Halbrook CJ, Lyssiotis CA, di Magliano MP, Maitra A. Pancreatic cancer: advances and challenges. Cell. 2023;186(8):1729–54.
CAS PubMed PubMed Central Google Scholar
Rojas LA, Sethna Z, Soares KC, Olcese C, Pang N, Patterson E, Lihm J, Ceglia N, Guasp P, Chu A. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature. 2023;618(7963):144–50.
CAS PubMed PubMed Central Google Scholar
Leidner R, Sanjuan Silva N, Huang H, Sprott D, Zheng C, Shih Y-P, Leung A, Payne R, Sutcliffe K, Cramer J. Neoantigen T-cell receptor gene therapy in pancreatic cancer. N Engl J Med. 2022;386(22):2112–9.
CAS PubMed PubMed Central Google Scholar
Baulu E, Gardet C, Chuvin N, Depil S. TCR-engineered T cell therapy in solid tumors: state of the Art and perspectives. Sci Adv. 2023;9(7):eadf3700.
CAS PubMed PubMed Central Google Scholar
Zheng C, Fass JN, Shih Y-P, Gunderson AJ, Silva NS, Huang H, Bernard BM, Rajamanickam V, Slagel J, Bifulco CB. Transcriptomic profiles of neoantigen-reactive T cells in human Gastrointestinal cancers. Cancer Cell. 2022;40(4):410–23. e417.
Fan C, Qu H, Wang X, Sobhani N, Wang L, Liu S, Xiong W, Zeng Z, Li Y. Cancer/testis antigens: from serology to mRNA cancer vaccine. Semin Cancer Biol. 2021:218–31.
Kwok DW, Stevers NO, Etxeberria I, Nejo T, Colton Cove M, Chen LH, Jung J, Okada K, Lakshmanachetty S, Gallus M. Tumour-wide RNA splicing aberrations generate actionable public neoantigens. Nature. 2025 1–11.
Poschke IC, Hassel JC, Rodriguez-Ehrenfried A, Lindner KA, Heras-Murillo I, Appel LM, Lehmann J, Lövgren T, Wickström SL, Lauenstein C. The outcome of ex vivo TIL expansion is highly influenced by Spatial heterogeneity of the tumor T-cell repertoire and differences in intrinsic in vitro growth capacity between T-cell clones. Clin Cancer Res. 2020;26(16):4289–301.
Lowery FJ, Krishna S, Yossef R, Parikh NB, Chatani PD, Zacharakis N, Parkhurst MR, Levin N, Sindiri S, Sachs A. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. Science. 2022;375(6583):877–84.
CAS PubMed PubMed Central Google Scholar
Tan CL, Lindner K, Boschert T, Meng Z, Rodriguez Ehrenfried A, De Roia A, Haltenhof G, Faenza A, Imperatore F, Bunse L. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy. Nat Biotechnol. 2024:1–9.
Zeng Z, Zhang T, Zhang J, Li S, Connor S, Zhang B, Zhao Y, Wilson J, Singh D, Kulikauskas R. A minimal gene set characterizes TIL specific for diverse tumor antigens across different cancer types. Nat Commun. 2025;16(1):1070.
CAS PubMed PubMed Central Google Scholar
Hongwei Sun XH, Du Z, Guo T, Xie F. Weiyue Gu and Zhiwen shi: A machine learning model that identifies neoantigen-reactive CD8 + T cells in human Gastrointestinal cancer. Br J Cancer. 2024:1–16. 131(2):387–402.
Meng Z, Rodriguez Ehrenfried A, Tan CL, Steffens LK, Kehm H, Zens S, Lauenstein C, Paul A, Schwab M, Förster JD. Transcriptome-based identification of tumor-reactive and bystander CD8 + T cell receptor clonotypes in human pancreatic cancer. Sci Transl Med. 2023;15(722):eadh9562.
Shi Z, Chen B, Han X, Gu W, Liang S, Wu L. Genomic and molecular landscape of homologous recombination deficiency across multiple cancer types. Sci Rep. 2023;13(1):8899.
CAS PubMed PubMed Central Google Scholar
McGinnis CS, Murrow LM, Gartner ZJ. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 2019;8(4):329–37. e324.
CAS PubMed PubMed Central Google Scholar
Haghverdi L, Lun AT, Morgan MD, Marioni JC. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat Biotechnol. 2018;36(5):421–7.
CAS PubMed PubMed Central Google Scholar
Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM III, Hao Y, Stoeckius M, Smibert P, Satija R. Comprehensive integration of single-cell data. Cell. 2019;177(7):1888–902. e1821.
CAS PubMed PubMed Central Google Scholar
Borcherding N, Bormann NL, Kraus G. scRepertoire: An R-based toolkit for single-cell immune receptor analysis. F1000Research. 2020;9.
Goncharov M, Bagaev D, Shcherbinin D, Zvyagin I, Bolotin D, Thomas PG, Minervina AA, Pogorelyy MV, Ladell K, McLaren JE. VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2. Nat Methods. 2022;19(9):1017–9.
Van de Sande B, Flerin C, Davie K, De Waegeneer M, Hulselmans G, Aibar S, Seurinck R, Saelens W, Cannoodt R. Rouchon qjnp: A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nat Protoc. 2020;15(7):2247–76.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W. Smyth gkjnar: Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47–47.
PubMed PubMed Central Google Scholar
Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan C-H, Myung P, Plikus MV. Nie qjnc: inference and analysis of cell-cell communication using cellchat. Nat Commun. 2021;12(1):1088.
CAS PubMed PubMed Central Google Scholar
Zheng L, Qin S, Si W, Wang A, Xing B, Gao R, Ren X, Wang L, Wu X, Zhang J. Pan-cancer single-cell landscape of tumor-infiltrating T cells. Science. 2021;374(6574):abe6474.
Lee JJ, Bernard V, Semaan A, Monberg ME, Huang J, Stephens BM, Lin D, Rajapakshe KI, Weston BR, Bhutani MS. Elucidation of tumor-stromal heterogeneity and the ligand-receptor interactome by single-cell transcriptomics in real-world pancreatic cancer biopsies. Clin Cancer Res. 2021;27(21):5912–21.
CAS PubMed PubMed Central Google Scholar
Werba G, Weissinger D, Kawaler EA, Zhao E, Kalfakakou D, Dhara S, Wang L, Lim HB, Oh G, Jing X. Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment. Nat Commun. 2023;14(1):797.
CAS PubMed PubMed Central Google Scholar
Zhang S, Fang W, Zhou S, Zhu D, Chen R, Gao X, Li Z, Fu Y, Zhang Y, Yang F. Single cell transcriptomic analyses implicate an immunosuppressive tumor microenvironment in pancreatic cancer liver metastasis. Nat Commun. 2023;14(1):5123.
CAS PubMed PubMed Central Google Scholar
Schalck A, Sakellariou-Thompson D, Forget M-A, Sei E, Hughes TG, Reuben A, Bai S, Hu M, Kumar T, Hurd MW. Single-cell sequencing reveals trajectory of tumor-infiltrating lymphocyte States in pancreatic cancer. Cancer Discov. 2022;12(10):2330–49.
CAS PubMed PubMed Central Google Scholar
Steele NG, Carpenter ES, Kemp SB, Sirihorachai VR, The S, Delrosario L, Lazarus J, Amir E-aD, Gunchick V, Espinoza C. Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer. Nat Cancer. 2020;1(11):1097–112.
CAS PubMed PubMed Central Google Scholar
Lee B, Namkoong H, Yang Y, Huang H, Heller D, Szot GL, Davis MM, Husain SZ, Pandol SJ, Bellin MD. Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis. Gut. 2022;71(9):1831–42.
Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(W1):W98–102.
CAS PubMed PubMed Central Google Scholar
Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, Treviño V, Shen H, Laird PW, Levine DA. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4(1):2612.
Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, Schinzel AC, Sandy P, Meylan E, Scholl C. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009;462(7269):108–12.
CAS PubMed PubMed Central Google Scholar
Hafemeister C, Satija R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 2019;20(1):296.
CAS PubMed PubMed Central Google Scholar
Kursa MB, Rudnicki WR. The all relevant feature selection using random forest. ArXiv Preprint arXiv:11065112 2011.
Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. J Exp Med. 2019;217(1):e20182009.
Shi Z, Zhao Q, Lv B, Qu X, Han X, Wang H, Qiu J, Hua K. Identification of biomarkers complementary to homologous recombination deficiency for improving the clinical outcome of ovarian serous cystadenocarcinoma. Clin Translational Med. 2021;11(5):e399.
Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using MACS. Nat Protoc. 2012;7(9):1728–40.
Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–92.
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