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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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Meliț LE, Mărginean CO, Borka Balas R. The Most Recent Insights into the Roots of Gastric Cancer. Life (Basel) 2024; 14:95. [PMID: 38255710 PMCID: PMC10817233 DOI: 10.3390/life14010095] [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: 11/29/2023] [Revised: 01/01/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Helicobacter pylori (H. pylori) is the most common bacterial infection worldwide, usually being acquired during childhood, and its persistence into adulthood represents one of the main contributors of gastric carcinogenesis. Based on these statements, it would be of great importance to know if the most early premalignant transformation occurs in children or later since, this would enable the development of effective anti-tumorigenesis strategies. The interplay between H. pylori virulence factors, the host's responses modified by this infection, and the gastric microecology are complex and eventually lead to the development of gastric cancer in susceptible individuals. Several biomarkers were identified as major contributors of this long-lasting process, such as pepsinogens, gastrin 17, lipid-, glucose- and iron-metabolism parameters, immunity players, aberrant bacterial DNA methylation, H. pylori virulence factors, and hallmarks of gastric dysbiosis. Several of these biomarkers were also identified in children with H. pylori infection, independently of the presence of premalignant lesions, which were also proven to be present in a subgroup of H. pylori-infected children, especially those carrying extremely virulent strains. Therefore, the most incipient premalignant gastric changes might indeed occur early during childhood, opening a promising research gate for further studies to delineate the border between infection and cancer.
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Affiliation(s)
| | - Cristina Oana Mărginean
- Department of Pediatrics I, “George Emil Palade” University of Medicine, Pharmacy, Sciences and Technology, Târgu Mureș, Gheorghe Marinescu Street, No. 38, 540136 Târgu Mureș, Romania; (L.E.M.)
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Usui G, Matsusaka K, Huang KK, Zhu F, Shinozaki T, Fukuyo M, Rahmutulla B, Yogi N, Okada T, Minami M, Seki M, Sakai E, Fujibayashi K, Kwok Tsao SK, Khor C, Ang TL, Abe H, Matsubara H, Fukayama M, Gunji T, Matsuhashi N, Morikawa T, Ushiku T, Yeoh KG, Tan P, Kaneda A. Integrated environmental, lifestyle, and epigenetic risk prediction of primary gastric neoplasia using the longitudinally monitored cohorts. EBioMedicine 2023; 98:104844. [PMID: 38251469 PMCID: PMC10755115 DOI: 10.1016/j.ebiom.2023.104844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND DNA methylation accumulates in non-malignant gastric mucosa after exposure to pathogens. To elucidate how environmental, methylation, and lifestyle factors interplay to influence primary gastric neoplasia (GN) risk, we analyzed longitudinally monitored cohorts in Japan and Singapore. METHODS Asymptomatic subjects who underwent a gastric mucosal biopsy on the health check-up were enrolled. We analyzed the association between clinical factors and GN development using Cox hazard models. We further conducted comprehensive methylation analysis on selected tissues, including (i) mucosae from subjects developing GN later, (ii) mucosae from subjects not developing GN later, and (iii) GN tissues and surrounding mucosae. We also use the methylation data of mucosa collected in Singapore. The association between methylation and GN risk, as well as lifestyle and methylation, were analyzed. FINDINGS Among 4234 subjects, GN was developed in 77 subjects. GN incidence was correlated with age, drinking, smoking, and Helicobacter pylori (HP) status. Accumulation of methylation in biopsied gastric mucosae was predictive of higher future GN risk and shorter duration to GN incidence. Whereas methylation levels were associated with HP positivity, lifestyle, and morphological alterations, DNA methylation remained an independent GN risk factor through multivariable analyses. Pro-carcinogenic epigenetic alterations initiated by HP exposure were amplified by unfavorable but modifiable lifestyle choices. Adding DNA methylation to the model with clinical factors improved the predictive ability for the GN risk. INTERPRETATION The integration of environmental, lifestyle, and epigenetic information can provide increased resolution in the stratification of primary GN risk. FUNDING The funds are listed in Acknowledgements section.
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Affiliation(s)
- Genki Usui
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tomohiro Shinozaki
- Faculty of Engineering, Department of Information and Computer Technology, Tokyo University of Science, Tokyo, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Norikazu Yogi
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoka Okada
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mizuki Minami
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Cancer Genomics Center, Chiba University Hospital, Chiba, Japan
| | - Eiji Sakai
- Department of Gastroenterology, NTT Medical Center Tokyo, Tokyo, Japan; Division of Gastroenterology, Yokohama Sakae Kyosai Hospital, Yokohama, Japan
| | - Kazutoshi Fujibayashi
- Center for Preventive Medicine, NTT Medical Center Tokyo, Tokyo, Japan; Department of General Medicine, Juntendo University Hospital, Tokyo, Japan
| | - Stephen Kin Kwok Tsao
- Department of Gastroenterology and Hepatology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Christopher Khor
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore, Singapore
| | - Tiing Leong Ang
- Department of Gastroenterology and Hepatology, Changi General Hospital, Singapore, Singapore
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiaki Gunji
- Center for Preventive Medicine, NTT Medical Center Tokyo, Tokyo, Japan
| | | | - Teppei Morikawa
- Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - 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.
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore; Genome Institute of Singapore, Singapore, Singapore; Cancer Science Institute of Singapore, Singapore, Singapore.
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Health and Disease Omics Center, Chiba University, Chiba, Japan.
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Vlasac IM, Christensen BC, Salas LA. Normal gastric tissue Helicobacter pylori infection is associated with epigenetic age acceleration, increased mitotic tick rate, tissue cell composition, and Natural Killer cell methylation alterations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546926. [PMID: 37425894 PMCID: PMC10327075 DOI: 10.1101/2023.06.28.546926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Background Gastric adenocarcinomas are a leading cause of global mortality, associated with chronic infection with Helicobacter pylori. The mechanisms by which infection with H. pylori contributes to carcinogenesis are not well understood. Recent studies from subjects with and without gastric cancer have identified significant DNA methylation alterations in normal gastric mucosa associated with H. pylori infection and gastric cancer risk. Here we further investigated DNA methylation alterations in normal gastric mucosa in gastric cancer cases (n = 42) and control subjects (n = 42) with H. pylori infection data. We assessed tissue cell type composition, DNA methylation alterations within cell populations, epigenetic aging, and repetitive element methylation. Results In normal gastric mucosa of both gastric cancer cases and control subjects, we observed increased epigenetic age acceleration associated with H. pylori infection. We also observed an increased mitotic tick rate associated with H. pylori infection in both gastric cancer cases and controls. Significant differences in immune cell populations associated with H. pylori infection in normal tissue from cancer cases and controls were identified using DNA methylation cell type deconvolution. We also found natural killer cell-specific methylation alterations in normal mucosa from gastric cancer patients with H. pylori infection. Conclusions Our findings from normal gastric mucosa provide insight into underlying cellular composition and epigenetic aspects of H. pylori associated gastric cancer etiology.
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Affiliation(s)
- Irma M. Vlasac
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Lucas A. Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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Zhou H, Nie C, Tian W, Han X, Wang J, Du X, Wang Q, Zhu X, Xiang G, Zhao Y. Joint Effects Between CDKN2B/P15 Methylation and Environmental Factors on the Susceptibility to Gastric Cancer. Dig Dis Sci 2023:10.1007/s10620-023-07917-1. [PMID: 36961670 DOI: 10.1007/s10620-023-07917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/14/2022] [Indexed: 03/25/2023]
Abstract
BACKGROUND The incidence of gastric cancer has long been at a high level in China, seriously affecting the health of Chinese people. AIMS This case‒control study was performed to identify gene methylation biomarkers of gastric cancer susceptibility. METHODS A total of 393 gastric cancer cases and 397 controls were included in this study. Gene methylation in peripheral blood leukocytes was detected by a methylation-sensitive high-resolution melting method, and the Helicobacter pylori antibody presence was semi-quantified in serum by ELISA. RESULTS Individuals with total methylation of CDKN2B/P15 had a 1.883-fold (95%CI: 1.166-3.040, P = 0.010) risk of gastric cancer compared with unmethylated individuals. Individuals with both CDKN2B/P15 and NEUROG1 methylation had a higher risk of gastric cancer (OR = 2.147, 95% CI: 1.137-4.073, P = 0.019). The interaction between CDKN2B/P15 and NEUROG1 total methylation on gastric cancer risk was affected by the pattern of adjustment. In addition, the joint effects between CDKN2B/P15 total methylation and environmental factors, such as freshwater fish intake (OR = 6.403, 95% CI = 2.970-13.802, P < 0.001), irregular diet (OR = 5.186, 95% CI = 2.559-10.510, P < 0.001), unsanitary water intake (OR = 2.238, 95% CI = 1.144-4.378, P = 0.019), smoking (OR = 2.421, 95% CI = 1.456-4.026, P = 0.001), alcohol consumption(OR = 2.163, 95% CI = 1.309-3.576, P = 0.003), and garlic intake(OR = 0.373, 95% CI = 0.196-0.709, P = 0.003) on GC risk were observed, respectively. However, CDKN2B/P15 and NEUROG1 total methylation were not associated with gastric cancer prognosis. CONCLUSION CDKN2B/P15 methylation in peripheral blood may be a potential biomarker for evaluating susceptibility to gastric cancer. The joint effects between CDKN2B/P15 methylation and environmental factors may also contribute to gastric cancer susceptibility.
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Affiliation(s)
- Haibo Zhou
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Chuang Nie
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Wenjing Tian
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Xu Han
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Jing Wang
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Xinyu Du
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Qi Wang
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Xiaojie Zhu
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Guanghui Xiang
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, 197 Xuefu Road, Harbin, 150081, Heilongjiang Province, People's Republic of China.
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Zhu C, Zhang S, Liu D, Wang Q, Yang N, Zheng Z, Wu Q, Zhou Y. A Novel Gene Prognostic Signature Based on Differential DNA Methylation in Breast Cancer. Front Genet 2021; 12:742578. [PMID: 34956313 PMCID: PMC8693898 DOI: 10.3389/fgene.2021.742578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 12/11/2022] Open
Abstract
Background: DNA methylation played essential roles in regulating gene expression. The impact of DNA methylation status on the occurrence and development of cancers has been well demonstrated. However, little is known about its prognostic role in breast cancer (BC). Materials: The Illumina Human Methylation450 array (450k array) data of BC was downloaded from the UCSC xena database. Transcriptomic data of BC was downloaded from the Cancer Genome Atlas (TCGA) database. Firstly, we used univariate and multivariate Cox regression analysis to screen out independent prognostic CpGs, and then we identified methylation-associated prognosis subgroups by consensus clustering. Next, a methylation prognostic model was developed using multivariate Cox analysis and was validated with the Illumina Human Methylation27 array (27k array) dataset of BC. We then screened out differentially expressed genes (DEGs) between methylation high-risk and low-risk groups and constructed a methylation-based gene prognostic signature. Further, we validated the gene signature with three subgroups of the TCGA-BRCA dataset and an external dataset GSE146558 from the Gene Expression Omnibus (GEO) database. Results: We established a methylation prognostic signature and a methylation-based gene prognostic signature, and there was a close positive correlation between them. The gene prognostic signature involved six genes: IRF2, KCNJ11, ZDHHC9, LRP11, PCMT1, and TMEM70. We verified their expression in mRNA and protein levels in BC. Both methylation and methylation-based gene prognostic signatures showed good prognostic stratification ability. The AUC values of 3-years, 5-years overall survival (OS) were 0.737, 0.744 in the methylation signature and 0.725, 0.715 in the gene signature, respectively. In the validation groups, high-risk patients were confirmed to have poorer OS. The AUC values of 3 years were 0.757, 0.735, 0.733 in the three subgroups of TCGA dataset and 0.635 in GSE146558 dataset. Conclusion: This study revealed the DNA methylation landscape and established promising methylation and methylation-based gene prognostic signatures that could serve as potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Chunmei Zhu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shuyuan Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Di Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qingqing Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ningning Yang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhewen Zheng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunfeng Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
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Boubrik F, Belmouden A, Kadmiri NE. Potential Non-invasive Biomarkers of Helicobacter pylori-Associated Gastric Cancer. J Gastrointest Cancer 2021; 53:1113-1120. [PMID: 34767179 DOI: 10.1007/s12029-021-00734-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Gastric cancer (GC) remains the fifth most common incident cancer with the highest incidence in East Asian countries and the third leading cause of cancer death worldwide. The causal association between non-cardia GC and Helicobacter pylori (H. pylori) has been firmly documented by clinical and epidemiological studies. According to the guidelines for diagnosis and treatment of H. pylori infection, eradication therapy is strongly recommended. Early detection of GC is critical and can save lives through rapid technological advancement. At present, endoscopy remains the most efficient technique. However, it is invasive and costs highly. METHODS An extensive bibliographic search was performed via PubMed/Medline, Web of Science, and EBSCO host databases to select studies conducted within the past 8 years. Forty-six relevant analyses were encompassed in this review. RESULTS Several non-invasive candidate biomarkers associated with H. pylori, divided into virulence markers, transcriptome markers, genomic markers, and inflammatory markers, have been shown to be potential predictors of GC at an early stage. CONCLUSION The discovery of non-invasive biomarkers offers new perspectives for screening, early detection, and monitoring of individuals at risk.
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Affiliation(s)
- Fatima Boubrik
- Laboratory of Cell Biology and Molecular Genetics, Faculty of Science, Ibn Zohr University, Agadir, Morocco
| | - Ahmed Belmouden
- Laboratory of Cell Biology and Molecular Genetics, Faculty of Science, Ibn Zohr University, Agadir, Morocco
| | - Nadia El Kadmiri
- Molecular Engineering, Valorization and Environment Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Hay El Mohammadi (Lastah), Taroudannt, BP: 271, 83000, Morocco.
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Gunathilake M, Lee J, Choi IJ, Kim YI, Kim J. Association between bacteria other than Helicobacter pylori and the risk of gastric cancer. Helicobacter 2021; 26:e12836. [PMID: 34268831 DOI: 10.1111/hel.12836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND The gastric microbiota, including Helicobacter pylori (HP), has a remarkable role in gastric cancer (GC) occurrence. Evidence for the role of non-HP bacteria in GC risk is limited. We aimed to observe the association between bacteria other than HP and risk of GC in a Korean population. METHODS In this study, 268 GC cases and 288 healthy controls were included. Demographic data and total energy intake data were collected using a general questionnaire and a semiquantitative food frequency questionnaire, respectively. 16S rRNA gene sequencing was performed using DNA extracted from gastric biopsy samples. RESULTS Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and non-HP Proteobacteria were the five main phyla in the gastric environment. The five phyla were negatively related to the relative abundance of Helicobacter species (all p < 0.001). The Shannon index, richness, and Pilou-evenness were negatively correlated with Helicobacter species (all p < 0.001), while the microbial dysbiosis index was positively correlated with Helicobacter species (p < 0.001). Participants with a higher relative abundance of Actinobacteria species showed a significantly increased risk of GC (OR: 3.16, 95% CI = 1.92-5.19, p-trend<0.001). The non-HP microbiota composition among the four groups (HP+cases, HP- cases, HP+controls, and HP- controls) was significantly different (ANOSIM R = 0.10, p = 0.001). CONCLUSION Other than HP, several bacterial species might be associated with GC risk. HP status and GC status could determine the differences in microbial compositions. Further large prospective studies are warranted to confirm our findings.
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Affiliation(s)
- Madhawa Gunathilake
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, South Korea
| | - Jeonghee Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, South Korea
| | - Il Ju Choi
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si, South Korea
| | - Young-Il Kim
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, South Korea
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Ghantous A, Novoloaca A, Bouaoun L, Cuenin C, Cros MP, Xu Y, Hernandez-Vargas H, Darboe MK, Prentice AM, Moore SE, Gong YY, Herceg Z, Routledge MN. Aflatoxin Exposure during Early Life Is Associated with Differential DNA Methylation in Two-Year-Old Gambian Children. Int J Mol Sci 2021; 22:8967. [PMID: 34445674 PMCID: PMC8396526 DOI: 10.3390/ijms22168967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022] Open
Abstract
Background: DNA methylation is an epigenetic control mechanism that may be altered by environmental exposures. We have previously reported that in utero exposure to the mycotoxin and liver carcinogen aflatoxin B1 from the maternal diet, as measured using biomarkers in the mothers' blood, was associated with differential DNA methylation in white blood cells of 6-month-old infants from The Gambia. Methods: Here we examined aflatoxin B1-associated differential DNA methylation in white blood cells of 24-month-old children from the same population (n = 244), in relation to the child's dietary exposure assessed using aflatoxin albumin biomarkers in blood samples collected at 6, 12 and 18 months of age. HM450 BeadChip arrays were used to assess DNA methylation, with data compared to aflatoxin albumin adduct levels using two approaches; a continuous model comparing aflatoxin adducts measured in samples collected at 18 months to DNA methylation at 24 months, and a categorical time-dose model that took into account aflatoxin adduct levels at 6, 12 and 18 months, for comparison to DNA methylation at 24 months. Results: Geometric mean (95% confidence intervals) for aflatoxin albumin levels were 3.78 (3.29, 4.34) at 6 months, 25.1 (21.67, 29.13) at 12 months and 49.48 (43.34, 56.49) at 18 months of age. A number of differentially methylated CpG positions and regions were associated with aflatoxin exposure, some of which affected gene expression. Pathway analysis highlighted effects on genes involved with with inflammatory, signalling and growth pathways. Conclusions: This study provides further evidence that exposure to aflatoxin in early childhood may impact on DNA methylation.
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Affiliation(s)
- Akram Ghantous
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Alexei Novoloaca
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Liacine Bouaoun
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Cyrille Cuenin
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Marie-Pierre Cros
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Ya Xu
- School of Medicine, University of Leeds, Leeds LS2 9JT, UK;
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun-Yat Sen University, Guangzhou 510006, China
| | - Hector Hernandez-Vargas
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
- Cancer Research Centre of Lyon (CRCL), Université de Lyon, 69008 Lyon, France
| | - Momodou K. Darboe
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, Banjul P.O. Box 273, The Gambia; (M.K.D.); (A.M.P.); (S.E.M.)
| | - Andrew M. Prentice
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, Banjul P.O. Box 273, The Gambia; (M.K.D.); (A.M.P.); (S.E.M.)
| | - Sophie E. Moore
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, Banjul P.O. Box 273, The Gambia; (M.K.D.); (A.M.P.); (S.E.M.)
- Department of Women and Children’s Health, King’s College London, St Thomas’ Hospital, London SE1 7EH, UK
| | - Yun Yun Gong
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK;
| | - Zdenko Herceg
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Michael N. Routledge
- School of Medicine, University of Leeds, Leeds LS2 9JT, UK;
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
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10
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Gunathilake M, Lee JH, Choi IJ, Kim YI, Kim JS. Effect of the Interaction between Dietary Patterns and the Gastric Microbiome on the Risk of Gastric Cancer. Nutrients 2021; 13:2692. [PMID: 34444852 PMCID: PMC8401549 DOI: 10.3390/nu13082692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
We aimed to observe the combined effects of Gaussian graphical model (GGM)-derived dietary patterns and the gastric microbiome on the risk of gastric cancer (GC) in a Korean population. The study included 268 patients with GC and 288 healthy controls. Food intake was assessed using a 106-item semiquantitative food frequency questionnaire. GGMs were applied to derive dietary pattern networks. 16S rRNA gene sequencing was performed using DNA extracted from gastric biopsy samples. The fruit pattern network was inversely associated with the risk of GC for the highest vs. lowest tertiles in the total population (odds ratio (OR): 0.47; 95% confidence interval (CI): 0.28-0.77; p for trend = 0.003) and in females (OR: 0.38; 95% CI: 0.17-0.83; p for trend = 0.021). Males who had a low microbial dysbiosis index (MDI) and high vegetable and seafood pattern score showed a significantly reduced risk of GC (OR: 0.44; 95% CI: 0.22-0.91; p-interaction = 0.021). Females who had a low MDI and high dairy pattern score showed a significantly reduced risk of GC (OR: 0.23; 95% CI: 0.07-0.76; p-interaction = 0.018). Our novel findings revealed that vegetable and seafood pattern might interact with dysbiosis to attenuate the risk of GC in males, whereas the dairy pattern might interact with dysbiosis to reduce the GC risk in females.
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Affiliation(s)
- Madhawa Gunathilake
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si 10408, Gyeonggi-do, Korea; (M.G.); (J.-H.L.)
| | - Jeong-Hee Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si 10408, Gyeonggi-do, Korea; (M.G.); (J.-H.L.)
| | - Il-Ju Choi
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si 10408, Gyeonggi-do, Korea; (I.-J.C.); (Y.-I.K.)
| | - Young-Il Kim
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si 10408, Gyeonggi-do, Korea; (I.-J.C.); (Y.-I.K.)
| | - Jeong-Seon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si 10408, Gyeonggi-do, Korea; (M.G.); (J.-H.L.)
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11
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Choe AR, Shim KN, Park Y, Song EM, Tae CH, Jung SA. Cost-Effectiveness, Efficacy, and Safety Analysis of Tailored Therapy in Patients with Helicobacter pylori Infection. J Clin Med 2021; 10:jcm10122619. [PMID: 34198677 PMCID: PMC8232140 DOI: 10.3390/jcm10122619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/06/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Recently in Korea, where triple therapy is accepted as the first-line Helicobacter pylori (H. pylori) eradication treatment, antibiotic resistance to clarithromycin has increased considerably, resulting in eradication rates of less than 80%. We investigated the efficacy of tailored therapy after a clarithromycin resistance test compared with empirical therapy for H. pylori eradication. The cost-effectiveness of H. pylori eradication success was evaluated according to the average medical cost per patient. A total of 364 patients were enrolled in the study. The first-line H. pylori eradication rate was significantly higher in patients who received tailored therapy than in those who received empirical therapy. The total medical costs for the tailored and empirical groups were 46,374 Won and 53,528 Won. The total treatment period for each ultimately successful eradication in the tailored group was 79.8 ± 2.8 days, which is shorter than that of the empirical group (99.2 ± 7.4 days). The rate of eradication-related adverse events for the tailored group and empirical group was 12.9% and 14.8%, respectively. Tailored therapy could be a useful option to achieve a higher successful eradication rate, shorter treatment periods, and lower medical costs than empirical therapy in the era of increasing antibiotic resistance.
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Affiliation(s)
| | - Ki-Nam Shim
- Correspondence: ; Tel.: +82-2-6986-3122; Fax: +82-6986-3129
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12
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Nie C, Han X, Wei R, Leonteva A, Hong J, Du X, Wang J, Zhu L, Zhao Y, Xue Y, Zhou H, Tian W. Association of ZNF331 and WIF1 methylation in peripheral blood leukocytes with the risk and prognosis of gastric cancer. BMC Cancer 2021; 21:551. [PMID: 33992091 PMCID: PMC8126111 DOI: 10.1186/s12885-021-08199-4] [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: 01/11/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
Background Peripheral blood leukocyte (PBL) DNA methylation may serve as a surrogate marker to evaluate the susceptibility to and prognosis of gastric cancer (GC). In this study, blood-derived DNA methylation levels of two tumour-related genes, namely, ZNF331 and WIF1, and their impacts on the risk and prognosis of GC were evaluated. Methods In total, 398 GC cases and 397 controls were recruited for the study. Then, all cases were followed up for 5 years. ZNF331 and WIF1 promoter methylation status in PBLs was measured using a methylation-sensitive high-resolution melting method. Logistic and Cox regression models were used to analyse the correlation between gene methylation and the risk and prognosis of GC. Confounders were balanced through propensity score (PS) matching. Results High ZNF331 methylation significantly decreased GC risk after PS adjustment (OR = 0.580, 95% CI: 0.375–0.898, P = 0.015), which also presented in males (OR = 0.577, 95% CI: 0.343–0.970, P = 0.038). However, WIF1 methylation was not associated with GC risk. Additionally, significant combined effects between ZNF331 methylation and the intake of green vegetables and garlic were observed (OR = 0.073, 95% CI: 0.027–0.196, P < 0.001 and OR = 0.138, 95% CI: 0.080–0.238, P < 0.001, respectively). Furthermore, ZNF331 and WIF1 methylation had no impact on the prognosis of GC. Conclusion ZNF331 methylation in PBLs may affect GC risk in combination with the consumption of green vegetables and garlic and may act as a potential biomarker of GC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08199-4.
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Affiliation(s)
- Chuang Nie
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Xu Han
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Rongrong Wei
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Anastasiia Leonteva
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Jia Hong
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Xinyu Du
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Jing Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Lin Zhu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yingwei Xue
- Department of Gastroenterological Surgery, Third Affiliated Hospital of Harbin Medical University, 150 Haping Road, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Haibo Zhou
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China.
| | - Wenjing Tian
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, 157 Baojian Road, Harbin, 150081, Heilongjiang Province, People's Republic of China.
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13
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Woo HD, Herceg Z. A Method to Investigate the Helicobacter pylori-Associated DNA Methylome. Methods Mol Biol 2021; 2283:75-81. [PMID: 33765311 DOI: 10.1007/978-1-0716-1302-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
The protocol described here for methylome profiling consists of two parts. One is the experimental part for a genome-wide analysis of methylation level, and the other is the bioinformatics analysis of the methylome data. DNA methylation measurement is conducted using the commercially available array-based "Infinium Human Methylation 450K BeadChip" kit (or its updated version, Infinium MethylationEPICBeadChip). This BeadChip allows the high-throughput DNA methylation analysis suitable for genome-wide studies with large sample size. The results give intensities of the beads providing information on the unmethylated and methylated CpG sites. Bioinformatics data analysis involves reading the intensities as methylation values using R packages. Here, we provide a detailed analysis tool for each of the data analysis steps.
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Affiliation(s)
- Hae Dong Woo
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France.
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14
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Alterations in Gastric Microbial Communities Are Associated with Risk of Gastric Cancer in a Korean Population: A Case-Control Study. Cancers (Basel) 2020; 12:cancers12092619. [PMID: 32937864 PMCID: PMC7563352 DOI: 10.3390/cancers12092619] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The gastric microbial community has been identified as a specific risk factor for the gastric cancer (GC) risk in recent molecular epidemiology studies. The equilibrium of the gastric microbial community and their functions are very important to keep a proper gastric related health. However, dysbiosis where there is an imbalance of the microbiome in gastric environment leads to several pathological conditions including GC. Thus, understanding how alterations in gastric microbial communities are associated with GC risk in large population-based studies is needed to implement possible preventive and curative strategies in the future. We derived a microbial dysbiosis index to observe the association with GC risk. Further, we predicted the microbial functions that are associated with GC risk. The findings of our study are important to understand certain pathogenic bacteria and their functions associated with GC risk. It might be helpful to develop novel preventive guidelines to prevent GC risk. Abstract Although the microbiome has a potential role in gastric cancer (GC), little is known about microbial dysbiosis and its functions. This study aimed to observe the associations between the alterations in gastric microbial communities and GC risk. The study participants included 268 GC patients and 288 controls. The 16S rRNA gene sequencing was performed to characterize the microbiome. Streptococcus_NCVM and Prevotella melaninogenica species were highly enriched in cases and controls, respectively. Those who were in the third tertile of P. melaninogenica showed a significantly decreased risk of GC in total (odds ratio (OR): 0.91, 95% confidence interval (CI): 0.38–0.96, p-trend = 0.071). Class Bacilli was phylogenetically enriched in cases, while phylum Actinobacteria, class Actinobacteria were related to the controls. The microbial dysbiosis index (MDI) was significantly higher for the cases compared with the healthy controls in the female population (p = 0.002). Females in the third tertile of the MDI showed a significantly increased risk of GC (OR: 2.66, 95% CI: 1.19-5.99, p-trend = 0.017). Secondary bile acid synthesis and biosynthesis of ansamycins pathways were highly abundant in cases and controls, respectively. Dysbiosis of gastric microbial communities is associated with an increased risk of GC specifically in females.
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15
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Zhu S, Khalafi S, Chen Z, Poveda J, Peng D, Lu H, Soutto M, Que J, Garcia-Buitrago M, Zaika A, El-Rifai W. Silencing of miR490-3p by H. pylori activates DARPP-32 and induces resistance to gefitinib. Cancer Lett 2020; 491:87-96. [PMID: 32735911 DOI: 10.1016/j.canlet.2020.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023]
Abstract
Infection with Helicobacter pylori (H. pylori) is the main risk factor for gastric carcinogenesis. In this study, we investigated the expression, molecular functions, and downstream effectors of miR490-3p in gastric cancer. We used in vitro and in vivo models to investigate the role of H. pylori in regulating miR490-3p, DARPP-32-dependent functions, and therapeutic resistance. Human and mouse neoplastic gastric lesions demonstrated a negative correlation between DARPP-32 and miR490-3p expression (R = -0.58, P < 0.01). This was also detected following infection with H. pylori (R = -0.66, P < 0.01). Molecular assays confirmed DARPP-32 as a direct target of miR490-3p. CHRM2, the host gene of miR490-3p, was hypermethylated and downregulated in neoplastic gastric tissues (P < 0.05). H. pylori induced methylation and downregulation of CHRM2 and miR490-3p. Functionally, the reconstitution of miR490-3p sensitized cancer cells to gefitinib by inactivating DRAPP-32-dependent AKT and STAT3 pathways. Patients with low miR490-3p or high DARPP-32 expression had decreased overall survival (P < 0.05). Hypermethylation-mediated silencing of CHRM2 and miR490-3p by H. pylori increased DARPP-32 expression. Downregulation of miR490-3p in gastric cancer plays a role in gefitinib response by inducing DARPP-32-mediated activation of PI3K/AKT, STAT3 signaling pathways.
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Affiliation(s)
- Shoumin Zhu
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA.
| | - Shayan Khalafi
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA.
| | - Zheng Chen
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA; Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA.
| | - Julio Poveda
- Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA.
| | - Dunfa Peng
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA.
| | - Heng Lu
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA.
| | - Mohammed Soutto
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA; Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA.
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY, USA.
| | | | - Alexander Zaika
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA; Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA
| | - Wael El-Rifai
- Department of Surgery and Department of Pathology, Miler School of Medicine, University of Miami, Miami, FL, USA; Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA.
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16
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Chung FFL, Herceg Z. The Promises and Challenges of Toxico-Epigenomics: Environmental Chemicals and Their Impacts on the Epigenome. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:15001. [PMID: 31950866 PMCID: PMC7015548 DOI: 10.1289/ehp6104] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND It has been estimated that a substantial portion of chronic and noncommunicable diseases can be caused or exacerbated by exposure to environmental chemicals. Multiple lines of evidence indicate that early life exposure to environmental chemicals at relatively low concentrations could have lasting effects on individual and population health. Although the potential adverse effects of environmental chemicals are known to the scientific community, regulatory agencies, and the public, little is known about the mechanistic basis by which these chemicals can induce long-term or transgenerational effects. To address this question, epigenetic mechanisms have emerged as the potential link between genetic and environmental factors of health and disease. OBJECTIVES We present an overview of epigenetic regulation and a summary of reported evidence of environmental toxicants as epigenetic disruptors. We also discuss the advantages and challenges of using epigenetic biomarkers as an indicator of toxicant exposure, using measures that can be taken to improve risk assessment, and our perspectives on the future role of epigenetics in toxicology. DISCUSSION Until recently, efforts to apply epigenomic data in toxicology and risk assessment were restricted by an incomplete understanding of epigenomic variability across tissue types and populations. This is poised to change with the development of new tools and concerted efforts by researchers across disciplines that have led to a better understanding of epigenetic mechanisms and comprehensive maps of epigenomic variation. With the foundations now in place, we foresee that unprecedented advancements will take place in the field in the coming years. https://doi.org/10.1289/EHP6104.
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Affiliation(s)
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
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17
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Yamashita S, Nanjo S, Rehnberg E, Iida N, Takeshima H, Ando T, Maekita T, Sugiyama T, Ushijima T. Distinct DNA methylation targets by aging and chronic inflammation: a pilot study using gastric mucosa infected with Helicobacter pylori. Clin Epigenetics 2019; 11:191. [PMID: 31829249 PMCID: PMC6907118 DOI: 10.1186/s13148-019-0789-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Background Aberrant DNA methylation is induced by aging and chronic inflammation in normal tissues. The induction by inflammation is widely recognized as acceleration of age-related methylation. However, few studies addressed target genomic regions and the responsible factors in a genome-wide manner. Here, we analyzed methylation targets by aging and inflammation, taking advantage of the potent methylation induction in human gastric mucosa by Helicobacter pylori infection-triggered inflammation. Results DNA methylation microarray analysis of 482,421 CpG probes, grouped into 270,249 genomic blocks, revealed that high levels of methylation were induced in 44,461 (16.5%) genomic blocks by inflammation, even after correction of the influence of leukocyte infiltration. A total of 61.8% of the hypermethylation was acceleration of age-related methylation while 21.6% was specific to inflammation. Regions with H3K27me3 were frequently hypermethylated both by aging and inflammation. Basal methylation levels were essential for age-related hypermethylation while even regions with little basal methylation were hypermethylated by inflammation. When limited to promoter CpG islands, being a microRNA gene and high basal methylation levels strongly enhanced hypermethylation while H3K27me3 strongly enhanced inflammation-induced hypermethylation. Inflammation was capable of overriding active transcription. In young gastric mucosae, genes with high expression and frequent mutations in gastric cancers were more frequently methylated than in old ones. Conclusions Methylation by inflammation was not simple acceleration of age-related methylation. Targets of aberrant DNA methylation were different between young and old gastric mucosae, and driver genes were preferentially methylated in young gastric mucosa.
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Affiliation(s)
- Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Sohachi Nanjo
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Emil Rehnberg
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takayuki Ando
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Takao Maekita
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Toshiro Sugiyama
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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18
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Gunathilake MN, Lee J, Choi IJ, Kim YI, Ahn Y, Park C, Kim J. Association between the relative abundance of gastric microbiota and the risk of gastric cancer: a case-control study. Sci Rep 2019; 9:13589. [PMID: 31537876 PMCID: PMC6753194 DOI: 10.1038/s41598-019-50054-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
The human gut hosts a diverse community of bacteria referred to as the gut microbiome. We investigated the association between the relative abundance of gastric microbiota and gastric cancer (GC) risk in a Korean population. The study participants included 268 GC patients and 288 controls. DNA was extracted from gastric biopsies, and 16S rRNA gene analysis was performed. Unconditional logistic regression models were used to observe the associations. Of the participants, those who had the highest level (highest tertile) of relative Helicobacter pylori and Propionibacterium acnes abundances showed a significantly higher risk for GC after adjusting for potential confounding variables (odds ratio (OR) = 1.86, 95% confidence interval (CI) = 1.17–2.97, p for trend = 0.017 and OR = 4.77, 95% CI = 2.94–7.74, p for trend <0.001, respectively). Subjects who carried Prevotella copri had a significantly higher risk of GC than noncarriers (OR = 2.54, 95% CI = 1.42–4.55, p for trend = 0.002). There was a lower risk of GC in subjects carrying Lactococcus lactis than in noncarriers (OR = 0.21, 95% CI = 0.10–0.44, p for trend <0.001). H. pylori, P. acnes and P. copri are strong risk factors, whereas L. lactis is a protective factor, for GC development in Koreans. Further microbiome studies are warranted to verify the findings of the current study.
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Affiliation(s)
- Madhawa Neranjan Gunathilake
- Department of Cancer Control and Population Health, Graduate School of Cancer Science and Policy, Goyang-si, 10408, Gyeonggi-do, South Korea
| | - Jeonghee Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, 10408, Gyeonggi-do, South Korea
| | - Il Ju Choi
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si, 10408, Gyeonggi-do, South Korea
| | - Young-Il Kim
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si, 10408, Gyeonggi-do, South Korea
| | - Yongju Ahn
- Microbiome Division, Theragen Etex, 145 Gwanggyo-ro, Gyeongtong-gu, Suwon-si, Gyeonggi-do, 16229, South Korea
| | - Chanhyeok Park
- Microbiome Division, Theragen Etex, 145 Gwanggyo-ro, Gyeongtong-gu, Suwon-si, Gyeonggi-do, 16229, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, 10408, Gyeonggi-do, South Korea.
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Thompson M, Chen ZJ, Rahmani E, Halperin E. CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasets. Genome Biol 2019; 20:138. [PMID: 31300005 PMCID: PMC6624895 DOI: 10.1186/s13059-019-1743-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/21/2019] [Indexed: 12/11/2022] Open
Abstract
Methylation datasets are affected by innumerable sources of variability, both biological (cell-type composition, genetics) and technical (batch effects). Here, we propose a reference-free method based on sparse canonical correlation analysis to separate the biological from technical sources of variability. We show through simulations and real data that our method, CONFINED, is not only more accurate than the state-of-the-art reference-free methods for capturing known, replicable biological variability, but it is also considerably more robust to dataset-specific technical variability than previous approaches. CONFINED is available as an R package as detailed at https://github.com/cozygene/CONFINED.
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Affiliation(s)
- Mike Thompson
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Zeyuan Johnson Chen
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Elior Rahmani
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Eran Halperin
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Anesthesiology and Perioperative Medicine, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Biomathematics, University of California Los Angeles, Los Angeles, CA, USA.
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20
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Yousefi B, Mohammadlou M, Abdollahi M, Salek Farrokhi A, Karbalaei M, Keikha M, Kokhaei P, Valizadeh S, Rezaiemanesh A, Arabkari V, Eslami M. Epigenetic changes in gastric cancer induction by
Helicobacter pylori. J Cell Physiol 2019; 234:21770-21784. [PMID: 31169314 DOI: 10.1002/jcp.28925] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Bahman Yousefi
- Department of Immunology Semnan University of Medical Sciences Semnan Iran
| | - Maryam Mohammadlou
- Department of Immunology Semnan University of Medical Sciences Semnan Iran
| | - Maryam Abdollahi
- Department of Immunology Semnan University of Medical Sciences Semnan Iran
| | | | - Mohsen Karbalaei
- Department of Microbiology and Virology, School of Medicine Jiroft University of Medical Sciences Jiroft Iran
| | - Masoud Keikha
- Department of Microbiology and Virology, School of Medicine Mashhad University of Medical Sciences Mashhad Iran
| | - Parviz Kokhaei
- Department of Immunology Semnan University of Medical Sciences Semnan Iran
- Immune and Gene Therapy Lab, Cancer Centre Karolinska Karolinska University Hospital Stockholm Sweden
| | - Saeid Valizadeh
- Department of Bacteriology and Virology Semnan University of Medical Sciences Semnan Iran
| | - Alireza Rezaiemanesh
- Department of Immunology, School of Medicine Kermanshah University of Medical Sciences Kermanshah Iran
| | - Vahid Arabkari
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology University College Dublin Dublin Ireland
| | - Majid Eslami
- Cancer Research Center Semnan University of Medical Sciences Semnan Iran
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Abstract
ABSTRACT
Successful bacterial colonizers and pathogens have evolved with their hosts and have acquired mechanisms to customize essential processes that benefit their lifestyle. In large part, bacterial survival hinges on shaping the transcriptional signature of the host, a process regulated at the chromatin level. Modifications of chromatin, either on histone proteins or on DNA itself, are common targets during bacterium-host cross talk and are the focus of this article.
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