High resolution genomic and epigenomic mapping of the human salivary gland

PROJECT SUMMARY A mechanistic and molecular examination of the differentiation programs and normal tissue homeostasis of the salivary glands (SG) is an important area of research since altered SG function is associated with multiple human disease conditions including Sjogren syndrome, cancer, and complications due to cancer chemo/radiation therapy. This necessitates an in-depth investigation of the complex ecosystem of SG that consists of a variety of epithelial and non-epithelial cell populations that cooperatively interact to facilitate SG function. The underlying molecular circuitry of the transcriptional and epigenomic gene-regulatory mechanisms that control SG biology, particularly as it pertains to individual cell types in the in vivo context of the human SG, however, is not very well-understood and thus presents a significant knowledge gap. Lack of this knowledge prevents a better understanding of principles of cell fate and lineage choices, cell-to-cell communication and transcriptional regulatory processes that are needed for guiding effective therapeutic interventions of human diseases. Our central hypothesis is that the establishment of the SG transcriptome, epigenome and gene regulatory networks is a dynamic process that results from reciprocal interactions between intracellular signaling pathways and the underlying hardwired genomic information of each cell-type. To test this hypothesis, three specific aims are proposed. Aim 1 is to generate single-cell RNA-sequencing (scRNA-seq), and scATAC-seq data from the same cells of the adult male and female SMG. The goals of Aim 2 are to use computational tools to define the cell fate trajectories and cell-to-cell communication systems that operate in the SG and identify crucial transcriptional regulators that define cell fate. Finally in Aim 3, the 3D chromatin state and the enhancer-promoter connectome map of the human SG will be established by HiChIP experiments. Such data will enable the establishment of the link between non-coding genetic variants and disease-associated genes that are relevant for disease such as Sjogren’s syndrome that primarily afflict the SG. This work is highly innovative and significant because our proposed use of cutting-edge technologies and sophisticated tools to examine fundamental transcriptional and epigenomic mechanisms of gene regulation and signaling pathways at a single cell resolution. Long term, such knowledge will substantially advance the fundamental understanding of SG biology and is anticipated to have a long-term impact on the treatment of complex genetic diseases of the SG.