Gene Expression Profiling Identifies Ferroptosis-Related Genes and Pathways in Human Colon Cancers Cell Lines

Michele Balik-Meisner¹D Phadke¹D Mav¹Ruchir Shah¹Keith Shockley²Carri Murphy²Erik J Tokar²Birandra Kumar Sinha^2*

• ¹Sciome LLC, Research Triangle Park, United States
• ²National Institute of Environmental Health Sciences (NIH), Durham, United States

Abstract Introduction: Colorectal cancer (CRC) is the third most diagnosed cancer worldwide and the second leading cause of cancer-related deaths. A major challenge in CRC treatment is drug resistance, which limits the efficacy of conventional therapies. Ferroptosis, an iron-dependent form of regulated cell death driven by the accumulation of reactive oxygen species (ROS), has emerged as a promising therapeutic strategy. Erastin (ER), a small-molecule compound, induces ferroptosis through ROS accumulation. Methods: We performed microarray gene expression analysis on two CRC cell lines, HCT116 and HT-29, to examine the transcriptional response to ER exposure and identify differentially expressed genes and pathways involved in ER-induced ferroptosis. Results: Our gene expression analysis revealed distinct transcriptional profiles between the two cell lines, and 26 transcripts commonly enriched in response to ER treatment were identified in both HCT116 and HT-29 cells. Notably, several of these genes— including ASNS, PCK2, CHAC1, and DDIT4—were significantly enriched, suggesting a conserved ferroptotic response. The induction of these genes was further confirmed in an additional CRC cell line, DLD-1. Interestingly, SOD1 and NQO1 genes, involved in oxidative stress response, were significantly upregulated by ER in HCT116 cells. Conclusion: Our findings highlight ASNS, CHAC1, PCK2, DDIT4, and ATF3/4 as potential biomarkers for ferroptosis in CRC. Monitoring the expression of these genes may help identify patients who are responsive to ferroptosis inducers and facilitate the development of personalized treatment strategies.