Integrative single cell and spatial transcriptomics of salivary glands in Sjogren's syndrome

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ABSTRACT Sjögren’s syndrome (SS) is a complex autoimmune disorder that affects 2-3.1 million Americans and is distinguished by irreversible exocrine gland damage that often results in debilitating dryness in the mouth and eyes. Severe systemic manifestations may include neuropathies, lymphomas, and clinically significant fatigue leading to considerable disability and reduced quality of life. Although dysregulation of innate and adaptive immune cells undoubtedly plays a role in exocrine gland dysfunction, why salivary gland ductal cells are targeted and immune cell infiltrates form foci around these structures is poorly understood. Known genetic risk variants in SS have been mapped to loci involved in antigen presentation, interferon responses, T and B cell activation, cell migration pathways, and autoantibody production, however the cell types in which functional effects of these genes operate in SS are unknown. Our central hypothesis is that salivary gland epithelial cells contribute directly to aberrant focal immune cell infiltration through dysregulation of normal homeostatic pathways and that these interactions are driven by recently identified SS genetic risk variants. This project seeks to define gene expression patterns that differ between ductal cells with presence or absence of immune cell foci and determine if these differences vary between risk and non-risk SS genotypes. We will apply a recently described integrative approach that couples 10X Genomics-based single cell RNA-sequencing with Spatial Transcriptomics data, thus allowing cellular expression levels to be interpreted in the context of very precise tissue morphology. In Aim 1, we will define transcriptional signatures of ductal cells involved in SS by comparing gene expression patterns of ductal cells surrounded by immune foci with those that are not through intrasubject analyses of 25 SS patients. Baseline ductal cell expression patterns obtained for 25 age, gender and racially matched healthy controls will also be compared. In Aim 2, we will define specific salivary gland and immune cell subsets that are functionally affected by known SS-associated expression quantitative trait loci (eQTLs). Using the same datasets generated for Aim 1, transcript levels will be compared between carriers of risk and non-risk variants in eQTLs for genes previously associated with SS. These data will identify the specific salivary gland (e.g. ductal, acinar, myoepithelial) and immune cells (e.g. T, B, dendritic, natural killer, etc.) subsets that are functionally affected by SS risk variants. We will leverage the extensive infrastructure and multidisciplinary expertise developed through the Oklahoma Sjögren’s Syndrome Center of Research Translation to accomplish the successful execution of this project. These studies will provide unprecedented depth and breadth of new knowledge regarding cell- specific dysregulation of genes and pathways. This knowledge is essential for development of novel therapeutics that target the right genes, pathways and cells and block the interactions between the immune system and exocrine glands that are fundamental to the pathogenesis of this complex disease.