Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities

Abstract

Every T cell receptor (TCR) repertoire is shaped by a complex probabilistic tangle of genetically determined biases and immune exposures. T cells combine a random V(D)J recombination process with a selection process to generate highly diverse and functional TCRs. The extent to which an individual’s genetic background is associated with their resulting TCR repertoire diversity has yet to be fully explored. Using a previously published repertoire sequencing dataset paired with high-resolution genome-wide genotyping from a large human cohort, we infer specific genetic loci associated with V(D)J recombination probabilities using genome-wide association inference. We show that V(D)J gene usage profiles are associated with variation in the TCRB locus and, specifically for the functional TCR repertoire, variation in the major histocompatibility complex locus. Further, we identify specific variations in the genes encoding the Artemis protein and the TdT protein to be associated with biasing junctional nucleotide deletion and N-insertion, respectively. These results refine our understanding of genetically-determined TCR repertoire biases by confirming and extending previous studies on the genetic determinants of V(D)J gene usage and providing the first examples of trans genetic variants which are associated with modifying junctional diversity. Together, these insights lay the groundwork for further explorations into how immune responses vary between individuals.

Statistical inference reveals the role of length, breathing, and nucleotide identity in V(D)J nucleotide trimming

“…We show that this model has high predictive accuracy for V- and J-gene sequences from an independent TCR β -sequencing data set, and also extends well to TCR α , TCR γ , and IGH sequences. Further, we demonstrate that genetic variations within the gene encoding the Artemis protein that were previously-identified as being associated with increasing the extent of trimming ( Russell et al, 2022 ) are also associated with changes in several mechanistic coefficients.…”

“…To explore this, we worked with paired SNP array and TCR β -immunosequencing data representing 611 of the original 666 individuals in the V-gene training data set used here. Our previous work ( Russell et al, 2022 ) used data from only 398 of these individuals, however, the conclusions of that paper held when using this expanded group of 611 individuals in the analysis. With these data, we asked whether the inferred coefficients from the V-gene-specific 1×2 motif + two-side base-count beyond model varied significantly in the context of the non-coding Artemis-locus SNP (rs41298872) that was found to be most strongly associated with increasing the extent of V-gene trimming in our previous work ( Russell et al, 2022 ).…”

“…Using a subset of the V-gene training data set used here, we previously identified a set of single nucleotide polymorphisms (SNPs) within the gene encoding the Artemis protein that are associated with increasing the extent of V-and J-gene trimming (Russell et al, 2022) Figure 5. Inferred SNP-parameter-interaction coefficients from fitting the 1x2 motif + two-side base-count beyond SNP interaction model.…”

“…The most dominant hairpin opening position leads to a single-stranded 3’ overhang that is 4 nucleotides in length (2 nucleotides of which are P-nucleotides) ( Lu et al, 2007 ). From here, nucleotides may be deleted from each gene end through an incompletely-understood mechanism suggested to involve Artemis ( Feeney et al, 1994 ; Nadel and Feeney, 1995, 1997 ; Jackson et al, 2004 ; Gu et al, 2010 ; Chang et al, 2015 ; Chang and Lieber, 2016 ; Zhao et al, 2020 ; Russell et al, 2022 ). This nucleotide trimming can remove traces of P-nucleotides ( Gauss and Lieber, 1996 ; Srivastava and Robins, 2012 ).…”

Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta and beta loci

“…Haplotyping and genotyping of the MHC/HLA loci is standard practice in many immune studies, thus, our method provides an opportunity to similarly operationalize genotyping of TR genes, including efforts to do this in conjunction with MHC/HLA typing to better understand genetic impacts on the function of TCR-MHC interactions. Additionally, partnering our method with adaptive immune receptor repertoire (AIRR) sequencing can facilitate the identification of TR variants that impact the composition of the TCR repertoire (9,40), as well as cross-talk between B and T cells, e.g. T cell dependent B cell activation.…”