Antibody Genetic Diversity within an African population

Abstract

Antibodies, also referred to as immunoglobulins, are a critical part of the adaptive immune response. They are produced through somatic recombination of immunoglobulin (IG) genes from genetically complex IG loci to form two chains - the heavy chain (IGH locus) and light chain (IGK and IGL loci). These highly variable IG loci contain extensive polymorphic diversity and structural variation; where insertion, deletion, and duplication events create copy number variation (CNV) in several IG genes. There is increasing evidence that genetic variation in antibody genes affects their expression, in addition to their affinity to bind antigens, and engage the broader immune system. In this thesis, we utilise transcriptomic and genomic techniques to characterise IG genetic diversity in a South African population. We examined the genes that encode the antigen binding site (variable genes: IGHV, IGKV, and IGLV), as well as those that interact with the broader immune system (constant genes: IGHG and IGHA). Chapter 1 examines the heavy chain variable (IGHV) genes, uncovering 53 novel alleles, including some with novel single nucleotide variants (SNVs) in the region of the gene that regulates antibody secretion. In addition to novel diversity, gene duplication was common in this African population, occurring in 18 genes of which ten are newly described. Furthermore, we provide evidence that duplication can enhance the expression of particular IGHV genes. In Chapter 2, we sequenced the IGHA and IGHG genes, that code for the IgA and IgG isotypes respectively. Genetic diversity in IGHA is poorly studied and here we report the addition of 26 novel alleles. While IGHG is more well-studied, this study provides an additional 29 novel genetic variants in this gene. The allelic variation uncovered for both of these genes resulted in protein variation that can affect how antibodies bind Fc receptors, enhancing or inhibiting effector functions, or altering the structural aspects of antibodies such as dimerisation. Chapter 3 examined the expressed light chain lambda and kappa (IGKV and IGLV) repertoires of three different populations (South Africa, Norway, and the United Kingdom). Despite significant genetic differences between these groups, the same limited set of light chain genes dominate the expressed repertoires of each group, with only five IGKV genes representing 50% of the expressed repertoire and only two IGLV genes accounting for between 20-50% of the repertoire. Overall, we report significant amounts of undiscovered genetic diversity in South African IG genes, uncovering 118 novel alleles across different IG genes. This variation can strongly affect the functional antibody repertoire. Understanding these dynamics will have implications for broader immunology and vaccinology, especially with the advent of germline targeting vaccine strategies for HIV and other pathogens. The work in this thesis serves as the foundation for further functional study of genetic IG variation.