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

 

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.

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

 

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.

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

 

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.

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.

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.

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.

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.

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.

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.

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.

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.