ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response [4C-seq]

AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here we show that ARID1A plays epigenetic roles to promote both DNA double-strand breaks (DSBs) repair pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). ARID1A is accumulated at DSBs after DNA damage and regulates chromatin loops formation by recruiting RAD21 and CTCF to DSBs. Simultaneously, ARID1A binds to and promotes the recruitment of HDAC1 and RSF1 to DSBs to control the distribution of activating histone marks and chromatin accessibility leading to eviction of RNAPII and silencing of transcription in transcriptionally active chromatin. ARID1A depletion resulted in enhanced accumulation of micronuclei, activation of cGAS-STING pathway, and an increased expression of immunomodulatory cytokines upon ionizing radiation. Furthermore, low ARID1A expression in cancer patients receiving radiotherapy was associated with higher infiltration of several immune cells. The high mutation rate of ARID1A in various cancer types highlights its clinical relevance as a promising biomarker that correlates with the level of immune regulatory cytokines and estimates the levels of tumor-infiltrating immune cells, which can predict the response to the combination of radio- and immunotherapy. We used both WT AID-DivA (Auxin-Inducible Degron DSB Inducible via AsiSI) cells and AID-DivA cells with an ARID1A knock-out. We used 2 different treatment types. For the first treatment, we used 3 different treatments: untreated (UT), treated with 300 nM 4-hydroxytamoxifen (4OHT) and incubated for 4h, then treated with Auxin to stop the enzymatic generation of the double-strand breaks, and cell collection either immediately after auxin treatment (T0) or 4h (T4) after addition of auxin. For the second treatment, we either used BRG1 inhibitors (brg1i) or not (nobrg1i). We used three viewpoints: one close to HR-prone DSB (DSB2), one close to NHEJ-prone DSB (DSB3), and one with no adjacent DSB (ctrl). A variable number of replicates was used for each condition.