Building cellular maps and dissecting gene regulation of the human body in health and disease

The human adult intestinal system is a key and complex organ regulating overall health and homeostasis of the body. The small intestine and colon play many important roles, including promoting digestion, enabling immune surveillance, maintaining symbiotic relationships with microbiota, and supporting overall health. Many diseases, such as inflammatory bowel disease (IBD), affect millions of people worldwide and are a result of disruption of these key processes performed by the gut. Despite the increasing disease burden of gut-related illnesses, our understanding of intestinal organization, function and regulation remains relatively limited. Furthermore, our understanding of healthy gut function enables our study of and ability to treat aberrant states for example in IBD and colorectal cancer. In our three major studies, we map key cell compositions, gene regulatory networks, and spatial organization in both the healthy gut and in early colorectal cancer. In this dissertation, I describe the use of genomic technologies for these three areas of interest, starting with the healthy body and moving towards higher resolution single cell studies of the early onset of cancer. In Chapter 2, we build high resolution cellular maps of the healthy human intestine using single nuclear RNA, open chromatin, and spatial proteomic imaging technologies. Previous studies have mapped cell types using single cell RNA sequencing (scRNA-seq) and have cataloged cell types across the intestine. We extend this work by the spatial mapping of cells and proteins using CODEX (CO-Detection by indEXing) to characterize approximately 1.2 million cells spatially. This study fills major gaps in our existing knowledge of cell types and compositional changes throughout different regions of the intestinal tract and provides a healthy tissue dataset for the community to use to improve our broader understanding of gut pathologies and diseases. In Chapter 3, we investigate molecular changes that drive colorectal cancer formation and subsequent transformation using genomic, transcriptomic, proteomic, metabolomic and lipidomic datasets. In our study, we examine hundreds of heterogeneous precancerous polyps and adenocarcinomas from high-risk patients. Multiomic analyses revealed a dynamic choreography of thousands of molecular and cellular events that occur during early hyperplasia, dysplasia and cancer formation. In Chapter 4, we transition to characterizing cancer formation and progression at the single cell level. We generated single-cell chromatin accessibility profiles and single-nuclear transcriptomes from 1K--10K cells per sample for 48 polyps, 27 normal tissues, and 6 colorectal tumors (CRC) collected from patients with and without germline APC mutations. We observed that a large fraction of polyp and CRC cells exhibit a stem-like phenotype, and we define a continuum of epigenetic and transcriptional changes occurring in these stem-like cells as they progress from normal to CRC

Keywords: Genetics.
Advisor: Snyder Michael
Curtis Christina
Ford James M. (James Matthew)
Montgomery Stephen