Characterization of cell type-specific enhancers in the human pancreas using a massively parallel reporter assay

FARE Award Winner

Authors

• RC Greochel
• AC Liu
• C Liu
• DS Knopman
• S Koton
• AM Kucharska-Newton
• PL Lutsey
• TH Mosley Jr
• P Palta
• AR Sharrett
• KA Walker
• DF Wong
• RF Gottesman

Abstract

Accurate control of cell identity is integral to maintaining healthy, functional systems, and deviations can lead to developmental defects and diseases, including cancer. Therefore, it is crucial to understand the regulatory mechanisms that drive cell type-specific functions. Enhancers are non-coding genetic elements that regulate transcription and are overwhelmingly responsible for cell type-specific gene expression. Additionally, over 80% of disease-associated genetic variants map to enhancer regions, emphasizing the need to understand their function. While nearly one million candidate enhancer regions have been identified, the functional characterization of enhancers has been a daunting challenge, particularly at genome-scale. The pancreas is a vital organ composed of multiple cell types. Our lab has identified candidate enhancer elements unique to the five major human pancreas cell types, and digital footprint analysis of chromatin accessibility data revealed that these regions are likely bound by cell type-specific transcription factors, underscoring the cell specificity. To systematically characterize the drivers of cell identity among the unique cell types, we are using a novel massively parallel reporter assay to quantify enhancer activity. We have prioritized candidate enhancers which contain differentially enriched transcription factor motifs, and those containing motifs of additional highly cell type-specific transcription factors. We have cloned thousands of candidate enhancers into lentiviral reporter libraries and are assessing activity of these elements in primary pancreas cells obtained from healthy donors. These results will yield the first functional enhancer map of human pancreas cells and advance our understanding of how these enhancers orchestrate the remarkable cell type-specific gene expression programs.

Scientific Focus Area: Genetics and Genomics

This page was last updated on Monday, September 25, 2023