ArticleFrontiers in immunology2026
A reproducible pipeline for TCR β-chain repertoire analysis from thoracic tumour RNA-seq and ICI-associated cardiac immunotoxicity.
Article in Frontiers in immunology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Background: 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-J-spanning assembly is rarely audited at the cohort level for non-small-cell lung cancer (NSCLC) and oesophageal squamous-cell carcinoma (ESCC). Objective: We built a reproducible, openly-released pipeline for productive T-cell-receptor β-chain (TRB) repertoire reconstruction from public thoracic-tumour RNA-seq, and extended it to immune-checkpoint-inhibitor (ICI)-associated cardiac immunotoxicity. Methods: Four GEO cohorts (NSCLC and ESCC bulk RNA-seq) were assembled with TRUST4 under a transparent cohort-level QC rule (≥ 10% V+J assemblies on ≥ 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). Results: 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 < 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. Conclusion: 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.
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