Project Summary Autoimmune diseases are a family of over 80 chronic, disabling illnesses in which defects in the immune system leads the body to attack normal components (self antigens) of its own tissues. Autoimmune disease affects 14.7 ? 23.5 million people in the U.S. alone (5 ? 8%), making it one of the most common classes of human diseases. However, despite considerable research being devoted to understanding autoimmunity, a coherent explanation of the critical causative events that initiate the autoimmune response is still lacking. Familial clustering of autoimmune disease indicates that an increased risk of disease, a genetic predisposition, can be inherited. But even in settings in which risk is inherited, disease onset is found to occur after a variable delay, suggesting that additional stochastic processes are necessary to trigger disease onset. This phenomenon is reminiscent of what has been observed in cancer where a genetic predisposition can be inherited, and yet cancer develops only after somatic mutations in additional target genes occur. Thus, the goal of the project described in this proposal is to test the hypothesis that somatic mutations in genes that regulate immune tolerance are required to initiate autoimmunity, by performing single cell RNA-seq-based expression profiling and sequence analysis of pathogenic lymphocytes from multiple sclerosis (MS) patients. Although the inflammatory lesions found in the central nervous system (CNS) of MS patients include a complex mixture of T cells, B cells and macrophages, the presence of clonally-expanded, receptor-edited and somatically-mutated memory B cells that express brain-reactive antibodies in the cerebrospinal fluid (CSF), and the dramatic clinical response to B cell depletion therapy, suggest that autoreactive B cells play a critical role in MS pathology, and are therefore the focus of the proposed studies. Three specific aims are proposed: 1. Determine if pathogenic B cells in the CSF of MS patients carry somatic mutations in genes involved in regulating B cell tolerance, 2. Determine if pathogenic B cells in the CSF of MS patients exhibit altered transcriptional profiles either constitutively or in response to activating signals, and 3. Investigate the functional relevance of somatic mutations detected on tolerance-related signaling pathways. Through the genome-wide comparative analysis of mRNA sequence and expression data of single CSF B cells from MS patients we expect to determine if somatic mutations and their effects can be identified in pathogenic cells. We will also have developed a validated single cell RNA-seq methodology for the conduct of similar studies in other autoimmune disease and immune response settings. The development of advanced single cell genomic methodologies that will allow us to explore the potential role of somatic mutations and differential gene expression in the etiology of MS will be a real game changer. Evidence for a role for somatic mutations in MS etiology and/or pathology would completely change the way we view autoimmune disease development and would have broad implications for the development of alternative personalized treatment approaches. OMB No. 0925-0001/0002 (Rev. 08/12 Approved Through 8/31/2015) Page Continuation Format Page