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Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal and malignant urothelial cells [RNA-seq]

ABSTRACT: Epigenetic regulators, such as the SWI/SNF complex, play an important role in tissue development and homeostasis, and are frequently mutated in cancer. ARID1A, a subunit of the SWI/SNF complex, is mutated in approximately 20% of all bladder tumors, however, our understanding of the consequences thereof remains limited. Here, we generated various loss- and gain-of-function models to conduct Omni-ATAC-Seq, RNA-Seq, interactome analyses, and first functional studies to characterize ARID1A-affected pathways potentially suitable for the treatment of ARID1A-deficient bladder cancers. We observed decreased cell proliferation and deregulation of stress-regulated pathways including DNA repair in ARID1A-deficient cells. Furthermore, ARID1A was linked to alternative splicing and translational regulation on RNA and interactome levels. The absence of ARID1A drastically impacted the accessibility of chromatin, displaying significantly less accessible chromatin especially around distal, but not proximal, enhancers. Less accessible chromatin areas were mapped to pathways such as DNA damage response and cell proliferation. Indeed, the G2/M checkpoint appeared impaired after DNA damage in ARID1A-deficient cells. Together, this highlights the broad impact of ARID1A and the possibility of targeting proliferative and DNA repair pathways.

ORGANISM(S): Homo sapiens

PROVIDER: GSE271301 | GEO | 2025/03/04

REPOSITORIES: GEO

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Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal and malignant urothelial cells

Project description:Epigenetic regulators, such as the SWI/SNF complex, play an important role in tissue development and homeostasis, and are frequently mutated in cancer. ARID1A, a subunit of the SWI/SNF complex, is mutated in approximately 20% of all bladder tumors, however, our understanding of the consequences thereof remains limited. Finding truncations to be the most common mutation, we generated loss- and gain-of-function models to conduct RNA-Seq, interactome analyses, Omni-ATAC-Seq, and first functional studies to characterize ARID1A-affected pathways potentially suitable for the treatment of ARID1A-deficient bladder cancers. We observed decreased cell proliferation and deregulation of stress-regulated pathways, including DNA repair in ARID1A-deficient cells. Furthermore, ARID1A was linked to alternative splicing and translational regulation on RNA and interactome levels. ARID1A deficiency drastically reduced the accessibility of chromatin, especially around introns and distal, but not proximal, enhancers. Less accessible chromatin areas were mapped to pathways such as cell proliferation and DNA damage response. Indeed, the G2/M checkpoint appeared impaired after DNA damage in ARID1A-deficient cells. Together, this highlights the broad impact of ARID1A and the possibility of targeting proliferative and DNA repair pathways.

2025-03-02 | PXD054817 | Pride

Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal and malignant urothelial cells [ATAC-seq]

Project description:Epigenetic regulators, such as the SWI/SNF complex, play an important role in tissue development and homeostasis, and are frequently mutated in cancer. ARID1A, a subunit of the SWI/SNF complex, is mutated in approximately 20% of all bladder tumors, however, our understanding of the consequences thereof remains limited. Here, we generated various loss- and gain-of-function models to conduct Omni-ATAC-Seq, RNA-Seq, interactome analyses, and first functional studies to characterize ARID1A-affected pathways potentially suitable for the treatment of ARID1A-deficient bladder cancers. We observed decreased cell proliferation and deregulation of stress-regulated pathways including DNA repair in ARID1A-deficient cells. Furthermore, ARID1A was linked to alternative splicing and translational regulation on RNA and interactome levels. The absence of ARID1A drastically impacted the accessibility of chromatin, displaying significantly less accessible chromatin especially around distal, but not proximal, enhancers. Less accessible chromatin areas were mapped to pathways such as DNA damage response and cell proliferation. Indeed, the G2/M checkpoint appeared impaired after DNA damage in ARID1A-deficient cells. Together, this highlights the broad impact of ARID1A and the possibility of targeting proliferative and DNA repair pathways.

2025-03-04 | GSE271587 | GEO

ARID1A regulates transcription and the epigenetic landscape via POLE and DMAP1 while ARID1A deficiency or pharmacological inhibition sensitizes germ cell tumor cells to ATR inhibition

Project description:Germ cell tumors (GCTs) are the most common solid malignancies in young men. Although high cure rates can be achieved at early stages, metastases, resistance to cisplatin-based therapy, and late toxicities still represent a lethal threat, arguing for the need of new therapeutic options. In a previous study, we identified downregulation of the chromatin-remodeling SWI/SNF complex member ARID1A as a key event in the mode of action of the histone deacetylase inhibitor romidepsin, subsequently leading to induction of stress, apoptosis and cell cycle regulators. Additionally, ARID1A is mutated in many different tumor types, like bladder, breast or ovarial cancer. There, the loss-of-function mutations re-sensitize these tumor types to various drugs, like EZH2-, PARP-, HDAC-, HSP90- or ATR-inhibitors. Thus, ARID1A presents as a promising target for synthetic lethality and combination therapy. In this study, we deciphered the molecular function of ARID1A and screened for the potential of two pharmacological ARID1A inhibitors as a new therapeutic strategy to treat GCTs. By CRISPR/Cas9, we generated ARID1A-deficient GCT cells and demonstrate that ARID1A regulates transcription, DNA repair and the epigenetic landscape on DNA and histone level via DNA Polymerase POLE and the DNA methyltransferase 1-associated protein DMAP1. Additionally, ARID1A deficiency or pharmacological inhibition considerably sensitized (cisplatin-resistant) GCT cells towards ATR inhibition. Thus, ARID1A might be new combination partner for ATR inhibitors in the treatment of GCTs.

2020-04-14 | PXD017898 | Pride

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [HCT116_ChIP-seq]

Project description:Genes encoding subunits of SWI/SNF chromatin remodeling complexes are collectively mutated in ~20% of all human cancers. Although ARID1A is the most frequent target of mutations, the mechanism by which its inactivation promotes tumorigenesis is unclear. Here, we demonstrate that Arid1a functions as a tumor suppressor in the mouse colon, but not the small intestine, and that invasive ARID1A-deficient adenocarcinomas resemble human colorectal cancer (CRC). These tumors lack deregulation of APC/beta-catenin, crucial gatekeepers in common forms of intestinal cancer. ARID1A normally targets SWI/SNF complexes to enhancers, where they function in coordination with transcription factors (TFs) to facilitate gene activation. ARID1B preserves SWI/SNF function in ARID1A-deficient cells, but defects in SWI/SNF targeting and control of enhancer activity cause extensive dysregulation of gene expression. These findings represent an advance in colon cancer modeling and implicate enhancer-mediated gene regulation as a principal tumor suppressor function of ARID1A.

2016-11-21 | GSE71510 | GEO

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [primary cells_RNA-seq]

2016-11-21 | GSE71513 | GEO

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [primary cells_ChIP-seq]

2016-11-21 | GSE71512 | GEO

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [HCT116_RNA-seq]

2016-11-21 | GSE71511 | GEO

Effect of EZH2 inhibition on ARID1A mutant bladder cancer cell lines

Project description:ARID1A, a subunit of SWI/SNF chromatin remodeling complex. SWI/SNF complex can regulate expression of genes involved in vital biological processes such as cell cycle, DNA damage repair and development. ARID1A is known to have high mutation rate in human cancers including bladder cancer, leading to its loss of function. Publicly available whole exome sequencing data for muscle invasive and non-muscle invasive bladder cancers, show fraction of tumors with truncated ARID1A. Thus identifying therapeutic strategies for ARID1A mutant cancers is of high importance. EZH2, a histone methyltransferase is known to over-express and play pivotal role in aggressive bladder cancer. Our preliminary studies show that treatment of EZH2 inhibitor (GSK126) on ARID1A mutant bladder cancer cells significantly reduced cancer cell viability, invasion and colony formation relative to wild type ARID1A containing cells. Here, we performed microarray experiments to assess the effect of EZH2 inhibitor on global transcriptome of both ARID1A mutant and wild type bladder cancer cell line.

2023-05-01 | GSE150249 | GEO

ARID-DNA interactions are essential for SWI/SNF function

Project description:Every known SWI/SNF chromatin-remodeling complex incorporates an ARID DNA binding domain-containing subunit. Despite being a ubiquitous component of these complexes, physiological roles for this domain remain undefined. We screened an N-ethyl-N-nitrosurea (ENU) mutagenized library for ARID domain point mutations and generated an Arid1a/Baf250a hypomorphic allele. The mutant ARID1a (V1068G) protein is stably expressed at wild-type levels, and it is capable of assembling into a SWI/SNF complex with in vitro mononucleosome disruption activity. However, its capacity to bind DNA is lost. Consistent with defective DNA binding, mutant protein occupancy at known SWI/SNF target genes is decreased. Loss of DNA binding is associated with concurrent changes in SWI/SNF target gene expression. Mutant embryos manifest heart defects, fail to establish proper yolk sac vasculature, and exhibit hemorrhaging. As a result of these phenotypes, mutant embryos fail to establish proper circulation, culminating in ischemic arrest in utero between days 9.5 and 11.5. These data support a role for ARID1a-containing, BAF-A complexes in heart and extraembryonic vascular development, and indicate the ARID domain of ARID1a is essential in this regard. Hence, intrinsic ARID subunit-DNA interactions are required for normal SWI/SNF function in vivo. Four-condition experiment, wild-type vs Baf250a/Arid1a^V1068G/V1068G yolk sacs isolated at E8.5 and E9.5. Biological replicates: 3 per condition.

2012-01-15 | E-GEOD-32116 | biostudies-arrayexpress

Catalytic subunits switch drives resistance to EZH2 inhibitors in ARID1A-mutated cells [RNA-seq]

Project description:The SWI/SNF chromatin remodeling complex is altered in ~20% of human cancers. ARID1A, a component of the SWI/SNF chromatin-remodeling complex, is the most frequently mutated epigenetic regulator in human cancers. Inactivation of the SWI/SNF complex is synthetically lethal with inhibition of EZH2 activity. EZH2 inhibitors are entering clinical trials for specific tumor types with SWI/SNF mutations. However, mechanisms of de novo or acquired resistance to EZH2 inhibitors in cancers with inactivating SWI/SNF mutations are unknown. Here we show that the switch of the SWI/SNF catalytic subunits from SMARCA4 to SMARCA2 drives resistance to EZH2 inhibitors in ARID1A-mutated ovarian cancer cells.

2019-02-10 | GSE110449 | GEO

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