Diversity in the preimmune immunoglobulin repertoire of SHR lines susceptible and resistant to end-organ injury

Abstract

We used next-generation sequencing to identify IGH genetic variation in two closely related hypertensive rat lines that differ in susceptibility to end-organ disease (SHR-A3 and SHR-B2). The two SHR lines differ extensively at the IGH locus from the rat reference genome sequence (RRGS) and from each other, creating 306 sequence unique IGH genes. Compared to IGH genes mapped in the RRGS, 98 are null gene alleles (31 are null in both SHR lines, 45 are null in SHR-A3 only, and 23 are null in SHR-B2 only). Of the 306 divergent gene sequences, 126 result in amino acid substitution and, among these, SHR-A3 and SHR-B2 differ from one another at the amino acid level in 96 segments. Twelve pseudogenes in the RRGS had changes displacing the stop codon and creating probable functional genes in either or both SHR-A3 and SHR-B2. A further 5 alleles that encoded functional RRGS genes or open reading frames were converted to pseudogenes in either or both SHR-A3 and SHR-B2. These studies reveal that the pre-immune immunoglobulin repertoire is highly divergent among SHR lines differing in end organ injury susceptibility and this may modify immune mechanisms in hypertensive renal injury.

Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity

“… 55 However, there are several examples demonstrating essential functions of IGHV germline-encoded variation in antigen specificity; for example, amino acids encoded by germline IGHV1-69 alleles have been shown to make important contributions to neutralizing antibody responses against influenza, hepatitis C and Middle East Respiratory Syndrome coronavirus. 10 , 56 , 57 A recent mapping effort in rates with two disease models of differing susceptibility to spontaneous hypertension revealed that the IGH region exhibited the highest sequence divergence genome-wide between these lines, 58 consistent with the results observed here. Whether increased genetic diversity in human IGHV is associated with a dominant role of the heavy chain in antibody function remains to be seen.…”

Hypertensive Renal Injury Is Associated With Gene Variation Affecting Immune Signaling

“…Our analysis of the whole genome sequences for the two SHR lines reveals that the IgH locus contains extensive variation between the two SHR lines, for SHR-B2 this is the most divergent region of the entire genome 20 . Variation at the IgH locus results in highly divergent serum levels of three of the four rat IgG subclasses and total serum IgG levels in SHR-A3.…”

“…Variation in the immunoglobulin heavy chain gene is very extensive and the complex, segmentally duplicated nature of this gene prevents a complete description of that variation here. In another manuscript we have completed an analysis of the variable, diversity, junctional and Fc gene segments of the IgH locus and the extensive divergence of the pre-immune immunoglobulin repertoire in these two rat lines 20 . Our findings for the other loci are summarized below and detailed in the Data Supplement.…”

“…It is further substantiated by the presence of extensive functional genetic variation, compared to SHR-B2, in the immunoglobulin heavy chain 8 . This variation in the IgH locus alters the pre-immune immunoglobulin repertoire (the germ-line encoded combinations of VDJ gene segments that provide initial interaction with antigen in the B cell lineage) 20 . IgH locus variation in SHR-A3 compared to SHR-B2 also determines large differences in serum immunoglobulin levels (and therefore Fc receptor ligand concentrations) and disrupts some IgG-Fc receptor interactions 8 .…”

Identification of subject-specific immunoglobulin alleles from expressed repertoire sequencing data

“…However, such IgGRdbs may be sparse or non-existent for certain species; IMGT/GENE-DB has only a single IgGRdb IGHV allele for most genes in mouse, and only a single allele for all genes in rat and rhesus macaque. Nevertheless, IGHV variation was observed in all of these species (for example, Mouse [24,25], Rat [26], Macaque [27,28]). In principle, the deep coverage of repertoire sequencing data could obviate the need for IgGRdbs by inferring the set of alleles for each subject based solely on the observed set of rearranged sequences.…”