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Sasaki A, Takeshima H, Yamashita S, Ichita C, Kawachi J, Naito W, Ohashi Y, Takeuchi C, Fukuda M, Furuichi Y, Yamamichi N, Ando T, Kobara H, Kotera T, Itoi T, Sumida C, Hamada A, Koizumi K, Ushijima T. Severe induction of aberrant DNA methylation by nodular gastritis in adults. J Gastroenterol 2024; 59:442-456. [PMID: 38499886 DOI: 10.1007/s00535-024-02094-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Nodular gastritis (NG) is characterized by marked antral lymphoid follicle formation, and is a strong risk factor for diffuse-type gastric cancer in adults. However, it is unknown whether aberrant DNA methylation, which is induced by atrophic gastritis (AG) and is a risk for gastric cancer, is induced by NG. Here, we analyzed methylation induction by NG. METHODS Gastric mucosal samples were obtained from non-cancerous antral tissues of 16 NG and 20 AG patients with gastric cancer and 5 NG and 6 AG patients without, all age- and gender-matched. Genome-wide methylation analysis and expression analysis were conducted by a BeadChip array and RNA-sequencing, respectively. RESULTS Clustering analysis of non-cancerous antral tissues of NG and AG patients with gastric cancer was conducted using methylation levels of 585 promoter CpG islands (CGIs) of methylation-resistant genes, and a large fraction of NG samples formed a cluster with strong methylation induction. Promoter CGIs of CDH1 and DAPK1 tumor-suppressor genes were more methylated in NG than in AG. Notably, methylation levels of these genes were also higher in the antrum of NG patients without cancer. Genes related to lymphoid follicle formation, such as CXCL13/CXCR5 and CXCL12/CXCR4, had higher expression in NG, and genes involved in DNA demethylation TET2 and IDH1, had only half the expression in NG. CONCLUSIONS Severe aberrant methylation, involving multiple tumor-suppressor genes, was induced in the gastric antrum and body of patients with NG, in accordance with their high gastric cancer risk.
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Affiliation(s)
- Akiko Sasaki
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Chikamasa Ichita
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Jun Kawachi
- Department of General Surgery, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Wataru Naito
- Department of Diagnostic Pathology, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Yui Ohashi
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Chihiro Takeuchi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Masahide Fukuda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yumi Furuichi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
- Department of Gastroenterological Surgery, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Nobutake Yamamichi
- Center for Epidemiology and Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takayuki Ando
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Hideki Kobara
- Department of Gastroenterology and Neurology, Kagawa University, Kagawa, Japan
| | - Tohru Kotera
- Department of Medical Examination, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Chihiro Sumida
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuya Koizumi
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
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Srivastava A, Srivastava S. Multiomics data identifies RSPO2 as a prognostic biomarker in human tumors associated with pan-cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:469-499. [PMID: 38448143 DOI: 10.1016/bs.apcsb.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
RSPO2 protein may provide valuable insights into the mechanism underlying various types of tumorigenesis. The role of RSPO2 in pan-cancer has not been reported so far. Therefore, this study aimed to provide a comprehensive analysis of RSPO2 from a pan-cancer perspective employing multiomics data. The expression profile and function of RSPO2 across different tumors were investigated using various web-based tools UALCAN, GEPIA, TIMER, Human Protein Atlas, cBioPortal, TISIDB, STRING, and Metascape to interpret the expression profile, promoter methylation status, genomic alterations, survival analysis, protein-protein interaction, correlation with immune cell subtypes, tumor immune microenvironment and enrichment analysis. Comprehensive pan-cancer analysis indicated that RSPO2 was significantly downregulated in eleven and upregulated in five tumor types compared to normal tissues, validation results further suggest RSPO2 was downregulated in most of the tumors. The protein level expression of RSPO2 was mostly low in malignant tissues. We found that RSPO2 was significantly related to individual pathological stages in BLCA, COAD, LUAD and LUSC. Prognostic analysis indicates that the high RSPO2 expression was significantly correlated with the poor prognosis in BRCA, KICH, KIRP, READ, and UCES. Furthermore, RSPO2 is frequently amplified, exhibits hypermethylated promoter in most cancers, and is associated with immune subtypes, molecular subtypes and immune cell infiltration. Finally, enrichment analysis showed that RSPO2 is involved in the regulation of the canonical Wnt pathway and neuronal development. The overall comprehensive pan-cancer analysis affirms that RSPO2 could be a promising diagnostic and prognostic biomarker and latent therapy target in the future.
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Affiliation(s)
- Ankit Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Uttar Pradesh, India
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Uttar Pradesh, India.
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Zhen Y, Pavez M, Li X. The role of Pcdh10 in neurological disease and cancer. J Cancer Res Clin Oncol 2023; 149:8153-8164. [PMID: 37058252 PMCID: PMC10374755 DOI: 10.1007/s00432-023-04743-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
BACKGROUND Protocadherin 10 (PCDH 10), a member of the superfamily of protocadherins, is a Ca2+-dependent homophilic cell-cell adhesion molecule expressed on the surface of cell membranes. Protocadherin 10 plays a critical role in the central nervous system including in cell adhesion, formation and maintenance of neural circuits and synapses, regulation of actin assembly, cognitive function and tumor suppression. Additionally, Pcdh10 can serve as a non-invasive diagnostic and prognostic indicator for various cancers. METHODS This paper collects and reviews relevant literature in Pubmed. CONCLUSION This review describes the latest research understanding the role of Pcdh10 in neurological disease and human cancer, highlighting the importance of scrutinizing its properties for the development of targeted therapies and identifying a need for further research to explore Pcdh10 functions in other pathways, cell types and human pathologies.
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Affiliation(s)
- Yilan Zhen
- Menzies Institute for Medical Research, University of Tasmania, Liverpool street, Hobart, 7000, Australia
| | - Macarena Pavez
- Department of Anatomy, University of Otago, Dunedin, Otago, New Zealand.
| | - Xinying Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China.
- School of Life Sciences, Anhui Medical University, Hefei, People's Republic of China.
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Vahidi S, Mirzajani E, Norollahi SE, Aziminezhad M, Samadani AA. Performance of DNA Methylation on the Molecular Pathogenesis of Helicobacter pylori in Gastric Cancer; targeted therapy approach. J Pharmacopuncture 2022; 25:88-100. [PMID: 35837145 PMCID: PMC9240405 DOI: 10.3831/kpi.2022.25.2.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Mohsen Aziminezhad
- Non-Communicable Disease Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
- UMR INSERM U 1122, Gene Environment Interactions in Cardiovascular Pathophysiology (IGE-PCV), University of Lorraine, Nancy, France
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Guilan University of Medical Sciences, Rasht, Iran
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Age-Related DNA Methylation in Normal Kidney Tissue Identifies Epigenetic Cancer Risk Susceptibility Loci in the ANKRD34B and ZIC1 Genes. Int J Mol Sci 2022; 23:ijms23105327. [PMID: 35628134 PMCID: PMC9141100 DOI: 10.3390/ijms23105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Both age-dependent and age-independent alteration of DNA methylation in human tissues are functionally associated with the development of many malignant and non-malignant human diseases. TCGA-KIRC data were biometrically analyzed to identify new loci with age-dependent DNA methylation that may contribute to tumor risk in normal kidney tissue. ANKRD34B and ZIC1 were evaluated as candidate genes by pyrosequencing of 539 tissues, including 239 normal autopsy, 157 histopathologically tumor-adjacent normal, and 143 paired tumor kidney samples. All candidate CpG loci demonstrated a strong correlation between relative methylation levels and age (R = 0.70−0.88, p < 2 × 10−16) and seven out of 10 loci were capable of predicting chronological age in normal kidney tissues, explaining 84% of the variance (R = 0.92). Moreover, significantly increased age-independent methylation was found for 9 out of 10 CpG loci in tumor-adjacent tissues, compared to normal autopsy tissues (p = 0.001−0.028). Comparing tumor and paired tumor-adjacent tissues revealed two patient clusters showing hypermethylation, one cluster without significant changes in methylation, and a smaller cluster demonstrating hypomethylation in the tumors (p < 1 × 10−10). Taken together, our results show the presence of additional methylation risk factors besides age for renal cancer in normal kidney tissue. Concurrent tumor-specific hypermethylation suggests a subset of these loci are candidates for epigenetic renal cancer susceptibility.
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Cai S, Yao D, Zhang Y, Li Z, Li X, Li L. Cautions should be taken when using cell models for gastric cancer research. Gene 2022; 806:145922. [PMID: 34454032 DOI: 10.1016/j.gene.2021.145922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 11/25/2022]
Abstract
Gastric cancer (GC)-derived cell lines were generally used in basic cancer research and drug screening. However, it is always concerned about the difference between cultured cells and primary tumor by oncologists. To address this question, we compared differentially expressed genes (DEGs) in primary cancers, healthy tissues, and cell lines both in vitro and in silico. Seven reported genes with decreased expression in GCs by DNA methylation were analyzed in our cohort studies and experimentally validation. Selected datasets from TCGA (The Cancer Genome Atlas), CCLE (The Broad Institute Cancer Cell Line Encyclopedia), and GTEx (The Genotype-Tissue Expression project) were used to represent GCs, GC-derived cell lines, and healthy tissues respectively in the in silico analysis. Thirty gastric tissues together with six cell lines were used for validations. Unexpectedly, we experimentally found that reported cancer-related downregulated genes were only found in cancer cell lines but not in biopsies. The unchanged gene expressions in primary GCs were generally consistent with our cohort study, using information from cancerous (TCGA) and healthy tissues (GETx). Substantial differences were also found between DEGs of cancer tissues (TGCA)/ healthy tissues (GTEx) pair and cell lines (CCLE)/ healthy tissues (GTEx) pair, which confirmed the significant differences between primary cancer and cancer cell lines. Moreover, elevated expression of YWHAQ (14-3-3 δ) and THBS1 were observed in the GC biopsies, which might be potential biomarkers for GC diagnosis, considering the increased YWHAQ and THBS1 associated with poor survival rates in gastric cancer patients. In sum, it is suggested that cautions should be taken when using GC cell lines to study genes that show great differences between cell lines and tissues.
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Affiliation(s)
- Siqi Cai
- Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Dan Yao
- Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Yuqi Zhang
- Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Zhaohe Li
- Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Xiaoyu Li
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao 266000, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266071, China.
| | - Li Li
- Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266071, China.
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7
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Zhou J, Wang L, Sun Q, Chen R, Zhang C, Yang P, Tan Y, Peng C, Wang T, Jin C, Ji J, Jin K, Sun Y. Hsa_circ_0001666 suppresses the progression of colorectal cancer through the miR-576-5p/PCDH10 axis. Clin Transl Med 2021; 11:e565. [PMID: 34841662 PMCID: PMC8567033 DOI: 10.1002/ctm2.565] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Though circular RNAs, new non-coding RNA classes have demonstrated that they have an essential role in the initiation as well as development of CRC (colorectal cancer), whereas in CRC the function and mechanism of hsa_circ_0001666 are less known. METHODS Hsa_circ_0001666 was identified by bioinformatics analysis of a circRNA microarray from the GEO database, and its expression in both CRC cell lines and tissues was analysed. A series of in vitro along with in vivo experiments were carried out for exploring the hsa_circ_0001666 functions, including transwell, wound healing, flow cytometry, colony formation, Edu, CCK-8, soft agar colony formation, tumor xenografts and lung/liver metastasis in mice. RNA pull-down, RIP (RNA immunoprecipitation), luciferase reporter assay, FISH (fluorescence in situ hybridization) and rescue experiments were used for determining the correlation among hsa_circ_0001666, miR-576-5p and PCDH10. RESULTS Hsa_circ_0001666 was downregulated in both CRC cell lines along with tumour tissues. A higher expression level of hsa_circ_0001666 indicated a better clinical prognosis in patients with CRC. Hsa_circ_0001666 knockdown significantly supported CRC cell proliferation along with invasion and inhibited cell apoptosis in vitro. Hsa_circ_0001666 knockdown accelerated the CRC growth and metastasis in vivo. Moreover, the mechanistic study showed that hsa_circ_0001666, acting as 'ceRNA' of miR-576-5p, prevented PCDH10 downregulation, as well as suppressed EMT and stemness of CRC cells, and the Wnt/β-catenin signalling pathway. Inhibiting miR-576-5p or overexpressing PCDH10 could reverse phenotypic changes caused by knocking down of hsa_circ_0001666. CONCLUSIONS Hsa_circ_0001666 suppresses CRC progression through the miR-576-5p/PCDH10 axis and may provide a new insight for the diagnosis and treatment of CRC.
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Affiliation(s)
- Jiahui Zhou
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lu Wang
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Qingyang Sun
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ranran Chen
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Chuan Zhang
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Peng Yang
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Yuqian Tan
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Chaofan Peng
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Tuo Wang
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Chi Jin
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jiangzhou Ji
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Kangpeng Jin
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Yueming Sun
- The First School of Clinical MedicineNanjing Medical UniversityNanjingChina
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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Li W, Guo L, Tang W, Ma Y, Wang X, Shao Y, Zhao H, Ying J. Identification of DNA methylation biomarkers for risk of liver metastasis in early-stage colorectal cancer. Clin Epigenetics 2021; 13:126. [PMID: 34108011 PMCID: PMC8190869 DOI: 10.1186/s13148-021-01108-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/31/2021] [Indexed: 12/23/2022] Open
Abstract
Background Liver metastases can occur even in CRC patients who underwent curative surgery. While evidence suggested that adjuvant chemotherapy can help to reduce the occurrence of liver metastases for certain patients, it is not a recommended routine as the side effects outweigh the potential benefits, especially in Stage II CRC patients. This study aims to construct a model for predicting liver metastasis risk using differential methylation signals in primary CRC tumors, which can facilitate the decision for adjuvant chemotherapy. Methods Fifty-nine stage I/II and IV CRC patients were enrolled. Primary tumor, adjacent normal tissue, and metastatic tumor tissues were subject to targeted bisulfite sequencing for DNA methylation. The Least Absolute Shrinkage and Selection Operator (LASSO) algorithm was used to identify potential DMRs for predicting liver metastasis of CRC. Results We identified a total of 241,573 DMRs by comparing the DNA methylation profile of primary tumors of stage II patients who developed metastasis to those who were metastasis-free during the follow up period. 213 DMRs were associated with poor prognosis, among which 182 DMRS were found to be hypermethylated in the primary tumor of patients with metastases. Furthermore, by using the LASSO regression model, we identified 23 DMRs that contributed to a high probability of liver metastasis of CRC. The leave-one-out cross validation (LOOCV) was used to evaluate model predictive performance at an AUC of 0.701. In particular, 7 out of those 23 DMRs were found to be in the promoter region of genes that were previously reported prognostic biomarkers in diverse tumor types, including TNNI2, PAX8, GUF1, KLF4, EVI2B, CEP112, and long non-coding RNA AC011298. In addition, the model was also able to distinguish metastases of different sites (liver or lung) at an AUC of 0.933. Conclusion We have identified DNA methylation biomarkers associated with the risk of cancer liver metastasis in early-stage CRC patients. A risk prediction model based on those epigenetic markers was proposed for outcome assessment. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01108-3.
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Affiliation(s)
- Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | | | - Yutong Ma
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Xiaonan Wang
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China.
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Chung HH, Lee CT, Hu JM, Chou YC, Lin YW, Shih YL. NKX6.1 Represses Tumorigenesis, Metastasis, and Chemoresistance in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21145106. [PMID: 32707737 PMCID: PMC7404324 DOI: 10.3390/ijms21145106] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Accumulating evidence suggests that NKX6.1 (NK homeobox 1) plays a role in various types of cancer. In our previous studies, we identified NKX6.1 hypermethylation as a promising marker and demonstrated that the NKX6.1 gene functions as a metastasis suppressor through the epigenetic regulation of the epithelial-to-mesenchymal transition (EMT) in cervical cancer. More recently, we have demonstrated that NKX6.1 methylation is related to the chemotherapy response in colorectal cancer (CRC). Nevertheless, the biological function of NKX6.1 in the tumorigenesis of CRC remains unclear. In this study, we showed that NKX6.1 suppresses tumorigenic and metastatic ability both in vitro and in vivo. NKX6.1 represses cell invasion partly through the modulation of EMT. The overexpression of NKX6.1 enhances chemosensitivity in CRC cells. To further explore how NKX6.1 exerts its tumor-suppressive function, we used RNA sequencing technology for comprehensive analysis. The results showed that differentially expressed genes (DEGs) were mainly related to cell migration, response to drug, transcription factor activity, and growth factor activity, suggesting that these DEGs are involved in the function of NKX6.1 suppressing cancer invasion and metastasis. Our results demonstrated that NKX6.1 functions as a tumor suppressor partly by repressing EMT and enhancing chemosensitivity in CRC, making it a potential therapeutic target.
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Affiliation(s)
- Hsin-Hua Chung
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
| | - Chun-Te Lee
- Division of Urological Surgery, Department of Surgery, Tri-Service General Hospital Songshan Branch, No.131, Jiankang Rd., Songshan District, Taipei 10581, Taiwan;
| | - Je-Ming Hu
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No.325, Sec.2, Chenggong Rd., Neihu District, Taipei 11490, Taiwan
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan;
| | - Ya-Wen Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan
| | - Yu-Lueng Shih
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei 11490, Taiwan
- Correspondence: ; Tel./Fax: +886-2-87917654
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Li C, Zheng Y, Pu K, Zhao D, Wang Y, Guan Q, Zhou Y. A four-DNA methylation signature as a novel prognostic biomarker for survival of patients with gastric cancer. Cancer Cell Int 2020; 20:88. [PMID: 32206039 PMCID: PMC7085204 DOI: 10.1186/s12935-020-1156-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 02/26/2020] [Indexed: 12/24/2022] Open
Abstract
Background Gastric cancer (GC) is the fifth most frequently diagnosed cancer and the third leading cause of cancer-related mortality. Lack of prognostic indicators for patient survival hinders GC treatment and survival. Methods and results Methylation profile data of patients with GC obtained from The Cancer Genome Atlas (TCGA) database were analyzed to identify methylation sites as biomarkers for GC prognosis. The cohort was divided into training and validation sets. Univariate Cox, LASSO regression,and multivariate Cox analyses revealed a close correlation of a four-DNA methylation signature as a risk score model with the overall survival of patients with GC. The survival between high-risk and low-risk score patients with GC was significantly different. Analyses of receiver operating characteristics revealed a high prognostic accuracy of the four-DNA methylation signature in patients with GC. The subgroup analysis indicated that the accuracy included that for anatomical region, histologic grade, TNM stage, pathological stage, and sex. The GC prognosis based on the four-DNA methylation signature was more precise than that based on known biomarkers. Conclusions The four-DNA methylation signature could serve as a novel independent prognostic factor that could be an important tool to predict the prognostic outcome of GC patients. This potential must be verified in a large-scale population cohort study and through basic research studies.
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Affiliation(s)
- Chunmei Li
- 1Key Laboratory for Gastrointestinal Diseases, Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China.,2Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- 1Key Laboratory for Gastrointestinal Diseases, Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China.,3Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ke Pu
- 1Key Laboratory for Gastrointestinal Diseases, Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China.,3Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Da Zhao
- 2Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- 1Key Laboratory for Gastrointestinal Diseases, Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China.,3Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Quanlin Guan
- 4Department of Oncology Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yongning Zhou
- 1Key Laboratory for Gastrointestinal Diseases, Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China.,3Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
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11
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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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12
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Tavera G, Morgan DR, Williams SM. Tipping the Scale Toward Gastric Disease: A Host-Pathogen Genomic Mismatch? CURRENT GENETIC MEDICINE REPORTS 2018; 6:199-207. [PMID: 30775159 PMCID: PMC6373874 DOI: 10.1007/s40142-018-0153-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Chronic infection with Helicobacter pylori infection is necessary but not sufficient to initiate development of intestinal-type gastric adenocarcinoma. It is not clear what additional factors tip the scale from commensal bacteria towards a pathogen that facilitates development of gastric cancer. Genetic variants in both the pathogen and host have been implicated, but neither alone explains a substantial portion of disease risk. RECENT FINDINGS In this review, we consider studies that address the important role of human and bacterial genetics, ancestry and their interactions in determining gastric disease risk. We observe gaps in the current literature that should guide future work to confirm the hypothesis of the interacting roles of host and bacterial genetics that will be necessary to translate these findings into clinically relevant information. SUMMARY We summarize genetic risk factors for gastric disease in both H. pylori and human hosts. However, genetic variation of one or the other organism in isolation insufficiently explains gastric disease risk. The most promising models of gastric disease risk simultaneously consider the genetic variation of both the H. pylori and human host, under a co-evolution model.
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Affiliation(s)
- Gloria Tavera
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Douglas R Morgan
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
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13
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Noto JM, Chopra A, Loh JT, Romero-Gallo J, Piazuelo MB, Watson M, Leary S, Beckett AC, Wilson KT, Cover TL, Mallal S, Israel DA, Peek RM. Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments. Gut 2018; 67:1793-1804. [PMID: 28924022 PMCID: PMC5857411 DOI: 10.1136/gutjnl-2017-313863] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/30/2017] [Accepted: 07/15/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease. DESIGN Whole genome sequencing of genetically related H. pylori strains that differ in virulence and targeted H. pylori sequencing following prolonged exposure of bacteria to in vitro carcinogenic conditions were performed. RESULTS A total of 180 unique single nucleotide polymorphisms (SNPs) were identified among the collective genomes when compared with a reference H. pylori genome. Importantly, common SNPs were identified in isolates harvested from iron-depleted and high salt carcinogenic microenvironments, including an SNP within fur (FurR88H). To investigate the direct role of low iron and/or high salt, H. pylori was continuously cultured in vitro under low iron or high salt conditions to assess fur genetic variation. Exposure to low iron or high salt selected for the FurR88H variant after only 5 days. To extend these results, fur was sequenced in 339 clinical H. pylori strains. Among the isolates examined, 17% (40/232) of strains isolated from patients with premalignant lesions harboured the FurR88H variant, compared with only 6% (6/107) of strains from patients with non-atrophic gastritis alone (p=0.0034). CONCLUSION These results indicate that specific genetic variation arises within H. pylori strains during in vivo adaptation to conditions conducive for gastric carcinogenesis.
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Affiliation(s)
- Jennifer M Noto
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - John T Loh
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Judith Romero-Gallo
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Blanca Piazuelo
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mark Watson
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Amber C Beckett
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy L Cover
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA,Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, Tennessee, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia,Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, Tennessee, USA
| | - Dawn A Israel
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard M Peek
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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14
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Zhou C, Ye M, Ni S, Li Q, Ye D, Li J, Shen Z, Deng H. DNA methylation biomarkers for head and neck squamous cell carcinoma. Epigenetics 2018; 13:398-409. [PMID: 29927694 DOI: 10.1080/15592294.2018.1465790] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA methylation plays an important role in the etiology and pathogenesis of head and neck squamous cell carcinoma (HNSCC). The current study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) by a comprehensive bioinformatics analysis. In addition, we screened for DEGs affected by DNA methylation modification and further investigated their prognostic values for HNSCC. We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus. Aberrantly methylated-DEGs were analyzed with R software. The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation. In total, 27 aberrantly methylated genes accompanied by altered expression were identified. After confirmation by The Cancer Genome Atlas (TCGA) database, 2 hypermethylated-low-expression genes (FAM135B and ZNF610) and 2 hypomethylated-high-expression genes (HOXA9 and DCC) were identified. A receiver operating characteristic (ROC) curve confirmed the diagnostic value of these four methylated genes for HNSCC. Multivariate Cox proportional hazards analysis showed that FAM135B methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients.
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Affiliation(s)
- Chongchang Zhou
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Meng Ye
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Shumin Ni
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Qun Li
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Dong Ye
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Jinyun Li
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhisen Shen
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Hongxia Deng
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
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15
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Amigo JD, Opazo JC, Jorquera R, Wichmann IA, Garcia-Bloj BA, Alarcon MA, Owen GI, Corvalán AH. The Reprimo Gene Family: A Novel Gene Lineage in Gastric Cancer with Tumor Suppressive Properties. Int J Mol Sci 2018; 19:E1862. [PMID: 29941787 PMCID: PMC6073456 DOI: 10.3390/ijms19071862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/20/2018] [Accepted: 04/21/2018] [Indexed: 12/18/2022] Open
Abstract
The reprimo (RPRM) gene family is a group of single exon genes present exclusively within the vertebrate lineage. Two out of three members of this family are present in humans: RPRM and RPRM-Like (RPRML). RPRM induces cell cycle arrest at G2/M in response to p53 expression. Loss-of-expression of RPRM is related to increased cell proliferation and growth in gastric cancer. This evidence suggests that RPRM has tumor suppressive properties. However, the molecular mechanisms and signaling partners by which RPRM exerts its functions remain unknown. Moreover, scarce studies have attempted to characterize RPRML, and its functionality is unclear. Herein, we highlight the role of the RPRM gene family in gastric carcinogenesis, as well as its potential applications in clinical settings. In addition, we summarize the current knowledge on the phylogeny and expression patterns of this family of genes in embryonic zebrafish and adult humans. Strikingly, in both species, RPRM is expressed primarily in the digestive tract, blood vessels and central nervous system, supporting the use of zebrafish for further functional characterization of RPRM. Finally, drawing on embryonic and adult expression patterns, we address the potential relevance of RPRM and RPRML in cancer. Active investigation or analytical research in the coming years should contribute to novel translational applications of this poorly understood gene family as potential biomarkers and development of novel cancer therapies.
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Affiliation(s)
- Julio D Amigo
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8330025 Santiago, Chile.
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, 5090000 Valdivia, Chile.
| | - Roddy Jorquera
- CORE Biodata, Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, 8330024 Santiago, Chile.
| | - Ignacio A Wichmann
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- CORE Biodata, Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, 8330024 Santiago, Chile.
| | - Benjamin A Garcia-Bloj
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
| | - Maria Alejandra Alarcon
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
| | - Gareth I Owen
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8330025 Santiago, Chile.
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.
| | - Alejandro H Corvalán
- Laboratory of Oncology, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- Departamento de Oncología y Hematología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8330034 Santiago, Chile.
- CORE Biodata, Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, 8330024 Santiago, Chile.
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16
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Fang JY, Du YQ, Liu WZ, Ren JL, Li YQ, Chen XY, Lv NH, Chen YX, Lv B. Chinese consensus on chronic gastritis (2017, Shanghai). J Dig Dis 2018; 19:182-203. [PMID: 29573173 DOI: 10.1111/1751-2980.12593] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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17
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Chang SY, Kuo CC, Wu CC, Hsiao CW, Hu JM, Hsu CH, Chou YC, Shih YL, Lin YW. NKX6.1 hypermethylation predicts the outcome of stage II colorectal cancer patients undergoing chemotherapy. Genes Chromosomes Cancer 2018; 57:268-277. [PMID: 29363224 DOI: 10.1002/gcc.22529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is a common malignancy worldwide. CRC patients in the same stage often present with dramatically different clinical scenarios. Thus, robust prognostic biomarkers are urgently needed to guide therapies and improve treatment outcomes. The NKX6.1 gene has been identified as a hypermethylation marker in cervical cancer, functioning as a metastasis suppressor by regulating epithelial-mesenchymal transition. Here, we investigated whether hypermethylation of NKX6.1 might be a prognostic biomarker for CRC. By analyzing the methylation and expression of NKX6.1 in CRC tissues and CRC cell lines. We quantitatively examined the NKX6.1 methylation levels in 151 pairs of CRC tissues by using methylation-specific polymerase chain reaction analysis and found that NKX6.1 was hypermethylated in 35 of 151 CRC tissues (23%). NKX6.1 gene expression was inversely correlated with the DNA methylation level in CRC cell lines in vitro. Then, we analyzed the association of NKX6.1 methylation with clinical characteristics of these CRC patients. Our data demonstrated that patients with NKX6.1 methylation presented poorer 5-year overall survival (P = 0.0167) and disease-free survival (P = 0.0083) than patients without NKX6.1 methylation after receiving adjuvant chemotherapy. Most importantly, these data revealed that stage II CRC patients with NKX6.1 methylation had poorer 5-year disease-free survival (P = 0.0322) than patients without NKX6.1 methylation after adjuvant chemotherapy. Our results demonstrate that methylation of NKX6.1 is a novel prognostic biomarker in CRC and that it may be used as a predictor of the response to chemotherapy.
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Affiliation(s)
- Sou-Yi Chang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Hematology & Oncology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Taipei, Taiwan, Republic of China
| | - Chih-Chi Kuo
- Teaching and Research Office, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chang-Chieh Wu
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Cheng-Wen Hsiao
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Je-Ming Hu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chih-Hsiung Hsu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,School of Medicine, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Yu-Lueng Shih
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Ya-Wen Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan, Republic of China
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18
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Naumova OY, Dozier M, Dobrynin PV, Grigorev K, Wallin A, Jeltova I, Lee M, Raefski A, Grigorenko EL. Developmental dynamics of the epigenome: A longitudinal study of three toddlers. Neurotoxicol Teratol 2017; 66:125-131. [PMID: 29247702 DOI: 10.1016/j.ntt.2017.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/20/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022]
Abstract
Epigenetic regulation plays an important role in development, at the embryonic stages and later during the lifespan. Some epigenetic marks are highly conserved throughout the lifespan whereas others are closely associated with specific age periods and/or particular environmental factors. Little is known about the dynamics of epigenetic regulation during childhood, especially during the period of rapid early development. Our study was aimed to determine whether the developmental program at the early stages of human development is accompanied by significant changes in the systems of genome regulation, specifically, by genome-wide changes in DNA methylation. Using a sequencing approach (MBD-seq) we investigated genome-wide DNA methylation patterns in the T-lymphocytes of three healthy toddlers at two timepoints within the second year of life. Pairwise comparison of the methylation patterns across the individuals and time points was conducted to determine common longitudinal changes in the DNA methylation patterns. Despite relatively high interindividual variability in their epigenetic profiles and the dynamics of these profiles during the second year of life, all children showed consistent changes in the DNA methylation patterns of genes involved in the control of the immune system and genes related to the development of the CNS. Thereby, we provide evidence that early development might be accompanied by epigenetic changes in specific functional groups of genes; many such epigenetic changes appear to be related to the rapid development of the CNS.
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Affiliation(s)
- Oxana Yu Naumova
- Dept. of Psychology, University of Houston, Houston, TX, USA; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Dept. of Psychology, Saint Petersburg State University, St. Petersburg, Russia
| | - Mary Dozier
- Dept. of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Pavel V Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Kirill Grigorev
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Allison Wallin
- Dept. of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Ida Jeltova
- Private Psychological Practice, Ridgewood, NJ, USA
| | - Maria Lee
- Child Study Center, Yale University, New Haven, CT, USA
| | - Adam Raefski
- Child Study Center, Yale University, New Haven, CT, USA
| | - Elena L Grigorenko
- Dept. of Psychology, University of Houston, Houston, TX, USA; Dept. of Psychology, Saint Petersburg State University, St. Petersburg, Russia; Child Study Center, Yale University, New Haven, CT, USA; Office of the Rector, Moscow State University of Psychology and Education, Moscow, Russia.
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19
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Abstract
Gastric cancer is a deadly malignancy afflicting close to a million people worldwide. Patient survival is poor and largely due to late diagnosis and suboptimal therapies. Disease heterogeneity is a substantial obstacle, underscoring the need for precision treatment strategies. Studies have identified different subgroups of gastric cancer displaying not just genetic, but also distinct epigenetic hallmarks. Accumulating evidence suggests that epigenetic abnormalities in gastric cancer are not mere bystander events, but rather promote carcinogenesis through active mechanisms. Epigenetic aberrations, induced by pathogens such as Helicobacter pylori, are an early component of gastric carcinogenesis, probably preceding genetic abnormalities. This Review summarizes our current understanding of the gastric cancer epigenome, highlighting key advances in recent years in both tumours and pre-malignant lesions, made possible through targeted and genome-wide technologies. We focus on studies related to DNA methylation and histone modifications, linking these findings to potential therapeutic opportunities. Lessons learned from the gastric cancer epigenome might also prove relevant for other gastrointestinal cancers.
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20
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Human and Helicobacter pylori Interactions Determine the Outcome of Gastric Diseases. Curr Top Microbiol Immunol 2017; 400:27-52. [PMID: 28124148 DOI: 10.1007/978-3-319-50520-6_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The innate immune response is a critical hallmark of Helicobacter pylori infection. Epithelial and myeloid cells produce effectors, including the chemokine CXCL8, reactive oxygen species (ROS), and nitric oxide (NO), in response to bacterial components. Mechanistic and epidemiologic studies have emphasized that dysregulated and persistent release of these products leads to the development of chronic inflammation and to the molecular and cellular events related to carcinogenesis. Moreover, investigations in H. pylori-infected patients about polymorphisms of the genes encoding CXCL8 and inducible NO synthase, and epigenetic control of the ROS-producing enzyme spermine oxidase, have further proven that overproduction of these molecules impacts the severity of gastric diseases. Lastly, the critical effect of the crosstalk between the human host and the infecting bacterium in determining the severity of H. pylori-related diseases has been supported by phylogenetic analysis of the human population and their H. pylori isolates in geographic areas with varying clinical and pathologic outcomes of the infection.
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21
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Nutrition and Helicobacter pylori: Host Diet and Nutritional Immunity Influence Bacterial Virulence and Disease Outcome. Gastroenterol Res Pract 2016; 2016:3019362. [PMID: 27688750 PMCID: PMC5027306 DOI: 10.1155/2016/3019362] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/03/2016] [Indexed: 12/19/2022] Open
Abstract
Helicobacter pylori colonizes the stomachs of greater than 50% of the world's human population making it arguably one of the most successful bacterial pathogens. Chronic H. pylori colonization results in gastritis in nearly all patients; however in a subset of people, persistent infection with H. pylori is associated with an increased risk for more severe disease outcomes including B-cell lymphoma of mucosal-associated lymphoid tissue (MALT lymphoma) and invasive adenocarcinoma. Research aimed at elucidating determinants that mediate disease progression has revealed genetic differences in both humans and H. pylori which increase the risk for developing gastric cancer. Furthermore, host diet and nutrition status have been shown to influence H. pylori-associated disease outcomes. In this review we will discuss how H. pylori is able to create a replicative niche within the hostile host environment by subverting and modifying the host-generated immune response as well as successfully competing for limited nutrients such as transition metals by deploying an arsenal of metal acquisition proteins and virulence factors. Lastly, we will discuss how micronutrient availability or alterations in the gastric microbiome may exacerbate negative disease outcomes associated with H. pylori colonization.
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22
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Sobota RS, Kodaman N, Mera R, Piazuelo MB, Bravo LE, Pazos A, Zabaleta J, Delgado AG, El-Rifai W, Morgan DR, Wilson KT, Correa P, Williams SM, Schneider BG. Epigenetic and genetic variation in GATA5 is associated with gastric disease risk. Hum Genet 2016; 135:895-906. [PMID: 27225266 PMCID: PMC4947561 DOI: 10.1007/s00439-016-1687-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 12/12/2022]
Abstract
Gastric cancer incidence varies considerably among populations, even those with comparable rates of Helicobacter pylori infection. To test the hypothesis that genetic variation plays a role in gastric disease, we assessed the relationship between genotypes and gastric histopathology in a Colombian study population, using a genotyping array of immune-related single nucleotide polymorphisms (SNPs). Two synonymous SNPs (rs6061243 and rs6587239) were associated with progression of premalignant gastric lesions in a dominant-effects model after correction for multiple comparisons (p = 2.63E-07 and p = 7.97E-07, respectively); effect sizes were β = -0.863 and β = -0.815, respectively, where β is an estimate of effect on histopathology scores, which ranged from 1 (normal) to 5 (dysplasia). In our replication cohort, a second Colombian population, both SNPs were associated with histopathology when additively modeled (β = -0.256, 95 % CI = -0.47, -0.039; and β = -0.239, 95 % CI = -0.45, -0.024), and rs6587239 was significantly associated in a dominant-effects model (β = -0.330, 95 % CI = -0.66, 0.00). Because promoter methylation of GATA5 has previously been associated with gastric cancer, we also tested for the association of methylation status with more advanced histopathology scores in our samples and found a significant relationship (p = 0.001). A multivariate regression model revealed that the effects of both the promoter methylation and the exonic SNPs in GATA5 were independent. A SNP-by-methylation interaction term was also significant. This interaction between GATA5 variants and GATA5 promoter methylation indicates that the association of either factor with gastric disease progression is modified by the other.
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Affiliation(s)
- Rafal S Sobota
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nuri Kodaman
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Robertino Mera
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Luis E Bravo
- Department of Pathology, School of Medicine, Universidad del Valle, Cali 760043, Colombia
| | - Alvaro Pazos
- Department of Biology, University of Nariño, Pasto 520002, Colombia
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Alberto G Delgado
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Wael El-Rifai
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs, Veterans Affairs Tennessee Valley Healthcare System and Office of Medical Research, Nashville, TN, USA
| | - Douglas R Morgan
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Keith T Wilson
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
- Department of Veterans Affairs, Veterans Affairs Tennessee Valley Healthcare System and Office of Medical Research, Nashville, TN, USA
| | - Pelayo Correa
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Scott M Williams
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Barbara G Schneider
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
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Servetas SL, Bridge DR, Merrell DS. Molecular mechanisms of gastric cancer initiation and progression by Helicobacter pylori. Curr Opin Infect Dis 2016; 29:304-10. [PMID: 26779778 PMCID: PMC5144489 DOI: 10.1097/qco.0000000000000248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Infection with the Gram-negative, microaerophilic pathogen Helicobacter pylori results in gastric cancer in a subset of infected individuals. As such, H. pylori is the only WHO classified bacterial class I carcinogen. Numerous studies have identified mechanisms by which H. pylori alters host cell signaling pathways to cause disease. The purpose of this review is to highlight recent studies that explore mechanisms associated with induction of gastric cancer. RECENT FINDINGS Over the last year and a half, new mechanisms contributing to the etiology of H. pylori-associated gastric cancer development have been discovered. In addition to utilizing the oncogenic CagA toxin to alter host cell signaling pathways, H. pylori also induces host DNA damage and alters DNA methylation to perturb downstream signaling. Furthermore, H. pylori activates numerous host cell pathways and proteins that result in epithelial-to-mesenchymal transition and induction of cell survival and proliferation. SUMMARY Mounting evidence suggests that H. pylori promotes gastric carcinogenesis using a multifactorial approach. Intriguingly, many of the targeted pathways and mechanisms show commonality with diverse forms of cancer.
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Affiliation(s)
| | | | - D. Scott Merrell
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland, 20814, United States of America
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24
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Gobert AP, Wilson KT. The Immune Battle against Helicobacter pylori Infection: NO Offense. Trends Microbiol 2016; 24:366-376. [PMID: 26916789 DOI: 10.1016/j.tim.2016.02.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 01/07/2023]
Abstract
Helicobacter pylori is a successful pathogen of the human stomach. Despite a vigorous immune response by the gastric mucosa, the bacterium survives in its ecological niche, thus favoring diseases ranging from chronic gastritis to adenocarcinoma. The current literature demonstrates that high-output of nitric oxide (NO) production by the inducible enzyme NO synthase-2 (NOS2) plays major functions in host defense against bacterial infections. However, pathogens have elaborated several strategies to counteract the deleterious effects of NO; this includes inhibition of host NO synthesis and transcriptional regulation in response to reactive nitrogen species, allowing the bacteria to face the nitrosative stress. Moreover, NO is also a critical mediator of inflammation and carcinogenesis. In this context, we review the recent findings on the expression of NOS2 in H. pylori-infected gastric tissues and epithelial cells, the role of NO in H. pylori-related diseases and H. pylori gene expression, and the mechanisms whereby H. pylori regulates NO synthesis by host cells.
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Affiliation(s)
- Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA.
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