结直肠癌放疗诱导表观遗传重组的生物信息学与实验整合分析

Colorectal cancer is the second-leading cause of cancer-related deaths in the US. Resistance to radiation therapy - known as radioresistance - often develops during treatment, leading to metastases and death. Current research overlooks the dynamic epigenetic changes that occur during therapy, limiting the development of effective therapeutics. My project aims to profile and interrogate these radiation-induced epigenetic alterations across multiple in vitro colorectal cancer models. To study this phenomenon across diverse colorectal cancer subtypes, I integrated high-throughput sequencing analyses with wet-lab CRISPR screens to identify radiotherapy-affected epigenetic regions and validate them in biologically relevant models. I performed RNA Sequencing (RNA-Seq), Gene Set Enrichment Analysis (GSEA), and Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq) on radiation-treated colorectal cancer cell lines to characterize radiation-induced epigenetic changes. I administered two courses of radiation treatments on HCT116, SW480, MDST8, and RKO lines to mimic clinically relevant radiation courses: (1) a single-dose treatment of 0, 2, or 5 Gy, and (2) a fractionated-dose treatment of 0 or 2 Gy administered daily for five consecutive days. To validate these bioinformatic analyses, I employed dual whole-genome-wide CRISPR knockout screens in both HCT116 and MDST8 colorectal cancer cell lines to experimentally identify radiation-induced epigenetic alterations, screening 180 million cells under 0 Gy control and 2 Gy multi-dose irradiation conditions. RNA-Seq revealed consistent post-radiation transcriptional changes in all four cell lines. The 5 Gy-irradiated RKO lines showed regions of the genome that had increases in gene expression with increasing radiation treatment, suggesting a potential radiation-induced epigenetic regulatory mechanism. In multi-radiation dose experiments, volcano plot analysis revealed increased expression of immune-related genes such as IFIT1 in HCT116 cells and similar lines. I ran additional GSEA analyses, which confirmed alterations in immune-sensing pathways following radiation treatment and suggest a potential link among immune response, radiation treatment, and epigenetic regulation in colorectal cancer. I am currently analyzing CRISPR and ATAC-Seq data, but anticipate overlap in radiation-altered epigenetic regions between datasets. We aim to integrate CRISPR-screen data with RNA-Seq, GSEA, and ATAC-Seq analyses. I expect these results to contribute to the novel characterization of key radiation-induced colorectal epigenetic alterations and provide a robust framework for studying radioresistance in colorectal cancer. Ultimately, we hope to use these results to develop personalized, time-sensitive therapies that may improve patient outcomes and quality of life.