Population genotyping of the germline immunoglobulin repertoire in AIDS-designated rhesus macaque breeding colonies

Emory University, Atlanta GA

Investigators

Linked publications, trials & patents

Abstract

PROJECT SUMMARY An urgent priority of contemporary HIV vaccine research is the development of strategies to elicit broadly neutralizing antibodies (bNAbs) capable of providing protection against diverse strains. Currently, some of the most promising vaccine strategies are those in which specific classes of germline immunoglobulin (IG) genes are targeted by immunogens and Ab evolution is directed by sequential immunization with a changing set of epitopes. As the early precursors of bNAbs have not yet acquired neutralization activity, a central metric to evaluate the success of candidate HIV vaccine immunogens is its ability to elicit bNAb precursors and induce somatic hypermutation (SHM). For this reason, the ability to accurately trace Ab evolution is a necessity for mechanistic studies of bNAb development and to ultimately judge the clinical potential of a candidate immunogen. Additionally, there is a growing appreciation for the fact that IG genetic polymorphism can directly contribute to the availability of bNAb precursors within the circulating repertoire, necessitating the inclusion of individual level IG germline gene and haplotype information; the value of these data have been demonstrated now in both human and animal model studies. The rhesus macaque (RM) model is a critical tool for the pre- clinical assessment of candidate HIV vaccines. However, despite recent improvements, the dearth of available sequence and haplotype information for the Ab-encoding IG loci of RM remains a barrier for optimal use of the model for HIV vaccine research. In our first iteration of this award, we generated long-read sequence assemblies of the IG loci with matching repertoire sequencing data for hundreds of Indian origin RMs, representing six different colonies, and shared these data with the community via novel public resources. Our initial data revealed that RM IG allelic and haplotype diversity is extensive at the population level, varying among animals both within and between colonies. The goal of this R24 renewal proposal is to build on the progress of our first award by characterizing IG haplotype diversity in an extended collection of AIDS designated RMs from U42- funded specific pathogen free colonies that serve major HIV vaccine stakeholders. This unique dataset will represent the largest collection of IG haplotypes, germline alleles, and expressed heavy and light chain Ab repertoires. With these data in hand, we will continue to optimize our existing bench protocols for improved efficiency and accuracy and develop novel analysis tools for expanding the integration of IG genetics directly into pre-clinical vaccine trials. Additionally, to make this resource broadly and readily accessible to the research community, we will leverage and augment existing repositories to: (i) create user-friendly resources that seamlessly feed into commonly used data workflows and software packages; and (ii) build novel data exploration tools that allow users to explore to explore these novel data types at the level of individual genomes and at population scale. Our development of resources and tools will be accompanied by the creation of online and in- person training modules and tutorials.