Outcomes in Men With Metastatic Castration-Resistant Prostate Cancer Treated With Enzalutamide: Secondary Analysis of the PREVAIL and AFFIRM Randomized Clinical Trials. Armstrong AJ, Al-Adhami M, Lin P, Parli T, Sugg J, Steinberg J, Tombal B, Sternberg CN, de Bono J, Scher HI, Beer TM. JAMA Oncol. 2019 Dec 12. doi: 10.1001/jamaoncol.2019.4636. [Epub ahead of print] PMID: 31830211

TPES: tumor purity estimation from SNVs. Locallo A, Prandi D, Fedrizzi T, Demichelis F. Bioinformatics. 2019 Nov 1;35(21):4433-4435. doi: 10.1093/bioinformatics/btz406. PMID: 31099386 PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC. Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18. PMID: 31628256 A Bayesian machine learning approach for drug target identification using diverse data types. Madhukar NS, Khade PK, Huang L, Gayvert K, Galletti G, Stogniew M, Allen JE, Giannakakou P, Elemento O. Nat Commun. 2019 Nov 19;10(1):5221. doi: 10.1038/s41467-019-12928-6. PMID: 31745082 An OCT2 / OCA-B / MEF2B Ternary Complex Controls the Activity and Architecture of an Essential Locus Control Region for Normal and Malignant Germinal Center B-Cells. Hellmuth JC, Chu CS, Singh R, Skrabanek LA, Doane A, Elemento O, Roeder RG, Melnick A. Blood. 2019 Nov 13;134(Supplement_1):24. doi: 10.1182/blood-2019-130692. PMID: 31723990 An approach that someday may boost testosterone biosynthesis in males with late-onset hypogonadism (low testosterone). Lamb DJ. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):22904-22906. doi: 10.1073/pnas.1916719116. Epub 2019 Oct 25. No abstract available. PMID: 31653760 Clinical features of neuroendocrine prostate cancer. Conteduca V, Oromendia C, Eng KW, Bareja R, Sigouros M, Molina A, Faltas BM, Sboner A, Mosquera JM, Elemento O, Nanus DM, Tagawa ST, Ballman KV, Beltran H. Eur J Cancer. 2019 Nov;121:7-18. doi: 10.1016/j.ejca.2019.08.011. Epub 2019 Sep 13. PMID: 31525487 Deep learning-based classification of mesothelioma improves prediction of patient outcome. Courtiol P, Maussion C, Moarii M, Pronier E, Pilcer S, Sefta M, Manceron P, Toldo S, Zaslavskiy M, Le Stang N, Girard N, Elemento O, Nicholson AG, Blay JY, Galateau-Sallé F, Wainrib G, Clozel T. Nat Med. 2019 Oct;25(10):1519-1525. doi: 10.1038/s41591-019-0583-3. Epub 2019 Oct 7. PMID: 31591589 Clonal Hematopoiesis and Premalignant Diseases. Kaner J, Desai P, Mencia-Trinchant N, Guzman ML, Roboz GJ, Hassane DC. Cold Spring Harb Perspect Med. 2019 Oct 15. pii: a035675. doi: 10.1101/cshperspect.a035675. [Epub ahead of print] PMID: 31615870 Organotypic tumor slice cultures provide a versatile platform for immuno-oncology and drug discovery. Sivakumar R, Chan M, Shin JS, Nishida-Aoki N, Kenerson HL, Elemento O, Beltran H, Yeung R, Gujral TS. Oncoimmunology. 2019 Oct 10;8(12):e1670019. doi: 10.1080/2162402X.2019.1670019. eCollection 2019. PMID: 31741771 Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants. Ricketts C, Seidman D, Popic V, Hormozdiari F, Batzoglou S, Hajirasouliha I. Bioinformatics. 2019 Oct 4. pii: btz737. doi: 10.1093/bioinformatics/btz737. [Epub ahead of print] PMID: 31584621 Obesity-Associated Extracellular Matrix Remodeling Promotes a Macrophage Phenotype Similar to Tumor-Associated Macrophages. Springer NL, Iyengar NM, Bareja R, Verma A, Jochelson MS, Giri DD, Zhou XK, Elemento O, Dannenberg AJ, Fischbach C. Am J Pathol. 2019 Oct;189(10):2019-2035. doi: 10.1016/j.ajpath.2019.06.005. Epub 2019 Jul 16. PMID: 31323189 Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2. Prandi D, Demichelis F. Curr Protoc Bioinformatics. 2019 Sep;67(1):e81. doi: 10.1002/cpbi.81. PMID: 31524989 Cancer-Specific Thresholds Adjust for Whole Exome Sequencing-based Tumor Mutational Burden Distribution. Fernandez EM, Eng K, Beg S, Beltran H, Faltas BM, Mosquera JM, Nanus DM, Pisapia DJ, Rao RA, Robinson BD, Rubin MA, Elemento O, Sboner A, Shah MA, Song W. JCO Precis Oncol. 2019;3. doi: 10.1200/PO.18.00400. Epub 2019 Jul 31. PMID: 31475242 PARP Inhibition Suppresses GR-MYCN-CDK5-RB1-E2F1 Signaling and Neuroendocrine Differentiation in Castration-Resistant Prostate Cancer. Liu B, Li L, Yang G, Geng C, Luo Y, Wu W, Manyam GC, Korentzelos D, Park S, Tang Z, Wu C, Dong Z, Sigouros M, Sboner A, Beltran H, Chen Y, Corn PG, Tetzlaff MT, Troncoso P, Broom B, Thompson TC. Clin Cancer Res. 2019 Nov 15;25(22):6839-6851. doi: 10.1158/1078-0432.CCR-19-0317. Epub 2019 Aug 22. PMID: 31439587 Incremental Utility of Adjuvant Chemotherapy in Muscle-invasive Bladder Cancer: Quantifying the Relapse Risk Associated with Therapeutic Effect. Pederzoli F, Bandini M, Briganti A, Plimack ER, Niegisch G, Yu EY, Bamias A, Agarwal N, Sridhar SS, Sternberg CN, Vaishampayan UN, Théodore C, Rosenberg JE, Harshman LC, Bellmunt J, Galsky MD, Gallina A, Salonia A, Montorsi F, Necchi A; RISC Investigators. Eur Urol. 2019 Oct;76(4):425-429. doi: 10.1016/j.eururo.2019.06.032. Epub 2019 Jul 11. PMID: 31303258 Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas. Lue JK, Prabhu SA, Liu Y, Gonzalez Y, Verma A, Mundi PS, Abshiru N, Camarillo JM, Mehta S, Chen EI, Qiao C, Nandakumar R, Cremers S, Kelleher NL, Elemento O, Amengual JE. Clin Cancer Res. 2019 Sep 1;25(17):5271-5283. doi: 10.1158/1078-0432.CCR-18-3989. Epub 2019 Apr 12. PMID: 30979734 Injectable mechanical pillows for attenuation of load-induced post-traumatic osteoarthritis. Holyoak DT, Wheeler TA, van der Meulen MCH, Singh A. Regen Biomater. 2019 Aug;6(4):211-219. doi: 10.1093/rb/rbz013. Epub 2019 Apr 22. PMID: 31402982 Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. Persi E, Prandi D, Wolf YI, Pozniak Y, Barnabas GD, Levanon K, Barshack I, Barbieri C, Gasperini P, Beltran H, Faltas BM, Rubin MA, Geiger T, Koonin EV, Demichelis F, Horn D. Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16987-16996. doi: 10.1073/pnas.1908790116. Epub 2019 Aug 6. PMID: 31387980 Somatic and germline sequencing in genitourinary oncology: genetics for the clinician. Shoag JE, Wise DR, Sharaf RN, Sternberg CN. Curr Opin Urol. 2019 Jul;29(4):315-318. doi: 10.1097/MOU.0000000000000643. PMID: 31158105 Supplemental estrogen and caloric restriction reduce obesity-induced periprostatic white adipose inflammation in mice. Bhardwaj P, Ikeda T, Zhou XK, Wang H, Zheng XE, Giri DD, Elemento O, Verma A, Miyazawa M, Mukherjee S, Falcone DJ, Wendel NK, Scherr DS, Dannenberg AJ. Carcinogenesis. 2019 Jul 20;40(7):914-923. doi: 10.1093/carcin/bgz088. PMID: 31067318 Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS). Playdon MC, Joshi AD, Tabung FK, Cheng S, Henglin M, Kim A, Lin T, van Roekel EH, Huang J, Krumsiek J, Wang Y, Mathé E, Temprosa M, Moore S, Chawes B, Eliassen AH, Gsur A, Gunter MJ, Harada S, Langenberg C, Oresic M, Perng W, Seow WJ, Zeleznik OA. Metabolites. 2019 Jul 17;9(7). pii: E145. doi: 10.3390/metabo9070145. PMID: 31319517 Early Post-treatment Prostate-specific Antigen at 4 Weeks and Abiraterone and Enzalutamide Treatment for Advanced Prostate Cancer: An International Collaborative Analysis. Rescigno P, Dolling D, Conteduca V, Rediti M, Bianchini D, Lolli C, Ong M, Li H, Omlin AG, Schmid S, Caffo O, Zivi A, Pezaro CJ, Morley C, Olmos D, Romero-Laorden N, Castro E, Saez MI, Mehra N, Smeenk S, Sideris S, Gil T, Banks P, Sandhu SK, Sternberg CN, De Giorgi U, De Bono JS. Eur Urol Oncol. 2019 Jul 12. pii: S2588-9311(19)30083-5. doi: 10.1016/j.euo.2019.06.008. [Epub ahead of print] PMID: 31307958 Landscape of innate immune system transcriptome and acute T cell-mediated rejection of human kidney allografts. Mueller FB, Yang H, Lubetzky M, Verma A, Lee JR, Dadhania DM, Xiang JZ, Salvatore SP, Seshan SV, Sharma VK, Elemento O, Suthanthiran M, Muthukumar T. JCI Insight. 2019 Jul 11;4(13). pii: 128014. doi: 10.1172/jci.insight.128014. eCollection 2019 Jul 11. PMID: 31292297 Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling. Robinson BD, Vlachostergios PJ, Bhinder B, Liu W, Li K, Moss TJ, Bareja R, Park K, Tavassoli P, Cyrta J, Tagawa ST, Nanus DM, Beltran H, Molina AM, Khani F, Miguel Mosquera J, Xylinas E, Shariat SF, Scherr DS, Rubin MA, Lerner SP, Matin SF, Elemento O, Faltas BM. Nat Commun. 2019 Jul 5;10(1):2977. doi: 10.1038/s41467-019-10873-y. PMID: 31278255 Association of Systemic Inflammation Index and Body Mass Index with Survival in Patients with Renal Cell Cancer Treated with Nivolumab. De Giorgi U, Procopio G, Giannarelli D, Sabbatini R, Bearz A, Buti S, Basso U, Mitterer M, Ortega C, Bidoli P, Ferraù F, Crinò L, Frassoldati A, Marchetti P, Mini E, Scoppola A, Verusio C, Fornarini G, Cartenì G, Caserta C, Sternberg CN. Clin Cancer Res. 2019 Jul 1;25(13):3839-3846. doi: 10.1158/1078-0432.CCR-18-3661. Epub 2019 Apr 9. PMID: 30967420 The Missing Pieces of Artificial Intelligence in Medicine. Gilvary C, Madhukar N, Elkhader J, Elemento O. Trends Pharmacol Sci. 2019 Aug;40(8):555-564. doi: 10.1016/j.tips.2019.06.001. Epub 2019 Jul 2. Review. PMID: 31277839 The application of precision medicine in diagnosing familial Mediterranean fever. Glynn S, Lipkin S, Zhang T, Sboner A, Elemento O, Van Besien K, Beltran H. Leuk Lymphoma. 2019 Aug;60(8):2091-2093. doi: 10.1080/10428194.2019.1571204. Epub 2019 Jan 30. No abstract available. PMID: 30698071 Artificial intelligence: its applications in reproductive medicine and the assisted reproductive technologies. Zaninovic N, Elemento O, Rosenwaks Z. Fertil Steril. 2019 Jul;112(1):28-30. doi: 10.1016/j.fertnstert.2019.05.019. No abstract available. PMID: 31277764 N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer. Berger A, Brady NJ, Bareja R, Robinson B, Conteduca V, Augello MA, Puca L, Ahmed A, Dardenne E, Lu X, Hwang I, Bagadion AM, Sboner A, Elemento O, Paik J, Yu J, Barbieri CE, Dephoure N, Beltran H, Rickman DS. J Clin Invest. 2019 Jul 1;130:3924-3940. doi: 10.1172/JCI127961. PMID: 31260412 Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM; PCF/SU2C International Prostate Cancer Dream Team, Schultz N, Van Allen EM. Nat Genet. 2019 Jul;51(7):1194. doi: 10.1038/s41588-019-0451-6. PMID: 31152158 FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes. Adams EJ, Karthaus WR, Hoover E, Liu D, Gruet A, Zhang Z, Cho H, DiLoreto R, Chhangawala S, Liu Y, Watson PA, Davicioni E, Sboner A, Barbieri CE, Bose R, Leslie CS, Sawyers CL. Nature. 2019 Jul;571(7765):408-412. doi: 10.1038/s41586-019-1318-9. Epub 2019 Jun 26. PMID: 31243370 Prostate Cancer Research at the Crossroads. Shen MM, Rubin MA. Cold Spring Harb Perspect Med. 2019 Jul 1;9(7). pii: a036277. doi: 10.1101/cshperspect.a036277. Review. No abstract available. PMID: 30348836 Radiation therapy and anti-tumor immunity: exposing immunogenic mutations to the immune system. Lhuillier C, Rudqvist NP, Elemento O, Formenti SC, Demaria S. Genome Med. 2019 Jun 20;11(1):40. doi: 10.1186/s13073-019-0653-7. Review. PMID: 31221199 Randomized phase III KEYNOTE-045 trial of pembrolizumab versus paclitaxel, docetaxel, or vinflunine in recurrent advanced urothelial cancer: results of >2 years of follow-up. Fradet Y, Bellmunt J, Vaughn DJ, Lee JL, Fong L, Vogelzang NJ, Climent MA, Petrylak DP, Choueiri TK, Necchi A, Gerritsen W, Gurney H, Quinn DI, Culine S, Sternberg CN, Nam K, Frenkl TL, Perini RF, de Wit R, Bajorin DF. Ann Oncol. 2019 Jun 1;30(6):970-976. doi: 10.1093/annonc/mdz127. PMID: 31050707 Integration of Metabolomic and Other Omics Data in Population-Based Study Designs: An Epidemiological Perspective. Chu SH, Huang M, Kelly RS, Benedetti E, Siddiqui JK, Zeleznik OA, Pereira A, Herrington D, Wheelock CE, Krumsiek J, McGeachie M, Moore SC, Kraft P, Mathé E, Lasky-Su J; Consortium of Metabolomics Studies Statistics Working Group. Metabolites. 2019 Jun 18;9(6). pii: E117. doi: 10.3390/metabo9060117. Review. PMID: 31216675 A Recurrent Activating Missense Mutation in Waldenström Macroglobulinemia Affects the DNA Binding of the ETS Transcription Factor SPI1 and Enhances Proliferation. Roos-Weil D, Decaudin C, Armand M, Della-Valle V, Diop MK, Ghamlouch H, Ropars V, Hérate C, Lara D, Durot E, Haddad R, Mylonas E, Damm F, Pflumio F, Stoilova B, Metzner M, Elemento O, Dessen P, Camara-Clayette V, Cosset FL, Verhoeyen E, Leblond V, Ribrag V, Cornillet-Lefebvre P, Rameau P, Azar N, Charlotte F, Morel P, Charbonnier JB, Vyas P, Mercher T, Aoufouchi S, Droin N, Guillouf C, Nguyen-Khac F, Bernard OA. Cancer Discov. 2019 Jun;9(6):796-811. doi: 10.1158/2159-8290.CD-18-0873. Epub 2019 Apr 24. PMID: 31018969 Characterization of Bulk Phosphatidylcholine Compositions in Human Plasma Using Side-Chain Resolving Lipidomics. Quell JD, Römisch-Margl W, Haid M, Krumsiek J, Skurk T, Halama A, Stephan N, Adamski J, Hauner H, Mook-Kanamori D, Mohney RP, Daniel H, Suhre K, Kastenmüller G. Metabolites. 2019 Jun 8;9(6). pii: E109. doi: 10.3390/metabo9060109. PMID: 31181753 BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples. Toosi H, Moeini A, Hajirasouliha I. BMC Bioinformatics. 2019 Jun 6;20(Suppl 11):282. doi: 10.1186/s12859-019-2824-3. PMID: 31167637 BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs. Meleshko D, Mohimani H, Tracanna V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA. Genome Res. 2019 Aug;29(8):1352-1362. doi: 10.1101/gr.243477.118. Epub 2019 Jun 3. PMID: 31160374 Dynamic modelling of an ACADS genotype in fatty acid oxidation – Application of cellular models for the analysis of common genetic variants. Matejka K, Stückler F, Salomon M, Ensenauer R, Reischl E, Hoerburger L, Grallert H, Kastenmüller G, Peters A, Daniel H, Krumsiek J, Theis FJ, Hauner H, Laumen H. PLoS One. 2019 May 23;14(5):e0216110. doi: 10.1371/journal.pone.0216110. eCollection 2019. PMID: 31120904 Where are we going with gene screening for male infertility? Thirumavalavan N, Gabrielsen JS, Lamb DJ. Fertil Steril. 2019 May;111(5):842-850. doi: 10.1016/j.fertnstert.2019.03.036. Review. PMID: 31029238 Function and clinical relevance of RHAMM isoforms in pancreatic tumor progression. Choi S, Wang D, Chen X, Tang LH, Verma A, Chen Z, Kim BJ, Selesner L, Robzyk K, Zhang G, Pang S, Han T, Chan CS, Fahey TJ 3rd, Elemento O, Du YN. Mol Cancer. 2019 May 9;18(1):92. doi: 10.1186/s12943-019-1018-y. PMID: 31072393 Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E. Cell Syst. 2019 May 22;8(5):446-455.e8. doi: 10.1016/j.cels.2019.04.001. Epub 2019 May 8. PMID: 31078526 Next-generation characterization of the Cancer Cell Line Encyclopedia. Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER 3rd, Barretina J, Gelfand ET, Bielski CM, Li H, Hu K, Andreev-Drakhlin AY, Kim J, Hess JM, Haas BJ, Aguet F, Weir BA, Rothberg MV, Paolella BR, Lawrence MS, Akbani R, Lu Y, Tiv HL, Gokhale PC, de Weck A, Mansour AA, Oh C, Shih J, Hadi K, Rosen Y, Bistline J, Venkatesan K, Reddy A, Sonkin D, Liu M, Lehar J, Korn JM, Porter DA, Jones MD, Golji J, Caponigro G, Taylor JE, Dunning CM, Creech AL, Warren AC, McFarland JM, Zamanighomi M, Kauffmann A, Stransky N, Imielinski M, Maruvka YE, Cherniack AD, Tsherniak A, Vazquez F, Jaffe JD, Lane AA, Weinstock DM, Johannessen CM, Morrissey MP, Stegmeier F, Schlegel R, Hahn WC, Getz G, Mills GB, Boehm JS, Golub TR, Garraway LA, Sellers WR. Nature. 2019 May;569(7757):503-508. doi: 10.1038/s41586-019-1186-3. Epub 2019 May 8. PMID: 31068700 The tech for the next decade: promises and challenges in genome biology. Hajirasouliha I, Tilgner HU. Genome Biol. 2019 Apr 30;20(1):86. doi: 10.1186/s13059-019-1695-2. PMID: 31039798 Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target. Lee RS, Zhang L, Berger A, Lawrence MG, Song J, Niranjan B, Davies RG, Lister NL, Sandhu SK, Rubin MA, Risbridger GP, Taylor RA, Rickman DS, Horvath LG, Daly RJ. Neoplasia. 2019 Apr;21(4):389-400. doi: 10.1016/j.neo.2019.02.005. Epub 2019 Mar 20. PMID: 30901730 Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation. Laimighofer M, Lickert R, Fuerst R, Theis FJ, Winkler C, Bonifacio E, Ziegler AG, Krumsiek J. Sci Rep. 2019 Apr 18;9(1):6250. doi: 10.1038/s41598-019-42750-5. PMID: 31000755 CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE. Cancer Cell. 2019 Apr 15;35(4):603-617.e8. doi: 10.1016/j.ccell.2019.03.001. Epub 2019 Mar 28. Erratum in: Cancer Cell. 2019 May 13;35(5):817-819. PMID: 30930119 A Novel Metabolic Signature To Predict the Requirement of Dialysis or Renal Transplantation in Patients with Chronic Kidney Disease. Zacharias HU, Altenbuchinger M, Schultheiss UT, Samol C, Kotsis F, Poguntke I, Sekula P, Krumsiek J, Köttgen A, Spang R, Oefner PJ, Gronwald W. J Proteome Res. 2019 Apr 5;18(4):1796-1805. doi: 10.1021/acs.jproteome.8b00983. Epub 2019 Mar 12. PMID: 30817158 Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization. Khosravi P, Kazemi E, Zhan Q, Malmsten JE, Toschi M, Zisimopoulos P, Sigaras A, Lavery S, Cooper LAD, Hickman C, Meseguer M, Rosenwaks Z, Elemento O, Zaninovic N, Hajirasouliha I. NPJ Digit Med. 2019 Apr 4;2:21. doi: 10.1038/s41746-019-0096-y. eCollection 2019. PMID: 31304368 Immunomodulatory nanogels overcome restricted immunity in a murine model of gut microbiome-mediated metabolic syndrome. Mosquera MJ, Kim S, Zhou H, Jing TT, Luna M, Guss JD, Reddy P, Lai K, Leifer CA, Brito IL, Hernandez CJ, Singh A. Sci Adv. 2019 Mar 27;5(3):eaav9788. doi: 10.1126/sciadv.aav9788. eCollection 2019 Mar. PMID: 30944865 Engineered microscale hydrogels for drug delivery, cell therapy, and sequencing. Wechsler ME, Stephenson RE, Murphy AC, Oldenkamp HF, Singh A, Peppas NA. Biomed Microdevices. 2019 Mar 23;21(2):31. doi: 10.1007/s10544-019-0358-0. Review. PMID: 30904963 Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer. Puca L, Gavyert K, Sailer V, Conteduca V, Dardenne E, Sigouros M, Isse K, Kearney M, Vosoughi A, Fernandez L, Pan H, Motanagh S, Hess J, Donoghue AJ, Sboner A, Wang Y, Dittamore R, Rickman D, Nanus DM, Tagawa ST, Elemento O, Mosquera JM, Saunders L, Beltran H. Sci Transl Med. 2019 Mar 20;11(484). pii: eaav0891. doi: 10.1126/scitranslmed.aav0891. PMID: 30894499 Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing. Grive KJ, Hu Y, Shu E, Grimson A, Elemento O, Grenier JK, Cohen PE. PLoS Genet. 2019 Mar 20;15(3):e1007810. doi: 10.1371/journal.pgen.1007810. eCollection 2019 Mar. PMID: 30893341 Generation of pulmonary neuroendocrine cells and SCLC-like tumors from human embryonic stem cells. Chen HJ, Poran A, Unni AM, Huang SX, Elemento O, Snoeck HW, Varmus H. J Exp Med. 2019 Mar 4;216(3):674-687. doi: 10.1084/jem.20181155. Epub 2019 Feb 8. PMID: 30737256 Identification of a therapeutic target using molecular sequencing for treatment of recurrent uterine serous adenocarcinoma. Musselman K, Glynn S, Mosquera JM, Elemento O, Sboner A, Beltran H, Holcomb K. Gynecol Oncol Rep. 2019 Feb 21;28:54-57. doi: 10.1016/j.gore.2019.01.013. eCollection 2019 May. PMID: 30906838 Gynecologic Organ Involvement During Radical Cystectomy for Bladder Cancer: Is It Time to Routinely Spare the Ovaries? Taylor BL, Matrai CE, Smith AL, Ayangbesan A, Xia L, Golombos DM, Mosquera JM, Nicolas J, Robinson BD, Scherr DS, Khani F. Clin Genitourin Cancer. 2019 Feb;17(1):e209-e215. doi: 10.1016/j.clgc.2018.10.009. Epub 2018 Oct 29. PMID: 30470630 Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate. Elfandy H, Armenia J, Pederzoli F, Pullman E, Pertega-Gomes N, Schultz N, Viswanathan K, Vosoughi A, Blattner M, Stopsack KH, Zadra G, Penney KL, Mosquera JM, Tyekucheva S, Mucci LA, Barbieri C, Loda M. Mol Cancer Res. 2019 Feb;17(2):446-456. doi: 10.1158/1541-7786.MCR-18-0440. Epub 2018 Oct 17. PMID: 30333152 DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns. Skvortsova K, Masle-Farquhar E, Luu PL, Song JZ, Qu W, Zotenko E, Gould CM, Du Q, Peters TJ, Colino-Sanguino Y, Pidsley R, Nair SS, Khoury A, Smith GC, Miosge LA, Reed JH, Kench JG, Rubin MA, Horvath L, Bogdanovic O, Lim SM, Polo JM, Goodnow CC, Stirzaker C, Clark SJ. Cancer Cell. 2019 Feb 11;35(2):297-314.e8. doi: 10.1016/j.ccell.2019.01.004. PMID: 30753827 Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics. Danko DC, Meleshko D, Bezdan D, Mason C, Hajirasouliha I. Genome Res. 2019 Jan;29(1):116-124. doi: 10.1101/gr.235499.118. Epub 2018 Dec 6. PMID: 30523036 RB1 Heterogeneity in Advanced Metastatic Castration-Resistant Prostate Cancer. Nava Rodrigues D, Casiraghi N, Romanel A, Crespo M, Miranda S, Rescigno P, Figueiredo I, Riisnaes R, Carreira S, Sumanasuriya S, Gasperini P, Sharp A, Mateo J, Makay A, McNair C, Schiewer M, Knudsen K, Boysen G, Demichelis F, de Bono JS. Clin Cancer Res. 2019 Jan 15;25(2):687-697. doi: 10.1158/1078-0432.CCR-18-2068. Epub 2018 Sep 26. PMID: 30257982 TETs Regulate Proepicardial Cell Migration through Extracellular Matrix Organization during Zebrafish Cardiogenesis. Lan Y, Pan H, Li C, Banks KM, Sam J, Ding B, Elemento O, Goll MG, Evans T. Cell Rep. 2019 Jan 15;26(3):720-732.e4. doi: 10.1016/j.celrep.2018.12.076. PMID: 30650362 Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. Boehm KM, Bhinder B, Raja VJ, Dephoure N, Elemento O. BMC Bioinformatics. 2019 Jan 5;20(1):7. doi: 10.1186/s12859-018-2561-z. PMID: 30611210 Revisiting the initial steps of sexual development in the malaria parasite Plasmodium falciparum. Bancells C, Llorà-Batlle O, Poran A, Nötzel C, Rovira-Graells N, Elemento O, Kafsack BFC, Cortés A. Nat Microbiol. 2019 Jan;4(1):144-154. doi: 10.1038/s41564-018-0291-7. Epub 2018 Nov 26. PMID: 30478286 Prostaglandin E₂ down-regulates sirtuin 1 (SIRT1), leading to elevated levels of aromatase, providing insights into the obesity-breast cancer connection. Subbaramaiah K, Iyengar NM, Morrow M, Elemento O, Zhou XK, Dannenberg AJ. J Biol Chem. 2019 Jan 4;294(1):361-371. doi: 10.1074/jbc.RA118.005866. Epub 2018 Nov 8. PMID: 30409902 Comprehensive characterization of the mutational landscape in multiple myeloma cell lines reveals potential drivers and pathways associated with tumor progression and drug resistance. Vikova V, Jourdan M, Robert N, Requirand G, Boireau S, Bruyer A, Vincent L, Cartron G, Klein B, Elemento O, Kassambara A, Moreaux J. Theranostics. 2019 Jan 1;9(2):540-553. doi: 10.7150/thno.28374. eCollection 2019. PMID: 30809292 A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers. Beltran H, Oromendia C, Danila DC, Montgomery B, Hoimes C, Szmulewitz RZ, Vaishampayan U, Armstrong AJ, Stein M, Pinski J, Mosquera JM, Sailer V, Bareja R, Romanel A, Gumpeni N, Sboner A, Dardenne E, Puca L, Prandi D, Rubin MA, Scher HI, Rickman DS, Demichelis F, Nanus DM, Ballman KV, Tagawa ST. Clin Cancer Res. 2019 Jan 1;25(1):43-51. doi: 10.1158/1078-0432.CCR-18-1912. Epub 2018 Sep 19. PMID: 30232224 Drug-Induced Expression-Based Computational Repurposing of Small Molecules Affecting Transcription Factor Activity. Gayvert K, Elemento O. Methods Mol Biol. 2019;1903:179-184. doi: 10.1007/978-1-4939-8955-3_10. PMID: 30547442

Immunological impact of cell death signaling driven by radiation on the tumor microenvironment.

Rodriguez-Ruiz ME, Vitale I, Harrington KJ, Melero I, Galluzzi L.

Nat Immunol. 2019 Dec 23. doi: 10.1038/s41590-019-0561-4. [Epub ahead of print] Review.

PMID: 31873291

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2018

A Randomized Multicenter Phase II Study of Docosahexaenoic Acid in Patients with a History of Breast Cancer, Premalignant Lesions or Benign Breast Disease.

Gucalp A, Zhou XK, Cook ED, Garber JE, Crew KD, Nangia JR, Bhardwaj P, Giri DD, Elemento O, Verma A, Wang H, Lee JJ, Vornik LA, Mays C, Weber D, Sepeda V, O’Kane H, Krasne M, Williams S, Morris PG, Heckman-Stoddard BM, Dunn BK, Hudis CA, Brown PH, Dannenberg AJ.
Cancer Prev Res (Phila). 2018 Feb 16. pii: canprevres.0354.2017. doi: 10.1158/1940-6207.CAPR-17-0354. [Epub ahead of print]
PMID: 29453232

Bioinformatics Approaches to Predict Drug Responses from Genomic Sequencing.

Madhukar NS, Elemento O.
Methods Mol Biol. 2018;1711:277-296. doi: 10.1007/978-1-4939-7493-1_14.
PMID: 29344895

Analyzing DNA Methylation Patterns During Tumor Evolution.

Pan H, Elemento O.
Methods Mol Biol. 2018;1711:27-53. doi: 10.1007/978-1-4939-7493-1_3.
PMID: 29344884

Chromosomal instability drives metastasis through a cytosolic DNA response.

Bakhoum SF, Ngo B, Laughney AM, Cavallo JA, Murphy CJ, Ly P, Shah P, Sriram RK, Watkins TBK, Taunk NK, Duran M, Pauli C, Shaw C, Chadalavada K, Rajasekhar VK, Genovese G, Venkatesan S, Birkbak NJ, McGranahan N, Lundquist M, LaPlant Q, Healey JH, Elemento O, Chung CH, Lee NY, Imielenski M, Nanjangud G, Pe’er D, Cleveland DW, Powell SN, Lammerding J, Swanton C, Cantley LC.
Nature. 2018 Jan 25;553(7689):467-472. doi: 10.1038/nature25432. Epub 2018 Jan 17.
PMID: 29342134

AICDA drives epigenetic heterogeneity and accelerates germinal center-derived lymphomagenesis.

Teater M, Dominguez PM, Redmond D, Chen Z, Ennishi D, Scott DW, Cimmino L, Ghione P, Chaudhuri J, Gascoyne RD, Aifantis I, Inghirami G, Elemento O, Melnick A, Shaknovich R.
Nat Commun. 2018 Jan 15;9(1):222. doi: 10.1038/s41467-017-02595-w.
PMID: 29335468

Drug knowledge bases and their applications in biomedical informatics research.

Zhu Y, Elemento O, Pathak J, Wang F.
Brief Bioinform. 2018 Jan 3. doi: 10.1093/bib/bbx169. [Epub ahead of print]
PMID: 29304188

Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images.

Khosravi P, Kazemi E, Imielinski M, Elemento O, Hajirasouliha I.
EBioMedicine. 2018 Jan;27:317-328. doi: 10.1016/j.ebiom.2017.12.026. Epub 2017 Dec 28.
PMID: 29292031

Author Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.

Verma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D.
Nat Genet. 2017 Dec 18. doi: 10.1038/s41588-017-0025-4. [Epub ahead of print]
PMID: 29255265

HN1L Promotes Triple-Negative Breast Cancer Stem Cells through LEPR-STAT3 Pathway.

Liu Y, Choi DS, Sheng J, Ensor JE, Liang DH, Rodriguez-Aguayo C, Polley A, Benz S, Elemento O, Verma A, Cong Y, Wong H, Qian W, Li Z, Granados-Principal S, Lopez-Berestein G, Landis MD, Rosato RR, Dave B, Wong S, Marchetti D, Sood AK, Chang JC.
Stem Cell Reports. 2018 Jan 9;10(1):212-227. doi: 10.1016/j.stemcr.2017.11.010. Epub 2017 Dec 14.
PMID: 29249663

STMN1 is Overexpressed in Adrenocortical Carcinoma and Promotes a More Aggressive Phenotype In Vitro.

Aronova A, Min IM, Crowley MJP, Panjwani SJ, Finnerty BM, Scognamiglio T, Liu YF, Whitsett TG, Garg S, Demeure MJ, Elemento O, Zarnegar R, Fahey Iii TJ.
Ann Surg Oncol. 2018 Mar;25(3):792-800. doi: 10.1245/s10434-017-6296-2. Epub 2017 Dec 6.
PMID: 29214451

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.

Verma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D.
Nat Genet. 2018 Jan;50(1):83-95. doi: 10.1038/s41588-017-0002-y. Epub 2017 Dec 4. Erratum in: Nat Genet. 2017 Dec 18;:. Nat Genet. 2017 Dec 18;:.
PMID: 29203910

Clinical Outcome of Prostate Cancer Patients with Germline DNA Repair Mutations: Retrospective Analysis from an International Study.

Mateo J, Cheng HH, Beltran H, Dolling D, Xu W, Pritchard CC, Mossop H, Rescigno P, Perez-Lopez R, Sailer V, Kolinsky M, Balasopoulou A, Bertan C, Nanus DM, Tagawa ST, Thorne H, Montgomery B, Carreira S, Sandhu S, Rubin MA, Nelson PS, de Bono JS.
Eur Urol. 2018 Jan 29. pii: S0302-2838(18)30019-8. doi: 10.1016/j.eururo.2018.01.010. [Epub ahead of print]
PMID: 29429804

Loss of an Androgen-Inactivating and Isoform-Specific HSD17B4 Splice Form Enables Emergence of Castration-Resistant Prostate Cancer.

Ko HK, Berk M, Chung YM, Willard B, Bareja R, Rubin M, Sboner A, Sharifi N.
Cell Rep. 2018 Jan 16;22(3):809-819. doi: 10.1016/j.celrep.2017.12.081.
PMID: 29346776

SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG.

Shoag J, Liu D, Blattner M, Sboner A, Park K, Deonarine L, Robinson BD, Mosquera JM, Chen Y, Rubin MA, Barbieri CE.
J Clin Invest. 2018 Jan 2;128(1):381-386. doi: 10.1172/JCI96551. Epub 2017 Dec 4.
PMID: 29202479

The Role of Next-Generation Sequencing in Precision Medicine: A Review of Outcomes in Oncology.

Morash M, Mitchell H, Beltran H, Elemento O, Pathak J.

J Pers Med. 2018 Sep 17;8(3). pii: E30. doi: 10.3390/jpm8030030. Review.

PMID: 30227640

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice.

Kindt A, Liebisch G, Clavel T, Haller D, Hörmannsperger G, Yoon H, Kolmeder D, Sigruener A, Krautbauer S, Seeliger C, Ganzha A, Schweizer S, Morisset R, Strowig T, Daniel H, Helm D, Küster B, Krumsiek J, Ecker J.

Nat Commun. 2018 Sep 14;9(1):3760. doi: 10.1038/s41467-018-05767-4.

PMID: 30218046

Does Solid Organ Transplantation Affect Male Reproduction?

Thirumavalavan N, Scovell JM, Link RE, Lamb DJ, Lipshultz LI.

Eur Urol Focus. 2018 Apr;4(3):307-310. doi: 10.1016/j.euf.2018.08.012. Epub 2018 Sep 5. Review.

PMID: 30194032

Linking prostate cancer cell AR heterogeneity to distinct castration and enzalutamide responses.

Li Q, Deng Q, Chao HP, Liu X, Lu Y, Lin K, Liu B, Tang GW, Zhang D, Tracz A, Jeter C, Rycaj K, Calhoun-Davis T, Huang J, Rubin MA, Beltran H, Shen J, Chatta G, Puzanov I, Mohler JL, Wang J, Zhao R, Kirk J, Chen X, Tang DG.

Nat Commun. 2018 Sep 6;9(1):3600. doi: 10.1038/s41467-018-06067-7.

PMID: 30190514

Fusion oncogenes-genetic musical chairs.

Imielinski M, Ladanyi M.

Science. 2018 Aug 31;361(6405):848-849. doi: 10.1126/science.aau8231. No abstract available.

PMID: 30166475

Publisher Correction: Suppression of insulin feedback enhances the efficacy of PI3K inhibitors.

Hopkins BD, Pauli C, Du X, Wang DG, Li X, Wu D, Amadiume SC, Goncalves MD, Hodakoski C, Lundquist MR, Bareja R, Ma Y, Harris EM, Sboner A, Beltran H, Rubin MA, Mukherjee S, Cantley LC.

Nature. 2018 Nov;563(7731):E24. doi: 10.1038/s41586-018-0506-3.

PMID: 30158705

Dilution correction for dynamically influenced urinary analyte data.

Hertel J, Rotter M, Frenzel S, Zacharias HU, Krumsiek J, Rathkolb B, Hrabe de Angelis M, Rabstein S, Pallapies D, Brüning T, Grabe HJ, Wang-Sattler R.

Anal Chim Acta. 2018 Nov 22;1032:18-31. doi: 10.1016/j.aca.2018.07.068. Epub 2018 Jul 28.

PMID: 30143216

A Systemic Inflammatory Signature Reflecting Cross Talk Between Innate and Adaptive Immunity Is Associated With Incident Polyneuropathy: KORA F4/FF4 Study.

Herder C, Kannenberg JM, Carstensen-Kirberg M, Strom A, Bönhof GJ, Rathmann W, Huth C, Koenig W, Heier M, Krumsiek J, Peters A, Meisinger C, Roden M, Thorand B, Ziegler D.

Diabetes. 2018 Nov;67(11):2434-2442. doi: 10.2337/db18-0060. Epub 2018 Aug 16.

PMID: 30115651

SPOP-Mutated/CHD1-Deleted Lethal Prostate Cancer and Abiraterone Sensitivity.

Boysen G, Rodrigues DN, Rescigno P, Seed G, Dolling D, Riisnaes R, Crespo M, Zafeiriou Z, Sumanasuriya S, Bianchini D, Hunt J, Moloney D, Perez-Lopez R, Tunariu N, Miranda S, Figueiredo I, Ferreira A, Christova R, Gil V, Aziz S, Bertan C, de Oliveira FM, Atkin M, Clarke M, Goodall J, Sharp A, MacDonald T, Rubin MA, Yuan W, Barbieri CE, Carreira S, Mateo J, de Bono JS.

Clin Cancer Res. 2018 Nov 15;24(22):5585-5593. doi: 10.1158/1078-0432.CCR-18-0937. Epub 2018 Aug 1.

PMID: 30068710

Suppression of insulin feedback enhances the efficacy of PI3K inhibitors.

Hopkins BD, Pauli C, Du X, Wang DG, Li X, Wu D, Amadiume SC, Goncalves MD, Hodakoski C, Lundquist MR, Bareja R, Ma Y, Harris EM, Sboner A, Beltran H, Rubin MA, Mukherjee S, Cantley LC.

Nature. 2018 Aug;560(7719):499-503. doi: 10.1038/s41586-018-0343-4. Epub 2018 Jul 4. Erratum in: Nature. 2018 Aug 29;:.

PMID: 30051890

Immune reprogramming via PD-1 inhibition enhances early-stage lung cancer survival.

Markowitz GJ, Havel LS, Crowley MJ, Ban Y, Lee SB, Thalappillil JS, Narula N, Bhinder B, Elemento O, Wong ST, Gao D, Altorki NK, Mittal V.

JCI Insight. 2018 Jul 12;3(13). pii: 96836. doi: 10.1172/jci.insight.96836.

PMID: 29997286

Somatic mutations precede acute myeloid leukemia years before diagnosis.

Desai P, Mencia-Trinchant N, Savenkov O, Simon MS, Cheang G, Lee S, Samuel M, Ritchie EK, Guzman ML, Ballman KV, Roboz GJ, Hassane DC.

Nat Med. 2018 Jul;24(7):1015-1023. doi: 10.1038/s41591-018-0081-z. Epub 2018 Jul 9.

PMID: 29988143

Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees.

Ricketts C, Popic V, Toosi H, Hajirasouliha I.

Curr Protoc Bioinformatics. 2018 Jun;62(1):e49. doi: 10.1002/cpbi.49. Epub 2018 May 16.

PMID: 29927069

Patient derived organoids to model rare prostate cancer phenotypes.

Puca L, Bareja R, Prandi D, Shaw R, Benelli M, Karthaus WR, Hess J, Sigouros M, Donoghue A, Kossai M, Gao D, Cyrta J, Sailer V, Vosoughi A, Pauli C, Churakova Y, Cheung C, Deonarine LD, McNary TJ, Rosati R, Tagawa ST, Nanus DM, Mosquera JM, Sawyers CL, Chen Y, Inghirami G, Rao RA, Grandori C, Elemento O, Sboner A, Demichelis F, Rubin MA, Beltran H.

Nat Commun. 2018 Jun 19;9(1):2404. doi: 10.1038/s41467-018-04495-z.

PMID: 29921838

Association of T-Cell Receptor Repertoire Use With Response to Combined Trastuzumab-Lapatinib Treatment of HER2-Positive Breast Cancer: Secondary Analysis of the NeoALTTO Randomized Clinical Trial.

Powles RL, Redmond D, Sotiriou C, Loi S, Fumagalli D, Nuciforo P, Harbeck N, de Azambuja E, Sarp S, Di Cosimo S, Huober J, Baselga J, Piccart-Gebhart M, Elemento O, Pusztai L, Hatzis C.

JAMA Oncol. 2018 Nov 1;4(11):e181564. doi: 10.1001/jamaoncol.2018.1564. Epub 2018 Nov 8.

PMID: 29902299

Molecular Subtypes of Prostate Cancer.

Arora K, Barbieri CE.

Curr Oncol Rep. 2018 Jun 1;20(8):58. doi: 10.1007/s11912-018-0707-9. Review.

PMID: 29858674

Single-Cell Transcriptome Profiling of Protozoan and Metazoan Parasites.

Nötzel C, Poran A, Kafsack BFC.

Trends Parasitol. 2018 Sep;34(9):731-734. doi: 10.1016/j.pt.2018.04.009. Epub 2018 May 26. Review.

PMID: 29807759

Accelerated lipid catabolism and autophagy are cancer survival mechanisms under inhibited glutaminolysis.

Halama A, Kulinski M, Dib SS, Zaghlool SB, Siveen KS, Iskandarani A, Zierer J, Prabhu KS, Satheesh NJ, Bhagwat AM, Uddin S, Kastenmüller G, Elemento O, Gross SS, Suhre K.

Cancer Lett. 2018 Aug 28;430:133-147. doi: 10.1016/j.canlet.2018.05.017. Epub 2018 May 17.

PMID: 29777783

Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy.

Lundquist MR, Goncalves MD, Loughran RM, Possik E, Vijayaraghavan T, Yang A, Pauli C, Ravi A, Verma A, Yang Z, Johnson JL, Wong JCY, Ma Y, Hwang KS, Weinkove D, Divecha N, Asara JM, Elemento O, Rubin MA, Kimmelman AC, Pause A, Cantley LC, Emerling BM.

Mol Cell. 2018 May 3;70(3):531-544.e9. doi: 10.1016/j.molcel.2018.03.037.

PMID: 29727621

How Biophysical Forces Regulate Human B Cell Lymphomas.

Apoorva F, Loiben AM, Shah SB, Purwada A, Fontan L, Goldstein R, Kirby BJ, Melnick AM, Cosgrove BD, Singh A.

Cell Rep. 2018 Apr 10;23(2):499-511. doi: 10.1016/j.celrep.2018.03.069.

PMID: 29642007

The long tail of oncogenic drivers in prostate cancer.

Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM; PCF/SU2C International Prostate Cancer Dream Team, Schultz N, Van Allen EM.

Nat Genet. 2018 May;50(5):645-651. doi: 10.1038/s41588-018-0078-z. Epub 2018 Apr 2. Erratum in: Nat Genet. 2019 Jul;51(7):1194.

PMID: 29610475

Beyond Tissue Stiffness and Bioadhesivity: Advanced Biomaterials to Model Tumor Microenvironments and Drug Resistance.

Singh A, Brito I, Lammerding J.

Trends Cancer. 2018 Apr;4(4):281-291. doi: 10.1016/j.trecan.2018.01.008. Epub 2018 Mar 10. Review.

PMID: 29606313

SvABA: genome-wide detection of structural variants and indels by local assembly.

Wala JA, Bandopadhayay P, Greenwald NF, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.

Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13.

PMID: 29535149

Intragenic DNA methylation of PITX1 and the adjacent long non-coding RNA C5orf66-AS1 are prognostic biomarkers in patients with head and neck squamous cell carcinomas.

Sailer V, Charpentier A, Dietrich J, Vogt TJ, Franzen A, Bootz F, Dietrich D, Schroeck A.

PLoS One. 2018 Feb 9;13(2):e0192742. doi: 10.1371/journal.pone.0192742. eCollection 2018.

PMID: 29425237

The Expanding World of N-MYC-Driven Tumors.

Rickman DS, Schulte JH, Eilers M.

Cancer Discov. 2018 Feb;8(2):150-163. doi: 10.1158/2159-8290.CD-17-0273. Epub 2018 Jan 22. Review.

PMID: 29358508

2017

Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models
Pisapia DJ, Salvatore S, Pauli C, Hissong E, Eng K, Prandi D, Sailer VW, Robinson BD, Park K, Cyrta J, Tagawa ST, Kossai M, Fontugne J, Kim R, Sigaras A, Rao R, Pancirer D, Faltas B, Bareja R, Molina AM, Nanus DM, Rajappa P, Souweidane MM, Greenfield J, Emde AK, Robine N, Elemento O, Sboner A, Demichelis F, Beltran H, Rubin MA, Mosquera JM
PMID: 29333526

Bone biopsy protocol for advanced prostate cancer in the era of precision medicine

Sailer V, Schiffman, MH, Kossai, M, Cyrta J, Beg, S, Sullivan B, Pua BB, Kyungmouk SL, Talendfeld AD, Nanus DM, Tagawa ST, Robinson BD, Rao RA, Pauli C, Bareja R, Beltran LS, Sigaras A, Eng KW, Elemento O, Sboner A, Rubin MA, Beltran H, Mosquera JM

Cancer. 2017 Dec 19. doi: 10.1002/cncr.31173. [Epub ahead of print]

STMN1 is Overexpressed in Adrenocortical Carcinoma and Promotes a More Aggressive Phenotype In Vitro.

Aronova A, Min IM, Crowley MJP, Panjwani SJ, Finnerty BM, Scognamiglio T, Liu YF, Whitsett TG, Garg S, Demeure MJ, Elemento O, Zarnegar R, Fahey Iii TJ.

Ann Surg Oncol. 2017 Dec 6. doi: 10.1245/s10434-017-6296-2. [Epub ahead of print]

PMID: 29214451

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.

Verma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D.

Nat Genet. 2017 Dec 4. doi: 10.1038/s41588-017-0002-y. [Epub ahead of print]

PMID: 29203910

Publisher Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.

Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple Negative Breast Cancer.

Liu H, Murphy CJ, Karreth FA, Emdal KB, White FM, Elemento O, Toker A, Wulf GM, Cantley LC.

Cancer Discov. 2017 Dec 4. pii: CD-17-0679. doi: 10.1158/2159-8290.CD-17-0679. [Epub ahead of print]

PMID: 29203461

Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites.

Poran A, Nötzel C, Aly O, Mencia-Trinchant N, Harris CT, Guzman ML, Hassane DC, Elemento O, Kafsack BFC.

Nature. 2017 Nov 2;551(7678):95-99. doi: 10.1038/nature24280. Epub 2017 Sep 25.

PMID: 29094698

Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance.

Shukla S, Cyrta J, Murphy DA, Walczak EG, Ran L, Agrawal P, Xie Y, Chen Y, Wang S, Zhan Y, Li D, Wong EWP, Sboner A, Beltran H, Mosquera JM, Sher J, Cao Z, Wongvipat J, Koche RP, Gopalan A, Zheng D, Rubin MA, Scher HI, Chi P, Chen Y.

Cancer Cell. 2017 Dec 11;32(6):792-806.e7. doi: 10.1016/j.ccell.2017.10.008. Epub 2017 Nov 16.

PMID: 29153843

Metastasectomy in older adults with urothelial carcinoma: Population-based analysis of use and outcomes.

Faltas BM, Gennarelli RL, Elkin E, Nguyen DP, Hu J, Tagawa ST.

Urol Oncol. 2018 Jan;36(1):9.e11-9.e17. doi: 10.1016/j.urolonc.2017.09.009. Epub 2017 Oct 5.

PMID: 28988653

Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine.

Pauli C, Hopkins BD, Prandi D, Shaw R, Fedrizzi T, Sboner A, Sailer V, Augello M, Puca L, Rosati R, McNary TJ, Churakova Y, Cheung C, Triscott J, Pisapia D, Rao R, Mosquera JM, Robinson B, Faltas BM, Emerling BE, Gadi VK, Bernard B, Elemento O, Beltran H, Demichelis F, Kemp CJ, Grandori C, Cantley LC, Rubin MA.

Cancer Discov. 2017 May;7(5):462-477. doi: 10.1158/2159-8290.CD-16-1154. Epub 2017 Mar 22 PMID: 28331002

Immune-checkpoint blockade in cisplatin-ineligible patients with urothelial cancer.

Faltas BM, Tagawa ST.

Lancet. 2017 Jan 7;389(10064):6-7. doi: 10.1016/S0140-6736(16)32516-8. Epub 2016 Dec 8. No abstract available.

PMID: 27939401

SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG.

Shoag J, Liu D, Blattner M, Sboner A, Park K, Deonarine L, Robinson BD, Mosquera JM, Chen Y, Rubin MA, Barbieri CE.

J Clin Invest. 2017 Dec 4. pii: 96551. doi: 10.1172/JCI96551. [Epub ahead of print]

PMID: 29202479

Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance.

Cancer Cell. 2017 Dec 11;32(6):792-806.e7. doi: 10.1016/j.ccell.2017.10.008. Epub 2017 Nov 16.

PMID: 29153843

Impact of Therapy on Genomics and Transcriptomics in High-Risk Prostate Cancer Treated with Neoadjuvant Docetaxel and Androgen Deprivation Therapy.

Beltran H, Wyatt AW, Chedgy EC, Donoghue A, Annala M, Warner EW, Beja K, Sigouros M, Mo F, Fazli L, Collins CC, Eastham J, Morris M, Taplin ME, Sboner A, Halabi S, Gleave ME.

Clin Cancer Res. 2017 Nov 15;23(22):6802-6811. doi: 10.1158/1078-0432.CCR-17-1034. Epub 2017 Aug 25.

PMID: 28842510

Molecular alterations in prostate cancer and association with MRI features.

Lee D, Fontugne J, Gumpeni N, Park K, MacDonald TY, Robinson BD, Sboner A, Rubin MA, Mosquera JM, Barbieri CE.

Prostate Cancer Prostatic Dis. 2017 Dec;20(4):430-435. doi: 10.1038/pcan.2017.33. Epub 2017 Aug 1.

PMID: 28762374

SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG.

Shoag J, Liu D, Blattner M, Sboner A, Park K, Deonarine L, Robinson BD, Mosquera JM, Chen Y, Rubin MA, Barbieri CE.

J Clin Invest. 2017 Dec 4. pii: 96551. doi: 10.1172/JCI96551. [Epub ahead of print]

PMID: 29202479

Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance.

Cancer Cell. 2017 Dec 11;32(6):792-806.e7. doi: 10.1016/j.ccell.2017.10.008. Epub 2017 Nov 16.

PMID: 29153843

Rapid autopsy of a patient with recurrent anaplastic ependymoma.

Lange KR, Fischer C, Rajappa P, Connors S, Pisapia D, Greenfield JP, Beltran H, Rubin M, Mosquera JM, Khakoo Y.

Palliat Support Care. 2017 Sep 25:1-5. doi: 10.1017/S1478951517000864. [Epub ahead of print]

PMID: 28942746

EZH2 enables germinal centre formation through epigenetic silencing of CDKN1A and an Rb-E2F1 feedback loop.
Béguelin W, Rivas MA, Calvo Fernández MT, Teater M, Purwada A, Redmond D, Shen H, Challman MF, Elemento O, Singh A, Melnick AM.
Nat Commun. 2017 Oct 12;8(1):877. doi: 10.1038/s41467-017-01029-x.
PMID:29026085.

A Predictive Model for Selective Targeting of the Warburg Effect through GAPDH Inhibition with a Natural Product.
Liberti MV, Dai Z, Wardell SE, Baccile JA, Liu X, Gao X, Baldi R, Mehrmohamadi M, Johnson MO, Madhukar NS, Shestov AA, Chio IIC, Elemento O, Rathmell JC, Schroeder FC, McDonnell DP, Locasale JW.
Cell Metab. 2017 Oct 3;26(4):648-659.e8. doi: 10.1016/j.cmet.2017.08.017. Epub 2017 Sep 14.
PMID: 28918937.

Broad Targeting Specificity during Bacterial Type III CRISPR-Cas Immunity Constrains Viral Escape.
Pyenson NC, Gayvert K, Varble A, Elemento O, Marraffini LA.
Cell Host Microbe. 2017 Sep 13;22(3):343-353.e3. doi: 10.1016/j.chom.2017.07.016. Epub 2017 Aug 17.
PMID: 28826839.

Cancer stem cell-related gene expression as a potential biomarker of response for first-in-class imipridone ONC201 in solid tumors.
Prabhu VV, Lulla AR, Madhukar NS, Ralff MD, Zhao D, Kline CLB, Van den Heuvel APJ, Lev A, Garnett MJ, McDermott U, Benes CH, Batchelor TT, Chi AS, Elemento O, Allen JE, El-Deiry WS.
PLoS One. 2017 Aug 2;12(8):e0180541. doi: 10.1371/journal.pone.0180541. eCollection 2017.
PMID: 28767654.

R-Spondin chromosome rearrangements drive Wnt-dependent tumour initiation and maintenance in the intestine.
Han T, Schatoff EM, Murphy C, Zafra MP, Wilkinson JE, Elemento O, Dow LE.
Nat Commun. 2017 Jul 11;8:15945. doi: 10.1038/ncomms15945.
PMID: 28695896.

Inherited determinants of early recurrent somatic mutations in prostate cancer.
Romanel A, Garritano S, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Soong D, Cotter KA, Petris G, Dhingra P, Gasperini P, Cereseto A, Elemento O, Sboner A, Khurana E, Inga A, Rubin MA, Demichelis F.
Nat Commun. 2017 Jun 29;8(1):48. doi: 10.1038/s41467-017-00046-0.
PMID: 28663546.

Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma.
Reichel JB, McCormick J, Fromm JR, Elemento O, Cesarman E, Roshal M.
J Vis Exp. 2017 Jun 10;(124). doi: 10.3791/54399.
PMID: 28654052.

Lymphatic endothelial S1P promotes mitochondrial function and survival in naive T cells.
Mendoza A, Fang V, Chen C, Serasinghe M, Verma A, Muller J, Chaluvadi VS, Dustin ML, Hla T, Elemento O, Chipuk JE, Schwab SR.
Nature. 2017 Jun 1;546(7656):158-161. doi: 10.1038/nature22352. Epub 2017 May 24.
PMID: 28538737.

Concerted regulation of retinal pigment epithelium basement membrane and barrier function by angiocrine factors.
Benedicto I, Lehmann GL, Ginsberg M, Nolan DJ, Bareja R, Elemento O, Salfati Z, Alam NM, Prusky GT, Llanos P, Rabbany SY, Maminishkis A, Miller SS, Rafii S, Rodriguez-Boulan E.
Nat Commun. 2017 May 19;8:15374. doi: 10.1038/ncomms15374.
PMID: 28524846.

Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells.
Liu Y, Pelham-Webb B, Di Giammartino DC, Li J, Kim D, Kita K, Saiz N, Garg V, Doane A, Giannakakou P, Hadjantonakis AK, Elemento O, Apostolou E.
Cell Rep. 2017 May 16;19(7):1283-1293. doi: 10.1016/j.celrep.2017.04.067.
PMID: 28514649.

Conversion of adult endothelium to immunocompetent haematopoietic stem cells.
Lis R, Karrasch CC, Poulos MG, Kunar B, Redmond D, Duran JGB, Badwe CR, Schachterle W, Ginsberg M, Xiang J, Tabrizi AR, Shido K, Rosenwaks Z, Elemento O, Speck NA, Butler JM, Scandura JM, Rafii S.
Nature. 2017 May 25;545(7655):439-445. doi: 10.1038/nature22326. Epub 2017 May 17.
PMID: 28514438.

An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data.
Carty M, Zamparo L, Sahin M, González A, Pelossof R, Elemento O, Leslie CS.
Nat Commun. 2017 May 17;8:15454. doi: 10.1038/ncomms15454.
PMID: 28513628.

Identification of a nucleoside analog active against adenosine kinase-expressing plasma cell malignancies.
Nayar U, Sadek J, Reichel J, Hernandez-Hopkins D, Akar G, Barelli PJ, Sahai MA, Zhou H, Totonchy J, Jayabalan D, Niesvizky R, Guasparri I, Hassane D, Liu Y, Sei S, Shoemaker RH, Warren JD, Elemento O, Kaye KM, Cesarman E.
J Clin Invest. 2017 Jun 1;127(6):2066-2080. doi: 10.1172/JCI83936. Epub 2017 May 15.
PMID: 28504647.

Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell.
Kassambara A, Jourdan M, Bruyer A, Robert N, Pantesco V, Elemento O, Klein B, Moreaux J.
Nucleic Acids Res. 2017 Jun 2;45(10):5639-5652. doi: 10.1093/nar/gkx327.
PMID: 28459970.

Stem Cell Lineage Infidelity Drives Wound Repair and Cancer.
Ge Y, Gomez NC, Adam RC, Nikolova M, Yang H, Verma A, Lu CP, Polak L, Yuan S, Elemento O, Fuchs E.
Cell. 2017 May 4;169(4):636-650.e14. doi: 10.1016/j.cell.2017.03.042. Epub 2017 Apr 20.
PMID: 28434617.

Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers.
Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME.
Cancer Discov. 2017 Aug;7(8):868-883. doi: 10.1158/2159-8290.CD-16-1032. Epub 2017 Apr 13.
PMID: 28408400.

EthSEQ: ethnicity annotation from whole exome sequencing data.
Romanel A, Zhang T, Elemento O, Demichelis F.
Bioinformatics. 2017 Aug 1;33(15):2402-2404. doi: 10.1093/bioinformatics/btx165.
PMID: 28369222.

Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression.
Anelli V, Villefranc JA, Chhangawala S, Martinez-McFaline R, Riva E, Nguyen A, Verma A, Bareja R, Chen Z, Scognamiglio T, Elemento O, Houvras Y.
Elife. 2017 Mar 28;6. pii: e20728. doi: 10.7554/eLife.20728.
PMID:28350298.

Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine.
Pauli C, Hopkins BD, Prandi D, Shaw R, Fedrizzi T, Sboner A, Sailer V, Augello M, Puca L, Rosati R, McNary TJ, Churakova Y, Cheung C, Triscott J, Pisapia D, Rao R, Mosquera JM, Robinson B, Faltas BM, Emerling BE, Gadi VK, Bernard B, Elemento O, Beltran H, Demichelis F, Kemp CJ, Grandori C, Cantley LC, Rubin MA.
Cancer Discov. 2017 May;7(5):462-477. doi: 10.1158/2159-8290.CD-16-1154. Epub 2017 Mar 22.
PMID: 28331002.

Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity.
Patnaik A, Swanson KD, Csizmadia E, Solanki A, Landon-Brace N, Gehring MP, Helenius K, Olson BM, Pyzer AR, Wang LC, Elemento O, Novak J, Thornley TB, Asara JM, Montaser L, Timmons JJ, Morgan TM, Wang Y, Levantini E, Clohessy JG, Kelly K, Pandolfi PP, Rosenblatt JM, Avigan DE, Ye H, Karp JM, Signoretti S, Balk SP, Cantley LC.
Cancer Discov. 2017 Jul;7(7):750-765. doi: 10.1158/2159-8290.CD-16-0778. Epub 2017 Mar 8.
PMID: 28274958.

BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells.
Valls E, Lobry C, Geng H, Wang L, Cardenas M, Rivas M, Cerchietti L, Oh P, Yang SN, Oswald E, Graham CW, Jiang Y, Hatzi K, Agirre X, Perkey E, Li Z, Tam W, Bhatt K, Leonard JP, Zweidler-McKay PA, Maillard I, Elemento O, Ci W, Aifantis I, Melnick A.
Cancer Discov. 2017 May;7(5):506-521. doi: 10.1158/2159-8290.CD-16-1189. Epub 2017 Feb 23.
PMID: 28232365.

Melanoma genome evolution across species.
Kansler ER, Verma A, Langdon EM, Simon-Vermot T, Yin A, Lee W, Attiyeh M, Elemento O, White RM.
BMC Genomics. 2017 Feb 7;18(1):136. doi: 10.1186/s12864-017-3518-8.
PMID: 28173755.

Effective Combination Therapies for B-cell Lymphoma Predicted by a Virtual Disease Model.
Du W, Goldstein R, Jiang Y, Aly O, Cerchietti L, Melnick A, Elemento O.
Cancer Res. 2017 Apr 15;77(8):1818-1830. doi: 10.1158/0008-5472.CAN-16-0476. Epub 2017 Jan 27.
PMID: 28130226.

Regulatory elements in molecular networks.
Doane AS, Elemento O.
Wiley Interdiscip Rev Syst Biol Med. 2017 May;9(3). doi: 10.1002/wsbm.1374. Epub 2017 Jan 17. Review.
PMID: 28093886.

Sox17 drives functional engraftment of endothelium converted from non-vascular cells.
Schachterle W, Badwe CR, Palikuqi B, Kunar B, Ginsberg M, Lis R, Yokoyama M, Elemento O, Scandura JM, Rafii S.
Nat Commun. 2017 Jan 16;8:13963. doi: 10.1038/ncomms13963.
PMID: 28091527.

A Computational Approach for Identifying Synergistic Drug Combinations.
Gayvert KM, Aly O, Platt J, Bosenberg MW, Stern DF, Elemento O.
PLoS Comput Biol. 2017 Jan 13;13(1):e1005308. doi: 10.1371/journal.pcbi.1005308. eCollection 2017 Jan.
PMID: 28085880.

Systems Structural Biology Analysis of Ligand Effects on ERα Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Nwachukwu JC, Srinivasan S, Bruno NE, Nowak J, Wright NJ, Minutolo F, Rangarajan ES, Izard T, Yao XQ, Grant BJ, Kojetin DJ, Elemento O, Katzenellenbogen JA, Nettles KW.
Cell Chem Biol. 2017 Jan 19;24(1):35-45. doi: 10.1016/j.chembiol.2016.11.014. Epub 2016 Dec 29.
PMID: 28042045.

Reversible methylation of m6Am in the 5′ cap controls mRNA stability.
Mauer J, Luo X, Blanjoie A, Jiao X, Grozhik AV, Patil DP, Linder B, Pickering BF, Vasseur JJ, Chen Q, Gross SS, Elemento O, Debart F, Kiledjian M, Jaffrey SR.
Nature. 2017 Jan 19;541(7637):371-375. doi: 10.1038/nature21022. Epub 2016 Dec 21.
PMID: 28002401.

Endothelial-specific inhibition of NF-κB enhances functional haematopoiesis.
Poulos MG, Ramalingam P, Gutkin MC, Kleppe M, Ginsberg M, Crowley MJ, Elemento O, Levine RL, Rafii S, Kitajewski J, Greenblatt MB, Shim JH, Butler JM.
Nat Commun. 2016 Dec 21;7:13829. doi: 10.1038/ncomms13829.
PMID: 28000664.

Mechanisms of Acquired Drug Resistance to the HDAC6 Selective Inhibitor Ricolinostat Reveals Rational Drug-Drug Combination with Ibrutinib.
Amengual JE, Prabhu SA, Lombardo M, Zullo K, Johannet PM, Gonzalez Y, Scotto L, Serrano XJ, Wei Y, Duong J, Nandakumar R, Cremers S, Verma A, Elemento O, O’Connor OA.
Clin Cancer Res. 2017 Jun 15;23(12):3084-3096. doi: 10.1158/1078-0432.CCR-16-2022. Epub 2016 Dec 19.
PMID: 27993968.

Systematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets.
Giannopoulou E, Elemento O.
Methods Mol Biol. 2017;1507:43-58.
PMID: 27832531.

The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations.
Huang L, Fernandes H, Zia H, Tavassoli P, Rennert H, Pisapia D, Imielinski M, Sboner A, Rubin MA, Kluk M, Elemento O.
J Am Med Inform Assoc. 2017 May 1;24(3):513-519. doi: 10.1093/jamia/ocw148.
PMID: 27789569.

CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas.
Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, Sharma S, Young JW, Chu CS, Roeder RG, Shaknovich R, Hiebert SW, Gascoyne RD, Tam W, Elemento O, Wendel HG, Melnick AM.
Cancer Discov. 2017 Jan;7(1):38-53. doi: 10.1158/2159-8290.CD-16-0975. Epub 2016 Oct 12.
PMID: 27733359.

SRRM4 Drives Neuroendocrine Transdifferentiation of Prostate Adenocarcinoma Under Androgen Receptor Pathway Inhibition.
Li Y, Donmez N, Sahinalp C, Xie N, Wang Y, Xue H, Mo F, Beltran H, Gleave M, Wang Y, Collins C, Dong X.
Eur Urol. 2017 Jan;71(1):68-78. doi: 10.1016/j.eururo.2016.04.028. Epub 2016 May 11.
PMID: 27180064.

The Master Neural Transcription Factor BRN2 Is an Androgen Receptor-Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer.
Bishop JL, Thaper D, Vahid S, Davies A, Ketola K, Kuruma H, Jama R, Nip KM, Angeles A, Johnson F, Wyatt AW, Fazli L, Gleave ME, Lin D, Rubin MA, Collins CC, Wang Y, Beltran H, Zoubeidi A.
Cancer Discov. 2017 Jan;7(1):54-71. doi: 10.1158/2159-8290.CD-15-1263. Epub 2016 Oct 26.
PMID: 27784708.

The clone wars.
Beltran H.
Sci Transl Med. 2017 Feb 15;9(377). pii: eaam6061. doi: 10.1126/scitranslmed.aam6061.
PMID: 28202773.

SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer.
Mu P, Zhang Z, Benelli M, Karthaus WR, Hoover E, Chen CC, Wongvipat J, Ku SY, Gao D, Cao Z, Shah N, Adams EJ, Abida W, Watson PA, Prandi D, Huang CH, de Stanchina E, Lowe SW, Ellis L, Beltran H, Rubin MA, Goodrich DW, Demichelis F, Sawyers CL.
Science. 2017 Jan 6;355(6320):84-88. doi: 10.1126/science.aah4307.
PMID: 28059768.

Unleashing the wrath of Ras.
Beltran H.
Sci Transl Med. 2017 Jan 4;9(371). pii: eaal4985. doi: 10.1126/scitranslmed.aal4985. No abstract available.
PMID: 28053152.

Prostate cancer in 2016: Improved outcomes and precision medicine come within reach.
Sternberg CN, Beltran H.
Nat Rev Urol. 2017 Feb;14(2):71-72. doi: 10.1038/nrurol.2016.270. Epub 2017 Jan 4. No abstract available.
PMID: 28050016.

Rapid autopsy of a patient with recurrent anaplastic ependymoma.
Lange KR, Fischer C, Rajappa P, Connors S, Pisapia D, Greenfield JP, Beltran H, Rubin M, Mosquera JM, Khakoo Y.
Palliat Support Care. 2017 Sep 25:1-5. doi: 10.1017/S1478951517000864.
PMID: 28942746.

A germline FANCA alteration that is associated with increased sensitivity to DNA damaging agents.
Wilkes DC, Sailer V, Xue H, Cheng H, Collins CC, Gleave M, Wang Y, Demichelis F, Beltran H, Rubin MA, Rickman DS.
Cold Spring Harb Mol Case Stud. 2017 Sep;3(5). pii: a001487. doi: 10.1101/mcs.a001487. Epub 2017 May 3.
PMID: 28864460.

Impact of therapy on genomics and transcriptomics in high-risk prostate cancer treated with neoadjuvant docetaxel and androgen deprivation therapy.
Beltran H, Wyatt AW, Chedgy E, Donoghue A, Annala M, Warner E, Beja K, Sigouros M, Mo F, Fazli L, Collins CC, Eastham JA, Morris MJ, Taplin ME, Sboner A, Halabi S, Gleave ME.
Clin Cancer Res. 2017 Aug 25. pii: clincanres.1034.2017. doi: 10.1158/1078-0432.CCR-17-1034.
PMID: 28842510.

Management of Patients with Advanced Prostate Cancer: The Report of the Advanced Prostate Cancer Consensus Conference APCCC 2017.
Gillessen S, Attard G, Beer TM, Beltran H, Bossi A, Bristow R, Carver B, Castellano D, Chung BH, Clarke N, Daugaard G, Davis ID, de Bono J, Dos Reis RB, Drake CG, Eeles R, Efstathiou E, Evans CP, Fanti S, Feng F, Fizazi K, Frydenberg M, Gleave M, Halabi S, Heidenreich A, Higano CS, James N, Kantoff P, Kellokumpu-Lehtinen PL, Khauli RB, Kramer G, Logothetis C, Maluf F, Morgans AK, Morris MJ, Mottet N, Murthy V, Oh W, Ost P, Padhani AR, Parker C, Pritchard CC, Roach M, Rubin MA, Ryan C, Saad F, Sartor O, Scher H, Sella A, Shore N, Smith M, Soule H, Sternberg CN, Suzuki H, Sweeney C, Sydes MR, Tannock I, Tombal B, Valdagni R, Wiegel T, Omlin A.
Eur Urol. 2017 Jun 24. pii: S0302-2838(17)30497-9. doi: 10.1016/j.eururo.2017.06.002.
PMID: 28655541.

ERF mutations reveal a balance of ETS factors controlling prostate oncogenesis.
Bose R, Karthaus WR, Armenia J, Abida W, Iaquinta PJ, Zhang Z, Wongvipat J, Wasmuth EV, Shah N, Sullivan PS, Doran MG, Wang P, Patruno A, Zhao Y; International SU2C/PCF Prostate Cancer Dream Team, Zheng D, Schultz N, Sawyers CL.
Nature. 2017 Jun 29;546(7660):671-675. doi: 10.1038/nature22820. Epub 2017 Jun 14.
PMID: 28614298.

Biology and evolution of poorly differentiated neuroendocrine tumors.
Rickman DS, Beltran H, Demichelis F, Rubin MA.
Nat Med. 2017 Jun 6;23(6):1-10. doi: 10.1038/nm.4341.
PMID: 28586335.

Personalizing Therapy for Metastatic Prostate Cancer: The Role of Solid and Liquid Tumor Biopsies.
Friedlander TW, Pritchard CC, Beltran H.
Am Soc Clin Oncol Educ Book. 2017;37:358-369. doi: 10.14694/EDBK_175510.
PMID: 28561699.

Erratum to: Unraveling the clonal hierarchy of somatic genomic aberrations.
Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.
Genome Biol. 2017 May 2;18(1):80. doi: 10.1186/s13059-017-1183-5. No abstract available.
PMID: 28464947.

Transplantation of engineered organoids enables rapid generation of metastatic mouse models of colorectal cancer.
O’Rourke KP, Loizou E, Livshits G, Schatoff EM, Baslan T, Manchado E, Simon J, Romesser PB, Leach B, Han T, Pauli C, Beltran H, Rubin MA, Dow LE, Lowe SW.
Nat Biotechnol. 2017 Jun;35(6):577-582. doi: 10.1038/nbt.3837. Epub 2017 May 1.
PMID: 28459450.

On-site Cytology for Development of Patient-Derived Three-dimensional Organoid Cultures – A Pilot Study.
Sailer V, Pauli C, Merzier EC, Mosquera JM, Beltran H, Rubin MA, Rao RA.
Anticancer Res. 2017 Apr;37(4):1569-1573.
PMID: 28373416.

Emerging Variants of Castration-Resistant Prostate Cancer.
Vlachostergios PJ, Puca L, Beltran H.
Curr Oncol Rep. 2017 May;19(5):32. doi: 10.1007/s11912-017-0593-6. Review.
PMID: 28361223.

Co-clinical Analysis of a Genetically Engineered Mouse Model and Human Prostate Cancer Reveals Significance of NKX3.1 Expression for Response to 5α-reductase Inhibition.
Dutta A, Panja S, Virk RK, Kim JY, Zott R, Cremers S, Golombos DM, Liu D, Mosquera JM, Mostaghel EA, Barbieri CE, Mitrofanova A, Abate-Shen C.
Eur Urol. 2017 Oct;72(4):499-506. doi: 10.1016/j.eururo.2017.03.031. Epub 2017 Apr 4.
PMID: 28385453.

A Precious Diagnostic “Pearl”: The Necklace Pattern in Germ Cell Tumors of the Testis.
Snow J, Mosquera JM, Scognamiglio T, Robinson BD, Khani F.
Int J Surg Pathol. 2017 Aug 1:1066896917729502. doi: 10.1177/1066896917729502. [Epub ahead of print]
PMID: 28862048.

Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics.
Wang H, Barbieri CE, He J, Gao Y, Shi T, Wu C, Schepmoes AA, Fillmore TL, Chae SS, Huang D, Mosquera JM, Qian WJ, Smith RD, Srivastava S, Kagan J, Camp DG 2nd, Rodland KD, Rubin MA, Liu T.
J Transl Med. 2017 Aug 15;15(1):175. doi: 10.1186/s12967-017-1276-7.
PMID: 28810879.

Molecular alterations in prostate cancer and association with MRI features.
Lee D, Fontugne J, Gumpeni N, Park K, MacDonald TY, Robinson BD, Sboner A, Rubin MA, Mosquera JM, Barbieri CE.
Prostate Cancer Prostatic Dis. 2017 Aug 1. doi: 10.1038/pcan.2017.33. [Epub ahead of print]
PMID: 28762374.

Characterization of CD34-deficient myofibroblastomas of the breast.
D’Alfonso TM, Subramaniyam S, Ginter PS, Mosquera JM, Croyle J, Liu YF, Rubin MA, Shin SJ.
Breast J. 2017 May 30. doi: 10.1111/tbj.12835.
PMID: 28557150.

Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.
Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW, Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F, Gabriel S, Van Allen EM, Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA.
Cancer Discov. 2017 Sep;7(9):973-983. doi: 10.1158/2159-8290.CD-16-0960. Epub 2017 May 17.
PMID: 28515055.

2016

Role of RPL39 in Metaplastic Breast Cancer.
Dave B, Gonzalez DD, Liu ZB, Li X, Wong H, Granados S, Ezzedine NE, Sieglaff DH, Ensor JE, Miller KD, Radovich M, KarinaEtrovic A, Gross SS, Elemento O, Mills GB, Gilcrease MZ, Chang JC.
J Natl Cancer Inst. 2016 Dec 31;109(6). pii: djw292. doi: 10.1093/jnci/djw292. Print 2017 Jun.
PMID: 28040796.

Clonal evolution of chemotherapy-resistant urothelial carcinoma.
Faltas BM, Prandi D, Tagawa ST, Molina AM, Nanus DM, Sternberg C, Rosenberg J, Mosquera JM, Robinson B, Elemento O, Sboner A, Beltran H, Demichelis F, Rubin MA.
Nat Genet. 2016 Dec;48(12):1490-1499. doi: 10.1038/ng.3692. Epub 2016 Oct 17.
PMID: 27749842.

Therapeutic efficacy of the bromodomain inhibitor OTX015/MK-8628 in ALK-positive anaplastic large cell lymphoma: an alternative modality to overcome resistant phenotypes.
Boi M, Todaro M, Vurchio V, Yang SN, Moon J, Kwee I, Rinaldi A, Pan H, Crescenzo R, Cheng M, Cerchietti L, Elemento O, Riveiro ME, Cvitkovic E, Bertoni F, Inghirami G; AIRC 5xMille Consortium ‘Genetics-Driven Targeted Management of Lymphoid Malignancies’.
Oncotarget. 2016 Nov 29;7(48):79637-79653. doi: 10.18632/oncotarget.12876.
PMID:27793034.

A Data-Driven Approach to Predicting Successes and Failures of Clinical Trials.
Gayvert KM, Madhukar NS, Elemento O.
Cell Chem Biol. 2016 Oct 20;23(10):1294-1301. doi: 10.1016/j.chembiol.2016.07.023. Epub 2016 Sep 15.
PMID: 27642066.

N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer.
Dardenne E, Beltran H, Benelli M, Gayvert K, Berger A, Puca L, Cyrta J, Sboner A, Noorzad Z, MacDonald T, Cheung C, Yuen KS, Gao D, Chen Y, Eilers M, Mosquera JM, Robinson BD, Elemento O, Rubin MA, Demichelis F, Rickman DS.
Cancer Cell. 2016 Oct 10;30(4):563-577. doi: 10.1016/j.ccell.2016.09.005.
PMID: 27728805.

Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region.
Bunting KL, Soong TD, Singh R, Jiang Y, Béguelin W, Poloway DW, Swed BL, Hatzi K, Reisacher W, Teater M, Elemento O, Melnick AM.
Immunity. 2016 Sep 20;45(3):497-512. doi: 10.1016/j.immuni.2016.08.012. Epub 2016 Sep 13.
PMID: 27637145.

Discovery and clinical introduction of first-in-class imipridone ONC201.
Allen JE, Kline CL, Prabhu VV, Wagner J, Ishizawa J, Madhukar N, Lev A, Baumeister M, Zhou L, Lulla A, Stogniew M, Schalop L, Benes C, Kaufman HL, Pottorf RS, Nallaganchu BR, Olson GL, Al-Mulla F, Duvic M, Wu GS, Dicker DT, Talekar MK, Lim B, Elemento O, Oster W, Bertino J, Flaherty K, Wang ML, Borthakur G, Andreeff M, Stein M, El-Deiry WS.
Oncotarget. 2016 Nov 8;7(45):74380-74392. doi: 10.18632/oncotarget.11814. Review.
PMID: 27602582.

An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer.
Xylinas E, Hassler MR, Zhuang D, Krzywinski M, Erdem Z, Robinson BD, Elemento O, Clozel T, Shariat SF.
Biomolecules. 2016 Sep 2;6(3). pii: E37. doi: 10.3390/biom6030037.
PMID: 27598218.

Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy.
Page DB, Yuan J, Redmond D, Wen YH, Durack JC, Emerson R, Solomon S, Dong Z, Wong P, Comstock C, Diab A, Sung J, Maybody M, Morris E, Brogi E, Morrow M, Sacchini V, Elemento O, Robins H, Patil S, Allison JP, Wolchok JD, Hudis C, Norton L, McArthur HL.
Cancer Immunol Res. 2016 Oct;4(10):835-844. Epub 2016 Sep 1. Erratum in: Cancer Immunol Res. 2017 Mar;5(3):269.
PMID: 27587469.

EZH2 and BCL6 Cooperate to Assemble CBX8-BCOR Complex to Repress Bivalent Promoters, Mediate Germinal Center Formation and Lymphomagenesis.
Béguelin W, Teater M, Gearhart MD, Calvo Fernández MT, Goldstein RL, Cárdenas MG, Hatzi K, Rosen M, Shen H, Corcoran CM, Hamline MY, Gascoyne RD, Levine RL, Abdel-Wahab O, Licht JD, Shaknovich R, Elemento O, Bardwell VJ, Melnick AM.
Cancer Cell. 2016 Aug 8;30(2):197-213. doi: 10.1016/j.ccell.2016.07.006.
PMID: 27505670.

KLF4: A new player in plasma cell development.
Elemento O.
Cell Cycle. 2016 Oct 17;15(20):2691-2. doi: 10.1080/15384101.2016.1214048. Epub 2016 Aug 2. No abstract available.
PMID: 27485539.

Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma.
Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang SN, Cohen J, Shaknovich R, Vanommeslaeghe K, Cheng H, Liang D, Cho HJ, Abbott J, Tam W, Du W, Leonard JP, Elemento O, Cerchietti L, Cierpicki T, Xue F, MacKerell AD Jr, Melnick AM.
J Clin Invest. 2016 Sep 1;126(9):3351-62. doi: 10.1172/JCI85795. Epub 2016 Aug 2.
PMID: 27482887.

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq.
Redmond D, Poran A, Elemento O.
Genome Med. 2016 Jul 27;8(1):80. doi: 10.1186/s13073-016-0335-7.
PMID: 27460926.

Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer.
Pritchard CC, Mateo J, Walsh MF, De Sarkar N, Abida W, Beltran H, Garofalo A, Gulati R, Carreira S, Eeles R, Elemento O, Rubin MA, Robinson D, Lonigro R, Hussain M, Chinnaiyan A, Vinson J, Filipenko J, Garraway L, Taplin ME, AlDubayan S, Han GC, Beightol M, Morrissey C, Nghiem B, Cheng HH, Montgomery B, Walsh T, Casadei S, Berger M, Zhang L, Zehir A, Vijai J, Scher HI, Sawyers C, Schultz N, Kantoff PW, Solit D, Robson M, Van Allen EM, Offit K, de Bono J, Nelson PS.
N Engl J Med. 2016 Aug 4;375(5):443-53. doi: 10.1056/NEJMoa1603144. Epub 2016 Jul 6.
PMID: 27433846.

A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors.
Gayvert KM, Dardenne E, Cheung C, Boland MR, Lorberbaum T, Wanjala J, Chen Y, Rubin MA, Tatonetti NP, Rickman DS, Elemento O.
Cell Rep. 2016 Jun 14;15(11):2348-56. doi: 10.1016/j.celrep.2016.05.037. Epub 2016 Jun 2.
PMID: 27264179.

Disruption of Adipose Rab10-Dependent Insulin Signaling Causes Hepatic Insulin Resistance.
Vazirani RP, Verma A, Sadacca LA, Buckman MS, Picatoste B, Beg M, Torsitano C, Bruno JH, Patel RT, Simonyte K, Camporez JP, Moreira G, Falcone DJ, Accili D, Elemento O, Shulman GI, Kahn BB, McGraw TE.
Diabetes. 2016 Jun;65(6):1577-89. doi: 10.2337/db15-1128. Epub 2016 Mar 25.
PMID: 27207531.

Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells.
Liu Y, Giannopoulou EG, Wen D, Falciatori I, Elemento O, Allis CD, Rafii S, Seandel M.
Nat Commun. 2016 Apr 27;7:11275. doi: 10.1038/ncomms11275.
PMID: 27117588.

Predictive features of ligand-specific signaling through the estrogen receptor.
Nwachukwu JC, Srinivasan S, Zheng Y, Wang S, Min J, Dong C, Liao Z, Nowak J, Wright NJ, Houtman R, Carlson KE, Josan JS, Elemento O, Katzenellenbogen JA, Zhou HB, Nettles KW.
Mol Syst Biol. 2016 Apr 22;12(4):864. doi: 10.15252/msb.20156701.
PMID: 27107013.

Practical Analysis of Genome Contact Interaction Experiments.
Carty MA, Elemento O.
Methods Mol Biol. 2016;1418:177-89. doi: 10.1007/978-1-4939-3578-9_9.
PMID: 27008015.

Nuclear envelope expansion is crucial for proper chromosomal segregation during a closed mitosis.
Takemoto A, Kawashima SA, Li JJ, Jeffery L, Yamatsugu K, Elemento O, Nurse P.
J Cell Sci. 2016 Mar 15;129(6):1250-9. doi: 10.1242/jcs.181560. Epub 2016 Feb 11.
PMID: 26869222.

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer.
Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F.
Nat Med. 2016 Mar;22(3):298-305. doi: 10.1038/nm.4045. Epub 2016 Feb 8.
PMID: 26855148.

Prostate-Specific Membrane Antigen Is a Potential Antiangiogenic Target in Adrenocortical Carcinoma.
Crowley MJ, Scognamiglio T, Liu YF, Kleiman DA, Beninato T, Aronova A, Liu H, Jhanwar YS, Molina A, Tagawa ST, Bander NH, Zarnegar R, Elemento O, Fahey TJ 3rd.
J Clin Endocrinol Metab. 2016 Mar;101(3):981-7. doi: 10.1210/jc.2015-4021. Epub 2016 Jan 15.
PMID: 26771706.

Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care.
Rennert H, Eng K, Zhang T, Tan A, Xiang J, Romanel A, Kim R, Tam W, Liu YC, Bhinder B, Cyrta J, Beltran H, Robinson B, Mosquera JM, Fernandes H, Demichelis F, Sboner A, Kluk M, Rubin MA, Elemento O.
NPJ Genom Med. 2016;1. pii: 16019. doi: 10.1038/npjgenmed.2016.19. Epub 2016 Jul 20.
PMID: 28781886.

Combinatorial targeting of nuclear export and translation of RNA inhibits aggressive B-cell lymphomas.
Culjkovic-Kraljacic B, Fernando TM, Marullo R, Calvo-Vidal N, Verma A, Yang S, Tabbò F, Gaudiano M, Zahreddine H, Goldstein RL, Patel J, Taldone T, Chiosis G, Ladetto M, Ghione P, Machiorlatti R, Elemento O, Inghirami G, Melnick A, Borden KL, Cerchietti L.
Blood. 2016 Feb 18;127(7):858-68. doi: 10.1182/blood-2015-05-645069. Epub 2015 Nov 24.
PMID: 26603836.

EBV-miR-BHRF1-2 targets PRDM1/Blimp1: potential role in EBV lymphomagenesis.
Ma J, Nie K, Redmond D, Liu Y, Elemento O, Knowles DM, Tam W.
Leukemia. 2016 Mar;30(3):594-604. doi: 10.1038/leu.2015.285. Epub 2015 Nov 4.
PMID: 26530011.

A primer on precision medicine informatics.
Sboner A, Elemento O.
Brief Bioinform. 2016 Jan;17(1):145-53. doi: 10.1093/bib/bbv032. Epub 2015 Jun 5. Review.
PMID: 26048401.

The Initial Detection and Partial Characterization of Circulating Tumor Cells in Neuroendocrine Prostate Cancer.
Beltran H, Jendrisak A, Landers M, Mosquera JM, Kossai M, Louw J, Krupa R, Graf RP, Schreiber NA, Nanus DM, Tagawa ST, Marrinucci D, Dittamore R, Scher HI.
Clin Cancer Res. 2016 Mar 15;22(6):1510-9. doi: 10.1158/1078-0432.CCR-15-0137. Epub 2015 Dec 15.
PMID: 26671992.

An emerging role for cytopathology in precision oncology.
Pauli C, Puca L, Mosquera JM, Robinson BD, Beltran H, Rubin MA, Rao RA.
Cancer Cytopathol. 2016 Mar;124(3):167-73. doi: 10.1002/cncy.21647. Epub 2015 Dec 7.
PMID: 26641771.

Update on the biology and management of neuroendocrine prostate cancer.
Beltran H.
Clin Adv Hematol Oncol. 2016 Jul;14(7):513-5. No abstract available.
PMID: 27379946.

Emerging Molecular Biomarkers in Advanced Prostate Cancer: Translation to the Clinic.
Beltran H, Antonarakis ES, Morris MJ, Attard G.
Am Soc Clin Oncol Educ Book. 2016;35:131-41. doi: 10.14694/EDBK_159248.
PMID: 27249694.

Characterization of the leiomyomatous variant of myofibroblastoma: a rare subset distinct from other smooth muscle tumors of the breast.
D’Alfonso TM, Subramaniyam S, Ginter PS, Mosquera JM, MacDonald TY, Noorzad Z, Orta LY, Liu YF, Rubin MA, Shin SJ.
Hum Pathol. 2016 Dec;58:54-61. doi: 10.1016/j.humpath.2016.07.018. Epub 2016 Aug 3.
PMID: 27498061.

Intracellular location of BRCA2 protein expression and prostate cancer progression in the Swedish Watchful Waiting Cohort.
Thorgeirsson T, Jordahl KM, Flavin R, Epstein MM, Fiorentino M, Andersson SO, Andren O, Rider JR, Mosquera JM, Ingoldsby H, Fall K, Tryggvadottir L, Mucci LA; Transdisciplinary Prostate Cancer Partnership (ToPCaP).
Carcinogenesis. 2016 Mar;37(3):262-8. doi: 10.1093/carcin/bgw001. Epub 2016 Jan 16.
PMID: 26775038.

Clonal evaluation of prostate cancer foci in biopsies with discontinuous tumor involvement by dual ERG/SPINK1 immunohistochemistry.
Fontugne J, Davis K, Palanisamy N, Udager A, Mehra R, McDaniel AS, Siddiqui J, Rubin MA, Mosquera JM, Tomlins SA.
Mod Pathol. 2016 Feb;29(2):157-65. doi: 10.1038/modpathol.2015.148. Epub 2016 Jan 8.
PMID: 26743468.

2015

5′ UTR m(6)A Promotes Cap-Independent Translation.
Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR.
Cell. 2015 Nov 5;163(4):999-1010. doi: 10.1016/j.cell.2015.10.012. Epub 2015 Oct 22.
PMID: 26593424.

Prediction of Genetic Interactions Using Machine Learning and Network Properties.
Madhukar NS, Elemento O, Pandey G.
Front Bioeng Biotechnol. 2015 Oct 26;3:172. doi: 10.3389/fbioe.2015.00172. eCollection 2015. Review.
PMID: 26579514.

Vitamin C selectively kills KRAS and BRAF mutant colorectal cancer cells by targeting GAPDH.
Yun J, Mullarky E, Lu C, Bosch KN, Kavalier A, Rivera K, Roper J, Chio II, Giannopoulou EG, Rago C, Muley A, Asara JM, Paik J, Elemento O, Chen Z, Pappin DJ, Dow LE, Papadopoulos N, Gross SS, Cantley LC.
Science. 2015 Dec 11;350(6266):1391-6. doi: 10.1126/science.aaa5004. Epub 2015 Nov 5.
PMID: 26541605.

Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma.
Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O.
Genome Med. 2015 Nov 1;7:110. doi: 10.1186/s13073-015-0230-7.
PMID: 26521025.

Vascular Platform to Define Hematopoietic Stem Cell Factors and Enhance Regenerative Hematopoiesis.
Poulos MG, Crowley MJ, Gutkin MC, Ramalingam P, Schachterle W, Thomas JL, Elemento O, Butler JM.
Stem Cell Reports. 2015 Nov 10;5(5):881-94. doi: 10.1016/j.stemcr.2015.08.018. Epub 2015 Oct 1.
PMID: 26441307.

The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development.
Ortega-Molina A, Boss IW, Canela A, Pan H, Jiang Y, Zhao C, Jiang M, Hu D, Agirre X, Niesvizky I, Lee JE, Chen HT, Ennishi D, Scott DW, Mottok A, Hother C, Liu S, Cao XJ, Tam W, Shaknovich R, Garcia BA, Gascoyne RD, Ge K, Shilatifard A, Elemento O, Nussenzweig A, Melnick AM, Wendel HG.
Nat Med. 2015 Oct;21(10):1199-208. doi: 10.1038/nm.3943. Epub 2015 Sep 14.
PMID: 26366710.

DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID.
Dominguez PM, Teater M, Chambwe N, Kormaksson M, Redmond D, Ishii J, Vuong B, Chaudhuri J, Melnick A, Vasanthakumar A, Godley LA, Papavasiliou FN, Elemento O, Shaknovich R.
Cell Rep. 2015 Sep 29;12(12):2086-98. doi: 10.1016/j.celrep.2015.08.036. Epub 2015 Sep 10.
PMID: 26365193.

Obesity-dependent changes in interstitial ECM mechanics promote breast tumorigenesis.
Seo BR, Bhardwaj P, Choi S, Gonzalez J, Andresen Eguiluz RC, Wang K, Mohanan S, Morris PG, Du B, Zhou XK, Vahdat LT, Verma A, Elemento O, Hudis CA, Williams RM, Gourdon D, Dannenberg AJ, Fischbach C.
Sci Transl Med. 2015 Aug 19;7(301):301ra130. doi: 10.1126/scitranslmed.3010467.
PMID: 26290412.

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.
Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA.
JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313.
PMID: 26181256.

Integrative Clinical Genomics of Advanced Prostate Cancer.
Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Sboner A, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM.
Cell. 2015 Jul 16;162(2):454. doi: 10.1016/j.cell.2015.06.053. Epub 2015 Jul 16. No abstract available.
PMID: 28843286.

Use of RNA sequencing to evaluate rheumatic disease patients.
Giannopoulou EG, Elemento O, Ivashkiv LB.
Arthritis Res Ther. 2015 Jul 1;17:167. doi: 10.1186/s13075-015-0677-3. Review.
PMID: 26126608.

Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia.
Rickman KA, Lach FP, Abhyankar A, Donovan FX, Sanborn EM, Kennedy JA, Sougnez C, Gabriel SB, Elemento O, Chandrasekharappa SC, Schindler D, Auerbach AD, Smogorzewska A.
Cell Rep. 2015 Jul 7;12(1):35-41. doi: 10.1016/j.celrep.2015.06.014. Epub 2015 Jun 25.
PMID: 26119737.

Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival.
Furlow PW, Zhang S, Soong TD, Halberg N, Goodarzi H, Mangrum C, Wu YG, Elemento O, Tavazoie SF.
Nat Cell Biol. 2015 Jul;17(7):943-52. doi: 10.1038/ncb3194. Epub 2015 Jun 22.
PMID: 26098574.

Identification of Reprogrammed Myeloid Cell Transcriptomes in NSCLC.
Durrans A, Gao D, Gupta R, Fischer KR, Choi H, El Rayes T, Ryu S, Nasar A, Spinelli CF, Andrews W, Elemento O, Nolan D, Stiles B, Rafii S, Narula N, Davuluri R, Altorki NK, Mittal V.
PLoS One. 2015 Jun 5;10(6):e0129123. doi: 10.1371/journal.pone.0129123. eCollection 2015.
PMID: 26046767.

Integrative clinical genomics of advanced prostate cancer.
Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM.
Cell. 2015 May 21;161(5):1215-1228. doi: 10.1016/j.cell.2015.05.001. Erratum in: Cell. 2015 Jul 16;162(2):454.
PMID: 26000489.

CCMCL1: a new model of aggressive mantle cell lymphoma.
Zhao X, Chen-Kiang S, Shetty S, Di Liberto M, Bodo J, Durkin L, Eng K, Elemento O, Smith MR, Hsi ED.
Blood. 2015 Apr 23;125(17):2730-2. doi: 10.1182/blood-2015-01-622795. No abstract available.
PMID: 25907904.

The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers.
Ceballos-Chávez M, Subtil-Rodríguez A, Giannopoulou EG, Soronellas D, Vázquez-Chávez E, Vicent GP, Elemento O, Beato M, Reyes JC.
PLoS Genet. 2015 Apr 20;11(4):e1005174. doi: 10.1371/journal.pgen.1005174. eCollection 2015 Apr.
PMID: 25894978.

Epigenomic evolution in diffuse large B-cell lymphomas.
Pan H, Jiang Y, Boi M, Tabbò F, Redmond D, Nie K, Ladetto M, Chiappella A, Cerchietti L, Shaknovich R, Melnick AM, Inghirami GG, Tam W, Elemento O.
Nat Commun. 2015 Apr 20;6:6921. doi: 10.1038/ncomms7921.
PMID: 25891015.

The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo.
Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U, Tay Y, Wu D, Seitzer N, Velasco-Herrera Mdel C, Bothmer A, Fung J, Langellotto F, Rodig SJ, Elemento O, Shipp MA, Adams DJ, Chiarle R, Pandolfi PP.
Cell. 2015 Apr 9;161(2):319-32. doi: 10.1016/j.cell.2015.02.043. Epub 2015 Apr 2.
PMID: 25843629.

Selective inhibition of protein arginine methyltransferase 5 blocks initiation and maintenance of B-cell transformation.
Alinari L, Mahasenan KV, Yan F, Karkhanis V, Chung JH, Smith EM, Quinion C, Smith PL, Kim L, Patton JT, Lapalombella R, Yu B, Wu Y, Roy S, De Leo A, Pileri S, Agostinelli C, Ayers L, Bradner JE, Chen-Kiang S, Elemento O, Motiwala T, Majumder S, Byrd JC, Jacob S, Sif S, Li C, Baiocchi RA.
Blood. 2015 Apr 16;125(16):2530-43. doi: 10.1182/blood-2014-12-619783. Epub 2015 Mar 5.
PMID: 25742700.

Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model.
Choi H, Sheng J, Gao D, Li F, Durrans A, Ryu S, Lee SB, Narula N, Rafii S, Elemento O, Altorki NK, Wong ST, Mittal V.
Cell Rep. 2015 Feb 24;10(7):1187-201. doi: 10.1016/j.celrep.2015.01.040. Epub 2015 Feb 19.
PMID: 25704820.

Vascular niche promotes hematopoietic multipotent progenitor formation from pluripotent stem cells.
Gori JL, Butler JM, Chan YY, Chandrasekaran D, Poulos MG, Ginsberg M, Nolan DJ, Elemento O, Wood BL, Adair JE, Rafii S, Kiem HP.
J Clin Invest. 2015 Mar 2;125(3):1243-54. doi: 10.1172/JCI79328. Epub 2015 Feb 9.
PMID: 25664855.

Lymphoblastic transformation of follicular lymphoma: a clinicopathologic and molecular analysis of 7 patients.
Geyer JT, Subramaniyam S, Jiang Y, Elemento O, Ferry JA, de Leval L, Nakashima MO, Liu YC, Martin P, Mathew S, Orazi A, Tam W.
Hum Pathol. 2015 Feb;46(2):260-71. doi: 10.1016/j.humpath.2014.10.021. Epub 2014 Nov 13.
PMID: 25529125.

Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells.
Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M.
Blood. 2015 Feb 12;125(7):1061-72. doi: 10.1182/blood-2014-11-610436. Epub 2014 Dec 8.
PMID: 25488972.

The transcriptional modulator BCL6 as a molecular target for breast cancer therapy.
Walker SR, Liu S, Xiang M, Nicolais M, Hatzi K, Giannopoulou E, Elemento O, Cerchietti L, Melnick A, Frank DA.
Oncogene. 2015 Feb 26;34(9):1073-82. doi: 10.1038/onc.2014.61. Epub 2014 Mar 24.
PMID: 24662818.

The spectrum of neuroendocrine tumors: histologic classification, unique features and areas of overlap.
Klimstra DS, Beltran H, Lilenbaum R, Bergsland E.
Am Soc Clin Oncol Educ Book. 2015:92-103. doi: 10.14694/EdBook_AM.2015.35.92. Review.
PMID: 25993147.

CRIPTO overexpression promotes mesenchymal differentiation in prostate carcinoma cells through parallel regulation of AKT and FGFR activities.
Terry S, El-Sayed IY, Destouches D, Maillé P, Nicolaiew N, Ploussard G, Semprez F, Pimpie C, Beltran H, Londono-Vallejo A, Allory Y, de la Taille A, Salomon DS, Vacherot F.
Oncotarget. 2015 May 20;6(14):11994-2008.
PMID: 25596738.

The Placental Gene PEG10 Promotes Progression of Neuroendocrine Prostate Cancer.
Akamatsu S, Wyatt AW, Lin D, Lysakowski S, Zhang F, Kim S, Tse C, Wang K, Mo F, Haegert A, Brahmbhatt S, Bell R, Adomat H, Kawai Y, Xue H, Dong X, Fazli L, Tsai H, Lotan TL, Kossai M, Mosquera JM, Rubin MA, Beltran H, Zoubeidi A, Wang Y, Gleave ME, Collins CC.
Cell Rep. 2015 Aug 11;12(6):922-36. doi: 10.1016/j.celrep.2015.07.012. Epub 2015 Jul 30.
PMID: 26235627.

Prostate cancer: Intrapatient heterogeneity in prostate cancer.
Beltran H, Demichelis F.
Nat Rev Urol. 2015 Aug;12(8):430-1. doi: 10.1038/nrurol.2015.182. Epub 2015 Jul 28. No abstract available.
PMID: 26215693.

MAGI3-AKT3 fusion in breast cancer amended.
Mosquera JM, Varma S, Pauli C, MacDonald TY, Yashinskie JJ, Varga Z, Sboner A, Moch H, Rubin MA, Shin SJ.
Nature. 2015 Apr 16;520(7547):E11-2. doi: 10.1038/nature14265. No abstract available.
PMID: 25877206.

Multicenter Evaluation of the Prostate Health Index to Detect Aggressive Prostate Cancer in Biopsy Naïve Men.
de la Calle C, Patil D, Wei JT, Scherr DS, Sokoll L, Chan DW, Siddiqui J, Mosquera JM, Rubin MA, Sanda MG.
J Urol. 2015 Jul;194(1):65-72. doi: 10.1016/j.juro.2015.01.091. Epub 2015 Jan 28.
PMID: 25636659.

2014

ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages.
Lu YC, Chang SH, Hafner M, Li X, Tuschl T, Elemento O, Hla T.
Cell Rep. 2014 Dec 24;9(6):2330-43. doi: 10.1016/j.celrep.2014.11.030. Epub 2014 Dec 18.
PMID: 25533351.

Dicer expression and microRNA dysregulation associate with aggressive features in thyroid cancer.
Erler P, Keutgen XM, Crowley MJ, Zetoune T, Kundel A, Kleiman D, Beninato T, Scognamiglio T, Elemento O, Zarnegar R, Fahey TJ 3rd.
Surgery. 2014 Dec;156(6):1342-50; discussion 1350. doi: 10.1016/j.surg.2014.08.007. Epub 2014 Nov 11.
PMID: 25456905.

ELAVL1 regulates alternative splicing of eIF4E transporter to promote postnatal angiogenesis.
Chang SH, Elemento O, Zhang J, Zhuang ZW, Simons M, Hla T.
Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18309-14. doi: 10.1073/pnas.1412172111. Epub 2014 Nov 24.
PMID: 25422430.

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer.
Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JM, Pauwels J, Park K, Kossai M, MacDonald TY, Fontugne J, Erho N, Vergara IA, Ghadessi M, Davicioni E, Jenkins RB, Palanisamy N, Chen Z, Nakagawa S, Hirose T, Bander NH, Beltran H, Fox AH, Elemento O, Rubin MA.
Nat Commun. 2014 Nov 21;5:5383. doi: 10.1038/ncomms6383.
PMID: 25415230.

Differentiation of human pluripotent stem cells to cells similar to cord-blood endothelial colony-forming cells.
Prasain N, Lee MR, Vemula S, Meador JL, Yoshimoto M, Ferkowicz MJ, Fett A, Gupta M, Rapp BM, Saadatzadeh MR, Ginsberg M, Elemento O, Lee Y, Voytik-Harbin SL, Chung HM, Hong KS, Reid E, O’Neill CL, Medina RJ, Stitt AW, Murphy MP, Rafii S, Broxmeyer HE, Yoder MC.
Nat Biotechnol. 2014 Nov;32(11):1151-1157. doi: 10.1038/nbt.3048. Epub 2014 Oct 12.
PMID: 25306246.

Tbx5 is required for avian and Mammalian epicardial formation and coronary vasculogenesis.
Diman NY, Brooks G, Kruithof BP, Elemento O, Seidman JG, Seidman CE, Basson CT, Hatcher CJ.
Circ Res. 2014 Oct 24;115(10):834-44. doi: 10.1161/CIRCRESAHA.115.304379. Epub 2014 Sep 22.
PMID: 25245104.

Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation.
Popovic R, Martinez-Garcia E, Giannopoulou EG, Zhang Q, Zhang Q, Ezponda T, Shah MY, Zheng Y, Will CM, Small EC, Hua Y, Bulic M, Jiang Y, Carrara M, Calogero RA, Kath WL, Kelleher NL, Wang JP, Elemento O, Licht JD.
PLoS Genet. 2014 Sep 4;10(9):e1004566. doi: 10.1371/journal.pgen.1004566. eCollection 2014 Sep.
PMID: 25188243.

Tracing the roots of cancer evolution.
Jiang Y, Elemento O.
Cancer Discov. 2014 Sep;4(9):995-7. doi: 10.1158/2159-8290.CD-14-0743.
PMID: 25185189.

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.
Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LH, Melnick AM, Tam W, Elemento O.
Genome Biol. 2014 Aug 15;15(8):432. doi: 10.1186/s13059-014-0432-0.
PMID: 25123191.

Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma.
Chiron D, Di Liberto M, Martin P, Huang X, Sharman J, Blecua P, Mathew S, Vijay P, Eng K, Ali S, Johnson A, Chang B, Ely S, Elemento O, Mason CE, Leonard JP, Chen-Kiang S.
Cancer Discov. 2014 Sep;4(9):1022-35. doi: 10.1158/2159-8290.CD-14-0098. Epub 2014 Jul 31.
PMID: 25082755.

Reprogramming human endothelial cells to haematopoietic cells requires vascular induction.
Sandler VM, Lis R, Liu Y, Kedem A, James D, Elemento O, Butler JM, Scandura JM, Rafii S.
Nature. 2014 Jul 17;511(7509):312-8. doi: 10.1038/nature13547. Epub 2014 Jul 2.
PMID: 25030167.

Impact of ERBB2 mutations on in vitro sensitivity of bladder cancer to lapatinib.
de Martino M, Zhuang D, Klatte T, Rieken M, Rouprêt M, Xylinas E, Clozel T, Krzywinski M, Elemento O, Shariat SF.
Cancer Biol Ther. 2014 Sep;15(9):1239-47. doi: 10.4161/cbt.29687. Epub 2014 Jul 14.
PMID: 24971884.

DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets.
Kasap C, Elemento O, Kapoor TM.
Nat Chem Biol. 2014 Aug;10(8):626-8. doi: 10.1038/nchembio.1551. Epub 2014 Jun 15.
PMID: 24929528.

Silencing of UCHL1 by CpG promoter hyper-methylation is associated with metastatic gastroenteropancreatic well-differentiated neuroendocrine (carcinoid) tumors.
Kleiman DA, Beninato T, Sultan S, Crowley MJ, Finnerty B, Kumar R, Panarelli NC, Liu YF, Lieberman MD, Seandel M, Evans T, Elemento O, Zarnegar R, Fahey TJ 3rd.
Ann Surg Oncol. 2014 Dec;21 Suppl 4:S672-9. doi: 10.1245/s10434-014-3787-2. Epub 2014 May 23.
PMID: 24854489.

Histone variant H3.3 is an essential maternal factor for oocyte reprogramming.
Wen D, Banaszynski LA, Liu Y, Geng F, Noh KM, Xiang J, Elemento O, Rosenwaks Z, Allis CD, Rafii S.
Proc Natl Acad Sci U S A. 2014 May 20;111(20):7325-30. doi: 10.1073/pnas.1406389111. Epub 2014 May 5.
PMID: 24799717.

Characterization of the human cumulus cell transcriptome during final follicular maturation and ovulation.
Yerushalmi GM, Salmon-Divon M, Yung Y, Maman E, Kedem A, Ophir L, Elemento O, Coticchio G, Dal Canto M, Mignini Renzinu M, Fadini R, Hourvitz A.
Mol Hum Reprod. 2014 Aug;20(8):719-35. doi: 10.1093/molehr/gau031. Epub 2014 Apr 25.
PMID: 24770949.

Double-stranded DNA in exosomes: a novel biomarker in cancer detection.
Thakur BK, Zhang H, Becker A, Matei I, Huang Y, Costa-Silva B, Zheng Y, Hoshino A, Brazier H, Xiang J, Williams C, Rodriguez-Barrueco R, Silva JM, Zhang W, Hearn S, Elemento O, Paknejad N, Manova-Todorova K, Welte K, Bromberg J, Peinado H, Lyden D.
Cell Res. 2014 Jun;24(6):766-9. doi: 10.1038/cr.2014.44. Epub 2014 Apr 8. No abstract available.
PMID: 24710597.

Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing.
Tan AY, Michaeel A, Liu G, Elemento O, Blumenfeld J, Donahue S, Parker T, Levine D, Rennert H.
J Mol Diagn. 2014 Mar;16(2):216-28. doi: 10.1016/j.jmoldx.2013.10.005. Epub 2013 Dec 27.
PMID: 24374109.

Exploring the role of anti-angiogenic therapies in prostate cancer: results from the phase 3 trial of sunitinib.
Beltran H, Kaur G, de España CG, Tagawa ST.
Asian J Androl. 2014 Jul-Aug;16(4):568-9. doi: 10.4103/1008-682X.127822. No abstract available.
PMID: 24875818.

Aggressive variants of castration-resistant prostate cancer.
Beltran H, Tomlins S, Aparicio A, Arora V, Rickman D, Ayala G, Huang J, True L, Gleave ME, Soule H, Logothetis C, Rubin MA.
Clin Cancer Res. 2014 Jun 1;20(11):2846-50. doi: 10.1158/1078-0432.CCR-13-3309. Epub 2014 Apr 11. Review.
PMID: 24727321.

The many faces of neuroendocrine differentiation in prostate cancer progression.
Terry S, Beltran H.
Front Oncol. 2014 Mar 25;4:60. doi: 10.3389/fonc.2014.00060. eCollection 2014. Review.
PMID: 24724054.

Proposed morphologic classification of prostate cancer with neuroendocrine differentiation.
Epstein JI, Amin MB, Beltran H, Lotan TL, Mosquera JM, Reuter VE, Robinson BD, Troncoso P, Rubin MA.
Am J Surg Pathol. 2014 Jun;38(6):756-67. doi: 10.1097/PAS.0000000000000208.
PMID: 24705311.

The N-myc Oncogene: Maximizing its Targets, Regulation, and Therapeutic Potential.
Beltran H.
Mol Cancer Res. 2014 Jun;12(6):815-22. doi: 10.1158/1541-7786.MCR-13-0536. Epub 2014 Mar 3. Review.
PMID: 24589438.

High fidelity patient-derived xenografts for accelerating prostate cancer discovery and drug development.
Lin D, Wyatt AW, Xue H, Wang Y, Dong X, Haegert A, Wu R, Brahmbhatt S, Mo F, Jong L, Bell RH, Anderson S, Hurtado-Coll A, Fazli L, Sharma M, Beltran H, Rubin M, Cox M, Gout PW, Morris J, Goldenberg L, Volik SV, Gleave ME, Collins CC, Wang Y.
Cancer Res. 2014 Feb 15;74(4):1272-83. doi: 10.1158/0008-5472.CAN-13-2921-T. Epub 2013 Dec 19.
PMID: 24356420.

ERG induces taxane resistance in castration-resistant prostate cancer.
Galletti G, Matov A, Beltran H, Fontugne J, Miguel Mosquera J, Cheung C, MacDonald TY, Sung M, O’Toole S, Kench JG, Suk Chae S, Kimovski D, Tagawa ST, Nanus DM, Rubin MA, Horvath LG, Giannakakou P, Rickman DS.
Nat Commun. 2014 Nov 25;5:5548. doi: 10.1038/ncomms6548.
PMID: 25420520.

Organoid cultures derived from patients with advanced prostate cancer.
Gao D, Vela I, Sboner A, Iaquinta PJ, Karthaus WR, Gopalan A, Dowling C, Wanjala JN, Undvall EA, Arora VK, Wongvipat J, Kossai M, Ramazanoglu S, Barboza LP, Di W, Cao Z, Zhang QF, Sirota I, Ran L, MacDonald TY, Beltran H, Mosquera JM, Touijer KA, Scardino PT, Laudone VP, Curtis KR, Rathkopf DE, Morris MJ, Danila DC, Slovin SF, Solomon SB, Eastham JA, Chi P, Carver B, Rubin MA, Scher HI, Clevers H, Sawyers CL, Chen Y.
Cell. 2014 Sep 25;159(1):176-187. doi: 10.1016/j.cell.2014.08.016. Epub 2014 Sep 4.
PMID: 25201530.

Unraveling the clonal hierarchy of somatic genomic aberrations.
Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.
Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6. Erratum in: Genome Biol. 2017 May 2;18(1):80.
PMID: 25160065.

Prostate cancer with Paneth cell-like neuroendocrine differentiation has recognizable histomorphology and harbors AURKA gene amplification.
Park K, Chen Z, MacDonald TY, Siddiqui J, Ye H, Erbersdobler A, Shevchuk MM, Robinson BD, Sanda MG, Chinnaiyan AM, Beltran H, Rubin MA, Mosquera JM.
Hum Pathol. 2014 Oct;45(10):2136-43. doi: 10.1016/j.humpath.2014.06.008. Epub 2014 Jun 26.
PMID: 25128228.

MYB-NFIB gene fusion in adenoid cystic carcinoma of the breast with special focus paid to the solid variant with basaloid features.
D’Alfonso TM, Mosquera JM, MacDonald TY, Padilla J, Liu YF, Rubin MA, Shin SJ.
Hum Pathol. 2014 Nov;45(11):2270-80. doi: 10.1016/j.humpath.2014.07.013. Epub 2014 Aug 7.
PMID: 25217885.

Evidence for molecular differences in prostate cancer between African American and Caucasian men.
Khani F, Mosquera JM, Park K, Blattner M, O’Reilly C, MacDonald TY, Chen Z, Srivastava A, Tewari AK, Barbieri CE, Rubin MA, Robinson BD.
Clin Cancer Res. 2014 Sep 15;20(18):4925-34. doi: 10.1158/1078-0432.CCR-13-2265. Epub 2014 Jul 23.
PMID: 25056375.

SPOP mutations in prostate cancer across demographically diverse patient cohorts.
Blattner M, Lee DJ, O’Reilly C, Park K, MacDonald TY, Khani F, Turner KR, Chiu YL, Wild PJ, Dolgalev I, Heguy A, Sboner A, Ramazangolu S, Hieronymus H, Sawyers C, Tewari AK, Moch H, Yoon GS, Known YC, Andrén O, Fall K, Demichelis F, Mosquera JM, Robinson BD, Barbieri CE, Rubin MA.
Neoplasia. 2014 Jan;16(1):14-20.
PMID: 24563616

Recurrent prostate cancer genomic alterations predict response to brachytherapy treatment.
Fontugne J, Lee D, Cantaloni C, Barbieri CE, Caffo O, Hanspeter E, Mazzoleni G, Dalla Palma P, Rubin MA, Fellin G, Mosquera JM, Barbareschi M, Demichelis F.
Cancer Epidemiol Biomarkers Prev. 2014 Apr;23(4):594-600. doi: 10.1158/1055-9965.EPI-13-1180. Epub 2014 Feb 10.
PMID: 24515272.

Diagnostic utility of MYC amplification and anti-MYC immunohistochemistry in atypical vascular lesions, primary or radiation-induced mammary angiosarcomas, and primary angiosarcomas of other sites.
Ginter PS, Mosquera JM, MacDonald TY, D’Alfonso TM, Rubin MA, Shin SJ.
Hum Pathol. 2014 Apr;45(4):709-16. doi: 10.1016/j.humpath.2013.11.002. Epub 2013 Nov 12.
PMID: 24457083.

2013

Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis.
Rath P, Huang C, Wang T, Wang T, Li H, Prados-Rosales R, Elemento O, Casadevall A, Nathan CF.
Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4790-7. doi: 10.1073/pnas.1320118110. Epub 2013 Nov 18.
PMID: 24248369.

EZH2 mutations are frequent and represent an early event in follicular lymphoma.
Bödör C, Grossmann V, Popov N, Okosun J, O’Riain C, Tan K, Marzec J, Araf S, Wang J, Lee AM, Clear A, Montoto S, Matthews J, Iqbal S, Rajnai H, Rosenwald A, Ott G, Campo E, Rimsza LM, Smeland EB, Chan WC, Braziel RM, Staudt LM, Wright G, Lister TA, Elemento O, Hills R, Gribben JG, Chelala C, Matolcsy A, Kohlmann A, Haferlach T, Gascoyne RD, Fitzgibbon J.
Blood. 2013 Oct 31;122(18):3165-8. doi: 10.1182/blood-2013-04-496893. Epub 2013 Sep 19.
PMID: 24052547.

Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling.
Qiao Y, Giannopoulou EG, Chan CH, Park SH, Gong S, Chen J, Hu X, Elemento O, Ivashkiv LB.
Immunity. 2013 Sep 19;39(3):454-69. doi: 10.1016/j.immuni.2013.08.009. Epub 2013 Sep 5.
PMID: 24012417.

Akt suppression of TGFβ signaling contributes to the maintenance of vascular identity in embryonic stem cell-derived endothelial cells.
Israely E, Ginsberg M, Nolan D, Ding BS, James D, Elemento O, Rafii S, Rabbany SY.
Stem Cells. 2014 Jan;32(1):177-90. doi: 10.1002/stem.1521.
PMID:23963623.

A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters.
Hatzi K, Jiang Y, Huang C, Garrett-Bakelman F, Gearhart MD, Giannopoulou EG, Zumbo P, Kirouac K, Bhaskara S, Polo JM, Kormaksson M, MacKerell AD Jr, Xue F, Mason CE, Hiebert SW, Prive GG, Cerchietti L, Bardwell VJ, Elemento O, Melnick A.
Cell Rep. 2013 Aug 15;4(3):578-88. doi: 10.1016/j.celrep.2013.06.016. Epub 2013 Aug 1.
PMID: 23911289.

Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration.
Nolan DJ, Ginsberg M, Israely E, Palikuqi B, Poulos MG, James D, Ding BS, Schachterle W, Liu Y, Rosenwaks Z, Butler JM, Xiang J, Rafii A, Shido K, Rabbany SY, Elemento O, Rafii S.
Dev Cell. 2013 Jul 29;26(2):204-19. doi: 10.1016/j.devcel.2013.06.017. Epub 2013 Jul 18.
PMID: 23871589.

The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry.
Hess ME, Hess S, Meyer KD, Verhagen LA, Koch L, Brönneke HS, Dietrich MO, Jordan SD, Saletore Y, Elemento O, Belgardt BF, Franz T, Horvath TL, Rüther U, Jaffrey SR, Kloppenburg P, Brüning JC.
Nat Neurosci. 2013 Aug;16(8):1042-8. doi: 10.1038/nn.3449. Epub 2013 Jun 30.
PMID: 23817550.

A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis.
Sun XJ, Wang Z, Wang L, Jiang Y, Kost N, Soong TD, Chen WY, Tang Z, Nakadai T, Elemento O, Fischle W, Melnick A, Patel DJ, Nimer SD, Roeder RG.
Nature. 2013 Aug 1;500(7460):93-7. doi: 10.1038/nature12287. Epub 2013 Jun 30.
PMID: 23812588.

AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes.
Kumar R, DiMenna L, Schrode N, Liu TC, Franck P, Muñoz-Descalzo S, Hadjantonakis AK, Zarrin AA, Chaudhuri J, Elemento O, Evans T.
Nature. 2013 Aug 1;500(7460):89-92. doi: 10.1038/nature12299. Epub 2013 Jun 26.
PMID: 23803762.

EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation.
Béguelin W, Popovic R, Teater M, Jiang Y, Bunting KL, Rosen M, Shen H, Yang SN, Wang L, Ezponda T, Martinez-Garcia E, Zhang H, Zheng Y, Verma SK, McCabe MT, Ott HM, Van Aller GS, Kruger RG, Liu Y, McHugh CF, Scott DW, Chung YR, Kelleher N, Shaknovich R, Creasy CL, Gascoyne RD, Wong KK, Cerchietti L, Levine RL, Abdel-Wahab O, Licht JD, Elemento O, Melnick AM.
Cancer Cell. 2013 May 13;23(5):677-92. doi: 10.1016/j.ccr.2013.04.011.
PMID: 23680150.

A novel approach for characterizing microsatellite instability in cancer cells.
Lu Y, Soong TD, Elemento O.
PLoS One. 2013 May 6;8(5):e63056. doi: 10.1371/journal.pone.0063056. Print 2013.
PMID: 23671654.

Punctuated evolution of prostate cancer genomes.
Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA.
Cell. 2013 Apr 25;153(3):666-77. doi: 10.1016/j.cell.2013.03.021.
PMID: 23622249.

Downregulation of FOXP1 is required during germinal center B-cell function.
Sagardoy A, Martinez-Ferrandis JI, Roa S, Bunting KL, Aznar MA, Elemento O, Shaknovich R, Fontán L, Fresquet V, Perez-Roger I, Robles EF, De Smedt L, Sagaert X, Melnick A, Martinez-Climent JA.
Blood. 2013 May 23;121(21):4311-20. doi: 10.1182/blood-2012-10-462846. Epub 2013 Apr 11.
PMID: 23580662.

Epigenomic alterations in localized and advanced prostate cancer.
Lin PC, Giannopoulou EG, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA, Elemento O.
Neoplasia. 2013 Apr;15(4):373-83.
PMID: 23555183.

Inferring chromatin-bound protein complexes from genome-wide binding assays.
Giannopoulou EG, Elemento O.
Genome Res. 2013 Aug;23(8):1295-306. doi: 10.1101/gr.149419.112. Epub 2013 Apr 3.
PMID: 23554462.

Metabolic alterations in lung cancer-associated fibroblasts correlated with increased glycolytic metabolism of the tumor.
Chaudhri VK, Salzler GG, Dick SA, Buckman MS, Sordella R, Karoly ED, Mohney R, Stiles BM, Elemento O, Altorki NK, McGraw TE.
Mol Cancer Res. 2013 Jun;11(6):579-92. doi: 10.1158/1541-7786.MCR-12-0437-T. Epub 2013 Mar 8.
PMID: 23475953.

NFIB is a governor of epithelial-melanocyte stem cell behaviour in a shared niche.
Chang CY, Pasolli HA, Giannopoulou EG, Guasch G, Gronostajski RM, Elemento O, Fuchs E.
Nature. 2013 Mar 7;495(7439):98-102. doi: 10.1038/nature11847. Epub 2013 Feb 6.
PMID: 23389444.

Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.
De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A, Michor F.
PLoS Genet. 2013;9(1):e1003137. doi: 10.1371/journal.pgen.1003137. Epub 2013 Jan 10.
PMID: 23326238.

Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression.
Lin PC, Chiu YL, Banerjee S, Park K, Mosquera JM, Giannopoulou E, Alves P, Tewari AK, Gerstein MB, Beltran H, Melnick AM, Elemento O, Demichelis F, Rubin MA.
Cancer Res. 2013 Feb 1;73(3):1232-44. doi: 10.1158/0008-5472.CAN-12-2968. Epub 2012 Dec 11.
PMID: 23233736.

Antagonistic function of the RNA-binding protein HuR and miR-200b in post-transcriptional regulation of vascular endothelial growth factor-A expression and angiogenesis.
Chang SH, Lu YC, Li X, Hsieh WY, Xiong Y, Ghosh M, Evans T, Elemento O, Hla T.
J Biol Chem. 2013 Feb 15;288(7):4908-21. doi: 10.1074/jbc.M112.423871. Epub 2012 Dec 6.
PMID: 23223443.

Human ESC-derived hemogenic endothelial cells undergo distinct waves of endothelial to hematopoietic transition.
Rafii S, Kloss CC, Butler JM, Ginsberg M, Gars E, Lis R, Zhan Q, Josipovic P, Ding BS, Xiang J, Elemento O, Zaninovic N, Rosenwaks Z, Sadelain M, Rafii JA, James D.
Blood. 2013 Jan 31;121(5):770-80. doi: 10.1182/blood-2012-07-444208. Epub 2012 Nov 20.
PMID: 23169780.

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, Sun J, Juhn F, Brennan K, Iwanik K, Maillet A, Buell J, White E, Zhao M, Balasubramanian S, Terzic S, Richards T, Banning V, Garcia L, Mahoney K, Zwirko Z, Donahue A, Beltran H, Mosquera JM, Rubin MA, Dogan S, Hedvat CV, Berger MF, Pusztai L, Lechner M, Boshoff C, Jarosz M, Vietz C, Parker A, Miller VA, Ross JS, Curran J, Cronin MT, Stephens PJ, Lipson D, Yelensky R.
Nat Biotechnol. 2013 Nov;31(11):1023-31. doi: 10.1038/nbt.2696. Epub 2013 Oct 20.
PMID: 24142049.

Cross modulation between the androgen receptor axis and protocadherin-PC in mediating neuroendocrine transdifferentiation and therapeutic resistance of prostate cancer.
Terry S, Maillé P, Baaddi H, Kheuang L, Soyeux P, Nicolaiew N, Ceraline J, Firlej V, Beltran H, Allory Y, de la Taille A, Vacherot F.
Neoplasia. 2013 Jul;15(7):761-72.
PMID: 23814488.

DNA mismatch repair in prostate cancer.
Beltran H.
J Clin Oncol. 2013 May 10;31(14):1782-4. doi: 10.1200/JCO.2012.48.4667. Epub 2013 Mar 25. No abstract available.
PMID: 23530097.

Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer.
Mosquera JM, Beltran H, Park K, MacDonald TY, Robinson BD, Tagawa ST, Perner S, Bismar TA, Erbersdobler A, Dhir R, Nelson JB, Nanus DM, Rubin MA.
Neoplasia. 2013 Jan;15(1):1-10.
PMID: 23358695.

New strategies in prostate cancer: translating genomics into the clinic.
Beltran H, Rubin MA.
Clin Cancer Res. 2013 Feb 1;19(3):517-23. doi: 10.1158/1078-0432.CCR-12-1452. Epub 2012 Dec 17. Review.
PMID: 23248095.

Novel MIR143-NOTCH fusions in benign and malignant glomus tumors.
Mosquera JM, Sboner A, Zhang L, Chen CL, Sung YS, Chen HW, Agaram NP, Briskin D, Basha BM, Singer S, Rubin MA, Tuschl T, Antonescu CR.
Genes Chromosomes Cancer. 2013 Nov;52(11):1075-87. doi: 10.1002/gcc.22102. Epub 2013 Sep 2.
PMID: 23999936.

V-ets erythroblastosis virus E26 oncogene homolog (avian)/Trefoil factor 3/high-molecular-weight cytokeratin triple immunostain: a novel tissue-based biomarker in prostate cancer with potential clinical application.
Park K, Chiu YL, Rubin MA, Demichelis F, Mosquera JM.
Hum Pathol. 2013 Oct;44(10):2282-92. doi: 10.1016/j.humpath.2013.05.010. Epub 2013 Jul 12.
PMID: 23856515.