1
|
Akanyibah FA, Zhu Y, Wan A, Ocansey DKW, Xia Y, Fang AN, Mao F. Effects of DNA methylation and its application in inflammatory bowel disease (Review). Int J Mol Med 2024; 53:55. [PMID: 38695222 DOI: 10.3892/ijmm.2024.5379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.
Collapse
Affiliation(s)
- Francis Atim Akanyibah
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| | - Yi Zhu
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, P.R. China
| | - Aijun Wan
- Zhenjiang College, Zhenjiang, Jiangsu 212028, P.R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - An-Ning Fang
- Basic Medical School, Anhui Medical College, Hefei, Anhui 230061, P.R. China
| | - Fei Mao
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| |
Collapse
|
2
|
Kim TO, Park DI, Han YK, Kang K, Park SG, Park HR, Yi JM. Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad ( FHIT) Gene as a New Promising Biomarker of Crohn's Disease. J Clin Med 2020; 9:jcm9051338. [PMID: 32375395 PMCID: PMC7291297 DOI: 10.3390/jcm9051338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel disease is known to be associated with a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interactions with environmental factors, particularly epigenetic factors, can also significantly contribute to the development of inflammatory bowel disease (IBD). Although many genome-wide association studies have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease, the role of epigenetic alterations based on molecular complications arising from Crohn’s disease (CD) is poorly understood. We employed an unbiased approach to define DNA methylation alterations in colonoscopy samples from patients with CD using the HumanMethylation450K BeadChip platform. Technical and functional validation was performed by methylation-specific PCR (MSP) and bisulfite sequencing of a validation set of 207 patients with CD samples. Immunohistochemistry (IHC) analysis was performed in the representative sample sets. DNA methylation profile in CD revealed that 135 probes (24 hypermethylated and 111 hypomethylated probes) were differentially methylated. We validated the methylation levels of 19 genes that showed hypermethylation in patients with CD compared with normal controls. We uniquely identified that the fragile histidine triad (FHIT) gene was hypermethylated in a disease-specific manner and its protein level was downregulated in patients with CD. Pathway analysis of the hypermethylated candidates further suggested putative molecular interactions relevant to IBD pathology. Our data provide information on the biological and clinical implications of DNA hypermethylated genes in CD, identifying FHIT methylation as a promising new biomarker for CD. Further study of the role of FHIT in IBD pathogenesis may lead to the development of new therapeutic targets.
Collapse
Affiliation(s)
- Tae-Oh Kim
- Department of Internal Medicine, Inje University, Haeundae Paik Hospital, Busan 48108, Korea;
| | - Dong-Il Park
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
| | - Yu Kyeong Han
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan 31116, Korea;
| | - Sae-Gwang Park
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Hae Ryoun Park
- Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan, Gyeongsangnam do 50612, Korea;
| | - Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
- Correspondence: ; Tel.: +82-51-890-6734
| |
Collapse
|
3
|
Kim TO, Han YK, Yi JM. Hypermethylated promoters of tumor suppressor genes were identified in Crohn's disease patients. Intest Res 2020; 18:297-305. [PMID: 32019290 PMCID: PMC7385571 DOI: 10.5217/ir.2019.00105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND/AIMS Overwhelming evidence suggests that inflammatory bowel disease (IBD) is caused by a complicated interplay between the multiple genes and abnormal epigenetic regulation in response to environmental factors. It is becoming apparent that epigenetic factors are significantly associated with the development of the disease. DNA methylation remains the most studied epigenetic modification, and hypermethylation of gene promoters is associated with gene silencing. METHODS DNA methylation alterations may contribute to the many complex diseases development by regulating the interplay between external and internal environmental factors and gene transcriptional expression. In this study, we used 15 tumor suppressor genes (TSGs), originally identified in colon cancer, to detect promoter methylation in patients with Crohn's disease (CD). Methylation specific polymerase chain reaction and bisulfite sequencing analyses were performed to assess methylation level of TSGs in CD patients. RESULTS We found 6 TSGs (sFRP1, sFRP2, sFRP5, TFPI2, Sox17, and GATA4) are robustly hypermethylated in CD patient samples. Bisulfite sequencing analysis confirmed the methylation levels of the sFRP1, sFRP2, sFRP5, TFPI2, Sox17, and GATA4 promoters in the representative CD patient samples. CONCLUSIONS In this study, the promoter hypermethylation of the TSGs observed indicates that CD exhibits specific DNA methylation signatures with potential clinical applications for the noninvasive diagnosis of IBD and the prognosis for patients with IBD.
Collapse
Affiliation(s)
- Tae-Oh Kim
- Department of Internal Medicine, Inje University Haeundae Paik Hospital, Busan, Korea
| | - Yu Kyeong Han
- Department of Microbiology and Immunology, Inje University College of Medicine, Busan, Korea
| | - Joo Mi Yi
- Department of Microbiology and Immunology, Inje University College of Medicine, Busan, Korea
| |
Collapse
|
4
|
Karatzas PS, Mantzaris GJ, Safioleas M, Gazouli M. DNA methylation profile of genes involved in inflammation and autoimmunity in inflammatory bowel disease. Medicine (Baltimore) 2014; 93:e309. [PMID: 25526479 PMCID: PMC4603097 DOI: 10.1097/md.0000000000000309] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 10/14/2014] [Accepted: 10/30/2014] [Indexed: 12/17/2022] Open
Abstract
The contribution of epigenetic alterations to disease pathogenesis is emerging as a research priority. In this study, we aimed to seek DNA methylation changes in peripheral blood and tissue biopsies from patients with inflammatory bowel disease. The promoter methylation status of genes involved in inflammation and autoimmunity was profiled using the Human Inflammatory Response and Autoimmunity EpiTect Methyl II Signature PCR Array profiles. Methylation was considered to be hypermethylated if >20% according to the instructions of the manufacturer. The microarrays were validated with Quantitative Real-time PCR. Regarding Crohn disease (CD) no gene appeared hypermethylated compared to healthy controls. In ulcerative colitis (UC) 5 genes (CXCL14, CXCL5, GATA3, IL17C, and IL4R) were hypermethylated compared to healthy controls. Some of the examined genes show different methylation patterns between CD and UC. Concerning tissue samples we found that all hypermethylated genes appear the same methylation pattern and confirmed a moderate-strong correlation between methylation levels in colon biopsies and peripheral blood (Pearson coefficients r=0.089-0.779, and r=0.023-0.353, respectively). The epigenetic changes observed in this study indicate that CD and UC exhibit specific DNA methylation signatures with potential clinical applications in IBD non-invasive diagnosis and prognosis.
Collapse
Affiliation(s)
- Pantelis S Karatzas
- From the 1 Department of Gastroenterology, Evaggelismos Hospital, Athens, Greece (PSK, GJM); 4 Department of Surgery, Attikon University Hospital, University of Athens, Athens, Greece (MS); and Department of Basic Medical Sciences, Laboratory of Biology, University of Athens, Athens, Greece (MG)
| | | | | | | |
Collapse
|
5
|
Yashiro M. Ulcerative colitis-associated colorectal cancer. World J Gastroenterol 2014; 20:16389-16397. [PMID: 25469007 PMCID: PMC4248182 DOI: 10.3748/wjg.v20.i44.16389] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/02/2014] [Accepted: 10/15/2014] [Indexed: 02/06/2023] Open
Abstract
The association between ulcerative colitis (UC) and colorectal cancer (CRC) has been acknowledged. One of the most serious and life threatening consequences of UC is the development of CRC (UC-CRC). UC-CRC patients are younger, more frequently have multiple cancerous lesions, and histologically show mucinous or signet ring cell carcinomas. The risk of CRC begins to increase 8 or 10 years after the diagnosis of UC. Risk factors for CRC with UC patients include young age at diagnosis, longer duration, greater anatomical extent of colonic involvement, the degree of inflammation, family history of CRC, and presence of primary sclerosing cholangitis. CRC on the ground of UC develop from non-dysplastic mucosa to indefinite dysplasia, low-grade dysplasia, high-grade dysplasia and finally to invasive adenocarcinoma. Colonoscopy surveillance programs are recommended to reduce the risk of CRC and mortality in UC. Genetic alterations might play a role in the development of UC-CRC. 5-aminosalicylates might represent a favorable therapeutic option for chemoprevention of CRC.
Collapse
|
6
|
Bae JH, Park J, Yang KM, Kim TO, Yi JM. Detection of DNA hypermethylation in sera of patients with Crohn's disease. Mol Med Rep 2013; 9:725-9. [PMID: 24317008 DOI: 10.3892/mmr.2013.1840] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/11/2013] [Indexed: 11/06/2022] Open
Abstract
Mounting evidence suggests that inflammatory bowel disease (IBD) is caused by genetic predisposition of various genes as well as an abnormal interaction with environmental factors, resulting in epigenetic alterations. It has become evident that epigenetic factors play a significant contributory role during disease development. Additionally, DNA methylation has been reported to be correlated with the development of IBD. In the present study, we examined the role of DNA hypermethylation in Crohn's disease (CD) patients. The transcription elongation regulator 1-like (TCERG1L) gene, which has been previously reported to be highly frequently methylated in colon tumors was selected as a candidate for the early detection of biomarkers for colon cancer patients. DNA methylation of TCERG1L in 101 serum samples of CD patients was examined. Results of conventional MSP analysis revealed high methylation [57% (58/101)] of serum samples in CD patients. The DNA methylation pattern of TCEEG1L was confirmed using bisulfate sequencing analysis. The results of the present study suggest that using regular colonoscopic surveillance sensitive DNA methylation markers may detect serum samples of CD patients, leading to reduced risk or prevention of the progression of advanced stages of disease.
Collapse
Affiliation(s)
- Jin-Han Bae
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, Republic of Korea
| | - Jongha Park
- Department of Internal Medicine, Inje University Haeundae Paik Hospital, Busan, Republic of Korea
| | - Kwang Mo Yang
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, Republic of Korea
| | - Tae-Oh Kim
- Department of Internal Medicine, Inje University Haeundae Paik Hospital, Busan, Republic of Korea
| | - Joo Mi Yi
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, Republic of Korea
| | | |
Collapse
|
7
|
Stein RA. Streptococcus infantarius and carcinogenesis: a new chapter in colorectal pathology. Int J Clin Pract 2013; 67:1220-4. [PMID: 24246203 DOI: 10.1111/ijcp.12295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/17/2013] [Indexed: 12/14/2022] Open
Abstract
As mirrored by several topics throughout history, the causal link between infectious diseases and cancer was initially viewed with disbelief and subsequently forgotten, only to be rediscovered decades later, when it started flourishing into a vibrant multidisciplinary field . Just a few years ago, it was estimated that over 20% of all cancers are causally linked to infectious diseases, most frequently caused by bacteria, viruses, and parasites .
Collapse
Affiliation(s)
- R A Stein
- Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA. ,
| |
Collapse
|
8
|
Lin Z, Hegarty JP, Yu W, Cappel JA, Chen X, Faber PW, Wang Y, Poritz LS, Fan JB, Koltun WA. Identification of disease-associated DNA methylation in B cells from Crohn's disease and ulcerative colitis patients. Dig Dis Sci 2012; 57:3145-53. [PMID: 22821069 DOI: 10.1007/s10620-012-2288-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 06/11/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Changes in the methylation status of inflammatory bowel disease (IBD)-associated genes could significantly alter levels of gene expression, thereby contributing to disease onset and progression. We previously identified seven disease-associated DNA methylation loci from intestinal tissues of IBD patients using the Illumina GoldenGate BeadArray assay. AIMS In this study, we extended this approach to identify IBD-associated changes in DNA methylation in B cells from 18 IBD patients [9 Crohn's disease (CD) and 9 ulcerative colitis (UC)]. B cell DNA methylation markers are particularly favorable for diagnosis due to the convenient access to peripheral blood. METHODS We examined DNA methylation profiles of B cell lines using the Illumina GoldenGate BeadArray assay. Disease-associated CpGs/genes with changes in DNA methylation were identified by comparison of methylation profiles between B cell lines from IBD patients and their siblings without IBD. BeadArray data were validated using a bisulfite polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method. To verify that observed changes in DNA methylation were not due to virus transformation, we compared specific CpG DNA methylation levels of GADD45A and POMC between B cell lines and matching peripheral blood B lymphocytes from five individuals. RESULTS Using this approach with strict statistical analysis, we identified 11 IBD-associated CpG sites, 14 CD-specific CpG sites, and 24 UC-specific CpG sites with methylation changes in B cells. CONCLUSIONS IBD- and subtype-specific changes in DNA methylation were identified in B cells from IBD patients. Many of these genes have important immune and inflammatory response functions including several loci within the interleukin (IL)-12/IL-23 pathway.
Collapse
Affiliation(s)
- Zhenwu Lin
- Department of Surgery, College of Medicine, The Pennsylvania State University, 500 University Drive, MC H 137, Hershey, PA 17033, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Lin Z, Hegarty JP, Cappel JA, Yu W, Chen X, Faber P, Wang Y, Kelly AA, Poritz LS, Peterson BZ, Schreiber S, Fan JB, Koltun WA. Identification of disease-associated DNA methylation in intestinal tissues from patients with inflammatory bowel disease. Clin Genet 2010; 80:59-67. [PMID: 20950376 DOI: 10.1111/j.1399-0004.2010.01546.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Overwhelming evidence supports the theory that inflammatory bowel disease (IBD) is caused by a complex interplay between genetic predispositions of multiple genes, combined with an abnormal interaction with environmental factors. It is becoming apparent that epigenetic factors can have a significant contribution in the pathogenesis of disease. Changes in the methylation state of IBD-associated genes could significantly alter levels of gene expression, potentially contributing to disease onset and progression. We have explored the role of DNA methylation in IBD pathogenesis. DNA methylation profiles (1505 CpG sites of 807 genes) of matched diseased (n = 26) and non-diseased (n = 26) intestinal tissues from 26 patients with IBD [Crohn's disease (CD) n = 9, ulcerative colitis (UC) n = 17] were profiled using the GoldenGate™ methylation assay. After an initial identification of a panel of 50 differentially methylated CpG sites from a training set (14 non-diseased and 14 diseased tissues) and subsequent validation with a testing set (12 non-diseased and 12 diseased tissues), we identified seven CpG sites that are differentially methylated in intestinal tissues of IBD patients. We have also identified changes in DNA methylation associated with the two major IBD subtypes, CD and UC. This study reports IBD-associated changes in DNA methylation in intestinal tissue, which may be disease subtype-specific.
Collapse
Affiliation(s)
- Z Lin
- Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA17033, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Marlowe J, Teo SS, Chibout SD, Pognan F, Moggs J. Mapping the epigenome--impact for toxicology. EXS 2009; 99:259-88. [PMID: 19157065 DOI: 10.1007/978-3-7643-8336-7_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in technological approaches for mapping and characterizing the epigenome are generating a wealth of new opportunities for exploring the relationship between epigenetic modifications, human disease and the therapeutic potential of pharmaceutical drugs. While the best examples for xenobiotic-induced epigenetic perturbations come from the field of non-genotoxic carcinogenesis, there is growing evidence for the relevance of epigenetic mechanisms associated with a wide range of disease areas and drug targets. The application of epigenomic profiling technologies to drug safety sciences has great potential for providing novel insights into the molecular basis of long-lasting cellular perturbations including increased susceptibility to disease and/or toxicity, memory of prior immune stimulation and/or drug exposure, and transgenerational effects.
Collapse
Affiliation(s)
- Jennifer Marlowe
- Novartis Pharma AG, Investigative Toxicology, Preclinical Safety, Basel, Switzerland.
| | | | | | | | | |
Collapse
|
11
|
Bäckdahl L, Bushell A, Beck S. Inflammatory signalling as mediator of epigenetic modulation in tissue-specific chronic inflammation. Int J Biochem Cell Biol 2008; 41:176-84. [PMID: 18793748 DOI: 10.1016/j.biocel.2008.08.023] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 08/18/2008] [Accepted: 08/19/2008] [Indexed: 12/19/2022]
Abstract
Recent successes of therapeutic intervention in chronic inflammatory diseases using epigenetic modifiers such as histone deacetylase inhibitors and inhibitors of DNA methylation suggest that epigenetic reprogramming plays a role in the aetiology of these diseases. The epigenetic signature of a given immune cell is reflected in the history of modifications from different signals the cell has been subjected to during differentiation. Like other cells, differentiating immune cells are dependent on a complex combination of inter- and intracell signalling as well as transcription machineries to modulate their epigenomes in order to mediate differentiation. Despite extensive research into these processes, the link between cellular signalling and epigenetic modulation remains poorly understood. Here, we review recent progress and discuss key factors driving epigenetic modulation in chronic inflammation.
Collapse
Affiliation(s)
- Liselotte Bäckdahl
- Medical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK.
| | | | | |
Collapse
|