18Concurrent ARID1A/PBRM1 loss reorganizes chromatin accessibility through SWI/SNF complex redistribution in Cholangiocarcinoma
M Dogukan Aksu, Jayla T Millender, Christine T Nguyen, Alexander Q Wixom, Keith D Robertson, Alexandre Gaspar-Maia, Gregory J Gores, Caitlin B ConboyAbstract
Background
Cholangiocarcinoma (CCA) is an aggressive primary liver cancer with remarkable molecular heterogeneity. Mutations in SWI/SNF chromatin remodeling components occur in > 20% of CCA cases, with ARID1A and PBRM1 being significantly co-mutated. However, how the dual loss of these subunits reshapes chromatin architecture and drives oncogenic programs remains unclear that we aimed to address by profiling SWI/SNF redistribution, chromatin accessibility, 3D chromatin structure, and transcriptome in a dual Arid1a/Pbrm1 knockout mouse model.
Methods
CCA was induced in Cas9 knock-in mice via biliary instillation of myr-AKT along with sgRNAs targeting Arid1a and Pbrm1, generating APAC cell line. AC cell line was derived from mice receiving myr-AKT alone. Isogenic dual knockout (AC-sgAP) and control (AC-NT) lines were then generated from AC cells. Multi-omics profiling included ChIP-seq for SMARCA4/BRG1 and DPF2, ATAC-seq, RNA-seq, and Hi-C.
Results
ChIP-seq revealed that AC-sgAP cells showed decreased BRG1 binding (9,217 vs. 20,769 peaks) but increased DPF2 binding (7,527 vs. 2,068 peaks) and co-occupancy (5,037 vs. 1,888 peaks) compared to AC-NT. In contrast, APAC cells exhibited depletion of both BRG1 (12,994 peaks) and particularly DPF2 (146 peaks) with minimal overlap (68 shared peaks). Genome-wide accessibility profiling demonstrated that APAC cells had 78,582 differentially accessible regions compared to AC-NT, the majority (>70%) representing loss of accessibility, whereas AC-sgAP cells showed only 6,587 differentially accessible regions. Transcriptional profiling identified both unique and common significantly differentially expressed genes in APAC and AC-sgAP relative to AC-NT controls. Interestingly, topologically associating domains (TADs) calling revealed that AC-sgAP cells displayed approximately three-fold more differential TADs compared to AC-NT than APAC cells relative to controls.
Conclusions
Concurrent Arid1a/Pbrm1 loss drives extensive chromatin and transcriptional reprogramming through SWI/SNF redistribution. APAC cells achieving greater transcriptional dysregulation with fewer TAD disruptions might suggest that intra-TAD regulatory changes are critical events in SWI/SNF-mutant cholangiocarcinoma.