Frame-specific depletion of the TRBV23-1 pseudogene in human TCR repertoires: Quantitative evidence and possible biological explanations

Abstract

V(D)J recombination generates T cell receptor diversity, but most rearrangements introduce frameshifts or premature termination codons that prevent formation of functional receptors. A quantitative model was developed to estimate the expected ratio of in-frame to out-of-frame arrangements. A statistical model was used to identify repertoires with anomalous frame usage. Applied to more than 6,000 repertoires from nine cohorts, the statistical model identified 14 repertoires with frame-dependent depletion in rearrangements involving the pseudogene TRBV23-1. The depletion is inconsistent with sequencing artifacts, contamination, or conventional thymic selection, but may reflect a biological process such as HLA class I-mediated targeting of TRBV23-1-derived peptides. RNA-seq analysis shows frame-specific RNA levels correlated with depletion rates, supporting the possibility of a post-transcriptional regulatory contribution. These observations suggest that pseudogenes, long considered inert, may influence immune repertoire structure. The findings establish a robust statistical signal of non-random TRBV23-1 depletion and provide testable mechanistic hypotheses for future validation.