Publications

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. 

Dejima H, Hu X, Chen R, Zhang J, Fujimoto J, Parra ER, Haymaker C, Hubert SM, Duose D, Solis LM, Su D, Fukuoka J, Tabata K, Pham HHN, Mcgranahan N, Zhang B, Ye J, Ying L, Little L, Gumbs C, Chow CW, Estecio MR, Godoy MCB, Antonoff MB, Sepesi B, Pass HI, Behrens C, Zhang J, Vaporciyan AA, Heymach JV, Scheet P, Lee JJ, Wu J, Futreal PA, Reuben A, Kadara H, Wistuba II, Zhang J. Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features. Nat Commun. 2021 May 11;12(1):2722. doi: 10.1038/s41467-021-22890-x. PubMed PMID: 33976164; PubMed Central PMCID: PMC8113327. 

Lee SH, Simoneau EB, Karpinets T, Futreal PA, Zhang J, Javle M, Zhang J, Vauthey JN, Lee JS, Estrella JS, Chun YS. Genomic profiling of multifocal intrahepatic cholangiocarcinoma reveals intraindividual concordance of genetic alterations. Carcinogenesis. 2021 Apr 17;42(3):436-441. doi: 10.1093/carcin/bgaa124. PubMed PMID: 33200197; PubMed Central PMCID: PMC8052956. 

Le X, Negrao MV, Reuben A, Federico L, Diao L, McGrail D, Nilsson M, Robichaux J, Munoz IG, Patel S, Elamin Y, Fan YH, Lee WC, Parra E, Solis Soto LM, Chen R, Li J, Karpinets T, Khairullah R, Kadara H, Behrens C, Sepesi B, Wang R, Zhu M, Wang L, Vaporciyan A, Roth J, Swisher S, Haymaker C, Zhang J, Wang J, Wong KK, Byers LA, Bernatchez C, Zhang J, Wistuba II, Gibbons DL, Akbay EA, Heymach JV. Characterization of the Immune Landscape of EGFR-Mutant NSCLC Identifies CD73/Adenosine Pathway as a Potential Therapeutic Target. J Thorac Oncol. 2021 Apr;16(4):583-600. doi: 10.1016/j.jtho.2020.12.010. Epub 2020 Dec 31. PubMed PMID: 33388477. 

Tsimberidou AM, Hong DS, Fu S, Karp DD, Piha-Paul S, Kies MS, Ravi V, Subbiah V, Patel SM, Tu SM, Janku F, Heymach J, Johnson A, Cartwright C, Zhao L, Zhang J, Berry DA, Vining DJ, Futreal A, Miller VA, Meric-Bernstam F. Precision medicine: preliminary results from the Initiative for Molecular Profiling and Advanced Cancer Therapy 2 (IMPACT2) study. NPJ Precis Oncol. 2021 Mar 19;5(1):21. doi: 10.1038/s41698-021-00159-2. PubMed PMID: 33742104; PubMed Central PMCID: PMC7979841. 

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. 

Ferrarotto R, Mitani Y, McGrail DJ, Li K, Karpinets TV, Bell D, Frank SJ, Song X, Kupferman ME, Liu B, Lee JJ, Glisson BS, Zhang J, Aster JC, Lin SY, Futreal PA, Heymach JV, El-Naggar AK. Proteogenomic Analysis of Salivary Adenoid Cystic Carcinomas Defines Molecular Subtypes and Identifies Therapeutic Targets. Clin Cancer Res. 2021 Feb 1;27(3):852-864. doi: 10.1158/1078-0432.CCR-20-1192. Epub 2020 Nov 10. PubMed PMID: 33172898; PubMed Central PMCID: PMC7854509. 

Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun. 2021 Jan 29;12(1):687. doi: 10.1038/s41467-021-20907-z. PubMed PMID: 33514726; PubMed Central PMCID: PMC7846738. 

Wang R, Dang M, Harada K, Han G, Wang F, Pool Pizzi M, Zhao M, Tatlonghari G, Zhang S, Hao D, Lu Y, Zhao S, Badgwell BD, Blum Murphy M, Shanbhag N, Estrella JS, Roy-Chowdhuri S, Abdelhakeem AAF, Wang Y, Peng G, Hanash S, Calin GA, Song X, Chu Y, Zhang J, Li M, Chen K, Lazar AJ, Futreal A, Song S, Ajani JA, Wang L. Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma. Nat Med. 2021 Jan;27(1):141-151. doi: 10.1038/s41591-020-1125-8. Epub 2021 Jan 4. PubMed PMID: 33398161; PubMed Central PMCID: PMC8074162. 

Gaudreau PO, Negrao MV, Mitchell KG, Reuben A, Corsini EM, Li J, Karpinets TV, Wang Q, Diao L, Wang J, Federico L, Parra-Cuentas ER, Khairullah R, Behrens C, Correa AM, Gomez D, Little L, Gumbs C, Kadara HN, Fujimoto J, McGrail DJ, Vaporciyan AA, Swisher SG, Walsh G, Antonoff MB, Weissferdt A, Tran H, Roarty E, Haymaker C, Bernatchez C, Zhang J, Futreal PA, Wistuba II, Cascone T, Heymach JV, Sepesi B, Zhang J, Gibbons DL.Neoadjuvant Chemotherapy Increases Cytotoxic T Cell, Tissue Resident Memory T Cell, and B Cell Infiltration in Resectable NSCLC. J Thorac Oncol. 2021 Jan;16(1):127-139. doi: 10.1016/j.jtho.2020.09.027. Epub 2020 Oct 21. PubMed PMID: 33096269; PubMed Central PMCID: PMC7775914.

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. 

Mitra A, Andrews MC, Roh W, De Macedo MP, Hudgens CW, Carapeto F, Singh S, Reuben A, Wang F, Mao X, Song X, Wani K, Tippen S, Ng KS, Schalck A, Sakellariou-Thompson DA, Chen E, Reddy SM, Spencer CN, Wiesnoski D, Little LD, Gumbs C, Cooper ZA, Burton EM, Hwu P, Davies MA, Zhang J, Bernatchez C, Navin N, Sharma P, Allison JP, Wargo JA, Yee C, Tetzlaff MT, Hwu WJ, Lazar AJ, Futreal PA. Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma. Nat Commun. 2020 Apr 15;11(1):1839. doi: 10.1038/s41467-020-15538-9. PubMed PMID: 32296058; PubMed Central PMCID: PMC7160105. 

Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK. Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer.Cell Rep. 2020 Apr 14;31(2):107502. doi: 10.1016/j.celrep.2020.03.066. PubMed PMID: 32294438; PubMed Central PMCID: PMC7234854. 

Subudhi SK, Vence L, Zhao H, Blando J, Yadav SS, Xiong Q, Reuben A, Aparicio A, Corn PG, Chapin BF, Pisters LL, Troncoso P, Tidwell RS, Thall P, Wu CJ, Zhang J, Logothetis CL, Futreal A, Allison JP, Sharma P. Neoantigen responses, immune correlates, and favorable outcomes after ipilimumab treatment of patients with prostate cancer. Sci Transl Med. 2020 Apr 1;12(537). doi: 10.1126/scitranslmed.aaz3577. PubMed PMID: 32238575. 

Dey P, Li J, Zhang J, Chaurasiya S, Strom A, Wang H, Liao WT, Cavallaro F, Denz P, Bernard V, Yen EY, Genovese G, Gulhati P, Liu J, Chakravarti D, Deng P, Zhang T, Carbone F, Chang Q, Ying H, Shang X, Spring DJ, Ghosh B, Putluri N, Maitra A, Wang YA, DePinho RA. Oncogenic KRAS-Driven Metabolic Reprogramming in Pancreatic Cancer Cells Utilizes Cytokines from the Tumor Microenvironment. Cancer Discov. 2020 Apr;10(4):608-625. doi: 10.1158/2159-8290.CD-19-0297. Epub 2020 Feb 11. PubMed PMID: 32046984; PubMed Central PMCID: PMC7125035. 

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. 

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. 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):1846-1859. doi: 10.1038/s41388-019-1104-z. Epub 2019 Nov 21. PubMed PMID: 31754213. 

Reuben A, Zhang J, Chiou SH, Gittelman RM, Li J, Lee WC, Fujimoto J, Behrens C, Liu X, Wang F, Quek K, Wang C, Kheradmand F, Chen R, Chow CW, Lin H, Bernatchez C, Jalali A, Hu X, Wu CJ, Eterovic AK, Parra ER, Yusko E, Emerson R, Benzeno S, Vignali M, Wu X, Ye Y, Little LD, Gumbs C, Mao X, Song X, Tippen S, Thornton RL, Cascone T, Snyder A, Wargo JA, Herbst R, Swisher S, Kadara H, Moran C, Kalhor N, Zhang J, Scheet P, Vaporciyan AA, Sepesi B, Gibbons DL, Robins H, Hwu P, Heymach JV, Sharma P, Allison JP, Baladandayuthapani V, Lee JJ, Davis MM, Wistuba II, Futreal PA, Zhang J. Comprehensive T cell repertoire characterization of non-small cell lung cancer. Nat Commun. 2020 Jan 30;11(1):603. doi: 10.1038/s41467-019-14273-0. PubMed PMID: 32001676; PubMed Central PMCID: PMC6992630. 

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.

Hu X, Fujimoto J, Ying L, Fukuoka J, Ashizawa K, Sun W, Reuben A, Chow CW, McGranahan N, Chen R, Hu J, Godoy MC, Tabata K, Kuroda K, Shi L, Li J, Behrens C, Parra ER, Little LD, Gumbs C, Mao X, Song X, Tippen S, Thornton RL, Kadara H, Scheet P, Roarty E, Ostrin EJ, Wang X, Carter BW, Antonoff MB, Zhang J, Vaporciyan AA, Pass H, Swisher SG, Heymach JV, Lee JJ, Wistuba II, Hong WK, Futreal PA, Su D, Zhang J. Multi-region exome sequencing reveals genomic evolution from preneoplasia to lung adenocarcinoma. Nat Commun. 2019 Jul 5;10(1):2978. doi: 10.1038/s41467-019-10877-8. PubMed PMID: 31278276; PubMed Central PMCID: PMC6611767.

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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.

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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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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.

Takahashi K, Hu B, Wang F, Yan Y, Kim E, Vitale C, Patel KP, Strati P, Gumbs C, Little L, Tippen S, Song X, Zhang J, Jain N, Thompson P, Garcia-Manero G, Kantarjian H, Estrov Z, Do KA, Keating M, Burger JA, Wierda WG, Futreal PA, Ferrajoli A. Clinical implications of cancer gene mutations in patients with chronic lymphocytic leukemia treated with lenalidomide. Blood. 2018 Apr 19;131(16):1820-1832. doi: 10.1182/blood-2017-11-817296. Epub 2018 Jan 22. PubMed PMID: 29358183; PubMed Central PMCID: PMC5909764.

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Morita K, Kantarjian HM, Wang F, Yan Y, Bueso-Ramos C, Sasaki K, Issa GC, Wang S, Jorgensen J, Song X, Zhang J, Tippen S, Thornton R, Coyle M, Little L, Gumbs C, Pemmaraju N, Daver N, DiNardo CD, Konopleva M, Andreeff M, Ravandi F, Cortes JE, Kadia T, Jabbour E, Garcia-Manero G, Patel KP, Futreal PA, Takahashi K. Clearance of Somatic Mutations at Remission and the Risk of Relapse in Acute Myeloid Leukemia. J Clin Oncol. 2018 Jun 20;36(18):1788-1797. doi: 10.1200/JCO.2017.77.6757. Epub 2018 Apr 27. PubMed PMID: 29702001; PubMed Central PMCID: PMC6008108.

Hillman RT, Celestino J, Terranova C, Beird HC, Gumbs C, Little L, Nguyen T, Thornton R, Tippen S, Zhang J, Lu KH, Gershenson DM, Rai K, Broaddus RR, Futreal PA. KMT2D/MLL2 inactivation is associated with recurrence in adult-type granulosa cell tumors of the ovary. Nat Commun. 2018 Jun 27;9(1):2496. doi: 10.1038/s41467-018-04950-x. PubMed PMID: 29950560; PubMed Central PMCID: PMC6021426.

Nguyen J, Jiao J, Smoot K, Watt GP, Zhao C, Song X, Stevenson HL, McCormick JB, Fisher-Hoch SP, Zhang J, Futreal PA, Beretta L. Toll-like receptor 4: a target for chemoprevention of hepatocellular carcinoma in obesity and steatohepatitis. Oncotarget. 2018 Jun 29;9(50):29495-29507. doi: 10.18632/oncotarget.25685. eCollection 2018 Jun 29. PubMed PMID: 30034633; PubMed Central PMCID: PMC6047684.

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Wu CC, Beird HC, Zhang J, Futreal PA. FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer. PLoS Comput Biol. 2018 Jul 24;14(7):e1006266. doi: 10.1371/journal.pcbi.1006266. eCollection 2018 Jul. PubMed PMID: 30040819; PubMed Central PMCID: PMC6075785.

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Liu B, Mitani Y, Rao X, Zafereo M, Zhang J, Zhang J, Futreal PA, Lozano G, El-Naggar AK. Spatio-Temporal Genomic Heterogeneity, Phylogeny, and Metastatic Evolution in Salivary Adenoid Cystic Carcinoma. Journal of the National Cancer Institute. 2017; 109(10). PMID: 29117356

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Takahashi K, Roh W, Zhang J, Propotopov A, Patel K, Strickland S, Kim A, Vnencak-Jones C, Pelletier S, Parmar S, Garcia-Manero G, Kornblau S, Chin L, Kantarjian H, Futreal PA, Ravandi F. Clonal evolution of acute myeloid leukemia relapsed after 19 years of remission. American journal of hematology. 2015; 90(7):E134-5. PMCID: PMC4948743.

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The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015; 163(4):1011-25. PMCID: PMC4695400.

Kahlert C, Melo SA, Protopopov A, Tang J, Seth S, Koch M, Zhang J, Weitz J, Chin L, Futreal A, Kalluri R. Identification of double-stranded genomic DNA spanning all chromosomes with mutated KRAS and p53 DNA in the serum exosomes of patients with pancreatic cancer. The Journal of Biological Chemistry. 2014; 289(7):3869-75. PMCID: PMC3924256.

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Zhang J, Fujimoto J, Zhang J, Wedge DC, Song X, Zhang J, Seth S, Chow CW, Cao Y, Gumbs C, Gold KA, Kalhor N, Little L, Mahadeshwar H, Moran C, Protopopov A, Sun H, Tang J, Wu X, Ye Y, William WN, Lee JJ, Heymach JV, Hong WK, Swisher S, Wistuba II, Futreal PA. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science (New York, N.Y.). 2014; 346(6206):256-9. PMCID: PMC4354858.

Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014; 159(3):676-90. PMC4243044.

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Hu J, Ho AL, Yuan L, Hu B, Hua S, Hwang SS, Zhang J, Hu T, Zheng H, Gan B, Wu G, Wang YA, Chin L, DePinho RA. From the Cover: Neutralization of terminal differentiation in gliomagenesis. Proceedings of the National Academy of Sciences of the United States of America. 2013; 110(36):14520-7. PMCID: PMC3767545.

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Ding Z, Wu CJ, Jaskelioff M, Ivanova E, Kost-Alimova M, Protopopov A, Chu GC, Wang G, Lu X, Labrot ES, Hu J, Wang W, Xiao Y, Zhang H, Zhang J, Zhang J, Gan B, Perry SR, Jiang S, Li L, Horner JW, Wang YA, Chin L, DePinho RA. Telomerase reactivation following telomere dysfunction yields murine prostate tumors with bone metastases. Cell. 2012; 148(5):896-907. PMCID: PMC3629723.

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Larman TC, DePalma SR, Hadjipanayis AG, Protopopov A, Zhang J, Gabriel SB, Chin L, Seidman CE, Kucherlapati R, Seidman JG. Spectrum of somatic mitochondrial mutations in five cancers. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109(35):14087-91. PMCID: PMC3435197.

Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012; 489(7417):519-25. PMCID: PMC3466113.

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Integrated genomic analyses of ovarian carcinoma. Nature. 2011; 474(7353):609-15. PMCID: PMC3163504.

Gutierrez A, Kentsis A, Sanda T, Holmfeldt L, Chen SC, Zhang J, Protopopov A, Chin L, Dahlberg SE, Neuberg DS, Silverman LB, Winter SS, Hunger SP, Sallan SE, Zha S, Alt FW, Downing JR, Mullighan CG, Look AT. The BCL11B tumor suppressor is mutated across the major molecular subtypes of T-cell acute lymphoblastic leukemia. Blood. 2011; 118(15):4169-73. PubMed [journal] PMID: 21878675, PMCID: PMC3204734

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Li M, Mukasa A, Inda MM, Zhang J, Chin L, Cavenee W, Furnari F. Guanylate binding protein 1 is a novel effector of EGFR-driven invasion in glioblastoma. The Journal of Experimental Medicine. 2011; 208(13):2657-73. PMCID: PMC3244036.

Gutierrez A, Sanda T, Ma W, Zhang J, Grebliunaite R, Dahlberg S, Neuberg D, Protopopov A, Winter SS, Larson RS, Borowitz MJ, Silverman LB, Chin L, Hunger SP, Jamieson C, Sallan SE, Look AT. Inactivation of LEF1 in T-cell acute lymphoblastic leukemia. Blood. 2010; 115(14):2845-51. PMCID: PMC2854430.

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Wiedemeyer WR, Dunn IF, Quayle SN, Zhang J, Chheda MG, Dunn GP, Zhuang L, Rosenbluh J, Chen S, Xiao Y, Shapiro GI, Hahn WC, Chin L. Pattern of retinoblastoma pathway inactivation dictates response to CDK4/6 inhibition in GBM. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107(25):11501-6. PMCID: PMC2895056.

Gutierrez A, Dahlberg SE, Neuberg DS, Zhang J, Grebliunaite R, Sanda T, Protopopov A, Tosello V, Kutok J, Larson RS, Borowitz MJ, Loh ML, Ferrando AA, Winter SS, Mullighan CG, Silverman LB, Chin L, Hunger SP, Sallan SE, Look AT. Absence of biallelic TCRgamma deletion predicts early treatment failure in pediatric T-cell acute lymphoblastic leukemia. Journal of clinical oncology. 2010; 28(24):3816-23. PMC2940399.