V(D)J Recombinase-Mediated Processing of Coding Junctions at Cryptic Recombination Signal Sequences in Peripheral T Cells during Human Development

Abstract

V(D)J recombinase mediates rearrangements at immune loci and cryptic recombination signal sequences (cRSS), resulting in a variety of genomic rearrangements in normal lymphocytes and leukemic cells from children and adults. The frequency at which these rearrangements occur and their potential pathologic consequences are developmentally dependent. To gain insight into V(D)J recombinase-mediated events during human development, we investigated 265 coding junctions associated with cRSS sites at the hypoxanthine-guanine phosphoribosyltransferase (HPRT) locus in peripheral T cells from 111 children during the late stages of fetal development through early adolescence. We observed a number of specific V(D)J recombinase processing features that were both age and gender dependent. In particular, TdT-mediated nucleotide insertions varied depending on age and gender, including percentage of coding junctions containing N-nucleotide inserts, predominance of GC nucleotides, and presence of inverted repeats (P r -nucleotides) at processed coding ends. In addition, the extent of exonucleolytic processing of coding ends was inversely related to age. We also observed a coding-partner-dependent difference in exonucleolytic processing and an age-specific difference in the subtypes of V(D)J-mediated events. We investigated these age-and gender-specific differences with recombination signal information content analysis of the cRSS sites in the human HPRT locus to gain insight into the mechanisms mediating these developmentally specific V(D)J recombinase-mediated rearrangements in humans.

The Ontogeny and Fate of NK Cells Marked by Permanent DNA Rearrangements

“…Cryptic recombination signal sequences are distributed every 40 -50 bp throughout the genome, including both immune and nonimmune loci (39), and it is becoming increasingly clear that rag-mediated rearrangements at these cryptic sites can occur in the absence of gross translocations. Nonpathogenic rearrangements have been most extensively studied at the HPRT locus in which rag activity is associated with three different deletions in T cells from healthy newborns and young adults (40,41). V(D)J rearrangements at cryptic recombination signal sequences are also detectable in ␥-satellite DNA, a highly repetitive DNA element encompassing ϳ6% of the mouse genome (42).…”

V(D)J Recombinase-Mediated TCR β Locus Gene Usage and Coding Joint Processing in Peripheral T Cells during Perinatal and Pediatric Development

“…We used these samples to compare coding joint processing at selected TCRb locus RSS with that previously observed in the same populations at a nonimmune cRSS at the HPRT locus (14). Mutant HPRT T cell clones were isolated using the HPRT T cell-cloning assay that selects for individual T cells that have acquired an in vivo mutation resulting in a loss of HPRT activity, as previously described (17,18).…”

“…V(D)J recombinase can also mediate rearrangements at nonimmune or "cryptic" RSS in normal and leukemic human peripheral T cells. We previously demonstrated age-and gender-specific developmental differences in V(D)J coding joint processing at cryptic RSS within the HPRT locus in peripheral T cells from healthy children (Murray et al 2006. J. Immunol.…”

“…We previously showed age and gender developmental differences in V(D)J recombinase-mediated coding joint processing at unselected nonimmune cryptic RSS (cRSS) sites at the HPRT locus (14) that results in the deletion of exons 2 and 3 (15,16). In this study, we examine coding joint gene usage and processing of V(D) J-mediated immune TCRb locus rearrangements at RSS in HPRT mutant peripheral T cells from the same study population to determine whether TCRb gene usage and coding joint processing at immune RSS also show evidence for developmental age and gender V(D)J recombinase specificity.…”

A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4+T cell receptor repertoire clonality

“…Studies by Murray et al have demonstrated genderspecific V(D)J recombinase-mediated TCRb gene usage and coding joint processing in human development that demonstrate direct effects on TCR diversity, though these studies were conducted on healthy children at a maximum age of 12.5 y. 63,64 In this study, these gender-specific differences in clonality did not occur across compartments -an observation that did occur with age-related associations, thus the strength of this gender-specific observation in NSCLC needs to be further evaluated in subsequent studies.…”