Level of human TCRBV3S1 (V beta 3) expression correlates with allelic polymorphism in the spacer region of the recombination signal sequence.

Abstract

SummaryOne of the causes of variations in the expressed human T cell receptor (TCR) BV (V~) repertoire is genetic variation in the germline DNA. Herein evidence is provided that allelic polymorphism may affect recombination frequency for a specific V gene. Two alleles of the TCR BV3 differ only at a single nucleotide position (C/T) within the 23-bp spacer region of the recombination signal sequence. These alleles are associated with variable percentages of BV3 cells in the peripheral blood, as shown in families and in unrelated normal donors. Individuals homozygous for allele 2 have a mean of 8.1% BV3 cells, heterozygous individuals have a mean of 4.7% BV3 cells, and homozygotes for allele 1 have a mean of 1.2% BV3 cells in CD3 § CD4 + peripheral blood T cells. Since the correlation is tight in unrelated individuals and other genetic differences were not found in the vicinity of BV3, we suggest that the spacer region sequence itself modifies recombination efficiency. This allelic system provides an example of a novel mechanism by which c/s-acting genetic elements may affect recombination in a natural in vivo system. T he vast diversity of TCR and immunoglobulins is created primarily by V(D)J recombination in maturing lymphocytes. As a result of this theoretically random process, a repertoire of highly diverse TCR is generated (1), but the observed repertoire in mature lymphocytes is skewed because of both genetic and environmental factors. Genetic control of the TCR repertoire is apparent because of highly similar profiles of TCR, Vot and V~ usage among monozygotic twins as opposed to unrelated individuals (2-6). Genes that influence the TCR repertoire include the MHC (2) and the TCR genes themselves. MHC genes mold the TCR repertoire because of recognition of peptide Ag in the context of MHC molecules. Thus, certain T cell subsets may be positively or negatively selected in the context of one MHC allele but not another.TCIL V gene segments are deleted in certain mouse haplotypes (7). Genomic deletions in the TCRBV locus also exist in humans (8) and directly affect the number of genomic V gene segments (9). In addition, a number of aUelic polymorphisms of TCR V gene exons have been described. Some of these result in null alleles (10, 11) and others result in different amino acid sequences at putative Ag/MHC or SAG-reactive sites (12)(13)(14)(15). It is also possible that TCR gene elements fail to rearrange efficiently because of structural constraints on some aspect of the recombinase machinery.This report describes a new type of polymorphism that can shape the TCR repertoire. AUelic variation in the TCRBV3 recombination signal sequence (R.SS) is associated with the level of BV3 gene segment utilization in the peripheral blood (formerly V~3, the new WHO-IUSIS recommended nomenclature is used throughout this manuscript. Bull. WHO 71:113-115, 1993). Variable expression of BV3 was first mapped to the TCRB locus in family studies and then shown to correlate with allelic variants of the BV3 RSS in unrelated individua...

Unequal VH Gene Rearrangement Frequency Within the Large VH7183 Gene Family Is Not Due to Recombination Signal Sequence Variation, and Mapping of the Genes Shows a Bias of Rearrangement Based on Chromosomal Location

“…However, for the VA2 genes we showed that two alleles differing at one position in the heptamer rearrange at ϳ5-fold different frequencies in vivo and in vitro, and the alleles presumably are identical in chromosomal location and sequence (only three changes were found in 700 bp) strongly suggesting that indeed the RSS was responsible for the differences in rearrangement frequencies in vivo vs in vitro (21). Similarly, two alleles of V␤3 have been shown to differ drastically in their representation in the peripheral repertoire (8.1 vs 1.2%), and the only difference in their sequence is 1 bp in the spacer sequence (34). Thus, we believe that these two latter cases of allelic differences in which chromosomal position is not a factor coupled with the extensive in vitro recombination substrate data demonstrate that RSS differences can indeed significantly affect rearrangement frequencies (24,31,35).…”

Contribution of TCR-β Locus and HLA to the Shape of the Mature Human Vβ Repertoire

“…However, Chen et al (30) showed that many of the differences were leveled off by rearrangement and/or ␤-selection, suggesting that other factors change the V␤ usage at different stages during thymocyte development, the most likely candidate being differences in RSS heptamer, nonamer, and 23-bp spacer region (32). Posnett et al (22) have shown that a SNP in the 23-bp spacer region of V␤28 strongly correlated with the usage of this V␤ by T cells. We have confirmed this in our data set.…”

“…The TCR-␤ locus contains 284 single nucleotide polymorphisms (SNPs) 3 which may affect V␤ usage by CD4 ϩ and CD8 ϩ T cells as has been established for V␤28 (22). The allelic effect was determined in adult and neonatal T cells by calculating the Spearman correlation coefficient between the V␤ repertoire in CD4 ϩ and CD8 ϩ T cells of the same individual.…”

Unifying model for molecular determinants of the preselection Vβ repertoire

“…Despite general conservation of the heptamer-spacer-nonamer configuration, RAG-1/2 substrates exhibit substantial variation compared with the consensus RSS sequence: (CACAGTG)-12-or 23-bp spacer-(ACAAAAACC) (32,33). In vivo replacement or natural variants of RSSs can alter the use of gene segments, including those within the Tcrb recombination center (34)(35)(36). In vitro studies using plasmid substrates have defined the effects of positional substitutions within the consensus RSS on recombination efficiency (32,37,38).…”