00:00 "The Hidden Diversity of Antibody Heavy Chains: Implications for Autoantibody Mediated Disease". Easton Ford, University of Louisville, Graduate Student
Current methods in Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) resolve variable region sequences of antibody transcripts with minimal detailed resolution of the constant region (IGHC) therefore hindering characterization of the extent of IGHC diversity. The variable region of the antibody is critical for binding of antigens but does not mediate many downstream antibody effector functions. Here, we utilized novel immunogenomics tools that resolve complete antibody heavy chain (IGH) genotypes from sample-derived genomic DNA (gDNA), and single-molecule resolution of near Full-Length Antibody Heavy Chain Repertoires (FLAIRR-seq) to define the immunogenomic and repertoire profiles of individuals with Acetylcholine Receptor Myasthenia Gravis (AChR MG) with the aim of identifying the impact of IG variation on disease.
Sample gDNA and RNA were co-extracted and processed for either IGH genotyping, or FLAIRR-seq repertoire profiling from both AChR MG and healthy donor peripheral blood mononuclear cells. The resulting libraries were sequenced on the Sequel IIe platform. From preliminary profiling of the IGHC regions in AChR MG and HD samples, 20 out of 49 alleles (40%) across IGHC genes were completely novel compared to the IMGT database, highlighting the diversity of IGHC. Profiling of variable genes from an initial sample set revealed biased usage of IGHV1 genes in AChR MG IgG1 repertoires vs HDs. Interestingly, the IGHV1-69 gene previously found in autoreactive monoclonals isolated from AChR MG individuals was significantly upregulated in IgG1 repertoires when compared to HD. Collectively, these methods enable some of the first nucleotide-level resolution of IGHC genes and how genomic variation may influence B cell autoimmunity. Future studies will extend these analyses to larger cohorts and integrate data with functional autoantibody characterization to identify residue signatures associated with response to therapy, providing a path to precision treatment plans with higher chances of success.
14:37 "Full-length assembly and immunogenetic analysis of immunoglobulin and T cell receptor loci from Mauritian cynomolgus macaques". Chaim Schramm, NIH/NIAID/VRC, Staff Scientist
Cynomolgus macaques are frequently used as experimental models for vaccine design, yet immunogenomic data for this species has lagged behind what is available for rhesus macaques. To begin to address this deficit, we sequenced the genomes of 13 Mauritian cynomolgus macaques using a combination of Nanopore and PacBio HiFi technologies. Reads corresponding to the immunoglobulin (IG) and T cell receptor (TR) loci were extracted and assembled with Hifiasm. We developed ALIGaToR, a de novo annotation pipeline to identify V, D, J, and C genes in the resulting contigs. For the IGH locus, we recovered 10 full-length haplotypes ranging in length from 1.9-2.3 megabases. From these, we annotated a total of 212 functional V genes. While the majority of these genes were monoallelic in our data, we observed 14 V genes with 4 or more alleles present among the 10 haplotypes. Similar analyses were conducted for the IGK, IGL, TRA/D, and TRB loci, as well. As Mauritian cynomolgus macaques have restricted genetic diversity, these new haplotypes are expected to cover nearly all of the immunogenetic diversity in this important model species.
AIRR Community Meeting VII - Learnings and Perspectives
June 3-6, 2024
University of Porto, Porto, Portugal
www.antibodysociety.org/the-a...