Selected Publications
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2023
A novel statistical method for decontaminating T-cell receptor sequencing data Opens a new window
Li R, Altan M, Reuben A, Lin R, Heymach JV, Tran H, Chen R, Little L, Hubert S, Zhang J, Li Z.Brief Bioinform. 2023 Jul 20;24(4):bbad230. doi: 10.1093/bib/bbad230. PMID: 37337757
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2023
MCT4-dependent lactate secretion suppresses antitumor immunity in LKB1-deficient lung adenocarcinoma Opens a new window
Qian Y, Galan-Cobo A, Guijarro I, Dang M, Molkentine D, Poteete A, Zhang F, Wang Q, Wang J, Parra E, Panda A, Fang J, Skoulidis F, Wistuba II, Verma S, Merghoub T, Wolchok JD, Wong KK, DeBerardinis RJ, Minna JD, Vokes NI, Meador CB, Gainor JF, Wang L, Reuben A, Heymach JV.Cancer Cell. 2023 Jul 10;41(7):1363-1380.e7. doi: 10.1016/j.ccell.2023.05.015. Epub 2023 Jun 15. PMID: 37327788
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2023
Analysis of Immune Intratumor Heterogeneity Highlights Immunoregulatory and Coinhibitory Lymphocytes as Hallmarks of Recurrence in Stage I Non-Small Cell Lung Cancer Opens a new window
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.Mod Pathol. 2023 Jan;36(1):100028. doi: 10.1016/j.modpat.2022.100028.PMID: 36788067 Free PMC article.
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2022
T cell receptor repertoire sequencing in the era of cancer immunotherapy Opens a new window
Frank ML, Lu K, Erdogan C, Han Y, Hu J, Wang T, Heymach JV, Zhang J, Reuben A. Clin Cancer Res. 2022 Nov 22:CCR-22-2469. doi: 10.1158/1078-0432.CCR-22-2469. Online ahead of print. PMID: 36413126
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2022
Immunogenomic profiling of lung adenocarcinoma reveals poorly differentiated tumors are associated with an immunogenic tumor microenvironment Opens a new window
Akhave N, Zhang J, Bayley E, Frank M, Chiou SH, Behrens C, Chen R, Hu X, Parra ER, Lee WC, Swisher S, Solis L, Weissferdt A, Moran C, Kalhor N, Zhang J, Scheet P, Vaporciyan AA, Sepesi B, Gibbons DL, Heymach JV, Lee JJ, Wistuba II, Andrew Futreal P, Zhang J, Fujimoto J, Reuben A. Lung Cancer. 2022 Oct;172:19-28. doi: 10.1016/j.lungcan.2022.08.007. Epub 2022 Aug 10. PMID: 35973335
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2022
Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma Opens a new window
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. J Exp Clin Cancer Res.
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2022
Combined IL-2, agonistic CD3 and 4-1BB stimulation preserve clonotype hierarchy in propagated non-small cell lung cancer tumor-infiltrating lymphocytes Opens a new window
Shah P, Forget MA, Frank ML, Jiang P, Sakellariou-Thompson D, Federico L, Khairullah R, Neutzler CA, Wistuba I, Chow CB, Long Y, Fujimoto J, Lin SY, Maitra A, Negrao MV, Mitchell KG, Weissferdt A, Vaporciyan AA, Cascone T, Roth JA, Zhang J, Sepesi B, Gibbons DL, Heymach JV, Haymaker CL, McGrail DJ, Reuben A, Bernatchez C. Journal for Immunotherapy of Cancer.
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2021
Distinct tumor-infiltrating lymphocyte landscapes are associated with clinical outcomes in localized non-small-cell lung cancer Opens a new window
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. Ann Oncol. 2022 Jan;33(1):42-56. doi: 10.1016/j.annonc.2021.09.021. Epub 2021 Oct 13. PubMed PMID: 34653632; NIHMSID:NIHMS1850169.
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2021
Neoadjuvant nivolumab or nivolumab plus ipilimumab in operable non-small cell lung cancer: the phase 2 randomized NEOSTAR trial Opens a new window
Cascone T, William WN Jr, Weissferdt A, Leung CH, Lin HY, Pataer A, Godoy MCB, Carter BW, Federico L, Reuben A, Khan MAW, Dejima H, Francisco-Cruz A, Parra ER, Solis LM, Fujimoto J, Tran HT, Kalhor N, Fossella FV, Mott FE, Tsao AS, Blumenschein G Jr, Le X, Zhang J, Skoulidis F, Kurie JM, Altan M, Lu C, Glisson BS, Byers LA, Elamin YY, Mehran RJ, Rice DC, Walsh GL, Hofstetter WL, Roth JA, Antonoff MB, Kadara H, Haymaker C, Bernatchez C, Ajami NJ, Jenq RR, Sharma P, Allison JP, Futreal A, Wargo JA, Wistuba II, Swisher SG, Lee JJ, Gibbons DL, Vaporciyan AA, Heymach JV, Sepesi B. Nat Med.
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2021
Deep learning-based prediction of the T cell receptor-antigen binding specificity Opens a new window
Lu T, Zhang Z, Zhu, J, Wang Y, Jiang P, Xiao X, Bernatchez C, Heymach JV, Gibbons DL, Wang J, Xu L, Reuben A, Wang T. Nature Machine Intelligence ().
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2021
Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer Opens a new window
Chen M, Chen R, Jin Y, Li J, Hu X, Zhang J, Fujimoto J, Hubert SM, Gay CM, Zhu B, Tian Y, McGranahan N, Lee WC, George J, Hu X, Chen Y, Wu M, Behrens C, Chow CW, Pham HHN, Fukuoka J, Wu J, Parra ER, Little LD, Gumbs C, Song X, Wu CJ, Diao L, Wang Q, Cardnell R, Zhang J, Wang J, Le X, Gibbons DL, Heymach JV, Jack Lee J, William WN Jr, Cheng C, Glisson B, Wistuba I, Andrew Futreal P, Thomas RK, Reuben A, Byers LA, Zhang J. Nature Communications
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2021
Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features Opens a new window
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. Nature Communications
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2021
Characterization of the Immune Landscape of EGFR-Mutant NSCLC Identifies CD73/Adenosine Pathway as a Potential Therapeutic Target Opens a new window
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. Journal of Thoracic Oncology.
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2021
Neoadjuvant Chemotherapy Increases Cytotoxic T Cell, Tissue Resident Memory T Cell, and B Cell Infiltration in Resectable NSCLC Opens a new window
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. Journal of Thoracic Oncology.
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2020
T-cell repertoire in combination with T-cell density predicts clinical outcomes in patients with Merkel cell carcinoma Opens a new window
Farah M, Reuben A, Spassova I, Yang RK, Kubat L, Nagarajan P, Ning J, Li W, Aung PP, Curry JL, Torres-Cabala CA, Hudgens CW, Ugurel S, Schadendorf D, Gumbs C, Little LD, Futreal A, Wistuba II, Prieto VG, Wang L, Wong MK, Wargo JA, Becker JC, Tetzlaff MT. T-Cell Repertoire in Combination with T-Cell Density Predicts Clinical Outcomes in Patients with Merkel Cell Carcinoma. J Invest Dermatol.
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2020
Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity Opens a new window
Lee WC, Reuben A, Hu X, McGranahan N, Chen R, Jalali A, Negrao MV, Hubert SM, Tang C, Wu CC, Lucas AS, Roh W, Suda K, Kim J, Tan AC, Peng DH, Lu W, Tang X, Chow CW, Fujimoto J, Behrens C, Kalhor N, Fukumura K, Coyle M, Thornton R, Gumbs C, Li J, Wu CJ, Little L, Roarty E, Song X, Lee JJ, Sulman EP, Rao G, Swisher S, Diao L, Wang J, Heymach JV, Huse JT, Scheet P, Wistuba II, Gibbons DL, Futreal PA, Zhang J, Gomez D, Zhang J. Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity. Genome Biol.