Abstract 1696: ACTL6A deficiency drives cell death through KLF4-involved chromatin accessibility changes in colorectal cancer

Abstract ACTL6A is a subunit of the SWI/SNF and INO80 chromatin remodeling complexes and plays roles in neural development and cancer cell proliferation. Additionally, it is known to be upregulated in various types of cancer and is associated with a decrease in patient survival rates. However, the mechanism of how chromatin remodelers including ACTL6A cause cell death has yet to be defined. Therefore, we would like to investigate how the depletion of ACTL6A promotes cell growth reduction by mediating changes in the epigenetic landscape in colorectal cancer cells. We engineered ACTL6A knockout by CRISPR-Cas9. We performed Assay for transposase-accessible chromatin using sequencing (ATAC-seq), RNA sequencing (RNA-seq), and Chromatin Immunoprecipitation sequencing (ChIP-seq) for SMARCB1 and INO80, as representative members of their respective families, and KLF4. Moreover, HCT116 cells stably transduced with doxycycline-inducible shGFP or shACTL6A were implanted into the flank of nude mice. One week after tumor implantation, mice were randomly allocated to 4 groups (n=13-15 per group) and doxycycline treated group was administered with doxycycline (1mg/ml) and 5% sucrose in the drinking water. Tumor volume was measured with calipers. Upon depletion of ACTL6A, the regions of increased chromatin accessibility were correlated with the upregulated genes. After the loss of ACTL6A, there was a significant increase in KLF4 expression and genomic binding largely increased, coinciding with an increase in newly accessible regions containing KLF4 motifs. Interestingly, there is a strong positive correlation between changes in chromatin accessibility and overall changes in the binding of KLF4, SWI/SNF, and INO80 complexes. We find that changes in chromatin accessibility are co-regulated by KLF4, the SWI/SNF and the INO80 complex, while SWI/SNF and INO80 complex have a low correlation in binding between the SWI/SNF and INO80 complexes at newly accessible regions, indicating no physical interactions between these two chromatin complexes. Overall, we demonstrated that the redistribution of ACTL6A-deficient two chromatin remodeling complexes and KLF4 is associated with changes in chromatin accessibility, which are also linked to upregulated genes that promote the p53 pathway. These findings revealed the role of KLF4 along with the SWI/SNF and INO80 complexes, in regulating the chromatin landscape and gene expression in ACTL6A-depleted colorectal cancer cells. Citation Format: Hye-Ju Yang, Eun-Ju Kim, Sang-Hyun Song, Tae-You Kim. ACTL6A deficiency drives cell death through KLF4-involved chromatin accessibility changes in colorectal cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 1696.