Abstract 124: Cell state regulation in early colorectal cancer through transcription factor and chromatin action

Abstract Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the United States, despite established treatment options and knowledge of causal mutations. CRC involves significant rewiring of cellular chromatin alongside mutational accumulation, which fuel aberrant cancer transcriptional programs. Many developmental gene regulatory mechanisms are also activated during early tumorigenesis. However, details of molecular controls in early tumor development and evolution are not fully understood. Mutations in tumor suppressor APC gene are essential for cancer initiation in the majority (>70%) of CRC patients. We ablated Apc in the mouse gastrointestinal stem cells resulting in their transformation leading to adenoma formation. We purified the transformed epithelial cells in adenoma using FACS and performed single nuclei ATAC and RNA sequencing to generate paired chromatin accessibility and transcriptional profiles using 10X genomics single cell multiome (scMultiome-seq) platform. By profiling the expression of known intestinal cell markers and comparing adenoma cells to wild type cells, we identified cell Apc-null cell populations with transcriptomic and chromatin landscape distinct from those of the wild-type cells. We identified differentially accessible genomic regions among wild-type and adenoma cells, the majority of which were located outside of gene promoters. This suggested changes in the cis-regulatory gene enhancer circuits potentially through altered transcription factor activity. MOTIF analysis using the differentially accessible peaks in adenoma cells revealed significant enrichment of several development specific transcription factors (TFs), including Sox17 and Foxa2. Such reappearance of developmental TFs in early adenomas may drive formation of unique cell states and cancer progression. Interestingly, immunostaining for Sox17 at various stages of adenoma development revealed heterogeneous enrichment within adenomas suggesting its involvement in early adenoma evolution. By profiling the histone modifications and transcription factor binding through chromatin immunoprecipitation sequencing, Sox17 directly binds to uniquely accessible enhancers in adenoma cells and promotes the activation of genes associated with cell-cell adhesion and migration. Our results using single-cell transcriptomic and epigenomic approaches reveal novel cell states formed during the birth and early growth of adenomas and how transformed cells utilize transcription factor activity to alter the cellular enhancer landscape as well as cellular properties during tumor evolution. Citation Format: Sweta Sharma, Alireza Lorzadeh, George Ye, Unmesh Jadhav. Cell state regulation in early colorectal cancer through transcription factor and chromatin action [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 124.