Common variable immunodeficiency (CVID) is a primary disease of germinal center (GC) dysfunction, yet most CVID mechanistic investigations have utilized patient blood samples, which do not contain bona fide GC cells. Similarly, genome-wide association studies (GWAS) of CVID patients have identified many disease-associated single nucleotide polymorphisms (SNPs), yet most lie in non-coding DNA and are of unclear relevance to disease pathogenesis. The long-range goal of the proposed work is to determine the full genetic basis of CVID. The objective of this grant is to determine which non-coding regions of DNA contribute to GC dysfunction. The working hypothesis is that CVID GWAS SNPs point to important non-coding genomic regions that interact with promoters of genes key to GC lymphocyte function. Further, genetic variation altering gene promoter interactions, or damage to these genes themselves, will lead to GC dysfunction and eventually the symptoms of CVID. Our rationale is that identifying gene promoter interactions critical to GC homeostasis will provide new diagnostic and therapeutic opportunities for patients suffering from diseases of GC dysfunction including, but not limited to, CVID.
Our specific aims will test the following hypotheses:
(Aim 1) CVID GWAS associated regions euchromatically interact with gene promoters in T follicular helper cells (Tfh) and/or follicular B cells (FO B cells);
(Aim 2) these interactions influence gene expression;
(Aim 3) non-coding variants altering gene expression or variants damaging coding genes are enriched in CVID patients and that rhese variants alter Tfh and FO B cell function. The contribution is significant because cataloguing the genes and gene promoter contacts vital to GC homeostasis/dysfunction will offer new disease discovery opportunities and provide new molecules to target with personalized therapies. The proposed work is innovative because we are reinterpreting published GWAS with a suite of interlocking genome-scale technologies capable of annotating individual SNPs with overlapping layers of cell type-specific epigenetic information including promoter contacts, chromatin availability and gene expression. Further, we are verifying our findings in CVID exomes and genomes, with genetically modified cell-lines, with patient lymph nodes and in co-cultures that recapitulate key transcriptional features of the GC environment.
PROJECT NARRITIVE: Common variable immune deficiency (CVID) patients are susceptible to death from infectious and/or autoimmune diseases because their lymph nodes cannot generate the right types of antibodies. The reasons for CVID antibody dysfunction are unknown, in part, because lymph nodes from patients are difficult to obtain and study. By determining how CVID genes interact with other parts of their DNA in lymph node and lymph node-like cells, we will identify the underlying genetic causes of CVID and determine what types of therapies will be most effective in treating CVID patient symptoms.
