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Dang T, Guan X, Cui L, Ruan Y, Chen Z, Zou H, Lan Y, Liu C, Zhang Y. Epigenetics and immunotherapy in colorectal cancer: progress and promise. Clin Epigenetics 2024; 16:123. [PMID: 39252116 PMCID: PMC11385519 DOI: 10.1186/s13148-024-01740-9] [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: 11/13/2023] [Accepted: 09/02/2024] [Indexed: 09/11/2024] Open
Abstract
Colorectal cancer (CRC) is a common malignant tumor with the third and second highest incidence and mortality rates among various malignant tumors. Despite significant advancements in the present therapy for CRC, the majority of CRC cases feature proficient mismatch repair/microsatellite stability and have no response to immunotherapy. Therefore, the search for new treatment options holds immense importance in the diagnosis and treatment of CRC. In recent years, clinical research on immunotherapy combined with epigenetic therapy has gradually increased, which may bring hope for these patients. This review explores the role of epigenetic regulation in exerting antitumor effects through its action on immune cell function and highlights the potential of certain epigenetic genes that can be used as markers of immunotherapy to predict therapeutic efficacy. We also discuss the application of epigenetic drug sensitization immunotherapy to develop new treatment options combining epigenetic therapy and immunotherapy.
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Affiliation(s)
- Tianjiao Dang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Xin Guan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Luying Cui
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Yuli Ruan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Zhuo Chen
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Haoyi Zou
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Ya Lan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Chao Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China.
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China.
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China.
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China.
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China.
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China.
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Zou H, Liu C, Ruan Y, Fang L, Wu T, Han S, Dang T, Meng H, Zhang Y. Colorectal medullary carcinoma: a pathological subtype with intense immune response and potential to benefit from immune checkpoint inhibitors. Expert Rev Clin Immunol 2024; 20:997-1008. [PMID: 38459764 DOI: 10.1080/1744666x.2024.2328746] [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: 12/03/2023] [Accepted: 03/06/2024] [Indexed: 03/10/2024]
Abstract
INTRODUCTION Different pathological types of colorectal cancer have distinguished immune landscape, and the efficacy of immunotherapy will be completely different. Colorectal medullary carcinoma, accounting for 2.2-3.2%, is characterized by massive lymphocyte infiltration. However, the attention to the immune characteristics of colorectal medullary carcinoma is insufficient. AREA COVERED We searched the literature about colorectal medullary carcinoma on PubMed through November 2023to investigate the hallmarks of colorectal medullary carcinoma's immune landscape, compare medullary carcinoma originating from different organs and provide theoretical evidence for precise treatment, including applying immunotherapy and BRAF inhibitors. EXPERT OPINION Colorectal medullary carcinoma is a pathological subtype with intense immune response, with six immune characteristics and has the potential to benefit from immunotherapy. Mismatch repair deficiency, ARID1A missing and BRAF V600E mutation often occurs. IFN-γ pathway is activated and PD-L1 expression is increased. Abundant lymphocyte infiltration performs tumor killing function. In addition, BRAF mutation plays an important role in the occurrence and development, and we can consider the combination of BRAF inhibitors and immunotherapy in patients with BRAF mutant. The exploration of colorectal medullary carcinoma will arouse researchers' attention to the correlation between pathological subtypes and immune response, and promote the process of precise immunotherapy.
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Affiliation(s)
- Haoyi Zou
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chao Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yuli Ruan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lin Fang
- Phase I Clinical Research Center, The Affiliated Hospital of Qingdao University in Shandong, Qingdao, China
| | - Tong Wu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuling Han
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tianjiao Dang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongxue Meng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin Medical University Cancer Hospital, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin Medical University Cancer Hospital, Harbin, China
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Maxwell MB, Hom-Tedla MS, Yi J, Li S, Rivera SA, Yu J, Burns MJ, McRae HM, Stevenson BT, Coakley KE, Ho J, Gastelum KB, Bell JC, Jones AC, Eskander RN, Dykhuizen EC, Shadel GS, Kaech SM, Hargreaves DC. ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity. Cell 2024; 187:3390-3408.e19. [PMID: 38754421 PMCID: PMC11193641 DOI: 10.1016/j.cell.2024.04.025] [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: 11/19/2022] [Revised: 02/26/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Clinical trials have identified ARID1A mutations as enriched among patients who respond favorably to immune checkpoint blockade (ICB) in several solid tumor types independent of microsatellite instability. We show that ARID1A loss in murine models is sufficient to induce anti-tumor immune phenotypes observed in ARID1A mutant human cancers, including increased CD8+ T cell infiltration and cytolytic activity. ARID1A-deficient cancers upregulated an interferon (IFN) gene expression signature, the ARID1A-IFN signature, associated with increased R-loops and cytosolic single-stranded DNA (ssDNA). Overexpression of the R-loop resolving enzyme, RNASEH2B, or cytosolic DNase, TREX1, in ARID1A-deficient cells prevented cytosolic ssDNA accumulation and ARID1A-IFN gene upregulation. Further, the ARID1A-IFN signature and anti-tumor immunity were driven by STING-dependent type I IFN signaling, which was required for improved responsiveness of ARID1A mutant tumors to ICB treatment. These findings define a molecular mechanism underlying anti-tumor immunity in ARID1A mutant cancers.
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Affiliation(s)
- Matthew B Maxwell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Marianne S Hom-Tedla
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Gynecologic Oncology, University of California, San Diego, San Diego, CA, USA
| | - Jawoon Yi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shitian Li
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Samuel A Rivera
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingting Yu
- Integrative Genomics and Bioinformatics Core, Salk Institute of Biological Studies, La Jolla, CA 92037, USA
| | - Mannix J Burns
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Helen M McRae
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Braden T Stevenson
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Katherine E Coakley
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Gynecologic Oncology, University of California, San Diego, San Diego, CA, USA
| | - Josephine Ho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Joshua C Bell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alexander C Jones
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ramez N Eskander
- Center for Personalized Cancer Therapy and Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Gerald S Shadel
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Ye L, Tong X, Pan K, Shi X, Xu B, Yao X, Zhuo L, Fang S, Tang S, Jiang Z, Xue X, Lu W, Guo G. Identification of potential novel N6-methyladenosine effector-related lncRNA biomarkers for serous ovarian carcinoma: a machine learning-based exploration in the framework of 3P medicine. Front Pharmacol 2024; 15:1351929. [PMID: 38895621 PMCID: PMC11185051 DOI: 10.3389/fphar.2024.1351929] [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: 12/07/2023] [Accepted: 03/04/2024] [Indexed: 06/21/2024] Open
Abstract
Background Serous ovarian carcinoma (SOC) is considered the most lethal gynecological malignancy. The current lack of reliable prognostic biomarkers for SOC reduces the efficacy of predictive, preventive, and personalized medicine (PPPM/3PM) in patients with SOC, leading to unsatisfactory therapeutic outcomes. N6-methyladenosine (m6A) modification-associated long noncoding RNAs (lncRNAs) are effective predictors of SOC. In this study, an effective risk prediction model for SOC was constructed based on m6A modification-associated lncRNAs. Methods Transcriptomic data and clinical information of patients with SOC were downloaded from The Cancer Genome Atlas. Candidate lncRNAs were identified using univariate and multivariate and least absolute shrinkage and selection operator-penalized Cox regression analyses. The molecular mechanisms of m6A effector-related lncRNAs were explored via Gene Ontology, pathway analysis, gene set enrichment analysis, and gene set variation analysis (GSVA). The extent of immune cell infiltration was assessed using various algorithms, including CIBERSORT, Microenvironment Cell Populations counter, xCell, European Prospective Investigation into Cancer and Nutrition, and GSVA. The calcPhenotype algorithm was used to predict responses to the drugs commonly used in ovarian carcinoma therapy. In vitro experiments, such as migration and invasion Transwell assays, wound healing assays, and dot blot assays, were conducted to elucidate the functional roles of candidate lncRNAs. Results Six m6A effector-related lncRNAs that were markedly associated with prognosis were used to establish an m6A effector-related lncRNA risk model (m6A-LRM) for SOC. Immune microenvironment analysis suggested that the high-risk group exhibited a proinflammatory state and displayed increased sensitivity to immunotherapy. A nomogram was constructed with the m6A effector-related lncRNAs to assess the prognostic value of the model. Sixteen drugs potentially targeting m6A effector-related lncRNAs were identified. Furthermore, we developed an online web application for clinicians and researchers (https://leley.shinyapps.io/OC_m6A_lnc/). Overexpression of the lncRNA RP11-508M8.1 promoted SOC cell migration and invasion. METTL3 is an upstream regulator of RP11-508M8.1. The preliminary regulatory axis METTL3/m6A/RP11-508M8.1/hsa-miR-1270/ARSD underlying SOC was identified via a combination of in vitro and bioinformatic analyses. Conclusion In this study, we propose an innovative prognostic risk model and provide novel insights into the mechanism underlying the role of m6A-related lncRNAs in SOC. Incorporating the m6A-LRM into PPPM may help identify high-risk patients and personalize treatment as early as possible.
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Affiliation(s)
- Lele Ye
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Women’s Reproductive Health Laboratory of Zhejiang Province, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xinyu Shi
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Binbing Xu
- First Clinical College, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuyang Yao
- First Clinical College, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Linpei Zhuo
- Haiyuan College, Kunming Medical University, Kunming, Yunnan, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Sangsang Tang
- Women’s Reproductive Health Laboratory of Zhejiang Province, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhuofeng Jiang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weiguo Lu
- Women’s Reproductive Health Laboratory of Zhejiang Province, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Gynecologic Oncology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Center of Uterine Cancer Diagnosis and Therapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-Related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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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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Yamashita H, Nakayama K, Kanno K, Ishibashi T, Ishikawa M, Iida K, Razia S, Kiyono T, Kyo S. Evaluation of ARID1A as a Potential Biomarker for Predicting Response to Immune Checkpoint Inhibitors in Patients with Endometrial Cancer. Cancers (Basel) 2024; 16:1999. [PMID: 38893118 PMCID: PMC11171230 DOI: 10.3390/cancers16111999] [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: 04/18/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND AT-rich interaction domain 1A (ARID1A) has been proposed as a new biomarker for predicting response to immune checkpoint inhibitors (ICIs). The predictive value of ARID1A for predicting ICI effectiveness has not been reported for endometrial cancer. Therefore, we investigated whether ARID1A negativity predicts ICI effectiveness for endometrial cancer treatment. METHODS We evaluated ARID1A expression, tumor-infiltrating lymphocytes (CD8+), and immune checkpoint molecules (PD-L1/PD-1) by immunostaining endometrial samples from patients with endometrial cancer. Samples in which any of the four mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2) were determined to be negative via immunostaining were excluded. In the ARID1A-negative group, microsatellite instability (MSI) status was confirmed via MSI analysis. RESULTS Of the 102 samples investigated, 25 (24.5%) were ARID1A-negative. CD8 and PD-1 expression did not differ significantly between the ARID1A-negative group and the ARID1A-positive group; however, the ARID1A-negative group showed significantly lower PD-L1 expression. Only three samples (14.2%) in the ARID1A-negative group showed high MSI. Sanger sequencing detected three cases of pathological mutation in the MSH2-binding regions. We also established an ARID1A-knockout human ovarian endometriotic epithelial cell line (HMOsisEC7 ARID1A KO), which remained microsatellite-stable after passage. CONCLUSION ARID1A negativity is not suitable as a biomarker for ICI effectiveness in treating endometrial cancer.
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Affiliation(s)
- Hitomi Yamashita
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan; (H.Y.); (K.K.); (M.I.); (K.I.)
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Nagoya City University East Medical Centre, Nagoya 464-8547, Japan;
| | - Kosuke Kanno
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan; (H.Y.); (K.K.); (M.I.); (K.I.)
| | - Tomoka Ishibashi
- Department of Obstetrics and Gynecology, Nagoya City University East Medical Centre, Nagoya 464-8547, Japan;
| | - Masako Ishikawa
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan; (H.Y.); (K.K.); (M.I.); (K.I.)
| | - Kouji Iida
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan; (H.Y.); (K.K.); (M.I.); (K.I.)
| | - Sultana Razia
- Department of Legal Medicine, Shimane University School of Medicine, Izumo 693-8501, Japan;
| | - Tohru Kiyono
- Project for Prevention of HPV-Related Cancer, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Kashiwa 277-8577, Japan;
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan; (H.Y.); (K.K.); (M.I.); (K.I.)
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Du J, Zhang E, Huang Z. The predictive value of next generation sequencing for matching advanced hepatocellular carcinoma patients to targeted and immunotherapy. Front Immunol 2024; 15:1358306. [PMID: 38665910 PMCID: PMC11043782 DOI: 10.3389/fimmu.2024.1358306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Background Targeted and Immunotherapy has emerged as a new first-line treatment for advanced hepatocellular carcinoma (aHCC). To identify the appropriate targeted and immunotherapy, we implemented next generation sequencing (NGS) to provide predictive and prognostic values for aHCC patients. Methods Pretreatment samples from 127 HCC patients were examined for genomic changes using 680-gene NGS, and PD-L1 expression was detected by immunohistochemistry. Demographic and treatment data were included for analyses of links among treatment outcomes, drug responses, and genetic profiles. A prognostic index model for predicting benefit from treatment was constructed, taking into account of biomarkers, including TP53, TERT, PD-L1, and tumor mutation burden (TMB) as possible independent prognostic factors. Results The multivariate Cox regression analyses showed that PD-L1≥1% (HR 25.07, 95%CI 1.56 - 403.29, p=0.023), TMB≥5Mb (HR 86.67, 95% CI 4.00 - 1876.48, p=0.004), TERT MU (HR 84.09, 95% CI 5.23 - 1352.70, p=0.002) and TP53 WT (HR 0.01, 95%CI 0.00 - 0.47, p=0.022) were independent risk factors for overall survival (OS), even after adjusting for various confounders. A prognostic nomogram for OS was developed, with an area under the ROC curve of 0.91, 0.85, and 0.98 at 1-, 2-, and 3- year, respectively, and a prognostic index cutoff of 1.2. According to the cutoff value, the patients were divided into the high-risk group (n=29) and low-risk group (n=98). The benefit of targeted and immunotherapy in the low-risk group was not distinguishable according to types of agents. However, treatment of Atezolizumab and Bevacizumab appeared to provide longer OS in the high-risk group (12 months vs 9.2, 9, or 5 months for other treatments, p<0.001). Conclusion The prognostic model constructed by PD-L1, TMB, TERT, and TP53 can identify aHCC patients who would benefit from targeted and immunotherapy, providing insights for the personalized treatment of HCC.
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Affiliation(s)
| | - Erlei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiyong Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Chaudhri A, Lizee G, Hwu P, Rai K. Chromatin Remodelers Are Regulators of the Tumor Immune Microenvironment. Cancer Res 2024; 84:965-976. [PMID: 38266066 DOI: 10.1158/0008-5472.can-23-2244] [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: 09/06/2023] [Revised: 11/24/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Immune checkpoint inhibitors show remarkable responses in a wide range of cancers, yet patients develop adaptive resistance. This necessitates the identification of alternate therapies that synergize with immunotherapies. Epigenetic modifiers are potent mediators of tumor-intrinsic mechanisms and have been shown to regulate immune response genes, making them prime targets for therapeutic combinations with immune checkpoint inhibitors. Some success has been observed in early clinical studies that combined immunotherapy with agents targeting DNA methylation and histone modification; however, less is known about chromatin remodeler-targeted therapies. Here, we provide a discussion on the regulation of tumor immunogenicity by the chromatin remodeling SWI/SNF complex through multiple mechanisms associated with immunotherapy response that broadly include IFN signaling, DNA damage, mismatch repair, regulation of oncogenic programs, and polycomb-repressive complex antagonism. Context-dependent targeting of SWI/SNF subunits can elicit opportunities for synthetic lethality and reduce T-cell exhaustion. In summary, alongside the significance of SWI/SNF subunits in predicting immunotherapy outcomes, their ability to modulate the tumor immune landscape offers opportunities for therapeutic intervention.
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Affiliation(s)
- Apoorvi Chaudhri
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Gregory Lizee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- MDACC Epigenomics Therapy Initiative, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Jia X, Li Z, Zhou R, Feng W, Yi L, Zhang H, Chen B, Li Q, Huang S, Zhu X. Single cell and bulk RNA sequencing identifies tumor microenvironment subtypes and chemoresistance-related IGF1 + cancer-associated fibroblast in gastric cancer. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167123. [PMID: 38484940 DOI: 10.1016/j.bbadis.2024.167123] [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: 08/02/2023] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND The tumor microenvironment (TME) significantly influences prognosis and drug resistance in various tumors, yet its heterogeneity and the mechanisms affecting therapeutic response remain unclear in gastric cancer (GC). METHODS The heterogenous TME were explored with single-cell RNA-sequencing (scRNA-seq) data of 50 primary GC samples. We then identified four GC TME subtypes with nonnegative matrix factorization (NMF) and constructed a pearson nearest-centroid classifier based on subtype-specific upregulated genes. Genomic features and clinical significance of four subtypes were comprehensively evaluated. We reclustered fibroblasts to identify cancer-associated fibroblast (CAF) subtype associated with poor clinical outcomes. RT-qPCR and double immunofluorescence staining were applied to validate the findings. Cellchat analysis elucidated potential molecular mechanisms of the CAF subtype in GC disease progression and chemotherapy resistance. FINDINGS The GC TME exhibited high heterogeneity, influencing chemo-sensitivity. Four TME-based subtypes predicting response to immunotherapy and chemotherapy were identified and validated in 1406 GC patients. Among which, ISG1 subtype displayed higher fibroblasts infiltration and heightened oncogenic pathways, and inferior response to chemotherapy with unfavorable prognosis. Microsatellite instability-high (MSI-H) GCs within four TME subtypes showed immunological heterogeneity. We then reported an IGF1-overexpressing CAF was associated with chemo-resistance and GC recurrence. Cell communication analysis revealed IGF1+ CAF may induce drug-resistant phenotypes in tumor cells through IGF1-α6β4 integrin ligand-receptor binding and activation of EMT biological process. INTERPRETATION We identified four TME-based subtypes with different clinical outcomes and IGF1+ CAFs contributing to poor clinical outcomes in GC, which might provide guidance for individualized treatment and facilitate the development of novel therapeutic targets.
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Affiliation(s)
- Xiya Jia
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ziteng Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Runye Zhou
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wanjing Feng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lixia Yi
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hena Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Bing Chen
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qin Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Shenglin Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Xiaodong Zhu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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10
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Guan X, Cui L, Ruan Y, Fang L, Dang T, Zhang Y, Liu C. Heterogeneous expression of ARID1A in colorectal cancer indicates distinguish immune landscape and efficacy of immunotherapy. Discov Oncol 2024; 15:92. [PMID: 38555560 PMCID: PMC10982246 DOI: 10.1007/s12672-024-00955-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
OBJECTIVE AT-rich interaction domain 1A (ARID1A) mutant tumors show active anti-tumor immune response, which is the potential indication of immunotherapy. However, the relationship between the heterogeneous ARID1A expression and the immune response and immunotherapy efficacy in colorectal cancer (CRC) is still unclear. METHODS We collected 1113 cases of patients with stage I-IV CRC who underwent primary resection at Harbin Medical University Cancer Hospital. ARID1A expression in CRC tissues was assessed via immunohistochemistry (IHC). CD8, CD163 and FOXP3 were stained by IHC to identify the immune landscape. Clinicopathological features of patients were compared using statistical tests like the Wilcoxon-Mann-Whitney test or χ2 tests. Kaplan-Meier survival analysis with log-rank tests were employed. RESULTS Heterogeneous ARID1A expression was categorized into integrity expression, complete expression deficiency (cd-ARID1A), partial expression deficiency (pd-ARID1A), and clonal expression deficiency (cld-ARID1A). ARID1A-deficient expression was significant association with dMMR (P value < 0.001). Patients with ARID1A deficiency, compared to ARID1A-proficient patients, exhibited increased infiltration levels of CD8 + P value < 0.0001), CD163 + P value < 0.001), and FOXP3 + P value < 0.001).cells within the tumor tissue. However, in different subgroups, only samples with complete or partial deficiency of ARID1A showed a higher abundance of lymphocyte infiltration. In patients with ARID1A-clonal expression deficiency tumor, the infiltration patterns of three immune cell types were comparable to those in ARID1A-proficient patients. Heterogeneous ARID1A expression is related to the different prognosis and immunotherapythe efficacy in CRC patients. CONCLUSION Heterogeneous ARID1A expression is accompanied by a different immune landscape. CRC patients with ARID1A-clonal expression deficiency do not benefit from the treatment of immune checkpoint inhibitors (ICIs).
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Affiliation(s)
- Xin Guan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping road, Harbin, Heilongjiang, 150001, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Luying Cui
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping road, Harbin, Heilongjiang, 150001, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Yuli Ruan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping road, Harbin, Heilongjiang, 150001, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Lin Fang
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
- Phase I Clinical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Tianjiao Dang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping road, Harbin, Heilongjiang, 150001, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping road, Harbin, Heilongjiang, 150001, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Chao Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping road, Harbin, Heilongjiang, 150001, People's Republic of China.
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China.
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China.
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11
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Peng H, Wu X, Zhang C, Liang Y, Cheng S, Zhang H, Shen L, Chen Y. Analyzing the associations between tertiary lymphoid structures and postoperative prognosis, along with immunotherapy response in gastric cancer: findings from pooled cohort studies. J Cancer Res Clin Oncol 2024; 150:153. [PMID: 38519621 PMCID: PMC10959798 DOI: 10.1007/s00432-024-05672-y] [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: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND The clinical significance of tertiary lymphoid structure (TLS) in gastric cancer (GC) was uncertain. METHODS A systematic search was performed in public databases for eligible studies as of April 2, 2023. Meta-analyses were performed to interrogate the associations between TLS levels and prognosis and immunotherapy response of GC. Bioinformatic analyses based on the nine-gene signature of TLS were further conducted to capture the biological underpinnings. RESULTS Eleven studies containing 4224 GC cases were enrolled in the meta-analysis. TLS levels positively correlated with smaller tumor size, earlier T stage and N stage. Moreover, higher TLS levels were detected in diffuse and mix subtypes of GC (P < 0.001). Higher TLS levels strongly predicted favorable postoperative overall survival of GC, with HR of 0.36 (95%CI 0.26-0.50, P < 0.001) and 0.55 (95%CI 0.45-0.68, P < 0.001) of univariate and multivariate Cox analysis, respectively. Higher TLS levels were also in favor of the treatment response of anti-PD-1 inhibitors as later-line therapy of GC. TLS levels positively correlated with immune effector cells infiltration, diversity and richness of T cell receptor and B cell receptor repertoire, immune checkpoint genes expression, and immune-related genes mutation of GC in the TCGA-STAD cohort, representing higher immunogenicity and immunoactivity. Moreover, moderate accuracy of TLS levels in predicting benefit from anti-PD-1 inhibitors in the PRJEB25780 cohort was also validated (AUC 0.758, 95%CI 0.583-0.933), higher than the microsatellite instability-score and Epstein-Barr virus status. CONCLUSIONS TLS levels demonstrated potential in predicting the postoperative prognosis and immunotherapy response of GC.
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Affiliation(s)
- Haoxin Peng
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiangrong Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Yueting Liang
- Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Siyuan Cheng
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
- Department of Tumor Chemotherapy and Radiation Sickness, Peking University Third Hospital, Beijing, China
| | - Honglang Zhang
- Department of Clinical Medicine, Nanshan School, Guangzhou Medical University, Jingxiu Road, Panyu District, Guangzhou, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
- Department of Gastrointestinal Oncology, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yang Chen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China.
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12
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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 2024; 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] [MESH Headings] [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 CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Youzhi Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- School of PharmacyHubei University of Science and TechnologyXianningChina
| | - Qiaoyun Zhang
- School of PharmacyHubei University of Science and TechnologyXianningChina
| | - Mengyao Lu
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiaoyu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery, Huai'an Second People's Hospitalthe Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuaianChina
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Liu Z, Jing C, Kong F. From clinical management to personalized medicine: novel therapeutic approaches for ovarian clear cell cancer. J Ovarian Res 2024; 17:39. [PMID: 38347608 PMCID: PMC10860311 DOI: 10.1186/s13048-024-01359-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
Ovarian clear-cell cancer is a rare subtype of epithelial ovarian cancer with unique clinical and biological features. Despite optimal cytoreductive surgery and platinum-based chemotherapy being the standard of care, most patients experience drug resistance and a poor prognosis. Therefore, novel therapeutic approaches have been developed, including immune checkpoint blockade, angiogenesis-targeted therapy, ARID1A synthetic lethal interactions, targeting hepatocyte nuclear factor 1β, and ferroptosis. Refining predictive biomarkers can lead to more personalized medicine, identifying patients who would benefit from chemotherapy, targeted therapy, or immunotherapy. Collaboration between academic research groups is crucial for developing prognostic outcomes and conducting clinical trials to advance treatment for ovarian clear-cell cancer. Immediate progress is essential, and research efforts should prioritize the development of more effective therapeutic strategies to benefit all patients.
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Affiliation(s)
- Zesi Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Chunli Jing
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Fandou Kong
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China.
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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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15
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Yang Y, Wu SF, Bao W. Molecular subtypes of endometrial cancer: Implications for adjuvant treatment strategies. Int J Gynaecol Obstet 2024; 164:436-459. [PMID: 37525501 DOI: 10.1002/ijgo.14969] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND When determining adjuvant treatment for endometrial cancer, the decision typically relies on factors such as cancer stage, histologic grade, subtype, and a few histopathologic markers. The Cancer Genome Atlas revealed molecular subtyping of endometrial cancer, which can provide more accurate prognostic information and guide personalized treatment plans. OBJECTIVE To summarize the expression and molecular basis of the main biomarkers of endometrial cancer. SEARCH STRATEGY PubMed was searched from January 2000 to March 2023. SELECTION CRITERIA Studies evaluating molecular subtypes of endometrial cancer and implications for adjuvant treatment strategies. DATA COLLECTION AND ANALYSIS Three authors independently performed a comprehensive literature search, collected and extracted data, and assessed the methodological quality of the included studies. MAIN RESULTS We summarized the molecular subtyping of endometrial cancer, including mismatch repair deficient, high microsatellite instability, polymerase epsilon (POLE) exonuclease domain mutated, TP53 gene mutation, and non-specific molecular spectrum. We also summarized planned and ongoing clinical trials and common therapy methods in endometrial cancer. POLE mutated endometrial cancer consistently exhibits favorable patient outcomes, regardless of adjuvant therapy. Genomic similarities between p53 abnormality endometrial cancer and high-grade serous ovarian cancer suggested possible overlapping treatment strategies. High levels of immune checkpoint molecules, such as programmed cell death 1 and programmed cell death 1 ligand 1 can counterbalance mismatch repair deficient endometrial cancer immune phenotype. Hormonal treatment is an appealing option for high-risk non-specific molecular spectrum endometrial cancers, which are typically endometrioid and hormone receptor positive. Combining clinical and pathologic characteristics to guide treatment decisions for patients, including concurrent radiochemotherapy, chemotherapy, inhibitor therapy, endocrine therapy, and immunotherapy, might improve the management of endometrial cancer and provide more effective treatment options for patients. CONCLUSIONS We have characterized the molecular subtypes of endometrial cancer and discuss their value in terms of a patient-tailored therapy in order to prevent significant under- or overtreatment.
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Affiliation(s)
- Ye Yang
- Obstetrics and Gynecology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Su Fang Wu
- Obstetrics and Gynecology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Wei Bao
- Obstetrics and Gynecology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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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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Li JJ, Lee CS. The Role of the AT-Rich Interaction Domain 1A Gene ( ARID1A) in Human Carcinogenesis. Genes (Basel) 2023; 15:5. [PMID: 38275587 PMCID: PMC10815128 DOI: 10.3390/genes15010005] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
The switch/sucrose non-fermentable (SWI/SNF) (SWI/SNF) complex uses energy from ATP hydrolysis to mobilise nucleosomes on chromatin. Components of SWI/SNF are mutated in 20% of all human cancers, of which mutations in AT-rich binding domain protein 1A (ARID1A) are the most common. ARID1A is mutated in nearly half of ovarian clear cell carcinoma and around one-third of endometrial and ovarian carcinomas of the endometrioid type. This review will examine in detail the molecular functions of ARID1A, including its role in cell cycle control, enhancer regulation, and the prevention of telomerase activity. ARID1A has key roles in the maintenance of genomic integrity, including DNA double-stranded break repair, DNA decatenation, integrity of the cohesin complex, and reduction in replication stress, and is also involved in mismatch repair. The role of ARID1A loss in the pathogenesis of some of the most common human cancers is discussed, with a particular emphasis on gynaecological cancers. Finally, several promising synthetic lethal strategies, which exploit the specific vulnerabilities of ARID1A-deficient cancer cells, are briefly mentioned.
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Affiliation(s)
- Jing Jing Li
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Cheok Soon Lee
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2010, Australia
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18
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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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19
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Zhang J, Zhao R, Xu H, Dong L, Chen X. The clinicopathological features of BRG1-deficient non-small cell lung cancer and its response to immunotherapy: A single-center retrospective study. Ann Diagn Pathol 2023; 67:152192. [PMID: 37639838 DOI: 10.1016/j.anndiagpath.2023.152192] [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: 08/01/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
PURPOSE BRG1-deficient NSCLCs have been more intriguing recently for its highly aggressive clinical behavior and no effective therapies. This study characterized the clinical and pathological features of BRG1-deficient NSCLCs and investigated their response to immunotherapy. METHODS Forty-seven cases with BRG1-deficient NSCLC were included. Immunohistochemical markers such as BRG1, CK7, TTF-1, NapsinA, P40, HepPar-1, Ki-67, BRM, ARID1A and ARID1B were stained. Additionally, the PD-L1 expression level, overall survival, progression-free survival and disease control rate of patients received immunotherapy were evaluated. RESULTS This study revealed that: (1) Patients with BRG1-deficient NSCLC have a male predominance (89.4 %), smoker enrichment (76.6 %) and poor prognosis (median OS: 7.0 months for advanced stage). (2) Histologically, BRG1-deficient NSCLCs presented significant morphological diversity and no lepidic pattern. Inflammatory infiltration and tumor necrosis was a prominent feature. Immunohistochemical analyses showed a distinctive uniform immunophenotype (TTF-1-/NapsinA-/CK7+) in 60.9 % (28/46) of cases and HepPar-1 positive in 46.5 % (20/43) of cases. BRM loss or significant reduction coexisted in 11.8 % (4/34) of cases. No case (0/37) showed loss of ARID1A or ARID1B. (3) Eight patients with advanced tumor stage had received immunotherapy and 4 cases achieved a sustainable clinical response with the disease control rate of 50 %. CONCLUSION BRG1-deficient NSCLC showed diverse histopathological patterns and a unique immunohistochemical phenotype. ICIs-based immunotherapy is a promising therapy needs to be investigated further for BRG1- deficient NSCLC.
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Affiliation(s)
- Jing Zhang
- Respiratory and Critical Care Medicine Department, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Runze Zhao
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haimin Xu
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyan Chen
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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20
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Anabel Sinberger L, Zahavi T, Sonnenblick A, Salmon-Divon M. Coexistent ARID1A-PIK3CA mutations are associated with immune-related pathways in luminal breast cancer. Sci Rep 2023; 13:20911. [PMID: 38017109 PMCID: PMC10684499 DOI: 10.1038/s41598-023-48002-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: 07/11/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
Up to 40% of luminal breast cancer patients carry activating mutations in the PIK3CA gene. PIK3CA mutations commonly co-occur with other mutations, but the implication of this co-occurrence may vary according to the specific genes involved. Here, we characterized a subgroup of luminal breast cancer expressing co-mutations in ARID1A and PIK3CA genes and identified their effect on important signaling pathways. Our study included 2609 primary breast cancer samples from the TCGA and METABRIC datasets that were classified based on tumor subtype and the existence of mutations in PIK3CA and ARID1A genes. Differential expression and WGCNA analyses were performed to detect molecular modules affected by the existence of the mutations. Our results reveal various evidence for the involvement of immune-related pathways in luminal tumors harboring ARID1A and PIK3CA mutations, as well as a unique Tumor-infiltrated immune cells composition. We also identified seven key hub genes in the ARID1A-PIK3CA mutated tumors associated with immune-related pathways: CTLA4, PRF1, LCK, CD3E, CD247, ZAP70, and LCP2. Collectively, these results indicate an immune system function that may contribute to tumor survival. Our data induced a hypothesis that ARID1A and PIK3CA mutations' co-occurrence might predict responses to immunotherapy in luminal BC and, if validated, could guide immunotherapy development.
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Affiliation(s)
| | - Tamar Zahavi
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Amir Sonnenblick
- Institute of Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Mali Salmon-Divon
- Department of Molecular Biology, Ariel University, Ariel, Israel.
- Adelson School of Medicine, Ariel University, Ariel, Israel.
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21
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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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22
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Zhang L, Zheng Y, Chien W, Ziman B, Billet S, Koeffler HP, Lin DC, Bhowmick NA. ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:5377. [PMID: 38001638 PMCID: PMC10670331 DOI: 10.3390/cancers15225377] [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: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
ARID1A, a member of the chromatin remodeling SWI/SNF complex, is frequently lost in many cancer types, including esophageal adenocarcinoma (EAC). Here, we study the impact of ARID1A deficiency on the anti-tumor immune response in EAC. We find that EAC tumors with ARID1A mutations are associated with enhanced tumor-infiltrating CD8+ T cell levels. ARID1A-deficient EAC cells exhibit heightened IFN response signaling and promote CD8+ T cell recruitment and cytolytic activity. Moreover, we demonstrate that ARID1A regulates fatty acid metabolism genes in EAC, showing that fatty acid metabolism could also regulate CD8+ T cell recruitment and CD8+ T cell cytolytic activity in EAC cells. These results suggest that ARID1A deficiency shapes both tumor immunity and lipid metabolism in EAC, with significant implications for immune checkpoint blockade therapy in EAC.
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Affiliation(s)
- Le Zhang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Wenwen Chien
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Benjamin Ziman
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
- Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Sandrine Billet
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - H. Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
- Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Neil A. Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
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23
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Chen L, Wu Z, Guo J, Wang X, Zhao Z, Liang H, Zhang R, Deng J. Initial clinical and experimental analyses of ALDOA in gastric cancer, as a novel prognostic biomarker and potential therapeutic target. Clin Exp Med 2023; 23:2443-2456. [PMID: 36422738 DOI: 10.1007/s10238-022-00952-8] [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: 07/01/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
The effect of ALDOA, an important regulator of tumor metabolism and immune cell function, on gastric cancer (GC) immune infiltration has not been elucidated. Hence, we explored the feasibility of using ALDOA combined with immune molecular markers as novel prognostic or therapeutic targets for GC patients. Bioinformatic analyses were initially performed in multiple databases to assess the prognostic prediction values of ALDOA expression in GC. Subsequently, both ALDOA expression and the clinicopathological characteristics of a total of 114 GC patients who underwent curative gastrectomy were collected to demonstrate the potential association between ALDOA expression and the biological behaviors of GC. Next, the expression of ALDOA and its effect on prognosis were determined at the mRNA and protein levels, respectively, using tissue microarrays and cellular experiments. Subsequently, several molecular mechanisms were revealed based on elaborate analyses, indicating that ALDOA expression was potentially involved in the progression of GC and could be considered a promising biomarker for evaluating the prognosis of GC. High ALDOA expression was frequently found in GC cells and GC tissues at the mRNA and protein levels. Based on survival analysis, the expression of ALDOA indicated comparatively poor overall survival (OS) in GC and was identified as an independent prognostic predictor of GC. Correlation analysis showed that ALDOA expression had a positive association with lymph node metastasis in GC patients. Additionally, microRNA-1179 was found to play a key role in inhibiting the expression of ALDOA in the metabolic pathways of GC cells, which might disrupt the expression of various immune molecules and be detrimental to the prognosis of GC. ALDOA should be considered a promising molecular target for evaluating the prognosis of GC, owing to its potential role in immune regulation.
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Affiliation(s)
- Liqiao Chen
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Zizhen Wu
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Jiamei Guo
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Xinyu Wang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Zhenzhen Zhao
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Han Liang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Rupeng Zhang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Jingyu Deng
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China.
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24
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Xu C, Huang KK, Law JH, Chua JS, Sheng T, Flores NM, Pizzi MP, Okabe A, Tan ALK, Zhu F, Kumar V, Lu X, Benitez AM, Lian BSX, Ma H, Ho SWT, Ramnarayanan K, Anene-Nzelu CG, Razavi-Mohseni M, Abdul Ghani SAB, Tay ST, Ong X, Lee MH, Guo YA, Ashktorab H, Smoot D, Li S, Skanderup AJ, Beer MA, Foo RSY, Wong JSH, Sanghvi K, Yong WP, Sundar R, Kaneda A, Prabhakar S, Mazur PK, Ajani JA, Yeoh KG, So JBY, Tan P. Comprehensive molecular phenotyping of ARID1A-deficient gastric cancer reveals pervasive epigenomic reprogramming and therapeutic opportunities. Gut 2023; 72:1651-1663. [PMID: 36918265 DOI: 10.1136/gutjnl-2022-328332] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023]
Abstract
OBJECTIVE Gastric cancer (GC) is a leading cause of cancer mortality, with ARID1A being the second most frequently mutated driver gene in GC. We sought to decipher ARID1A-specific GC regulatory networks and examine therapeutic vulnerabilities arising from ARID1A loss. DESIGN Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of ARID1A inactivation across molecular subtypes. Single-cell transcriptomic profiles of ARID1A-mutated GCs were analysed to examine tumour microenvironmental changes arising from ARID1A loss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks of ARID1A-mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. RESULTS We observed prevalent ARID1A inactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment. ARID1A-depletion caused loss of H3K27ac activation signals at ARID1A-occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as NFKB1 and NFKB2. Promoter activation in ARID1A-mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific to ARID1A-genomic status. CONCLUSION Our results suggest a therapeutic strategy for ARID1A-mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.
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Affiliation(s)
- Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jia Hao Law
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joy Shijia Chua
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Taotao Sheng
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Melissa Pool Pizzi
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vikrant Kumar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xiaoyin Lu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ana Morales Benitez
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Haoran Ma
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Shamaine Wei Ting Ho
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore
- Human Genetics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
- Montreal Heart Institute, Quebec, Québec, Canada
- Department of Medicine, University of Montreal, Quebec, Québec, Canada
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Baltimore, Maryland, USA
| | | | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Duane Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, Tennessee, USA
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore
- Human Genetics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Kaushal Sanghvi
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | - Wei Peng Yong
- Department of Haematology-Oncology, National University Health System, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
- The N.1 Institute for Health, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Pawel Karol Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaffer A Ajani
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Jimmy Bok-Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- Division of Surgical Oncology, National University Cancer Institute, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
- Cellular and Molecular Research, National Cancer Centre, Singapore
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25
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Ji JH, Ha SY, Lee D, Sankar K, Koltsova EK, Abou-Alfa GK, Yang JD. Predictive Biomarkers for Immune-Checkpoint Inhibitor Treatment Response in Patients with Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:7640. [PMID: 37108802 PMCID: PMC10144688 DOI: 10.3390/ijms24087640] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among solid cancers. Late diagnosis and a lack of efficacious treatment options contribute to the dismal prognosis of HCC. Immune checkpoint inhibitor (ICI)-based immunotherapy has presented a new milestone in the treatment of cancer. Immunotherapy has yielded remarkable treatment responses in a range of cancer types including HCC. Based on the therapeutic effect of ICI alone (programmed cell death (PD)-1/programmed death-ligand1 (PD-L)1 antibody), investigators have developed combined ICI therapies including ICI + ICI, ICI + tyrosine kinase inhibitor (TKI), and ICI + locoregional treatment or novel immunotherapy. Although these regimens have demonstrated increasing treatment efficacy with the addition of novel drugs, the development of biomarkers to predict toxicity and treatment response in patients receiving ICI is in urgent need. PD-L1 expression in tumor cells received the most attention in early studies among various predictive biomarkers. However, PD-L1 expression alone has limited utility as a predictive biomarker in HCC. Accordingly, subsequent studies have evaluated the utility of tumor mutational burden (TMB), gene signatures, and multiplex immunohistochemistry (IHC) as predictive biomarkers. In this review, we aim to discuss the current state of immunotherapy for HCC, the results of the predictive biomarker studies, and future direction.
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Affiliation(s)
- Jun Ho Ji
- Division of Hematology and Oncology, Department of Internal Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon 51353, Republic of Korea
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sang Yun Ha
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 03181, Republic of Korea
| | - Danbi Lee
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Kamya Sankar
- Division of Medical Oncology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ekaterina K. Koltsova
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ghassan K. Abou-Alfa
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weil Cornell Medicine, Cornell University, New York, NY 14853, USA
| | - Ju Dong Yang
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Chen MC, Su HY, Su YH, Huang KH, Fang WL, Lin CW, Chen MH, Chao Y, Lo SS, Fen-Yau Li A, Wu CW. Reply to "Is it possible that advanced-stage gastric cancer patients can be cured by surgery alone?". J Chin Med Assoc 2023; 86:350. [PMID: 36599153 DOI: 10.1097/jcma.0000000000000875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Meng-Chao Chen
- Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan, ROC
- Department of Neurosurgery, China Medical University Hospital, Taipei Branch, Taipei, Taiwan, ROC
| | - Hsuan-Yu Su
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Yen-Hao Su
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, ROC
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan, ROC
- Division of General Surgery, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, ROC
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan, ROC
| | - Kuo-Hung Huang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Gastric Cancer Medical Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Wen-Liang Fang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Gastric Cancer Medical Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Chii-Wann Lin
- Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Ming-Huang Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yee Chao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Su-Shun Lo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- National Yang Ming Chiao Tung University Hospital, Yilan, Taiwan, ROC
| | - Anna Fen-Yau Li
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Chew-Wun Wu
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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27
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Kung CY, Fang WL, Hung YP, Huang KH, Chen MH, Chao Y, Lin SC, Li AFY, Lo SS, Wu CW. Comparison of the mutation patterns between tumor tissue and cell-free DNA in stage IV gastric cancer. Aging (Albany NY) 2023; 15:777-790. [PMID: 36779847 PMCID: PMC9970310 DOI: 10.18632/aging.204512] [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: 09/07/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023]
Abstract
Compared to stage I-III gastric cancer (GC), the level of cell-free DNA (cfDNA) was significantly higher in stage IV GC. The mutation patterns of different metastatic patterns between cfDNA and tumor DNA in stage IV GC have not yet been reported. We used next-generation sequencing (NGS) to analyze cfDNA and tumor DNA in 56 stage IV GC patients. Tumor DNA and cfDNA were analyzed using a 29-gene NGS panel. In tumor samples, the most commonly mutated gene was TP53 (64%), followed by ARID1A (62%), KMT2C (60%) and KMT2D (58%). In cfDNA samples, the most commonly mutated genes were FAT4 (19%) and MACF1 (19%), followed by KMT2D (18%), ARID1A (14%) and LRP1B (14%). The concordance of mutation patterns in these 29 genes was 42.0% between cfDNA and tumor DNA. A specificity of 100% was found when using the mutation status of cfDNA to predict mutations in tumor samples. The sensitivity of the mutation status of cfDNA to predict mutation in tumor samples was highest in FAT4 (88.9%), followed by MACF1 (80%), CDH1 (75%) and PLB1 (75%). For cfDNA with PLB1 mutations, patients were more likely to develop distant lymphatic metastasis than peritoneal metastasis. Patients with multiple-site metastases had significantly more mutated spots than patients with single-site metastasis. Due to the high sensitivity and specificity of some genes in the prediction of mutation in tumor samples, monitoring the mutation pattern of cfDNA may be useful in the stage IV GC treatment.
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Affiliation(s)
- Ching-Yun Kung
- Department of Surgery, Division of General Surgery, Taipei Veterans General Hospital, Taipei, Taiwan,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wen-Liang Fang
- Department of Surgery, Division of General Surgery, Taipei Veterans General Hospital, Taipei, Taiwan,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Ping Hung
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,Department of Oncology, Center of Immuno-Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuo-Hung Huang
- Department of Surgery, Division of General Surgery, Taipei Veterans General Hospital, Taipei, Taiwan,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ming-Huang Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,Department of Oncology, Center of Immuno-Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yee Chao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,Department of Oncology, Center of Immuno-Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shih-Chieh Lin
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Anna Fen-Yau Li
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,Department of Anatomical Pathology, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Su-Shun Lo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,National Yang Ming Chiao Tung University Hospital, Yilan, Taiwan
| | - Chew-Wun Wu
- Department of Surgery, Division of General Surgery, Taipei Veterans General Hospital, Taipei, Taiwan,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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28
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Chen MC, Su HY, Su YH, Huang KH, Fang WL, Lin CW, Chen MH, Chao Y, Lo SS, Fen-Yau Li A, Wu CW. The clinicopathological and genetic differences among gastric cancer patients with no recurrence, early recurrence, and late recurrence after curative surgery. J Chin Med Assoc 2023; 86:57-64. [PMID: 36374529 DOI: 10.1097/jcma.0000000000000846] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND To date, few reports have investigated the genetic alterations and clinicopathological features among gastric cancer (GC) patients with no tumor recurrence, early recurrence, and late recurrence following curative surgery. METHODS A total of 473 GC patients undergoing curative surgery were included. The clinicopathological characteristics, patient prognosis, recurrence patterns, and genetic alterations were compared between GC patients with early recurrence and late recurrence. RESULTS Among the 473 GC patients, 119 had early recurrence (<2 years) and 45 had late recurrence (≥2 years). Patients with early recurrence had tumor size larger than 5 cm, fewer superficial-type tumors, more lymphovascular invasion, more advanced pathological T and N categories and Tumor, Node, Metastasis (TNM) stages, and worse 5-year overall survival than patients with late recurrence and no recurrence. For intestinal-type GC, patients with no tumor recurrence had more Helicobacter pylori infection than patients with early recurrence and late recurrence; for diffuse-type GC patients, the frequency of PIK3CA amplification was the highest in early recurrence, followed by late recurrence and no recurrence. GC patients with single-site recurrence had more ARID1A mutations than those with multiple-site recurrence. Multivariate analysis demonstrated that age, tumor recurrence, and pathological N categories were independent prognostic factors. CONCLUSION PIK3CA amplifications were more common in diffuse-type GC with early recurrence, whereas ARID1A mutations were more common in patients with single-site recurrence. Targeted therapy and immunotherapy might be helpful for these patients.
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Affiliation(s)
- Meng-Chao Chen
- Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan, ROC
- Department of Neurosurgery, China Medical University Hospital, Taipei Branch, Taipei, Taiwan, ROC
| | - Hsuan-Yu Su
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Yen-Hao Su
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, ROC
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan, ROC
- Division of General Surgery, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, ROC
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan, ROC
| | - Kuo-Hung Huang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Gastric Cancer Medical Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Wen-Liang Fang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Gastric Cancer Medical Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Chii-Wann Lin
- Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Ming-Huang Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yee Chao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Su-Shun Lo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Department of Surgery, National Yang Ming Chiao Tung University Hospital, Yilan, Taiwan, ROC
| | - Anna Fen-Yau Li
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Chew-Wun Wu
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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29
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Zhang R, Gan W, Zong J, Hou Y, Zhou M, Yan Z, Li T, Lv S, Zeng Z, Wang W, Zhang F, Yang M. Developing an m5C regulator-mediated RNA methylation modification signature to predict prognosis and immunotherapy efficacy in rectal cancer. Front Immunol 2023; 14:1054700. [PMID: 36911744 PMCID: PMC9992543 DOI: 10.3389/fimmu.2023.1054700] [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: 09/27/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
Background Currently, a very small number of patients with colorectal cancer (CRC) respond to immune checkpoint inhibitor (ICI) treatment. Therefore, there is an urgent need to investigate effective biomarkers to determine the responsiveness to ICI treatment. Recently, aberrant 5-methylcytosine (m5C) RNA modification has emerged as a key player in the pathogenesis of cancer. Thus, we aimed to explore the predictive signature based on m5C regulator-related genes for characterizing the immune landscapes and predicting the prognosis and response to therapies. Methods The Cancer Genome Atlas (TCGA) cohort was used as the training set, while GEO data sets, real-time quantitative PCR (RT-qPCR) analysis from paired frozen tissues, and immunohistochemistry (IHC) data from tissue microarray (TMA) were used for validation. We constructed a novel signature based on three m5C regulator-related genes in patients with rectal adenocarcinoma (READ) using a least absolute shrinkage and selection operator (LASSO)-Cox regression and unsupervised consensus clustering analyses. Additionally, we correlated the three-gene signature risk model with the tumor immune microenvironment, immunotherapy efficiency, and potential applicable drugs. Results The m5C methylation-based signature was an independent prognostic factor, where low-risk patients showed a stronger immunoreactivity phenotype and a superior response to ICI therapy. Conversely, the high-risk patients had enriched pathways of cancer hallmarks and presented immune-suppressive state, which demonstrated that they are more insensitive to immunotherapy. Additionally, the signature markedly correlated with drug susceptibility. Conclusions We developed a reliable m5C regulator-based risk model to predict the prognosis, clarify the molecular and tumor microenvironment status, and identify patients who would benefit from immunotherapy or chemotherapy. Our study could provide vital guidance to improve prognostic stratification and optimize personalized therapeutic strategies for patients with rectal cancer.
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Affiliation(s)
- Rixin Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenqiang Gan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinbao Zong
- Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China.,Qingdao Hospital of Traditional Chinese Medicine, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Yufang Hou
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingxuan Zhou
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Yan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tiegang Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Silin Lv
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zifan Zeng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiqi Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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30
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Li M, Gao X, Wang X. Identification of tumor mutation burden-associated molecular and clinical features in cancer by analyzing multi-omics data. Front Immunol 2023; 14:1090838. [PMID: 36911742 PMCID: PMC9998480 DOI: 10.3389/fimmu.2023.1090838] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/06/2023] [Indexed: 03/14/2023] Open
Abstract
Background Tumor mutation burden (TMB) has been recognized as a predictive biomarker for immunotherapy response in cancer. Systematic identification of molecular features correlated with TMB is significant, although such investigation remains insufficient. Methods We analyzed associations of somatic mutations, pathways, protein expression, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), competing endogenous RNA (ceRNA) antitumor immune signatures, and clinical features with TMB in various cancers using multi-omics datasets from The Cancer Genome Atlas (TCGA) program and datasets for cancer cohorts receiving the immune checkpoint blockade therapy. Results Among the 32 TCGA cancer types, melanoma harbored the highest percentage of high-TMB (≥ 10/Mb) cancers (49.4%), followed by lung adenocarcinoma (36.9%) and lung squamous cell carcinoma (28.1%). Three hundred seventy-six genes had significant correlations of their mutations with increased TMB in various cancers, including 11 genes (ARID1A, ARID1B, BRIP1, NOTCH2, NOTCH4, EPHA5, ROS1, FAT1, SPEN, NSD1,and PTPRT) with the characteristic of their mutations associated with a favorable response to immunotherapy. Based on the mutation profiles in three genes (ROS1, SPEN, and PTPRT), we defined the TMB prognostic score that could predict cancer survival prognosis in the immunotherapy setting but not in the non-immunotherapy setting. It suggests that the TMB prognostic score's ability to predict cancer prognosis is associated with the positive correlation between immunotherapy response and TMB. Nine cancer-associated pathways correlated positively with TMB in various cancers, including nucleotide excision repair, DNA replication, homologous recombination, base excision repair, mismatch repair, cell cycle, spliceosome, proteasome, and RNA degradation. In contrast, seven pathways correlated inversely with TMB in multiple cancers, including Wnt, Hedgehog, PI3K-AKT, MAPK, neurotrophin, axon guidance, and pathways in cancer. High-TMB cancers displayed higher levels of antitumor immune signatures and PD-L1 expression than low-TMB cancers in diverse cancers. The association between TMB and survival prognosis was positive in bladder, gastric, and endometrial cancers and negative in liver and head and neck cancers. TMB also showed significant associations with age, gender, height, weight, smoking, and race in certain cohorts. Conclusions The molecular and clinical features significantly associated with TMB could be valuable predictors for TMB and immunotherapy response and therefore have potential clinical values for cancer management.
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Affiliation(s)
- Mengyuan Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xuejiao Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiaosheng Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
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Xia W, Gao Z, Jiang X, Jiang L, Qin Y, Zhang D, Tian P, Wang W, Zhang Q, Zhang R, Zhang N, Xu S. Alzheimer's risk factor FERMT2 promotes the progression of colorectal carcinoma via Wnt/β-catenin signaling pathway and contributes to the negative correlation between Alzheimer and cancer. PLoS One 2022; 17:e0278774. [PMID: 36480537 PMCID: PMC9731493 DOI: 10.1371/journal.pone.0278774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Increasing evidence from epidemiological studies indicate that Alzheimer's disease (AD) has a negative relationship with the incidence of cancers. Whether the Alzheimer's genetic risk factor, named as fermitin family homolog-2 (FERMT2), plays a pivotal part in the progressive process of colorectal carcinoma (CRC) yet remains unclear. This study revealed that FERMT2 was upregulated in CRC tissues which predicted an unfavorable outcome of CRC using the PrognoScan web tool. FERMT2 was co-expressed with a variety of genes have been linked with CRC occurrence and implicated in the infiltration of immune cell in CRC tissues. Overexpressing FERMT2 promoted CRC progression with upregulation of Wnt/β-catenin signaling. Knockdown of FERMT2 suppressed the cell multiplication, colony formation rate, migration and invasion, along with the epithelial to mesenchymal transition (EMT) with downregulation Wnt/β-catenin proteins in cells of CRC, while overexpressing β-catenin reversed the inhibitory effects of silencing FERMT2 on the migration or invasion of CRC cells. Furthermore, Aβ1-42 treated HT22 cells induced downregulation of FERMT2 and inhibited the migration, invasion and EMT in co-cultured CT26 cells through Wnt/β-catenin signaling. Our results revealed that the downregulated FERMT2 gene during AD is prominently activated in CRC, which promotes its progression via Wnt/β-catenin pathway.
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Affiliation(s)
- Wenzhen Xia
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhaoyu Gao
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China,Hebei International Joint Research Center for Brain Science, Shijiazhuang, Hebei, China,Hebei Key Laboratory of Brain Science and Psychiatric-Psychologic Disease, Shijiazhuang, Hebei, China
| | - Xia Jiang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China,Key Laboratory for Colorectal Cancer Precision Diagnosis and Treatment of Hebei Province, Shijiazhuang, Hebei, China
| | - Lei Jiang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China,Hebei International Joint Research Center for Brain Science, Shijiazhuang, Hebei, China,Hebei Key Laboratory of Brain Science and Psychiatric-Psychologic Disease, Shijiazhuang, Hebei, China
| | - Yushi Qin
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Di Zhang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Pei Tian
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Wanchang Wang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Qi Zhang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Rui Zhang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China,Hebei International Joint Research Center for Brain Science, Shijiazhuang, Hebei, China,Hebei Key Laboratory of Brain Science and Psychiatric-Psychologic Disease, Shijiazhuang, Hebei, China
| | - Nan Zhang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China,Hebei International Joint Research Center for Brain Science, Shijiazhuang, Hebei, China,Hebei Key Laboratory of Brain Science and Psychiatric-Psychologic Disease, Shijiazhuang, Hebei, China
| | - Shunjiang Xu
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China,Hebei International Joint Research Center for Brain Science, Shijiazhuang, Hebei, China,Hebei Key Laboratory of Brain Science and Psychiatric-Psychologic Disease, Shijiazhuang, Hebei, China,* E-mail:
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32
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Chen G, Li X, Ji C, Liu P, Zhou L, Xu D, Wang D, Li J, Yu J. Early myeloid-derived suppressor cells accelerate epithelial-mesenchymal transition by downregulating ARID1A in luminal A breast cancer. Front Bioeng Biotechnol 2022; 10:973731. [PMID: 36329699 PMCID: PMC9623091 DOI: 10.3389/fbioe.2022.973731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/03/2022] [Indexed: 11/18/2022] Open
Abstract
Early myeloid-derived suppressor cells (eMDSCs) are a newly characterized subclass of MDSCs, which exhibit more potent immunosuppressive capacity than classical MDSCs. Previously, we found high eMDSCs infiltration was correlated with poor prognosis of breast cancer, though the regulatory mechanisms have not been fully understood. Here, we constructed a 21-gene signature to evaluate the status of eMDSCs infiltration within breast cancer tissues and found that highly infiltrated eMDSCs affected the prognosis of breast cancer patients, especially in luminal A subtype. We also found that eMDSCs promoted epithelial-mesenchymal transition (EMT) and accelerated cell migration and invasion in vitro. Meanwhile, eMDSCs significantly downregulated ARID1A expression in luminal A breast cancer, which was closely associated with EMT and was an important prognostic factor in breast cancer patients. Moreover, significant changes of EMT-related genes were detected in luminal A breast cancer cells after co-cultured with eMDSCs or ARID1A knock-down and overexpression of ARID1A significantly reversed this procedure. These results implied that eMDSCs might suppress the ARID1A expression to promote EMT in luminal A breast cancer cells, which might provide a new light on developing novel treatment regimens for relapsed luminal A breast cancer after conventional therapies.
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Affiliation(s)
- Guidong Chen
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Xingchen Li
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Chenyan Ji
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Pengpeng Liu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Li Zhou
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Dechen Xu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Dong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
- *Correspondence: Jinpu Yu, ; Jie Li,
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- *Correspondence: Jinpu Yu, ; Jie Li,
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Identification and Validation of a Novel Multiomics Signature for Prognosis and Immunotherapy Response of Endometrial Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:8998493. [PMID: 36281289 PMCID: PMC9587907 DOI: 10.1155/2022/8998493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/31/2022] [Accepted: 08/06/2022] [Indexed: 11/17/2022]
Abstract
Purpose Cancer development and immune escape involve DNA methylation, copy number variation, and other molecular events. However, there are remarkably few studies integrating multiomics genetic profiles into endometrial cancer (EC). This study aimed to develop a multiomics signature for the prognosis and immunotherapy response of endometrial carcinoma. Methods The gene expression, somatic mutation, copy number alteration, and DNA methylation data of EC were analyzed from the UCSC Xena database. Then, a multiomics signature was constructed by a machine learning model, with the ROC curve comparing its prognostic power with traditional clinical features. Two computational strategies were utilized to estimate the signature's performance in predicting immunotherapy response in EC. Further validation focused on the most frequently mutant molecule, ARID1A, in the signature. The association of ARID1A with survival, MSI (Microsatellite-instability), immune checkpoints, TIL (tumor-infiltrating lymphocyte), and downstream immune pathways was explored. Results The signature consisted of 22 multiomics molecules, showing excellent prognostic performance in predicting the overall survival of patients with EC (AUC = 0.788). After stratifying patients into a high and low-risk group according to the signature's median value, low-risk patients displayed a greater possibility of respond to immunotherapy. Further validation on ARID1A suggested it could induce immune checkpoints upregulation, promote interferon response pathway, and interact with Treg (regulatory T cell) to facilitate immune activation in EC. Conclusion A novel multiomics prognostic signature of EC was identified and validated in this study, which could guide clinical management of EC and benefit personalized immunotherapy.
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Wang N, Qin Y, Du F, Wang X, Song C. Prevalence of SWI/SNF genomic alterations in cancer and association with the response to immune checkpoint inhibitors: A systematic review and meta-analysis. Gene X 2022; 834:146638. [PMID: 35680019 DOI: 10.1016/j.gene.2022.146638] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/02/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The association between SWI/SNF genomic alterations and responses to immune checkpoint inhibitors (ICIs) remains conflicting. This meta-analysis was performed to systematically assess the impact of SWI/SNF genomic alterations on response to ICIs in cancer. METHODS Relevant studies were searched in multiple databases updated to April 29, 2021. Outcomes of interest included prevalence of SWI/SNF alterations, overall survival (OS), progression-free survival (PFS) and time to treatment failure (TTF). For survival data, the hazard ratio (HR) was adopted, and the effect size was described as 95% confidence intervals (CI). RESULTS 15 studies involving 10,849 patients were included, with the overall frequency of 18.5% in SWI/SNF alterations. Across different cancer types, the mutational frequency of PBRM1 (32.0%) was the highest, followed by ARID1A (18.1%), SMARCA4 (15.6%), SMARCA2 (10.3%), ARID2 (8.1%), SMARCC2 (6.4%) and SMARCB1 (5.0%). Overall analysis showed that SWI/SNF alterations were not associated with improved OS (HR: 0.822, 95 %CI: 0.583-1.158, p = 0.262), PFS (HR: 0.608, 95 %CI: 0.434-1.067, p = 0.094) and TTF (HR: 0.923, 95 %CI: 0.757-1.125, p = 0.427) in patients treated with ICIs. In subgroup analysis, PBRM1 mutations were observed to be linked with improved OS (HR: 0.650, 95 %CI: 0.440-0.960, p = 0.030), PFS (HR: 0.539, 95 %CI: 0.314-0.926, p = 0.025) and TTF (HR: 0.490, 95 %CI: 0.271-0.885, p = 0.018) in RCC patients receiving ICIs. CONCLUSIONS The overall prevalence of SWI/SNF alterations was 18.5% across different cancer types. Except for PBRM1 mutations in RCC, SWI/SNF alterations may be uncorrelated with improved clinical outcomes in cancer.
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Affiliation(s)
- Nanya Wang
- Cancer Center, The First Hospital of Jilin University, Changchun 130021, China.
| | - Yong Qin
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210042, China
| | - Furong Du
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210042, China; Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing 210042, China
| | - Xiaoxuan Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210042, China; Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing 210042, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210042, China; Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing 210042, China
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Jiang Y, Wang X, Li L, He J, Jin Q, Long D, Liu C, Zhou W, Liu K. A systematic analysis of C5ORF46 in gastrointestinal tumors as a potential prognostic and immunological biomarker. Front Genet 2022; 13:926943. [PMID: 35991552 PMCID: PMC9389054 DOI: 10.3389/fgene.2022.926943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Chromosome 5 open reading frame 46 (C5ORF46), also known as antimicrobial peptide with 64 amino acid residues (AP-64) and skin and saliva-secreted protein 1 (SSSP1), belongs to the family of open reading frame genes and encodes a small exosomal protein. C5ORF46 has been implicated in antibacterial activity and associated with patient prognosis in pancreatic cancer, colorectal cancer, and stomach cancer. These findings highlight the importance of C5ORF46 in gastrointestinal (GI) tumor inception and development. However, the prognostic and immunological value of C5ORF46 in human GI tumors remains largely unknown. In this study, we sought to explore the potential value of C5ORF46 in GI tumor prognosis and immunology.Method: RNA sequencing (RNA-seq) was performed on the tumor and tumor-adjacent normal samples we collected to identify potential target genes for GI tumors. Apart from our RNA-seq data, all original data were downloaded from The Cancer Genome Atlas (TCGA) database and integrated via Strawberry Perl (v 5.32.0) and R (v 4.1.1). The differential expression of C5ORF46 was examined with Oncomine, Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), Cancer Cell Line Encyclopedia (CCLE), the Human Protein Atlas (HPA) and TCGA databases. The c-BioPortal database was used to investigate the genomic alterations of C5ORF46. The effect of C5ORF46 on prognosis and clinical phenotypes was explored via bioinformatics analyses on the TCGA and GEPIA databases. We used the bioinformatics analyses based on the TCGA database to analyze tumor mutational burden (TMB), microsatellite instability (MSI), tumor immune cell infiltration, and the correlations between C5ORF46 expression and several immune-related genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was carried out via the DAVID website and presented as bubble charts using ShengXinRen online tools. Gene set enrichment analysis (GSEA) was performed using R scripts based on data downloaded from the GSEA website. Immunohistochemistry (IHC) was used to validate the expression of C5ORF46 in GI tumors.Results: The results of our RNA-seq data indicated a critical role for C5ORF46 in colon carcinogenesis. Consistently, we demonstrated that C5ORF46 was highly expressed in tumor tissues compared to normal tissues in human GI tumors. Moreover, a strong correlation was observed between C5ORF46 expression levels and patient prognosis, staging, TMB, MSI, and immune cell infiltration. Further, C5ORF46 presented as an important regulator in the tumor microenvironment (TME) and was active in the regulation of cancer immune functions. C5ORF46 is significantly correlated with genes regulating inflammation and immune responses.Conclusion:C5ORF46 may serve as a biomarker for GI tumor prognosis and immunology. C5ORF46 could be a novel target for GI tumor immunotherapy.
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Affiliation(s)
- Yuhong Jiang
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaobo Wang
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lun Li
- Department of Breast-Thyroid Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jun He
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qianqian Jin
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Dongju Long
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chao Liu
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Weihan Zhou
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Kuijie Liu
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- *Correspondence: Kuijie Liu,
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Zhou Z, Huang D, Yang S, Liang J, Wang X, Rao Q. Clinicopathological Significance, Related Molecular Changes and Tumor Immune Response Analysis of the Abnormal SWI/SNF Complex Subunit PBRM1 in Gastric Adenocarcinoma. PATHOLOGY AND ONCOLOGY RESEARCH 2022; 28:1610479. [PMID: 35928964 PMCID: PMC9344308 DOI: 10.3389/pore.2022.1610479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022]
Abstract
Background: PBRM1 gene abnormalities were recently found to play a role in tumor development and tumor immune activity. This article will explore the clinicopathological and molecular changes and tumor immune activity of the abnormal SWI/SNF complex subunit PBRM1 in gastric adenocarcinoma (GAC) and its significance. Methods: The cBioPortal, LinkedOmics and TISIDB datasets were used to analyze the abnormality of the PBRM1 gene in GAC and its relationship with prognosis, related molecular changes and tumor-infiltrating lymphocytes (TILs). In addition, 198 GAC cases were collected to further study the relationship between the loss/attenuation of PBRM1 expression and clinicopathology, prognosis, microsatellite stability, PD-L1 expression and TIL in GAC. DNA whole-exome sequencing was performed on 7 cases of gastric cancer with loss of PBRM1 expression. Results: The cBioPortal data showed that PBRM1 deletion/mutation accounted for 7.32% of GAC and was significantly associated with several molecular changes, such as molecular subtypes of GAC. The LinkedOmics dataset showed that PBRM1 mutation and its promoter DNA methylation showed lower PBRM1 mRNA expression, and PBRM1 mutation cases showed significantly higher mRNA expression of PD-L1 (CD274). TISIDB data showed that PBRM1 abnormalities were significantly positively associated with multiple TILs. In our group of 198 cases, the loss/attenuation of PBRM1 expression was significantly positively correlated with intra-tumoral tumor infiltrating lymphocytes (iTILs) and deficient MMR and PD-L1 expression. Kaplan–Meier survival analysis showed that the overall survival of GAC patients with loss/attenuation of PBRM1 expression was significantly better (p = 0.023). iTIL was an independent prognostic factor of GAC. Loss of PBRM1 expression often co-occurs with mutations in other SWI/SNF complex subunit genes, and there are some repetitive KEGG signaling changes. Conclusion: Abnormality of the PBRM1 gene may be related to the occurrence of some GACs and can affect tumor immune activity, thereby affecting clinicopathology and prognosis. It may be a potentially effective predictive marker for immunotherapy and a novel therapeutic approach associated with synthetic lethality.
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Affiliation(s)
- Zhiyi Zhou
- Department of Pathology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Dandan Huang
- Digestive Endoscopic Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Shudong Yang
- Department of Pathology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Jiabei Liang
- Department of Pathology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Xuan Wang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qiu Rao
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- *Correspondence: Qiu Rao,
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Conde M, Frew IJ. Therapeutic significance of ARID1A mutation in bladder cancer. Neoplasia 2022; 31:100814. [PMID: 35750014 PMCID: PMC9234250 DOI: 10.1016/j.neo.2022.100814] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Bladder cancer (BC) develops from the tissues of the urinary bladder and is responsible for nearly 200,000 deaths annually. This review aims to integrate knowledge of recently discovered functions of the chromatin remodelling tumour suppressor protein ARID1A in bladder urothelial carcinoma with a focus on highlighting potential new avenues for the development of personalised therapies for ARID1A mutant bladder tumours. ARID1A is a component of the SWI/SNF chromatin remodelling complex and functions to control many important biological processes such as transcriptional regulation, DNA damage repair (DDR), cell cycle control, regulation of the tumour microenvironment and anti-cancer immunity. ARID1A mutation is emerging as a truncal driver mutation that underlies the development of a sub-set of urothelial carcinomas, in cooperation with other driver mutations, to cause dysregulation of a number of key cellular processes. These processes represent tumour drivers but also represent potentially attractive therapeutic targets.
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Affiliation(s)
- Marina Conde
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre - University of Freiburg, Freiburg, Baden-Württemberg, Germany
| | - Ian J Frew
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre - University of Freiburg, Freiburg, Baden-Württemberg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany; Signalling Research Centre BIOSS, University of Freiburg, Freiburg, Baden-Württemberg, Germany; Comprehensive Cancer Center Freiburg (CCCF), Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Baden-Württemberg, Germany.
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High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration. J Immunol Res 2022; 2022:2922832. [PMID: 35707002 PMCID: PMC9192325 DOI: 10.1155/2022/2922832] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Purpose To elucidate the clinical and prognostic role of PDZ and LIM domain protein (PDLIM) genes and the association to epithelial-mesenchymal transition (EMT) and immune cell infiltration in patients with prostate cancer (PRAD). Methods The data of RNA-seq, DNA methylation, and clinical features of PRAD patients were collected from The Cancer Genome Atlas (TCGA) database to define the prognostic value of PDLIM gene expression and the association with EMT and immune cell infiltration. A tissue microarray including 134 radical prostatectomy specimens was served as validation by immunohistochemistry (IHC) staining analysis. Results The mRNA levels of PDLIM1/2/3/4/6/7 were significantly downregulated, while PDLIM5 was upregulated in PRAD (P < 0.05). High expression of PDLIM2 mRNA suggests poor progression free interval in PRAD patients. DNA methylation of PDLIM2 was correlated with its mRNA expression level, and that the cg22973076 methylation site in PDLIM2 was associated with shorter PFI (P < 0.05) in PRAD. Single-sample gene-set enrichment and gene functional enrichment results showed that PDLIM2 was correlated with EMT and immune processes. Spearman's test showed a significant correlation with six reported EMT signatures and several EMT signature-related genes. Tumor microenvironment analysis revealed that the PDLIM2 mRNA expression was positively correlated with the immune score, stromal score, and various tumor infiltrating immune cells. Additionally, the results showed that patients in the high-PDLIM2 mRNA expression group may be more sensitive to immune checkpoint blockade therapy. Finally, IHC analysis further implicated the protein level of PDLIM2 was upregulated in PRAD and acts as a novel potential biomarker in predicting tumor progression. Conclusion Our study suggests that PDLIM family genes might be significantly correlated with oncogenesis and the progression of PRAD. PDLIM2 correlated with EMT and immune cell infiltration by acting as an oncogene in PRAD, which may serve as a potential prognostic biomarker for PRAD patients.
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Genetic and Clinical Characteristics of ARID1A Mutated Melanoma Reveal High Tumor Mutational Load without Implications on Patient Survival. Cancers (Basel) 2022; 14:cancers14092090. [PMID: 35565222 PMCID: PMC9101535 DOI: 10.3390/cancers14092090] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Melanoma is a highly malignant skin cancer with the highest mortality of all cutaneous tumors. Relevant genetic events have been identified, which shape the tumor and also the response to treatment. Recurrent ARID1A mutations have been identified, which are associated with improved outcomes to immune checkpoint inhibition in various tumors. Not much was known about the role of ARID1A mutations in melanoma to date. We investigated the largest cohort of ARID1A mutated melanoma to date and were able to show that despite a high mutational load the described beneficial treatment response is not apparent in melanoma. Abstract (1) Background: Melanoma has the highest mortality of all cutaneous tumors, despite recent treatment advances. Many relevant genetic events have been identified in the last decade, including recurrent ARID1A mutations, which in various tumors have been associated with improved outcomes to immunotherapy. (2) Methods: Retrospective analysis of 116 melanoma samples harboring ARID1A mutations. Assessment of clinical and genetic characteristics was performed as well as correlations with treatment outcome applying Kaplan–Meier (log-rank test), Fisher’s exact and Chi-squared tests. (3) Results: The majority of ARID1A mutations were in cutaneous and occult melanoma. ARID1A mutated samples had a higher number of mutations than ARID1A wild-type samples and harbored UV-mutations. A male predominance was observed. Many samples also harbored NF1 mutations. No apparent differences were noted between samples harboring genetically inactivating (frame-shift or nonsense) mutations and samples with other mutations. No differences in survival or response to immunotherapy of patients with ARID1A mutant melanoma were observed. (4) Conclusions: ARID1A mutations primarily occur in cutaneous melanomas with a higher mutation burden. In contrast to findings in other tumors, our data does not support ARID1A mutations being a biomarker of favorable response to immunotherapies in melanoma. Larger prospective studies would still be warranted.
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Wedge ME, Jennings VA, Crupi MJF, Poutou J, Jamieson T, Pelin A, Pugliese G, de Souza CT, Petryk J, Laight BJ, Boileau M, Taha Z, Alluqmani N, McKay HE, Pikor L, Khan ST, Azad T, Rezaei R, Austin B, He X, Mansfield D, Rose E, Brown EEF, Crawford N, Alkayyal A, Surendran A, Singaravelu R, Roy DG, Migneco G, McSweeney B, Cottee ML, Jacobus EJ, Keller BA, Yamaguchi TN, Boutros PC, Geoffrion M, Rayner KJ, Chatterjee A, Auer RC, Diallo JS, Gibbings D, tenOever BR, Melcher A, Bell JC, Ilkow CS. Virally programmed extracellular vesicles sensitize cancer cells to oncolytic virus and small molecule therapy. Nat Commun 2022; 13:1898. [PMID: 35393414 PMCID: PMC8990073 DOI: 10.1038/s41467-022-29526-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
Recent advances in cancer therapeutics clearly demonstrate the need for innovative multiplex therapies that attack the tumour on multiple fronts. Oncolytic or “cancer-killing” viruses (OVs) represent up-and-coming multi-mechanistic immunotherapeutic drugs for the treatment of cancer. In this study, we perform an in-vitro screen based on virus-encoded artificial microRNAs (amiRNAs) and find that a unique amiRNA, herein termed amiR-4, confers a replicative advantage to the VSVΔ51 OV platform. Target validation of amiR-4 reveals ARID1A, a protein involved in chromatin remodelling, as an important player in resistance to OV replication. Virus-directed targeting of ARID1A coupled with small-molecule inhibition of the methyltransferase EZH2 leads to the synthetic lethal killing of both infected and uninfected tumour cells. The bystander killing of uninfected cells is mediated by intercellular transfer of extracellular vesicles carrying amiR-4 cargo. Altogether, our findings establish that OVs can serve as replicating vehicles for amiRNA therapeutics with the potential for combination with small molecule and immune checkpoint inhibitor therapy. RNA-based viruses can be engineered to express artificial microRNAs (amiRNAs). Here, the authors identify a candidate amiRNA that confers a replicative advantage to oncolytic viruses, enhancing their anticancer potency, and show that intercellular transfer of extracellular vesicles carrying the amiRNA promotes bystander killing of uninfected cancer cells.
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Affiliation(s)
- Marie-Eve Wedge
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Victoria A Jennings
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Institute of Cancer Research, London, UK.,Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Mathieu J F Crupi
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Joanna Poutou
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Taylor Jamieson
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Giuseppe Pugliese
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | | | - Julia Petryk
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Brian J Laight
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Meaghan Boileau
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Zaid Taha
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Nouf Alluqmani
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hayley E McKay
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Larissa Pikor
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Sarwat Tahsin Khan
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Taha Azad
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Reza Rezaei
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Bradley Austin
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Xiaohong He
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | | | - Elaine Rose
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Emily E F Brown
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Natalie Crawford
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Almohanad Alkayyal
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Abera Surendran
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ragunath Singaravelu
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Dominic G Roy
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Gemma Migneco
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Benjamin McSweeney
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Mary Lynn Cottee
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Egon J Jacobus
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Oncology, University of Oxford, Oxford, UK
| | - Brian A Keller
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Takafumi N Yamaguchi
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paul C Boutros
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.,Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Katey J Rayner
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.,University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Avijit Chatterjee
- The Ottawa Hospital, Division of Gastroenterology, Ottawa, Ontario, Canada
| | - Rebecca C Auer
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.,Department of Surgery, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-Simon Diallo
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John C Bell
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carolina S Ilkow
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada. .,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.
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Nan L, Wang C, Wang J, Zhang S, Bo X, Wang Y, Liu H. ARID1A Downregulation Predicts High PD-L1 Expression and Worse Clinical Outcome in Patients With Gallbladder Cancer. Front Oncol 2022; 12:787897. [PMID: 35198440 PMCID: PMC8858979 DOI: 10.3389/fonc.2022.787897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
BackgroundRecent studies have confirmed that AT-rich interactive domain-containing protein 1A (ARID1A) plays a critical role in tumorigenesis, but its role in gallbladder cancer (GBC) remains unclear.MethodsIn total, 224 patients from Zhongshan Hospital were recruited for this retrospective study. The clinicopathological and baseline characteristics of the patients were collected. Bioinformatics analysis was performed to reveal variations in genes and signaling pathways, and ARID1A and PD-L1 expression and the number of PD1+ tumor-infiltrating lymphocytes (TILs) were measured by immunohistochemical staining.ResultsARID1A expression was negatively correlated with overall survival in patients with GBC, and multivariate analysis identified ARID1A as an independent prognostic factor for overall survival. A heatmap and gene set enrichment analysis suggested that cytotoxic T lymphocyte signatures and immune-related signaling pathways were downregulated in ARID1A low tumors. Subsequent immunohistochemical staining confirmed that ARID1A expression was negatively correlated with PD-L1 expression and PD1+ TILs in the tumor microenvironment. The Kaplan–Meier analysis suggested that high ARID1A expression combined with low PD-L1 expression or low PD1+ TIL counts is associated with the best prognosis in patients with GBC.ConclusionARID1A inactivation can lead to a worse prognosis in patients with GBC, potentially by mediating immune evasion through the PD1/PD-L1 pathway.
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Affiliation(s)
- Lingxi Nan
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Biliary Tract Diseases Institute, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
| | - Changcheng Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Biliary Tract Diseases Institute, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
| | - Jie Wang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Shulong Zhang
- Biliary Tract Diseases Institute, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Department of General Surgery, Xuhui District Central Hospital, Shanghai, China
| | - Xiaobo Bo
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Biliary Tract Diseases Institute, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- *Correspondence: Yueqi Wang, ; Xiaobo Bo, ; Houbao Liu,
| | - Yueqi Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yueqi Wang, ; Xiaobo Bo, ; Houbao Liu,
| | - Houbao Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Biliary Tract Diseases Institute, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, Shanghai, China
- Department of General Surgery, Xuhui District Central Hospital, Shanghai, China
- *Correspondence: Yueqi Wang, ; Xiaobo Bo, ; Houbao Liu,
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Hwang J, Kim H, Han J, Lee J, Hong S, Kim S, Yoon SK, Choi K, Yang J, Park U, Kim K, Yim K, Kim Y, Choi Y. Identification of Survival-Specific Genes in Clear Cell Renal Cell Carcinoma Using a Customized Next-Generation Sequencing Gene Panel. J Pers Med 2022; 12:jpm12010113. [PMID: 35055428 PMCID: PMC8778284 DOI: 10.3390/jpm12010113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
Purpose: Although mutations are associated with carcinogenesis, little is known about survival-specific genes in clear cell renal cell carcinoma (ccRCC). We developed a customized next-generation sequencing (NGS) gene panel with 156 genes. The purpose of this study was to investigate whether the survival-specific genes we found were present in Korean ccRCC patients, and their association with clinicopathological findings. Materials and Methods: DNA was extracted from the formalin-fixed, paraffin-embedded tissue of 22 ccRCC patients. NGS was performed using our survival-specific gene panel with an Illumina MiSeq. We analyzed NGS data and the correlations between mutations and clinicopathological findings and also compared them with data from the Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) and Renal Cell Cancer-European Union (RECA-EU). Results: We found a total of 100 mutations in 37 of the 156 genes (23.7%) in 22 ccRCC patients. Of the 37 mutated genes, 11 were identified as clinicopathologically significant. Six were novel survival-specific genes (ADAMTS10, CARD6, NLRP2, OBSCN, SECISBP2L, and USP40), and five were top-ranked mutated genes (AKAP9, ARID1A, BAP1, KDM5C, and SETD2). Only CARD6 was validated as an overall survival-specific gene in this Korean study (p = 0.04, r = −0.441), TCGA-KIRC cohort (p = 0.0003), RECA-EU (p = 0.0005). The 10 remaining gene mutations were associated with clinicopathological findings; disease-free survival, mortality, nuclear grade, sarcomatoid component, N-stage, sex, and tumor size. Conclusions: We discovered 11 survival-specific genes in ccRCC using data from TCGA-KIRC, RECA-EU, and Korean patients. We are the first to find a correlation between CARD6 and overall survival in ccRCC. The 11 genes, including CARD6, NLRP2, OBSCN, and USP40, could be useful diagnostic, prognostic, and therapeutic markers in ccRCC.
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Affiliation(s)
- Jia Hwang
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Heeeun Kim
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Jinseon Han
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Jieun Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Sunghoo Hong
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.H.); (S.K.)
| | - Saewoong Kim
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.H.); (S.K.)
| | - Sungjoo Kim Yoon
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.K.Y.); (K.C.)
| | - Keonwoo Choi
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.K.Y.); (K.C.)
| | - Jihoon Yang
- Department of Computer Science and Engineering, Sogang University, Seoul 04107, Korea; (J.Y.); (U.P.)
| | - Unsang Park
- Department of Computer Science and Engineering, Sogang University, Seoul 04107, Korea; (J.Y.); (U.P.)
| | | | - Kwangil Yim
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Yuil Kim
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Yeongjin Choi
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
- Correspondence: ; Tel.: +82-(22)-2581616; Fax: +82-(22)-2581627
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Fountzilas E, Kurzrock R, Vo HH, Tsimberidou AM. Wedding of Molecular Alterations and Immune Checkpoint Blockade: Genomics as a Matchmaker. J Natl Cancer Inst 2021; 113:1634-1647. [PMID: 33823006 PMCID: PMC9890928 DOI: 10.1093/jnci/djab067] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/21/2021] [Accepted: 03/10/2021] [Indexed: 02/05/2023] Open
Abstract
The development of checkpoint blockade immunotherapy has transformed the medical oncology armamentarium. But despite its favorable impact on clinical outcomes, immunotherapy benefits only a subset of patients, and a substantial proportion of these individuals eventually manifest resistance. Serious immune-related adverse events and hyperprogression have also been reported. It is therefore essential to understand the molecular mechanisms and identify the drivers of therapeutic response and resistance. In this review, we provide an overview of the current and emerging clinically relevant genomic biomarkers implicated in checkpoint blockade outcome. US Food and Drug Administration-approved molecular biomarkers of immunotherapy response include mismatch repair deficiency and/or microsatelliteinstability and tumor mutational burden of at least 10 mutations/megabase. Investigational genomic-associated biomarkers for immunotherapy response include alterations of the following genes/associated pathways: chromatin remodeling (ARID1A, PBRM1, SMARCA4, SMARCB1, BAP1), major histocompatibility complex, specific (eg, ultraviolet, APOBEC) mutational signatures, T-cell receptor repertoire, PDL1, POLE/POLD1, and neo-antigens produced by the mutanome, those potentially associated with resistance include β2-microglobulin, EGFR, Keap1, JAK1/JAK2/interferon-gamma signaling, MDM2, PTEN, STK11, and Wnt/Beta-catenin pathway alterations. Prospective clinical trials are needed to assess the role of a composite of these biomarkers to optimize the implementation of precision immunotherapy in patient care.
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Affiliation(s)
- Elena Fountzilas
- Department of Medical Oncology, Euromedica General Clinic, Thessaloniki, Greece
- European University Cyprus, Limassol, Cyprus
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, USA
| | - Henry Hiep Vo
- The University of Texas MD Anderson Cancer Center, Department of Investigational Cancer Therapeutics, Houston, TX, USA
| | - Apostolia-Maria Tsimberidou
- The University of Texas MD Anderson Cancer Center, Department of Investigational Cancer Therapeutics, Houston, TX, USA
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Cheng X, Zhao JX, Dong F, Cao XC. ARID1A Mutation in Metastatic Breast Cancer: A Potential Therapeutic Target. Front Oncol 2021; 11:759577. [PMID: 34804958 PMCID: PMC8599951 DOI: 10.3389/fonc.2021.759577] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/15/2021] [Indexed: 12/05/2022] Open
Abstract
Distant metastasis is the principal cause of mortality for breast cancer patients. Targeting specific mutations that have been acquired during the evolution process of advanced breast cancer is a potential means of enhancing the clinical efficacy of treatment strategies. In metastatic breast cancer, ARID1A is the most prevalent mutation of the SWI/SNF complex, which regulates DNA repair, recombination, and gene transcription. The low expression of ARID1A is associated with poor disease-free survival and overall survival of patients with luminal A or HER2-rich breast cancer. In addition, ARID1A plays a prominent role in maintaining luminal characteristics and has an advantage for identifying responses to treatment, including endocrine therapies, HDAC inhibitors and CDK4/6 inhibitors. The therapeutic vulnerabilities initiated by ARID1A alterations encourage us to explore new approaches to cope with ARID1A mutant-related drug resistance or metastasis. In this review, we describe the mutation profiles of ARID1A in metastatic breast cancer and the structure and function of ARID1A and the SWI/SNF complex as well as discuss the potential mechanisms of ARID1A-mediated endocrine resistance and therapeutic potential.
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Affiliation(s)
- Xuan Cheng
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jian-Xiong Zhao
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Feng Dong
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, China
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Xu-Chen Cao
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
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Chen Z, Chen C, Li L, Zhang T, Wang X. The spliceosome pathway activity correlates with reduced anti-tumor immunity and immunotherapy response, and unfavorable clinical outcomes in pan-cancer. Comput Struct Biotechnol J 2021; 19:5428-5442. [PMID: 34667536 PMCID: PMC8501672 DOI: 10.1016/j.csbj.2021.09.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 12/12/2022] Open
Abstract
Alterations in the spliceosome pathway (SP) have been associated with diverse human cancers. In this study, we explored associations of the SP activity with various clinical features, anti-tumor immune signatures, tumor immunity-related genomic and molecular features, and the response to immunotherapies and targeted therapies in 29 cancer types from The Cancer Genome Atlas (TCGA) database. We showed that the SP activity was an oncogenic signature, as evidenced by its hyperactivation in cancer and invasive cancer subtypes and correlations with unfavorable clinical outcomes and anti-tumor immunosuppression in various cancers. The SP activity showed positive correlations with tumor mutation burden (TMB) and aneuploidy in diverse cancers, suggesting its association with genomic instability. However, the negative association between the SP activity and anti-tumor immune response was independent of its associations with aneuploidy and TMB. Furthermore, we supported that the SP activity had a negative correlation with immunotherapy response in four cancer cohorts treated by immune checkpoint inhibitors. Moreover, elevated SP activity is correlated with increased drug sensitivity for a broad spectrum of anti-tumor targeted therapies. In conclusion, the SP activity is a negative biomarker for anti-tumor immune response, prognosis, and the response to immunotherapeutic and targeted drugs in pan-cancer.
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Affiliation(s)
- Zuobing Chen
- Department of Rehabilitation Medicine, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Canping Chen
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Tianfang Zhang
- Department of Rehabilitation Medicine, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
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Li M, Ma Y, Zhong Y, Liu Q, Chen C, Qiang L, Wang X. KALRN mutations promote antitumor immunity and immunotherapy response in cancer. J Immunother Cancer 2021; 8:jitc-2019-000293. [PMID: 33037113 PMCID: PMC7549479 DOI: 10.1136/jitc-2019-000293] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2020] [Indexed: 12/26/2022] Open
Abstract
Background kalirin RhoGEF kinase (KALRN) is mutated in a wide range of cancers. Nevertheless, the association between KALRN mutations and the pathogenesis of cancer remains unexplored. Identification of biomarkers for cancer immunotherapy response is crucial because immunotherapies only show beneficial effects in a subset of patients with cancer. Methods We explored the correlation between KALRN mutations and antitumor immunity in 10 cancer cohorts from The Cancer Genome Atlas program by the bioinformatics approach. Moreover, we verified the findings from the bioinformatics analysis with in vitro and in vivo experiments. We explored the correlation between KALRN mutations and immunotherapy response in five cancer cohorts receiving immune checkpoint blockade therapy. Results Antitumor immune signatures were more enriched in KALRN-mutated than KALRN-wildtype cancers. Moreover, KALRN mutations displayed significant correlations with increased tumor mutation burden and the microsatellite instability or DNA damage repair deficiency genomic properties, which may explain the high antitumor immunity in KALRN-mutated cancers. Also, programmed cell death 1 ligand (PD-L1) expression was markedly upregulated in KALRN-mutated versus KALRN-wildtype cancers. The increased antitumor immune signatures and PD-L1 expression in KALRN-mutated cancers may favor the response to immune checkpoint blockade therapy in this cancer subtype, as evidenced in five cancer cohorts receiving antiprogrammed cell death protein 1 (PD-1)/PD-L1/cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) immunotherapy. Furthermore, the significant association between KALRN mutations and increased antitumor immunity was associated with the fact that KALRN mutations compromised the function of KALRN in targeting Rho GTPases for the regulation of DNA damage repair pathways. In vitro and in vivo experiments validated the association of KALRN deficiency with antitumor immunity and the response to immune checkpoint inhibitors. Conclusions The KALRN mutation is a useful biomarker for predicting the response to immunotherapy in patients with cancer.
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Affiliation(s)
- Mengyuan Li
- Biomedical Informatics Research Lab,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Yuxiang Ma
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - You Zhong
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qian Liu
- Biomedical Informatics Research Lab,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Canping Chen
- Biomedical Informatics Research Lab,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Lei Qiang
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China .,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
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Feng Q, Song D, Wang X. Pan-cancer analysis reveals that neurotrophin signaling correlates positively with anti-tumor immunity, clinical outcomes, and response to targeted therapies and immunotherapies in cancer. Life Sci 2021; 282:119848. [PMID: 34293398 DOI: 10.1016/j.lfs.2021.119848] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 12/23/2022]
Abstract
AIMS The crosstalk between cancer cells and nerves plays an important role in tumor biology. However, the correlation between the neurotrophin signaling (NS) and anti-tumor immunity and immunotherapy response in cancer remains unexplored. MATERIALS AND METHODS We analyzed associations of NS with anti-tumor immune signatures, tumor immunity-related molecular and genomic features, and clinical features in 33 TCGA cancer types. We also explored the association between NS and the response to immune checkpoint inhibitors (ICIs) in four cancer cohorts. KEY FINDINGS NS scores had significant positive correlations with the enrichment scores of anti-tumor immune signatures, including CD8+ T cells, interferon response, natural killer cells, Toll-like receptor and NOD-like receptor signaling pathways in most cancer types. NS scores were inversely correlated with the scores of DNA damage repair pathways, tumor mutation burden, copy number alterations, intra-tumor heterogeneity, and tumor stemness in diverse cancers. In contrast, NS scores were significantly and positively correlated with the apoptosis pathway's scores in 32 of the 33 cancer types. NS scores were significantly lower in early-stage versus late-stage and in primary versus metastatic tumors in diverse cancers. Higher NS scores were correlated with better survival in pan-cancer and in eight individual cancer types. Moreover, the response rate to ICIs was higher in higher-NS-score than in lower-NS-score tumors in four cancer cohorts. Elevated NS was correlated with increased drug sensitivity for numerous anti-tumor targeted drugs. SIGNIFICANCE NS is a positive biomarker for anti-tumor immune response, prognosis, and the response to targeted and immunotherapeutic drugs in cancer.
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Affiliation(s)
- Qiushi Feng
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Dandan Song
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
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Xing Z, Ma B, Sun W, Sun Y, Liu C. Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers. Hereditas 2021; 158:38. [PMID: 34598711 PMCID: PMC8487138 DOI: 10.1186/s41065-021-00203-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/18/2021] [Indexed: 01/04/2023] Open
Abstract
Background Alterations in genes encoding chromatin regulatory proteins are prevalent in cancers and may confer oncogenic properties and molecular changes linked to therapy resistance. However, the impact of copy number alterations (CNAs) of the SWItch/Sucrose NonFermentable (SWI/SNF) complex on the oncogenic and immunologic properties has not been systematically explored across human cancer types. Methods We comprehensively analyzed the genomic, transcriptomic and clinical data of The Cancer Genome Atlas (TCGA) dataset across 33 solid cancers. Results CNAs of the SWI/SNF components were identified in more than 25% of all queried cancers, and tumors harboring SWI/SNF CNAs demonstrated a worse overall survival (OS) than others in several cancer types. Mechanistically, the SCNA events in the SWI/SNF complex are correlated with dysregulated genomic features and oncogenic pathways, including the cell cycle, DNA damage and repair. Notably, the SWI/SNF CNAs were associated with homologous recombination deficiency (HRD) and improved clinical outcomes of platinum-treated ovarian cancer. Furthermore, we observed distinct immune infiltrating patterns and immunophenotypes associated with SWI/SNF CNAs in different cancer types. Conclusion The CNA events of the SWI/SNF components are a key process linked to oncogenesis, immune infiltration and therapeutic responsiveness across human cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00203-y.
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Affiliation(s)
- Zhiwei Xing
- The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, China
| | - Buhuan Ma
- Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, China
| | - Weiting Sun
- Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, China
| | - Yimin Sun
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, China.,Department of Biomedical Engineering, Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing, 100084, China
| | - Caixia Liu
- The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, China.
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Sun D, Zhu Y, Zhao H, Bian T, Li T, Liu K, Feng L, Li H, Hou H. Loss of ARID1A expression promotes lung adenocarcinoma metastasis and predicts a poor prognosis. Cell Oncol (Dordr) 2021; 44:1019-1034. [PMID: 34109546 DOI: 10.1007/s13402-021-00616-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/26/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND ARID1A is an essential subunit of SWI/SNF chromatin remodeling complexes. ARID1A gene mutations and loss of ARID1A expression have been observed in a variety of cancers, and to be correlated with invasion, immune escape and synthetic lethality. As yet, however, the biological effect of ARID1A expression and its role in the prognosis of lung adenocarcinoma (LUAD) patients have remained unclear. In this study we aimed to further elucidate the role of ARID1A expression in LUAD in vitro and in vivo and to assess its effect on the clinical prognosis of LUAD patients. METHODS ARID1A expression was detected by IHC in tissue samples from LUAD patients. After regular culturing of LUAD cell lines and constructing stable ARID1A knockdown lines, wound healing and Transwell assays were used to assess the role of ARID1A in cell migration and invasion. The effect of ARID1A knockdown on metastasis was verified in vivo. Western blotting was used to examine the expression of target proteins. Univariate and multivariate analyses were performed to assess survival and to provide variables for nomogram construction. In addition, we used the "rms" package to construct a prognostic nomogram based on a Cox regression model. RESULTS We found that ARID1A expression serves as an effective prognostic marker for LUAD patients. Loss of ARID1A expression correlated with a poor prognosis, as verified with a nomogram based on a Cox regression model. In addition, we found that ARID1A knockdown promoted LUAD cell proliferation, migration and invasion in vitro and enhanced LUAD metastasis in vivo by activating the Akt signaling pathway. CONCLUSIONS Our data indicate that loss of ARID1A expression promotes LUAD metastasis and predicts a poor prognosis in LUAD patients.
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Affiliation(s)
- Dantong Sun
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, 59 Haier Road, Shandong, 266000, Qingdao, China
| | - Yan Zhu
- Department of Medical Oncology, The Municipal Hospital of Qingdao, 266000, Qingdao, China
| | - Han Zhao
- Department of Pathology, The Affiliated Hospital of Qingdao University, 266000, Qingdao, China
| | - Tiantian Bian
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao University, 266100, Qingdao, China
| | - Tianjun Li
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, 59 Haier Road, Shandong, 266000, Qingdao, China
| | - Kewei Liu
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, 59 Haier Road, Shandong, 266000, Qingdao, China
| | - Lizong Feng
- Department of General Surgery, Qingdao Eighth People's Hospital, 266041, Qingdao, China
| | - Hong Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China.
| | - Helei Hou
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, 59 Haier Road, Shandong, 266000, Qingdao, China.
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Mutations in Epigenetic Regulation Genes in Gastric Cancer. Cancers (Basel) 2021; 13:cancers13184586. [PMID: 34572812 PMCID: PMC8467700 DOI: 10.3390/cancers13184586] [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: 08/06/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Epigenetic mechanisms, such as DNA methylation/demethylation, covalent modifications of histone proteins, and chromatin remodeling, create specific patterns of gene expression. Epigenetic deregulations are associated with oncogenesis, relapse of the disease and metastases, and can serve as a useful clinical marker. We assessed the clinical relevance of integrity of the genes coding for epigenetic regulator proteins by mutational profiling of 25 genes in 135 gastric cancer (GC) samples. Overall, mutations in the epigenetic regulation genes were found to be significantly associated with reduced overall survival of patients in the group with metastases and in the group with tumors with signet ring cells. We have also discovered mutual exclusivity of somatic mutations in the KMT2D, KMT2C, ARID1A, and CHD7 genes in our cohort. Our results suggest that mutations in epigenetic regulation genes may be valuable clinical markers and deserve further exploration in independent cohorts. Abstract We have performed mutational profiling of 25 genes involved in epigenetic processes on 135 gastric cancer (GC) samples. In total, we identified 79 somatic mutations in 49/135 (36%) samples. The minority (n = 8) of mutations was identified in DNA methylation/demethylation genes, while the majority (n = 41), in histone modifier genes, among which mutations were most commonly found in KMT2D and KMT2C. Somatic mutations in KMT2D, KMT2C, ARID1A and CHD7 were mutually exclusive (p = 0.038). Mutations in ARID1A were associated with distant metastases (p = 0.03). The overall survival of patients in the group with metastases and in the group with tumors with signet ring cells was significantly reduced in the presence of mutations in epigenetic regulation genes (p = 0.036 and p = 0.041, respectively). Separately, somatic mutations in chromatin remodeling genes correlate with low survival rate of patients without distant metastasis (p = 0.045) and in the presence of signet ring cells (p = 0.0014). Our results suggest that mutations in epigenetic regulation genes may be valuable clinical markers and deserve further exploration in independent cohorts.
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