Mapping inflammatory bowel disease variants to genes and functional phenotypes in human macrophages

Abstract Inflammatory Bowel Disease (IBD) is a complex genetic disorder marked by dysregulated gut immune responses to environmental factors, influenced by numerous genetic variants. Affecting over 0.7% of Americans and millions worldwide, IBD's genetic and molecular underpinnings remain incompletely understood. Although genome-wide association studies (GWAS) have successfully identified hundreds of IBD- associated loci, the prioritization of regulated genes and their functional relevance in disease-relevant cells remain unclear. This project seeks to fill these gaps by utilizing a large-scale CRISPRi Perturb-seq screen in primary human monocytes, a key cell type in IBD pathogenesis.The specific aims of this proposal are to: (1) elucidate the transcriptional consequences of IBD candidate genes in monocytes from diverse populations using a GWAS-guided Perturb-seq approach, and (2) functionally characterize non-coding variants from East Asian (EAS) IBD-associated loci. This innovative approach will identify key regulatory pathways and gene programs involved in monocyte and macrophage function, and highlight potential ancestry-specific differences. Furthermore, this study will improve understanding of how non-coding IBD-associated variants shape immune responses by linking these variants to their target genes. In the mentored K99 phase, the research goal is to map the genotype-phenotype landscape of IBD candidate genes in human monocyte-derived macrophages and systematically link GWAS-nominated variants to their target genes. During the R00 phase, the focus will shift to exploring the genetic effects on macrophage differentiation and immune responses within their native tissue environment using in vivo Perturb-seq, with particular emphasis on genes identified during the K99 phase as key regulators of macrophage plasticity, and functionally characterizing select non-coding variants to gain mechanistic insights into gene regulation. The short-term career goal is to complete the proposed research, develop a multi-pronged pipeline for GWAS guided functional study, and receive multidisciplinary training under the mentorship of Dr. Cho and a diverse advisory committee. The long-term career goal is to lead a research lab focused on understanding how genetic variants contribute to dysregulated immune responses in chronic inflammatory diseases, ultimately guiding the development of more precise and personalized therapeutic strategies. The collaborative and resource-rich environment of the New York area provides an ideal setting for achieving these goals.