Type 1 Diabetes (T1D) is a complex autoimmune disease that commonly afflicts children. We need to identify the underlying pathogenic cellular pathways in order to develop effective therapies for this disease. Human genetics has the potential to provide an unbiased view of the causative disease mechanisms. T1D already has been the subject of intensive genetic investigations, including genome-wide association studies (GWAS) that have uncovered dozens of risk loci. However, mechanistic understanding of these risk loci has been a challenge because the vast majority falls outside of genes, in non-coding regions of the genome. In contrast to protein- coding regions of the genome where we understand the amino acid code, we still do not have a clear framework to understand how non-coding genome variants alter cell function and contribute to disease. To learn how DNA variation throughout the genome affects cellular pathways and contributes to T1D, we now need a deeper understanding of the function of non-coding genome elements in the specific cell types that drive the pathology. We propose an integrated strategy to pinpoint the molecular and cellular effects of T1D risk variants. We will perform a population-based study of how natural genetic variation alters the transcriptional and epigenomic state of human immune cells in vivo. We have unique access to human T subsets sorted directly out of the pancreatic draining lymph nodes of organ donors with and without T1D. We will identify specific gene regulatory circuits in T cells that are disrupted as a result of T1D risk variants at the site of inflammation. These studies will be complemented by rigorous functional testing of candidate causal variants in primary human and mouse cells. We will leverage our recent genome editing advances to alter specific disease-associated genome sequences and directly test effects on gene regulation, cell differentiation and murine models of T1D. We will generate isogenic edited primary human and mouse T cells to validate mechanistic effects of T1D variants. To test the hypothesis that a subset of T1D variants impairs beta cells, we will also edit human ES cells and assess direct effects on in vitro beta cell differentiation and function. Understanding how causal non-coding T1D risk variants disrupt key gene programs in human cells has potential to accelerate development of targeted therapeutic approaches.
Much of the genetic risk for T1D resides in the vast stretches of human genome that do not contain protein- encoding genes. We recently developed pinpointed specific sites of genetic variation that confer risk of T1D diseases to genomic elements with putative roles in gene regulation in T cells and beta cells. We now propose rigorous functional testing of how naturally occurring T1D risk variants and variants experimentally introduced by CRISPR-Cas9 cause impaired gene expression, chromatin state and cellular function in human immune cells and beta cells.
| Roth, Theodore L; Puig-Saus, Cristina; Yu, Ruby et al. (2018) Reprogramming human T cell function and specificity with non-viral genome targeting. Nature 559:405-409 |
| Simeonov, Dimitre R; Gowen, Benjamin G; Boontanrart, Mandy et al. (2017) Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature 549:111-115 |
