{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T11:17:41Z","timestamp":1788347861374,"version":"build-2803163510"},"reference-count":60,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:00:00Z","timestamp":1788307200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Bulk RNA-sequencing of thoracic tumours is routine, but the T-cell receptor (TCR) repertoires it contains are rarely re-mined with a uniform pipeline, and library-prep compatibility for productive V\u2013J-spanning assembly is rarely audited at the cohort level for non-small-cell lung cancer (NSCLC) and oesophageal squamous-cell carcinoma (ESCC).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>We built a reproducible, openly-released pipeline for productive T-cell-receptor \u03b2-chain (TRB) repertoire reconstruction from public thoracic-tumour RNA-seq, and extended it to immune-checkpoint-inhibitor (ICI)-associated cardiac immunotoxicity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Four GEO cohorts (NSCLC and ESCC bulk RNA-seq) were assembled with TRUST4 under a transparent cohort-level QC rule (\u2265 10% V+J assemblies on \u2265 1 representative sample), and antigens were annotated by exact CDR3-amino-acid matching to VDJdb. The identical pipeline was applied to 23 peripheral-blood TRB repertoires from an ICI-irAE single-cell cohort (GSE180045; 10 discovery and 13 validation libraries).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The retained pilot dataset comprised 12 productive samples and 916 productive TRB clones; ESCC (n = 1 after QC) was oligoclonal versus diverse NSCLC. Of 37 VDJdb hits, 33 were viral and 4 tumour or self, with no clone shared across cohorts. Thoracic-tumour tissue repertoires were significantly more oligoclonal than peripheral ICI-irAE repertoires (top-10 clone fraction 0.76 vs 0.18; inverse Simpson 8.8 vs 177; Mann-Whitney BH-FDR &amp;lt; 0.001), whereas depth-normalised metrics did not differ (FDR = 0.61), indicating an assay-platform (bulk RNA-seq versus 10x single-cell), sequencing-depth and tissue-versus-blood effect rather than intrinsic clonal architecture; within-patient cardiac contrasts were not significant and are reported descriptively.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>One uniform pipeline transparently re-mines public thoracic-tumour and cardiac-immunotoxicity RNA-seq for TCR repertoires. These findings are descriptive and hypothesis-generating rather than statistically generalisable, with the ESCC-versus-NSCLC contrast resting on a single ESCC sample.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1892720","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T11:00:29Z","timestamp":1788346829000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["A reproducible pipeline for TCR \u03b2-chain repertoire analysis from thoracic tumour RNA-seq and ICI-associated cardiac immunotoxicity"],"prefix":"10.3389","volume":"17","author":[{"given":"Xu","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Cardiovascular Surgery, Henan Provincial Chest Hospital","place":["Zhengzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaojun","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Cardiovascular Surgery, Henan Provincial Chest Hospital","place":["Zhengzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuaifei","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Cardiovascular Surgery, Henan Provincial Chest Hospital","place":["Zhengzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiquan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Cardiovascular Surgery, Henan Provincial Chest Hospital","place":["Zhengzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Cardiovascular Surgery, Henan Provincial Chest Hospital","place":["Zhengzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenwei","family":"Ge","sequence":"additional","affiliation":[{"name":"Department of Cardiovascular Surgery, Henan Provincial Chest Hospital","place":["Zhengzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.21417\/b7z59d","article-title":"Pd-1 blockade induces responses by inhibiting adaptive immune resistance","volume":"515","author":"Tumeh","year":"2014","journal-title":"Nature"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1056\/nejmoa1716078","article-title":"Neoadjuvant pd-1 blockade in resectable lung cancer","volume":"378","author":"Forde","year":"2018","journal-title":"N Engl J Med"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1056\/nejmoa1801946","article-title":"Nivolumab plus ipilimumab in lung cancer with a high tumor mutational burden","volume":"378","author":"Hellmann","year":"2018","journal-title":"N Engl J Med"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1056\/nejmoa1606774","article-title":"Pembrolizumab versus chemotherapy for pd-l1-positive non-small-cell lung cancer","volume":"375","author":"Reck","year":"2016","journal-title":"N Engl J Med"},{"key":"B5","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1016\/j.cell.2017.09.028","article-title":"Tumor and microenvironment evolution during immunotherapy with nivolumab","volume":"171","author":"Riaz","year":"2017","journal-title":"Cell"},{"key":"B6","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s40425-015-0070-4","article-title":"Peripheral t cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma","volume":"3","author":"Postow","year":"2015","journal-title":"J Immunother Cancer"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.ccr-13-2648","article-title":"Ctla4 blockade broadens the peripheral t-cell receptor repertoire","volume":"20","author":"Robert","year":"2014","journal-title":"Clin Cancer Res"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.122092","article-title":"T cell receptor repertoire features associated with survival in immunotherapy-treated pancreatic ductal adenocarcinoma","volume":"3","author":"Hopkins","year":"2018","journal-title":"JCI Insight"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.21417\/b7mg68","article-title":"Contribution of systemic and somatic factors to clinical response and resistance to pd-l1 blockade in urothelial cancer: an exploratory multi-omic analysis","volume":"14","author":"Snyder","year":"2017","journal-title":"PloS Med"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.21417\/sv2020nm","article-title":"Immune-awakening revealed by peripheral t cell dynamics after one cycle of immunotherapy","volume":"1","author":"Valpione","year":"2020","journal-title":"Nat Cancer"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1056\/nejmoa2032125","article-title":"Adjuvant nivolumab in resected esophageal or gastroesophageal junction cancer","volume":"384","author":"Kelly","year":"2021","journal-title":"N Engl J Med"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1111\/cas.14541","article-title":"Tumor immune microenvironment and immune checkpoint inhibitors in esophageal squamous cell carcinoma","volume":"111","author":"Baba","year":"2020","journal-title":"Cancer Sci"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.799455","article-title":"Therapeutic implications of tumor microenvironment in lung cancer: focus on immune checkpoint blockade","volume":"12","author":"Genova","year":"2021","journal-title":"Front Immunol"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1056\/nejmoa1609214","article-title":"Fulminant myocarditis with combination immune checkpoint blockade","volume":"375","author":"Johnson","year":"2016","journal-title":"N Engl J Med"},{"key":"B15","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1016\/s0140-6736(18)30533-6","article-title":"Increased reporting of fatal immune checkpoint inhibitor-associated myocarditis","volume":"391","author":"Moslehi","year":"2018","journal-title":"Lancet"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1016\/s0735-1097(18)31240-3","article-title":"Myocarditis in patients treated with immune checkpoint inhibitors","volume":"71","author":"Mahmood","year":"2018","journal-title":"J Am Coll Cardiol"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1016\/s1470-2045(18)30608-9","article-title":"Cardiovascular toxicities associated with immune checkpoint inhibitors: an observational, retrospective, pharmacovigilance study","volume":"19","author":"Salem","year":"2018","journal-title":"Lancet Oncol"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1161\/circulationaha.121.056730","article-title":"Identification of pathogenic immune cell subsets associated with checkpoint inhibitor-induced myocarditis","volume":"146","author":"Zhu","year":"2022","journal-title":"Circulation"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2555","article-title":"Mitcr: software for t-cell receptor sequencing data analysis","volume":"10","author":"Bolotin","year":"2013","journal-title":"Nat Methods"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201242517","article-title":"Next generation sequencing for tcr repertoire profiling: platform-specific features and correction algorithms","volume":"42","author":"Bolotin","year":"2012","journal-title":"Eur J Immunol"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3364","article-title":"Mixcr: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat Methods"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw526","article-title":"Assembly-based inference of b-cell receptor repertoires from short read rna sequencing data with v'djer","volume":"32","author":"Mose","year":"2016","journal-title":"Bioinformatics"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.21417\/b7301w","article-title":"Landscape of tumor-infiltrating t cell repertoire of human cancers","volume":"48","author":"Li","year":"2016","journal-title":"Nat Genet"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa432","article-title":"An ultra-sensitive t-cell receptor detection method for tcr-seq and rna-seq data","volume":"36","author":"Chen","year":"2020","journal-title":"Bioinformatics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"3126","DOI":"10.1038\/s41467-020-16857-7","article-title":"Profiling immunoglobulin repertoires across multiple human tissues using rna sequencing","volume":"11","author":"Mandric","year":"2020","journal-title":"Nat Commun"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01142-2","article-title":"Trust4: immune repertoire reconstruction from bulk and single-cell rna-seq data","volume":"18","author":"Song","year":"2021","journal-title":"Nat Methods"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3979","article-title":"Antigen receptor repertoire profiling from rna-seq data","volume":"35","author":"Bolotin","year":"2017","journal-title":"Nat Biotechnol"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad220","article-title":"Rigorous benchmarking of t-cell receptor repertoire profiling methods for cancer rna sequencing","volume":"24","author":"Peng","year":"2023","journal-title":"Brief Bioinform"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx760","article-title":"Vdjdb: a curated database of t-cell receptor sequences with known antigen specificity","volume":"46","author":"Shugay","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx286","article-title":"Mcpas-tcr: a manually curated catalogue of pathology-associated t cell receptor sequences","volume":"33","author":"Tickotsky","year":"2017","journal-title":"Bioinformatics"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1006","article-title":"The immune epitope database (iedb): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa796","article-title":"Tcrdb: a comprehensive database for t-cell receptor sequences with powerful search function","volume":"49","author":"Chen","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"B33","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/bioinformatics\/btz474","article-title":"Arcashla: high-resolution hla typing from rnaseq","volume":"36","author":"Orenbuch","year":"2020","journal-title":"Bioinformatics"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu548","article-title":"Optitype: precision hla typing from next-generation sequencing data","volume":"30","author":"Szolek","year":"2014","journal-title":"Bioinformatics"},{"key":"B35","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btz235","article-title":"Hla*la \u2014 hla typing from linearly projected graph alignments","volume":"35","author":"Dilthey","year":"2019","journal-title":"Bioinformatics"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0130-2","article-title":"Bystander cd8+ t cells are abundant and phenotypically distinct in human tumour infiltrates","volume":"557","author":"Simoni","year":"2018","journal-title":"Nature"},{"key":"B37","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/s41591-018-0266-5","article-title":"Low and variable tumor reactivity of the intratumoral tcr repertoire in human cancers","volume":"25","author":"Scheper","year":"2019","journal-title":"Nat Med"},{"key":"B38","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41467-019-08534-1","article-title":"Virus-specific memory t cells populate tumors and can be repurposed for tumor immunotherapy","volume":"10","author":"Rosato","year":"2019","journal-title":"Nat Commun"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1601064","article-title":"Virus-specific cd8+ t cells infiltrate melanoma lesions and retain function independently of pd-1 expression","volume":"198","author":"Erkes","year":"2017","journal-title":"J Immunol"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1126\/science.abe6474","article-title":"Pan-cancer single-cell landscape of tumor-infiltrating t cells","volume":"374","author":"Zheng","year":"2021","journal-title":"Science"},{"key":"B41","doi-asserted-by":"publisher","first-page":"2965","DOI":"10.1038\/s41467-021-23324-4","article-title":"Interpretation of t cell states from single-cell transcriptomics data using reference atlases","volume":"12","author":"Andreatta","year":"2021","journal-title":"Nat Commun"},{"key":"B42","doi-asserted-by":"publisher","first-page":"6268","DOI":"10.1038\/s41467-020-20019-0","article-title":"Immune suppressive landscape in the human esophageal squamous cell carcinoma microenvironment","volume":"11","author":"Zheng","year":"2020","journal-title":"Nat Commun"},{"key":"B43","doi-asserted-by":"publisher","first-page":"5291","DOI":"10.1038\/s41467-021-25539-x","article-title":"Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat Commun"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1067","article-title":"The european nucleotide archive in 2023","volume":"52","author":"Yuan","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"B46","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1145\/584091.584093","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst Tech J"},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.2307\/1934352","article-title":"Diversity and evenness: a unifying notation and its consequences","volume":"54","author":"Hill","year":"1973","journal-title":"Ecology"},{"key":"B48","article-title":"Nonparametric estimation of the number of classes in a population","volume":"11","author":"Chao","year":"1984","journal-title":"Scand J Stat"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1038\/163688a0","article-title":"Measurement of diversity","volume":"163","author":"Simpson","year":"1949","journal-title":"Nature"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1016\/0022-5193(67)90048-3","article-title":"The measurement of diversity in different types of biological collections","volume":"13","author":"Pielou","year":"1966","journal-title":"J Theor Biol"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1038\/s12276-020-00493-8","article-title":"Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer","volume":"52","author":"Cho","year":"2020","journal-title":"Exp Mol Med"},{"key":"B52","doi-asserted-by":"publisher","first-page":"4278","DOI":"10.1038\/s41467-019-12159-9","article-title":"DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load","volume":"10","author":"Jung","year":"2019","journal-title":"Nat Commun"},{"key":"B53","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1038\/s41419-022-05057-4","article-title":"Single-cell profiling of immune cells after neoadjuvant pembrolizumab and chemotherapy in IIIA non-small cell lung cancer (NSCLC)","volume":"13","author":"Hui","year":"2022","journal-title":"Cell Death Dis"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1038\/nature22976","article-title":"Identifying specificity groups in the T cell receptor repertoire","volume":"547","author":"Glanville","year":"2017","journal-title":"Nature"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0505-4","article-title":"Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening","volume":"38","author":"Huang","year":"2020","journal-title":"Nat Biotechnol"},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.7554\/elife.68605","article-title":"TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs","volume":"10","author":"Mayer-Blackwell","year":"2021","journal-title":"Elife"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1200\/jco.2010.32.2537","article-title":"Tumor regression in patients with metastatic synovial cell sarcoma and melanoma using genetically engineered lymphocytes reactive with NY-ESO-1","volume":"29","author":"Robbins","year":"2011","journal-title":"J Clin Oncol"},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1126\/science.1129003","article-title":"Cancer regression in patients after transfer of genetically engineered lymphocytes","volume":"314","author":"Morgan","year":"2006","journal-title":"Science"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.ccr-11-1513","article-title":"Merkel cell polyomavirus-specific CD8+ and CD4+ T-cell responses identified in Merkel cell carcinomas and blood","volume":"17","author":"Iyer","year":"2011","journal-title":"Clin Cancer Res"},{"key":"B60","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in cancer immunotherapy","volume":"348","author":"Schumacher","year":"2015","journal-title":"Science"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1892720\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T11:00:32Z","timestamp":1788346832000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1892720\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,2]]},"references-count":60,"alternative-id":["10.3389\/fimmu.2026.1892720"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1892720","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,2]]},"article-number":"1892720"}}