1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Li L, Song Q, Zhou J, Ji Q. Controllers of histone methylation-modifying enzymes in gastrointestinal cancers. Biomed Pharmacother 2024; 174:116488. [PMID: 38520871 DOI: 10.1016/j.biopha.2024.116488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024] Open
Abstract
Gastrointestinal (GI) cancers have been considered primarily genetic malignancies, caused by a series of progressive genetic alterations. Accumulating evidence shows that histone methylation, an epigenetic modification program, plays an essential role in the different pathological stages of GI cancer progression, such as precancerous lesions, tumorigenesis, and tumor metastasis. Histone methylation-modifying enzymes, including histone methyltransferases (HMTs) and demethylases (HDMs), are the main executor of post-transcriptional modification. The abnormal expression of histone methylation-modifying enzymes characterizes GI cancers with complex pathogenesis and progression. Interactions between upstream controllers and histone methylation-modifying enzymes have recently been revealed, and have provided numerous opportunities to elucidate the pathogenesis of GI cancers in depth and clearly. Here we focus on the association between histone methylation-modifying enzymes and their controllers, aiming to provide a new perspective on the molecular research and clinical management of GI cancers.
Collapse
Affiliation(s)
- Ling Li
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qing Song
- Department of Medical Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu 215007, China
| | - Jing Zhou
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Liver Disease Department of Integrative Medicine, Ningbo No.2 Hospital, Ningbo, Zhejiang 315000, China.
| | - Qing Ji
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| |
Collapse
|
3
|
Nishiyama K, Nishinakamura H, Takeshima H, Yuyu L, Takeuchi C, Hattori N, Takeda H, Yamashita S, Wakabayashi M, Sato K, Obama K, Ushijima T. Mouse methylation profiles for leukocyte cell types, and estimation of leukocyte fractions in inflamed gastrointestinal DNA samples. PLoS One 2023; 18:e0290034. [PMID: 37797047 PMCID: PMC10553802 DOI: 10.1371/journal.pone.0290034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/31/2023] [Indexed: 10/07/2023] Open
Abstract
Precise analysis of tissue DNA and RNA samples is often hampered by contaminating non-target cells whose amounts are highly variable. DNA methylation profiles are specific to cell types, and can be utilized for assessment of the fraction of such contaminating non-target cells. Here, we aimed 1) to identify methylation profiles specific to multiple types of mouse leukocytes, and 2) to estimate the fraction of leukocytes infiltrating inflamed tissues using DNA samples. First, genome-wide DNA methylation analysis was conducted for three myeloid-lineage cells and four lymphoid-lineage cells isolated by fluorescence-activated cell sorting after magnetic-activated cell sorting from leukocytes in the spleen. Clustering analysis using CpG sites within enhancers separated the three myeloid-lineage cells and four lymphoid-lineage cells while that using promoter CpG islands (TSS200CGIs) did not. Among the 266,108 CpG sites analyzed, one CpG site was specifically hypermethylated (β value ≥ 0.7) in B cells, and four, seven, 183, and 34 CpG sites were specifically hypomethylated (β value < 0.2) in CD4+ T cells, CD8+ T cells, B cells, and NK cells, respectively. Importantly, cell type-specific hypomethylated CpG sites were located at genes involved in cell type-specific biological functions. Then, marker CpG sites to estimate the leukocyte fraction in a tissue with leukocyte infiltration were selected, and an estimation algorithm was established. The fractions of infiltrating leukocytes were estimated to be 1.6-12.4% in the stomach (n = 10) with Helicobacter pylori-induced inflammation and 1.5-4.3% in the colon with dextran sulfate sodium-induced colitis (n = 4), and the fractions were highly correlated with those estimated histologically using Cd45-stained tissue sections [R = 0.811 (p = 0.004)]. These results showed that mouse methylation profiles at CpG sites within enhancers reflected leukocyte cell lineages, and the use of marker CpG sites successfully estimated the leukocyte fraction in inflamed gastric and colon tissues.
Collapse
Affiliation(s)
- Kazuhiro Nishiyama
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Division of Surgery, University of Kyoto, Kyoto, Japan
| | - Hitomi Nishinakamura
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, 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
| | - Liu Yuyu
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- 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
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Haruna Takeda
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Life Engineering, Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Kotomi Sato
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, 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
| |
Collapse
|
4
|
Irie T, Yamada H, Takeuchi C, Liu YY, Charvat H, Shimazu T, Ando T, Maekita T, Abe S, Takamaru H, Kodama M, Murakami K, Sugimoto K, Sakamoto K, Ushijima T. The methylation level of a single cancer risk marker gene reflects methylation burden in gastric mucosa. Gastric Cancer 2023; 26:667-676. [PMID: 37219707 DOI: 10.1007/s10120-023-01399-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Gastric cancer risk can be accurately predicted by measuring the methylation level of a single marker gene in gastric mucosa. However, the mechanism is still uncertain. We hypothesized that the methylation level measured reflects methylation alterations in the entire genome (methylation burden), induced by Helicobacter pylori (H. pylori) infection, and thus cancer risk. METHODS Gastric mucosa of 15 healthy volunteers without H. pylori infection (G1), 98 people with atrophic gastritis (G2), and 133 patients with gastric cancer (G3) after H. pylori eradication were collected. Methylation burden of an individual was obtained by microarray analysis as an inverse of the correlation coefficient between the methylation levels of 265,552 genomic regions in the person's gastric mucosa and those in an entirely healthy mucosa. RESULTS The methylation burden significantly increased in the order of G1 (n = 4), G2 (n = 18), and G3 (n = 19) and was well correlated with the methylation level of a single marker gene (r = 0.91 for miR124a-3). The average methylation levels of nine driver genes tended to increase according to the risk levels (P = 0.08 between G2 vs G3) and was also correlated with the methylation level of a single marker gene (r = 0.94). Analysis of more samples (14 G1, 97 G2, and 131 G3 samples) yielded significant increases of the average methylation levels between risk groups. CONCLUSIONS The methylation level of a single marker gene reflects the methylation burden, which includes driver gene methylation, and thus accurately predicts cancer risk.
Collapse
Affiliation(s)
- Takahiro Irie
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
- Department of Coloproctological Surgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Harumi Yamada
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
- Department of Surgery, Kyoto University, Kyoto, Japan
| | - Chihiro Takeuchi
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Yu-Yu Liu
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Hadrien Charvat
- Faculty of International Liberal Arts, Juntendo University, Tokyo, Japan
| | - Taichi Shimazu
- Division of Behavioral Sciences, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, 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
| | - Seiichiro Abe
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | | | - Masaaki Kodama
- Department of Gastroenterology Faculty of Medicine, Oita University, Oita, Japan
| | - Kazunari Murakami
- Department of Gastroenterology Faculty of Medicine, Oita University, Oita, Japan
| | - Kiichi Sugimoto
- Department of Coloproctological Surgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazuhiro Sakamoto
- Department of Coloproctological Surgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshikazu Ushijima
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
IL-1β, an important cytokine affecting Helicobacter pylori-mediated gastric carcinogenesis. Microb Pathog 2023; 174:105933. [PMID: 36494022 DOI: 10.1016/j.micpath.2022.105933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Infection with Helicobacter pylori (H. pylori) is prevalent around the world and responsible for gastric cancer (GC). The development of GC from gastritis is closely associated with the bacterial virulence and the body's immune response ability. In this process, interleukin-1β (IL-1β) plays an important role. Under H. pylori infection, IL-1β is highly expressed that result in gastric acid inhibition, GC-related gene methylations and disfunctions, angiogenesis. Nod-like receptor pyrin domain containing 3 (NLRP3) inflammasome mediates IL-1β maturation in cells such as macrophages, neutrophils and dendritic cells. But how does IL-1β get released across the cell membrane still unclear. In this review, we focus on the secretion mechanism of IL-1β across the membrane, and to explore the role of IL-1β in the progression of GC.
Collapse
|
7
|
Abdusalam AAA. In-silico identification of novel inhibitors for human Aurora kinase B form the ZINC database using molecular docking-based virtual screening. RESEARCH RESULTS IN PHARMACOLOGY 2022. [DOI: 10.3897/rrpharmacology.8.82977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Introduction: Aurora kinase enzymes play critical functions in mammals. Aurora kinases are mitotic regulators that are involved in a variety of processes during cell division. The overexpression of these enzymes is associated with tumour formation and is symptomatic of clinical circumstances in cancer patients who have been diagnosed.
Materials and methods: The current study reports an in-silico virtual screening (VS) and molecular docking analysis of 2500 compounds retrieved from the ZINC database and five current clinical trial compounds against Aurora Kinase B using AutoDock Vina to identify potential inhibitors.
Results and discussion: The top six compounds that resulted from the screening were ZINC00190959, ZINC07889110, ZINC0088285, ZINC01404326, ZINC00882846 and ZINC08813187, which showed lower free energy of binding (FEB) against the target protein binding pocket. The FEB were as follows: -11.92, -11.85, -11.46, -11.33, -11.21 and -11.1 kcal/mol, using AutoDock, and -11.7, -11.5, -11.2, -11.0, -10.8 and -10.6 kcal/mol for AutoDock Vina, respectively. These findings were superior to those obtained with the co-crystallized ligand VX-680, with a -7.5 kcal/mol and the current clinical trial drug. Finally, using a VS and molecular docking approach, novel Aurora kinase B inhibitors were effectively identified from the ZINC database fulfilling the Lipinski rule of five with low FEB and functional molecular interactions with the target protein.
Conclusion: The findings suggest that the six compounds could be used as a potential agent for cancer treatments.
Graphical abstract
Collapse
|
8
|
Aberrant Methylation of Somatostatin Receptor 2 Gene Is Initiated in Aged Gastric Mucosa Infected with Helicobacter pylori and Consequential Gene Silencing Is Associated with Establishment of Inflammatory Microenvironment In Vitro Study. Cancers (Basel) 2022; 14:cancers14246183. [PMID: 36551669 PMCID: PMC9777158 DOI: 10.3390/cancers14246183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The loss-of-function variants are thought to be associated with inflammation in the stomach. We here aimed to evaluate the extent and role of methylation at the SSTR2 promoter in inflammation and gastric tumor formation. A whole-genome bisulfite sequencing analysis revealed that the SSTR2 promoter was significantly hypermethylated in gastric tumors, dysplasia, and intestinal metaplasia compared to non-tumor tissues from patients with gastric cancer. Using public data, we confirmed SSTR2 promoter methylation in primary gastric tumors and intestinal metaplasia, and even aged gastric mucosae infected with Helicobacter pylori, suggesting that aberrant methylation is initiated in normal gastric mucosa. The loss-of-function of SSTR2 in SNU638 cell-induced cell proliferation in vitro, while stable transfection of SSTR2 in AGS and MKN74 cells inhibited cell proliferation and tumorigenesis in vitro and in vivo. As revealed by a comparison of target genes differentially expressed in these cells with hallmark molecular signatures, inflammation-related pathways were distinctly induced in SSTR2-KO SNU638 cell. By contrast, inflammation-related pathways were inhibited in AGS and MKN74 cells ectopically expressing SSTR2. Collectively, we propose that SSTR2 silencing upon promoter methylation is initiated in aged gastric mucosae infected with H. pylori and promotes the establishment of an inflammatory microenvironment via the intrinsic pathway. These findings provide novel insights into the initiation of gastric carcinogenesis.
Collapse
|
9
|
Tanaka I, Ono S, Watanabe Y, Yamamoto H, Oikawa R, Matsumoto S, Kubo M, Nishimura Y, Shimoda Y, Ono M, Yamamoto K, Sakamoto N. Long-term changes in aberrant DNA methylation and gastritis after Helicobacter pylori eradication focused on metachronous gastric cancer. Helicobacter 2022; 27:e12915. [PMID: 35939560 DOI: 10.1111/hel.12915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND A persistently high methylation level in gastric mucosa after Helicobacter pylori (H. pylori) eradication is presumed to be a risk for metachronous gastric cancer (MGC); however, long-term changes in aberrant DNA methylation and histological gastritis have been unclear. Our aim was to examine changes in DNA methylation and histological gastritis according to the occurrence of MGC. METHODS Subjects were classified into three groups: 25 patients in whom MGCs occurred after the initial endoscopic resection (ER) for early gastric cancer and H. pylori eradication (MGC group), 17 patients in whom MGC did not occur for more than 5 years after the initial ER and H. pylori eradication (non-MGC group) and 29 patients without a history of gastric cancer who succeeded in eradication more than 5 years ago (HP group). Aberrance of DNA methylation in three genes (miR-124a-3, EMX1, NKX6-1) and histological score of atrophy and intestinal metaplasia (IM) were evaluated using biopsy samples before and more than a mean of 5 years after H. pylori eradication. Also, the mean Z-score was calculated using Z-score values of the three genes. RESULTS The methylation level of miR-124a-3 in the HP group and non-MGC group and that of EMX1 in the HP group significantly decreased in the long term after eradication. In the MGC group, H. pylori eradication did not improve aberrant methylation, and the mean Z-score significantly increased. There were significant positive correlations between methylation levels in miR-124a-3 and EMX1 and histological findings after eradication. CONCLUSIONS A persistently high methylation level after H. pylori eradication reflected precancerous mucosal conditions and led to long-term MGC.
Collapse
Affiliation(s)
- Ikko Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Shoko Ono
- Division of Endoscopy, Hokkaido University Hospital, Sapporo, Japan
| | - Yoshiyuki Watanabe
- Department of Internal Medicine, Kawasaki Rinko General Hospital, Kawasaki, Japan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroyuki Yamamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan.,Department of Bioinformatics, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Ritsuko Oikawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Shogo Matsumoto
- Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Marina Kubo
- Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yusuke Nishimura
- Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshihiko Shimoda
- Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Masayoshi Ono
- Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Keiko Yamamoto
- Division of Endoscopy, Hokkaido University Hospital, Sapporo, Japan
| | - Naoya Sakamoto
- Department of Gastroenterology and Hepatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| |
Collapse
|
10
|
Takeuchi C, Sato J, Yamashita S, Sasaki A, Akahane T, Aoki R, Yamamichi M, Liu YY, Ito M, Furuta T, Nakajima S, Sakaguchi Y, Takahashi Y, Tsuji Y, Niimi K, Tomida S, Fujishiro M, Yamamichi N, Ushijima T. Autoimmune gastritis induces aberrant DNA methylation reflecting its carcinogenic potential. J Gastroenterol 2022; 57:144-155. [PMID: 35034200 DOI: 10.1007/s00535-021-01848-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Autoimmune gastritis (AIG) is a chronic inflammatory condition in gastric mucosa and is associated with increased cancer risk, though not as high as that by Helicobacter pylori (H. pylori)-associated gastritis (HPG). Although aberrant DNA methylation is induced by HPG and the level correlates with the risk of gastric cancer, DNA methylation induction by AIG is unknown. METHODS Gastric mucosa samples from the corpus were collected from 12 people with AIG without H. pylori infection, 10 people with HPG, and eight healthy volunteers. Genome-wide DNA methylation analysis was conducted using Infinium Methylation EPIC array. Gene expression was analyzed by quantitative RT-PCR. RESULTS The AIG samples had extensive aberrant DNA methylation but presented unique methylation profiles against the HPG samples after correction of leucocyte fractions. Comparison between the AIG and HPG samples showed that AIG induced methylation, but less than HPG, in overall CpG sites and also in promoter CpG islands. Promoter CpG islands of tumor-suppressor genes in the pathway of cell cycle, cell adhesion, p53, and WNT were highly methylated in the AIG samples, but more so in the HPG samples. The expression levels of IL1B and IL8, secreted by macrophage, were significantly lower in the AIG samples than in the HPG samples, suggesting that a difference in inflammatory response affected the degree and patterns of aberrant DNA methylation. CONCLUSIONS AIG induced aberrant DNA methylation in gastric mucosa. However, the degree of DNA methylation was less than that by HPG, which reflected carcinogenic risk.
Collapse
Affiliation(s)
- Chihiro Takeuchi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Junichi Sato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akiko Sasaki
- Department of Gastroenterology, Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Takemi Akahane
- Department of Gastroenterology, Nara Medical University, Nara, Japan
| | - Rika Aoki
- Tokushima Health Screening Center, Tokushima, Japan
| | - Mitsue Yamamichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yu-Yu Liu
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Masayoshi Ito
- Department of Gastroenterology, Yotsuya Medical Cube, Tokyo, Japan
| | - Takahisa Furuta
- Center for Clinical Research, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Shigemi Nakajima
- Department of General Medicine, Consortium for Community Medicine, Japan Community Healthcare Organization Shiga Hospital, Shiga University of Medical Science, Shiga, Japan
| | - Yoshiki Sakaguchi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yu Takahashi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tsuji
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keiko Niimi
- Center for Epidemiology and Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobutake Yamamichi
- Center for Epidemiology and Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
| |
Collapse
|
11
|
Zhang CD, Takeshima H, Sekine S, Yamashita S, Liu YY, Hattori N, Abe H, Yamashita H, Fukuda M, Imamura Y, Ushiku T, Katai H, Makino H, Watanabe M, Seto Y, Ushijima T. Prediction of tissue origin of adenocarcinomas in the esophagogastric junction by DNA methylation. Gastric Cancer 2022; 25:336-345. [PMID: 34557982 DOI: 10.1007/s10120-021-01252-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Prediction of tissue origin of esophagogastric junction (EGJ) adenocarcinomas can be important for therapeutic decision, but no molecular marker is available. Here, we aimed to develop such a marker taking advantage of tissue-specific profiles of DNA methylation. METHODS DNA methylation profiles of gastric adenocarcinomas (GACs) were obtained by an Infinium HumanMethylation450 BeadChip array, and those of esophageal adenocarcinoma (EACs) were obtained from the TCGA database. DNA from formalin-fixed paraffin-embedded (FFPE) samples was analyzed by bisulfite pyrosequencing. RESULTS In the screening set, 51 of 145,841 CpG sites in CpG islands were methylated at significantly higher levels in 30 GACs compared to those in 30 EACs. Among them, SLC46A3 and cg09177106 were unmethylated in all the 30 EACs. Predictive powers of these two markers were successfully confirmed in an independent validation set (18 GACs and 18 EACs) (SLC46A3, sensitivity = 77.8%, specificity = 100%; cg09177106, sensitivity = 83.3%, specificity = 94.4%), and could be applied to FFPE samples (37 GACs and 18 EACs) (SLC46A3, P = 0.0001; cg09177106, P = 0.0028). On the other hand, EAC-specific markers informative in the FFPE samples could not be isolated. Using these GAC-specific markers, nine of 46 (19.6%) TCGA EGJ adenocarcinomas were predicted to be GACs. CONCLUSIONS Two GAC-specific markers, SLC46A3 and cg09177106, had a high specificity for identifying the tissue origin of EGJ adenocarcinoma.
Collapse
Affiliation(s)
- Chun-Dong Zhang
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yu-Yu Liu
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroharu Yamashita
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Masahide Fukuda
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hitoshi Katai
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Hiroshi Makino
- Department of Surgery, Tama-Nagayama Hospital, Nippon Medical School, Tokyo, 206-8512, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| |
Collapse
|
12
|
ARID1A loss-of-function induces CpG island methylator phenotype. Cancer Lett 2022; 532:215587. [DOI: 10.1016/j.canlet.2022.215587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
|
13
|
Abstract
BACKGROUND There is a need for a model of diffuse-type gastric cancer that captures the features of the disease, facilitates the study of its mechanisms, and aids the development of potential therapies. One such model may be Cdh1 and Trp53 double conditional knockout (DCKO) mice, which have histopathological features similar to those of human diffuse-type gastric cancer. However, a genomic profile of this mouse model has yet to be completed. METHODS Whole-genome sequences of tumors from eight DCKO mice were analyzed and their molecular features were compared with those of human gastric adenocarcinoma. RESULTS DCKO mice gastric cancers harbored single nucleotide variations and indel patterns comparable to those of human genomically stable gastric cancers, whereas their copy number variation fraction and ploidy were more similar to human chromosomal instability gastric cancers (perhaps due to Trp53 knockout). Copy number variations dominated changes in cancer-related genes in DCKO mice, with typical high-level amplifications observed for oncogenic drivers, e.g., Myc, Ccnd1, and Cdks, as well as gastrointestinal transcription factors, e.g., Gata4, Foxa1, and Sox9. Interestingly, frequent alterations in gastrointestinal transcription factors in DCKO mice indicated their potential role in tumorigenesis. Furthermore, mouse gastric cancer had a reproducible but smaller number of mutational signatures than human gastric cancer, including the potentially acid-related signature 17, indicating shared tumorigenic etiologies in humans and mice. CONCLUSIONS Cdh1/Trp53 DCKO mice have similar genomic features to those found in human gastric cancer; hence, this is a suitable model for further studies of diffuse-type gastric cancer mechanisms and therapies.
Collapse
|
14
|
Ushijima T, Clark SJ, Tan P. Mapping genomic and epigenomic evolution in cancer ecosystems. Science 2021; 373:1474-1479. [PMID: 34554797 DOI: 10.1126/science.abh1645] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW 2010, Australia
| | - Patrick Tan
- Cancer and Stem Cell Biology, Duke-NUS Medical School Singapore, Singapore 169857, Singapore.,Epigenomic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore 138672, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| |
Collapse
|
15
|
Shock T, Badang L, Ferguson B, Martinez-Guryn K. The interplay between diet, gut microbes, and host epigenetics in health and disease. J Nutr Biochem 2021; 95:108631. [PMID: 33789148 PMCID: PMC8355029 DOI: 10.1016/j.jnutbio.2021.108631] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/31/2021] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
The mechanisms linking the function of microbes to host health are becoming better defined but are not yet fully understood. One recently explored mechanism involves microbe-mediated alterations in the host epigenome. Consumption of specific dietary components such as fiber, glucosinolates, polyphenols, and dietary fat has a significant impact on gut microbiota composition and function. Microbial metabolism of these dietary components regulates important epigenetic functions that ultimately influences host health. Diet-mediated alterations in the gut microbiome regulate the substrates available for epigenetic modifications like DNA methylation or histone methylation and/or acetylation. In addition, generation of microbial metabolites such as butyrate inhibits the activity of core epigenetic enzymes like histone deacetylases (HDACs). Reciprocally, the host epigenome also influences gut microbial composition. Thus, complex interactions exist between these three factors. This review comprehensively examines the interplay between diet, gut microbes, and host epigenetics in modulating host health. Specifically, the dietary impact on gut microbiota structure and function that in-turn regulates host epigenetics is evaluated in terms of promoting protection from disease development.
Collapse
Affiliation(s)
- Tori Shock
- Biomedical Sciences Program, Midwestern University, Downers Grove, IL, USA
| | - Luis Badang
- Biomedical Sciences Program, Midwestern University, Downers Grove, IL, USA
| | - Bradley Ferguson
- Department of Nutrition, University of Nevada Reno, Reno, NV, USA; Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada Reno, Reno, NV, USA
| | | |
Collapse
|
16
|
Padmanabhan N, Kyon HK, Boot A, Lim K, Srivastava S, Chen S, Wu Z, Lee HO, Mukundan VT, Chan C, Chan YK, Xuewen O, Pitt JJ, Isa ZFA, Xing M, Lee MH, Tan ALK, Ting SHW, Luftig MA, Kappei D, Kruger WD, Bian J, Ho YS, Teh M, Rozen SG, Tan P. Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation. Genome Biol 2021; 22:167. [PMID: 34074348 PMCID: PMC8170989 DOI: 10.1186/s13059-021-02375-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative analysis in 50 GC cell lines and 467 primary GCs. Results We identify the cystathionine beta-synthase enzyme (CBS) as a highly recurrent target of epigenetic silencing in CIMP GC. Likewise, we show that CBS epimutations are significantly associated with CIMP in various other cancers, occurring even in premalignant gastroesophageal conditions and longitudinally linked to clinical persistence. Of note, CRISPR deletion of CBS in normal gastric epithelial cells induces widespread DNA methylation changes that overlap with primary GC CIMP patterns. Reflecting its metabolic role as a gatekeeper interlinking the methionine and homocysteine cycles, CBS loss in vitro also causes reductions in the anti-inflammatory gasotransmitter hydrogen sulfide (H2S), with concomitant increase in NF-κB activity. In a murine genetic model of CBS deficiency, preliminary data indicate upregulated immune-mediated transcriptional signatures in the stomach. Conclusions Our results implicate CBS as a bi-faceted modifier of aberrant DNA methylation and inflammation in GC and highlights H2S donors as a potential new therapy for CBS-silenced lesions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02375-2.
Collapse
Affiliation(s)
- Nisha Padmanabhan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Huang Kie Kyon
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kevin Lim
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Zhiyuan Wu
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Hyung-Ok Lee
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yarn Kit Chan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ong Xuewen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zul Fazreen Adam Isa
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Manjie Xing
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ming Hui Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Angie Lay Keng Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Shamaine Ho Wei Ting
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Centre for Virology, Duke University School of Medicine, Durham, NC, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Warren D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.,National University of Singapore (Suzhou) Research Institute, Suzhou, 215123, China
| | - Ying Swan Ho
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, 119228, Singapore
| | - Steve George Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Genome Institute of Singapore, Singapore, 138672, Singapore. .,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 169856, Singapore. .,Singapore Gastric Cancer Consortium, Singapore, 119074, Singapore. .,Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
| |
Collapse
|
17
|
Hong C, Yang S, Wang Q, Zhang S, Wu W, Chen J, Zhong D, Li M, Li L, Li J, Yu H, Chen H, Zeng Q, Zhang C. Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis. Front Genet 2021; 12:563051. [PMID: 33815458 PMCID: PMC8012546 DOI: 10.3389/fgene.2021.563051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Abnormal DNA methylation (DNAm) age has been assumed to be an indicator for canceration and all-cause mortality. However, associations between DNAm age and molecular features of stomach adenocarcinoma (STAD), and its prognosis have not been systematically studied. Method: We calculated the DNAm age of 591 STAD samples and 115 normal stomach samples from The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) database using the Horvath’s clock model. Meanwhile, we utilized survival analysis to evaluate the prognostic value of DNAm age and epigenetic age acceleration shift. In addition, we performed weighted gene co-expression network analysis (WGCNA) to identify DNAm age-associated gene modules and pathways. Finally, the association between DNAm age and molecular features was performed by correlation analysis. Results: DNA methylation age was significantly correlated with chronological age in normal gastric tissues (r = 0.85, p < 0.0001), but it was not associated with chronological age in STAD samples (r = 0.060, p = 0.2369). Compared with tumor adjacent normal tissue, the DNAm age of STAD tissues was significantly decreased. Meanwhile, chronological age in STAD samples was higher than its DNAm age. Both DNAm age and epigenetic acceleration shift were associated with the prognosis of STAD patients. By using correlation analysis, we also found that DNAm age was associated with immunoactivation and stemness in STAD samples. Conclusion: In summary, epigenetic age acceleration of STAD was associated with tumor stemness, immunoactivation, and favorable prognosis.
Collapse
Affiliation(s)
- Chunhong Hong
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shaohua Yang
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qiaojin Wang
- Department of Surgical Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Zhang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Wenhui Wu
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jinyao Chen
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Danhui Zhong
- Department of Physiotherapy, The University of Hongkong-Shenzhen Hospital, Shenzhen, China
| | - Mingzhe Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liang Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jianfeng Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hong Yu
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hong Chen
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qianlin Zeng
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Changhua Zhang
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| |
Collapse
|
18
|
Han Q, Kono TJY, Knutson CG, Parry NM, Seiler CL, Fox JG, Tannenbaum SR, Tretyakova NY. Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2-/-/ Il10-/- Mouse Model. Int J Mol Sci 2020; 22:ijms22010364. [PMID: 33396408 PMCID: PMC7795000 DOI: 10.3390/ijms22010364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/26/2022] Open
Abstract
Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.
Collapse
Affiliation(s)
- Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Thomas J. Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Nicola M. Parry
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Christopher L. Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: ; Tel.: +1-612-626-3432
| |
Collapse
|
19
|
Ramos-Lopez O, Milagro FI, Riezu-Boj JI, Martinez JA. Epigenetic signatures underlying inflammation: an interplay of nutrition, physical activity, metabolic diseases, and environmental factors for personalized nutrition. Inflamm Res 2020; 70:29-49. [PMID: 33231704 PMCID: PMC7684853 DOI: 10.1007/s00011-020-01425-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 12/12/2022] Open
Abstract
Aim and objective Emerging translational evidence suggests that epigenetic alterations (DNA methylation, miRNA expression, and histone modifications) occur after external stimuli and may contribute to exacerbated inflammation and the risk of suffering several diseases including diabetes, cardiovascular diseases, cancer, and neurological disorders. This review summarizes the current knowledge about the harmful effects of high-fat/high-sugar diets, micronutrient deficiencies (folate, manganese, and carotenoids), obesity and associated complications, bacterial/viral infections, smoking, excessive alcohol consumption, sleep deprivation, chronic stress, air pollution, and chemical exposure on inflammation through epigenetic mechanisms. Additionally, the epigenetic phenomena underlying the anti-inflammatory potential of caloric restriction, n-3 PUFA, Mediterranean diet, vitamin D, zinc, polyphenols (i.e., resveratrol, gallic acid, epicatechin, luteolin, curcumin), and the role of systematic exercise are discussed. Methods Original and review articles encompassing epigenetics and inflammation were screened from major databases (including PubMed, Medline, Science Direct, Scopus, etc.) and analyzed for the writing of the review paper. Conclusion Although caution should be exercised, research on epigenetic mechanisms is contributing to understand pathological processes involving inflammatory responses, the prediction of disease risk based on the epigenotype, as well as the putative design of therapeutic interventions targeting the epigenome.
Collapse
Affiliation(s)
- Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana, Baja California, Mexico
| | - Fermin I Milagro
- Department of Nutrition, Food Science and Physiology, Center for Nutrition Research, University of Navarra, 1 Irunlarrea Street, 31008, Pamplona, Spain.
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.
- CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, Spain.
| | - Jose I Riezu-Boj
- Department of Nutrition, Food Science and Physiology, Center for Nutrition Research, University of Navarra, 1 Irunlarrea Street, 31008, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - J Alfredo Martinez
- Department of Nutrition, Food Science and Physiology, Center for Nutrition Research, University of Navarra, 1 Irunlarrea Street, 31008, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, Spain
- Precision Nutrition and Cardiometabolic Health, IMDEA-Food Institute (Madrid Institute for Advanced Studies), Madrid, Spain
| |
Collapse
|
20
|
Abstract
The original strategies developed by Helicobacter pylori to persistently colonise its host and to deregulate its cellular functions make this bacterium an outstanding model to study host-pathogen interaction and the mechanisms responsible for bacterial-induced carcinogenesis. During the last year, significant results were obtained on the role of bacterial factors essential for gastric colonisation such as spiral shape maintenance, orientation through chemotaxis and the formation of bacteria clonal population islands inside the gastric glands. Particularities of the H pylori cell surface, a structure important for immune escape, were demonstrated. New insights in the bacterial stress response revealed the importance of DNA methylation-mediated regulation. Further findings were reported on H pylori components that mediate natural transformation and mechanisms of bacterial DNA horizontal transfer which maintain a high level of H pylori genetic variability. Within-host evolution was found to be niche-specific and probably associated with physiological differences between the antral and oxyntic gastric mucosa. In addition, with the progress of CryoEM, high-resolution structures of the major virulence factors, VacA and CagT4SS, were obtained. The use of gastric organoid models fostered research revealing, preferential accumulation of bacteria at the site of injury during infection. Several studies further characterised the role of CagA in the oncogenic properties of H pylori, identifying the activation of novel CagA-dependent pathways, leading to the promotion of genetic instabilities, epithelial-to-mesenchymal transition and finally carcinogenesis. Recent studies also highlight that microRNA-mediated regulation and epigenetic modifications, through DNA methylation, are key events in the H pylori-induced tumorigenesis process.
Collapse
Affiliation(s)
- Milica Denic
- Département de Microbiologie, Institut Pasteur, UMR CNRS 2001, Unité Pathogenèse de Helicobacter, Paris, France.,Sorbonne Paris Cité, Cellule Pasteur, Université Paris Diderot, Paris, France
| | - Eliette Touati
- Département de Microbiologie, Institut Pasteur, UMR CNRS 2001, Unité Pathogenèse de Helicobacter, Paris, France
| | - Hilde De Reuse
- Département de Microbiologie, Institut Pasteur, UMR CNRS 2001, Unité Pathogenèse de Helicobacter, Paris, France
| |
Collapse
|
21
|
Gastric cancer: genome damaged by bugs. Oncogene 2020; 39:3427-3442. [PMID: 32123313 PMCID: PMC7176583 DOI: 10.1038/s41388-020-1241-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022]
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related death worldwide. The role of the microorganisms in gastric tumorigenesis attracts much attention in recent years. These microorganisms include bacteria, virus, and fungi. Among them, Helicobacter pylori (H. pylori) infection is by far the most important risk factor for GC development, with special reference to the early-onset cases. H. pylori targets multiple cellular components by utilizing various virulence factors to modulate the host proliferation, apoptosis, migration, and inflammatory response. Epstein–Barr virus (EBV) serves as another major risk factor in gastric carcinogenesis. The virus protein, EBER noncoding RNA, and EBV miRNAs contribute to the tumorigenesis by modulating host genome methylation and gene expression. In this review, we summarized the related reports about the colonized microorganism in the stomach and discussed their specific roles in gastric tumorigenesis. Meanwhile, we highlighted the therapeutic significance of eradicating the microorganisms in GC treatment.
Collapse
|