ARID1A

Overview

ARID1A encodes a SWI/SNF chromatin-remodeling complex subunit and is recurrently altered across lymphoid and solid tumors, where loss-of-function events shape disease subtype and metastatic behavior.

Alterations observed in the corpus

  • Driver mutations enriched in IGHV-unmutated CLL (U-CLL), reinforced by 1p36.11 copy loss (4.4%) in the cBioPortal CLL map PMID:35927489.
  • Altered more often in LUAD metastases than in matched primary tumors in the MSK LUAD organotropism cohort PMID:37084736.
  • Enriched in primary LUAD tumors from patients who later developed brain metastasis compared with non-metastatic primaries PMID:37591896.
  • ARID1A alterations were positively associated with SETD2 driver mutations in LUAD (q<0.05) in the MSK-CHORD cohort PMID:39506116.
  • ARID1A enriched in KRAS other-MAPK-mutant PAAD (21% vs 8% in KRAS-mutant, P = 2.4 × 10⁻⁴) and in KRAS G12D vs G12R tumors (10% vs 5%, P = 0.002) in a 2,336-tumor PDAC genomic study PMID:39753968.
  • ARID1A mutations less frequent in Black endometrial carcinoma (EC) patients than in White patients (19% vs 47%), consistent with fewer endometrioid histology cases in the Black cohort (1,025-patient molecular characterization study) PMID:37651310.
  • ARID1A mutations present in >10% of both early-onset and average-onset esophagogastric cancer patients without significant differential frequency between age groups (n=1,123) PMID:37699004.
  • ARID1A missense/frameshift/nonsense mutations detected in 18% of advanced HCC patients by cfDNA profiling (MSK-ACCESS, 51 patients); 100% concordance with tissue sequencing (kappa 0.91) PMID:37769223.
  • ARID1A mutated in 82% of dMMR/MSI-H gynecologic cancers treated with nivolumab (n=35); not differentially associated with response or resistance to PD-1 blockade PMID:38653864.
  • ARID1A is a frequent co-mutation in BRAF fusion-positive colorectal cancers (36% of CRC with BRAF fusions) in a tumor-agnostic BRAF fusion analysis across 97,024 MSK-sequenced samples PMID:38922339.
  • Alteration frequency not independently associated with VTE risk after controlling for ctDNA detection in a 4,141-patient liquid biopsy VTE prediction study PMID:39147831.
  • ARID1A mutations absent in cervical adenosquamous carcinoma; present in mesonephric carcinoma (2/3 cases) in a 177-patient cervical cancer genomic landscape study PMID:37643132.
  • Truncating mutations (e.g., E1783*) enriched in metastatic bladder cancer (28%) vs low-grade non-invasive (14%); when discordant, always exclusive to metastasis PMID:36543146
  • ARID1A is a chromatin-modifying gene with high prevalence of non-silent variants in metastatic UC (UC-GENOME cohort) PMID:36333289
  • ARID1A LOF mutations in 18% of GBC PMID:36228155
  • ARID1A mutation not significantly associated with immunotherapy outcomes in advanced NSCLC (P = 0.44) PMID:36038778
  • ARID1A loss-of-function mutations sensitize ovarian cancer cells to BET bromodomain inhibition (JQ1), establishing a synthetic lethal relationship exploitable therapeutically PMID:22037554
  • ARID1A truncating mutations identified in breast cancer WES of 100 tumors as a recurrent driver PMID:22722201
  • ARID1A is recurrently mutated in colorectal adenocarcinoma among 276 TCGA CRC tumors, implicating SWI/SNF chromatin remodeling complex disruption in CRC pathogenesis PMID:22810696
  • ARID1A is identified as a significantly mutated gene in melanoma WES of 121 tumors (Broad cohort), expanding its known role beyond gynecologic cancers to cutaneous melanoma PMID:22817889
  • Mutated in lung adenocarcinoma WES study (Broad, 183 tumors); identified in comprehensive genomic characterization of lung adenocarcinoma PMID:22980975
  • Somatically mutated in pancreatic cancer (ICGC WES, 142 tumors); ARID1A truncating mutations identified among significantly mutated genes PMID:23103869
  • Mutated in neuroblastoma (Broad WES/WGS, 240 tumors); ARID1A identified among recurrently mutated chromatin-remodeling genes PMID:23334666
  • SWI/SNF and broader chromatin-remodeling mutations (including ARID1A, ARID2, SMARCA4, PBRM1, JARID2) present in 24% of EACs (esca_broad cohort, 145 tumors) PMID:23525077
  • High mutation rate in non-serous endometrial carcinoma subgroups (ucec_tcga_pub); decreased protein expression by RPPA consistent with inactivating mutations; differential frequencies across POLE-ultramutated, MSI, and copy-number-low subtypes PMID:23636398
  • Single somatic mutation observed in adenoid cystic carcinoma (ACC) WES cohort (n=60); classified as SWI/SNF complex alteration PMID:23685749
  • Co-occurs in HotNet PBAF subnetwork with PBRM1 and SMARCA4 in CCRCC (TCGA, n=446) PMID:23792563
  • Chromatin-remodeling gene mutated in transitional cell carcinoma (TCC) of the bladder; mutations in ARID1A/ARID4A subgroup contribute to the 58% prevalence of chromatin-remodeling gene alterations in bladder cancer PMID:24121792
  • SWI/SNF complex subunit mutated in 9/64 (14%) intrahepatic cholangiocarcinoma; not previously reported in cholangiocarcinoma at time of publication PMID:24185509
  • Somatic mutation in 2/23 (9%) pancreatic carcinomas with acinar differentiation PMID:24293293
  • Single in-frame deletion p.Tyr560_Gln561delinsTer identified in sinonasal AdCC (1/21 sequenced cases); SWI/SNF complex component PMID:24418857
  • Singleton expressed mutation flagged as a candidate driver in rhabdomyosarcoma (RMS); not previously reported in RMS PMID:24436047
  • Mutated in 25% of muscle-invasive bladder carcinomas (BLCA, n=131); truncating mutations enriched; identified as a significantly mutated gene by MutSig; encodes SWI/SNF chromatin-remodeling complex component PMID:24476821
  • SWI/SNF subunit mutated in ccRCC (RMH004, p.Arg1020Lys) alongside PBRM1 and SMARCA4 hits; identified as a branch driver in multi-region sequencing of 10 ccRCC tumors PMID:24487277
  • Non-catalytic BAF subunit (BAF250A) invoked in the context of SWI/SNF biology in SCCOHT; not mutated in this cohort but noted as relevant to ovarian tumorigenesis PMID:24658004
  • Chromatin remodeling driver identified by NGS in HCC; listed among the newly identified HCC driver genes PMID:24735922
  • Loss-of-function mutation in 8% (range 4–12%) of HCCs (WES, n=1,289); chromatin-modifier trunk driver classified as non-actionable PMID:24798001
  • Mutated in 14% overall in gastric adenocarcinoma; especially common in EBV-positive (55%) and GS subtypes; chromatin remodeler loss implicated in EBV-driven tumorigenesis PMID:25079317
  • Mutated in 7% of LUAD (chromatin modifier); part of the chromatin remodeling alteration landscape of lung adenocarcinoma PMID:25079552
  • Truncating alterations in 28% of muscle-invasive urothelial carcinoma (UCB); mutually exclusive with SMARCA4 mutations; not associated with post-cystectomy outcomes PMID:25092538
  • Significantly mutated (MutSigCV) across muscle-invasive urothelial carcinoma cohort PMID:25096233
  • Truncating mutations in 7/22 (32%) uterine/ovarian carcinosarcoma cases; enriched in MSS ovarian cases (4/5 ovarian vs 0/uterine MSS) PMID:25233892
  • Recurrently mutated in chRCC but not reaching q-score significance in the non-clear-cell RCC cohort PMID:25401301
  • Loss-of-function mutations in 18–23% of intrahepatic CCA and 14% of extrahepatic CCA; mechanistically represses ALDH1A1 via HDAC1/H3K27ac axis; loss enhances cancer stemness and correlates with poor prognosis; co-occurring with activating KRAS mutations synergistically accelerates CCA development; ARID1A-mutant tumors trend toward high MSI/TMB and ICI sensitivity PMID:25526346
  • Significantly enriched in the Low-clonality (LoC) subtype of gastric cancer; associated with younger onset and longer survival in a 294-patient Tianjin WES cohort PMID:25583476
  • Chromatin remodeler truncated or hit at COSMIC sites in cutaneous squamous cell carcinoma; part of SWI/SNF complex alterations observed in 48% of 29-tumor cSCC cohort PMID:25589618
  • Chromatin-remodeling gene recurrently mutated in HCC; part of SWI/SNF pathway altered in 28% of 243 HCC tumors PMID:25822088
  • Mutated in 6% of PDA by sequencing; protein loss by IHC in independent 296-case cohort significantly associated with poor outcome (P=0.0202); ARID1A-deficient PDA cell lines are synthetically lethal with ARID1B depletion PMID:25855536
  • Chromatin-modifier gene mutated in 13.6% of UTUC vs 27.5% of UCB (p=0.050); mutations are early/clonal events concordant across spatial tumor components in UTUC PMID:26278805
  • Inactivating mutations in the SWI/SNF complex in desmoplastic melanoma; protein loss confirmed by IHC; co-occurs with ARID2 inactivation PMID:26343386
  • One of the most frequent SWI/SNF chromatin-remodelling alterations in periampullary adenocarcinomas (AMPAC, DUOAC, CAC); equally distributed across the three tumour types PMID:26804919
  • Identified as a putative MYB transcriptional target in adenoid cystic carcinoma (ACC); mutated in ACC per prior sequencing studies cited in this analysis PMID:26829750
  • ARID1A, as part of the SWI/SNF complex, mutated in 36% ATC vs 6% PDTC (P = 1×10⁻⁴) in a 341-gene targeted sequencing cohort (n=117 advanced thyroid tumors); mutations were largely mutually exclusive within the SWI/SNF complex PMID:26878173
  • ARID1A recurrently mutated in plasmacytoid-variant bladder cancer at frequencies comparable to conventional urothelial carcinoma, NOS, as part of a broader chromatin-remodeler mutation pattern PMID:26901067
  • Inactivating mutations detected in lung ADC by pan-lung WES (TCGA); identified as a significantly mutated gene in the lung cancer landscape PMID:27158780
  • SWI/SNF member; inactivating mutations identified as Mut-drivers in breast cancer (METABRIC 2,433-sample cohort); ARID1B synthetic-lethal dependency proposed as therapeutic strategy in ARID1A-deficient tumors PMID:27161491
  • ARID1A (SWI/SNF complex) more frequently altered in esophageal adenocarcinoma (EAC) than ESCC; part of a recurrent SWI/SNF complex alteration pattern in upper GI cancers PMID:28052061
  • Y551Lfs*72 frameshift mutation detected in 1/19 sequenced 1p/19q-codeleted anaplastic oligodendrogliomas PMID:28472509
  • Stop-gain driver SNV detected in the para-vertebral metastasis of NSCLC patient CRUK0063, below multi-region sequencing calling threshold in the primary tumor region from which the metastatic subclone derived; illustrates subclonal metastatic seeding in LUAD PMID:28445469
  • Mutated in 15.9% of clear-cell endometrial carcinomas (CCEC; n=63); one of the top recurrently altered genes in this histology PMID:28485815
  • Mutated in 21% of non-muscle-invasive bladder cancers (NMIBC); the only single gene significantly associated with recurrence after BCG immunotherapy (HR = 3.14, p = 0.002); ARID1A mutations may predict BCG failure and motivate testing of EZH2 inhibitors (synthetic lethality in ARID1A-deficient tumors) PMID:28583311
  • ARID1A enriched in Cluster 1 of cholangiocarcinoma (p < 0.01) and also a recurrent structural variant target PMID:28667006
  • ARID1A is a SWI/SNF subunit mutated in medulloblastoma; together with SMARCA4 and ARID2, SWI/SNF subunits are altered in 33% of WNT MBs, providing rationale for PRC2 inhibitors (trial NCT02601937) PMID:28726821
  • SWI/SNF chromatin remodeler with recurrent inactivating mutations and 4.2% deletions in MIBC (TCGA, n=412) PMID:28988769
  • Mutated in 15% of metastatic esophagogastric cancer (EGC) tumors profiled by MSK-IMPACT (n=200) PMID:29122777
  • ARID1A is a SWI/SNF member altered in ~5% of 1,013 prostate cancers (prad_p1000), enriched in ETS-fusion-negative tumors alongside ARID2, ARID4A, and SMARCA1. PMID:29610475

Cancer types (linked)

  • CLL — ARID1A is a U-CLL-enriched driver tied to chromatin-remodeling dysfunction PMID:35927489.
  • LUAD — ARID1A alterations accumulate in metastatic lesions and in primary tumors that will later seed brain metastases PMID:37084736 PMID:37591896.
  • UCEC — ARID1A is depleted in Black EC patients (19% vs 47%), reflecting lower endometrioid histology prevalence in this population PMID:37651310.
  • HCC — ARID1A mutations detectable in cfDNA at high concordance with tissue profiling (100%, kappa 0.91) PMID:37769223.
  • UCEC / gynecologic cancers (dMMR) — ARID1A mutated in 82% of dMMR/MSI-H cases but not predictive of nivolumab response PMID:38653864.
  • COAD / colorectal — ARID1A frequent co-mutation (36%) in BRAF fusion-positive colorectal cancer PMID:38922339.

Co-occurrence and mutual exclusivity

Therapeutic relevance

Open questions

  • Whether ARID1A loss is causal for metastatic progression in LUAD or a marker of broader chromatin-remodeling instability remains unresolved PMID:37084736 PMID:37591896.

Sources

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