Heterogeneity and evolution of tumour immune microenvironment in metastatic gastroesophageal adenocarcinoma

Sugarbaker PH. Gastric cancer: prevention and treatment of peritoneal metastases. J Cancer Metastasis Treat. 2018;4(2):7.

Article  CAS  Google Scholar 

Baxter MA, Middleton F, Cagney HP, Petty RD. Resistance to immune checkpoint inhibitors in advanced gastro-oesophageal cancers. Br J Cancer. 2021;125:1068–79.

PubMed  PubMed Central  Article  Google Scholar 

Aversa I, Malanga D, Fiume G, Palmieri C. Molecular T-cell repertoire analysis as source of prognostic and predictive biomarkers for checkpoint blockade immunotherapy. Int J Mol Sci. 2020;21(7):2378.

CAS  PubMed Central  Article  Google Scholar 

Kidman J, Principe N, Watson M, Lassmann T, Holt RA, Nowak AK, Lesterhuis WJ, Lake RA, Chee J. Characteristics of TCR repertoire associated with successful immune checkpoint therapy responses. Front Immunol. 2020;11: 587014.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hopkins AC, Yarchoan M, Durham JN, Yusko EC, Rytlewski JA, Robins HS, Laheru DA, Le DT, Lutz ER, Jaffee EM. T cell receptor repertoire features associated with survival in immunotherapy-treated pancreatic ductal adenocarcinoma. JCI Insight. 2018;3(13): e122092.

PubMed Central  Article  Google Scholar 

Looney TJ, Topacio-Hall D, Lowman G, Conroy J, Morrison C, Oh D, Fong L, Zhang L. TCR Convergence in individuals treated with immune checkpoint inhibition for cancer. Front Immunol. 2020;10:2985.

PubMed  PubMed Central  Article  CAS  Google Scholar 

Khunger A, Rytlewski JA, Fields P, Yusko EC, Tarhini AA. The impact of CTLA-4 blockade and interferon-α on clonality of T-cell repertoire in the tumour microenvironment and peripheral blood of metastatic melanoma patients. Oncoimmunology. 2019;8(11): e1652538.

PubMed  PubMed Central  Article  Google Scholar 

Han J, Duan J, Bai H, Wang Y, Wan R, Wang X, Chen S, Tian Y, Wang D, Fei K, Yao Z, Wang S, Lu Z, Wang Z, Wang J. TCR repertoire diversity of peripheral PD-1þCD8þ T cells predicts clinical outcomes after immunotherapy in patients with non–small cell lung cancer. Cancer Immunol Res. 2020;8(1):146–54.

CAS  PubMed  Article  Google Scholar 

Galon J, Bruni D. Tumour immunology and tumour evolution: intertwined histories. Immunity. 2020;52(1):55–81.

CAS  PubMed  Article  Google Scholar 

Lee JS, Won HS, Sun DS, Hong JH, Ko YH. Prognostic role of tumour-infiltrating lymphocytes in gastric cancer: a systematic review and meta-analysis. Medicine (Baltimore). 2018;97(32):1–8.

Article  CAS  Google Scholar 

Son SM, Woo CG, Kim DH, Yun HY, Kim H, Kim HK, Yang Y, Kwon J, Kwon M, Kim TY, Kim HD, Koh JY, Park SH, Shin EC, Han HS. Distinct tumour immune microenvironments in primary and metastatic lesions in gastric cancer patients. Sci Rep. 2020;10(1):1–12.

Article  CAS  Google Scholar 

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, et al. Comprehensive T cell repertoire characterization of non-small cell lung cancer. Nat Commun. 2020;11(1):603.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Zhang C, Ding H, Huang H, Palashati H, Miao Y, Xiong H, Lu Z. TCR repertoire intratumour heterogeneity of CD4 + and CD8 + T cells in centers and margins of localized lung adenocarcinomas. Int J Cancer. 2019;144(4):818–27.

CAS  PubMed  Article  Google Scholar 

Rosenthal R, Cadieux EL, Salgado R, Al-Bakir M, Moore DA, Hiley CT, Lund T, Tanić M, Reading JL, Joshi K, Henry JY, Ghorani E, Wilson GA, Birkbak NJ, Jamal-Hanjani M, Veeriah S, Szallasi Z, Loi S, Hellmann MD, et al. Neoantigen-directed immune escape in lung cancer evolution. Nature. 2019;567(7749):479–85.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Jia Q, Wu W, Wang Y, Alexander PB, Sun C, Gong Z, Cheng JN, Sun H, Guan Y, Xia X, Yang L, Yi X, Wan YY, Wang H, He J, Futreal PA, Li QJ, Zhu B. Local mutational diversity drives intratumoural immune heterogeneity in non-small cell lung cancer. Nat Commun. 2018;9(1):1–10.

Article  CAS  Google Scholar 

Mani NL, Schalper KA, Hatzis C, Saglam O, Tavassoli F, Butler M, Chagpar AB, Pusztai L, Rimm DL. Quantitative assessment of the spatial heterogeneity of tumour-infiltrating lymphocytes in breast cancer. Breast Cancer Res. 2016;18(1):1–10.

Article  CAS  Google Scholar 

Jiménez-Sánchez A, Cybulska P, Mager KLV, Koplev S, Cast O, Couturier DL, Memon D, Selenica P, Nikolovski I, Mazaheri Y, Bykov Y, Geyer FC, Macintyre G, Gavarró LM, Drews RM, Gill MB, Papanastasiou AD, Sosa RE, Soslow RA, et al. Unraveling tumour–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy. Nat Genet. 2020;52(6):582–93.

PubMed  PubMed Central  Article  CAS  Google Scholar 

Gerlinger M, Quezada SA, Peggs KS, Furness AJS, Fisher R, Marafioti T, Shende VH, McGranahan N, Rowan AJ, Hazell S, Hamm D, Robins HS, Pickering L, Gore M, Nicol DL, Larkin J, Swanton C. Ultra-deep T cell receptor sequencing reveals the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas. J Pathol. 2013;231(4):424–32.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics. 2014;30(15):2114–20.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Reiter JG, Makohon-Moore AP, Gerold JM, Bozic I, Chatterjee K, Iacobuzio-Donahue CA, Vogelstein B, Nowak MA. Reconstructing metastatic seeding patterns of human cancers. Nat Commun. 2017;8:1–10.

CAS  Article  Google Scholar 

Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM. MiXCR: Software for comprehensive adaptive immunity profiling. Nat Methods. 2015;12(5):380–1.

CAS  PubMed  Article  Google Scholar 

Arnaud-Haond S, Duarte CM, Alberto F, Serrão EA. Standardizing methods to address clonality in population studies. Mol Ecol. 2007;16(24):5115–39.

CAS  PubMed  Article  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.

CAS  PubMed  Article  Google Scholar 

Li B, Colin ND. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12(323):21–40.

Google Scholar 

Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling tumour infiltrating immune cells with CIBERSORT. Methods Mol Biol. 2018;1711:243–59.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, et al. The immune landscape of cancer. Immunity. 2018;48(4):812-830.e14.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumours associated with local immune cytolytic activity. Cell. 2015;160(1–2):48–61.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody MC, Pfeifer JD. ATHLATES: accurate typing of human leukocyte antigen through exome sequencing. Nucleic Acids Res. 2013;41(14):1–8.

Google Scholar 

Hundal J, Carreno BM, Petti AA, Linette GP, Griffith OL, Mardis ER, Griffith M. pVAC-Seq : a genome-guided in silico approach to identifying tumour neoantigens. Genome Med. 2016;8:1–11.

Article  CAS  Google Scholar 

Galili T. dendextend: An R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics. 2015;31(22):3718–20.

CAS  PubMed  PubMed Central  Article  Google Scholar 

De Mattos-Arruda L, Sammut S-J, Ross EM, Markowetz F, Seoane J, Caldas CC. The genomic and immune landscapes of lethal metastatic breast cancer. Cell Rep. 2019. https://doi.org/10.1016/j.celrep.2019.04.098.

PubMed  PubMed Central  Article  Google Scholar 

Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, Rudolph JE, Yaeger R, Soumerai T, Nissan MH, Chang MT, Chandarlapaty S, Traina TA, Paik PK, Ho AL, Hantash FM, Grupe A, Baxi SS, Callahan MK, Snyder A, Chi P, Danila D, Gounder M, Harding JJ, Schultz N. OncoKB : a precision oncology knowledge base. JCO Precis Oncol. 2017. https://doi.org/10.1200/PO.17.00011.

PubMed  PubMed Central  Article  Google Scholar 

Eyles J, Puaux AL, Wang X, Toh B, Prakash C, Hong M, Tan TG, Zheng L, Ong LC, Jin Y, Kato M, Prévost-Blondel A, Chow P, Yang H, Abastado JP. Tumour cells disseminate early, but immunosurveillance limits metastatic outgrowth, in a mouse model of melanoma. J Clin Invest. 2010;120(6):2030–9.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Guo FF, Cui JW. The role of tumour-infiltrating B cells in tumour immunity. J Oncol. 2019. https://doi.org/10.1155/2019/2592419.

PubMed  PubMed Central  Article  Google Scholar 

Poran A, Scherer J, Bushway ME, Besada R, Balogh KN, Wanamaker A, Williams RG, Prabhakara J, Ott PA, Hu-Lieskovan S, Khondker ZS, Gaynor RB, Rooney MS, Srinivasan L. Combined TCR Repertoire Profiles and Blood Cell Phenotypes Predict Melanoma Patient Response to Personalized Neoantigen Therapy plus Anti-PD-1. Cell Rep Med. 2020;1(8): 100141.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Vroman H, Balzaretti G, Belderbos RA, Klarenbeek PL, Van Nimwegen M, Bezemer K, Cornelissen R, Niewold ITG, Van Schaik BD, Van Kampen AH, Aerts JGJV, De Vries N, Hendriks RW. T cell receptor repertoire characteristics both before and following immunotherapy correlate with clinical response in mesothelioma. J Immunother Cancer. 2020;8(1):1–8.

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