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Zhi Y, Qiaoyun T. Screening of pivotal oncogenes modulated by DNA methylation in hepatocellular carcinoma and identification of atractylenolide I as an anti-cancer drug. Hum Cell 2025; 38:97. [PMID: 40325252 DOI: 10.1007/s13577-025-01224-9] [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: 07/30/2024] [Accepted: 04/18/2025] [Indexed: 05/07/2025]
Abstract
This study was performed to identify crucial oncogenes modulated by DNA methylation in hepatocellular carcinoma (HCC) and look for new drugs for HCC treatment. The data of TCGA-LIHC cohort were obtained from UCSC database. Weighted gene co-expression network analysis and multiple machine learning algorithms were applied to screen the crucial prognosis-related genes in HCC. Then these genes were further screened by DNA methylation status. Ten-eleven translocation 1 (TET1) was overexpressed in HCC cell lines, and its biological functions and regulatory effects on the oncogenes were explored by qPCR, methylation-specific polymerase chain reaction, cell viability assay, Western blot, etc. Molecular docking was applied to evaluate the binding affinity between atractylenolide I (AT-I) and TET1, and the tumor-suppressive functions of AT-I were examined with both in vitro and in vivo models. In this work, 12 crucial genes related to HCC prognosis were obtained, among which six genes were with differential methylation status in HCC tissues, including AKR1B10, ALPK3, NQO1, NT5DC2, SFN, and SPP1. The expression levels of ALPK3 and NT5DC2 were positively regulated by TET1, the crucial mediator of demethylation. TET1 overexpression increased the viability and stemness of HCC cells. AT-I had good binding affinity with TET1, and repressed its activity. AT-I promoted the methylation of ALPK3 and NT5DC2 promoter regions, and reduced their expression, and repressed the growth of HCC cells. In summary, DNA methylation contributes to HCC progression, and AT-I represses the malignancy of HCC cells by inhibiting TET1-mediated abnormal DNA demethylation.
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Affiliation(s)
- Yang Zhi
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Institute of Digestive Disease, Affiliated Central People's Hospital of China Three Gorges University, China Three Gorges University, Yichang, China
- Department of Gastroenterology, Yichang Central People's Hospital, Yichang, China
| | - Tong Qiaoyun
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China.
- Institute of Digestive Disease, Affiliated Central People's Hospital of China Three Gorges University, China Three Gorges University, Yichang, China.
- Department of Gastroenterology, Yichang Central People's Hospital, Yichang, China.
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2
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Kalra A, Meltzer SJ. The Role of DNA Methylation in Gastrointestinal Disease: An Expanded Review of Malignant and Nonmalignant Gastrointestinal Diseases. Gastroenterology 2025; 168:245-266. [PMID: 38971197 PMCID: PMC11698954 DOI: 10.1053/j.gastro.2024.07.001] [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: 10/10/2023] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Esophageal, colorectal, pancreatic, hepatocellular, and gastric cancer together impact millions of patients worldwide each year, with high overall mortality rates, and are increasing in incidence. Additionally, premalignant gastrointestinal diseases, such as Barrett's esophagus and inflammatory bowel disease, are also increasing in incidence. However, involvement of aberrant DNA methylation in these diseases is incompletely understood, especially given recent research advancements in this field. Here, we review knowledge of this epigenetic mechanism in gastrointestinal preneoplasia and neoplasia, considering mechanisms of action, genetic and environmental factors, and 5'-C-phosphate-G-3' island methylator phenotype. We also highlight developments in translational research, focusing on genomic-wide data, methylation-based biomarkers and diagnostic tests, machine learning, and therapeutic epigenetic strategies.
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Affiliation(s)
- Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Wang X, Zhou Z, Chai X, Li J, Wang W, Pang Z, Cheng L, Cheng C, Qiao L, Pan Y, Yang K, Liu W, Liu J. Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat. Animals (Basel) 2024; 15:36. [PMID: 39794979 PMCID: PMC11718830 DOI: 10.3390/ani15010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 12/24/2024] [Accepted: 12/26/2024] [Indexed: 01/13/2025] Open
Abstract
Lüliang black goat (LBG) is a unique livestock genetic resource of great significance for the local agriculture and economic development of Shanxi, China. However, the kidding rate of LBG is relatively low, which limits efforts to improve the reproductive performance and economic benefits of this breed. Therefore, improving the kidding characteristics of LBG is crucial for increasing its economic benefits. In this study, 20 LBG does were selected for whole-genome resequencing and divided into two groups: 10 in the T group (does with three consecutive kiddings of twin kids) and 10 in the S group (does with three consecutive kiddings of single kids). Based on whole-genome resequencing data, this study comprehensively assessed the population structure and genetic diversity of LBG and explored the related genes that affect reproductive performance. Three selection signal analysis methods-Fst (Fixation Index), π (nucleotide diversity), and XP-CLR (Cross Population Composite Likelihood Ratio)-were applied to screen a total of 838 genes, and enrichment analysis was performed to identify genes closely related to the reproductive performance of LBG, including ENPP3, APC, and GLI2. A generalized linear model was used to conduct a correlation analysis between non-synonymous mutations in the three genes and the number of kids produced. Two loci that were significantly correlated with kidding number were identified (p < 0.05): GLI2 g.63400363 C>T and GLI2 g.63417538 C>T. In general, the LBG population has high genetic diversity and good prospects for genetic improvement. The findings revealed that mining high-fecundity selection characteristics provides a basis for research on goat reproductive mechanisms.
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Affiliation(s)
- Xu Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Zhenqi Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Xinrui Chai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Jie Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Wannian Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Zhixu Pang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Lifen Cheng
- Shanxi Animal Husbandry Technology Extension Service Center, Taiyuan 030001, China; (L.C.); (C.C.)
| | - Caihong Cheng
- Shanxi Animal Husbandry Technology Extension Service Center, Taiyuan 030001, China; (L.C.); (C.C.)
| | - Liying Qiao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Yangyang Pan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Kaijie Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Wenzhong Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
| | - Jianhua Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (X.W.); (Z.Z.); (X.C.); (J.L.); (W.W.); (Z.P.); (L.Q.); (Y.P.); (K.Y.); (W.L.)
- Key Laboratory of Farm Animal Genetic Resources Exploration and Precision Breeding of Shanxi Province, Jinzhong 030801, China
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Liu W, Kuai Y, Wang D, Chen J, Xiong F, Wu G, Wang Q, Huang W, Qi Y, Wang B, Chen Y. PPM1G Inhibits Epithelial-Mesenchymal Transition in Cholangiocarcinoma by Catalyzing TET1 Dephosphorylation for Destabilization to Impair Its Targeted Demethylation of the CLDN3 Promoter. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2407323. [PMID: 39477806 DOI: 10.1002/advs.202407323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 10/22/2024] [Indexed: 12/19/2024]
Abstract
Ten-eleven translocation protein 1 (TET1) functions as an epigenetic regulatory molecule, mediating the majority of DNA demethylation, and plays a role in the development of different types of cancers by regulating the expression of proto-oncogenes and oncogenes. Here it is found that TET1 is highly expressed in cholangiocarcinoma (CCA) and is associated with a poor prognosis. In addition, TET1 promotes claudin-3 (CLDN3) transcription by targeting the CLDN3 promoter region between -16 and 512 for demethylation. PPM1G functions as a protein dephosphorylase, catalyzing the dephosphorylation of TET1. This results in the destabilization of the TET1 protein, thereby impairing the targeting of the CLDN3 promoter for demethylation. Two phosphatase inhibitors, staurosporine and AZD0156, inhibit epithelial-to-mesenchymal transition (EMT) in cholangiocarcinoma cells by suppressing TET1 expression. In conclusion, it is also demonstrated that PPM1G can be employed as a therapeutic target to impede the progression of CCA by catalyzing the dephosphorylation of TET1, which diminishes the capacity of TET1 to target the CLDN3 promoter to activate transcription and inhibit EMT in CCA.
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Affiliation(s)
- Wenzheng Liu
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Yiyang Kuai
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Da Wang
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Junsheng Chen
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Fei Xiong
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Guanhua Wu
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Qi Wang
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Wenhua Huang
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430074, China
| | - Yongqiang Qi
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Bing Wang
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Yongjun Chen
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
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El Osmani N, Prévostel C, Picque Lasorsa L, El Harakeh M, Radwan Z, Mawlawi H, El Sabban M, Shirinian M, Dassouki Z. Vitamin C enhances co-localization of novel TET1 nuclear bodies with both Cajal and PML bodies in colorectal cancer cells. Epigenetics 2024; 19:2337142. [PMID: 38583183 PMCID: PMC11000620 DOI: 10.1080/15592294.2024.2337142] [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: 08/16/2023] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Deregulation of ten-eleven Translocation protein 1 (TET1) is commonly reported to induce imbalances in gene expression and subsequently to colorectal cancer development (CRC). On the other hand, vitamin C (VitC) improves the prognosis of colorectal cancer by reprogramming the cancer epigenome and limiting chemotherapeutic drug resistance events. In this study, we aimed to characterize TET1-specific subcellular compartments and evaluate the effect of VitC on TET1 compartmentalization in colonic tumour cells. We demonstrated that TET1 is concentrated in coarse nuclear bodies (NB) and 5-hydroxymethylcytosine (5hmC) in foci in colorectal cancer cells (HCT116, Caco-2, and HT-29). To our knowledge, this is the first report of a novel intracellular localization profile of TET1 and its demethylation marker, 5hmC, in CRC cells. Interestingly, we found that TET1-NBs frequently interacted with Cajal bodies, but not with promyelocytic leukaemia (PML) bodies. In addition, we report that VitC treatment of HCT116 cells induces 5hmC foci biogenesis and triggers 5hmC marks to form active complexes with nuclear body components, including both Cajal and PML proteins. Our data highlight novel NB-concentrating TET1 in CRC cells and demonstrate that VitC modulates TET1-NBs' interactions with other nuclear structures. These findings reveal novel TET1-dependent cellular functions and potentially provide new insights for CRC management.
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Affiliation(s)
- Nour El Osmani
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
- Laboratory of Applied Biotechnology (LBA3B), AZM Center for Research in Biotechnology and its Applications, Doctoral School for Sciences and Technology, Tripoli, Lebanon
| | - Corinne Prévostel
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
- INSERM, Montpellier, France
- ICM, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Laurence Picque Lasorsa
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
- INSERM, Montpellier, France
- ICM, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Mohammad El Harakeh
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Zeina Radwan
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hiba Mawlawi
- Laboratory of Applied Biotechnology (LBA3B), AZM Center for Research in Biotechnology and its Applications, Doctoral School for Sciences and Technology, Tripoli, Lebanon
- Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan El Sabban
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Margret Shirinian
- Department of Experiment Pathology, Immunology, and Microbiology, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Zeina Dassouki
- Laboratory of Applied Biotechnology (LBA3B), AZM Center for Research in Biotechnology and its Applications, Doctoral School for Sciences and Technology, Tripoli, Lebanon
- Department of Medical Laboratory Sciences, University of Balamand, Faculty of Health Sciences, Tripoli, Lebanon
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Chen Y, Shen YQ. Role of reactive oxygen species in regulating epigenetic modifications. Cell Signal 2024; 125:111502. [PMID: 39521028 DOI: 10.1016/j.cellsig.2024.111502] [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: 08/25/2024] [Revised: 10/24/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024]
Abstract
Reactive oxygen species (ROS) originate from diverse sources and regulate multiple signaling pathways within the cellular environment. Their generation is intricately controlled, and disruptions in their signaling or atypical levels can precipitate pathological conditions. Epigenetics, the examination of heritable alterations in gene expression independent of changes in the genetic code, has been implicated in the pathogenesis of various diseases through aberrant epigenetic modifications. The significant contribution of epigenetic modifications to disease progression underscores their potential as crucial therapeutic targets for a wide array of medical conditions. This study begins by providing an overview of ROS and epigenetics, followed by a discussion on the mechanisms of epigenetic modifications such as DNA methylation, histone modification, and RNA modification-mediated regulation. Subsequently, a detailed examination of the interaction between ROS and epigenetic modifications is presented, offering new perspectives and avenues for exploring the mechanisms underlying specific epigenetic diseases and the development of novel therapeutics.
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Affiliation(s)
- Yutong Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China.
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7
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Tajali R, Zali N, Naderi Noukabadi F, Jalili M, Valinezhad M, Ghasemian F, Cheraghpour M, Savabkar S, Nazemalhosseini Mojarad E. The implication of TET1, miR-200, and miR-494 expression with tumor formation in colorectal cancer: through targeting Wnt signaling. Mol Biol Rep 2024; 51:1119. [PMID: 39495308 PMCID: PMC11535070 DOI: 10.1007/s11033-024-10060-3] [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: 09/07/2024] [Accepted: 10/24/2024] [Indexed: 11/05/2024]
Abstract
OBJECTIVE Colorectal cancer (CRC) is a diverse and multifaceted disease characterized by genetic and epigenetic changes that contribute to tumor initiation and progression. CRC pathophysiology has been linked to the deregulation of the Wnt signaling pathway and the ten-eleven translocation (TET) DNA demethylases. This study aimed to evaluate the expression level of selective miRNAs (miR-200 and miR-494), TET1, and Wnt1 in colorectal polyps, actual colorectal tumors, and normal adjacent tissues. We also evaluated the effect of 5-aza cytidine on the expression level of TET1 and wnt1 in the HT29 cell line. MATERIALS AND METHODS In this study, we assessed TET1 and Wnt1 expression in 5-azacytidine-treated HT29 cells, a demethylating agent commonly used in cancer therapy. Additionally, we enrolled 114 individuals who underwent radical surgical colon resection, including 47 with cancerous tissues and 67 with polyps. We utilized qRT-PCR to measure miR-200, miR-494, TET1, and Wnt1 mRNA levels in colorectal polyps, actual colorectal tumors, and normal adjacent tissues. RESULTS Our study revealed that TET1 expression was notably lower in both polyps and CRC tissue compared to adjacent normal tissue, with higher TET1 expression in tumors than polyps. We also observed significant differences in miR-200 and miR-494 expression in tumor samples compared to adjacent normal tissue. Our in vitro experiments revealed that 5-azacytidine administration increased TET1 and decreased Wnt1 expression in CRC cell lines. This suggests that DNA-demethylating drugs may have a therapeutic role in modifying TET1 and Wnt signaling in the development of CRC. CONCLUSIONS Overall, our findings shed light on the intricate interactions between TET1, Wnt1, and specific miRNAs in colorectal cancer (CRC) and their potential implications for diagnosis and treatment.
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Affiliation(s)
- Raziye Tajali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran
| | - Neda Zali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran
| | - Fatemeh Naderi Noukabadi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran
| | - Meysam Jalili
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran
| | - Morteza Valinezhad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran
| | - Farnaz Ghasemian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran
| | - Makan Cheraghpour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran
| | - Sanaz Savabkar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17411, Tehran, Iran.
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman Street, Chamran Expressway, P.O. Box: 19857-17411, Tehran, Iran.
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands.
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8
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Conway K, Edmiston SN, Vondras A, Reiner A, Corcoran DL, Shen R, Parrish EA, Hao H, Lin L, Kenney JM, Ilelaboye G, Kostrzewa CE, Kuan PF, Busam KJ, Lezcano C, Lee TK, Hernando E, Googe PB, Ollila DW, Moschos S, Gorlov I, Amos CI, Ernstoff MS, Cust AE, Wilmott JS, Scolyer RA, Mann GJ, Vergara IA, Ko J, Rees JR, Yan S, Nagore E, Bosenberg M, Rothberg BG, Osman I, Lee JE, Saenger Y, Bogner P, Thompson CL, Gerstenblith M, Holmen SL, Funchain P, Brunsgaard E, Depcik-Smith ND, Luo L, Boyce T, Orlow I, Begg CB, Berwick M, Thomas NE, InterMEL Study Group.. DNA Methylation Classes of Stage II and III Primary Melanomas and Their Clinical and Prognostic Significance. JCO Precis Oncol 2024; 8:e2400375. [PMID: 39509669 PMCID: PMC11737429 DOI: 10.1200/po-24-00375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 09/05/2024] [Accepted: 09/20/2024] [Indexed: 11/15/2024] Open
Abstract
PURPOSE Patients with stage II and III cutaneous primary melanoma vary considerably in their risk of melanoma-related death. We explore the ability of methylation profiling to distinguish primary melanoma methylation classes and their associations with clinicopathologic characteristics and survival. MATERIALS AND METHODS InterMEL is a retrospective case-control study that assembled primary cutaneous melanomas from American Joint Committee on Cancer (AJCC) 8th edition stage II and III patients diagnosed between 1998 and 2015 in the United States and Australia. Cases are patients who died of melanoma within 5 years from original diagnosis. Controls survived longer than 5 years without evidence of melanoma recurrence or relapse. Methylation classes, distinguished by consensus clustering of 850K methylation data, were evaluated for their clinicopathologic characteristics, 5-year survival status, and differentially methylated gene sets. RESULTS Among 422 InterMEL melanomas, consensus clustering revealed three primary melanoma methylation classes (MethylClasses): a CpG island methylator phenotype (CIMP) class, an intermediate methylation (IM) class, and a low methylation (LM) class. CIMP and IM were associated with higher AJCC stage (both P = .002), Breslow thickness (CIMP P = .002; IM P = .006), and mitotic index (both P < .001) compared with LM, while IM had higher N stage than CIMP (P = .01) and LM (P = .007). CIMP and IM had a 2-fold higher likelihood of 5-year death from melanoma than LM (CIMP odds ratio [OR], 2.16 [95% CI, 1.18 to 3.96]; IM OR, 2.00 [95% CI, 1.12 to 3.58]) in a multivariable model adjusted for age, sex, log Breslow thickness, ulceration, mitotic index, and N stage. Despite more extensive CpG island hypermethylation in CIMP, CIMP and IM shared similar patterns of differential methylation and gene set enrichment compared with LM. CONCLUSION Melanoma MethylClasses may provide clinical value in predicting 5-year death from melanoma among patients with primary melanoma independent of other clinicopathologic factors.
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Affiliation(s)
- Kathleen Conway
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
- Department of Dermatology, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sharon N. Edmiston
- Department of Dermatology, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Amanda Vondras
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Allison Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David L. Corcoran
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eloise A. Parrish
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Honglin Hao
- Department of Dermatology, University of North Carolina, Chapel Hill, NC
| | - Lan Lin
- Department of Dermatology, University of North Carolina, Chapel Hill, NC
| | - Jessica M Kenney
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gbemisola Ilelaboye
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caroline E. Kostrzewa
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pei Fen Kuan
- Department of Applied Mathematics and Statistics, State University of New York, Stony Brook, NY
| | - Klaus J. Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Cecilia Lezcano
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tim K. Lee
- British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - Eva Hernando
- Grossman School of Medicine, New York University, New York, NY
| | - Paul B. Googe
- Department of Dermatology, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - David W. Ollila
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Stergios Moschos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Medicine, Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ivan Gorlov
- Department of Medicine, Baylor Medical Center, Houston, TX
| | | | | | - Anne E. Cust
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, Australia
- Melanoma Institute of Australia, The University of Sydney, New South Wales, Australia
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - James S. Wilmott
- Melanoma Institute of Australia, The University of Sydney, New South Wales, Australia
| | - Richard A. Scolyer
- Melanoma Institute of Australia, The University of Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Graham J. Mann
- Melanoma Institute of Australia, The University of Sydney, New South Wales, Australia
- John Curtin School of Medical Research, Australian National University, ACT 2601, Australia
| | - Ismael A. Vergara
- Melanoma Institute of Australia, The University of Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Judy R. Rees
- Department of Epidemiology, Dartmouth Medical School, Lebanon NH
| | - Shaofeng Yan
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon NH
| | - Eduardo Nagore
- Instituto Valenciano de Oncologia, Valencia, Spain
- Universidad Católica de Valencia San Vicente Mártir, Valencia, Spain
| | | | | | - Iman Osman
- Grossman School of Medicine, New York University, New York, NY
| | - Jeffrey E. Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yvonne Saenger
- Columbia University Medical School, New York, NY
- Albert Einstein School of Medicine, New York, NY
| | - Paul Bogner
- Departments of Pathology and Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Cheryl L. Thompson
- Case Western Reserve University, Cleveland, OH
- Penn State University, Hershey, PA
| | | | - Sheri L. Holmen
- Department of Surgery, University of Utah Health Sciences Center and Huntsman Cancer Institute, Salt Lake City, UT
| | | | - Elise Brunsgaard
- Department of Dermatology, Rush University Medical Center, Chicago, Il
| | | | - Li Luo
- Department of Internal Medicine and the UNM Comprehensive Cancer Center, Albuquerque, NM
| | - Tawny Boyce
- Department of Internal Medicine and the UNM Comprehensive Cancer Center, Albuquerque, NM
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Colin B. Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marianne Berwick
- Department of Internal Medicine and the UNM Comprehensive Cancer Center, Albuquerque, NM
| | - Nancy E. Thomas
- Department of Dermatology, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
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9
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Kim JH, Hong J, Lee JA, Jung M, Choi E, Cho NY, Kang GH, Kim S. Immune microenvironmental heterogeneity according to tumor DNA methylation phenotypes in microsatellite instability-high colorectal cancers. Cancer Immunol Immunother 2024; 73:215. [PMID: 39235590 PMCID: PMC11377388 DOI: 10.1007/s00262-024-03805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
The detailed association between tumor DNA methylation, including CpG island methylation, and tumor immunity is poorly understood. CpG island methylator phenotype (CIMP) is observed typically in sporadic colorectal cancers (CRCs) with microsatellite instability-high (MSI-H). Here, we investigated the differential features of the tumor immune microenvironment according to CIMP status in MSI-H CRCs. CIMP-high (CIMP-H) or CIMP-low/negative (CIMP-L/0) status was determined using MethyLight assay in 133 MSI-H CRCs. All MSI-H CRCs were subjected to digital pathology-based quantification of CD3 + /CD8 + /CD4 + /FoxP3 + /CD68 + /CD204 + /CD177 + tumor-infiltrating immune cells using whole-slide immunohistochemistry. Programmed death-ligand 1 (PD-L1) immunohistochemistry was evaluated using the tumor proportion score (TPS) and combined positive score (CPS). Representative cases were analyzed using whole-exome and RNA-sequencing. In 133 MSI-H CRCs, significantly higher densities of CD8 + tumor-infiltrating lymphocytes (TILs) were observed in CIMP-H tumors compared with CIMP-L/0 tumors. PD-L1 TPS and CPS in CIMP-H tumors were higher than in CIMP-L/0 tumors. Next-generation sequencing revealed that, compared with CIMP-L/0 tumors, CIMP-H tumors had higher fractions of CD8 + T cells/cytotoxic lymphocytes, higher cytolytic activity scores, and activated immune-mediated cell killing pathways. In contrast to CIMP-L/0 tumors, most CIMP-H tumors were identified as consensus molecular subtype 1, an immunogenic transcriptomic subtype of CRC. However, there were no differences in tumor mutational burden (TMB) between CIMP-H and CIMP-L/0 tumors in MSI-H CRCs. In conclusion, CIMP-H is associated with abundant cytotoxic CD8 + TILs and PD-L1 overexpression independent of TMB in MSI-H CRCs, suggesting that CIMP-H tumors represent a typical immune-hot subtype and are optimal candidates for immunotherapy in MSI-H tumors.
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Affiliation(s)
- Jung Ho Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
| | - Jiyun Hong
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Ji Ae Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Minsun Jung
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Eunwoo Choi
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Nam-Yun Cho
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
- Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea.
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10
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Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
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Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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11
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Mecca M, Picerno S, Cortellino S. The Killer's Web: Interconnection between Inflammation, Epigenetics and Nutrition in Cancer. Int J Mol Sci 2024; 25:2750. [PMID: 38473997 DOI: 10.3390/ijms25052750] [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: 12/20/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Inflammation is a key contributor to both the initiation and progression of tumors, and it can be triggered by genetic instability within tumors, as well as by lifestyle and dietary factors. The inflammatory response plays a critical role in the genetic and epigenetic reprogramming of tumor cells, as well as in the cells that comprise the tumor microenvironment. Cells in the microenvironment acquire a phenotype that promotes immune evasion, progression, and metastasis. We will review the mechanisms and pathways involved in the interaction between tumors, inflammation, and nutrition, the limitations of current therapies, and discuss potential future therapeutic approaches.
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Affiliation(s)
- Marisabel Mecca
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Simona Picerno
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Salvatore Cortellino
- Laboratory of Preclinical and Translational Research, Responsible Research Hospital, 86100 Campobasso, CB, Italy
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, 80138 Naples, NA, Italy
- S.H.R.O. Italia Foundation ETS, 10060 Candiolo, TO, Italy
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12
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Chen W, Sun J, Mao Y, Tang Y, Wang J, Liu Z. Endogenously Gated DNA Walking Machine for Prescreened MicroRNA Detection in Extracellular Vesicles. Anal Chem 2024; 96:2244-2252. [PMID: 38253329 DOI: 10.1021/acs.analchem.3c05595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Tumor-derived extracellular vesicle (T-EV) microRNAs have been investigated as promising biomarkers in clinical diagnosis as well as disease progression monitoring. However, the expression profiles of microRNA in different tissues vary widely, the precise monitoring of microRNA levels in EVs originating from diseased tissues is susceptible to background interference, thus remains a challenge. Conventional assays require extensive processing, such as EV isolation and even sample lysis, which is both slow and laborious, and the cumbersome pretreatment could spoil the downstream analysis. To address this issue, we developed a generalizable strategy for T-EVs-selective activation and therefore specific amplified microRNA imaging. The conditional signal amplification is established by integrating a traditional DNA walker system with endogenously activated motif to achieve sensitized microRNA imaging in T-EVs. The preorganized endogenous activation with additional sensing criteria narrowed the scope against the complex specimens, and the amplified sensing with reduced off-target signals was supposed to be sensitive to monitor the tiny changes of microRNA expression during the disease course, which holds great potential for accurate diagnosis and prognosis.
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Affiliation(s)
- Weiming Chen
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Jiale Sun
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Yuqing Mao
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Yuhao Tang
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Jing Wang
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Zhihong Liu
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
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13
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Park PH, Keith K, Calendo G, Jelinek J, Madzo J, Gharaibeh RZ, Ghosh J, Sapienza C, Jobin C, Issa JPJ. Association between gut microbiota and CpG island methylator phenotype in colorectal cancer. Gut Microbes 2024; 16:2363012. [PMID: 38860458 PMCID: PMC11174071 DOI: 10.1080/19490976.2024.2363012] [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: 01/23/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
The intestinal microbiota is an important environmental factor implicated in CRC development. Intriguingly, modulation of DNA methylation by gut microbiota has been reported in preclinical models, although the relationship between tumor-infiltrating bacteria and CIMP status is currently unexplored. In this study, we investigated tumor-associated bacteria in 203 CRC tumor cases and validated the findings using The Cancer Genome Atlas datasets. We assessed the abundance of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae through qPCR analysis and observed enrichment of all four bacterial species in CRC samples. Notably, except for E. coli, all exhibited significant enrichment in cases of CIMP. This enrichment was primarily driven by a subset of cases distinguished by high levels of these bacteria, which we labeled as "Superhigh". The bacterial Superhigh status showed a significant association with CIMP (odds ratio 3.1, p-value = 0.013) and with MLH1 methylation (odds ratio 4.2, p-value = 0.0025). In TCGA CRC cases (393 tumor and 45 adj. normal), bacterial taxa information was extracted from non-human whole exome sequencing reads, and the bacterial Superhigh status was similarly associated with CIMP (odds ratio 2.9, p < 0.001) and MLH1 methylation (odds ratio 3.5, p < 0.001). Finally, 16S ribosomal RNA gene sequencing revealed high enrichment of Bergeyella spp. C. concisus, and F. canifelinum in CIMP-Positive tumor cases. Our findings highlight that specific bacterial taxa may influence DNA methylation, particularly in CpG islands, and contribute to the development and progression of CIMP in colorectal cancer.
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Affiliation(s)
- Pyoung Hwa Park
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Gennaro Calendo
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
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14
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Lee SW, Frankston CM, Kim J. Epigenome editing in cancer: Advances and challenges for potential therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:191-230. [PMID: 38359969 DOI: 10.1016/bs.ircmb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cancers are diseases caused by genetic and non-genetic environmental factors. Epigenetic alterations, some attributed to non-genetic factors, can lead to cancer development. Epigenetic changes can occur in tumor suppressors or oncogenes, or they may contribute to global cell state changes, making cells abnormal. Recent advances in gene editing technology show potential for cancer treatment. Herein, we will discuss our current knowledge of epigenetic alterations occurring in cancer and epigenetic editing technologies that can be applied to developing therapeutic options.
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Affiliation(s)
- Seung-Won Lee
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Connor Mitchell Frankston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Biomedical Engineering Graduate Program, Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Jungsun Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States; Cancer Biology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States.
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15
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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