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2 "Joo Mi Yi"
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Original Article
Inflammatory bowel diseases
Hypermethylated promoters of tumor suppressor genes were identified in Crohn’s disease patients
Tae-Oh Kim, Yu Kyeong Han, Joo Mi Yi
Intest Res 2020;18(3):297-305.   Published online February 7, 2020
DOI: https://doi.org/10.5217/ir.2019.00105
AbstractAbstract PDFPubReaderePub
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.

Citations

Citations to this article as recorded by  
  • Colorectal cancer patient outcome is influenced by tumour-adherent bacteria through epigenetic regulation of cardinal genes including PHLPP1
    Iradj Sobhani, Nilmara De Oliveiro Alves, Cecile Charpy, Emma Bergsten, Caroline Barau, Amaury Vaysse, Mathias Chamaillard, Shatha Awaad, Aurelien Amiot, Mohammad Sadeghi, Denis Mestivier, Khashayarsha Khazaie
    BMJ Oncology.2025; 4(1): e000859.     CrossRef
  • Effects of DNA methylation and its application in inflammatory bowel disease (Review)
    Francis Akanyibah, Yi Zhu, Aijun Wan, Dickson Ocansey, Yuxuan Xia, An-Ning Fang, Fei Mao
    International Journal of Molecular Medicine.2024;[Epub]     CrossRef
  • Transcriptomic Module Discovery of Diarrhea-Predominant Irritable Bowel Syndrome: A Causal Network Inference Approach
    Davide Guido, Fatima Maqoud, Michelangelo Aloisio, Domenica Mallardi, Blendi Ura, Nicolò Gualandi, Massimiliano Cocca, Francesco Russo
    International Journal of Molecular Sciences.2024; 25(17): 9322.     CrossRef
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    Ehsan Gharib, Gilles A. Robichaud
    International Journal of Molecular Sciences.2024; 25(17): 9463.     CrossRef
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    Raquel Francés, Yuanji Fu, Christophe Desterke, Jorge Mata-Garrido
    J.2024; 7(4): 489.     CrossRef
  • Epigenotoxicity: a danger to the future life
    Farzaneh Kefayati, Atoosa Karimi Babaahmadi, Taraneh Mousavi, Mahshid Hodjat, Mohammad Abdollahi
    Journal of Environmental Science and Health, Part A.2023; 58(4): 382.     CrossRef
  • Evaluating the Clinical Performance of a Dual-Target Stool DNA Test for Colorectal Cancer Detection
    Zhongxin Wang, Jian Shang, Guannan Zhang, Lingjun Kong, Feng Zhang, Ye Guo, Yaling Dou, Jun Lin
    The Journal of Molecular Diagnostics.2022; 24(2): 131.     CrossRef
  • Lipocalin 2 potentially contributes to tumorigenesis from colitis via IL-6/STAT3/NF-κB signaling pathway
    Se Lim Kim, Min Woo Shin, Seung Young Seo, Sang Wook Kim
    Bioscience Reports.2022;[Epub]     CrossRef
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    Su Hyun Park, Sang Hyoung Park
    Journal of Gastroenterology and Hepatology.2022; 37(8): 1434.     CrossRef
  • Landscape of sialylation patterns identify biomarkers for diagnosis and prediction of response to anti-TNF therapy in crohn’s disease
    Chenglin Ye, Sizhe Zhu, Yuan Gao, Yabing Huang
    Frontiers in Genetics.2022;[Epub]     CrossRef
  • The role of epigenetic modifications for the pathogenesis of Crohn's disease
    M. Hornschuh, E. Wirthgen, M. Wolfien, K. P. Singh, O. Wolkenhauer, J. Däbritz
    Clinical Epigenetics.2021;[Epub]     CrossRef
  • SFRP5 inhibits melanin synthesis of melanocytes in vitiligo by suppressing the Wnt/β-catenin signaling
    Dao-Pei Zou, Yang-Mei Chen, Ling-Zhao Zhang, Xiao-Hui Yuan, Yu-Jie Zhang, Adelina Inggawati, Pham Thi Kieu Nguyet, Tian-Wen Gao, Jin Chen
    Genes & Diseases.2021; 8(5): 677.     CrossRef
  • 7,970 View
  • 142 Download
  • 10 Web of Science
  • 12 Crossref
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Review
Epigenetic Alterations in Inflammatory Bowel Disease and Cancer
Joo Mi Yi, Tae Oh Kim
Intest Res 2015;13(2):112-121.   Published online April 27, 2015
DOI: https://doi.org/10.5217/ir.2015.13.2.112
AbstractAbstract PDFPubReader

Overwhelming evidences supports the idea that inflammatory bowel disease (IBD) is caused by a complex interplay between genetic alterations of multiple genes and an aberrant interaction with environmental factors. There is growing evidence that epigenetic factors can play a significant part in the pathogenesis of IBD. Significant effort has been invested in uncovering genetic and epigenetic factors, which may increase the risk of IBD, but progress has been slow, and few IBD-specific factors have been detected so far. It has been known for decades that DNA methylation is the most well studied epigenetic modification, and analysis of DNA methylation is leading to a new generation of cancer biomarkers. Therefore, in this review, we summarize the role of DNA methylation alteration in IBD pathogenesis, and discuss specific genes or genetic loci using recent molecular technology advances. Here, we suggest that DNA methylation should be studied in depth to understand the molecular pathways of IBD pathogenesis, and discuss epigenetic studies of IBD that may have a significant impact on the field of IBD research.

Citations

Citations to this article as recorded by  
  • From Exposure to Dysfunction: The Intestinal Toxicity of Per- and Polyfluoroalkyl Substances
    Kashi Brunetti, Giulia Serena Galletti, Elisabetta Catalani, Davide Cervia, Simona Del Quondam
    Toxics.2025; 14(1): 39.     CrossRef
  • Personalized Medicine for IBD Patients
    Nina Fadeeva, Igor Khatkov, Natalia Bodunova, Oleg Knyazev, Dmitry Bordin, Asfold Parfenov, Karina Nikolskaya, Sergey Nikolaev, Konstantin Rumyantsev, Vera Polyakova, Tatiana Yanova
    BioNanoScience.2023; 13(1): 330.     CrossRef
  • Epigenetic Changes and Its Intervention in Age-Related Neurodegenerative Diseases
    Nuraqila Mohd Murshid, Faridah Aminullah Lubis, Suzana Makpol
    Cellular and Molecular Neurobiology.2022; 42(3): 577.     CrossRef
  • Role of diet and nutrition in inflammatory bowel disease
    Marina Moreira de Castro, Lívia Bitencourt Pascoal, Karine Mariane Steigleder, Beatriz Piatezzi Siqueira, Ligiana Pires Corona, Maria de Lourdes Setsuko Ayrizono, Marciane Milanski, Raquel Franco Leal
    World Journal of Experimental Medicine.2021; 11(1): 1.     CrossRef
  • Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad (FHIT) Gene as a New Promising Biomarker of Crohn’s Disease
    Tae-Oh Kim, Dong-Il Park, Yu Han, Keunsoo Kang, Sae-Gwang Park, Hae Park, Joo Yi
    Journal of Clinical Medicine.2020; 9(5): 1338.     CrossRef
  • Aberrant methylation and microRNA-target regulation are associated with downregulated NEURL1B: a diagnostic and prognostic target in colon cancer
    Jiaxin Liu, Zhao Liu, Xiaozhi Zhang, Yanli Yan, Shuai Shao, Demao Yao, Tuotuo Gong
    Cancer Cell International.2020;[Epub]     CrossRef
  • Effect of Perfluorooctanoic Acid on the Epigenetic and Tight Junction Genes of the Mouse Intestine
    Faizan Rashid, Saeed Ahmad, Joseph Maria Kumar Irudayaraj
    Toxics.2020; 8(3): 64.     CrossRef
  • Epigenetics, DNA Organization, and Inflammatory Bowel Disease
    Greeshma Ray, Michelle S Longworth
    Inflammatory Bowel Diseases.2019; 25(2): 235.     CrossRef
  • Impaired nutritional status in outpatients in remission or with active Crohn's disease – classified by objective endoscopic and imaging assessments
    Marina Moreira de Castro, Ligiana Pires Corona, Lívia Bitencourt Pascoal, Bruno Lima Rodrigues, Maria de Lourdes Setsuko Ayrizono, Claudio Saddy Rodrigues Coy, Raquel Franco Leal, Marciane Milanski
    Clinical Nutrition ESPEN.2019; 33: 60.     CrossRef
  • Hepatitis B Virus Infection Is Independently Associated With Advanced Colorectal Adenoma
    Su Hwan Kim, Ji Won Kim, Kook Lae Lee, Seohui Lee, Seong-Joon Koh, Ji Bong Jeong, Byeong Gwan Kim
    The American Journal of the Medical Sciences.2018; 356(2): 141.     CrossRef
  • Protocol for Fecal Microbiota Transplantation in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis
    Haiming Fang, Lian Fu, Jiajia Wang
    BioMed Research International.2018; 2018: 1.     CrossRef
  • Epigenetic modulation of intestinal Na+/H+ exchanger-3 expression
    Anoop Kumar, Pooja Malhotra, Hayley Coffing, Shubha Priyamvada, Arivarasu N. Anbazhagan, Harish R. Krishnan, Ravinder K. Gill, Waddah A. Alrefai, David P. Gavin, Subhash C. Pandey, Pradeep K. Dudeja, Seema Saksena
    American Journal of Physiology-Gastrointestinal and Liver Physiology.2018; 314(3): G309.     CrossRef
  • Is there a potential role of fecal microbiota transplantation in the treatment of inflammatory bowel disease?
    Chang Soo Eun
    Intestinal Research.2017; 15(2): 145.     CrossRef
  • Lack of Aberrant Methylation in an Adjacent Area of Left-Sided Colorectal Cancer
    Otgontuya Sambuudash, Hyun-Soo Kim, Mee Yon Cho
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    C.A. Gonzalez-Correa, E. Mulett-Vásquez, D.A. Miranda, C.H. Gonzalez-Correa, P.A. Gómez-Buitrago
    Medical Hypotheses.2017; 108: 133.     CrossRef
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    Eirini Zacharopoulou, Maria Gazouli, Maria Tzouvala, Antonios Vezakis, George Karamanolis
    Digestive and Liver Disease.2017; 49(10): 1067.     CrossRef
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    Italia Loddo, Claudio Romano
    Frontiers in Immunology.2015;[Epub]     CrossRef
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    Isabelle Cleynen, Séverine Vermeire
    Current Opinion in Gastroenterology.2015;[Epub]     CrossRef
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    Integrative Medicine International.2015; 2(1-2): 63.     CrossRef
  • 22,624 View
  • 71 Download
  • 26 Web of Science
  • 20 Crossref
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