OUR PUBLICATIONS
Selected Publications
For a full list of publications, see Dr. Berchuck’s profile on PubMed.
2024
A panel-based mutational signature of homologous recombination deficiency associates with response to PARP inhibition in metastatic castration-resistant prostate cancer.
Boiarsky D, Tewari AK, Gulhan DC, Bakouny Z, Ananda G, Savignano H, Lakshminarayanan G, McClure HM, Silver R, Choueiri TK, Taplin ME, Park PJ, Berchuck JE. The Prostate. 2024 Sep 9. Epub ahead of print.
Detecting small cell transformation in patients with advanced EGFR mutant lung adenocarcinoma through epigenomic cfDNA profiling.
El Zarif T, Meador CB, Qiu X, Seo JH, Davidsohn MP, Savignano H, Lakshminarayanan G, McClure HM, Canniff J, Fortunato B, Li R, Banwait MK, Semaan K, Eid M, Long H, Hung YP, Mahadevan NR, Barbie DA, Oser MG, Piotrowska Z, Choueiri TK, Baca SC, Hata AN, Freedman ML, Berchuck JE. Clinical Cancer Research. 2024 Sep 3;30(17):3798-3811.
Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma.
El Zarif T, Semaan K, Eid M, Seo JH, Garinet S, Davidsohn MP, Sahgal P, Fortunato B, Canniff J, Nassar AH, Abou Alaiwi S, Bakouny Z, Lakshminarayanan G, Savignano H, Lyons K, Matar S, Ali A, Saad E, Saliby RM, Cordeiro P, Zhang Z, El Ahmar N, Laimon YN, Labaki C, Shah V, Freeman D, O’Toole J, Lee GM, Hwang J, Pomerantz M, Signoretti S, Van Allen EM, Xie W, Berchuck JE, Viswanathan SR, Braun DA, Choueiri TK, Freedman ML, Baca SC. Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma. Cell Reports. 2024 Jun 25;43(6):114350.
A panel-based mutational signature of mismatch repair deficiency is associated with durable response to pembrolizumab in metastatic castration-resistant prostate cancer.
Boiarsky D, Gulhan DC, Savignano H, Lakshminarayanan G, McClure HM, Silver R, Hirsch MS, Sholl LM, Choudhury AD, Ananda G, Park PJ, Tewari AK, Berchuck JE. Clinical Genitourinary Cancer. 2024 Apr;22(2):558-568.e3.
2023
Liquid biopsy epigenomic profiling for cancer subtyping.
Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Nature Medicine. 2023 Nov;29(11):2737-2741.
Nucleosome patterns in circulating tumor DNA reveal transcriptional regulation of advanced prostate cancer phenotypes.
De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Cancer Discovery. 2023 Mar 1;13(3):632-653.
Epigenomic charting and functional annotation of risk loci in renal cell carcinoma.
Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O’Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Nature Communications. 2023 Jan 21;14(1):346.
2022
The clinical landscape of cell-free DNA alterations in 1671 patients with advanced biliary tract cancer.
Berchuck JE, Facchinetti F, DiToro DF, Baiev I, Majeed U, Reyes S, Chen C, Zhang K, Sharman R, Uson Junior PLS, Maurer J, Shroff RT, Pritchard CC, Wu MJ, Catenacci DVT, Javle M, Friboulet L, Hollebecque A, Bardeesy N, Zhu AX, Lennerz JK, Tan B, Borad M, Parikh AR, Kiedrowski LA, Kelley RK, Mody K, Juric D, Goyal L. Annals of Oncology. 2022 Dec;33(12):1269-1283.
Addition of germline testing to tumor-only sequencing improves detection of pathogenic germline variants in men with advanced prostate cancer.
Berchuck JE, Boiarsky D, Silver R, Sunkara R, McClure HM, Tsai HK, Siegmund S, Tewari AK, Nowak JA, Lindeman NI, Rana HQ, Choudhury AD, Pomerantz MM, Freedman ML, Van Allen EM, Taplin ME. JCO Precision Oncology. 2022 Aug;6:e2200329.
The prostate cancer androgen receptor cistrome in African American men associates with upregulation of lipid metabolism and immune response.
Berchuck JE, Adib E, Abou Alaiwi S, Dash AK, Shin JN, Lowder D, McColl C, Castro P, Carelli R, Benedetti E, Deng J, Robertson M, Baca SC, Bell C, McClure HM, El Zarif T, Davidsohn MP, Lakshminarayanan G, Rizwan K, Skapura DG, Grimm SL, Davis CM, Ehli EA, Kelleher KM, Seo JH, Mitsiades N, Coarfa C, Pomerantz MM, Loda M, Ittmann M, Freedman ML, Kaochar S. Cancer Research. 2022 Aug 16;82(16):2848-2859.
HOXB13 suppresses de novo lipogenesis through HDAC3-mediated epigenetic reprogramming in prostate cancer.
Lu X, Fong KW, Gritsina G, Wang F, Baca SC, Brea LT, Berchuck JE, Spisak S, Ross J, Morrissey C, Corey E, Chandel NS, Catalona WJ, Yang X, Freedman ML, Zhao JC, Yu J. Nature Genetics. 2022 May;54(5):670-683.
Detecting neuroendocrine prostate cancer through tissue-informed cell-free DNA methylation analysis.
Berchuck JE, Baca SC, McClure HM, Korthauer K, Tsai HK, Nuzzo PV, 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. Clinical Cancer Research. 2022 Mar 1;28(5):928-938.
2021
Impact of pathogenic germline DNA damage repair alterations on response to intense neoadjuvant androgen deprivation therapy in high-risk localized prostate cancer.
Berchuck JE, Zhang Z, Silver R, Kwak L, Xie W, Lee GM, Freedman ML, Kibel AS, Van Allen EM, McKay RR, Taplin ME. European Urology. 2021 Sep;80(3):295-303.
Clinical considerations for the management of androgen indifferent prostate cancer.
Berchuck JE, Viscuse PV, Beltran H, Aparicio A. Prostate Cancer and Prostatic Diseases. 2021 Sep;24(3):623-637.
Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer.
Baca SC, Takeda DY, Seo JH, Hwang J, Ku SY, Arafeh R, Arnoff T, Agarwal S, Bell C, O’Connor E, Qiu X, Alaiwi SA, Corona RI, Fonseca MAS, Giambartolomei C, Cejas P, Lim K, He M, Sheahan A, Nassar A, Berchuck JE, Brown L, Nguyen HM, Coleman IM, Kaipainen A, De Sarkar N, Nelson PS, Morrissey C, Korthauer K, Pomerantz MM, Ellis L, Pasaniuc B, Lawrenson K, Kelly K, Zoubeidi A, Hahn WC, Beltran H, Long HW, Brown M, Corey E, Freedman ML. Nature Communications. 2021 Mar 30;12(1):1979.
2020
Plasma cell-free DNA variant analysis compared with methylated DNA analysis in renal cell carcinoma.
Lasseter K*, Nassar AH*, Hamieh L*, Berchuck JE*, Nuzzo PV*, Korthauer K, Shinagare AB, Ogorek B, McKay R, Thorner AR, Lee GM, Braun DA, Bhatt RS, Freedman M, Choueiri TK, Kwiatkowski DJ. Genetics in Medicine. 2020 Aug;22(8):1366-1373. *These authors contributed equally
Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes.
Nuzzo PV*, Berchuck JE*, Korthauer K*, Spisak S*, Nassar AH, Abou Alaiwi S, Chakravarthy A, Shen SY, Bakouny Z, Boccardo F, Steinharter J, Bouchard G, Curran CR, Pan W, Baca SC, Seo JH, Lee GM, Michaelson MD, Chang SL, Waikar SS, Sonpavde G, Irizarry RA, Pomerantz M, De Carvalho DD, Choueiri TK, Freedman ML. Nature Medicine. 2020 Jul;26(7):1041-1043. *These authors contributed equally
Association of mental health treatment with outcomes for US veterans diagnosed with non-small cell lung cancer.
Berchuck JE, Meyer CS, Zhang N, Berchuck CM, Trivedi NN, Cohen B, Wang S. JAMA Oncology. 2020 Jul 1;6(7):1055-1062.
2009
Proteomic and genetic approaches identify Syk as an AML target.
Hahn CK*, Berchuck JE*, Ross KN, Kakoza RM, Clauser K, Schinzel AC, Ross L, Galinsky I, Davis TN, Silver SJ, Root DE, Stone RM, DeAngelo DJ, Carroll M, Hahn WC, Carr SA, Golub TR, Kung AL, Stegmaier K. Cancer Cell. 2009 Oct 6;16(4):281-294. *These authors contributed equally