PROJECT SUMMARY/ABSTRACT A comprehensive genome-wide map of DNA regulatory elements and gene expression in human cells is of critical importance for understanding how genomic variation impacts human health and disease. Since regulatory DNA elements are exceptionally cell type-, tissue-, and disease state-specific, a comprehensive catalog of these elements has been difficult to achieve. The overall mission of this IGVF Mapping Center is to create a high- quality, open-access, and single cell-resolution reference map of human regulatory elements and gene expression in immune cells during human development, across organ systems in healthy adults, and in tissues from diverse immune-related diseases. Our Mapping Center will leverage: (i) our recent advances in developing scalable and cost-efficient single-cell epigenome and multi-omic technologies to simultaneously map open chromatin sites, gene expression, intracellular and cell surface proteins, and clonal lineage tracing in each tissue sample, (ii) our prior technical improvements and application of these methods to primary tissues from humans, and (iii) our pre-existing human tissue biobank consisting of samples from more than 500 human individuals, 20 organ systems, and 15 disease conditions, consented for unrestricted access, genomic sequencing, and data sharing. In Specific Aim 1, we will work closely with the IGVF Consortium to establish cross-center plans for data generation, analyses, and effective coordination of sample access and sharing. In Specific Aim 2, we will generate a single-cell multi-omic atlas of immune cell types (and non-immune cells types, as determined with the IGVF) during development in early life, healthy aging, and across human organ systems. In Specific Aim 3, we will generate a single-cell multi-omic atlas in immune cell types from primary tissues in patients with autoimmunity, cancer, neurodegenerative disease, and infection. In Specific Aim 4, we will analyze regulatory sites and gene expression in the context of clonal differentiation trajectories inferred from mitochondrial lineage tracing and develop and maintain an integrated reference map of each datatype and tissue sample for the research community. Our Mapping Center, composed of 7 new investigators with extensive experience in single- cell genomic technologies and human disease analysis, will work closely with the IGVF to share technologies, resources, data, and tissue samples towards the shared goal of developing a comprehensive single-cell atlas of cell types, functional regulatory elements, and gene expression in humans.

PROJECT NARRATIVE A comprehensive genome-wide identification of cell type-specific gene regulatory elements and gene expression in human cells is of critical importance for understanding how genomic variation impacts human health and disease. We propose to develop an IGVF Mapping Center that utilizes our recent development of high- throughput genome-wide technologies to simultaneously map open chromatin sites, gene and protein expression, and clonal lineage tracing in single cells from human tissues during development, adult health, and several disease conditions, including cancer, neurodegeneration, infection, and autoimmunity. We will work closely with the IGVF Consortium to share technologies, resources, data, and human samples towards the goal of understanding the relationship between functional element-cell type associations and genome function.