Formation of ultralong DH regions through genomic rearrangement

Abstract

Background Cow antibodies are very unusual in having exceptionally long CDR H3 regions. The genetic basis for this length largely derives from long heavy chain diversity (DH) regions, with a single “ultralong” DH, IGHD8–2, encoding over 50 amino acids. Many bovine IGHD regions have sequence similarity but have several nucleotide repeating units that diversify their lengths. Genomically, most DH regions exist in three clusters that appear to have formed from DNA duplication events. However, the relationship between the genomic arrangement and long CDR lengths is unclear. Results The DH cluster containing IGHD8–2 underwent a rearrangement and deletion event in relation to the other clusters in the region corresponding to IGHD8–2, with possible fusion of two DH regions and expansion of short repeats to form the ultralong IGHD8–2 gene. Conclusions Length heterogeneity within DH regions is a unique evolutionary genomic mechanism to create immune diversity, including formation of ultralong CDR H3 regions.

Evolution of immunogenetic components encoding ultralong CDR H3

“…The 148-bp (48 amino acid) IGHD gene segment in zebu, a subspecies of Bos taurus , was nearly identical to the ultralong-encoding IGHD in cattle, sharing 92% amino acid (93% nucleotide) identity. The ultralong IGHD sequence for wild yak was 139-bp in length and encoded 45 amino acids (Smider and Smider 2020 ) and shared 75% amino acid (81% nucleotide) identity with cattle, while the gayal genome contained a 148-bp (48 amino acid) IGHD but was less conserved (64% amino acid/78% nucleotide identity). Finally, the bison genome contained one IGHD gene segment (IGHD8-2) that was similar in both sequence length and identity to the ultralong-encoding IGHD8-2 of cattle, with a sequence length of 139-bp encoding 45 amino acids.…”

“…To date, studies have reported expressed ultralong-encoding IGHV or IGHD gene segments only in cattle and yak (Saini et al 1999 ; Smider and Smider 2020 ; Wang et al 2013 ; Wu et al 2023 ). Nucleotide BLASTs of cattle ultralong transcripts against all other Bovidae species produced hits only to transcripts containing conventional IGHV gene segments, indicating that either no other bovid species expresses ultralong V regions (including those species with an ultralong-encoding IGHV) or (more likely) there simply have not been enough studies generating these data in other species.…”

“…Within the knob, repetitive codons for glycine (GGT), tyrosine (TAT), and serine (AGT) residues can be somatically mutated to cysteine (TGT) with a single base change, and rearranged loci undergo extensive SHM within the sequences encoding knob domains, thereby altering the number of noncanonical cysteine residues within the knob (Wang et al 2013 ). The paired cysteines form disulfide bonds, designing unique loop patterns that ultimately shape the final paratope diversity (Deiss et al 2019 ; Di et al 2022 ; Haakenson et al 2019 , 2018 ; Smider and Smider 2020 ; Stanfield et al 2018 ). Finally, the end of IGHD8-2 encodes a pattern of alternating aromatic tyrosine residues (YxYxY) that (with the beginning of IGHJ2-4) forms the descending strand of the stalk domain and is critical for the integrity of the stalk structure.…”

“…For example, cattle immunized with stabilized HIV spike trimer protein generated broadly neutralizing ultralong antibodies against HIV (Sok et al 2017 ). While clinical applications progress, however, we are only just beginning to understand the genomic mechanisms that yielded ultralong-encoding IGHV and IGHD gene segments in the species that make them (Smider and Smider 2020 ; Warner Jenkins et al 2022 ). The evolutionary origin of these two gene segments—as well as any specific functional purpose of ultralong antibodies in cattle—remains unknown.…”

Benefits of immunoglobulin substitution in primary and secondary immunodeficiencies: Interim analysis of a prospective, long-term non-interventional study

“…Some guidelines [ 11 ] and publications [ 12 ] argue that treatment should be initiated with at least 0.4 g/kg and that the dose should then be adjusted according to the patient’s treatment needs. A recent study by Weide et al [ 13 ] showed that SID patients with IgG trough levels (7 g/L or more) had a significantly reduced incidence of all types of infections as well as less severe infections requiring antibiotic treatment, compared to patients with lower IgG levels (< 7 g/L). Furthermore, a meta-analysis [ 9 ] provided evidence that in SID patients the risk of pneumonia can be progressively reduced by higher trough IgG levels of up to at least 10 g/L, with a median IVIG dose administered of 0.5 g/kg body weight every 4 weeks.…”