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Lau DK, Collin JP, Mariadason JM. Clinical Developments and Challenges in Treating FGFR2-Driven Gastric Cancer. Biomedicines 2024; 12:1117. [PMID: 38791079 PMCID: PMC11118914 DOI: 10.3390/biomedicines12051117] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Recent advances in the treatment of gastric cancer (GC) with chemotherapy, immunotherapy, anti-angiogenic therapy and targeted therapies have yielded some improvement in survival outcomes; however, metastatic GC remains a lethal malignancy and amongst the leading causes of cancer-related mortality worldwide. Importantly, the ongoing molecular characterisation of GCs continues to uncover potentially actionable molecular targets. Among these, aberrant FGFR2-driven signalling, predominantly arising from FGFR2 amplification, occurs in approximately 3-11% of GCs. However, whilst several inhibitors of FGFR have been clinically tested to-date, there are currently no approved FGFR-directed therapies for GC. In this review, we summarise the significance of FGFR2 as an actionable therapeutic target in GC, examine the recent pre-clinical and clinical data supporting the use of small-molecule inhibitors, antibody-based therapies, as well as novel approaches such as proteolysis-targeting chimeras (PROTACs) for targeting FGFR2 in these tumours, and discuss the ongoing challenges and opportunities associated with their clinical development.
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Affiliation(s)
- David K. Lau
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Oncology, Monash Health, Clayton, VIC 3168, Australia
| | - Jack P. Collin
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - John M. Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
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2
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Kuwata T. Molecular classification and intratumoral heterogeneity of gastric adenocarcinoma. Pathol Int 2024. [PMID: 38651937 DOI: 10.1111/pin.13427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Gastric cancers frequently harbor striking histological complexity and diversity between lesions as well as within single lesions, known as inter- and intratumoral heterogeneity, respectively. The latest World Health Organization Classification of Tumors designated more than 30 histological subtypes for gastric epithelial tumors, assigning 12 subtypes for gastric adenocarcinoma (GAD). Meanwhile, recent advances in genome-wide analyses have provided molecular aspects to the histological classification of GAD, and consequently revealed different molecular traits underlying these histological subtypes. Moreover, accumulating knowledge of comprehensive molecular profiles has led to establishing molecular classifications of GAD, which are often associated with clinical biomarkers for therapeutics and prognosis. However, most of our knowledge of GAD molecular profiles is based on inter-tumoral heterogeneity, and the molecular profiles underlying intratumoral heterogeneity are yet to be determined. In this review, recently established molecular classifications of GAD are introduced in the aspect of pathological diagnosis and are discussed in the context of intratumoral heterogeneity.
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Affiliation(s)
- Takeshi Kuwata
- Department of Genetic Medicine and Services, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
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3
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Wang X, Dong Y, Zhang H, Zhao Y, Miao T, Mohseni G, Du L, Wang C. DNA methylation drives a new path in gastric cancer early detection: Current impact and prospects. Genes Dis 2024; 11:847-860. [PMID: 37692483 PMCID: PMC10491876 DOI: 10.1016/j.gendis.2023.02.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/24/2023] [Indexed: 03/31/2023] Open
Abstract
Gastric cancer (GC) is one of the most common and deadly cancers worldwide. Early detection offers the best chance for curative treatment and reducing its mortality. However, the optimal population-based early screening for GC remains unmet. Aberrant DNA methylation occurs in the early stage of GC, exhibiting cancer-specific genetic and epigenetic changes, and can be detected in the media such as blood, gastric juice, and feces, constituting a valuable biomarker for cancer early detection. Furthermore, DNA methylation is a stable epigenetic alteration, and many innovative methods have been developed to quantify it rapidly and accurately. Nonetheless, large-scale clinical validation of DNA methylation serving as tumor biomarkers is still lacking, precluding their implementation in clinical practice. In conclusion, after a critical analysis of the recent existing literature, we summarized the evolving roles of DNA methylation during GC occurrence, expounded the newly discovered noninvasive DNA methylation biomarkers for early detection of GC, and discussed its challenges and prospects in clinical applications.
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Affiliation(s)
- Xinhui Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
| | - Yaqi Dong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
| | - Hong Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Department of Clinical Laboratory, Fuling Hospital, Chongqing University, Chongqing 402774, China
| | - Yinghui Zhao
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Suzhou Research Institute of Shandong University, Suzhou, Jiangsu 215123, China
| | - Tianshu Miao
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, Shandong 250012, China
| | - Ghazal Mohseni
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong 250033, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong 250033, China
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4
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Blua F, Monge C, Gastaldi S, Clemente N, Pizzimenti S, Lazzarato L, Senetta R, Vittorio S, Gigliotti CL, Boggio E, Dianzani U, Vistoli G, Altomare AA, Aldini G, Dianzani C, Marini E, Bertinaria M. Discovery of a septin-4 covalent binder with antimetastatic activity in a mouse model of melanoma. Bioorg Chem 2024; 144:107164. [PMID: 38306824 DOI: 10.1016/j.bioorg.2024.107164] [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: 12/06/2023] [Revised: 01/23/2024] [Accepted: 01/28/2024] [Indexed: 02/04/2024]
Abstract
Cancer spreading through metastatic processes is one of the major causes of tumour-related mortality. Metastasis is a complex phenomenon which involves multiple pathways ranging from cell metabolic alterations to changes in the biophysical phenotype of cells and tissues. In the search for new effective anti-metastatic agents, we modulated the chemical structure of the lead compound AA6, in order to find the structural determinants of activity, and to identify the cellular target responsible of the downstream anti-metastatic effects observed. New compounds synthesized were able to inhibit in vitro B16-F10 melanoma cell invasiveness, and one selected compound, CM365, showed in vivo anti-metastatic effects in a lung metastasis mouse model of melanoma. Septin-4 was identified as the most likely molecular target responsible for these effects. This study showed that CM365 is a promising molecule for metastasis prevention, remarkably effective alone or co-administered with drugs normally used in cancer therapy, such as paclitaxel.
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Affiliation(s)
- Federica Blua
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Chiara Monge
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Simone Gastaldi
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Nausicaa Clemente
- Settore Centri di Ricerca e Infrastrutture di Ateneo e Laboratori - Polo di NO, University of Piemonte Orientale, Novara, Italy
| | - Stefania Pizzimenti
- Department of Clinical and Biological Science, University of Turin, Torino, Italy
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Rebecca Senetta
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Serena Vittorio
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | | | - Elena Boggio
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Umberto Dianzani
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | | | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Chiara Dianzani
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Elisabetta Marini
- Department of Drug Science and Technology, University of Turin, Turin, Italy.
| | - Massimo Bertinaria
- Department of Drug Science and Technology, University of Turin, Turin, Italy
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5
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Du Y, Lin Y, Gan L, Wang S, Chen S, Li C, Hou S, Hu B, Wang B, Ye Y, Shen Z. Potential crosstalk between SPP1 + TAMs and CD8 + exhausted T cells promotes an immunosuppressive environment in gastric metastatic cancer. J Transl Med 2024; 22:158. [PMID: 38365757 PMCID: PMC10870525 DOI: 10.1186/s12967-023-04688-1] [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: 07/24/2023] [Accepted: 10/31/2023] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Immunotherapy brings new hope to patients with advanced gastric cancer. However, liver metastases can reduce the efficacy of immunotherapy in patients. Tumor-associated macrophages (TAMs) may be the cause of this reduction in efficacy. SPP1 + TAMs are considered to have immunosuppressive properties. We aimed to investigate the involvement of SPP1 + TAMs in the metastasis of gastric cancer. METHODS The single-cell transcriptome was combined with batched BULK datasets for analysis. Animal models were used to verify the analysis results. RESULTS We reveal the interaction of SPP1 + TAMs with CD8 + exhausted T cells in metastatic cancer. Among these interactions, GDF15-TGFBR2 may play a key immunosuppressive role. We constructed an LR score to quantify interactions based on ligands and receptors. The LR score is highly correlated with various immune features and clinical molecular subtypes. The LR score may also guide the prediction of the efficacy of immunotherapy and prognosis. CONCLUSIONS The crosstalk between SPP1 + TAMs and CD8 + exhausted T cells plays a key immunosuppressive role in the gastric metastatic cancer microenvironment.
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Affiliation(s)
- Yan Du
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Lin Gan
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Shuo Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Shuang Chen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Chen Li
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Sen Hou
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Bozhi Hu
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Bo Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
- Laboratory of Surgical Oncology, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.
- Laboratory of Surgical Oncology, Peking University People's Hospital, Beijing, China.
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China.
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.
- Laboratory of Surgical Oncology, Peking University People's Hospital, Beijing, China.
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, China.
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6
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Draškovič T, Hauptman N. Discovery of novel DNA methylation biomarker panels for the diagnosis and differentiation between common adenocarcinomas and their liver metastases. Sci Rep 2024; 14:3095. [PMID: 38326602 PMCID: PMC10850119 DOI: 10.1038/s41598-024-53754-1] [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: 10/25/2023] [Accepted: 02/05/2024] [Indexed: 02/09/2024] Open
Abstract
Differentiation between adenocarcinomas is sometimes challenging. The promising avenue for discovering new biomarkers lies in bioinformatics using DNA methylation analysis. Utilizing a 2853-sample identification dataset and a 782-sample independent verification dataset, we have identified diagnostic DNA methylation biomarkers that are hypermethylated in cancer and differentiate between breast invasive carcinoma, cholangiocarcinoma, colorectal cancer, hepatocellular carcinoma, lung adenocarcinoma, pancreatic adenocarcinoma and stomach adenocarcinoma. The best panels for cancer type exhibit sensitivity of 77.8-95.9%, a specificity of 92.7-97.5% for tumors, a specificity of 91.5-97.7% for tumors and normal tissues and a diagnostic accuracy of 85.3-96.4%. We have shown that the results can be extended from the primary cancers to their liver metastases, as the best panels diagnose and differentiate between pancreatic adenocarcinoma liver metastases and breast invasive carcinoma liver metastases with a sensitivity and specificity of 83.3-100% and a diagnostic accuracy of 86.8-91.9%. Moreover, the panels could detect hypermethylation of selected regions in the cell-free DNA of patients with liver metastases. At the same time, these were unmethylated in the cell-free DNA of healthy donors, confirming their applicability for liquid biopsies.
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Affiliation(s)
- Tina Draškovič
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Hauptman
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia.
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7
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Preston-Alp S, Caruso LB, Su C, Keith K, Soldan SS, Maestri D, Madzo J, Kossenkov A, Napoletani G, Gewurz B, Lieberman PM, Tempera I. Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer. mBio 2023; 14:e0039623. [PMID: 37606370 PMCID: PMC10653948 DOI: 10.1128/mbio.00396-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE Epstein-Barr virus (EBV) latency is controlled by epigenetic silencing by DNA methylation [5-methyl cytosine (5mC)], histone modifications, and chromatin looping. However, how they dictate the transcriptional program in EBV-associated gastric cancers remains incompletely understood. EBV-associated gastric cancer displays a 5mC hypermethylated phenotype. A potential treatment for this cancer subtype is the DNA hypomethylating agent, which induces EBV lytic reactivation and targets hypermethylation of the cellular DNA. In this study, we identified a heterogeneous pool of EBV epialleles within two tumor-derived gastric cancer cell lines that are disrupted with a hypomethylating agent. Stochastic DNA methylation patterning at critical regulatory regions may be an underlying mechanism for spontaneous reactivation. Our results highlight the critical role of epigenetic modulation on EBV latency and life cycle, which is maintained through the interaction between 5mC and the host protein CCCTC-binding factor.
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Affiliation(s)
| | | | - Chenhe Su
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Kelsey Keith
- The Coriell Institute for Medical Research, Camden, New Jersey, USA
| | | | | | - Jozef Madzo
- The Coriell Institute for Medical Research, Camden, New Jersey, USA
| | | | | | - Benjamin Gewurz
- Division of Infectious Diseases, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Italo Tempera
- The Wistar Institute, Philadelphia, Pennsylvania, USA
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8
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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9
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Guo J, Li J, Chang J, Wang L, Xi Y. Value of Methylation Status of RPRM, SDC2, and TCF4 Genes in Plasma for Gastric Adenocarcinoma Screening. Int J Gen Med 2023; 16:673-681. [PMID: 36855658 PMCID: PMC9968426 DOI: 10.2147/ijgm.s395951] [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: 11/17/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
Objective To explore the clinical value of the combined screening of the methylation statuses of the RPRM, SDC2, and TCF4 genes in plasma of gastric cancer patients. Methods Differential expressed genes (DEGs) were selected from the Gene Expression Omnibus database, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using DAVID, and a protein-protein interaction network was constructed. Hub genes were obtained using Cytoscape. Screening results combined with literature reports identified three genes (RPRM, SDC2, and TCF4). Further analysis was done using biopsies collected through gastroscopy at Shanxi Cancer Hospital from January 8, 2020 to February 22, 2021. The patients were divided into two groups: gastric adenocarcinoma group, and control group which are not gastric adenocarcinoma according to pathological or gastroscopic results. The methylation statuses of the three genes in peripheral blood plasma were detected by fluorescence polymerase chain reaction, and the relationships between the positive rates of the three combined genes with pathology and/or gastroscopy results were analyzed. The clinical value of the combined detection of the three genes was evaluated according to these indicators. The diagnostic specificity and sensitivity of this detective method were analyzed. Results A total of 197 DEGs were identified and 12 hub genes were obtained. The enriched functions and pathways of DEGs include regulation of cell proliferation, extracellular space, cytokine activity, and pathways in cancer. The combination of RPRM, SDC2, and TCF4 gene methylation had a specificity of 93.39% and sensitivity of 80.33%. The combined positive rate of RPRM, SDC2, and TCF4 gene methylation in patients with gastric adenocarcinoma was significantly higher compared with those without gastric adenocarcinoma (χ2=151.179, P<0.05). Conclusion Combined detection of RPRM, SDC2, and TCF4 gene methylation in peripheral blood plasma maybe helpful in screening for gastric adenocarcinoma, and maybe a complementary method to gastroscopy and serum tumor markers.
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Affiliation(s)
- Jianghong Guo
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, People’s Republic of China
| | - Jing Li
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, People’s Republic of China
| | - Jiang Chang
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, People’s Republic of China
| | - Li Wang
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, People’s Republic of China
| | - Yanfeng Xi
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, People’s Republic of China,Correspondence: Yanfeng Xi, Email
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10
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Li B, Zhang F, Niu Q, Liu J, Yu Y, Wang P, Zhang S, Zhang H, Wang Z. A molecular classification of gastric cancer associated with distinct clinical outcomes and validated by an XGBoost-based prediction model. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:224-240. [PMID: 36700042 PMCID: PMC9843270 DOI: 10.1016/j.omtn.2022.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Gastric cancer (GC) is a heterogeneous disease and a leading cause of cancer-related deaths. Discovering robust, clinically relevant molecular classifications is critical for guiding personalized therapies for GC. Here, we propose a refined molecular classification scheme for GC using integrated optimal algorithms and multi-omics data. Based on the important features of mRNA, microRNA, and DNA methylation data selected by the multivariate Cox regression model, three subtypes linked to distinct clinical outcomes were identified by combining similarity network fusion and consensus clustering methods. Three subtypes were validated by an extreme gradient boosting machine learning prediction model with 125 differentially expressed genes in multiple independent cohorts. The molecular characteristics of mutation signatures, characteristic gene sets, driver genes, and chemotherapy sensitivity for each subtype were also identified: subtype 1 was associated with favorable prognosis and characterized by high ARID1A and PIK3CA mutations, subtype 2 was associated with a poor prognosis and harbored high recurrent TP53 mutations, and subtype 3 was associated with high CHD1, APOA1 mutations, and a poor prognosis. The proposed three-subtype scheme achieved a better clinical prediction performance (area under the curve value = 0.71) than The Cancer Genome Atlas classification, which may provide a practical subtyping framework to improve the treatment of GC.
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Affiliation(s)
- Bing Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fengbin Zhang
- Department of Gastroenterology and Hepatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Qikai Niu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yanan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Pengqian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Siqi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Huamin Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,Corresponding author: Huamin Zhang, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China,Corresponding author: Zhong Wang, Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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11
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Fennell LJ, Hartel G, McKeone DM, Bond CE, Kane A, Leggett BA, Patch AM, Whitehall VL. Comparative analysis of Illumina Mouse Methylation BeadChip and reduced-representation bisulfite sequencing for routine DNA methylation analysis. CELL REPORTS METHODS 2022; 2:100323. [PMID: 36452869 PMCID: PMC9701610 DOI: 10.1016/j.crmeth.2022.100323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/14/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
Researching the murine epigenome in disease models has been hampered by the lack of appropriate and cost-effective DNA methylation arrays. Here we perform a comprehensive, comparative analysis between the Mouse Methylation BeadChip (MMB) and reduced-representation bisulfite sequencing (RRBS) in two murine models of colorectal carcinogenesis. We evaluate the coverage, variability, and ability to identify differential DNA methylation of RRBS and MMB. We show that MMB is an effective tool for profiling the murine methylome that performs comparably with RRBS, identifying similar differentially methylated pathways. Although choice of technology is experiment dependent and will be predicated on the underlying biology being probed, these analyses provide insights into the relative strengths and weaknesses of each approach.
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Affiliation(s)
- Lochlan J. Fennell
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Science, Monash University, 19 Innovation Walk, Clayton, VIC, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
| | - Gunter Hartel
- Statistics Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Diane M. McKeone
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Catherine E. Bond
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
| | - Alexandra Kane
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
- Conjoint Internal Medical Laboratories, Pathology Queensland, Brisbane, QLD, Australia
| | - Barbara A. Leggett
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
- Department of Gastroenterology and Hepatology, Royal Brisbane and Womens’ Hospital, Brisbane, QLD, Australia
| | - Ann-Marie Patch
- Clinical Genomics Laboratory, Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Vicki L.J. Whitehall
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
- Conjoint Internal Medical Laboratories, Pathology Queensland, Brisbane, QLD, Australia
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12
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Coutzac C, Funk-Debleds P, Cattey-Javouhey A, Desseigne F, Guibert P, Marolleau P, Rochefort P, de la Fouchardière C. Targeting HER2 in metastatic gastroesophageal adenocarcinomas: What is new? Bull Cancer 2022; 110:552-559. [PMID: 36229267 DOI: 10.1016/j.bulcan.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/19/2022] [Accepted: 08/27/2022] [Indexed: 11/07/2022]
Abstract
Gastric and esophageal adenocarcinomas represent a biologically heterogeneous disease. The identification, in early eighties, of human epidermal growth factor receptor 2 (HER2) overexpression, being present in 12 to 20% of the cases, marked a major milestone in the efforts of unraveling the molecular complexity of this disease. This led to the development of anti-HER2-therapies, trastuzumab being the first to demonstrate, in combination with cisplatin and 5FU/capecitabine chemotherapy, an improvement in response rate and survival in the first-line setting of patients with metastatic, HER2-positive gastroesophageal adenocarcinomas. Afterwards, during a decade, several studies have tried new strategies either to block HER2 pathway differently or to combine different anti-HER2, without efficacy. Everything changed with studies demonstrating additive effect between anti-HER2 and immune checkpoint inhibitors and leading to phase III clinical trials combining anti-HER2 and anti-PD-L1/PD1 therapies. Pembrolizumab, a PD-1 inhibitor, was recently granted by FDA an accelerated approval, in patients with HER2-positive gastro-oesophageal adenocarcinomas, in combination with trastuzumab and platinum-based chemotherapy following meaningful improvement in overall response rate over standard treatment. Progression-free and overall-survival results are still awaited to change our first-line standard treatment. Furthermore, new HER2 inhibitors have been developed, blocking HER2-mediated pathway signaling via different mechanisms from pan-HER inhibition to anti-HER2 antibody drug conjugates with promising results in pretreated patients. Trastuzumab-deruxtecan has in particular showed interesting results in pretreated patients. We present here a review of the recent data and perspectives in HER2-positive metastatic gastroesophageal adenocarcinomas.
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13
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Katz-Summercorn AC, Jammula S, Frangou A, Peneva I, O'Donovan M, Tripathi M, Malhotra S, di Pietro M, Abbas S, Devonshire G, Januszewicz W, Blasko A, Nowicki-Osuch K, MacRae S, Northrop A, Redmond AM, Wedge DC, Fitzgerald RC. Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity. Nat Commun 2022; 13:1407. [PMID: 35301290 PMCID: PMC8931005 DOI: 10.1038/s41467-022-28237-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/14/2022] [Indexed: 12/11/2022] Open
Abstract
Barrett's esophagus is a pre-malignant lesion that can progress to esophageal adenocarcinoma. We perform a multi-omic analysis of pre-cancer samples from 146 patients with a range of outcomes, comprising 642 person years of follow-up. Whole genome sequencing reveals complex structural variants and LINE-1 retrotransposons, as well as known copy number changes, occurring even prior to dysplasia. The structural variant burden captures the most variance across the cohort and genomic profiles do not always match consensus clinical pathology dysplasia grades. Increasing structural variant burden is associated with: high levels of chromothripsis and breakage-fusion-bridge events; increased expression of genes related to cell cycle checkpoint, DNA repair and chromosomal instability; and epigenetic silencing of Wnt signalling and cell cycle genes. Timing analysis reveals molecular events triggering genomic instability with more clonal expansion in dysplastic samples. Overall genomic complexity occurs early in the Barrett's natural history and may inform the potential for cancer beyond the clinically discernible phenotype.
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Affiliation(s)
- A C Katz-Summercorn
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - A Frangou
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - I Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - M O'Donovan
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - M Tripathi
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - S Malhotra
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - M di Pietro
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S Abbas
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - G Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - W Januszewicz
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - A Blasko
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - K Nowicki-Osuch
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S MacRae
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - A Northrop
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - A M Redmond
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - D C Wedge
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK
| | - R C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK.
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14
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Yates J, Boeva V. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. Brief Bioinform 2022; 23:6520307. [PMID: 35134107 PMCID: PMC8921629 DOI: 10.1093/bib/bbab610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.
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Affiliation(s)
- Josephine Yates
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland
| | - Valentina Boeva
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland.,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.,Cochin Institute, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris 75014, France
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15
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Abstract
Gastric cancer (GC) is a leading contributor to global cancer incidence and mortality. Pioneering genomic studies, focusing largely on primary GCs, revealed driver alterations in genes such as ERBB2, FGFR2, TP53 and ARID1A as well as multiple molecular subtypes. However, clinical efforts targeting these alterations have produced variable results, hampered by complex co-alteration patterns in molecular profiles and intra-patient genomic heterogeneity. In this Review, we highlight foundational and translational advances in dissecting the genomic cartography of GC, including non-coding variants, epigenomic aberrations and transcriptomic alterations, and describe how these alterations interplay with environmental influences, germline factors and the tumour microenvironment. Mapping of these alterations over the GC life cycle in normal gastric tissues, metaplasia, primary carcinoma and distant metastasis will improve our understanding of biological mechanisms driving GC development and promoting cancer hallmarks. On the translational front, integrative genomic approaches are identifying diverse mechanisms of GC therapy resistance and emerging preclinical targets, enabled by technologies such as single-cell sequencing and liquid biopsies. Validating these insights will require specifically designed GC cohorts, converging multi-modal genomic data with longitudinal data on therapeutic challenges and patient outcomes. Genomic findings from these studies will facilitate 'next-generation' clinical initiatives in GC precision oncology and prevention.
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Affiliation(s)
- Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
| | - Patrick Tan
- Singapore Gastric Cancer Consortium, Singapore, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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16
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ARID1A loss-of-function induces CpG island methylator phenotype. Cancer Lett 2022; 532:215587. [DOI: 10.1016/j.canlet.2022.215587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
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17
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Lyu M, Yi X, Huang Z, Chen Y, Ai Z, Liang Y, Feng Q, Xiang Z. A transcriptomic analysis based on aberrant methylation levels revealed potential novel therapeutic targets for nasopharyngeal carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:47. [PMID: 35282089 PMCID: PMC8848444 DOI: 10.21037/atm-21-6628] [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: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 12/24/2022]
Abstract
Background This study aimed to identify potential novel therapeutic targets for nasopharyngeal carcinoma (NPC) by identifying aberrantly methylated-differentially expressed genes (DEGs) and pathways based on a comprehensive bioinformatics analysis. Methods Eight gene expression data sets and 2 methylation microarray data sets that included NPC and control groups from the Gene Expression Omnibus were identified. Meta-analyses of the DEGs were performed using the online analysis database “NetworkAnalyst”. Aberrantly methylated gene loci were obtained from the GEO2R. Aberrantly methylated DEGs were obtained from Venn diagrams. The enrichment analysis was carried out on the “Metascape” website, and the protein-protein interaction (PPI) network construction, network analysis, and visualization of the analysis results were carried out on the “String” website using “Cytoscape” software. Results In total, 544 hypomethylation high-expression genes and 164 hypermethylation low-expression genes were obtained. The enrichment and PPI network analyses suggested that several pathways and hub genes with abnormal gene expression accompanied by methylation change, including inositol-trisphosphate 3-kinase B (ITPKB), G protein subunit beta 5 (GNB5), FYN proto-oncogene, Src family tyrosine kinase (FYN), LCK proto-oncogene, Src family tyrosine kinase (LCK), nuclear factor of activated T cells 1 (NFATC1), GNAS complex locus (GNAS), protein kinase C beta (PRKCB), zeta chain of T cell receptor associated protein kinase 70 (ZAP70), lysophosphatidic acid receptor 1 (LPAR1), protein kinase C epsilon (PRKCE), tumor protein p53 (TP53), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fibronectin 1 (FN1), cyclin D1 (CCND1), vascular endothelial growth factor A (VEGFA), HRas proto-oncogene, GTPase (HRAS), signal transducer and activator of transcription 3 (STAT3), fibroblast growth factor 2 (FGF2), amyloid beta precursor protein (APP), and matrix metallopeptidase 2 (MMP2), may be related to the occurrence of nasopharyngeal carcinoma . Conclusions The identification of novel and important pathways and hub genes and their roles in the occurrence and development of NPC will guide clinical research and the development of pharmaceutical targets.
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Affiliation(s)
- Mo Lyu
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xinzhu Yi
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhiwei Huang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yirong Chen
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhu Ai
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Yuying Liang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Qili Feng
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhiming Xiang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
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18
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Manuel Lopes de Sousa H, Patrícia Costa Ribeiro J, Basílio Timóteo M. Epstein-Barr Virus-Associated Gastric Cancer: Old Entity with New Relevance. Infect Dis (Lond) 2021. [DOI: 10.5772/intechopen.93649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Gastric cancer (GC) represents a major public health issue worldwide, being the fifth most common cancer and one of the leading causes of death by cancer. In 2014, The Cancer Genome Atlas (TCGA) established that tumors positive for Epstein-Barr virus (EBV) are considered a specific subtype of GC (EBVaGC). Several meta-analyses have shown that EBVaGC represents almost 10% of all gastric cancer worldwide, with small differences in the geographic distribution. This tumor subtype has a high potential of being clinically relevant and studies have shown that it has specific features, a better prognosis, and increased overall survival. In this review, we summarize some of the most frequent aspects of EBVaGC, including the specific features of this GC subtype, data regarding the potential steps of EBVaGC carcinogenesis, and perspectives on treatment opportunities.
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19
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Ren J, Lu P, Zhou X, Liao Y, Liu X, Li J, Wang W, Wang J, Wen L, Fu W, Tang F. Genome-Scale Methylation Analysis of Circulating Cell-Free DNA in Gastric Cancer Patients. Clin Chem 2021; 68:354-364. [PMID: 34791072 DOI: 10.1093/clinchem/hvab204] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Aberrant DNA hypermethylation of CpG islands (CGIs) occurs frequently and is genome-wide in human gastric cancer (GC). A DNA methylation approach in plasma cell-free DNA (cfDNA) is attractive for the noninvasive detection of GC. Here, we performed genome-scale cfDNA methylation analysis in patients with GC. METHODS We used MCTA-Seq, a genome-scale DNA methylation analysis method, on the plasma samples of patients with GC (n = 89) and control participants (n = 82), as well as 28 pairs of GC and adjacent noncancerous tissues. The capacity of the method for detecting GC and discriminating GC from colorectal cancer (CRC) and hepatocellular carcinoma (HCC) was assessed. RESULTS We identified 153 cfDNA methylation biomarkers, including DOCK10, CABIN1, and KCNQ5, for detecting GC in blood. A panel of these biomarkers gave a sensitivity of 44%, 59%, 78%, and 100% for stage I, II, III, and IV tumors, respectively, at a specificity of 92%. CpG island methylation phenotype (CIMP) tumors and NON-CIMP tumors could be distinguished and detected effectively. We also identified several hundreds of cfDNA biomarkers differentially methylated between GC, CRC, and HCC, and showed that MCTA-Seq can discriminate early-stage GC, CRC, and HCC in blood by using a high specificity (approximately 100%) algorithm. CONCLUSIONS Our comprehensive analyses provided valuable data on cfDNA methylation biomarkers of GC and showed the promise of cfDNA methylation for the blood-based noninvasive detection of GC.
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Affiliation(s)
- Jie Ren
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ping Lu
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China
| | - Yuhan Liao
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Xiaomeng Liu
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China
| | - Jingyi Li
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China
| | - Wendong Wang
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China
| | - Jilian Wang
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China
| | - Lu Wen
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Wei Fu
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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20
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Chen Q, Wu Q, Peng Y. ADHFE1 is a correlative factor of patient survival in cancer. Open Life Sci 2021; 16:571-582. [PMID: 34179501 PMCID: PMC8216228 DOI: 10.1515/biol-2021-0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022] Open
Abstract
Alcohol dehydrogenase iron containing 1 (ADHFE1) encodes a hydroxyacid-oxoacid transhydrogenase participating in multiple biological processes. The role of ADHFE1 in cancer has not been fully uncovered. Herein, we performed data analysis to investigate the expression of ADHFE1 and the underlying regulatory mechanisms, its relationship with cancer patients’ survival, and the relevant pathways in cancer. A range of recognized, web-available databases and bioinformatics tools were used in this in silico study. We found that ADHFE1 was frequently downregulated and hypermethylated in various cancer cell lines and tissue samples. High expression of ADHFE1 was positively associated with favorable patient prognosis in breast, colon, and gastric cancers. Pathway analysis revealed its potential role in cancer-related biological processes, including energy metabolism, DNA replication, and cell cycle regulation. AHDFE1 mRNA expression and DNA methylation can potentially be used as diagnostic markers in cancer and might be of great value in predicting the survival of patients with cancer.
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Affiliation(s)
- Qi Chen
- Department of Traditional Chinese Medicine, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Qiyan Wu
- Cancer Center Key Lab, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Yaojun Peng
- Department of Emergency, The First Medical Centre, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
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21
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Padmanabhan N, Kyon HK, Boot A, Lim K, Srivastava S, Chen S, Wu Z, Lee HO, Mukundan VT, Chan C, Chan YK, Xuewen O, Pitt JJ, Isa ZFA, Xing M, Lee MH, Tan ALK, Ting SHW, Luftig MA, Kappei D, Kruger WD, Bian J, Ho YS, Teh M, Rozen SG, Tan P. Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation. Genome Biol 2021; 22:167. [PMID: 34074348 PMCID: PMC8170989 DOI: 10.1186/s13059-021-02375-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative analysis in 50 GC cell lines and 467 primary GCs. Results We identify the cystathionine beta-synthase enzyme (CBS) as a highly recurrent target of epigenetic silencing in CIMP GC. Likewise, we show that CBS epimutations are significantly associated with CIMP in various other cancers, occurring even in premalignant gastroesophageal conditions and longitudinally linked to clinical persistence. Of note, CRISPR deletion of CBS in normal gastric epithelial cells induces widespread DNA methylation changes that overlap with primary GC CIMP patterns. Reflecting its metabolic role as a gatekeeper interlinking the methionine and homocysteine cycles, CBS loss in vitro also causes reductions in the anti-inflammatory gasotransmitter hydrogen sulfide (H2S), with concomitant increase in NF-κB activity. In a murine genetic model of CBS deficiency, preliminary data indicate upregulated immune-mediated transcriptional signatures in the stomach. Conclusions Our results implicate CBS as a bi-faceted modifier of aberrant DNA methylation and inflammation in GC and highlights H2S donors as a potential new therapy for CBS-silenced lesions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02375-2.
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Affiliation(s)
- Nisha Padmanabhan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Huang Kie Kyon
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kevin Lim
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Zhiyuan Wu
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Hyung-Ok Lee
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yarn Kit Chan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ong Xuewen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zul Fazreen Adam Isa
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Manjie Xing
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ming Hui Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Angie Lay Keng Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Shamaine Ho Wei Ting
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Centre for Virology, Duke University School of Medicine, Durham, NC, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Warren D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.,National University of Singapore (Suzhou) Research Institute, Suzhou, 215123, China
| | - Ying Swan Ho
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, 119228, Singapore
| | - Steve George Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Genome Institute of Singapore, Singapore, 138672, Singapore. .,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 169856, Singapore. .,Singapore Gastric Cancer Consortium, Singapore, 119074, Singapore. .,Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
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22
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Luo C, Huang J, Guo Z, Guo J, Zeng X, Li Y, Liu M. Methylated biomarkers for breast cancer identified through public database analysis and plasma target capture sequencing. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:683. [PMID: 33987381 PMCID: PMC8106113 DOI: 10.21037/atm-21-1128] [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] [Indexed: 11/09/2022]
Abstract
Background Aberrant methylation is common during the early stage of cancer development. This study was designed to investigate DNA methylation as biomarker for breast cancer. Methods Public database analysis and methylation-specific whole-gene sequencing were conducted to identify methylated biomarkers that would enable early non-invasive diagnosis of breast cancer. Firstly, the data was obtained from the TCGA Database and the Blueprint Epigenome Database. Secondly, methylation-specific whole-gene sequencing was conducted in 10 female patients with early-stage breast cancer and 10 healthy female volunteers from Nanfang Hospital of Southern Medical University between March 2018 and July 2018. Thirdly, the R language was used for data analysis, and KEGG and DAVID online tool was used for annotations. Results We found that methylation levels at 13 cytosine-phosphate-guanine (CpG) sites (cg04066177, cg04281344, cg05995576, cg06221609, cg08642731, cg11388802, cg12665414, cg14557216, cg19404723, cg19457909, cg24570211, cg25818763, and cg26215982) in the malignant tissue DNA were highly comparable to those of circulating cell-free DNA (cfDNA) of breast cancer patients, but were significantly different from those of normal tissue DNA, cfDNA of healthy women, and leukocyte DNA. In addition, three CpG sites (cg04281344, cg24570211, and cg26215982) were confirmed in clinical research, which showed that the sensitivity and specificity of these CpGs as biomarkers for breast cancer were 69.4–83.7% and 85.7–88.6%, respectively. Conclusions New biomarkers were identified and confirmed for breast cancer by comparing the methylation of tumour tissues, leukocytes, and non-plasma DNA.
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Affiliation(s)
- Can Luo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaheng Huang
- Department of Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhaoze Guo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jingyun Guo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoqi Zeng
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yimin Li
- General Surgery, Yangjiang Hospital, Qiongzhong, China
| | - Minfeng Liu
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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23
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Zhang G, Xue Z, Yan C, Wang J, Luo H. A Novel Biomarker Identification Approach for Gastric Cancer Using Gene Expression and DNA Methylation Dataset. Front Genet 2021; 12:644378. [PMID: 33868380 PMCID: PMC8044773 DOI: 10.3389/fgene.2021.644378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/16/2021] [Indexed: 01/09/2023] Open
Abstract
As one type of complex disease, gastric cancer has high mortality rate, and there are few effective treatments for patients in advanced stage. With the development of biological technology, a large amount of multiple-omics data of gastric cancer are generated, which enables computational method to discover potential biomarkers of gastric cancer. That will be very important to detect gastric cancer at earlier stages and thus assist in providing timely treatment. However, most of biological data have the characteristics of high dimension and low sample size. It is hard to process directly without feature selection. Besides, only using some omic data, such as gene expression data, provides limited evidence to investigate gastric cancer associated biomarkers. In this research, gene expression data and DNA methylation data are integrated to analyze gastric cancer, and a feature selection approach is proposed to identify the possible biomarkers of gastric cancer. After the original data are pre-processed, the mutual information (MI) is applied to select some top genes. Then, fold change (FC) and T-test are adopted to identify differentially expressed genes (DEG). In particular, false discover rate (FDR) is introduced to revise p_value to further screen genes. For chosen genes, a deep neural network (DNN) model is utilized as the classifier to measure the quality of classification. The experimental results show that the approach can achieve superior performance in terms of accuracy and other metrics. Biological analysis for chosen genes further validates the effectiveness of the approach.
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Affiliation(s)
- Ge Zhang
- School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Zijing Xue
- School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Chaokun Yan
- School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Jianlin Wang
- School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Huimin Luo
- School of Computer and Information Engineering, Henan University, Kaifeng, China
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24
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Hong C, Yang S, Wang Q, Zhang S, Wu W, Chen J, Zhong D, Li M, Li L, Li J, Yu H, Chen H, Zeng Q, Zhang C. Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis. Front Genet 2021; 12:563051. [PMID: 33815458 PMCID: PMC8012546 DOI: 10.3389/fgene.2021.563051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Abnormal DNA methylation (DNAm) age has been assumed to be an indicator for canceration and all-cause mortality. However, associations between DNAm age and molecular features of stomach adenocarcinoma (STAD), and its prognosis have not been systematically studied. Method: We calculated the DNAm age of 591 STAD samples and 115 normal stomach samples from The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) database using the Horvath’s clock model. Meanwhile, we utilized survival analysis to evaluate the prognostic value of DNAm age and epigenetic age acceleration shift. In addition, we performed weighted gene co-expression network analysis (WGCNA) to identify DNAm age-associated gene modules and pathways. Finally, the association between DNAm age and molecular features was performed by correlation analysis. Results: DNA methylation age was significantly correlated with chronological age in normal gastric tissues (r = 0.85, p < 0.0001), but it was not associated with chronological age in STAD samples (r = 0.060, p = 0.2369). Compared with tumor adjacent normal tissue, the DNAm age of STAD tissues was significantly decreased. Meanwhile, chronological age in STAD samples was higher than its DNAm age. Both DNAm age and epigenetic acceleration shift were associated with the prognosis of STAD patients. By using correlation analysis, we also found that DNAm age was associated with immunoactivation and stemness in STAD samples. Conclusion: In summary, epigenetic age acceleration of STAD was associated with tumor stemness, immunoactivation, and favorable prognosis.
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Affiliation(s)
- Chunhong Hong
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shaohua Yang
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qiaojin Wang
- Department of Surgical Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Zhang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Wenhui Wu
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jinyao Chen
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Danhui Zhong
- Department of Physiotherapy, The University of Hongkong-Shenzhen Hospital, Shenzhen, China
| | - Mingzhe Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liang Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jianfeng Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hong Yu
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hong Chen
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qianlin Zeng
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Changhua Zhang
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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25
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Giacopelli B, Wang M, Cleary A, Wu YZ, Schultz AR, Schmutz M, Blachly JS, Eisfeld AK, Mundy-Bosse B, Vosberg S, Greif PA, Claus R, Bullinger L, Garzon R, Coombes KR, Bloomfield CD, Druker BJ, Tyner JW, Byrd JC, Oakes CC. DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia. Genome Res 2021; 31:747-761. [PMID: 33707228 PMCID: PMC8092005 DOI: 10.1101/gr.269233.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a molecularly complex disease characterized by heterogeneous tumor genetic profiles and involving numerous pathogenic mechanisms and pathways. Integration of molecular data types across multiple patient cohorts may advance current genetic approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed genome-wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed “epitypes”) using unbiased clustering. Integration of genetic data revealed that most epitypes were associated with a certain recurrent mutation (or combination) in a majority of patients, yet other epitypes were largely independent. Epitypes showed developmental blockage at discrete stages of myeloid differentiation, revealing epitypes that retain arrested hematopoietic stem-cell-like phenotypes. Detailed analyses of DNA methylation patterns identified unique patterns of aberrant hyper- and hypomethylation among epitypes, with variable involvement of transcription factors influencing promoter, enhancer, and repressed regions. Patients in epitypes with stem-cell-like methylation features showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients, and rare epitype switching accompanied loss of the dominant epitype mutations and reversion to stem-cell-like methylation patterns. These results show that DNA methylation-based classification integrates important molecular features of AML to reveal the diverse pathogenic and biological aspects of the disease.
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Affiliation(s)
- Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Min Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ada Cleary
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Yue-Zhong Wu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Anna Reister Schultz
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Maximilian Schmutz
- Hematology and Oncology, Medical Faculty, University of Augsburg, 86159 Augsburg, Germany
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Bethany Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Munich, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rainer Claus
- Department of Medicine II, Stem Cell Transplantation Unit, Klinikum Augsburg, Ludwig-Maximilians University Munich, 86156 Munich, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumorimmunology, Charité-Universitätsmedizin, 13353 Berlin, Germany
| | - Ramiro Garzon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Kevin R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Clara D Bloomfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
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26
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A decade in unravelling the etiology of gastric carcinogenesis in Kashmir, India – A high risk region. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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27
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Chen P, Guo H, Wu X, Li J, Duan X, Ba Q, Wang H. Epigenetic silencing of microRNA-204 by Helicobacter pylori augments the NF-κB signaling pathway in gastric cancer development and progression. Carcinogenesis 2020; 41:430-441. [PMID: 31873718 DOI: 10.1093/carcin/bgz143] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/30/2019] [Indexed: 12/22/2022] Open
Abstract
Helicobacter pylori infection induces gastric cancer (GC) development through a progressive cascade; however, the roles of the microRNAs that are involved in the cascade and the underlying mechanisms are still unclear. Here, we found that microRNA-204 was suppressed in gastric mucosal cells in response to H.pylori infection and downregulated in GC tissues due to aberrant methylation of the promoter of its host gene, TRPM3. Helicobacter pylori induced a progressive downregulation of microRNA-204 from superficial gastritis to intestinal metaplasia, with an accompanying increment of the methylated levels of CpG sites in the TRPM3 promoter. With the GC cellular models of AGS, MGC-803 or BGC-823, we found that microRNA-204 suppressed the tumor necrosis factor (TNF)-α-induced activation of NF-κB signaling pathways and, in animal models, inhibited tumor growth and metastasis. The conditional supernatant of microRNA-204 overexpression GC cells led to reduced tube formation of human umbilical vein endothelial cells. A target gene for microRNA-204 was BIRC2, and in GC cells, BIRC2 knockdown recapitulated the biological phenotype of microRNA-204 overexpression. BIRC2 overexpression promoted the metastasis of GC cells and rescued the inhibition activities of microRNA-204 on cell migration and the NF-κB signaling pathway. Moreover, lower microRNA-204 and higher BIRC2 expression levels were associated with a poorer prognosis of GC patients. These results demonstrate that epigenetic silencing of microRNA-204 induced by H.pylori infection augments the NF-κB signaling pathway in H.pylori-induced gastritis and GC, potentially providing novel intervention targets for these diseases. MicroRNA-204 was epigenetically down-regulated by H. pylori infection in gastric mucosal cells. It led to enhanced BIRC2 expression level and BIRC2/TNF-a/NF-kB signaling pathway activities, which promoted angiogenesis and metastasis of gastric cancer cells.
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Affiliation(s)
- Peizhan Chen
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
| | - He Guo
- Key Laboratory of Food Safety Research, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, P. R. China
| | - Xuming Wu
- Nantong Center for Disease Control and Prevention, Nantong, P.R. China.,Nantong Tumor Hospital, Nantong, P. R. China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
| | - Xiaohua Duan
- Key Laboratory of Food Safety Research, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, P. R. China
| | - Qian Ba
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China.,Key Laboratory of Food Safety Research, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, P. R. China
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28
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Yamamoto H, Watanabe Y, Sato Y, Maehata T, Itoh F. Non-Invasive Early Molecular Detection of Gastric Cancers. Cancers (Basel) 2020; 12:E2880. [PMID: 33036473 PMCID: PMC7600616 DOI: 10.3390/cancers12102880] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC) is a significant source of global cancer death with a high mortality rate, because the majority of patients with GC are diagnosed at a late stage, with limited therapeutic choices and poor outcomes. Therefore, development of minimally invasive or noninvasive biomarkers which are specific to GC is crucially needed. The latest advancements in the understanding of GC molecular landscapes and molecular biological methods have accelerated attempts to diagnose GC at an early stage. Body fluids, including peripheral blood, saliva, gastric juice/wash, urine, and others, can be a source of biomarkers, offering new methods for the early detection of GC. Liquid biopsy-based methods using circulating sources of cancer nucleic acids could also be considered as alternative strategies. Moreover, investigating gastric juices/washes could represent an alternative for the detection of GC via invasive biopsy. This review summarizes recently reported biomarkers based on DNA methylation, microRNA, long noncoding RNA, circular RNA, or extracellular vesicles (exosomes) for the detection of GC. Although the majority of studies have been conducted to detect these alterations in advanced-stage GC and only a few in population studies or early-stage GC, some biomarkers are potentially valuable for the development of novel approaches for an early noninvasive detection of GC.
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Affiliation(s)
- Hiroyuki Yamamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8511, Japan; (Y.W.); (Y.S.); (T.M.); (F.I.)
| | - Yoshiyuki Watanabe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8511, Japan; (Y.W.); (Y.S.); (T.M.); (F.I.)
- Department of Internal Medicine, Kawasaki Rinko General Hospital, Kawasaki 210-0806, Japan
| | - Yoshinori Sato
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8511, Japan; (Y.W.); (Y.S.); (T.M.); (F.I.)
| | - Tadateru Maehata
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8511, Japan; (Y.W.); (Y.S.); (T.M.); (F.I.)
| | - Fumio Itoh
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8511, Japan; (Y.W.); (Y.S.); (T.M.); (F.I.)
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29
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Xia D, Leon AJ, Cabanero M, Pugh TJ, Tsao MS, Rath P, Siu LLY, Yu C, Bedard PL, Shepherd FA, Zadeh G, Chetty R, Aldape K. Minimalist approaches to cancer tissue-of-origin classification by DNA methylation. Mod Pathol 2020; 33:1874-1888. [PMID: 32415265 PMCID: PMC8808378 DOI: 10.1038/s41379-020-0547-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 11/09/2022]
Abstract
Classification of cancers by tissue-of-origin is fundamental to diagnostic pathology. While the combination of clinical data, tissue histology, and immunohistochemistry is usually sufficient, there remains a small but not insignificant proportion of difficult-to-classify cases. These challenging cases provide justification for ancillary molecular testing, including high-throughput DNA methylation array profiling, which promises cell-of-origin information and compatibility with formalin-fixed specimens. While diagnostically powerful, methylation profiling platforms are costly and technically challenging to implement, particularly for less well-resourced laboratories. To address this, we simulated the performance of "minimalist" methylation-based tests for cancer classification using publicly-available and internal institutional profiling data. These analyses showed that small and focused sets of the most informative CpG biomarkers from the arrays are sufficient for accurate diagnoses. As an illustrative example, one classifier, using information from just 53 out of about 450,000 available CpG probes, achieved an accuracy of 94.5% on 2575 fresh primary validation cases across 28 cancer types from The Cancer Genome Atlas Network. By training minimalist classifiers on formalin-fixed primary and metastatic cases, generally high accuracies were also achieved on additional datasets. These results support the potential of minimalist methylation testing, possibly via quantitative PCR and targeted next-generation sequencing platforms, in cancer classification.
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Affiliation(s)
- Daniel Xia
- Division of Hematopathology and Transfusion Medicine, University Health Network, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | | | - Michael Cabanero
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Division of Anatomical Pathology, University Health Network, Toronto, ON, Canada
| | | | - Ming Sound Tsao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Division of Anatomical Pathology, University Health Network, Toronto, ON, Canada
| | - Prisni Rath
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Lillian Lai-Yun Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Celeste Yu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | | | - Gelareh Zadeh
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Runjan Chetty
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Division of Anatomical Pathology, University Health Network, Toronto, ON, Canada
| | - Kenneth Aldape
- Laboratory of Pathology, Center of Cancer Research, National Cancer Institute, Bethesda, MD, USA
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30
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Shi XJ, Wei Y, Ji B. Systems Biology of Gastric Cancer: Perspectives on the Omics-Based Diagnosis and Treatment. Front Mol Biosci 2020; 7:203. [PMID: 33005629 PMCID: PMC7479200 DOI: 10.3389/fmolb.2020.00203] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is the fifth most diagnosed cancer in the world, affecting more than a million people and causing nearly 783,000 deaths each year. The prognosis of advanced gastric cancer remains extremely poor despite the use of surgery and adjuvant therapy. Therefore, understanding the mechanism of gastric cancer development, and the discovery of novel diagnostic biomarkers and therapeutics are major goals in gastric cancer research. Here, we review recent progress in application of omics technologies in gastric cancer research, with special focus on the utilization of systems biology approaches to integrate multi-omics data. In addition, the association between gastrointestinal microbiota and gastric cancer are discussed, which may offer insights in exploring the novel microbiota-targeted therapeutics. Finally, the application of data-driven systems biology and machine learning approaches could provide a predictive understanding of gastric cancer, and pave the way to the development of novel biomarkers and rational design of cancer therapeutics.
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Affiliation(s)
- Xiao-Jing Shi
- Laboratory Animal Center, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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31
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Li JC, Chang X, Chen Y, Li XZ, Zhang XL, Yang SM, Hu CJ, Zhang H. Loss of the Tumor Suppressor HACE1 Contributes to Cancer Progression. Curr Drug Targets 2020; 20:1018-1028. [PMID: 30827236 DOI: 10.2174/1389450120666190227184654] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/20/2019] [Accepted: 02/14/2019] [Indexed: 12/15/2022]
Abstract
HACE1 belongs to the family of HECT domain-containing E3 ligases, which plays an important role in the occurrence, invasion and metastatic process in many human malignancies. HACE1 is a tumor suppressor gene that is reduced in most cancer tissues compared to adjacent normal tissue. The loss or knocking out of HACE1 leads to enhanced tumor growth, invasion, and metastasis; in contrast, the overexpression of HACE1 can inhibit the development of tumors. Hypermethylation reduces the expression of HACE1, thereby promoting tumor development. HACE1 can inhibit the development of inflammation or tumors via the ubiquitination pathway. Therefore, HACE1 may be a potential therapeutic target, providing new strategies for disease prevention and treatment.
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Affiliation(s)
- Jun-Chen Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.,Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Xing Chang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Yang Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Xin-Zhe Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Xiang-Lian Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Guangxi 530021, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Chang-Jiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Hao Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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32
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Pisanic TR, Wang Y, Sun H, Considine M, Li L, Wang TH, Wang TL, Shih IM. Methylomic Landscapes of Ovarian Cancer Precursor Lesions. Clin Cancer Res 2020; 26:6310-6320. [PMID: 32817081 DOI: 10.1158/1078-0432.ccr-20-0270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/11/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE The current paradigm in the development of high-grade serous ovarian carcinoma (HGSC) proposes that the majority of HGSCs arise from precursor serous tubal intraepithelial carcinoma (STIC) lesions of the fallopian tube. Here we survey genome-wide methylation in HGSC precursor lesions to identify genomic regions that exhibit high-specificity differential hypermethylation for potential use as biomarkers for detecting STIC and HGSC at stages when curative intervention likely remains feasible. EXPERIMENTAL DESIGN We first identified quality control criteria for performing reliable methylomic analysis of DNA-limited tubal precursor lesions with the Illumina Infinium MethylationEPIC array. We then used this platform to compare genome-wide methylation among 12 STICs with paired adjacent-normal epithelia, one p53 signature lesion and two samples of concurrent HGSC. The resulting methylomic data were analyzed by unsupervised hierarchical clustering and multidimensional analysis. Regions of high-confidence STIC-specific differential hypermethylation were identified using selective bioinformatic criteria and compared with published MethylationEPIC data from 23 HGSC tumors and 11 healthy fallopian tube mucosae. RESULTS Unsupervised analysis showed that STICs largely clustered with HGSCs, but were clearly distinct from adjacent-normal fallopian tube epithelia. Forty-two genomic regions exhibited high-confidence STIC-specific differential hypermethylation, of which 17 (40.5%) directly overlapped with HGSC-specific differentially methylated regions. Methylation at these shared loci was able to completely distinguish STIC and HGSC samples from normal and adjacent-normal specimens. CONCLUSIONS Our results suggest that most STICs are epigenetically similar to HGSCs and share regions of differential hypermethylation that warrant further evaluation for potential use as biomarkers for early detection of ovarian HGSC.See related commentary by Ishak and De Carvalho, p. 6083.
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Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
| | - Yeh Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hanru Sun
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Michael Considine
- Department of Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lihong Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Canale M, Casadei-Gardini A, Ulivi P, Arechederra M, Berasain C, Lollini PL, Fernández-Barrena MG, Avila MA. Epigenetic Mechanisms in Gastric Cancer: Potential New Therapeutic Opportunities. Int J Mol Sci 2020; 21:E5500. [PMID: 32752096 PMCID: PMC7432799 DOI: 10.3390/ijms21155500] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) is one of the deadliest malignancies worldwide. Complex disease heterogeneity, late diagnosis, and suboptimal therapies result in the poor prognosis of patients. Besides genetic alterations and environmental factors, it has been demonstrated that alterations of the epigenetic machinery guide cancer onset and progression, representing a hallmark of gastric malignancies. Moreover, epigenetic mechanisms undergo an intricate crosstalk, and distinct epigenomic profiles can be shaped under different microenvironmental contexts. In this scenario, targeting epigenetic mechanisms could be an interesting therapeutic strategy to overcome gastric cancer heterogeneity, and the efforts conducted to date are delivering promising results. In this review, we summarize the key epigenetic events involved in gastric cancer development. We conclude with a discussion of new promising epigenetic strategies for gastric cancer treatment.
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Affiliation(s)
- Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (M.C.); (P.U.)
| | - Andrea Casadei-Gardini
- Department of Oncology and Hematology, Division of Oncology, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (M.C.); (P.U.)
| | - Maria Arechederra
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (C.B.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Carmen Berasain
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (C.B.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Pier-Luigi Lollini
- Laboratory of Immunology and Biology of Metastasis, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy;
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (C.B.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Matías A. Avila
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (C.B.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
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Li Y, Sun R, Zhang Y, Yuan Y, Miao Y. A methylation-based mRNA signature predicts survival in patients with gastric cancer. Cancer Cell Int 2020; 20:284. [PMID: 32647495 PMCID: PMC7336496 DOI: 10.1186/s12935-020-01374-w] [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: 04/01/2020] [Accepted: 06/22/2020] [Indexed: 11/22/2022] Open
Abstract
Background Evidence suggests that altered DNA methylation plays a causative role in the occurrence, progression and prognosis of gastric cancer (GC). Thus, methylated-differentially expressed genes (MDEGs) could potentially serve as biomarkers and therapeutic targets in GC. Methods Four genomics profiling datasets were used to identify MDEGs. Gene Ontology enrichment and Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis were used to explore the biological roles of MDEGs in GC. Univariate Cox and LASSO analysis were used to identify survival-related MDEGs and to construct a MDEGs-based signature. The prognostic performance was evaluated in two independent cohorts. Results We identified a total of 255 MDEGs, including 192 hypermethylation-low expression and 63 Hypomethylation-high expression genes. The univariate Cox regression analysis showed that 83 MDEGs were associated with overall survival. Further we constructed an eight-MDEGs signature that was independent predictive of prognosis in the training cohort. By applying the eight-MDEGs signature, patients in the training cohort could be categorized into high-risk or low-risk subgroup with significantly different overall survival (HR = 2.62, 95% CI 1.71–4.02, P < 0.0001). The prognostic value of the eight-MDEGs signature was confirmed in another independent GEO cohort (HR = 1.35, 95% CI 1.03–1.78, P = 0.0302) and TCGA-GC cohort (HR = 1.85, 95% CI 1.16–2.94, P = 0.0084). Multivariate cox regression analysis proved the eight-MDEGs signature was an independent prognostic factor for GC. Conclusion We have thus established an innovative eight-MDEGs signature that is predictive of overall survival and could be a potentially useful guide for personalized treatment of GC patients.
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Affiliation(s)
- Yang Li
- Department of Central Laboratory, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, 221009 China
| | - Rongrong Sun
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, 221009 China
| | - Youwei Zhang
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, 221009 China
| | - Yuan Yuan
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, 221009 China
| | - Yufeng Miao
- Department of Medical Oncology, The First Peoples' Hospital of Wenling City, Wenling, 317500 China
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LEPR hypomethylation is significantly associated with gastric cancer in males. Exp Mol Pathol 2020; 116:104493. [PMID: 32659237 DOI: 10.1016/j.yexmp.2020.104493] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/28/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Previous study has shown LEPR is a candidate gene of prediction and treatment of gastric cancer (GC). The purpose of this study was to test whether LEPR methylation could predict the risk of GC. MATERIALS AND METHODS Tumor tissues and 5-cm adjacent non-tumor tissues from 117 newly diagnosed and untreated GC patients were collected for the current methylation study. LEPR methylation levels were determined by quantitative methylation specific PCR (qMSP), and the methylation level of LEPR was described by the percentage of methylated reference (PMR). RESULTS Our results showed that LEPR methylation levels were significantly lower in tumor tissues than those in adjacent non-tumor tissues (median PMR: 36.64% vs. 50.29%, P = 1E-4). In addition, LEPR methylation levels were found to be significantly associated with platelet (r = -0.198, P = .037). Further subgroup analysis showed that the association of LEPR promoter hypomethylation with GC was specific to males (males: P = 7E-5; females: P = .500). Notably, significant hypomethylation of LEPR promoter was found only in GC patients without recurrence (P = .002) but not in GC patients with recurrence (P = .146). The AUC of LEPR hypomethylation for identification of GC risk was 0.649 with a sensitivity of 67.5% and a specificity of 63.2%. In addition, the AUC of LEPR hypomethylation in males was 0.685 with a sensitivity of 68.4% and a specificity of 69.6%. CONCLUSION LEPR hypomethylation can be used to predict the risk of GC in males. And it might also have the potential to predict the recurrence in GC patients.
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Abstract
Nasopharyngeal carcinoma (NPC) is the most common malignant tumor with a remarkable racial and geographical distribution including people in southern China, South East Asia, and the Middle East/North Africa. DNA methylation is an important manifestation of epigenetic modification, has been studied over several decades, and by regulating and controlling the expression of cancer-related genesits, abnormal DNA methylation can influence in a variety of human malignancy tumors.Until now, there is no analysis focus on differentially methylated, differential expressed genes (MDEGs) study, so we make a joint analysis for both gene methylation profiling microarray and gene expression profiling microarray in NPC. Two gene expression datasets (GSE64634 and GSE12452) and gene methylation profiling data set (GSE62336) were downloaded from GEO and analyzed using the online tool GEO2R to identify MDEGs. Gene ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially methylated genes were performed. The STRING database was used to evaluate the interactions of MDEGs and to construct a protein-protein interaction (PPI) network using Cytoscape software. Hub genes were validated with the cBioPortal database.The overlap among the 3 datasets contained 135 hypermethylation genes and 541 hypomethylation genes between NPC and non-NPC samples. A total of 4 genes (TROAP, PCOLCE2, HOXA4, and C1QB) in Hyper-LGs and 14 genes (DYNC1H1, LNX1, RAB37, ALDH3A1, SLC24A4, CP, CEP250, ANK2, DNAI2, MUC13, ACACB, GABRP, STX7, and TTC9) in Hypo-HGs were identified as hub genes.The study of DNA methylation and gene expression provides us a strong support as well as new comprehensive information of MDEGs to the revelation of nasopharyngeal carcinoma's complex pathogenesis. However, further studies are needed to elucidate the biological function of these genes in NPC in the future.
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Affiliation(s)
- Zeng-hong Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hai-Ying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA
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Zhai S, Lin S, Lin Z, Xu J, Ji T, Chen K, Wu K, Liu H, Ying H, Fei W, Wang J, Fu G, Wang Y, Hu X, Cai X. eIF4EBP3 was downregulated by methylation and acted as a tumor suppressor by targeting eIF4E/β-catenin in gastric cancer. Gastric Cancer 2020; 23:483-496. [PMID: 31853750 DOI: 10.1007/s10120-019-01030-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Epigenetic aberrations of tumor suppressor genes (TSGs), particularly DNA methylation, are frequently involved in the pathogenesis of gastric cancer (GC). Through a methylome study, we identified eIF4EBP3 as a methylated gene in GC. However, the role of eIF4EBP3 in GC progression has not been explored. METHODS The expression and promoter region methylation of eIF4EBP3 in GC and healthy tissues were analyzed in public datasets. eIF4EBP3 expression in GC was detected by semi-quantitative RT-PCR, western blot and immunohistochemistry. We also studied epigenetic alterations and functions in GC. The effects of eIF4EBP3 on cell proliferation, migration and invasion were conducted by functional experiments in vitro and in vivo. Label-free proteomic analysis was applied to identify targets of eIF4EBP3. RESULTS The expression level of eIF4EBP3 was downregulated in gastric cancer due to promoter region methylation, and was associated with poor survival and tumor progression. Ectopic expression of eIF4EBP3 significantly inhibited tumor cell growth, migration and invasion both in vitro and in vivo. Label-free proteomic analysis indicated eIF4EBP3 downregulated the protein level of β-catenin, which was confirmed by western blot. Overexpression of β-catenin reversed the inhibitory effects of eIF4EBP3 on cell growth and migration, indicating that eIF4EBP3 acts on GC cells by targeting the eIF4E/β-catenin axis. CONCLUSION These results suggest that eIF4EBP3 is a novel TSG methylated in gastric cancer that may play important roles in GC development and liver metastasis and indicate eIF4EBP3 as a potential metastasis and survival biomarker for GC.
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Affiliation(s)
- Shuting Zhai
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Shuang Lin
- Department of Lung Transplantation, Department of Thoracic Surgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Zhongjie Lin
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Junjie Xu
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Tong Ji
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Ke Chen
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Ke Wu
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Hui Liu
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Hanning Ying
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Weiqiang Fei
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Jin Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Guoxiang Fu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Yifan Wang
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China.
| | - Xiaotong Hu
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, Zhejiang, China.
| | - Xiujun Cai
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310016, Zhejiang, China.
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Song P, Wu L, Guan W. Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer. Front Genet 2020; 11:91. [PMID: 32174965 PMCID: PMC7056837 DOI: 10.3389/fgene.2020.00091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Abnormal DNA methylation, an epigenetic modification, has increasingly been linked to the pathogenesis of many human cancers. However, there has been little focus on the DNA methylation patterns of genes encoding long noncoding RNAs (lncRNAs) in gastric cancer (GC). This study comprehensively determined DNA methylation and lncRNA expression profiles in GC through genome-wide analysis. Differentially methylated loci and lncRNAs were identified by integrating multi-omics data. In total, 548 differentially methylated CpG sites in lncRNA promoters and 2,399 differentially expressed lncRNAs were screened that were capable of distinguishing GC from normal tissues. Among them, 22 differentially methylation sites in 17 lncRNAs were inversely related to expression levels. Further analysis of DNA methylation status and gene expression level in GC revealed that three CpG sites (cg01550148, cg22497867, and cg20001829) and two lncRNAs (RP11-366F6.2 and RP5-881L22.5) were significantly associated with GC patient overall survival. Molecular function analysis showed that these abnormally methylated lncRNAs were mainly involved in transcriptional activator activity. Our study identified several lncRNAs regulated by aberrant DNA methylation that have clinical utility as novel prognostic biomarkers in GC. These findings help improve the understanding of methylated patterns of lncRNAs and further our knowledge of the role of epigenetics in cancer development.
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Affiliation(s)
- Peng Song
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Lei Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenxian Guan
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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Liu D, Zhou B, Liu R. A transcriptional co-expression network-based approach to identify prognostic biomarkers in gastric carcinoma. PeerJ 2020; 8:e8504. [PMID: 32095347 PMCID: PMC7025707 DOI: 10.7717/peerj.8504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
Abstract
Background Gastric carcinoma is a very diverse disease. The progression of gastric carcinoma is influenced by complicated gene networks. This study aims to investigate the actual and potential prognostic biomarkers related to survival in gastric carcinoma patients to further our understanding of tumor biology. Methods A weighted gene co-expression network analysis was performed with a transcriptome dataset to identify networks and hub genes relevant to gastric carcinoma prognosis. Data was obtained from 300 primary gastric carcinomas (GSE62254). A validation dataset (GSE34942 and GSE15459) and TCGA dataset confirmed the results. Gene ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene set enrichment analysis (GSEA) were performed to identify the clusters responsible for the biological processes and pathways of this disease. Results A brown transcriptional module enriched in the organizational process of the extracellular matrix was significantly correlated with overall survival (HR = 1.586, p = 0.005, 95% CI [1.149–2.189]) and disease-free survival (HR = 1.544, p = 0.008, 95% CI [1.119–2.131]). These observations were confirmed in the validation dataset (HR = 1.664, p = 0.006, 95% CI [1.155–2.398] in overall survival). Ten hub genes were identified and confirmed in the validation dataset from this brown module; five key biomarkers (COL8A1, FRMD6, TIMP2, CNRIP1 and GPR124 (ADGRA2)) were identified for further research in microsatellite instability (MSI) and epithelial-tomesenchymal transition (MSS/EMT) gastric carcinoma molecular subtypes. A high expression of these genes indicated a poor prognosis. Conclusion A transcriptional co-expression network-based approach was used to identify prognostic biomarkers in gastric carcinoma. This method may have potential for use in personalized therapies, however, large-scale randomized controlled clinical trials and replication experiments are needed before these key biomarkers can be applied clinically.
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Affiliation(s)
- Danqi Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, People's Republic of China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Boting Zhou
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, People's Republic of China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Rangru Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, People's Republic of China.,Key Laboratory of Tropical Diseases and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine, Hainan Medical College, Haikou, People's Republic of China
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Ho SWT, Tan P. Dissection of gastric cancer heterogeneity for precision oncology. Cancer Sci 2019; 110:3405-3414. [PMID: 31495054 PMCID: PMC6825006 DOI: 10.1111/cas.14191] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) remains the fifth most prevalent cancer worldwide and the third leading cause of global cancer mortality. Comprehensive ‐omic studies have unveiled a heterogeneous GC landscape, with considerable molecular diversity both between and within tumors. Given the complex nature of GC, a long‐sought goal includes effective identification of distinct patient subsets with prognostic and/or predictive outcomes to enable tailoring of specific treatments (“precision oncology”). In this review, we highlight various approaches to molecular classification in GC, covering recent genomic, transcriptomic, proteomic and epigenomic features. We pay special attention to the translational significance of classifier systems and examine potential confounding factors which deserve further investigation. In particular, we discuss recent advancements in our knowledge of intra‐subtype, intra‐patient and intra‐tumor heterogeneity, and the pivotal role of the tumor stromal microenvironment.
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Affiliation(s)
- Shamaine Wei Ting Ho
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Cellular and Molecular Research, National Cancer Centre, Singapore.,Singapore Gastric Cancer Consortium, Singapore
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Identification of DNA methylation-regulated differentially-expressed genes and related pathways using Illumina 450K BeadChip and bioinformatic analysis in gastric cancer. Pathol Res Pract 2019; 215:152570. [PMID: 31378454 DOI: 10.1016/j.prp.2019.152570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/16/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
In the current research, we aimed to identify and analyze methylation-regulated differentially-expressed genes (MeDEGs) and related pathways using bioinformatic methods. We downloaded RNA-seq, Illumina Human Methylation 450 K BeadChip and clinical information of gastric cancer (GC) from The Cancer Genome Atlas (TCGA) project. Differentially-expressed genes (DEGs) were identified using the edgeR package. Then, we performed Spearman's correlation analysis between DEG expression levels and methylation levels. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in the DAVID database. We then conducted Kaplan-Meier survival analysis to explore the relationship between methylation, expression and prognosis. The protein-protein interaction networks were further analyzed using the STRING database. A total of 204 down-regulated DEGs and 164 up-regulated DEGs were identified as MeDEGs. GO and KEGG pathway analyses showed that MeDEGs were enriched in multiple cancer-related terms. Kaplan-Meier survival analysis showed that eight up-regulated MeDEGs (CAMKV, COMP, FGF3, FGF19, FOXL2, IGF2BP1, IGFBP1 and NPPB) and five down-regulated MeDEGs (ALDH3B2, CALML3, FLRT1, G6PC and HRASLS2) were associated with prognosis of GC patients. In addition, PPI networks and KEGG pathway analyses further confirmed the critical role of prognosis-related MeDEGs. In conclusion, methylation plays a critical role in GC progression. Multiple MeDEGs are related to prognosis, suggesting that they may be potential targets in tumor treatment.
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Lingohr P, Dohmen J, Semaan A, Branchi V, Dietrich J, Bootz F, Kalff JC, Matthaei H, Dietrich D. Clinicopathological, immune and molecular correlates of PD-L2 methylation in gastric adenocarcinomas. Epigenomics 2019; 11:639-653. [DOI: 10.2217/epi-2018-0149] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: We investigated the significance of PD-L2 DNA methylation in gastric adenocarcinomas. Methods: We analyzed the methylation at different CpG sites within the PD-L2-encoding gene PDCD1LG2 with regard to correlations and associations with gene expression, clinicopathological parameters, molecular features and immune cell infiltrates in two publicly available cohorts (The Cancer Genome Atlas and Singapore cohorts) of a total of 594 gastric adenocarcinoma patients. Results: PD-L2 methylation is significantly associated with transcriptional activity, survival, Epstein–Barr virus infection, PD-L2 gene amplification, CD8+ T-cell infiltration, microsatellite instability and high mutational load (tumor mutational burden, hypermutation). Conclusion: PD-L2 methylation is associated with known predictive biomarkers of response to anti-PD-1 immunotherapies.
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Affiliation(s)
- Philipp Lingohr
- Department of Surgery, University Hospital Bonn, Bonn, Germany
| | - Jonas Dohmen
- Department of Surgery, University Hospital Bonn, Bonn, Germany
| | | | | | - Jörn Dietrich
- Department of Otolaryngology, Head & Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Friedrich Bootz
- Department of Otolaryngology, Head & Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Jörg C Kalff
- Department of Surgery, University Hospital Bonn, Bonn, Germany
| | - Hanno Matthaei
- Department of Surgery, University Hospital Bonn, Bonn, Germany
| | - Dimo Dietrich
- Department of Otolaryngology, Head & Neck Surgery, University Hospital Bonn, Bonn, Germany
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43
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Sammarco G, Varricchi G, Ferraro V, Ammendola M, De Fazio M, Altomare DF, Luposella M, Maltese L, Currò G, Marone G, Ranieri G, Memeo R. Mast Cells, Angiogenesis and Lymphangiogenesis in Human Gastric Cancer. Int J Mol Sci 2019; 20:E2106. [PMID: 31035644 PMCID: PMC6540185 DOI: 10.3390/ijms20092106] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/15/2019] [Accepted: 04/19/2019] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer is diagnosed in nearly one million new patients each year and it remains the second leading cause of cancer-related deaths worldwide. Although gastric cancer represents a heterogeneous group of diseases, chronic inflammation has been shown to play a role in tumorigenesis. Cancer development is a multistep process characterized by genetic and epigenetic alterations during tumour initiation and progression. The stromal microenvironment is important in maintaining normal tissue homeostasis or promoting tumour development. A plethora of immune cells (i.e., lymphocytes, macrophages, mast cells, monocytes, myeloid-derived suppressor cells, Treg cells, dendritic cells, neutrophils, eosinophils, natural killer (NK) and natural killer T (NKT) cells) are components of gastric cancer microenvironment. Mast cell density is increased in gastric cancer and there is a correlation with angiogenesis, the number of metastatic lymph nodes and the survival of these patients. Mast cells exert a protumorigenic role in gastric cancer through the release of angiogenic (VEGF-A, CXCL8, MMP-9) and lymphangiogenic factors (VEGF-C and VEGF-F). Gastric mast cells express the programmed death ligands (PD-L1 and PD-L2) which are relevant as immune checkpoints in cancer. Several clinical undergoing trials targeting immune checkpoints could be an innovative therapeutic strategy in gastric cancer. Elucidation of the role of subsets of mast cells in different human gastric cancers will demand studies of increasing complexity beyond those assessing merely mast cell density and microlocalization.
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Affiliation(s)
- Giuseppe Sammarco
- Department of Health Science, General Surgery, Magna Graecia University, Medicine School of Germaneto, 88100 Catanzaro, Italy.
| | - Gilda Varricchi
- Department of Translational Medical Sciences (DISMET) and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131 Naples, Italy.
- WAO Center of Excellence, 80131 Naples, Italy.
| | - Valentina Ferraro
- Department of Biomedical Sciences and Human Oncology, Unit of Endocrine, Digestive and Emergency Surgery, Aldo Moro University, 74124 Bari, Italy.
| | - Michele Ammendola
- Department of Health Science, General Surgery, Magna Graecia University, Medicine School of Germaneto, 88100 Catanzaro, Italy.
| | - Michele De Fazio
- Department of Emergency and Organ Transplantation, Aldo Moro University, 74124 Bari, Italy.
| | | | - Maria Luposella
- Cardiovascular Disease Unit, San Giovanni di Dio Hospital, 88900 Crotone, Italy.
| | - Lorenza Maltese
- Pathology Unit, Pugliese-Ciaccio Hospital, 88100 Catanzaro, Italy.
| | - Giuseppe Currò
- Department of Health Science, General Surgery, Magna Graecia University, Medicine School of Germaneto, 88100 Catanzaro, Italy.
- Department of Human Pathology of Adult and Evolutive Age G. Barresi, University of Messina, 98122 Messina, Italy.
| | - Gianni Marone
- Department of Translational Medical Sciences (DISMET) and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131 Naples, Italy.
- WAO Center of Excellence, 80131 Naples, Italy.
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), 80131 Naples, Italy.
| | - Girolamo Ranieri
- Interventional Oncology Unit with Integrated Section of Translational Medical Oncology, National Cancer Research Centre, Istituto Tumori Giovanni Paolo II, 74124 Bari, Italy.
| | - Riccardo Memeo
- Department of Emergency and Organ Transplantation, Aldo Moro University, 74124 Bari, Italy.
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44
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Chen S, Pu W, Guo S, Jin L, He D, Wang J. Genome-Wide DNA Methylation Profiles Reveal Common Epigenetic Patterns of Interferon-Related Genes in Multiple Autoimmune Diseases. Front Genet 2019; 10:223. [PMID: 31024609 PMCID: PMC6459983 DOI: 10.3389/fgene.2019.00223] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/28/2019] [Indexed: 11/13/2022] Open
Abstract
Graves’ disease (GD), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are complex autoimmune diseases sharing common clinical, genetic and pathogenetic features. However, the commonalities of the DNA methylation profiles for these diseases are still unknown. We conducted an integrative analysis of the multiple-autoimmune disease methylation dataset including GD, RA, SLE, and SSc samples, to identify the common methylation patterns of autoimmune diseases. We identified 15,289 differentially methylated sites between multiple-autoimmune disease patients and controls in CD4+ T cells. We found that the most significant differentially methylated sites had a remarkable enrichment in type I interferon (IFN) pathway genes. Similarly, we identified 9,295 differentially methylated sites between GD/SSc patients and controls in CD8+ T cells. The overall IFN-related gene panel annotated by gene ontology (GO) showed an excellent diagnostic capacity in CD4+ T cells (Sensitivity = 0.82, specificity = 0.82 and AUC = 0.90), while IFI44L, another IFN-related gene not annotated by GO, showed high prediction ability in both CD4+ (AUC = 0.86) and CD8+ (AUC = 0.75) T cells. In conclusion, our study demonstrated that hypomethylation of IFN-related genes is a common feature of GD/RA/SLE/SSc patients in CD4+ T cells, and the DNA methylation profile of IFN-related genes could be promising biomarkers for the diagnosis of GD, RA, SLE, and SSc.
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Affiliation(s)
- Sidi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Weilin Pu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Shicheng Guo
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Traditional Chinese Medicine Research Institute, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China.,Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
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45
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LINC00162 confers sensitivity to 5-Aza-2'-deoxycytidine via modulation of an RNA splicing protein, HNRNPH1. Oncogene 2019; 38:5281-5293. [PMID: 30914798 DOI: 10.1038/s41388-019-0792-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/13/2022]
Abstract
DNA demethylation therapy is now expanding from hematological tumors to solid tumors. To exploit its maximum efficacy, long-term treatment is needed, and stratification of sensitive patients is critically important. Here, we identified a long non-coding RNA, LINC00162, as highly and frequently expressed in gastric cancer cell lines sensitive to 5-aza-2'-deoxycytidine (5-aza-dC). Knockdown of LINC00162 decreased the sensitivity while its overexpression increased the sensitivity. In vivo experiments also showed that LINC00162 overexpression increased the sensitivity. LINC00162 enhanced cell cycle arrest and apoptosis induced by 5-aza-dC, but did not affect its DNA demethylation effect. Mechanistically, LINC00162 interacted with an RNA splicing protein, HNRNPH1, and decreased splicing of an anti-apoptotic splicing variant, BCL-XL. LINC00162 may have translational value to predict patients who will respond to 5-aza-dC.
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46
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Dai D, Zhou B, Xu W, Jin H, Wang X. CHFR Promoter Hypermethylation Is Associated with Gastric Cancer and Plays a Protective Role in Gastric Cancer Process. J Cancer 2019; 10:949-956. [PMID: 30854101 PMCID: PMC6400794 DOI: 10.7150/jca.27224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Background: Chromosomally unstable tumors account for 50% of gastric cancer. CHFR plays a role in controlling chromosomal instability and its inactivation will eventually lead to tumorigenesis. In addition to genetic deletion, DNA methylation could silence the expression of many cancer-related genes including CHFR. Its methylation was found to be associated with the initiation and progression of gastric cancer. Methods: We performed a meta-analysis involving methylation analyses of CHFR promoter in gastric cancer. Nineteen studies with 1,249 tumor tissues and 745 normal tissues had been included in current study. Results: We found that CHFR methylation was significantly higher in gastric cancer (studies numbers = 15, cases/controls = 862/745, odds ratio (OR) = 7.46, 95% confidence index (95% CI) = 4.99-11.14). Methylation array data was also obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas network (TCGA). There were 7 out of 13 CHFR methylation probes target to the same CpG island region (hg19, 131973620-131975130) showed the CHFR methylation was higher in gastric cancers than normal controls. Eight probes showed CHFR promoter hypermethylation was associated with longer overall survival of gastric cancer patients (Hazard Ratio < 1). Conclusions: The CHFR promoter hypermethylation was associated with gastric cancer and played a protective role in gastric cancer process. Its methylation could be a potential biomarker for the diagnosis and prognosis of gastric cancer.
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Affiliation(s)
- Dongjun Dai
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Bingluo Zhou
- Laboratory of Cancer Biology, Key Lab of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Wenxia Xu
- Laboratory of Cancer Biology, Key Lab of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Lab of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
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47
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Fluctuations of epigenetic regulations in human gastric Adenocarcinoma: How does it affect? Biomed Pharmacother 2019; 109:144-156. [DOI: 10.1016/j.biopha.2018.10.094] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
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48
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Ge Y, Wu Q, Ma G, Shao W, Liu H, Zhang Q, Xin J, Xue Y, Du M, Zhao Q, Wang M, Chu H, Zhang Z. Hypermethylation of EIF4E promoter is associated with early onset of gastric cancer. Carcinogenesis 2018; 39:66-71. [PMID: 29342273 DOI: 10.1093/carcin/bgx110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/29/2017] [Indexed: 12/14/2022] Open
Abstract
Although gastric cancer (GC) in young adults (≤ 45 years) accounts for fewer than 10% of newly diagnosed cases, the young patients are more likely to have advanced disease at presentation compared with elderly patients. Previous studies have identified that the DNA methylation of genomes are different during aging. Our study aimed to explore the association between DNA methylation and the onset of GC. We applied Illumina HumanMethylation450 BeadChip to examine methylation expression profiles and compared methylation expression patterns in five early onset GC patients and seven elderly patients. Additionally, we evaluated the associations of methylation expression with different clinicopathological characteristics of GC. Our results showed that the pattern of genome-wide methylation expression was significantly different between early onset and elderly GC. The top 10 hypomethylation and hypermethylation CpG sites were selected for further analyses in The Cancer Genome Atlas (TCGA) database. We found that the hypermethylation of cg11037477, located at the promoter of EIF4E, was significantly associated with age at diagnosis and the expression of EIF4E. Besides, GC patients with high level of cg11037477 were more likely to have advance disease with T3/T4 invasion and III/IV stage. The cg11037477 hypermethylation and EIF4E down-expression were significantly related to poor survival of GC patients. Our study provides new insights into the molecular mechanism of early onset patients with GC and suggests that methylation of cg11037477 and expression of EIF4E may act as prognostic markers in GC.
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Affiliation(s)
- Yuqiu Ge
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qin Wu
- Department of Medical Technology, Yancheng Insititute of Health Sciences, Yancheng, China
| | - Gaoxiang Ma
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Shao
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hanting Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiang Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yao Xue
- Department of Hematology and oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qinghong Zhao
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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49
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Baek DW, Kang BW, Kim JG. The Predictive Value of Epstein-Barr Virus-Positivity in Patients Undergoing Gastrectomy Followed by Adjuvant Chemotherapy. Chonnam Med J 2018; 54:173-177. [PMID: 30288373 PMCID: PMC6165919 DOI: 10.4068/cmj.2018.54.3.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
The present study evaluated the survival impact of standard adjuvant chemotherapy and prognostic differences between Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC) and EBV-negative gastric cancer (EBVnGC). A total of 276 patients were enrolled according to the following criteria: 1) pathologically diagnosed with primary gastric adenocarcinoma, 2) test results from EBV-encoded RNA in situ hybridization, 3) stage II/III according to the 7th edition of UICC/AJCC staging system for gastric cancer, and 4) postoperative adjuvant chemotherapy. Fifty-nine (21.4%) and 217 (78.6%) patients exhibited EBVaGC and EBVnGC, respectively, while 129 (46.7%) patients were classified as stage II and 147 (53.3%) as stage III. As for adjuvant chemotherapy, 87 (31.5%) patients received capecitabine and oxaliplatin, while 189 (68.5%) received S-1 monotherapy. With a median follow-up duration of 21.3 (6.4-89.0) months, the estimated 3-year disease-free survival (DFS) and overall survival (OS) rates were 74.8% and 83.0%, respectively. In univariate analysis and multivariate analysis using a Cox proportional hazard model including age, gender, stage, Lauren classification, and the type of chemotherapy, EBV-positivity was not significantly associated with DFS (p-value= 0.630) regardless of the type of chemotherapy. Therefore, no association was found between EBV positivity and the survival outcomes in patients with curatively resected gastric cancer who received standard adjuvant chemotherapy.
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Affiliation(s)
- Dong Won Baek
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Kyungpook National University Cancer Research Institute, Daegu, Korea
| | - Byung Woog Kang
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Kyungpook National University Cancer Research Institute, Daegu, Korea
| | - Jong Gwang Kim
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Kyungpook National University Cancer Research Institute, Daegu, Korea
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50
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Transcriptome-wide analysis of alternative mRNA splicing signature in the diagnosis and prognosis of stomach adenocarcinoma. Oncol Rep 2018; 40:2014-2022. [PMID: 30106437 PMCID: PMC6111597 DOI: 10.3892/or.2018.6623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
Alternative mRNA splicing (AS) contributes greatly to expanding the diversity and function of the proteome. Increasing evidence has suggested that dysregulation of mRNA splicing may be associated with various types of cancer. In the present study, RNA sequencing data were used to investigate alterations to the global mRNA splicing landscape of cellular genes from 452 stomach adenocarcinoma (STAD) tissues available in The Cancer Genome Atlas. Seven types of AS events, including the profiles of exon skipping events, were analyzed using SpliceSeq software. A total of 60,754 AS events in 10,611 genes were detected, more than half of which were exon skipping events. The AS events were compared between 415 STAD tissues and 37 normal tissues, and 3,895 differentially spliced cancer-specific events were identified. In addition, the association of the AS events with the overall survival of 373 STAD patients was analyzed. Multivariate Cox regression analysis revealed that prognosis prediction models based on the AS events with clinical parameters had an excellent performance in predicting the survival of STAD patients. This study provides a comprehensive portrait of global changes in mRNA splicing signatures that occur in gastric cancer. These results allowed the identification of a core set of AS in gastric cancer and indicated that AS events may serve as prognostic indicators.
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