DNA damage-induced activation of ATM promotes β-TRCP-mediated ARID1A ubiquitination and destruction in gastric cancer cells
AT-rich interactive domain-containing protein 1A (ARID1A) is a subunit of the mammary SWI/SNF chromatin remodeling complex and a tumor suppressor protein. The loss of ARID1A been observed in several types of human cancers and associated with poor patient prognosis. Previously, we have reported that ARID1A protein was rapidly ubiquitinated and destructed in gastric cancer cells during DNA damage response. However, the ubiquitin e3 ligase that mediated this process remains unclear.
Materials and methods
The interaction between ARID1A and β-TRCP was verified by co-immunoprecipitation (Co-IP) assay. The degron site of ARID1A protein was analyzed by bioinformatics assay. Short hairpin RNAs (shRNAs) were used to knockdown (KD) gene expression.
Here we show that DNA damage promotes ARID1A ubiquitination and subsequent destruction via the ubiquitin E3 ligase complex SCFβ-TRCP. β-TRCP recognizes ARID1A through a canonical degron site (DSGXXS) after its phosphorylation in response to DNA damage. Notably, genetic inactivation of the Ataxia Telangiectasia Mutated (ATM) kinase impaired DNA damage-induced ARID1A destruction.
Our studies provide a novel molecular mechanism for the negative regulation of ARID1A by β-TRCP and ATM in DNA damaged gastric cancer cells.
KeywordsARID1A β-TRCP Phosphodegron DNA damage
AT-rich interactive domain-containing protein 1A
genome-wide association studies
Skp1-Cul1-F box protein
short hairpin RNAs
Ataxia Telangiectasia Mutated
Recent genome-wide association studies (GWAS) have demonstrated that the AT-rich interactive domain 1A (ARID1A) gene is frequently mutated in a wide variety of cancer [1, 2, 3]. The majority of mutations of ARID1A are insertions/deletions, suggesting ARID1A is a tumor suppressor gene . Indeed, ARID1A collaborates with p53 to regulate genes transcription and tumor growth in gynecologic cancers [5, 6]. ARID1A encodes a large nuclear protein and is a component of the switch/sucrose non-fermentable (SWI/SNF) complex by interacting with several other proteins including SMARCD3 . SWI/SNF, is a master regulator of transcription factor action and enable gene transcription and/or repressing by promoting or preventing transcription factors to bind to promoters and/or enhancers and plays a critical role in DNA damage response, mitosis and genomic instability [8, 9].
Gastric cancer (GC) is the fourth most common cancer and the second leading cause of cancer death worldwide . The raising of gastric cancer is known to be involve by multiple genetic and epigenetic alterations, which resulted in the aberrant regulation of many cancer-associated genes, which play critical role in diverse cellular processes [11, 12]. It has been shown that ARID1A was mutated and downregulated in GC and restoring ARID1A expression in gastric cancer cells significantly inhibited cell proliferation and colony formation [6, 13, 14]. However, how to regulate ARID1A itself is still not fully understood. Previously, we found that ARID1A was rapidly ubiquitinated and destructed in response to DNA damage and associated with both SKP1 and Cullin1 which are the components of Skp1-Cul1-F box protein (SCF) ubiquitin ligases .
There are 69 SCF ligases in human cells, and are distinguished by the exchangeable F box proteins that provide specificity for the SCF E3 ligases . Phosphorylation on specific sites are requested for most SCF substrates which are recognized by F box proteins . However, there are only 3 out of the entire F box proteins, including Skp2, β-TRCP, and Fbxw7 that have well-established substrates . Human cells express two distinct β-TRCP proteins (β-TRCP1 and β-TRCP2), but with undistinguishable biochemical function, therefore we use the term β-TRCP to refer to both proteins .
The aim of this study is therefore to determine which F-box protein is involved in the degradation of ARID1A. By using an unbiased F-box proteins binding screen assay, we identified β-TRCP is the E3 ligase for ARID1A degradation and found that β-TRCP interacted and ubiquitinated ARID1A in a phosphorylation-dependent manner during DNA damage response.
Materials and methods
HEK293T cells and gastric cancer cells line NCI-N87 and AGS cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% fetal calf serum (Gibco BRL, Gaithersburg, MD). All these cells were cultured in a 5% CO2/95% air at 37 °C. DMSO, proteasome inhibitor MG132, cycloheximide (CHX), λ-ppase and VP16 (Etoposide) were purchased from sigma.
Plasmids and transfection
ARID1A plasmid was purchased from Addgene (#39475). Flag-tagged F-box protein plasmids were gifts from Liu . ARID1A and β-TRCP mutants were generated using QuickChange Site-Directed Mutagenesis Kit (Stratagene). All cDNAs were completely sequenced. The following shRNA-expression lentiviral plasmids were made in PLKO.1 and purchased from sigma, with the clone numbers indicated: β-TRCP (TRCN0000314899 and TRCN0000314972) and ATM (TRCN0000194969 and TRCN0000195732). All the transient transfections were performed with Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions.
Protein extracts were loaded on 10–12% SDS-PAGE, electrophoresed, and transferred to nitrocellulose (NC) membrane. After blocking with 5% nonfat milk in PBS, the membranes were then incubated with the primary antibodies and followed by horseradish peroxidase (HRP)—linked secondary antibodies. The signals were detected by chemiluminescence phototope-HRP kit WBKLS0100 (Millipore, USA) according to manufacturer’s instructions. Antibodies were obtained from the following sources: anti-ARID1A (Santa Cruz Biotech, Santa Cruz, CA), anti-β-TRCP (D13F10) Rabbit mAb (Cell Signaling, Beverly, MA), anti-ATM (Santa Cruz Biotech, Santa Cruz, CA), anti-Flag M2 (Sigma, USA), anti-HA (Sigma, USA), anti-Cullin1 (Santa Cruz Biotech, Santa Cruz, CA), anti-SKP1 (Santa Cruz Biotech, Santa Cruz, CA) and anti-β-actin (Cell Signaling, Beverly, MA).
Cells were lysed in 5 ml of lysis buffer (150 mM Tris–HCl pH 7.5, 150 mM NaCl, 0.5% Nonidet P40, and 50 mM PMSF) for 20 min at 4 °C and sonicated for 4 min. Lysates were cleared using centrifugation (13,000 rpm, 20 min), the supernatant was then subjected to IP with 15 μl anti-mouse IgG or HA antibody with 20 μl protein G beads (Sigma) overnight at 4 °C with gentle rotation. Beads containing immune complexes were washed with lysis buffer 6 times. Precipitates were denatured in 2× SDS buffer at 99 °C for 5 min. For Flag-tagged protein IP, the supernatant was then subjected to IP with 20 μl Flag M2 beads (Sigma) overnight at 4 °C with gentle rotation.
To analyze protein half-life, cells were treated with CHX (25 μg/ml) for different durations followed by western blot assay.
Values were shown as mean ± SEM. Statistical differences were determined by a Student t test. Statistical significance is displayed as *P < 0.05, **P < 0.01 or ***P < 0.001.
β-TrCP associated with ARID1A
β-TrCP controls ARID1A protein levels
A canonical DSGXXS in ARID1A mediated the interaction between β-TrCP and ARID1A
ATM-induced ARID1A phosphorylation promoted β-TrCP-induced ARID1A destruction
By epigenetically regulating gene expression, the SWI/SNF chromatin remodeling complex mediates diverse biological pathways including DNA damage response . ARID1A, a component of the SWI/SNF complex, is a tumor suppressor with a high frequency of inactivating mutations in many cancers and plays an important role in targeting the complex to gene promoters . ARID1A and the SWI/SNF complex are capable of activating or repressing the transcription of hundreds of target genes. For example, p21 (CDKN1A) has been identified as a target gene of ARID1A and mediated the growth-suppressive effects of ARID1A .
In the present study, our data reveal a novel molecular event taking place in DNA damage response which is mediated by ATM and β-TrCP. Our previous studies suggest that ARID1A was associated with a SCF complex. Thus, we focus on identification the exact F-box protein which is responsible for the recognizing and destruction of ARID1A. By using unbiased F-box protein library screen, we identify that β-TrCP controls the stability of ARID1A. Our biochemical data reveal that ARID1A is a novel substrate of β-TrCP which interacts and targets phosphorylated ARID1A for ubiquitination and degradation. We show that ARID1A is recognized by β-TrCP through a DSGXXS motif after phosphorylation of two serine residues (S1316 and S1320). Although we have not identified the kinase directly responsible for phosphorylation of residues S1316 and S1320, we still able to provide evidence to show that the DNA damage-activated kinase ATM is involved in the degradation of ARID1A. As genetic or pharmacologic inactivation of the Ataxia Telangiectasia Mutated (ATM) kinase impaired DNA damage-induced ARID1A destruction. However, the in vitro kinase assay should be utilized in the future to clarify whether ATM is the direct kinase or the upstream kinase. The phosphorylation of ARID1A would ensure rapid degradation of ARID1A to transcriptional activate or repress the expression of some genes needs for DNA damage checkpoint activation and preventing the cell death, as we previously have found that overexpression of ARID1A protein caused significant cell death after DNA damage insult in gastric cancer cells.
By using unbiased F-box protein library screen, our study is the first to show F box protein β-TrCP controls the stability of ARID1A. We further found that ARID1A is recognized and ubiquitinated by β-TrCP through a DSGXXS motif after phosphorylation of two serine residues (S1316 and S1320) during DNA damage response. We provide a novel molecular mechanism for the negative regulation of ARID1A by β-TRCP and ATM in gastric cancer cells in response to DNA damage insult. Our data suggest that ARID1A acts as a participant in the damage response pathway, the fine tune of which might contribute to tumorigenesis prevention and affect the response of patients towards DNA-damaging chemotherapies.
ZJ participated in the design of the study, performed the experience and drafted the manuscript. TP and HQ performed the primary experience. CL and FQ performed the statistical analyses. ZJ and SZ were major contributors to the design of this study and revised the manuscript. All authors read and approved the final manuscript.
This work was supported by The Scientific Innovation Team Project of Ningbo (Grant No. 2013B82010). Ningbo Health Branding Subject Fund (PPXK2018-03) and Natural Science Foundation of Ningbo (Grant No. 2017A610152).
Ethics approval and consent to participate
The study was approved by the Ethics Committee of the Second Affiliated Hospital, Zhejiang University School of Medicine. All procedures performed in this study were in accordance with the 1964 Helsinki Declaration and its later amendments. Written informed consent was obtained from all patients included in the study.
Consent for publication
All listed authors have actively participated in the study and have read and approved the submitted manuscript.
The authors declare that they have no competing interests.
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