Publications

Sammouri J, Wong MC, Lynn EJ, El Alam MB, Lo DK, Lin D, Harris TH, Karpinets TV, Court K, Napravnik TC, Wu X, Zhang J, Klopp AH, Ajami NJ, Colbert LE. Serial Genotyping of the Human Papillomavirus in Cervical Cancer: An Insight Into Virome Dynamics During Chemoradiation Therapy. Int J Radiat Oncol Biol Phys. 2023 Feb 16;. doi: 10.1016/j.ijrobp.2023.02.018. [Epub ahead of print] PubMed PMID: 36801350.

Yoshida-Court K, Karpinets TV, Mitra A, Solley TN, Dorta-Estremera S, Sims TT, Delgado Medrano AY, El Alam MB, Ahmed-Kaddar M, Lynn EJ, Sastry KJ, Zhang J, Futreal A, Nick A, Lu K, Colbert LE, Klopp AH. Immune environment and antigen specificity of the T cell receptor repertoire of malignant ascites in ovarian cancer. PLoS One. 2023;18(1):e0279590. doi: 10.1371/journal.pone.0279590. eCollection 2023. PubMed PMID: 36607962; PubMed Central PMCID: PMC9821423.

Hahn AW, Menk AV, Rivadeneira DB, Augustin RC, Xu M, Li J, Wu X, Mishra AK, Gide TN, Quek C, Zang Y, Spencer CN, Menzies AM, Daniel CR, Hudgens CW, Nowicki T, Haydu LE, Khan MAW, Gopalakrishnan V, Burton EM, Malke J, Simon JM, Bernatchez C, Putluri N, Woodman SE, Vashisht Gopal YN, Guerrieri R, Fischer GM, Wang J, Wani KM, Thompson JF, Lee JE, Hwu P, Ajami N, Gershenwald JE, Long GV, Scolyer RA, Tetzlaff MT, Lazar AJ, Schadendorf D, Wargo JA, Kirkwood JM, DeBerardinis RJ, Liang H, Futreal A, Zhang J, Wilmott JS, Peng W, Davies MA, Delgoffe GM, Najjar YG, McQuade JL. Obesity Is Associated with Altered Tumor Metabolism in Metastatic Melanoma. Clin Cancer Res. 2023 Jan 4;29(1):154-164. doi: 10.1158/1078-0432.CCR-22-2661. PubMed PMID: 36166093.

Francisco-Cruz A, Rocha P, Reuben A, Krishnan SN, Das P, Chen R, Quek K, Li J, Parra ER, Solis LM, Barua S, Jiang M, Lazcano R, Chow CW, Behrens C, Gumb C, Little L, Fukuoka J, Kalhor N, Weissferdt A, Kadara H, Heymach JV, Swisher S, Sepesi B, Rao A, Moran C, Zhang J, Lee JJ, Fujimoto J, Futreal PA, Wistuba II, Peterson CB, Zhang J. Analysis of Immune Intratumor Heterogeneity Highlights Immunoregulatory and Coinhibitory Lymphocytes as Hallmarks of Recurrence in Stage I Non-Small Cell Lung Cancer. Mod Pathol. 2023 Jan;36(1):100028. doi: 10.1016/j.modpat.2022.100028. PubMed PMID: 36788067.

Wong KK, Bateman NW, Ng CW, Tsang YTM, Sun CS, Celestino J, Nguyen TV, Malpica A, Hillman RT, Zhang J, Futreal PA, Rojas C, Conrads KA, Hood BL, Dalgard CL, Wilkerson MD, Phippen NT, Conrads TP, Maxwell GL, Sood AK, Gershenson DM. Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors. J Transl Med. 2022 Dec 17;20(1):606. doi: 10.1186/s12967-022-03820-x. PubMed PMID: 36528667; PubMed Central PMCID: PMC9758924.

Hao D, Han G, Sinjab A, Gomez-Bolanos LI, Lazcano R, Serrano A, Hernandez SD, Dai E, Cao X, Hu J, Dang M, Wang R, Chu Y, Song X, Zhang J, Parra ER, Wargo JA, Swisher SG, Cascone T, Sepesi B, Futreal AP, Li M, Dubinett SM, Fujimoto J, Solis Soto LM, Wistuba II, Stevenson CS, Spira A, Shalapour S, Kadara H, Wang L. The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma. Cancer Discov. 2022 Nov 2;12(11):2626-2645. doi: 10.1158/2159-8290.CD-21-1658. PubMed PMID: 36098652; PubMed Central PMCID: PMC9633381.

Sperling AS, Guerra VA, Kennedy JA, Yan Y, Hsu JI, Wang F, Nguyen AT, Miller PG, McConkey ME, Quevedo Barrios VA, Furudate K, Zhang L, Kanagal-Shamanna R, Zhang J, Little L, Gumbs C, Daver N, DiNardo CD, Kadia T, Ravandi F, Kantarjian H, Garcia-Manero G, Futreal PA, Ebert BL, Takahashi K. Lenalidomide promotes the development of TP53-mutated therapy-related myeloid neoplasms. Blood. 2022 Oct 20;140(16):1753-1763. doi: 10.1182/blood.2021014956. PubMed PMID: 35512188; PubMed Central PMCID: PMC9837415.

Bronk JK, Kapadia C, Wu X, Chapman BV, Wang R, Karpinets TV, Song X, Futreal AM, Zhang J, Klopp AH, Colbert LE. Feasibility of a novel non-invasive swab technique for serial whole-exome sequencing of cervical tumors during chemoradiation therapy. PLoS One. 2022;17(10):e0274457. doi: 10.1371/journal.pone.0274457. eCollection 2022. PubMed PMID: 36201462; PubMed Central PMCID: PMC9536567.

Handley KF, Sims TT, Bateman NW, Glassman D, Foster KI, Lee S, Yao J, Yao H, Fellman BM, Liu J, Lu Z, Conrads KA, Hood BL, Barakat W, Zhao L, Zhang J, Westin SN, Celestino J, Rangel KM, Badal S, Pereira I, Ram PT, Maxwell GL, Eberlin LS, Futreal PA, Bast RC Jr, Fleming ND, Conrads TP, Sood AK. Classification of High-Grade Serous Ovarian Cancer Using Tumor Morphologic Characteristics. JAMA Netw Open. 2022 Oct 3;5(10):e2236626. doi: 10.1001/jamanetworkopen.2022.36626. PubMed PMID: 36239936; PubMed Central PMCID: PMC9568802.

Karpinets TV, Wu X, Solley T, El Alam MB, Sims TT, Yoshida-Court K, Lynn E, Ahmed-Kaddar M, Biegert G, Yue J, Song X, Sun H, Petrosino JF, Mezzari MP, Okhuysen P, Eifel PJ, Jhingran A, Lin LL, Schmeler KM, Ramondetta L, Ajami N, Jenq RR, Futreal A, Zhang J, Klopp AH, Colbert LE. Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure. BMC Cancer. 2022 Sep 1;22(1):945. doi: 10.1186/s12885-022-09997-0. PubMed PMID: 36050658; PubMed Central PMCID: PMC9438314.

Zhao L, Corvigno S, Ma S, Celestino J, Fleming ND, Hajek RA, Lankenau Ahumada A, Jennings NB, Thompson EJ, Tang H, Westin SN, Jazaeri AA, Zhang J, Futreal PA, Sood AK, Lee S. Molecular Profiles of Serum-Derived Extracellular Vesicles in High-Grade Serous Ovarian Cancer. Cancers (Basel). 2022 Jul 23;14(15). doi: 10.3390/cancers14153589. PubMed PMID: 35892848; PubMed Central PMCID: PMC9330879.

Andrews MC, Oba J, Wu CJ, Zhu H, Karpinets T, Creasy CA, Forget MA, Yu X, Song X, Mao X, Robertson AG, Romano G, Li P, Burton EM, Lu Y, Sloane RS, Wani KM, Rai K, Lazar AJ, Haydu LE, Bustos MA, Shen J, Chen Y, Morgan MB, Wargo JA, Kwong LN, Haymaker CL, Grimm EA, Hwu P, Hoon DSB, Zhang J, Gershenwald JE, Davies MA, Futreal PA, Bernatchez C, Woodman SE. Multi-modal molecular programs regulate melanoma cell state. Nat Commun. 2022 Jul 9;13(1):4000. doi: 10.1038/s41467-022-31510-1. PubMed PMID: 35810190; PubMed Central PMCID: PMC9271073.

Schmidt ST, Akhave N, Knightly RE,Lips EH, Kumar T, Megalios A, Visser LL, Sheinman M, Fortunato A, Shah V, Hoogstraat M, Sei E, Mallo D, Roman-Escorza M, Ahmed AA, Xu M, van den Belt-Dusebout AW, Brugman W, Casasent AK, Clements K, Davies HR, Fu L, Grigoriadis A, Hardman TM, King LM, Krete M, Kristel P, de Maaker M, Maley CC, Marks JR, Menegaz BA, Mulder L, Nieboer F, Nowinski S, Pinder S, Quist J, Salinas-Souza C, Schaapveld M, Schmidt MK, Shaaban AM, Shami R, Sridharan M, Zhang J, Stobart H, Collyar D, Nik-Zainal S, Wessels LFA, Hwang ES, Navin NE, Futreal PA, Thompson AM, Wesseling J, Sawyer EJ. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer. Nat Genet. 2022 Jun 9;. doi: 10.1038/s41588-022-01082-3. [Epub ahead of print] PubMed PMID: 35681052.

Lips EH, Kumar T, Megalios A, Visser LL, Sheinman M, Fortunato A, Shah V, Hoogstraat M, Sei E, Mallo D, Roman-Escorza M, Ahmed AA, Xu M, van den Belt-Dusebout AW, Brugman W, Casasent AK, Clements K, Davies HR, Fu L, Grigoriadis A, Hardman TM, King LM, Krete M, Kristel P, de Maaker M, Maley CC, Marks JR, Menegaz BA, Mulder L, Nieboer F, Nowinski S, Pinder S, Quist J, Salinas-Souza C, Schaapveld M, Schmidt MK, Shaaban AM, Shami R, Sridharan M, Zhang J, Stobart H, Collyar D, Nik-Zainal S, Wessels LFA, Hwang ES, Navin NE, Futreal PA, Thompson AM, Wesseling J, Sawyer EJ. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer. Nat Genet. 2022 Jun;54(6):850-860. doi: 10.1038/s41588-022-01082-3. Epub 2022 Jun 9. PubMed PMID: 35681052; PubMed Central PMCID: PMC9197769.

Chen R, Li J, Fujimoto J, Hong L, Hu X, Quek K, Tang M, Mitra A, Behrens C, Chow CW, Jiang P, Little LD, Gumbs C, Song X, Zhang J, Tan D, Heymach JV, Wistuba I, Futreal PA, Gibbons DL, Byers LA, Zhang J, Reuben A. Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma. J Exp Clin Cancer Res. 2022 May 11;41(1):172. doi: 10.1186/s13046-022-02361-x. PubMed PMID: 35546239; PubMed Central PMCID: PMC9092788.

Sperling AS, Guerra VA, Kennedy JA, Yan Y, Hsu JI, Wang F, Nguyen AT, Miller PG, McConkey ME, Quevedo Barrios VA, Furudate K, Zhang L, Kanagal-Shamanna R, Zhang J, Little LD, Gumbs CE, Daver NG, DiNardo CD, Kadia TM, Ravandi F, Kantarjian HM, Garcia-Manero G, Futreal A, Ebert BL, Takahashi K. Lenalidomide promotes the development of TP53-mutated therapy-related myeloid neoplasms. Blood. 2022 May 5;. doi: 10.1182/blood.2021014956. [Epub ahead of print] PubMed PMID: 35512188.

Song X, Chang S, Seminario-Vidal L, de Mingo Pulido A, Tordesillas L, Song X, Reed RA, Harkins A, Whiddon S, Nguyen JV, Segura CM, Zhang C, Yoder S, Sayegh Z, Zhao Y, Messina JL, Harro CM, Zhang X, Conejo-Garcia JR, Berglund A, Sokol L, Zhang J, Rodriguez PC, Mulé JJ, Futreal AP, Tsai KY, Chen PL. Genomic and Single-Cell Landscape Reveals Novel Drivers and Therapeutic Vulnerabilities of Transformed Cutaneous T-cell Lymphoma. Cancer Discov. 2022 May 2;12(5):1294-1313. doi: 10.1158/2159-8290.CD-21-1207. PubMed PMID: 35247891.

Creasy CA, Meng YJ, Forget MA, Karpinets T, Tomczak K, Stewart C, Torres-Cabala CA, Pilon-Thomas S, Sarnaik AA, Mulé JJ, Garraway L, Bustos M, Zhang J, Patel SP, Diab A, Glitza IC, Yee C, Tawbi H, Wong MK, McQuade J, Hoon DSB, Davies MA, Hwu P, Amaria RN, Haymaker C, Beroukhim R, Bernatchez C. Genomic Correlates of Outcome in Tumor-Infiltrating Lymphocyte Therapy for Metastatic Melanoma. Clin Cancer Res. 2022 May 2;28(9):1911-1924. doi: 10.1158/1078-0432.CCR-21-1060. PubMed PMID: 35190823; PubMed Central PMCID: PMC9064946.

Wu CC, Beird HC, Lamhamedi-Cherradi SE, Soeung M, Ingram D, Truong DD, Porter RW, Krishnan S, Little L, Gumbs C, Zhang J, Titus M, Genovese G, Ludwig JA, Lazar AJ, Hayes-Jordan A, Futreal PA. Multi-site desmoplastic small round cell tumors are genetically related and immune-cold. NPJ Precis Oncol. 2022 Apr 4;6(1):21. doi: 10.1038/s41698-022-00257-9. PubMed PMID: 35379887; PubMed Central PMCID: PMC8980094.

Kwan SY, Jiao J, Joon A, Wei P, Petty LE, Below JE, Daniel CR, Wu X, Zhang J, Jenq RR, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Beretta L. Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease. Hepatology. 2022 Apr;75(4):955-967. doi: 10.1002/hep.32197. Epub 2021 Dec 13. PubMed PMID: 34633706; PubMed Central PMCID: PMC8930512.

Glassman D, Bateman NW, Lee S, Zhao L, Yao J, Tan Y, Ivan C, Rangel KM, Zhang J, Conrads KA, Hood BL, Abulez T, Futreal PA, Fleming ND, Afshar-Kharghan V, Maxwell GL, Conrads TP, Chen K, Sood AK. Molecular Correlates of Venous Thromboembolism (VTE) in Ovarian Cancer. Cancers (Basel). 2022 Mar 15;14(6). doi: 10.3390/cancers14061496. PubMed PMID: 35326647; PubMed Central PMCID: PMC8946269.

Li J, Lu H, Ng PK, Pantazi A, Ip CKM, Jeong KJ, Amador B, Tran R, Tsang YH, Yang L, Song X, Dogruluk T, Ren X, Hadjipanayis A, Bristow CA, Lee S, Kucherlapati M, Parfenov M, Tang J, Seth S, Mahadeshwar HS, Mojumdar K, Zeng D, Zhang J, Protopopov A, Seidman JG, Creighton CJ, Lu Y, Sahni N, Shaw KR, Meric-Bernstam F, Futreal A, Chin L, Scott KL, Kucherlapati R, Mills GB, Liang H. A functional genomic approach to actionable gene fusions for precision oncology. Sci Adv. 2022 Feb 11;8(6):eabm2382. doi: 10.1126/sciadv.abm2382. Epub 2022 Feb 9. PubMed PMID: 35138907; PubMed Central PMCID: PMC8827659.

Hong Y, Limback D, Elsarraj HS, Harper H, Haines H, Hansford H, Ricci M, Kaufman C, Wedlock E, Xu M, Zhang J, May L, Cusick T, Inciardi M, Redick M, Gatewood J, Winblad O, Aripoli A, Huppe A, Balanoff C, Wagner JL, Amin AL, Larson KE, Ricci L, Tawfik O, Razek H, Meierotto RO, Madan R, Godwin AK, Thompson J, Hilsenbeck SG, Futreal A, Thompson A, Hwang ES, Fan F, Behbod F. Mouse-INtraDuctal (MIND): an in vivo model for studying the underlying mechanisms of DCIS malignancy. J Pathol. 2022 Feb;256(2):186-201. doi: 10.1002/path.5820. Epub 2021 Dec 13. PubMed PMID: 34714554; PubMed Central PMCID: PMC8738143.

Colbert LE, El MB, Lynn EJ, Bronk J, Karpinets TV, Wu X, Chapman BV, Sims TT, Lin D, Kouzy R, Sammouri J, Biegert G, Delgado Medrano AY, Olvera A, Sastry KJ, Eifel PJ, Jhingran A, Lin L, Ramondetta LM, Futreal AP, Jazaeri AA, Schmeler KM, Yue J, Mitra A, Yoshida-Court K, Wargo JA, Solley TN, Hegde V, Nookala SS, Yanamandra AV, Dorta-Estremera S, Mathew G, Kavukuntla R, Papso C, Ahmed-Kaddar M, Kim M, Zhang J, Reuben A, Holliday EB, Minsky BD, Koong AC, Koay EJ, Das P, Taniguchi CM, Klopp A. Expansion of Candidate HPV-Specific T Cells in the Tumor Microenvironment during Chemoradiotherapy Is Prognostic in HPV16+ Cancers. Cancer Immunol Res. 2022 Feb;10(2):259-271. doi: 10.1158/2326-6066.CIR-21-0119. Epub 2022 Jan 19. PubMed PMID: 35045973.

Wu CC, Wang YA, Livingston JA, Zhang J, Futreal PA. Prediction of biomarkers and therapeutic combinations for anti-PD-1 immunotherapy using the global gene network association. Nat Commun. 2022 Jan 10;13(1):42. doi: 10.1038/s41467-021-27651-4. PubMed PMID: 35013211; PubMed Central PMCID: PMC8748689.

Federico L, McGrail DJ, Bentebibel SE, Haymaker C, Ravelli A, Forget MA, Karpinets T, Jiang P, Reuben A, Negrao MV, Li J, Khairullah R, Zhang J, Weissferdt A, Vaporciyan AA, Antonoff MB, Walsh G, Lin SY, Futreal A, Wistuba I, Roth J, Byers LA, Gaudreau PO, Uraoka N, Cruz AF, Dejima H, Lazcano RN, Solis LM, Parra ER, Lee JJ, Swisher S, Cascone T, Heymach JV, Zhang J, Sepesi B, Gibbons DL, Bernatchez C. Distinct tumor-infiltrating lymphocyte landscapes are associated with clinical outcomes in localized non-small-cell lung cancer. Ann Oncol. 2022 Jan;33(1):42-56. doi: 10.1016/j.annonc.2021.09.021. Epub 2021 Oct 13. PubMed PMID: 34653632.
 

Tang M, Abbas HA, Negrao MV, Ramineni M, Hu X, Hubert SM, Fujimoto J, Reuben A, Varghese S, Zhang J, Li J, Chow CW, Mao X, Song X, Lee WC, Wu J, Little L, Gumbs C, Behrens C, Moran C, Weissferdt A, Lee JJ, Sepesi B, Swisher S, Cheng C, Kurie J, Gibbons D, Heymach JV, Wistuba II, Futreal PA, Kalhor N, Zhang J. The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics. Nat Commun. 2021 Dec 6;12(1):7081. doi: 10.1038/s41467-021-27341-1. PubMed PMID: 34873156. 

Hong Y, Limback D, Elsarraj HS, Harper H, Haines H, Hansford H, Ricci M, Kaufman C, Wedlock E, Xu M, Zhang J, May L, Cusick T, Inciardi M, Redick M, Gatewood J, Winblad O, Aripoli A, Huppe A, Balanoff C, Wagner JL, Amin AL, Larson KE, Ricci L, Tawfik O, Razek H, Meierotto RO, Madan R, Godwin AK, Thompson J, Hilsenbeck SG, Futreal A, Thompson A, Hwang ES, Fan F, Behbod F. Mouse-INtraDuctal (MIND): an in vivo model for studying the underlying mechanisms of DCIS malignancy. J Pathol. 2021 Oct 29;. doi: 10.1002/path.5820. [Epub ahead of print] PubMed PMID: 34714554. 

Abbas HA, Hao D, Tomczak K, Barrodia P, Im JS, Reville PK, Alaniz Z, Wang W, Wang R, Wang F, Al-Atrash G, Takahashi K, Ning J, Ding M, Beird HC, Mathews JT, Little L, Zhang J, Basu S, Konopleva M, Marques-Piubelli ML, Solis LM, Parra ER, Lu W, Tamegnon A, Garcia-Manero G, Green MR, Sharma P, Allison JP, Kornblau SM, Rai K, Wang L, Daver N, Futreal A. Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy. Nat Commun. 2021 Oct 18;12(1):6071. doi: 10.1038/s41467-021-26282-z. PubMed PMID: 34663807; PubMed Central PMCID: PMC8524723. 

Federico L, McGrail DJ, Bentebibel SE, Haymaker C, Ravelli A, Forget MA, Karpinets T, Jiang P, Reuben A, Negrao MV, Li J, Khairullah R, Zhang J, Weissferdt A, Vaporciyan AA, Antonoff MB, Walsh G, Lin SY, Futreal A, Wistuba I, Roth J, Byers LA, Gaudreau PO, Uraoka N, Cruz AF, Dejima H, Lazcano RN, Solis LM, Parra ER, Lee JJ, Swisher S, Cascone T, Heymach JV, Zhang J, Sepesi B, Gibbons DL, Bernatchez C. Distinct tumor-infiltrating lymphocyte landscapes are associated with clinical outcomes in localized non-small-cell lung cancer. Ann Oncol. 2021 Oct 13;. doi: 10.1016/j.annonc.2021.09.021. [Epub ahead of print] PubMed PMID: 34653632. 

Kwan SY, Jiao J, Joon A, Wei P, Petty LE, Below JE, Daniel CR, Wu X, Zhang J, Jenq RR, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Beretta L. Gut Microbiome Features Associated with Liver Fibrosis in Hispanics, a Population at High Risk for Fatty Liver Disease. Hepatology. 2021 Oct 11;. doi: 10.1002/hep.32197. [Epub ahead of print] PubMed PMID: 34633706. 

Hou P, Ma X, Yang Z, Zhang Q, Wu CJ, Li J, Tan L, Yao W, Yan L, Zhou X, Kimmelman AC, Lorenzi PL, Zhang J, Jiang S, Spring D, Wang YA, DePinho RA. USP21 deubiquitinase elevates macropinocytosis to enable oncogenic KRAS bypass in pancreatic cancer. Genes Dev. 2021 Oct 1;35(19-20):1327-1332. doi: 10.1101/gad.348787.121. Epub 2021 Sep 16. PubMed PMID: 34531315; PubMed Central PMCID: PMC8494209. 

Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen Q, Enos R, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla S, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal A, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu CJ. Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network. Clin Cancer Res. 2021 Sep 15;27(18):5049-5061. doi: 10.1158/1078-0432.CCR-20-3251. Epub 2020 Dec 15. PubMed PMID: 33323402; PubMed Central PMCID: PMC8203757. 

Kochat V, Raman AT, Landers SM, Tang M, Schulz J, Terranova C, Landry JP, Bhalla AD, Beird HC, Wu CC, Jiang Y, Mao X, Lazcano R, Gite S, Ingram DR, Yi M, Zhang J, Keung EZ, Scally CP, Roland CL, Hunt KK, Feig BW, Futreal PA, Hwu P, Wang WL, Lazar AJ, Slopis JM, Wilson-Robles H, Wiener DJ, McCutcheon IE, Wustefeld-Janssens B, Rai K, Torres KE. Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state. Acta Neuropathol. 2021 Sep;142(3):565-590. doi: 10.1007/s00401-021-02341-z. Epub 2021 Jul 20. PubMed PMID: 34283254. 

Abbas HA, Mohanty V, Wang R, Huang Y, Liang S, Wang F, Zhang J, Qiu Y, Hu CW, Qutub AA, Dail M, Bolen CR, Daver N, Konopleva M, Futreal A, Chen K, Wang L, Kornblau SM. Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes. Front Oncol. 2021;11:705627. doi: 10.3389/fonc.2021.705627. eCollection 2021. PubMed PMID: 34422660; PubMed Central PMCID: PMC8372368. 

Andrews MC, Duong CPM, Gopalakrishnan V, Iebba V, Chen WS, Derosa L, Khan MAW, Cogdill AP, White MG, Wong MC, Ferrere G, Fluckiger A, Roberti MP, Opolon P, Alou MT, Yonekura S, Roh W, Spencer CN, Curbelo IF, Vence L, Reuben A, Johnson S, Arora R, Morad G, Lastrapes M, Baruch EN, Little L, Gumbs C, Cooper ZA, Prieto PA, Wani K, Lazar AJ, Tetzlaff MT, Hudgens CW, Callahan MK, Adamow M, Postow MA, Ariyan CE, Gaudreau PO, Nezi L, Raoult D, Mihalcioiu C, Elkrief A, Pezo RC, Haydu LE, Simon JM, Tawbi HA, McQuade J, Hwu P, Hwu WJ, Amaria RN, Burton EM, Woodman SE, Watowich S, Diab A, Patel SP, Glitza IC, Wong MK, Zhao L, Zhang J, Ajami NJ, Petrosino J, Jenq RR, Davies MA, Gershenwald JE, Futreal PA, Sharma P, Allison JP, Routy B, Zitvogel L, Wargo JA. Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade. Nat Med. 2021 Aug;27(8):1432-1441. doi: 10.1038/s41591-021-01406-6. Epub 2021 Jul 8. PubMed PMID: 34239137. 

Chakravarti D, Lee R, Multani AS, Santoni A, Keith Z, Hsu WH, Chang K, Reyes L, Rashid A, Wu CJ, Li J, Zhang J, Shim HS, Chandra K, Deng P, Spring DJ, Nielsen OH, Riis LB, Mayigegowda KK, Blutt SE, Zhang J, Younes M, DuPont A, Thirumurthi S, Vilar E, Estes MK, Colla S, Shroyer NF, DePinho RA.Telomere dysfunction instigates inflammation in inflammatory bowel disease. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29). doi: 10.1073/pnas.2024853118. PubMed PMID: 34253611; PubMed Central PMCID: PMC8307535. 

Karpinets TV, Mitani Y, Liu B, Zhang J, Pytynia KB, Sellen LD, Karagiannis DT, Ferrarotto R, Futreal AP, El-Naggar AK. Whole-Genome Sequencing of Common Salivary Gland Carcinomas: Subtype-Restricted and Shared Genetic Alterations. Clin Cancer Res. 2021 Jul 15;27(14):3960-3969. doi: 10.1158/1078-0432.CCR-20-4071. Epub 2021 May 19. PubMed PMID: 34011559; PubMed Central PMCID: PMC8598082. 

Jiao J, Sanchez JI, Thompson EJ, Mao X, McCormick JB, Fisher-Hoch SP, Futreal PA, Zhang J, Beretta L. Somatic Mutations in Circulating Cell-Free DNA and Risk for Hepatocellular Carcinoma in Hispanics. Int J Mol Sci. 2021 Jul 10;22(14). doi: 10.3390/ijms22147411. PubMed PMID: 34299031; PubMed Central PMCID: PMC8304329. 

Zhang S, Jiang VC, Han G, Hao D, Lian J, Liu Y, Zhang R, McIntosh J, Wang R, Dang M, Dai E, Wang Y, Santos D, Badillo M, Leeming A, Chen Z, Hartig K, Bigcal J, Zhou J, Kanagal-Shamanna R, Ok CY, Lee H, Steiner RE, Zhang J, Song X, Nair R, Ahmed S, Rodriquez A, Thirumurthi S, Jain P, Wagner-Bartak N, Hill H, Nomie K, Flowers C, Futreal A, Wang L, Wang M. Longitudinal single-cell profiling reveals molecular heterogeneity and tumor-immune evolution in refractory mantle cell lymphoma. Nat Commun. 2021 May 17;12(1):2877. doi: 10.1038/s41467-021-22872-z. PubMed PMID: 34001881; PubMed Central PMCID: PMC8128874. 

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Lee S, Zhao L, Little LD, Westin SN, Jazarei AA, Fleming ND, Zhang J, Futreal PA, Sood AK. Distinct T cell receptor repertoire diversity of clinically defined high-grade serous ovarian cancer treatment subgroups. iScience. 2021 Feb 19;24(2):102053. doi: 10.1016/j.isci.2021.102053. eCollection 2021 Feb 19. PubMed PMID: 33537658; PubMed Central PMCID: PMC7840469. 

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Hou P, Kapoor A, Zhang Q, Li J, Wu CJ, Li J, Lan Z, Tang M, Ma X, Ackroyd JJ, Kalluri R, Zhang J, Jiang S, Spring DJ, Wang YA, DePinho RA. Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer. Cancer Discov. 2020 Jul;10(7):1058-1077. doi: 10.1158/2159-8290.CD-19-0597. Epub 2020 Apr 27. PubMed PMID: 32341020; PubMed Central PMCID: PMC7334087. 

Mitra A, Grossman Biegert GW, Delgado AY, Karpinets TV, Solley TN, Mezzari MP, Yoshida-Court K, Petrosino JF, Mikkelson MD, Lin L, Eifel P, Zhang J, Ramondetta LM, Jhingran A, Sims TT, Schmeler K, Okhuysen P, Colbert LE, Klopp AH. Microbial Diversity and Composition Is Associated with Patient-Reported Toxicity during Chemoradiation Therapy for Cervical Cancer.Int J Radiat Oncol Biol Phys. 2020 May 1;107(1):163-171. doi: 10.1016/j.ijrobp.2019.12.040. Epub 2020 Jan 25. PubMed PMID: 31987960. 

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Jain P, Zhang S, Kanagal-Shamanna R, Ok CY, Nomie K, Gonzalez GN, Gonzalez-Pagan O, Hill HA, Lee HJ, Fayad L, Westin J, Nastoupil L, Hagemeister F, Chen W, Oriabure O, Badillo M, Jiang C, Yixin Y, Li S, Tang G, Yin CC, Patel KP, Medeiros LJ, Nair R, Ahmed S, Iyer SP, Thirumurthi S, Champlin R, Xu G, Tinsu P, Santos D, Wang R, Han G, Zhang J, Song X, Neelapu S, Romaguera J, Futreal A, Flowers C, Fowler N, Wang L, Wang ML. Genomic profiles and clinical outcomes of de novo blastoid/pleomorphic MCL are distinct from those of transformed MCL. Blood Adv. 2020 Mar 24;4(6):1038-1050. doi: 10.1182/bloodadvances.2019001396. PubMed PMID: 32191807; PubMed Central PMCID: PMC7094021. 

Jin Y, Bao H, Le X, Fan X, Tang M, Shi X, Zhao J, Yan J, Xu Y, Quek K, Elamin YY, Zhang J, Futreal PA, Wistuba II, Heymach JV, Lou G, Shao L, He Q, Lin C, Wu X, Shao YW, Wang X, He J, Chen Y, Stebbing J, Chen M, Zhang J, Yu X. Correction: Distinct co-acquired alterations and genomic evolution during TKI treatment in non-small-cell lung cancer patients with or without acquired T790M mutation. Oncogene. 2020 Feb;39(9):2027. doi: 10.1038/s41388-019-1143-5. PubMed PMID: 31831835. 

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Fountzilas E, Kotoula V, Koliou GA, Giannoulatou E, Gogas H, Papadimitriou C, Tikas I, Zhang J, Papadopoulou K, Zagouri F, Christodoulou C, Koutras A, Makatsoris T, Chrisafi S, Linardou H, Varthalitis I, Papatsibas G, Razis E, Papakostas P, Samantas E, Aravantinos G, Bafaloukos D, Kosmidis P, Koumarianou A, Psyrri A, Pentheroudakis G, Pectasides D, Futreal A, Fountzilas G, Tsimberidou AM. Pathogenic mutations and overall survival in 3,084 patients with cancer: the Hellenic Cooperative Oncology Group Precision Medicine Initiative. Oncotarget. 2020 Jan 7;11(1):1-14. doi: 10.18632/oncotarget.27338. eCollection 2020 Jan 7. PubMed PMID: 32002119; PubMed Central PMCID: PMC6967777. 

Wang R, Song S, Harada K, Ghazanfari Amlashi F, Badgwell B, Pizzi MP, Xu Y, Zhao W, Dong X, Jin J, Wang Y, Scott A, Ma L, Huo L, Vicente D, Blum Murphy M, Shanbhag N, Tatlonghari G, Thomas I, Rogers J, Kobayashi M, Vykoukal J, Estrella JS, Roy-Chowdhuri S, Han G, Zhang S, Mao X, Song X, Zhang J, Gu J, Johnson RL, Calin GA, Peng G, Lee JS, Hanash SM, Futreal A, Wang Z, Wang L, Ajani JA. Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response. Gut. 2020 Jan;69(1):18-31. doi: 10.1136/gutjnl-2018-318070. Epub 2019 Jun 6. PubMed PMID: 31171626; PubMed Central PMCID: PMC6943252. 

Kapoor A, Yao W, Ying H, Hua S, Liewen A, Wang Q, Zhong Y, Wu CJ, Sadanandam A, Hu B, Chang Q, Chu GC, Al-Khalil R, Jiang S, Xia H, Fletcher-Sananikone E, Lim C, Horwitz GI, Viale A, Pettazzoni P, Sanchez N, Wang H, Protopopov A, Zhang J, Heffernan T, Johnson RL, Chin L, Wang YA, Draetta G, DePinho RA. Yap1 Activation Enables Bypass of Oncogenic Kras Addiction in Pancreatic Cancer. Cell. 2019 Nov 14;179(5):1239. doi: 10.1016/j.cell.2019.10.037. PubMed PMID: 31730860.

Hou P, Ma X, Zhang Q, Wu CJ, Liao W, Li J, Wang H, Zhao J, Zhou X, Guan C, Ackroyd J, Jiang S, Zhang J, Spring DJ, Wang YA, DePinho RA. USP21 deubiquitinase promotes pancreas cancer cell stemness via Wnt pathway activation. Genes Dev. 2019 Oct 1;33(19-20):1361-1366. doi: 10.1101/gad.326314.119. Epub 2019 Sep 5. PubMed PMID: 31488580; PubMed Central PMCID: PMC6771391.

Manasanch EE, Han G, Mathur R, Qing Y, Zhang Z, Lee H, Weber DM, Amini B, Berkova Z, Eterovic K, Zhang S, Zhang J, Song X, Mao X, Morgan M, Feng L, Baladandayuthapani V, Futreal A, Wang L, Neelapu SS, Orlowski RZ. A pilot study of pembrolizumab in smoldering myeloma: report of the clinical, immune, and genomic analysis. Blood Adv. 2019 Aug 13;3(15):2400-2408. doi: 10.1182/bloodadvances.2019000300. PubMed PMID: 31405950; PubMed Central PMCID: PMC6693011.

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Wang R, Song S, Harada K, Ghazanfari Amlashi F, Badgwell B, Pizzi MP, Xu Y, Zhao W, Dong X, Jin J, Wang Y, Scott A, Ma L, Huo L, Vicente D, Blum Murphy M, Shanbhag N, Tatlonghari G, Thomas I, Rogers J, Kobayashi M, Vykoukal J, Estrella JS, Roy-Chowdhuri S, Han G, Zhang S, Mao X, Song X, Zhang J, Gu J, Johnson RL, Calin GA, Peng G, Lee JS, Hanash SM, Futreal A, Wang Z, Wang L, Ajani JA. Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response. Gut. 2019 Jun 6;. doi: 10.1136/gutjnl-2018-318070. [Epub ahead of print] PubMed PMID: 31171626.

Zhang L, Yao Y, Zhang S, Liu Y, Guo H, Ahmed M, Bell T, Zhang H, Han G, Lorence E, Badillo M, Zhou S, Sun Y, Di Francesco ME, Feng N, Haun R, Lan R, Mackintosh SG, Mao X, Song X, Zhang J, Pham LV, Lorenzi PL, Marszalek J, Heffernan T, Draetta G, Jones P, Futreal A, Nomie K, Wang L, Wang M. Metabolic reprogramming toward oxidative phosphorylation identifies a therapeutic target for mantle cell lymphoma. Sci Transl Med. 2019 May 8;11(491). doi: 10.1126/scitranslmed.aau1167. PubMed PMID: 31068440.

Liao W, Overman MJ, Boutin AT, Shang X, Zhao D, Dey P, Li J, Wang G, Lan Z, Li J, Tang M, Jiang S, Ma X, Chen P, Katkhuda R, Korphaisarn K, Chakravarti D, Chang A, Spring DJ, Chang Q, Zhang J, Maru DM, Maeda DY, Zebala JA, Kopetz S, Wang YA, DePinho RA. KRAS-IRF2 Axis Drives Immune Suppression and Immune Therapy Resistance in Colorectal Cancer. Cancer Cell.2019 Apr 15;35(4):559-572.e7. doi: 10.1016/j.ccell.2019.02.008. Epub 2019 Mar 21. PubMed PMID: 30905761; PubMed Central PMCID: PMC6467776.

Seth S, Li CY, Ho IL, Corti D, Loponte S, Sapio L, Del Poggetto E, Yen EY, Robinson FS, Peoples M, Karpinets T, Deem AK, Kumar T, Song X, Jiang S, Kang Y, Fleming J, Kim M, Zhang J, Maitra A, Heffernan TP, Giuliani V, Genovese G, Futreal A, Draetta GF, Carugo A, Viale A. Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors. Cell Rep. 2019 Feb 5;26(6):1518-1532.e9. doi: 10.1016/j.celrep.2019.01.048. PubMed PMID: 30726735.

Yilmaz M, Wang F, Loghavi S, Bueso-Ramos C, Gumbs C, Little L, Song X, Zhang J, Kadia T, Borthakur G, Jabbour E, Pemmaraju N, Short N, Garcia-Manero G, Estrov Z, Kantarjian H, Futreal A, Takahashi K, Ravandi F. Late relapse in acute myeloid leukemia (AML): clonal evolution or therapy-related leukemia?. Blood Cancer J. 2019 Jan 16;9(2):7. doi: 10.1038/s41408-019-0170-3. PubMed PMID: 30651532; PubMed Central PMCID: PMC6335405.

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Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC, Cogdill AP, Zhao L, Hudgens CW, Hutchinson DS, Manzo T, Petaccia de Macedo M, Cotechini T, Kumar T, Chen WS, Reddy SM, Szczepaniak Sloane R, Galloway-Pena J, Jiang H, Chen PL, Shpall EJ, Rezvani K, Alousi AM, Chemaly RF, Shelburne S, Vence LM, Okhuysen PC, Jensen VB, Swennes AG, McAllister F, Marcelo Riquelme Sanchez E, Zhang Y, Le Chatelier E, Zitvogel L, Pons N, Austin-Breneman JL, Haydu LE, Burton EM, Gardner JM, Sirmans E, Hu J, Lazar AJ, Tsujikawa T, Diab A, Tawbi H, Glitza IC, Hwu WJ, Patel SP, Woodman SE, Amaria RN, Davies MA, Gershenwald JE, Hwu P, Lee JE, Zhang J, Coussens LM, Cooper ZA, Futreal PA, Daniel CR, Ajami NJ, Petrosino JF, Tetzlaff MT, Sharma P, Allison JP, Jenq RR, Wargo JA. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2018 Jan 5;359(6371):97-103. doi: 10.1126/science.aan4236. Epub 2017 Nov 2. PubMed PMID: 29097493; PubMed Central PMCID: PMC5827966 

Montalban-Bravo G, Takahashi K, Patel K, Wang F, Xingzhi S, Nogueras GM, Huang X, Pierola AA, Jabbour E, Colla S, Gañan-Gomez I, Borthakur G, Daver N, Estrov Z, Kadia T, Pemmaraju N, Ravandi F, Bueso-Ramos C, Chamseddine A, Konopleva M, Zhang J, Kantarjian H, Futreal A, Garcia-Manero G. Impact of the number of mutations in survival and response outcomes to hypomethylating agents in patients with myelodysplastic syndromes or myelodysplastic/myeloproliferative neoplasms. Oncotarget. 2018 Jan 3;9(11):9714-9727. doi: 10.18632/oncotarget.23882. eCollection 2018 Feb 9. PubMed PMID: 29515765; PubMed Central PMCID: PMC5839396.

Wang JF, Pu X, Zhang X, Chen K, Xi Y, Wang J, Mao X, Zhang J, Heymach JV, Antonoff MB, Hofstetter WL, Mehran RJ, Rice DC, Roth JA, Sepesi B, Swisher SG, Vaporciyan AA, Walsh GL, Meng QH, Shaw KR, Eterovic AK, Fang B. Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing.Cancer. 2018 Mar 1;124(5):1061-1069. doi: 10.1002/cncr.31152. Epub 2017 Nov 27. PubMed PMID: 29178133; PubMed Central PMCID: PMC5821585.

Karpinets TV, Gopalakrishnan V, Wargo J, Futreal AP, Schadt CW, Zhang J. Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks. Front Microbiol. 2018 Mar 7;9:297. doi: 10.3389/fmicb.2018.00297. eCollection 2018. PubMed PMID: 29563898; PubMed Central PMCID: PMC5850922.

Beird HC, Wu CC, Ingram DR, Wang WL, Alimohamed A, Gumbs C, Little L, Song X, Feig BW, Roland CL, Zhang J, Benjamin RS, Hwu P, Lazar AJ, Futreal PA, Somaiah N. Genomic profiling of dedifferentiated liposarcoma compared to matched well-differentiated liposarcoma reveals higher genomic complexity and a common origin. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002386. doi: 10.1101/mcs.a002386. Print 2018 Apr. PubMed PMID: 29610390; PubMed Central PMCID: PMC5880260.

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