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Zhang Y, Qian HS, Hu G, Wang L, Zhu Y. ARID1A is involved in DNA double-strand break repair in gastric cancer. J Gastrointest Oncol 2024; 15:862-872. [PMID: 38989399 PMCID: PMC11231857 DOI: 10.21037/jgo-24-283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024] Open
Abstract
Background Defects in DNA damage repair can cause genetic mutations, which in turn can cause different types of cancers. Chromatin remodeling complexes, which help repair damaged DNA, can cause the chromatin structure to change as a result of DNA damage. ARID1A may play a role in the process of DNA damage repair, and arid1a may be related to the occurrence and development of gastric cancer (GC). This study aimed to investigate the mechanism of ARID1A regulating the DNA damage repair of gastric adenocarcinoma cell lines AGS and SGC-7901 and its effect on migration, proliferation and apoptosis. Methods The expression of ARID1A plasmid was detected by Western blot and real-time polymerase chain reaction (PCR). The effect of etoposide (ETO) on the survival rate of AGS and SGC-7901 gastric adenocarcinoma cell lines was detected by MTT assay. The DNA double-strand break model was established by ETO and then passed through the comet assay and immunofluorescence co-localization to observe DNA damage; western blot method was used to detect the effect of ARID1A on the expression of related proteins in DNA damage repair pathway in gastric adenocarcinoma cells; scratch test and colony formation experiments were used to observe ARID1A migration and proliferation of gastric adenocarcinoma cells. The flow cytometry was used to detect the effect of ARID1A on apoptosis of gastric adenocarcinoma cells. Results The expression of mRNA and protein was increased after transfection of ARID1A plasmid. ETO was confirmed by MTT assay to inhibit cell survival in a dose-dependent manner. After the DNA double-strand break model was established by ETO, the expression levels of phospho-ataxia telangiectasia mutated (p-ATM) protein increased in the overexpressed ARID1A group. Meanwhile, the overexpressed ARID1A group had a shortened tail moment, and γ-H2AX and ARID1A co-localized in the DNA damage site of the nucleus. The over-expressed ARID1A group had weaker wound healing ability, reduced number of clone formation, and increased apoptosis rate. Conclusions ARID1A may repair DNA double-strand breaks caused by ETO by p-ATM pathway; ARID1A can inhibit the migration and proliferation of gastric adenocarcinoma cells and promote apoptosis. Our findings indicate that ARID1A could serve as a therapeutic target and biomarker for GC patients.
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Affiliation(s)
- Ying Zhang
- Department of Oncology, Fuyang Cancer Hospital, Fuyang, China
| | - He-Sheng Qian
- Department of Oncology, Fuyang Cancer Hospital, Fuyang, China
| | - Gengwei Hu
- Department of Cardiovascular Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Lu Wang
- Department of Oncology, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Yiping Zhu
- Department of Oncology, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
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2
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Trejo-Villegas OA, Heijink IH, Ávila-Moreno F. Preclinical evidence in the assembly of mammalian SWI/SNF complexes: Epigenetic insights and clinical perspectives in human lung disease therapy. Mol Ther 2024:S1525-0016(24)00409-X. [PMID: 38910326 DOI: 10.1016/j.ymthe.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
The SWI/SNF complex, also known as the BRG1/BRM-associated factor (BAF) complex, represents a critical regulator of chromatin remodeling mechanisms in mammals. It is alternatively referred to as mSWI/SNF and has been suggested to be imbalanced in human disease compared with human health. Three types of BAF assemblies associated with it have been described, including (1) canonical BAF (cBAF), (2) polybromo-associated BAF (PBAF), and (3) non-canonical BAF (ncBAF) complexes. Each of these BAF assemblies plays a role, either functional or dysfunctional, in governing gene expression patterns, cellular processes, epigenetic mechanisms, and biological processes. Recent evidence increasingly links the dysregulation of mSWI/SNF complexes to various human non-malignant lung chronic disorders and lung malignant diseases. This review aims to provide a comprehensive general state-of-the-art and a profound examination of the current understanding of mSWI/SNF assembly processes, as well as the structural and functional organization of mSWI/SNF complexes and their subunits. In addition, it explores their intricate functional connections with potentially dysregulated transcription factors, placing particular emphasis on molecular and cellular pathogenic processes in lung diseases. These processes are reflected in human epigenome aberrations that impact clinical and therapeutic levels, suggesting novel perspectives on the diagnosis and molecular therapies for human respiratory diseases.
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Affiliation(s)
- Octavio A Trejo-Villegas
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México
| | - Irene H Heijink
- Departments of Pathology & Medical Biology and Pulmonology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9713 Groningen, the Netherlands
| | - Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México; Research Unit, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, 14080, Ciudad de México, México; Research Tower, Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), 14080, Ciudad de México, México.
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3
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Zhu T, Li Q, Zhang Z, Shi J, Li Y, Zhang F, Li L, Song X, Shen J, Jia R. ARID1A loss promotes RNA editing of CDK13 in an ADAR1-dependent manner. BMC Biol 2024; 22:132. [PMID: 38835016 PMCID: PMC11151582 DOI: 10.1186/s12915-024-01927-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/22/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is thought to play a significant role both in tumor suppression and tumor initiation, which is highly dependent upon context. Previous studies have suggested that ARID1A deficiency may contribute to cancer development. The specific mechanisms of whether ARID1A loss affects tumorigenesis by RNA editing remain unclear. RESULTS Our findings indicate that the deficiency of ARID1A leads to an increase in RNA editing levels and alterations in RNA editing categories mediated by adenosine deaminases acting on RNA 1 (ADAR1). ADAR1 edits the CDK13 gene at two previously unidentified sites, namely Q113R and K117R. Given the crucial role of CDK13 as a cyclin-dependent kinase, we further observed that ADAR1 deficiency results in changes in the cell cycle. Importantly, the sensitivity of ARID1A-deficient tumor cells to SR-4835, a CDK12/CDK13 inhibitor, suggests a promising therapeutic approach for individuals with ARID1A-mutant tumors. Knockdown of ADAR1 restored the sensitivity of ARID1A deficient cells to SR-4835 treatment. CONCLUSIONS ARID1A deficiency promotes RNA editing of CDK13 by regulating ADAR1.
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Affiliation(s)
- Tianyu Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Jiahao Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Yongyun Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Feng Zhang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xin Song
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China.
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China.
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4
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Yamamoto H, Watanabe Y, Arai H, Umemoto K, Tateishi K, Sunakawa Y. Microsatellite instability: A 2024 update. Cancer Sci 2024; 115:1738-1748. [PMID: 38528657 PMCID: PMC11145116 DOI: 10.1111/cas.16160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Deficient mismatch repair (dMMR) results in microsatellite instability (MSI), a pronounced mutator phenotype. High-frequency MSI (MSI-H)/dMMR is gaining increasing interest as a biomarker for advanced cancer patients to determine their eligibility for immune checkpoint inhibitors (ICIs). Various methods based on next-generation sequencing (NGS) have been developed to assess the MSI status. Comprehensive genomic profiling (CGP) testing can precisely ascertain the MSI status as well as genomic alterations in a single NGS test. The MSI status can be also ascertained through the liquid biopsy-based CGP assays. MSI-H has thus been identified in various classes of tumors, resulting in a greater adoption of immunotherapy, which is hypothesized to be effective against malignancies that possess a substantial number of mutations and/or neoantigens. NGS-based studies have also characterized MSI-driven carcinogenesis, including significant rates of fusion kinases in colorectal cancers (CRCs) with MSI-H that are targets for therapeutic kinase inhibitors, particularly in MLH1-methylated CRCs with wild-type KRAS/BRAF. NTRK fusion is linked to the colorectal serrated neoplasia pathway. Recent advances in investigations of MSI-H malignancies have resulted in the development of novel diagnostic or therapeutic techniques, such as a synthetic lethal therapy that targets the Werner gene. DNA sensing in cancer cells is required for antitumor immunity induced by dMMR, opening up novel avenues and biomarkers for immunotherapy. Therefore, clinical relevance exists for analyses of MSI and MSI-H-associated genomic alterations in malignancy. In this article, we provide an update on MSI-driven carcinogenesis, with an emphasis on unique landscapes of diagnostic and immunotherapeutic strategies.
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Affiliation(s)
- Hiroyuki Yamamoto
- Department of BioinformaticsSt. Marianna University Graduate School of MedicineKawasakiJapan
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yoshiyuki Watanabe
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
- Department of Internal MedicineKawasaki Rinko General HospitalKawasakiJapan
| | - Hiroyuki Arai
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Kumiko Umemoto
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Keisuke Tateishi
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yu Sunakawa
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
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5
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Pejovic T, Cathcart AM, Alwaqfi R, Brooks MN, Kelsall R, Nezhat FR. Genetic Links between Endometriosis and Endometriosis-Associated Ovarian Cancer-A Narrative Review (Endometriosis-Associated Cancer). Life (Basel) 2024; 14:704. [PMID: 38929687 PMCID: PMC11204815 DOI: 10.3390/life14060704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Endometriosis is a frequent, estrogen-dependent, chronic disease, characterized by the presence of endometrial glands and stroma outside of the uterine cavity. Although it is not considered a precursor of cancer, endometriosis is associated with ovarian cancer. In this review, we summarized the evidence that clear-cell and endometrioid ovarian carcinomas (endometriosis-associated ovarian carcinoma-EAOC) may arise in endometriosis. The most frequent genomic alterations in these carcinomas are mutations in the AT-rich interaction domain containing protein 1A (ARID1A) gene, a subunit of the SWI/SNF chromatin remodeling complex, and alterations in phosphatidylinositol 3-kinase (PI3K) which frequently coexist. Recent studies have also suggested the simultaneous role of the PTEN tumor-suppressor gene in the early malignant transformation of endometriosis and the contribution of deficient MMR (mismatch repair) protein status in the pathogenesis of EAOC. In addition to activating and inactivating mutations in cancer driver genes, the complex pathogenesis of EAOC involves multiple other mechanisms such as the modulation of cancer driver genes via the transcriptional and post-translational (miRNA) modulation of cancer driver genes and the interplay with the inflammatory tissue microenvironment. This knowledge is being translated into the clinical management of endometriosis and EAOC. This includes the identification of the new biomarkers predictive of the risk of endometriosis and cancer, and it will shape the precision oncology treatment of EAOC.
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Affiliation(s)
- Tanja Pejovic
- Department of Obstetrics and Gynecology, Providence Medical Center and Providence Cancer Institute, Medford, OR 97504, USA;
| | - Ann M. Cathcart
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR 97201, USA;
| | - Rofieda Alwaqfi
- Department of Pathology and Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; (R.A.); (F.R.N.)
| | - Marjorie N. Brooks
- Department of Obstetrics and Gynecology, Providence Medical Center and Providence Cancer Institute, Medford, OR 97504, USA;
| | - Rachel Kelsall
- Pacific Northwest University of Health Sciences, Yakima, WA 98901, USA;
| | - Farr R. Nezhat
- Department of Pathology and Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; (R.A.); (F.R.N.)
- Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- NYU Long Island School of Medicine, Mineola, NY 11501, USA
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6
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Angelico G, Attanasio G, Colarossi L, Colarossi C, Montalbano M, Aiello E, Di Vendra F, Mare M, Orsi N, Memeo L. ARID1A Mutations in Gastric Cancer: A Review with Focus on Clinicopathological Features, Molecular Background and Diagnostic Interpretation. Cancers (Basel) 2024; 16:2062. [PMID: 38893181 PMCID: PMC11171396 DOI: 10.3390/cancers16112062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
AT-rich interaction domain 1 (ARID1A) is a pivotal gene with a significant role in gastrointestinal tumors which encodes a protein referred to as BAF250a or SMARCF1, an integral component of the SWI/SNF (SWItch/sucrose non-fermentable) chromatin remodeling complex. This complex is instrumental in regulating gene expression by modifying the structure of chromatin to affect the accessibility of DNA. Mutations in ARID1A have been identified in various gastrointestinal cancers, including colorectal, gastric, and pancreatic cancers. These mutations have the potential to disrupt normal SWI/SNF complex function, resulting in aberrant gene expression and potentially contributing to the initiation and progression of these malignancies. ARID1A mutations are relatively common in gastric cancer, particularly in specific adenocarcinoma subtypes. Moreover, such mutations are more frequently observed in specific molecular subtypes, such as microsatellite stable (MSS) cancers and those with a diffuse histological subtype. Understanding the presence and implications of ARID1A mutations in GC is of paramount importance for tailoring personalized treatment strategies and assessing prognosis, particularly given their potential in predicting patient response to novel treatment strategies including immunotherapy, poly(ADP) ribose polymerase (PARP) inhibitors, mammalian target of rapamycin (mTOR) inhibitors, and enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) inhibitors.
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Affiliation(s)
- Giuseppe Angelico
- Department of Medicine and Surgery, Kore University of Enna, 94100 Enna, Italy;
| | - Giulio Attanasio
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, Anatomic Pathology, University of Catania, 95123 Catania, Italy;
| | - Lorenzo Colarossi
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
| | - Cristina Colarossi
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
| | - Matteo Montalbano
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
- PhD Program in Precision Medicine, University of Palermo, 90144 Palermo, Italy
| | - Eleonora Aiello
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
| | - Federica Di Vendra
- Department of Chemical, Biological and Environmental Chemistry, University of Messina, 98122 Messina, Italy
| | - Marzia Mare
- Medical Oncology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, Viagrande, 95029 Catania, Italy
| | - Nicolas Orsi
- Leeds Institute of Medical Research, St James’s University Hospital, The University of Leeds, Leeds LS9 7TF, UK;
| | - Lorenzo Memeo
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
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7
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Zhao T, Fan J, Abu-Zaid A, Burley SK, Zheng XS. Nuclear mTOR Signaling Orchestrates Transcriptional Programs Underlying Cellular Growth and Metabolism. Cells 2024; 13:781. [PMID: 38727317 PMCID: PMC11083943 DOI: 10.3390/cells13090781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
mTOR is a central regulator of cell growth and metabolism in response to mitogenic and nutrient signals. Notably, mTOR is not only found in the cytoplasm but also in the nucleus. This review highlights direct involvement of nuclear mTOR in regulating transcription factors, orchestrating epigenetic modifications, and facilitating chromatin remodeling. These effects intricately modulate gene expression programs associated with growth and metabolic processes. Furthermore, the review underscores the importance of nuclear mTOR in mediating the interplay between metabolism and epigenetic modifications. By integrating its functions in nutrient signaling and gene expression related to growth and metabolism, nuclear mTOR emerges as a central hub governing cellular homeostasis, malignant transformation, and cancer progression. Better understanding of nuclear mTOR signaling has the potential to lead to novel therapies against cancer and other growth-related diseases.
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Affiliation(s)
- Tinghan Zhao
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jialin Fan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Ahmed Abu-Zaid
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Stephen K. Burley
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - X.F. Steven Zheng
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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8
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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9
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Künstner A, Schwarting J, Witte HM, Xing P, Bernard V, Stölting S, Lohneis P, Janke F, Salehi M, Chen X, Kusch K, Sültmann H, Chteinberg E, Fischer A, Siebert R, von Bubnoff N, Merz H, Busch H, Feller AC, Gebauer N. Genome-wide DNA methylation-analysis of blastic plasmacytoid dendritic cell neoplasm identifies distinct molecular features. Leukemia 2024; 38:1086-1098. [PMID: 38600314 DOI: 10.1038/s41375-024-02240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) constitutes a rare and aggressive malignancy originating from plasmacytoid dendritic cells (pDCs) with a primarily cutaneous tropism followed by dissemination to the bone marrow and other organs. We conducted a genome-wide analysis of the tumor methylome in an extended cohort of 45 BPDCN patients supplemented by WES and RNA-seq as well as ATAC-seq on selected cases. We determined the BPDCN DNA methylation profile and observed a dramatic loss of DNA methylation during malignant transformation from early and mature DCs towards BPDCN. DNA methylation profiles further differentiate between BPDCN, AML, CMML, and T-ALL exhibiting the most striking global demethylation, mitotic stress, and merely localized DNA hypermethylation in BPDCN resulting in pronounced inactivation of tumor suppressor genes by comparison. DNA methylation-based analysis of the tumor microenvironment by MethylCIBERSORT yielded two, prognostically relevant clusters (IC1 and IC2) with specific cellular composition and mutational spectra. Further, the transcriptional subgroups of BPDCN (C1 and C2) differ by DNA methylation signatures in interleukin/inflammatory signaling genes but also by higher transcription factor activity of JAK-STAT and NFkB signaling in C2 in contrast to an EZH2 dependence in C1-BPDCN. Our integrative characterization of BPDCN offers novel molecular insights and potential diagnostic applications.
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Affiliation(s)
- Axel Künstner
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Julian Schwarting
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hanno M Witte
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Hematology and Oncology, Federal Armed Forces Hospital Ulm, Oberer Eselsberg 40, 89081, Ulm, Germany
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Veronica Bernard
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Stephanie Stölting
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Philipp Lohneis
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Maede Salehi
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Kathrin Kusch
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Emil Chteinberg
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Hartmut Merz
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Alfred C Feller
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Niklas Gebauer
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany.
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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10
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Gao Y, Vakoc CR. Therapeutic index of targeting select chromatin complexes in human cancer patients. Curr Opin Genet Dev 2024; 85:102162. [PMID: 38401489 PMCID: PMC11072572 DOI: 10.1016/j.gde.2024.102162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 02/26/2024]
Abstract
Aberrant chromatin regulation can promote the initiation and progression of human cancer. An improved understanding of such mechanisms has resulted in the identification of cancers with an enhanced dependency on specific chromatin regulatory proteins relative to nonmalignant cell types. Hence, targeting of such complexes with small molecules has significant therapeutic potential in oncology. In recent years, several drugs have been developed and evaluated in human cancer patients, which can influence tumor biology by reprogramming of chromatin structure. In this review, we summarize several of the known mechanisms that endow cancer cells with a powerful dependency on chromatin regulation that exceeds the requirements for normal tissue homeostasis. We also summarize the remarkable small-molecule inhibitors that exploit chromatin regulator dependencies with a clear therapeutic benefit in human cancer patients.
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Affiliation(s)
- Yuan Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. https://twitter.com/@yuangao_yg
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11
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Zhang J, Chen F, Tang M, Xu W, Tian Y, Liu Z, Shu Y, Yang H, Zhu Q, Lu X, Peng B, Liu X, Xu X, Gullerova M, Zhu WG. The ARID1A-METTL3-m6A axis ensures effective RNase H1-mediated resolution of R-loops and genome stability. Cell Rep 2024; 43:113779. [PMID: 38358891 DOI: 10.1016/j.celrep.2024.113779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
R-loops are three-stranded structures that can pose threats to genome stability. RNase H1 precisely recognizes R-loops to drive their resolution within the genome, but the underlying mechanism is unclear. Here, we report that ARID1A recognizes R-loops with high affinity in an ATM-dependent manner. ARID1A recruits METTL3 and METTL14 to the R-loop, leading to the m6A methylation of R-loop RNA. This m6A modification facilitates the recruitment of RNase H1 to the R-loop, driving its resolution and promoting DNA end resection at DSBs, thereby ensuring genome stability. Depletion of ARID1A, METTL3, or METTL14 leads to R-loop accumulation and reduced cell survival upon exposure to cytotoxic agents. Therefore, ARID1A, METTL3, and METTL14 function in a coordinated, temporal order at DSB sites to recruit RNase H1 and to ensure efficient R-loop resolution. Given the association of high ARID1A levels with resistance to genotoxic therapies in patients, these findings open avenues for exploring potential therapeutic strategies for cancers with ARID1A abnormalities.
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Affiliation(s)
- Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Yuxin Shu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Hui Yang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Bin Peng
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China; Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China; School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China; Department of Biochemistry and Molecular Biology, Peking University Health Science Centre, Beijing 100191, China.
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12
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Li K, Wang B, Hu H. Research progress of SWI/SNF complex in breast cancer. Epigenetics Chromatin 2024; 17:4. [PMID: 38365747 PMCID: PMC10873968 DOI: 10.1186/s13072-024-00531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
In the past decade, numerous epigenetic mechanisms have been discovered to be associated with cancer. The mammalian SWI/SNF complex is an ATP-dependent chromatin remodeling complex whose mutations are associated with various malignancies including breast cancer. As the SWI/SNF complex has become one of the most commonly mutated complexes in cancer, targeting epigenetic mutations acquired during breast cancer progress is a potential means of improving clinical efficacy in treatment strategies. This article reviews the composition of the SWI/SNF complex, its main roles and research progress in breast cancer, and links these findings to the latest discoveries in cancer epigenomics to discuss the potential mechanisms and therapeutic potential of SWI/SNF in breast cancer.
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Affiliation(s)
- Kexuan Li
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Baocai Wang
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Haolin Hu
- Breast Center, Zhongda Hospital, School of Medicine, Southeast University, 87 Dingjiaqiao Road, Nanjing, 210009, Jiangsu, China.
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13
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Wadapurkar RM, Sivaram A, Vyas R. Computational investigations into structure and function impact of novel mutations identified in targeted exons from ovarian cancer cell lines. J Biomol Struct Dyn 2024:1-15. [PMID: 38334284 DOI: 10.1080/07391102.2024.2310776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/20/2024] [Indexed: 02/10/2024]
Abstract
The lack of sensitive and specific biomarkers for ovarian cancer leads to late stage diagnosis of the disease in a majority of the cases. Mutation accumulation is the basis for cancer progression, thus identifying mutations is an important step in the disease diagnosis. In the present study, a comprehensive analysis of fifteen Next Generation Sequencing samples from thirteen ovarian cancer cell lines was carried out for the identification of new mutations. The study revealed eight clinically significant novel mutations in six ovarian cancer oncogenes, viz. SMARCA4, ARID1A, PPP2R1A, CTNNB1, DICER1 and PIK3CA. In-depth computational analysis revealed that the mutations affected the structure of the proteins in terms of stability, solvent accessible surface area and molecular dynamics. Moreover, the mutations were present in functionally significant domains of the proteins, thereby adversely affecting the protein functionality. PPI network for SMARCA4, CTNNB1, DICER1, PIK3CA, PPP2R1A and ARID1A showed that these genes were involved in certain significant pathways affecting various hallmarks of cancer. For further validation, in vitro studies were performed that revealed hypermutability of the CTNNB1 gene. Through this study we have identified some key mutations and have analysed their structural and functional impact. The study establishes some key mutations, which can be potentially explored as biomarker and drug target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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14
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Kaushik K, Kumar H, Mehta S, Palanichamy JK. Hypoxia increases the biogenesis of IGF2BP3-bound circular RNAs. Mol Biol Rep 2024; 51:288. [PMID: 38329630 DOI: 10.1007/s11033-024-09230-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND Insulin-like Growth Factor 2 Binding Protein 3 (IGF2BP3) promotes cancer migration and invasion by binding to several coding and non-coding RNAs. Hypoxia stimulates tumor progression by upregulating Hypoxia Inducible Factors and downstream signaling. Quaking (QKI) gene, which is upregulated in hypoxia and promotes epithelial to mesenchymal transition (EMT), induces circular RNAs. Therefore, the axis between IGF2BP3, QKI, circular RNAs and their respective host genes under hypoxia was studied. METHODS AND RESULTS Several IGF2BP3-bound circular RNAs were previously identified in HepG2. There were 13 circRNAs originating from 8 host genes bound to IGF2BP3. We confirmed their binding to IGF2BP3 in U87MG using an RNA Immunoprecipitation assay. MALAT1, an oncogenic lncRNA was also found to be associated with IGF2BP3. Three adherent cell lines expressing high levels of IGF2BP3 viz., HeLa, HepG2 and U87MG were cultured under normoxia (20%O2) and hypoxia (<0.2%O2) for 48-168 h. Expression of IGF2BP3, QKI, EMT markers, IGF2BP3-bound circRNAs and their host mRNAs expression were assessed by quantitative real-time PCR (qRT-PCR) in both normoxia and hypoxia. The hypoxia markers viz., VEGF and CA9 were upregulated in all the cell lines in hypoxia at all time points along with an increase in SNAIL. We found 6 genes, viz., PHC3, CDYL, ANKRD17, ARID1A, NEIL3 and FNDC3B with increased expression both at the mRNA and circRNA level indicating their synergistic role in tumor initiation. Overall, we found that circRNA to mRNA expression was observed to be increased for most of the genes and time points of hypoxia in all the cell lines. IGF2BP3 and QKI were also upregulated in hypoxia indicating their role in circRNA biogenesis and stability. CONCLUSION Our data implies that hypoxia augments circRNA biogenesis which might subsequently play a role in tumor progression.
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Affiliation(s)
- Kriti Kaushik
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, Convergence Block, New Delhi, 110029, India
| | - Hemant Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, Convergence Block, New Delhi, 110029, India
| | - Samriddhi Mehta
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Jayanth Kumar Palanichamy
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, Convergence Block, New Delhi, 110029, India.
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15
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Hein KZ, Stephen B, Fu S. Therapeutic Role of Synthetic Lethality in ARID1A-Deficient Malignancies. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2024; 7:41-52. [PMID: 38327752 PMCID: PMC10846636 DOI: 10.36401/jipo-22-37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/28/2023] [Accepted: 09/21/2023] [Indexed: 02/09/2024]
Abstract
AT-rich interaction domain 1A (ARID1A), a mammalian switch/sucrose nonfermenting complex subunit, modulates several cellular processes by regulating chromatin accessibility. It is encoded by ARID1A, an immunosuppressive gene frequently disrupted in a many tumors, affecting the proliferation, migration, and invasion of cancer cells. Targeting molecular pathways and epigenetic regulation associated with ARID1A loss, such as inhibiting the PI3K/AKT pathway or modulating Wnt/β-catenin signaling, may help suppress tumor growth and progression. Developing epigenetic drugs like histone deacetylase or DNA methyltransferase inhibitors could restore normal chromatin structure and function in cells with ARID1A loss. As ARID1A deficiency correlates with enhanced tumor mutability, microsatellite instability, high tumor mutation burden, increased programmed death-ligand 1 expression, and T-lymphocyte infiltration, ARID1A-deficient cells can be a potential therapeutic target for immune checkpoint inhibitors that warrants further exploration. In this review, we discuss the role of ARID1A in carcinogenesis, its crosstalk with other signaling pathways, and strategies to make ARID1A-deficient cells a potential therapeutic target for patients with cancer.
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Affiliation(s)
- Kyaw Z. Hein
- Department of Internal Medicine, HCA Florida Westside Hospital, Plantation, FL, USA
| | - Bettzy Stephen
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Abraham A, Samaniego-Castruita D, Paladino J, Han I, Ramesh P, Tran MT, Southern RM, Shukla A, Shukla V. Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient Germinal Center B cell responses. RESEARCH SQUARE 2024:rs.3.rs-3871185. [PMID: 38313292 PMCID: PMC10836118 DOI: 10.21203/rs.3.rs-3871185/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Differentiating B cells in germinal centers (GC) require tightly coordinated transcriptional and epigenetic transitions to generate efficient humoral immune responses. The mammalian Brg1/Brm-associated factor (BAF) complexes are major regulators of nucleosomal remodeling, crucial for cellular differentiation and development, and are commonly mutated in several cancers, including GC-derived B cell lymphomas. However, the specific roles of distinct BAF complexes in GC B cell biology and generation of functional humoral immune responses are not well understood. Here, we show that the A-T Rich Interaction Domain 1a (Arid1a) containing canonical BAF (cBAF) complex is required for maintenance of GCs and therefore high affinity antibody responses. While Arid1a-deficient B cells undergo activation to initiate GC responses, they fail to sustain the GC program resulting in premature GC collapse. We discovered that Arid1a-dependent cBAF activity establishes permissive chromatin landscapes during B cell activation and is concomitantly required to suppress inflammatory gene programs to maintain transcriptional fidelity in early GC B cells. Interestingly, the inflammatory signatures instigated by Arid1a deficiency in early GC B cells recruited neutrophils and inflammatory monocytes and eventually disrupted GC homeostasis. Dampening of inflammatory cues with anti-inflammatory glucocorticoid receptor signaling rescued GC B cell differentiation of Arid1a-deficient B cells, thus highlighting a critical role of inflammation in impeding GC responses. In sum, our work identifies essential functions of Arid1a-dependent BAF activity in promoting efficient GC responses. These findings further support an emerging paradigm in which unrestrained inflammation limits GC-derived humoral responses, as reported in the context of severe bacterial and viral infections.
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Affiliation(s)
- Ajay Abraham
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
- Center for Human Immunobiology, Northwestern University, Chicago, Illinois, USA, 60611
| | | | - Jillian Paladino
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Isabella Han
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Prathyaya Ramesh
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Mi Thao Tran
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Rebecca M Southern
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Ashima Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA, 60611
- Center for Human Immunobiology, Northwestern University, Chicago, Illinois, USA, 60611
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17
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Xing T, Li L, Rao X, Zhao J, Chen Y, Ju G, Xu Y, Gao X, Dong G, Xia X, Guan Y, Zhang L, Wen Z, Liang J. ARID1A deficiency promotes progression and potentiates therapeutic antitumour immunity in hepatitis B virus-related hepatocellular carcinoma. BMC Gastroenterol 2024; 24:11. [PMID: 38166741 PMCID: PMC10759659 DOI: 10.1186/s12876-023-03059-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Exploring predictive biomarkers and therapeutic strategies of ICBs has become an urgent need in clinical practice. Increasing evidence has shown that ARID1A deficiency might play a critical role in sculpting tumor environments in various tumors and might be used as pan-cancer biomarkers for immunotherapy outcomes. The current study aims to explored the immune-modulating role of ARID1A deficiency in Hepatitis B virus (HBV) related hepatocellular carcinoma (HBV-HCC) and its potential immunotherapeutic implications. METHODS In the current study, we performed a comprehensive analysis using bioinformatics approaches and pre-clinical experiments to evaluate the ARID1A regulatory role on the biological behavior, and immune landscape of Hepatitis B virus (HBV) related hepatocellular carcinoma (HBV-HCC). A total of 425 HBV-related hepatocellular carcinoma patients from TCGA-LIHC, AMC and CHCC-HBV cohort were enrolled in bioinformatics analysis. Immunohistochemical staining of HBV-HCC specimens and ARID1A deficiency cellular models were used to validate the results of the analysis. RESULTS Our results have shown that ARID1A deficiency promoted tumor proliferation and metastasis. More importantly, ARID1A deficiency in HBV-HCC was associated with the higher TMB, elevated immune activity, and up-regulated expression of immune checkpoint proteins, especially TIM-3 in HBV-HCC. Further, the expression of Galectin-9, which is the ligand of TIM-3, was elevated in the ARID1A knockout HBV positive cell line. CONCLUSION To conclude, we have shown that the ARID1A deficiency was correlated with more active immune signatures and higher expression of immune checkpoints in HBV-HCC. Additionally, the present study provides insights to explore the possibility of the predictive role of ARID1A in HBV-HCC patients responsive to immunotherapy.
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Affiliation(s)
- Tao Xing
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No. 52, Fucheng Road, Haidian District, Beijing, 100142, China
| | - Li Li
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China
| | - Xiaosong Rao
- HAINAN YILING Medical Industry Development Co.,Ldt, Qionghai, Hainan, 571442, China
| | - Jing Zhao
- Department of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, 72074, Germany
| | - Yiran Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Gaoda Ju
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China
| | - Yaping Xu
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Guilan Dong
- Tangshan People's Hospital, Tangshan, Hebei, 063001, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Lingling Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No. 52, Fucheng Road, Haidian District, Beijing, 100142, China.
| | - Zhenping Wen
- Inner Mongolia Cancer Hospital, 42 Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia, 010020, P. R. China.
| | - Jun Liang
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China.
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No. 52, Fucheng Road, Haidian District, Beijing, 100142, China.
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18
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Mandal J, Yu ZC, Shih IM, Wang TL. ARID1A loss activates MAPK signaling via DUSP4 downregulation. J Biomed Sci 2023; 30:94. [PMID: 38071325 PMCID: PMC10709884 DOI: 10.1186/s12929-023-00985-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/12/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND ARID1A, a tumor suppressor gene encoding BAF250, a protein participating in chromatin remodeling, is frequently mutated in endometrium-related malignancies, including ovarian or uterine clear cell carcinoma (CCC) and endometrioid carcinoma (EMCA). However, how ARID1A mutations alter downstream signaling to promote tumor development is yet to be established. METHODS We used RNA-sequencing (RNA-seq) to explore transcriptomic changes in isogenic human endometrial epithelial cells after deleting ARID1A. Chromatin immunoprecipitation sequencing (ChIP-seq) was employed to assess the active or repressive histone marks on DUSP4 promoter and regulatory regions. We validated our findings using genetically engineered murine endometroid carcinoma models, human endometroid carcinoma tissues, and in silico approaches. RESULTS RNA-seq revealed the downregulation of the MAPK phosphatase dual-specificity phosphatase 4 (DUSP4) in ARID1A-deficient cells. ChIP-seq demonstrated decreased histone acetylation marks (H3K27Ac, H3K9Ac) on DUSP4 regulatory regions as one of the causes for DUSP4 downregulation in ARID1A-deficient cells. Ectopic DUSP4 expression decreased cell proliferation, and pharmacologically inhibiting the MAPK pathway significantly mitigated tumor formation in vivo. CONCLUSIONS Our findings suggest that ARID1A protein transcriptionally modulates DUSP4 expression by remodeling chromatin, subsequently inactivating the MAPK pathway, leading to tumor suppression. The ARID1A-DUSP4-MAPK axis may be further considered for developing targeted therapies against ARID1A-mutated cancers.
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Affiliation(s)
- Jayaprakash Mandal
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zheng-Cheng Yu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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19
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Zhang X, Zhang Y, Zhang Q, Lu M, Chen Y, Zhang X, Zhang P. Role of AT-rich interaction domain 1A in gastric cancer immunotherapy: Preclinical and clinical perspectives. J Cell Mol Med 2023; 28:e18063. [PMID: 38041544 PMCID: PMC10902580 DOI: 10.1111/jcmm.18063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/31/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
The application of immune checkpoint inhibitor (ICI) using monoclonal antibodies has brought about a profound transformation in the clinical outcomes for patients grappling with advanced gastric cancer (GC). Nonetheless, despite these achievements, the quest for effective functional biomarkers for ICI therapy remains constrained. Recent research endeavours have shed light on the critical involvement of modified epigenetic regulators in the pathogenesis of gastric tumorigenesis, thus providing a glimpse into potential biomarkers. Among these regulatory factors, AT-rich interaction domain 1A (ARID1A), a pivotal constituent of the switch/sucrose non-fermentable (SWI/SNF) complex, has emerged as a promising candidate. Investigations have unveiled the pivotal role of ARID1A in bridging the gap between genome instability and the reconfiguration of the tumour immune microenvironment, culminating in an enhanced response to ICI within the landscape of gastric cancer treatment. This all-encompassing review aims to dissect the potential of ARID1A as a valuable biomarker for immunotherapeutic approaches in gastric cancer, drawing from insights garnered from both preclinical experimentation and clinical observations.
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Affiliation(s)
- Xuemei Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Youzhi Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Qiaoyun Zhang
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Mengyao Lu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery, Huai'an Second People's Hospital, the Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Xing B, Zhang X, Gu X, Xiang L, Wang C, Jin Y. Explore the alterations of downstream molecular pathways caused by ARID1A mutation/knockout in human endometrial cancer cells. J Cancer Res Clin Oncol 2023; 149:17529-17541. [PMID: 37906351 DOI: 10.1007/s00432-023-05471-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023]
Abstract
PURPOSE As one of the most common gynecologic malignancies, endometrial cancer (EC) is driven by multiple genetic alterations that may be targeted for treatments. AT-rich interaction domain 1A (ARID1A) gene mutations were reported as early events in endometrial carcinogenesis. METHODS To explore the alterations of downstream molecular pathways caused by ARID1A mutations and the associated therapeutic implications, we edited ARID1A gene in human endometrial cancer cell line Ishikawa using the Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-Associated Proteins (CRISPR/Cas9) technology. We successfully constructed a stable Ishikawa cell line with a confirmed 10 bp deletion on the ARID1A gene, which resulted in a code-shift mutation and gene knockout. RESULTS Compared with unedited wild-type cells, ARID1A knockout (KO) led to reduced apoptosis, accelerated transformation from G0/G1 to S phase, and enhanced cell proliferation. ARID1A deficiency would reduce the protein levels of p21, caspase 7, and caspase 9 in Ishikawa endometrial cancer cells compared with the wild-type cells. In addition, ARID1A KO resulted in high levels of microsatellite instability (MSI-H). Moreover, transcriptomic analyses showed that ARID1A KO can lead to activated phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling. Furthermore, experimental analyses demonstrated that ARID1A KO cells had reduced expression of genetic instability-associated markers mutL homologue 1 (MLH1) and progesterone receptor B (PR) and increased p-Akt expression. CONCLUSION These findings support further exploration of ARID1A as a therapeutic target for EC and provide insight into developing more effective treatments in EC, such as the combinatory use of immune checkpoint inhibitors.
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Affiliation(s)
- Baoling Xing
- Department of Pathology, Affiliated Zhoupu Hospital of Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
| | - Xiaoying Zhang
- Department of Pathology, Affiliated Zhoupu Hospital of Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Xia Gu
- Department of Pathology, Affiliated Zhoupu Hospital of Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Lintao Xiang
- Department of Pathology, Affiliated Zhoupu Hospital of Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Cuiping Wang
- College of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yueling Jin
- Management Department of Scientific Research, Shanghai Science and Technology Museum, Shanghai, 200127, China
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Lu S, Duan R, Cong L, Song Y. The effects of ARID1A mutation in gastric cancer and its significance for treatment. Cancer Cell Int 2023; 23:296. [PMID: 38008753 PMCID: PMC10676575 DOI: 10.1186/s12935-023-03154-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023] Open
Abstract
Gastric cancer (GC) has emerged as a significant issue in public health all worldwide as a result of its high mortality rate and dismal prognosis. AT-rich interactive domain 1 A (ARID1A) is a vital component of the switch/sucrose-non-fermentable (SWI/SNF) chromatin remodeling complex, and ARID1A mutations occur in various tumors, leading to protein loss and decreased expression; it then affects the tumor biological behavior or prognosis. More significantly, ARID1A mutations will likely be biological markers for immune checkpoint blockade (ICB) treatment and selective targeted therapy. To provide theoretical support for future research on the stratification of individuals with gastric cancer with ARID1A as a biomarker to achieve precision therapy, we have focused on the clinical significance, predictive value, underlying mechanisms, and possible treatment strategies for ARID1A mutations in gastric cancer in this review.
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Affiliation(s)
- Shan Lu
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China
| | - Ruifeng Duan
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China
| | - Liang Cong
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China
| | - Ying Song
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China.
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Xing T, Li L, Chen Y, Ju G, Li G, Zhu X, Ren Y, Zhao J, Cheng Z, Li Y, Xu D, Liang J. Targeting the TCA cycle through cuproptosis confers synthetic lethality on ARID1A-deficient hepatocellular carcinoma. Cell Rep Med 2023; 4:101264. [PMID: 37939712 PMCID: PMC10694624 DOI: 10.1016/j.xcrm.2023.101264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/10/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023]
Abstract
ARID1A is among the most commonly mutated tumor suppressor genes in hepatocellular carcinoma (HCC). In this study, we conduct a CRISPR-Cas9 synthetic lethality screen using ARID1A-deficient HCC cells to identify approaches to treat HCC patients harboring ARID1A deficiency. This strategy reveals that the survival of these ARID1A-deficient HCC cells is highly dependent on genes related to the tricarboxylic acid (TCA) cycle. Mechanistically, ARID1A loss represses expression of key glycolysis-related gene PKM, shifting cellular glucose metabolism from aerobic glycolysis to dependence on the TCA cycle and oxidative phosphorylation. Cuproptosis is a recently defined form of copper-induced cell death reported to directly target the TCA cycle. Here, we find that ARID1A-deficient HCC cells and xenograft tumors are highly sensitive to copper treatment. Together, these results offer evidence of the synthetic lethality between ARID1A deficiency and mitochondrial respiration impairment, suggesting that copper treatment constitutes a promising therapeutic strategy for selectively targeting ARID1A-deficient HCC.
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Affiliation(s)
- Tao Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Li Li
- Department of Oncology, Peking University International Hospital, Beijing 102206, China
| | - Yiran Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China
| | - Gaoda Ju
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Guilan Li
- Department of Pathology, Peking University International Hospital, Beijing 102206, China
| | - Xiaoyun Zhu
- Department of Pathology, Peking University International Hospital, Beijing 102206, China
| | - Yubo Ren
- Department of Pathology, Peking University International Hospital, Beijing 102206, China
| | - Jing Zhao
- Department of Pathology and Neuropathology, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Zhilei Cheng
- Department of Hepatobiliary Surgery, Peking University International Hospital, Beijing 102206, China
| | - Yan Li
- Department of Hematology, Peking University International Hospital, Beijing 102206, China
| | - Da Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Hepatopancreatobiliary Surgery Department I, Peking University Cancer Hospital & Institute, Beijing 100142, China.
| | - Jun Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China; Department of Oncology, Peking University International Hospital, Beijing 102206, China.
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23
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Li Y, Liu Y, Yang K, Jin L, Yang J, Huang S, Liu Y, Hu B, Liu R, Liu W, Liu A, Zheng Q, Zhang Y. Impact of ARID1A and TP53 mutations in pediatric refractory or relapsed mature B-Cell lymphoma treated with CAR-T cell therapy. Cancer Cell Int 2023; 23:281. [PMID: 37981695 PMCID: PMC10657579 DOI: 10.1186/s12935-023-03122-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/02/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR)-T cell therapy has been used to treat pediatric refractory or relapsed mature B-cell non-Hodgkin lymphoma (r/r MB-NHL) with significantly improved outcomes, but a proportion of patients display no response or experience relapse after treatment. To investigate whether tumor-intrinsic somatic genetic alterations have an impact on CAR-T cell treatment, the genetic features and treatment outcomes of 89 children with MB-NHL were analyzed. METHODS 89 pediatric patients treated at multiple clinical centers of the China Net Childhood Lymphoma (CNCL) were included in this study. Targeted next-generation sequencing for a panel of lymphoma-related genes was performed on tumor samples. Survival rates and relapse by genetic features and clinical factors were analyzed. Survival curves were calculated using a log-rank (Mantel-Cox) test. The Wilcox sum-rank test and Fisher's exact test were applied to test for group differences. RESULTS A total of 89 driver genes with somatic mutations were identified. The most frequently mutated genes were TP53 (66%), ID3 (55%), and ARID1A (31%). The incidence of ARID1A mutation and co-mutation of TP53 and ARID1A was high in patients with r/r MB-NHL (P = 0.006; P = 0.018, respectively). CAR-T cell treatment significantly improved survival in r/r MB-NHL patients (P = 0.00081), but patients with ARID1A or ARID1A and TP53 co-mutation had poor survival compared to those without such mutations. CONCLUSION These results indicate that children with MB-NHL harboring ARID1A or TP53 and ARID1A co-mutation are insensitive to initial conventional chemotherapy and subsequent CAR-T cell treatment. Examination of ARID1A and TP53 mutation status at baseline might have prognostic value, and risk-adapted or more effective therapies should be considered for patients with these high-risk genetic alterations.
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Affiliation(s)
- Yang Li
- Molecular diagnostics laboratory, Beijing GoBroad Boren Hospital, Beijing, China
| | - Yang Liu
- Department of Pediatric Lymphoma, Beijing GoBroad Boren Hospital, Beijing, China
| | - Keyan Yang
- Molecular diagnostics laboratory, Beijing GoBroad Boren Hospital, Beijing, China
| | - Ling Jin
- Department of Hematology/Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jing Yang
- Department of Hematology/Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Shuang Huang
- Department of Hematology/Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Ying Liu
- Department of Pediatric Lymphoma, Beijing GoBroad Boren Hospital, Beijing, China
| | - Bo Hu
- Department of Pediatric Lymphoma, Beijing GoBroad Boren Hospital, Beijing, China
| | - Rong Liu
- Department of Hematology/Oncology, Capital institute of pediatric, Beijing, China
| | - Wei Liu
- Department of Hematology/Oncology, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Ansheng Liu
- Department of Hematology/Oncology, Xian Children's Hospital, Xi'An, China
| | - Qinlong Zheng
- Molecular diagnostics laboratory, Beijing GoBroad Boren Hospital, Beijing, China.
| | - Yonghong Zhang
- Department of Pediatric Lymphoma, Beijing GoBroad Boren Hospital, Beijing, China.
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Kordowitzki P, Mechsner S, Sehouli J. ARID1a Gene as a Potential Early Marker to Tackle Endometriosis-Associated Ovarian Cancer. Aging Dis 2023:AD.2023.1109. [PMID: 38029403 DOI: 10.14336/ad.2023.1109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
The worries of women with endometriosis - a chronic gynecological disease affecting approximately 10% of women of childbearing age - about the increased risk of ovarian cancer are present worldwide. Endometriosis is a common, often painful, but benign gynecological disease that affects women. However, the pathogenesis remains elusive but is certainly multifactorial. Interestingly, endometriosis shares similarities with cancer. Therefore, women suffering from endometriosis fear an increased risk of ovarian cancer. In addition, these patients suffer from anxiety and depression. Previous studies have provided evidence that epithelial mutations in endometriosis or in the endometrium include certain inactivating mutations responsible for ovarian cancer, such as in the ARID1A gene.
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Affiliation(s)
- Pawel Kordowitzki
- Department of Preclinical and Basic Sciences, Nicolaus Copernicus University, Torun, Poland
- Department of Gynecology including Center of Oncological Surgery (CVK) and Department of Gynecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany
| | - Sylvia Mechsner
- Department of Gynecology including Center of Oncological Surgery (CVK) and Department of Gynecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany
| | - Jalid Sehouli
- Department of Gynecology including Center of Oncological Surgery (CVK) and Department of Gynecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany
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25
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Guo CC, Xu HE, Ma X. ARID3a from the ARID family: structure, role in autoimmune diseases and drug discovery. Acta Pharmacol Sin 2023; 44:2139-2150. [PMID: 37488425 PMCID: PMC10618457 DOI: 10.1038/s41401-023-01134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/09/2023] [Indexed: 07/26/2023] Open
Abstract
The AT-rich interaction domain (ARID) family of DNA-binding proteins is a group of transcription factors and chromatin regulators with a highly conserved ARID domain that recognizes specific AT-rich DNA sequences. Dysfunction of ARID family members has been implicated in various human diseases including cancers and intellectual disability. Among them, ARID3a has gained increasing attention due to its potential involvement in autoimmunity. In this article we provide an overview of the ARID family, focusing on the structure and biological functions of ARID3a. It explores the role of ARID3a in autoreactive B cells and its contribution to autoimmune diseases such as systemic lupus erythematosus and primary biliary cholangitis. Furthermore, we also discuss the potential for drug discovery targeting ARID3a and present a plan for future research in this field.
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Affiliation(s)
- Cheng-Cen Guo
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
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26
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Hahn E, Xu B, Katabi N, Dogan S, Smith SM, Perez-Ordonez B, Patel PB, MacMillan C, Lubin DJ, Gagan J, Weinreb I, Bishop JA. Comprehensive Molecular Characterization of Polymorphous Adenocarcinoma, Cribriform Subtype: Identifying Novel Fusions and Fusion Partners. Mod Pathol 2023; 36:100305. [PMID: 37595638 PMCID: PMC11225962 DOI: 10.1016/j.modpat.2023.100305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
Polymorphous adenocarcinoma (PAC) is a common, usually low-grade salivary gland carcinoma. While conventional PACs are most associated with PRKD1 p.E710D hotspot mutations, the cribriform subtype is often associated with gene fusions in PRKD1, PRKD2, or PRKD3. These fusions have been primarily identified by fluorescence in situ hybridization (FISH) analysis, with a minority evaluated by next-generation sequencing (NGS). Many of the reported fusions were detected by break-apart FISH probes and therefore have unknown partners or were negative by FISH altogether. In this study, we aimed to further characterize the fusions associated with PAC with NGS. Fifty-four PACs (exclusively cribriform and mixed/intermediate types to enrich the study for fusion-positive cases) were identified and subjected to NGS. Fifty-one cases were successfully sequenced, 28 of which demonstrated gene fusions involving PRKD1, PRKD2, or PRKD3. There were 10 cases with the PRKD1 p.E710D mutation. We identified a diverse group of fusion partners, including 13 novel partners, 3 of which were recurrent. The most common partners for the PRKD genes were ARID1A and ARID1B. The wide variety of involved genes is unlike in other salivary gland malignancies and warrants a broader strategy of sequencing for molecular confirmation for particularly challenging cases, as our NGS study shows.
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Affiliation(s)
- Elan Hahn
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada.
| | - Bin Xu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen M Smith
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Bayardo Perez-Ordonez
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | | | - Christina MacMillan
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Daniel J Lubin
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ilan Weinreb
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
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27
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Rock A, Uche A, Yoon J, Agulnik M, Chow W, Millis S. Bioinformatic Analysis of Recurrent Genomic Alterations and Corresponding Pathway Alterations in Ewing Sarcoma. J Pers Med 2023; 13:1499. [PMID: 37888109 PMCID: PMC10608227 DOI: 10.3390/jpm13101499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
Ewing Sarcoma (ES) is an aggressive, mesenchymal malignancy associated with a poor prognosis in the recurrent or metastatic setting with an estimated overall survival (OS) of <30% at 5 years. ES is characterized by a balanced, reciprocal chromosomal translocation involving the EWSR1 RNA-binding protein and ETS transcription factor gene (EWS-FLI being the most common). Interestingly, murine ES models have failed to produce tumors phenotypically representative of ES. Genomic alterations (GA) in ES are infrequent and may work synergistically with EWS-ETS translocations to promote oncogenesis. Aberrations in fibroblast growth factor receptor (FGFR4), a receptor tyrosine kinase (RTK) have been shown to contribute to carcinogenesis. Mouse embryonic fibroblasts (MEFs) derived from knock-in strain of homologous Fgfr4G385R mice display a transformed phenotype with enhanced TGF-induced mammary carcinogenesis. The association between the FGFRG388R SNV in high-grade soft tissue sarcomas has previously been demonstrated conferring a statistically significant association with poorer OS. How the FGFR4G388R SNV specifically relates to ES has not previously been delineated. To further define the genomic landscape and corresponding pathway alterations in ES, comprehensive genomic profiling (CGP) was performed on the tumors of 189 ES patients. The FGFR4G388R SNV was identified in a significant proportion of the evaluable cases (n = 97, 51%). In line with previous analyses, TP53 (n = 36, 19%), CDK2NA/B (n = 33, 17%), and STAG2 (n = 22, 11.6%) represented the most frequent alterations in our cohort. Co-occurrence of CDK2NA and STAG2 alterations was observed (n = 5, 3%). Notably, we identified a higher proportion of TP53 mutations than previously observed. The most frequent pathway alterations affected MAPK (n = 89, 24% of pathological samples), HRR (n = 75, 25%), Notch1 (n = 69, 23%), Histone/Chromatin remodeling (n = 57, 24%), and PI3K (n = 64, 20%). These findings help to further elucidate the genomic landscape of ES with a novel investigation of the FGFR4G388R SNV revealing frequent aberration.
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Affiliation(s)
- Adam Rock
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - An Uche
- Alameda Health System, 1411 E. 31st St., Oakland, CA 94602, USA;
| | - Janet Yoon
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Mark Agulnik
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Warren Chow
- UCI Health, 101 The City Drive, South Orange, CA 92868, USA;
| | - Sherri Millis
- Foundation Medicine, Inc., 150 Second St., Cambridge, MA 02141, USA;
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Liu PP, Lu SP, Li X, Tang GB, Liu X, Dai SK, Jiao LF, Lin XW, Li XG, Hu B, Jiao J, Teng ZQ, Han CS, Liu CM. Abnormal chromatin remodeling caused by ARID1A deletion leads to malformation of the dentate gyrus. Cell Death Differ 2023; 30:2187-2199. [PMID: 37543710 PMCID: PMC10483045 DOI: 10.1038/s41418-023-01199-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/15/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
ARID1A, an SWI/SNF chromatin-remodeling gene, is commonly mutated in cancer and hypothesized to be a tumor suppressor. Recently, loss-of-function of ARID1A gene has been shown to cause intellectual disability. Here we generate Arid1a conditional knockout mice and investigate Arid1a function in the hippocampus. Disruption of Arid1a in mouse forebrain significantly decreases neural stem/progenitor cells (NSPCs) proliferation and differentiation to neurons within the dentate gyrus (DG), increasing perinatal and postnatal apoptosis, leading to reduced hippocampus size. Moreover, we perform single-cell RNA sequencing (scRNA-seq) to investigate cellular heterogeneity and reveal that Arid1a is necessary for the maintenance of the DG progenitor pool and survival of post-mitotic neurons. Transcriptome and ChIP-seq analysis data demonstrate that ARID1A specifically regulates Prox1 by altering the levels of histone modifications. Overexpression of downstream target Prox1 can rescue proliferation and differentiation defects of NSPCs caused by Arid1a deletion. Overall, our results demonstrate a critical role for Arid1a in the development of the hippocampus and may also provide insight into the genetic basis of intellectual disabilities such as Coffin-Siris syndrome, which is caused by germ-line mutations or microduplication of Arid1a.
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Affiliation(s)
- Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Shi-Ping Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xiao Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gang-Bin Tang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin-Fei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Wen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences, China Medical University, No.91, Hsueh-Shih Road, Taichung, 40402, Taiwan
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chun-Sheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Hinsberger M, Becker-Kettern J, Jürgens-Wemheuer WM, Oertel J, Schulz-Schaeffer WJ. Development of an Enzyme-Linked Immunosorbent Assay (ELISA) for the Quantification of ARID1A in Tissue Lysates. Cancers (Basel) 2023; 15:4096. [PMID: 37627124 PMCID: PMC10452747 DOI: 10.3390/cancers15164096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
ARID1A is a subunit of the mammalian SWI/SNF complex, which is thought to regulate gene expression through restructuring chromatin structures. Its gene ARID1A is frequently mutated and ARID1A levels are lowered in several human cancers, especially gynecologic ones. A functional ARID1A loss may have prognostic or predictive value in terms of therapeutic strategies but has not been proposed based on a quantitative method. Hardly any literature is available on ARID1A levels in tumor samples. We developed an indirect enzyme-linked immunosorbent assay (ELISA) for ARID1A based on the current EMA and FDA criteria. We demonstrated that our ELISA provides the objective, accurate, and precise quantification of ARID1A concentrations in recombinant protein solutions, cell culture standards, and tissue lysates of tumors. A standard curve analysis yielded a 'goodness of fit' of R2 = 0.99. Standards measured on several plates and days achieved an inter-assay accuracy of 90.26% and an inter-assay precision with a coefficient of variation of 4.53%. When tumor lysates were prepared and measured multiple times, our method had an inter-assay precision with a coefficient of variation of 11.78%. We believe that our suggested method ensures a high reproducibility and can be used for a high sample throughput to determine the ARID1A concentration in different tumor entities. The application of our ELISA on various tumor and control tissues will allow us to explore whether quantitative ARID1A measurements in tumor samples are of predictive value.
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Affiliation(s)
- Manuel Hinsberger
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
| | - Julia Becker-Kettern
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
| | - Wiebke M. Jürgens-Wemheuer
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
| | - Joachim Oertel
- Department of Neurosurgery, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany;
| | - Walter J. Schulz-Schaeffer
- Institute for Neuropathology, Medical Faculty, Saarland University, Building 90.3, 66421 Homburg, Saar, Germany (J.B.-K.); (W.M.J.-W.)
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Achom M, Sadagopan A, Bao C, McBride F, Xu Q, Konda P, Tourdot RW, Li J, Nakhoul M, Gallant DS, Ahmed UA, O’Toole J, Freeman D, Mary Lee GS, Hecht JL, Kauffman EC, Einstein DJ, Choueiri TK, Zhang CZ, Viswanathan SR. A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552029. [PMID: 37577497 PMCID: PMC10418269 DOI: 10.1101/2023.08.04.552029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Xp11 translocation renal cell carcinoma (tRCC) is a female-predominant kidney cancer driven by translocations between the TFE3 gene on chromosome Xp11.2 and partner genes located on either chrX or on autosomes. The rearrangement processes that underlie TFE3 fusions, and whether they are linked to the female sex bias of this cancer, are largely unexplored. Moreover, whether oncogenic TFE3 fusions arise from both the active and inactive X chromosomes in females remains unknown. Here we address these questions by haplotype-specific analyses of whole-genome sequences of 29 tRCC samples from 15 patients and by re-analysis of 145 published tRCC whole-exome sequences. We show that TFE3 fusions universally arise as reciprocal translocations with minimal DNA loss or insertion at paired break ends. Strikingly, we observe a near exact 2:1 female:male ratio in TFE3 fusions arising via X:autosomal translocation (but not via X inversion), which accounts for the female predominance of tRCC. This 2:1 ratio is at least partially attributable to oncogenic fusions involving the inactive X chromosome and is accompanied by partial re-activation of silenced chrX genes on the rearranged chromosome. Our results highlight how somatic alterations involving the X chromosome place unique constraints on tumor initiation and exemplify how genetic rearrangements of the sex chromosomes can underlie cancer sex differences.
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Affiliation(s)
- Mingkee Achom
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Chunyang Bao
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Fiona McBride
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Qingru Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Richard W. Tourdot
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Maria Nakhoul
- Department of Informatics & Analytics, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Daniel S. Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Usman Ali Ahmed
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jillian O’Toole
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jonathan L. Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Eric C Kauffman
- Department of Urology, Roswell Park Comprehensive Cancer Center; Buffalo, New York, USA
| | - David J Einstein
- Division of Medical Oncology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
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Qu J, Tao D, Huang W, Lu L, Fan J, Zhang S, Huang F. Assessment of prognostic role of a novel 7-lncRNA signature in HCC patients. Heliyon 2023; 9:e18493. [PMID: 37520979 PMCID: PMC10382640 DOI: 10.1016/j.heliyon.2023.e18493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is characterized by extensive risk factors, high morbidity and mortality. Clinical prognostic evaluation assay assumes a nonspecific quality. Better HCC prognostics are urgently needed. Long noncoding RNAs (lncRNAs) exerts a crucial role in tumorigenesis and development. Excavating specific lncRNAs signature to ameliorate the high-risk survival prediction in HCC patients is worthwhile. Methods Differentially expressed lncRNAs (DElncRNAs) profile was acquired from The Cancer Genome Atlas database (TCGA). Then, the lncRNAs high-risk survival prognostic model was established using the least absolute shrinkage and selection operator (LASSO)-Cox regression algorithm. The lncRNAs were evaluated in clinical specimen by PCR. The receiver operating characteristic curve (ROC) analysis was further conducted to assess the potential prognostic value of the model. Moreover, a visible nomogram containing clinicopathological features and prognostic model was developed for prediction of survival property. Potential molecular mechanism was assessed by GO, KEGG, GSEA enrichment analysis and CIBERSORT immune infiltration analysis. Results A novel 7-lncRNA risk model (AL161937.2, LINC01063, AC145207.5, POLH-AS1, LNCSRLR, MKLN1-AS, AC105345.1) was constructed and validated for HCC prognosis prediction. Kaplan-Meier analysis revealed that patients in the high-risk group suffered a poor prognosis (p = 1.813 × 10-8). These genes were detected by PCR, and the expression trend was in accordance with TCGA database. Interestingly, the risk score served as an independent risk factor for HCC patients (HR: 1.166, 95% CI:1.119-1.214, p < 0.001). The nomogram was established, and the predictive accuracy in the nomogram was prior to the TNM stage according to the ROC curve analysis. Cell proliferation related pathway, decreased CD4+ T cell, CD8+ T cell, NK cell and elevated Neutrophil, Macrophage M0 were observed in high-risk group. Besides, suppression of MKLN1-AS expression inhibited cell proliferation of HCC cells by CCK8 assay in vitro. Conclusion The 7-lncRNA signature may exert a particular prognostic prediction role in HCC and provide new insight in HCC carcinogenesis.
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Affiliation(s)
- Junchi Qu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Gastroenterology, The First People's Hospital of PingJiang, Yueyang 410400, China
| | - Di Tao
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wei Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Liting Lu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Junming Fan
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Shineng Zhang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Fengting Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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Chui MH, Ellenson LH. Mixed Ovarian Neoplasms With Gastrointestinal-type Mucinous and Mullerian Epithelial Components: A Rare Group of Tumors Demonstrating the Phenotypic Plasticity of the Mullerian Epithelial Cell. Am J Surg Pathol 2023; 47:756-765. [PMID: 37125505 PMCID: PMC10959257 DOI: 10.1097/pas.0000000000002045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Primary mucinous ovarian neoplasms, gastrointestinal-type (GI-type), are composed of mucin-producing tumor cells resembling intestinal goblet cells or gastric foveolar epithelium. In contrast to seromucinous tumors, which exhibit endocervical-type mucinous differentiation and are thought to be derived from endometriosis, the cell/tissue-of-origin of most GI-type mucinous ovarian tumors is unknown. We identified 8 GI-type mucinous ovarian tumors (cystadenomas, n=4; borderline tumor/carcinoma, n=4) with spatially distinct areas that showed morphologic features of Mullerian-type epithelial differentiation (ciliated cells or endometrioid-type glands). Immunohistochemistry for cell lineage markers and Alcian blue (pH 2.5)/Periodic Acid-Schiff staining were performed. Morphologically distinct components were isolated by microdissection, from which extracted DNA was analyzed by targeted next-generation sequencing. In all cases, immunohistochemistry demonstrated mucin-producing cells to be positive for at least one GI marker (CK20 or CDX2), while areas with morphologic features of Mullerian differentiation were positive for PAX8, ER and/or PR, and lacked expression of CK20 and CDX2; CK7 was strongly and diffusely positive in all tumor cells. Tumor cells with a gastric-type phenotype produced neutral mucin, while acidic mucin was present within intestinal-type goblet cells. Targeted sequencing revealed ARID1A mutations in all mixed borderline tumors/carcinomas (n=4); other recurrent genetic alterations included KRAS (n=2) and TP53 mutations (n=2). Shared mutations were present in paired Mullerian and GI-type mucinous tumor components in 4 mixed borderline tumors/carcinomas, with more shared mutations between components than private mutations specific to each component. All mixed borderline tumors/carcinomas were associated with endometriosis (n=3) or Mullerian inclusion cysts (n=1); mutation or loss of ARID1A expression was seen in these putative precursor lesions in 2 cases. Hence, ovarian neoplasms composed of clonally related GI-type mucinous and Mullerian-type epithelial components harbor ARID1A mutations and are frequently associated with endometriosis. The existence of a Mullerian stem/progenitor cell with the capacity to differentiate toward cell lineages within the GI-tract may be involved in the pathogenesis of at least a subset of GI-type mucinous ovarian neoplasms.
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Affiliation(s)
- Michael Herman Chui
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Wang H, Bienz M, Yan XX, Xu W. Structural basis of the interaction between BCL9-Pygo and LDB-SSBP complexes in assembling the Wnt enhanceosome. Nat Commun 2023; 14:3702. [PMID: 37349336 PMCID: PMC10287724 DOI: 10.1038/s41467-023-39439-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
The Wnt enhanceosome is responsible for transactivation of Wnt-responsive genes and a promising therapeutic target for treatment of numerous cancers with Adenomatous Polyposis Coli (APC) or β-catenin mutations. How the Wnt enhanceosome is assembled remains poorly understood. Here we show that B-cell lymphoma 9 protein (BCL9), Pygopus (Pygo), LIM domain-binding protein 1 (LDB1) and single-stranded DNA-binding protein (SSBP) form a stable core complex within the Wnt enhanceosome. Their mutual interactions rely on a highly conserved N-terminal asparagine proline phenylalanine (NPF) motif of Pygo, through which the BCL9-Pygo complex binds to the LDB-SSBP core complex. Our crystal structure of a ternary complex comprising the N-terminus of human Pygo2, LDB1 and SSBP2 reveals a single LDB1-SSBP2 complex binding simultaneously to two Pygo2 molecules via their NPF motifs. These interactions critically depend on the NPF motifs which bind to a deep groove formed between LDB1 and SSBP2, potentially constituting a binding site for drugs blocking Wnt/β-catenin signaling. Analysis of human cell lines lacking LDB or Pygo supports the functional relevance of the Pygo-LDB1-SSBP2 interaction for Wnt/β-catenin-dependent transcription.
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Affiliation(s)
- Hongyang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mariann Bienz
- Medical Research Council Laboratory of Molecular Biology, CB2 0QH, Cambridge, United Kingdom
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Wenqing Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Shi Y, Shin DS. Dysregulation of SWI/SNF Chromatin Remodelers in NSCLC: Its Influence on Cancer Therapies including Immunotherapy. Biomolecules 2023; 13:984. [PMID: 37371564 DOI: 10.3390/biom13060984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Molecularly targeted therapeutics and immunotherapy revolutionized the clinical care of NSCLC patients. However, not all NSCLC patients harbor molecular targets (e.g., mutated EGFR), and only a subset benefits from immunotherapy. Moreover, we are lacking reliable biomarkers for immunotherapy, although PD-L1 expression has been mainly used for guiding front-line therapeutic options. Alterations of the SWI/SNF chromatin remodeler occur commonly in patients with NSCLC. This subset of NSCLC tumors tends to be undifferentiated and presents high heterogeneity in histology, and it shows a dismal prognosis because of poor response to the current standard therapies. Catalytic subunits SMARCA4/A2 and DNA binding subunits ARID1A/ARID1B/ARID2 as well as PBRM1 were identified to be the most commonly mutated subunits of SWI/SNF complexes in NSCLC. Mechanistically, alteration of these SWI/SNF subunits contributes to the tumorigenesis of NSCLC through compromising the function of critical tumor suppressor genes, enhancing oncogenic activity as well as impaired DNA repair capacity related to genomic instability. Several vulnerabilities of NSCLCS with altered SWI/SNF subunits were detected and evaluated clinically using EZH2 inhibitors, PROTACs of mutual synthetic lethal paralogs of the SWI/SNF subunits as well as PARP inhibitors. The response of NSCLC tumors with an alteration of SWI/SNF to ICIs might be confounded by the coexistence of mutations in genes capable of influencing patients' response to ICIs. High heterogenicity in the tumor with SWI/SNF deficiency might also be responsible for the seemingly conflicting results of ICI treatment of NSCLC patients with alterations of SWI/SNF. In addition, an alteration of each different SWI/SNF subunit might have a unique impact on the response of NSCLC with deficient SWI/SNF subunits. Prospective studies are required to evaluate how the alterations of the SWI/SNF in the subset of NSCLC patients impact the response to ICI treatment. Finally, it is worthwhile to point out that combining inhibitors of other chromatin modulators with ICIs has been proven to be effective for the treatment of NSCLC with deficient SWI/SNF chromatin remodelers.
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Affiliation(s)
- Yijiang Shi
- Division of Hematology/Oncology, Department of Medicine, Los Angeles, CA 90073, USA
- Division of Hematology/Oncology, Department of Medicine, VA Greater Los Angeles Healthcare System, 11301 Wilshire Blvd, Los Angeles, CA 90073, USA
| | - Daniel Sanghoon Shin
- Division of Hematology/Oncology, Department of Medicine, Los Angeles, CA 90073, USA
- Division of Hematology/Oncology, Department of Medicine, VA Greater Los Angeles Healthcare System, 11301 Wilshire Blvd, Los Angeles, CA 90073, USA
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He J, Xu T, Zhao F, Guo J, Hu Q. SETD2-H3K36ME3: an important bridge between the environment and tumors. Front Genet 2023; 14:1204463. [PMID: 37359376 PMCID: PMC10288198 DOI: 10.3389/fgene.2023.1204463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Epigenetic regulation plays an important role in the occurrence, development and treatment of tumors. The histone methyltransferase SET-domain-containing 2 (SETD2) plays a key role in mammalian epigenetic regulation by catalyzing histone methylation and interacting with RNA polymerase II to mediate transcription elongation and mismatch repair. As an important bridge between the environment and tumors, SETD2-H3K36me3 plays an important role in the occurrence and development of tumors. Many tumors, including renal cancer, gastric cancer, lung cancer, are closely related to SETD2 gene mutations. As a key component of common tumor suppressor mechanisms, SETD2-H3K36me3is an important target for clinical disease diagnosis and treatment. Here, we reviewed the structure and function of the SETD2 and how SETD2-H3K36me3 functions as a bridge between the environment and tumors to provide an in-depth understanding of its role in the occurrence and development of various tumors, which is of great significance for future disease diagnosis and treatment.
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Affiliation(s)
- Jiahui He
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Tangpeng Xu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Fangrui Zhao
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jin Guo
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qinyong Hu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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Nourbakhsh A, Dinh CT. Updates on Tumor Biology in Vestibular Schwannoma. Otolaryngol Clin North Am 2023; 56:421-434. [PMID: 37121611 DOI: 10.1016/j.otc.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Vestibular schwannomas (VSs) are benign tumors that develop after biallelic inactivation of the neurofibromatosis type 2 (NF2) gene that encodes the tumor suppressor merlin. Merlin inactivation leads to cell proliferation by dysregulation of receptor tyrosine kinase signaling and other intracellular pathways. In VS without NF2 mutations, dysregulation of non-NF2 genes can promote pathways favoring cell proliferation and tumorigenesis. The tumor microenvironment of VS consists of multiple cell types that influence VS tumor biology through complex intercellular networking and communications.
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Affiliation(s)
- Aida Nourbakhsh
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 Northwest 14th Street, Suite 579, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, 1475 Northwest 12th Avenue, Miami, FL 33136, USA
| | - Christine T Dinh
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 Northwest 14th Street, Suite 579, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, 1475 Northwest 12th Avenue, Miami, FL 33136, USA.
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Jiang YK, Shuai YJ, Ding HM, Zhang H, Huang C, Wang L, Sun JY, Wei WJ, Xiao XY, Jiang GS. ARID1A Inactivation Increases Expression of circ0008399 and Promotes Cisplatin Resistance in Bladder Cancer. Curr Med Sci 2023; 43:560-571. [PMID: 37142816 DOI: 10.1007/s11596-023-2731-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 05/06/2023]
Abstract
OBJECTIVE Cisplatin (CDDP)-based chemotherapy is a first-line, drug regimen for muscle-invasive bladder cancer (BC) and metastatic bladder cancer. Clinically, resistance to CDDP restricts the clinical benefit of some bladder cancer patients. AT-rich interaction domain 1A (ARID1A) gene mutation occurs frequently in bladder cancer; however, the role of CDDP sensitivity in BC has not been studied. METHODS We established ARID1A knockout BC cell lines using CRISPR/Cas9 technology. IC50 determination, flow cytometry analysis of apoptosis, and tumor xenograft assays were performed to verify changes in the CDDP sensitivity of BC cells losing ARID1A. qRT-PCR, Western blotting, RNA interference, bioinformatic analysis, and ChIP-qPCR analysis were performed to further explore the potential mechanism of ARID1A inactivation in CDDP sensitivity in BC. RESULTS It was found that ARID1A inactivation was associated with CDDP resistance in BC cells. Mechanically, loss of ARID1A promoted the expression of eukaryotic translation initiation factor 4A3 (EIF4A3) through epigenetic regulation. Increased expression of EIF4A3 promoted the expression of hsa_circ_0008399 (circ0008399), a novel circular RNA (circRNA) identified in our previous study, which, to some extent, showed that ARID1A deletion caused CDDP resistance through the inhibitory effect of circ0008399 on the apoptosis of BC cells. Importantly, EIF4A3-IN-2 specifically inhibited the activity of EIF4A3 to reduce circ0008399 production and restored the sensitivity of ARID1A inactivated BC cells to CDDP. CONCLUSION Our research deepens the understanding of the mechanisms of CDDP resistance in BC and elucidates a potential strategy to improve the efficacy of CDDP in BC patients with ARID1A deletion through combination therapy targeting EIF4A3.
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Affiliation(s)
- Yang-Kai Jiang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yu-Jun Shuai
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hua-Min Ding
- Department of Urology, Jingshan Union Hospital of Huazhong University of Science and Technology (People's Hospital of Jingshan), Jingshan, 431899, China
| | - Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chao Huang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jia-Yin Sun
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wen-Jie Wei
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xing-Yuan Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Guo-Song Jiang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Ashcroft CR, Penney SW, Whiteway SL. Treatment Refractory Soft Tissue Myoepithelial Carcinoma With an ARID1A Mutation. J Pediatr Hematol Oncol 2023; 45:e539-e542. [PMID: 37083274 DOI: 10.1097/mph.0000000000002650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/02/2023] [Indexed: 04/22/2023]
Abstract
Soft tissue myoepithelial carcinoma is a rare tumor first reported in the salivary gland. There is considerable tumor heterogeneity between pathology findings, tumor aggressiveness, and response to treatment. Recent molecular testing has identified recurrent genetic changes with PLAG mutations in salivary gland primary tumors and loss of SMARCB1 and EWSR1/FUS gene changes in myoepithelial carcinoma. SMARCB1 is a component of the switch/sucrose nonfermentable (SWI/SNF) complex, an essential cellular regulator. ARID1A is another SWI/SNF complex subunit and is a potent oncogenic driver in other tumor types. In this case, we describe the case of an adolescent/young adult patient with treatment refractory soft tissue myoepithelial carcinoma and a previously unreported ARID1A mutation.
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Affiliation(s)
| | - Scott W Penney
- Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX
| | - Susan L Whiteway
- Department of Pediatrics, Walter Reed National Military Medical Center, Bethesda, MD
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Dang DD, Rosenblum JS, Shah AH, Zhuang Z, Doucet-O’Hare TT. Epigenetic Regulation in Primary CNS Tumors: An Opportunity to Bridge Old and New WHO Classifications. Cancers (Basel) 2023; 15:2511. [PMID: 37173979 PMCID: PMC10177493 DOI: 10.3390/cancers15092511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Originally approved in 1979, a specific grading classification for central nervous system (CNS) tumors was devised by the World Health Organization (WHO) in an effort to guide cancer treatment and better understand prognosis. These "blue books" have since undergone several iterations based on tumor location, advancements in histopathology, and most recently, diagnostic molecular pathology in its fifth edition. As new research methods have evolved to elucidate complex molecular mechanisms of tumorigenesis, a need to update and integrate these findings into the WHO grading scheme has become apparent. Epigenetic tools represent an area of burgeoning interest that encompasses all non-Mendelian inherited genetic features affecting gene expression, including but not limited to chromatin remodeling complexes, DNA methylation, and histone regulating enzymes. The SWItch/Sucrose non-fermenting (SWI/SNF) chromatin remodeling complex is the largest mammalian family of chromatin remodeling proteins and is estimated to be altered in 20-25% of all human malignancies; however, the ways in which it contributes to tumorigenesis are not fully understood. We recently discovered that CNS tumors with SWI/SNF mutations have revealed an oncogenic role for endogenous retroviruses (ERVs), remnants of exogenous retroviruses that integrated into the germline and are inherited like Mendelian genes, several of which retain open reading frames for proteins whose expression putatively contributes to tumor formation. Herein, we analyzed the latest WHO classification scheme for all CNS tumors with documented SWI/SNF mutations and/or aberrant ERV expression, and we summarize this information to highlight potential research opportunities that could be integrated into the grading scheme to better delineate diagnostic criteria and therapeutic targets.
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Affiliation(s)
- Danielle D. Dang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared S. Rosenblum
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ashish H. Shah
- Section of Virology and Immunotherapy, Department of Neurosurgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Zhengping Zhuang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara T. Doucet-O’Hare
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Wang Y, Chen X, Qiao X, Xie Y, Guo D, Li B, Cao J, Tao Z, Hu X. Chromatin Remodelling Molecule ARID1A Determines Metastatic Heterogeneity in Triple-Negative Breast Cancer by Competitively Binding to YAP. Cancers (Basel) 2023; 15:cancers15092447. [PMID: 37173914 PMCID: PMC10177047 DOI: 10.3390/cancers15092447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Heterogeneity represents a pivotal factor in the therapeutic failure of triple-negative breast cancer (TNBC). In this study, we retrospectively collected and analysed clinical and pathological data from 258 patients diagnosed with TNBC at the Fudan University Cancer Hospital. Our findings show that low ARID1A expression is an independent prognostic indicator for poor overall survival (OS) and recurrence-free survival (RFS) in TNBC patients. Mechanistically, both nuclear and cytoplasmic protein analyses and immunofluorescent localisation assays confirm that ARID1A recruits the Hippo pathway effector YAP into the nucleus in human triple-negative breast cancer cells. Subsequently, we designed a YAP truncator plasmid and confirmed through co-immunoprecipitation that ARID1A can competitively bind to the WW domain of YAP, forming an ARID1A/YAP complex. Moreover, the downregulation of ARID1A promoted migration and invasion in both human triple-negative breast cancer cells and xenograft models through the Hippo/YAP signalling axis. Collectively, these findings demonstrate that ARID1A orchestrates the molecular network of YAP/EMT pathways to affect the heterogeneity in TNBC.
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Affiliation(s)
- Ye Wang
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Xinyu Chen
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Xiaosu Qiao
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Yizhao Xie
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Duancheng Guo
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Bin Li
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Jianing Cao
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Zhonghua Tao
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
| | - Xichun Hu
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, 270, Dong'an Road, Xuhui District, Shanghai 200032, China
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Czegle I, Huang C, Soria PG, Purkiss DW, Shields A, Wappler-Guzzetta EA. The Role of Genetic Mutations in Mitochondrial-Driven Cancer Growth in Selected Tumors: Breast and Gynecological Malignancies. Life (Basel) 2023; 13:life13040996. [PMID: 37109525 PMCID: PMC10145875 DOI: 10.3390/life13040996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
There is an increasing understanding of the molecular and cytogenetic background of various tumors that helps us better conceptualize the pathogenesis of specific diseases. Additionally, in many cases, these molecular and cytogenetic alterations have diagnostic, prognostic, and/or therapeutic applications that are heavily used in clinical practice. Given that there is always room for improvement in cancer treatments and in cancer patient management, it is important to discover new therapeutic targets for affected individuals. In this review, we discuss mitochondrial changes in breast and gynecological (endometrial and ovarian) cancers. In addition, we review how the frequently altered genes in these diseases (BRCA1/2, HER2, PTEN, PIK3CA, CTNNB1, RAS, CTNNB1, FGFR, TP53, ARID1A, and TERT) affect the mitochondria, highlighting the possible associated individual therapeutic targets. With this approach, drugs targeting mitochondrial glucose or fatty acid metabolism, reactive oxygen species production, mitochondrial biogenesis, mtDNA transcription, mitophagy, or cell death pathways could provide further tailored treatment.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary
| | - Chelsea Huang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Priscilla Geraldine Soria
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Dylan Wesley Purkiss
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Andrea Shields
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
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Zhou W, Liu H, Yuan Z, Zundell J, Towers M, Lin J, Lombardi S, Nie H, Murphy B, Yang T, Wang C, Liao L, Goldman AR, Kannan T, Kossenkov AV, Drapkin R, Montaner LJ, Claiborne DT, Zhang N, Wu S, Zhang R. Targeting the mevalonate pathway suppresses ARID1A-inactivated cancers by promoting pyroptosis. Cancer Cell 2023; 41:740-756.e10. [PMID: 36963401 PMCID: PMC10085864 DOI: 10.1016/j.ccell.2023.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/22/2023] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
ARID1A, encoding a subunit of the SWI/SNF complex, is mutated in ∼50% of clear cell ovarian carcinoma (OCCC) cases. Here we show that inhibition of the mevalonate pathway synergizes with immune checkpoint blockade (ICB) by driving inflammasome-regulated immunomodulating pyroptosis in ARID1A-inactivated OCCCs. SWI/SNF inactivation downregulates the rate-limiting enzymes in the mevalonate pathway such as HMGCR and HMGCS1, which creates a dependence on the residual activity of the pathway in ARID1A-inactivated cells. Inhibitors of the mevalonate pathway such as simvastatin suppresses the growth of ARID1A mutant, but not wild-type, OCCCs. In addition, simvastatin synergizes with anti-PD-L1 antibody in a genetic OCCC mouse model driven by conditional Arid1a inactivation and in a humanized immunocompetent ARID1A mutant patient-derived OCCC mouse model. Our data indicate that inhibition of the mevalonate pathway simultaneously suppresses tumor cell growth and boosts antitumor immunity by promoting pyroptosis, which synergizes with ICB in suppressing ARID1A-mutated cancers.
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Affiliation(s)
- Wei Zhou
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Heng Liu
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Zhe Yuan
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Joseph Zundell
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Martina Towers
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jianhuang Lin
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Simona Lombardi
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Hao Nie
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Brennah Murphy
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Tyler Yang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Chen Wang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Liping Liao
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Aaron R Goldman
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Toshitha Kannan
- Bioinformatics Facility, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Andrew V Kossenkov
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ronny Drapkin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luis J Montaner
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Daniel T Claiborne
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Nan Zhang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Shuai Wu
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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Wang L, Tang J. SWI/SNF complexes and cancers. Gene 2023; 870:147420. [PMID: 37031881 DOI: 10.1016/j.gene.2023.147420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/11/2023]
Abstract
Epigenetics refers to the study of genetic changes that can affect gene expression without altering the underlying DNA sequence, including DNA methylation, histone modification, chromatin remodelling, X chromosome inactivation and non-coding RNA regulation. Of these, DNA methylation, histone modification and chromatin remodelling constitute the three classical modes of epigenetic regulation. These three mechanisms alter gene transcription by adjusting chromatin accessibility, thereby affecting cell and tissue phenotypes in the absence of DNA sequence changes. In the presence of ATP hydrolases, chromatin remodelling alters the structure of chromatin and thus changes the transcription level of DNA-guided RNA. To date, four types of ATP-dependent chromatin remodelling complexes have been identified in humans, namely SWI/SNF, ISWI, INO80 and NURD/MI2/CHD. SWI/SNF mutations are prevalent in a wide variety of cancerous tissues and cancer-derived cell lines as discovered by next-generation sequencing technologies.. SWI/SNF can bind to nucleosomes and use the energy of ATP to disrupt DNA and histone interactions, sliding or ejecting histones, altering nucleosome structure, and changing transcriptional and regulatory mechanisms. Furthermore, mutations in the SWI/SNF complex have been observed in approximately 20% of all cancers. Together, these findings suggest that mutations targeting the SWI/SNF complex may have a positive impact on tumorigenesis and cancer progression.
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Affiliation(s)
- Liyuan Wang
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Oncology and Hematology, Jinan 250000, Shandong Province, China
| | - Jinglong Tang
- Adicon Medical Laboratory Center, Molecular Genetic Diagnosis Center, Pathological Diagnosis Center, Jinan 250014, Shandong Province, China.
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Lebedev T, Kousar R, Patrick B, Usama M, Lee MK, Tan M, Li XG. Targeting ARID1A-Deficient Cancers: An Immune-Metabolic Perspective. Cells 2023; 12:cells12060952. [PMID: 36980292 PMCID: PMC10047504 DOI: 10.3390/cells12060952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Epigenetic remodeling and metabolic reprogramming, two well-known cancer hallmarks, are highly intertwined. In addition to their abilities to confer cancer cell growth advantage, these alterations play a critical role in dynamically shaping the tumor microenvironment and antitumor immunity. Recent studies point toward the interplay between epigenetic regulation and metabolic rewiring as a potentially targetable Achilles' heel in cancer. In this review, we explore the key metabolic mechanisms that underpin the immunomodulatory role of AT-rich interaction domain 1A (ARID1A), the most frequently mutated epigenetic regulator across human cancers. We will summarize the recent advances in targeting ARID1A-deficient cancers by harnessing immune-metabolic vulnerability elicited by ARID1A deficiency to stimulate antitumor immune response, and ultimately, to improve patient outcome.
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Affiliation(s)
- Timofey Lebedev
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Rubina Kousar
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Bbumba Patrick
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Muhammad Usama
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Meng-Kuei Lee
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Ming Tan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
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Meng GX, Yang CC, Yan LJ, Yang YF, Yan YC, Hong JG, Chen ZQ, Dong ZR, Li T. The somatic mutational landscape and role of the ARID1A gene in hepatocellular carcinoma. Heliyon 2023; 9:e14307. [PMID: 36950649 PMCID: PMC10025035 DOI: 10.1016/j.heliyon.2023.e14307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is one of the most common malignant tumours worldwide. Clarification of the somatic mutational landscape of important genes could reveal new therapeutic targets and facilitate individualized therapeutic approaches for HCC patients. The mutation and expression changes in the ARID1A gene in HCC remain controversial. Methods First, cBioPortal was used to visualize genetic alterations and DNA copy number alterations (CNAs) in ARID1A. The relationships between ARID1A mutation status and HCC patient clinicopathological features and overall survival (OS) were also determined. Then, a meta-analysis was performed to evaluate the effect of ARID1A mutation or expression on the prognosis of HCC patients. Finally, the role of ARID1A in HCC progression was verified by in vitro experiments. Results ARID1A mutation was detected in 9.35% (33/353) of sequenced HCC cases, and ARID1A mutation decreased ARID1A mRNA expression. Patients with ARID1A alterations presented worse OS than those without ARID1A alterations. Meta-analysis and human HCC tissue microarray (TMA) analysis revealed that HCC patients with low ARID1A expression had worse OS and relapse-free survival (RFS), and low ARID1A expression was negatively correlated with tumour size. Then, ARID1A gain-of-function and loss-of-function experiments demonstrated the tumour suppressor role of ARID1A in HCC in vitro. In terms of the mechanism, we found that ARID1A could inhibit HCC progression by regulating retinoblastoma-like 1 (RBL1) expression via the JNK/FOXO3 pathway. Conclusions ARID1A can be considered a potential prognostic biomarker and candidate therapeutic target for HCC.
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Affiliation(s)
- Guang-Xiao Meng
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Chun-Cheng Yang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Lun-Jie Yan
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Ya-Fei Yang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yu-Chuan Yan
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Jian-Guo Hong
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Zhi-Qiang Chen
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Zhao-Ru Dong
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
- Corresponding author. Department of General Surgery Qilu Hospital, Shandong University Jinan, China.
| | - Tao Li
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
- Department of Hepatobiliary Surgery, The Second Hospital of Shandong University, Jinan, 250000, China
- Corresponding author. Department of General Surgery Qilu Hospital, Shandong University Jinan, China.
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Chow RD, Michaels T, Bellone S, Hartwich TM, Bonazzoli E, Iwasaki A, Song E, Santin AD. Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti-PD-1 Immunotherapy in Endometrial Carcinoma. Cancer Discov 2023; 13:312-331. [PMID: 36301137 PMCID: PMC9905265 DOI: 10.1158/2159-8290.cd-22-0686] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/29/2022] [Accepted: 10/19/2022] [Indexed: 02/07/2023]
Abstract
Mismatch repair-deficient (MMRd) cancers have varied responses to immune-checkpoint blockade (ICB). We conducted a phase II clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared with epigenetic MMRd; however, within each category of MMRd, mutation burden was not correlated with ICB response. Pretreatment JAK1 mutations were not associated with primary resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of antitumor immunity for mutational versus epigenetic MMRd cancers. Whereas effector CD8+ T cells correlated with regression of mutational MMRd tumors, activated CD16+ NK cells were associated with ICB-responsive epigenetic MMRd tumors. These data highlight the interplay between tumor-intrinsic and tumor-extrinsic factors that influence ICB response. SIGNIFICANCE The molecular mechanism of MMRd is associated with response to anti-PD-1 immunotherapy in endometrial carcinoma. Tumors with epigenetic MMRd or mutational MMRd are correlated with NK cell or CD8+ T cell-driven immunity, respectively. Classifying tumors by the mechanism of MMRd may inform clinical decision-making regarding cancer immunotherapy. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Ryan D. Chow
- Department of Genetics, Yale University, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
| | - Tai Michaels
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
| | - Stefania Bellone
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tobias M.P. Hartwich
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elena Bonazzoli
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Eric Song
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
| | - Alessandro D. Santin
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
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Molina Pimienta L, Salgado Sánchez JC, Hernández Cuello I. Implicaciones en el tratamiento de pacientes con cáncer de mama y alteraciones en ARID1A. UNIVERSITAS MÉDICA 2023. [DOI: 10.11144/javeriana.umed64-1.tpcm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
ARID1A (AT-rich interaction domain 1A) es una subunidad de los complejos SWI/SNF específicamente mutada en ~20 % de los cánceres humanos primarios. La inactivación de ARID1A a través de mutaciones somáticas y otros mecanismos epigenéticos da como resultado la pérdida de las funciones de guardián y cuidador en las células, lo que promueve la iniciación del tumor. Se ha documentado una correlación entre mutaciones de pérdida de función en ARID1A y la presencia de mutaciones activadoras en PIK3CA, pérdida de la expresión de PTEN y la pérdida de la función de p53. Las mutaciones de ARID1A estaban presentes en el 2,5 % de todos los cánceres de mama; no obstante, el porcentaje de cáncer de mama con mutaciones en ARID1A aumenta en los cánceres metastásicos un 12 %, o en los inflamatorios, un 10 %. La pérdida de la función de la ARID1A en cáncer de mama se adquiere con mayor frecuencia posterior al tratamiento y está asociada con la resistencia al tratamiento hormonal y con agentes quimioterapéuticos. Además, conduce a una reparación deficiente de las rupturas de doble cadena, que sensibilizan las células a los inhibidores de PARP. Por último, las alteraciones en ARID1A podrían ser un biomarcador de respuesta a inhibidores de punto de control.
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Chromatin complex dependencies reveal targeting opportunities in leukemia. Nat Commun 2023; 14:448. [PMID: 36707513 PMCID: PMC9883437 DOI: 10.1038/s41467-023-36150-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Chromatin regulators are frequently mutated in human cancer and are attractive drug targets. They include diverse proteins that share functional domains and assemble into related multi-subunit complexes. To investigate functional relationships among these regulators, here we apply combinatorial CRISPR knockouts (KOs) to test over 35,000 gene-gene pairings in leukemia cells, using a library of over 300,000 constructs. Top pairs that demonstrate either compensatory non-lethal interactions or synergistic lethality enrich for paralogs and targets that occupy the same protein complex. The screen highlights protein complex dependencies not apparent in single KO screens, for example MCM histone exchange, the nucleosome remodeling and deacetylase (NuRD) complex, and HBO1 (KAT7) complex. We explore two approaches to NuRD complex inactivation. Paralog and non-paralog combinations of the KAT7 complex emerge as synergistic lethal and specifically nominate the ING5 PHD domain as a potential therapeutic target when paired with other KAT7 complex member losses. These findings highlight the power of combinatorial screening to provide mechanistic insight and identify therapeutic targets within redundant networks.
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Yakovlev VA, Sullivan SA, Fields EC, Temkin SM. PARP inhibitors in the treatment of ARID1A mutant ovarian clear cell cancer: PI3K/Akt1-dependent mechanism of synthetic lethality. Front Oncol 2023; 13:1124147. [PMID: 36910637 PMCID: PMC9992988 DOI: 10.3389/fonc.2023.1124147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Poly(ADP-ribose) polymerase (PARP) is a nuclear enzyme involved in the repair of DNA single-strand breaks (SSB). The recent development of poly(ADP-ribose) polymerase inhibitors (PARPi) results from over 45 years of studies. When the activity of PARP1 or PARP2 is compromised, DNA SSB lesions are unresolved and can be converted to DNA double-strand breaks (DSBs) by the cellular transcription mechanisms. ARID1A (also called BAF250a) is an important component of the mammalian Switch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex. ARID1A gene demonstrates >50% of mutation rate in ovarian clear-cell carcinomas (OCCC). Mutated or downregulated ARID1A significantly compromises the Homologous Recombination Repair (HRR) of DNA DSB. Results The present study demonstrated that downregulated or mutated ARID1A attenuates DNA HRR through stimulation of the PI3K/Akt1 pathway and makes tumor cells highly sensitive to PARPi and PARPi/ionizing radiation (IR) combination. We showed that PI3K/Akt1 pathway plays an important role in the sensitization of cancer cell lines with compromised function of ARID1A to PARPi treatment. Discussion We believe that using of PARPi monotherapy or in combination with radiation therapy is an appealing strategy for treating ARID1A-mutated cancers, as well as many other types of PI3K/Akt1-driven cancers.
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Affiliation(s)
- Vasily A Yakovlev
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Stephanie A Sullivan
- Gynecologic Oncology Division, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Emma C Fields
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Sarah M Temkin
- Gynecologic Oncology Division, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
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Kuo TL, Cheng KH, Chen LT, Hung WC. ARID1A loss in pancreas leads to islet developmental defect and metabolic disturbance. iScience 2022; 26:105881. [PMID: 36654862 PMCID: PMC9840936 DOI: 10.1016/j.isci.2022.105881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
ARID1A is a tumor suppressor gene mutated in 7-10% of pancreatic cancer patients. However, its function in pancreas development and endocrine regulation is unclear. We generated mice that lack Arid1a expression in the pancreas. Our results showed that deletion of the Arid1a gene in mice caused a reduction in islet numbers and insulin production, both of which are associated with diabetes mellitus (DM) phenotype. RNA sequencing of isolated islets confirmed DM gene signature and decrease of developmental lineage genes. We identified neurogenin3, a transcription factor that controls endocrine fate specification, is a direct target of Aird1a. Gene set enrichment analysis indicated the enhancement of histone deacetylase (HDAC) pathway after Arid1a depletion and a clinically approved HDAC inhibitor showed therapeutic benefit by suppressing disease onset. Our data suggest that Arid1a is required for the development of pancreatic islets by regulating Ngn3+-mediated transcriptional program and is important in maintaining endocrine function.
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Affiliation(s)
- Tzu-Lei Kuo
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Kuang-Hung Cheng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan,Division of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan,Corresponding author
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