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Miranda Furtado CL, Hansen M, Kogure GS, Ribeiro VB, Taylor N, Racy Soares M, Ferriani RA, Aston KI, Jenkins T, dos Reis RM. Resistance and aerobic training increases genome-wide DNA methylation in women with polycystic ovary syndrome. Epigenetics 2024; 19:2305082. [PMID: 38245873 PMCID: PMC10802204 DOI: 10.1080/15592294.2024.2305082] [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: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Physical activity is a first-line treatment for polycystic ovary syndrome (PCOS). Resistance or aerobic exercise improves metabolic complications, reproductive outcomes, and quality of life in PCOS. DNA methylation reprogramming during exercise may be the major modifier behind these changes. We sought to evaluate genome-wide DNA methylation changes after supervised resistance and aerobic exercise in women with PCOS. Exercises were performed in 56 women with PCOS (resistance, n = 30; aerobic, n = 26), for 16 weeks (wks), three times per week, in 50-minute to one-hour sessions. Anthropometric indices and hormonal and metabolic parameters were measured before and after training. Genome-wide leukocyte DNA methylation was analysed by Infinium Human MethylationEPIC 850K BeadChip microarrays (Illumina). Both resistance and aerobic exercise improved anthropometric indices, metabolic dysfunction, and hyperandrogenism in PCOS after the training programme, but no differences were observed between the two exercises. Resistance and aerobic exercise increased genome-wide DNA methylation, although resistance changed every category in the CpG island context (islands, shores, shelve, and open sea), whereas aerobic exercise altered CpG shores and the open sea. Using a stringent FDR (>40), 6 significantly differentially methylated regions (DMRs) were observed in the resistance exercise cohort and 14 DRMs in the aerobic cohort, all of which were hypermethylated. The increase in genome-wide DNA methylation may be related to the metabolic and hormonal changes observed in PCOS after resistance and aerobic exercise. Since the mammalian genome is hypermethylated globally to prevent genomic instability and ageing, resistance and aerobic exercise may promote health and longevity through environmentally induced epigenetic changes.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Experimental Biology Center, Graduate Program in Medical Sciences, University of Fortaleza, Fortaleza, Ceará, Brazil
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Megan Hansen
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Gislaine Satyko Kogure
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Victor Barbosa Ribeiro
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Nathanael Taylor
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Murilo Racy Soares
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Kenneth Ivan Aston
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Timothy Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rosana Maria dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
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Lewis SA, Ruttenberg A, Iyiyol T, Kong N, Jin SC, Kruer MC. Potential clinical applications of advanced genomic analysis in cerebral palsy. EBioMedicine 2024; 106:105229. [PMID: 38970919 PMCID: PMC11282942 DOI: 10.1016/j.ebiom.2024.105229] [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: 02/15/2024] [Revised: 04/26/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Cerebral palsy (CP) has historically been attributed to acquired insults, but emerging research suggests that genetic variations are also important causes of CP. While microarray and whole-exome sequencing based studies have been the primary methods for establishing new CP-gene relationships and providing a genetic etiology for individual patients, the cause of their condition remains unknown for many patients with CP. Recent advancements in genomic technologies offer additional opportunities to uncover variations in human genomes, transcriptomes, and epigenomes that have previously escaped detection. In this review, we outline the use of these state-of-the-art technologies to address the molecular diagnostic challenges experienced by individuals with CP. We also explore the importance of identifying a molecular etiology whenever possible, given the potential for genomic medicine to provide opportunities to treat patients with CP in new and more precise ways.
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Affiliation(s)
- Sara A Lewis
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States
| | - Andrew Ruttenberg
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tuğçe Iyiyol
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Nahyun Kong
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States; Programs in Neuroscience and Molecular & Cellular Biology, School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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3
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Xiao C, Peng G, Conneely KN, Zhao H, Felger JC, Wommack EC, Higgins KA, Shin DM, Saba NF, Bruner DW, Miller AH. DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism. Mol Psychiatry 2024:10.1038/s41380-024-02652-z. [PMID: 38977918 DOI: 10.1038/s41380-024-02652-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 06/19/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Cancer patients are commonly affected by fatigue. Herein, we sought to examine epigenetic modifications (i.e., DNA methylation) related to fatigue in peripheral blood among patients during and after treatment for head and neck cancer (HNC). Further, we determined whether these modifications were associated with gene expression and inflammatory protein markers, which we have previously linked to fatigue in HNC. This prospective, longitudinal study enrolled eligible patients with data collected at pre-radiotherapy, end of radiotherapy, and six months and one-year post-radiotherapy. Fatigue data were reported by patients using the Multidimensional Fatigue Inventory (MFI)-20. DNA methylation (Illumina MethylationEPIC) and gene expression (Applied Biosystems Clariom S) arrays and assays for seven inflammatory markers (R&D Systems multiplex) were performed. Mixed models and enrichment analyses were applied to establish the associations. A total of 386 methylation loci were associated with fatigue among 145 patients (False Discovery Rate [FDR] < 0.05). Enrichment analyses showed the involvement of genes related to immune and inflammatory responses, insulin and lipid metabolism, neuropsychological disorders, and tumors. We further identified 16 methylation-gene expression pairs (FDR < 0.05), which were linked to immune and inflammatory responses and lipid metabolism. Ninety-one percent (351) of the 386 methylation loci were also significantly associated with inflammatory markers (e.g., interleukin 6, c-reactive protein; FDR < 0.05), which further mediated the association between methylation and fatigue (FDR < 0.05). These data suggest that epigenetic modifications associated with inflammation and immunometabolism, in conjunction with relevant gene expression and protein markers, are potential targets for treating fatigue in HNC patients. The findings also merit future prospective studies in other cancer populations as well as interventional investigations.
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Affiliation(s)
- Canhua Xiao
- Emory University School of Nursing, Atlanta, GA, USA.
| | - Gang Peng
- Indianan University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN, USA
| | - Karen N Conneely
- Emory University School of Medicine, Department of Human Genetics, Atlanta, GA, USA
| | - Hongyu Zhao
- Yale University School of Medicine, Department of Genetics, New Haven, CT, USA
| | - Jennifer C Felger
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Evanthia C Wommack
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Kristin A Higgins
- Emory University School of Medicine, Department of Radiation Oncology, Atlanta, GA, USA
| | - Dong M Shin
- Emory University School of Medicine, Department of Hematology and Medical Oncology, Atlanta, GA, USA
| | - Nabil F Saba
- Emory University School of Medicine, Department of Hematology and Medical Oncology, Atlanta, GA, USA
| | | | - Andrew H Miller
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
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4
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Zhao N, Lai C, Wang Y, Dai S, Gu H. Understanding the role of DNA methylation in colorectal cancer: Mechanisms, detection, and clinical significance. Biochim Biophys Acta Rev Cancer 2024; 1879:189096. [PMID: 38499079 DOI: 10.1016/j.bbcan.2024.189096] [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: 10/05/2023] [Revised: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Colorectal cancer (CRC) is one of the deadliest malignancies worldwide, ranking third in incidence and second in mortality. Remarkably, early stage localized CRC has a 5-year survival rate of over 90%; in stark contrast, the corresponding 5-year survival rate for metastatic CRC (mCRC) is only 14%. Compounding this problem is the staggering lack of effective therapeutic strategies. Beyond genetic mutations, which have been identified as critical instigators of CRC initiation and progression, the importance of epigenetic modifications, particularly DNA methylation (DNAm), cannot be underestimated, given that DNAm can be used for diagnosis, treatment monitoring and prognostic evaluation. This review addresses the intricate mechanisms governing aberrant DNAm in CRC and its profound impact on critical oncogenic pathways. In addition, a comprehensive review of the various techniques used to detect DNAm alterations in CRC is provided, along with an exploration of the clinical utility of cancer-specific DNAm alterations.
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Affiliation(s)
- Ningning Zhao
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuanxi Lai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou 310000, China
| | - Sheng Dai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China.
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5
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Ajithkumar P, Vasantharajan SS, Pattison S, McCall JL, Rodger EJ, Chatterjee A. Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis. Int J Mol Sci 2024; 25:874. [PMID: 38255946 PMCID: PMC10815915 DOI: 10.3390/ijms25020874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Metastatic progression is a complex, multistep process and the leading cause of cancer mortality. There is growing evidence that emphasises the significance of epigenetic modification, specifically DNA methylation and histone modifications, in influencing colorectal (CRC) metastasis. Epigenetic modifications influence the expression of genes involved in various cellular processes, including the pathways associated with metastasis. These modifications could contribute to metastatic progression by enhancing oncogenes and silencing tumour suppressor genes. Moreover, specific epigenetic alterations enable cancer cells to acquire invasive and metastatic characteristics by altering cell adhesion, migration, and invasion-related pathways. Exploring the involvement of DNA methylation and histone modification is crucial for identifying biomarkers that impact cancer prediction for metastasis in CRC. This review provides a summary of the potential epigenetic biomarkers associated with metastasis in CRC, particularly DNA methylation and histone modifications, and examines the pathways associated with these biomarkers.
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Affiliation(s)
- Priyadarshana Ajithkumar
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sai Shyam Vasantharajan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sharon Pattison
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - John L. McCall
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
- School of Health Sciences and Technology, UPES University, Dehradun 248007, India
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6
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Donson AM, Bertrand KC, Riemondy KA, Gao D, Zhuang Y, Sanford B, Norris GA, Chapman RJ, Fu R, Willard N, Griesinger AM, Ribeiro de Sousa G, Amani V, Grimaldo E, Hankinson TC, Booker F, Sill M, Grundy RG, Pajtler KW, Ellison DW, Foreman NK, Ritzmann TA. Significant increase of high-risk chromosome 1q gain and 6q loss at recurrence in posterior fossa group A ependymoma: A multicenter study. Neuro Oncol 2023; 25:1854-1867. [PMID: 37246777 PMCID: PMC10547517 DOI: 10.1093/neuonc/noad096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Ependymoma (EPN) posterior fossa group A (PFA) has the highest rate of recurrence and the worst prognosis of all EPN molecular groups. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent PFA remains largely unknown; however, the increasing use of surgery at first recurrence has now provided access to clinical samples to facilitate a better understanding of this. METHODS In this large longitudinal international multicenter study, we examined matched samples of primary and recurrent disease from PFA patients to investigate the biology of recurrence. RESULTS DNA methylome derived copy number variants (CNVs) revealed large-scale chromosome gains and losses at recurrence in PFA. CNV changes were dominated by chromosome 1q gain and/or 6q loss, both previously identified as high-risk factors in PFA, which were present in 23% at presentation but increased to 61% at first recurrence. Multivariate survival analyses of this cohort showed that cases with 1q gain or 6q loss at first recurrence were significantly more likely to recur again. Predisposition to 1q+/6q- CNV changes at recurrence correlated with hypomethylation of heterochromatin-associated DNA at presentation. Cellular and molecular analyses revealed that 1q+/6q- PFA had significantly higher proportions of proliferative neuroepithelial undifferentiated progenitors and decreased differentiated neoplastic subpopulations. CONCLUSIONS This study provides clinically and preclinically actionable insights into the biology of PFA recurrence. The hypomethylation predisposition signature in PFA is a potential risk-classifier for trial stratification. We show that the cellular heterogeneity of PFAs evolves largely because of genetic evolution of neoplastic cells.
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Affiliation(s)
- Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | | | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dexiang Gao
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- University of Colorado Cancer Center Biostatistics and Bioinformatics Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yonghua Zhuang
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- University of Colorado Cancer Center Biostatistics and Bioinformatics Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bridget Sanford
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregory A Norris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Rebecca J Chapman
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Rui Fu
- Computational Biology, New York Genome Center, New York, New York, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, Colorado, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Graziella Ribeiro de Sousa
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Vladimir Amani
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Enrique Grimaldo
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Todd C Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, Colorado, USA
| | - Ffyona Booker
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Martin Sill
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Richard G Grundy
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Timothy A Ritzmann
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
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Hansford JR, Eisenstat DD. No safe harbors for recurrent posterior fossa group A ependymoma: A time for change in risk assignment? Neuro Oncol 2023; 25:1868-1870. [PMID: 37487035 PMCID: PMC10547506 DOI: 10.1093/neuonc/noad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Indexed: 07/26/2023] Open
Affiliation(s)
- Jordan R Hansford
- Michael Rice Cancer Centre, Women’s and Children’s Hospital, North Adelaide, South Australia, Australia
- Precision Cancer Medicine, South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia Immunogenomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - David D Eisenstat
- Children’s Cancer Centre, Royal Children’s Hospital, Parkville, Victoria, Australia
- Stem Cell Biology, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
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8
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Chao CR, Slezak J, Siegmund K, Cannavale K, Shu Y, Chien GW, Chen X, Shi F, Song N, Van Den Eeden SK, Huang J. Genome-wide methylation profiling of diagnostic tumor specimens identified DNA methylation markers associated with metastasis among men with untreated localized prostate cancer. Cancer Med 2023; 12:18837-18849. [PMID: 37694549 PMCID: PMC10557825 DOI: 10.1002/cam4.6507] [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: 06/16/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND We used a genome-wide discovery approach to identify methylation markers associated with metastasis in men with localized prostate cancer (PCa), as better identification of those at high risk of metastasis can inform treatment decision-making. METHODS We identified men with localized PCa at Kaiser Permanente California (January 1, 1997-December 31, 2006) who did not receive curative treatment and followed them for 10 years to determine metastasis status. Cases were chart review-confirmed metastasis, and controls were matched using density sampling. We extracted DNA from the cancerous areas in the archived diagnostic tissue blocks. We used Illumina's Infinium MethylationEPIC BeadChip for methylation interrogation. We used conditional logistic regression and Bonferroni's correction to identify methylation markers associated with metastasis. In a separate validation cohort (2007), we evaluated the added predictive utility of the methylation score beyond clinical risk score. RESULTS Among 215 cases and 404 controls, 31 CpG sites were significantly associated with metastasis status. Adding the methylation score to the clinical risk score did not meaningfully improve the c-statistic (0.80-0.81) in the validation cohort, though the score itself was statistically significant (p < 0.01). In the validation cohort, both clinical risk score alone and methylation marker score alone are well calibrated for predicted 10-year metastasis risks. Adding the methylation score to the clinical risk score only marginally improved predictive risk calibration. CONCLUSION Our findings do not support the use of these markers to improve clinical risk prediction. The methylation markers identified may inform novel hypothesis in the roles of these genetic regions in metastasis development.
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Affiliation(s)
- Chun R. Chao
- Department of Research and EvaluationKaiser Permanente Southern CaliforniaPasadenaCaliforniaUSA
- Department of Health Systems ScienceKaiser Permanente Bernard J Tyson School of MedicinePasadenaCaliforniaUSA
| | - Jeff Slezak
- Department of Research and EvaluationKaiser Permanente Southern CaliforniaPasadenaCaliforniaUSA
| | - Kimberly Siegmund
- Department of Population and Public Health Sciences, USC Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Kimberly Cannavale
- Department of Research and EvaluationKaiser Permanente Southern CaliforniaPasadenaCaliforniaUSA
| | - Yu‐Hsiang Shu
- Department of Research and EvaluationKaiser Permanente Southern CaliforniaPasadenaCaliforniaUSA
| | - Gary W. Chien
- Department of Urology, Los Angeles Medical CenterKaiser Permanente Southern CaliforniaLos AngelesCaliforniaUSA
| | - Xu‐Feng Chen
- Department of Pathology, School of MedicineDuke UniversityDurhamNorth CarolinaUSA
| | - Feng Shi
- Department of Pathology, Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Nan Song
- Department of Urology Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | | | - Jiaoti Huang
- Department of Pathology, School of MedicineDuke UniversityDurhamNorth CarolinaUSA
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9
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Sergeeva A, Davydova K, Perenkov A, Vedunova M. Mechanisms of human DNA methylation, alteration of methylation patterns in physiological processes and oncology. Gene 2023:147487. [PMID: 37211289 DOI: 10.1016/j.gene.2023.147487] [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: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
DNA methylation is one of the epigenetic modifications of the genome, the essence of which is the attachment of a methyl group to nitrogenous bases. In the eukaryote genome, cytosine is methylated in the vast majority of cases. About 98% of cytosines are methylated as part of CpG dinucleotides. They, in turn, form CpG islands, which are clusters of these dinucleotides. Islands located in the regulatory elements of genes are in particular interest. They are assumed to play an important role in the regulation of gene expression in humans. Besides that, cytosine methylation serves the functions of genomic imprinting, transposon suppression, epigenetic memory maintenance, X- chromosome inactivation, and embryonic development. Of particular interest are the enzymatic processes of methylation and demethylation. The methylation process always depends on the work of enzymatic complexes and is very precisely regulated. The methylation process largely depends on the functioning of three groups of enzymes: writers, readers and erasers. Writers include proteins of the DNMT family, readers are proteins containing the MBD, BTB/POZ or SET- and RING-associated domains and erasers are proteins of the TET family. Whereas demethylation can be performed not only by enzymatic complexes, but also passively during DNA replication. Hence, the maintenance of DNA methylation is important. Changes in methylation patterns are observed during embryonic development, aging, and cancers. In both aging and cancer, massive hypomethylation of the genome with local hypermethylation is observed. In this review, we will review the current understanding of the mechanisms of DNA methylation and demethylation in humans, the structure and distribution of CpG islands, the role of methylation in the regulation of gene expression, embryogenesis, aging, and cancer development.
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Affiliation(s)
- A Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - K Davydova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - A Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - M Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
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10
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Besselink N, Keijer J, Vermeulen C, Boymans S, de Ridder J, van Hoeck A, Cuppen E, Kuijk E. The genome-wide mutational consequences of DNA hypomethylation. Sci Rep 2023; 13:6874. [PMID: 37106015 PMCID: PMC10140063 DOI: 10.1038/s41598-023-33932-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/21/2023] [Indexed: 04/29/2023] Open
Abstract
DNA methylation is important for establishing and maintaining cell identity and for genomic stability. This is achieved by regulating the accessibility of regulatory and transcriptional elements and the compaction of subtelomeric, centromeric, and other inactive genomic regions. Carcinogenesis is accompanied by a global loss in DNA methylation, which facilitates the transformation of cells. Cancer hypomethylation may also cause genomic instability, for example through interference with the protective function of telomeres and centromeres. However, understanding the role(s) of hypomethylation in tumor evolution is incomplete because the precise mutational consequences of global hypomethylation have thus far not been systematically assessed. Here we made genome-wide inventories of all possible genetic variation that accumulates in single cells upon the long-term global hypomethylation by CRISPR interference-mediated conditional knockdown of DNMT1. Depletion of DNMT1 resulted in a genomewide reduction in DNA methylation. The degree of DNA methylation loss was similar to that observed in many cancer types. Hypomethylated cells showed reduced proliferation rates, increased transcription of genes, reactivation of the inactive X-chromosome and abnormal nuclear morphologies. Prolonged hypomethylation was accompanied by increased chromosomal instability. However, there was no increase in mutational burden, enrichment for certain mutational signatures or accumulation of structural variation to the genome. In conclusion, the primary consequence of hypomethylation is genomic instability, which in cancer leads to increased tumor heterogeneity and thereby fuels cancer evolution.
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Affiliation(s)
- Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Janneke Keijer
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carlo Vermeulen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Arne van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
- Regenerative Medicine Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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11
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Mouat JS, Li X, Neier K, Zhu Y, Mordaunt CE, La Merrill MA, Lehmler HJ, Jones MP, Lein PJ, Schmidt RJ, LaSalle JM. Networks of placental DNA methylation correlate with maternal serum PCB concentrations and child neurodevelopment. ENVIRONMENTAL RESEARCH 2023; 220:115227. [PMID: 36608759 PMCID: PMC10518186 DOI: 10.1016/j.envres.2023.115227] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Gestational exposure to polychlorinated biphenyls (PCBs) has been associated with elevated risk for neurodevelopmental disorders. Placental epigenetics may serve as a potential mechanism of risk or marker of altered placental function. Prior studies have associated differential placental DNA methylation with maternal PCB exposure or with increased risk of autism spectrum disorder (ASD). However, sequencing-based placental methylomes have not previously been tested for simultaneous associations with maternal PCB levels and child neurodevelopmental outcomes. OBJECTIVES We aimed to identify placental DNA methylation patterns associated with maternal PCB levels and child neurodevelopmental outcomes in the high-risk ASD MARBLES cohort. METHODS We measured 209 PCB congeners in 104 maternal serum samples collected at delivery. We identified networks of DNA methylation from 147 placenta samples using the Comethyl R package, which performs weighted gene correlation network analysis for whole genome bisulfite sequencing data. We tested placental DNA methylation modules for association with maternal serum PCB levels, child neurodevelopment, and other participant traits. RESULTS PCBs 153 + 168, 170, 180 + 193, and 187 were detected in over 50% of maternal serum samples and were highly correlated with one another. Consistent with previous findings, maternal age was the strongest predictor of serum PCB levels, alongside year of sample collection, pre-pregnancy BMI, and polyunsaturated fatty acid levels. Twenty seven modules of placental DNA methylation were identified, including five which significantly correlated with one or more PCBs, and four which correlated with child neurodevelopment. Two modules associated with maternal PCB levels as well as child neurodevelopment, and mapped to CSMD1 and AUTS2, genes previously implicated in ASD and identified as differentially methylated regions in mouse brain and placenta following gestational PCB exposure. CONCLUSIONS Placental DNA co-methylation modules were associated with maternal PCBs and child neurodevelopment. Methylation of CSMD1 and AUTS2 could be markers of altered placental function and/or ASD risk following maternal PCB exposure.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Xueshu Li
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Kari Neier
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Michele A La Merrill
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Michael P Jones
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Pamela J Lein
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA; Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA; Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA.
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12
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Reale A, Tagliatesta S, Zardo G, Zampieri M. Counteracting aged DNA methylation states to combat ageing and age-related diseases. Mech Ageing Dev 2022; 206:111695. [PMID: 35760211 DOI: 10.1016/j.mad.2022.111695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation (DNAm) overwrites information about multiple extrinsic factors on the genome. Age is one of these factors. Age causes characteristic DNAm changes that are thought to be not only major drivers of normal ageing but also precursors to diseases, cancer being one of these. Although there is still much to learn about the relationship between ageing, age-related diseases and DNAm, we now know how to interpret some of the effects caused by age in the form of changes in methylation marks at specific loci. In fact, these changes form the basis of the so called "epigenetic clocks", which translate the genomic methylation profile into an "epigenetic age". Epigenetic age does not only estimate chronological age but can also predict the risk of chronic diseases and mortality. Epigenetic age is believed to be one of the most accurate metrics of biological age. Initial evidence has recently been gathered pointing to the possibility that the rate of epigenetic ageing can be slowed down or even reversed. In this review, we discuss some of the most relevant advances in this field. Expected outcome is that this approach can provide insights into how to preserve health and reduce the impact of ageing diseases in humans.
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Affiliation(s)
- Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Stefano Tagliatesta
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00161 Rome, Italy.
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
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13
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Osteogenic Commitment of Human Periodontal Ligament Cells Is Predetermined by Methylation, Chromatin Accessibility and Expression of Key Transcription Factors. Cells 2022; 11:cells11071126. [PMID: 35406691 PMCID: PMC8997528 DOI: 10.3390/cells11071126] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Periodontal ligament stem cells (PDLCs) can be used as a valuable source in cell therapies to regenerate bone tissue. However, the potential therapeutic outcomes are unpredictable due to PDLCs’ heterogeneity regarding the capacity for osteoblast differentiation and mineral nodules production. Here, we identify epigenetic (DNA (hydroxy)methylation), chromatin (ATAC-seq) and transcriptional (RNA-seq) differences between PDLCs presenting with low (l) and high (h) osteogenic potential. The primary cell populations were investigated at basal state (cultured in DMEM) and after 10 days of osteogenic stimulation (OM). At a basal state, the expression of transcription factors (TFs) and the presence of gene regulatory regions related to osteogenesis were detected in h-PDLCs in contrast to neuronal differentiation prevalent in l-PDLCs. These differences were also observed under stimulated conditions, with genes and biological processes associated with osteoblast phenotype activated more in h-PDLCs. Importantly, even after the induction, l-PDLCs showed hypermethylation and low expression of genes related to bone development. Furthermore, the analysis of TFs motifs combined with TFs expression suggested the relevance of SP1, SP7 and DLX4 regulation in h-PDLCs, while motifs for SIX and OLIG2 TFs were uniquely enriched in l-PDLCs. Additional analysis including a second l-PDLC population indicated that the high expression of OCT4, SIX3 and PPARG TFs could be predictive of low osteogenic commitment. In summary, several biological processes related to osteoblast commitment were activated in h-PDLCs from the onset, while l-PDLCs showed delay in the activation of the osteoblastic program, restricted by the persistent methylation of gene related to bone development. These processes are pre-determined by distinguishable epigenetic and transcriptional patterns, the recognition of which could help in selection of PDLCs with pre-osteoblastic phenotype.
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14
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Yates J, Boeva V. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. Brief Bioinform 2022; 23:6520307. [PMID: 35134107 PMCID: PMC8921629 DOI: 10.1093/bib/bbab610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.
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Affiliation(s)
- Josephine Yates
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland
| | - Valentina Boeva
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland.,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.,Cochin Institute, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris 75014, France
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15
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Pagotto S, Colorito ML, Nicotra A, Apuzzo T, Tinari N, Protasi F, Stassi G, Visone R, Di Franco S, Veronese A. A perspective analysis: microRNAs, glucose metabolism, and drug resistance in colon cancer stem cells. Cancer Gene Ther 2022; 29:4-9. [PMID: 33526845 DOI: 10.1038/s41417-021-00298-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 01/29/2023]
Affiliation(s)
- Sara Pagotto
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Maria Luisa Colorito
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Annalisa Nicotra
- Cellular and Molecular Pathophysiology Laboratory, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Tiziana Apuzzo
- Cellular and Molecular Pathophysiology Laboratory, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Nicola Tinari
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Feliciano Protasi
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Science, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Giorgio Stassi
- Cellular and Molecular Pathophysiology Laboratory, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Rosa Visone
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Simone Di Franco
- Cellular and Molecular Pathophysiology Laboratory, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy.
| | - Angelo Veronese
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy. .,Department of Neuroscience, Imaging, and Clinical Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.
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16
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Yeoh Y, Low TY, Abu N, Lee PY. Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance. PeerJ 2021; 9:e12338. [PMID: 34733591 PMCID: PMC8544255 DOI: 10.7717/peerj.12338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.
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Affiliation(s)
- Yeelon Yeoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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17
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Turpín-Sevilla MDC, Pérez-Sanz F, García-Solano J, Sebastián-León P, Trujillo-Santos J, Carbonell P, Estrada E, Tuomisto A, Herruzo I, Fennell LJ, Mäkinen MJ, Rodríguez-Braun E, Whitehall VLJ, Conesa A, Conesa-Zamora P. Global Methylome Scores Correlate with Histological Subtypes of Colorectal Carcinoma and Show Different Associations with Common Clinical and Molecular Features. Cancers (Basel) 2021; 13:cancers13205165. [PMID: 34680315 PMCID: PMC8533997 DOI: 10.3390/cancers13205165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The typical methylation patterns associated with cancer are hypermethylation at gene promoters and global genome hypomethylation. Aberrant CpG island hypermethylation at promoter regions and global genome hypomethylation have not been associated with histological colorectal carcinomas (CRC) subsets. Using Illumina's 450 k Infinium Human Methylation beadchip, the methylome of 82 CRCs were analyzed, comprising different histological subtypes: 40 serrated adenocarcinomas (SAC), 32 conventional carcinomas (CC) and 10 CRCs showing histological and molecular features of microsatellite instability (hmMSI-H), and, additionally, 35 normal adjacent mucosae. Scores reflecting the overall methylation at 250 bp, 1 kb and 2 kb from the transcription starting site (TSS) were studied. RESULTS SAC has an intermediate methylation pattern between CC and hmMSI-H for the three genome locations. In addition, the shift from promoter hypermethylation to genomic hypomethylation occurs at a small sequence between 250 bp and 1 Kb from the gene TSS, and an asymmetric distribution of methylation was observed between both sides of the CpG islands (N vs. S shores). CONCLUSION These findings show that different histological subtypes of CRC have a particular global methylation pattern depending on sequence distance to TSS and highlight the so far underestimated importance of CpGs aberrantly hypomethylated in the clinical phenotype of CRCs.
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Affiliation(s)
- María del Carmen Turpín-Sevilla
- Facultad de Medicina, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda, Km 1800, Pozuelo de Alarcón, 28223 Madrid, Spain; (M.d.C.T.-S.); (I.H.)
| | - Fernando Pérez-Sanz
- Biomedical Informatics & Bioinformatics Platform, Institute for Biomedical Research of Murcia (IMIB)/Foundation for Healthcare Training & Research of the Region of Murcia (FFIS), Calle Luis Fontes Pagán 9, 30003 Murcia, Spain;
| | - José García-Solano
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain;
- Facultad de Ciencias de la Salud, Universidad Católica de Murcia (UCAM), Campus Los Jerónimos, 30107 Guadalupe, Spain
- Group of Molecular Pathology and Pharmacogenetics, Institute for Biomedical Research from Murcia (IMIB), HGUSL, 30202 Cartagena, Spain
| | - Patricia Sebastián-León
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain;
| | - Javier Trujillo-Santos
- Department of Internal Medicine, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain;
| | - Pablo Carbonell
- Biochemistry and Clinical Genetic Center, Virgen de la Arrixaca University Hospital, 30100 Murcia, Spain;
| | - Eduardo Estrada
- Department of Social Psychology and Methodology, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - Anne Tuomisto
- Cancer and Translational Medicine Research Unit, Department of Pathology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.T.); (M.J.M.)
| | - Irene Herruzo
- Facultad de Medicina, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda, Km 1800, Pozuelo de Alarcón, 28223 Madrid, Spain; (M.d.C.T.-S.); (I.H.)
| | - Lochlan J. Fennell
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (L.J.F.); (V.L.J.W.)
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4072, Australia
| | - Markus J. Mäkinen
- Cancer and Translational Medicine Research Unit, Department of Pathology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.T.); (M.J.M.)
| | - Edith Rodríguez-Braun
- Clinical Oncology Department, Santa Lucía General University Hospital (HGUSL). C/Mezquita s/n, 30202 Cartagena, Spain;
| | - Vicki L. J. Whitehall
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (L.J.F.); (V.L.J.W.)
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4072, Australia
| | - Ana Conesa
- Microbiology and Cell Sciences Department, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, FL 32611, USA;
| | - Pablo Conesa-Zamora
- Facultad de Ciencias de la Salud, Universidad Católica de Murcia (UCAM), Campus Los Jerónimos, 30107 Guadalupe, Spain
- Group of Molecular Pathology and Pharmacogenetics, Institute for Biomedical Research from Murcia (IMIB), HGUSL, 30202 Cartagena, Spain
- Clinical Oncology Department, Santa Lucía General University Hospital (HGUSL). C/Mezquita s/n, 30202 Cartagena, Spain;
- Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain
- Correspondence: ; Tel.: +34-968128600 (ext. 951615)
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18
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Cao L, Chen E, Zhang H, Ba Y, Yan B, Li T, Yang J. Construction of a novel methylation-related prognostic model for colorectal cancer based on microsatellite status. J Cell Biochem 2021; 122:1781-1790. [PMID: 34397105 DOI: 10.1002/jcb.30131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022]
Abstract
The present study aimed to construct a novel methylation-related prognostic model based on microsatellite status that may enhance the prognosis of colorectal cancer (CRC) from methylation and microsatellite status perspective. DNA methylation and mRNA expression data with clinical information were downloaded from The Cancer Genome Atlas (TCGA) data set. The samples were divided into microsatellite stability and microsatellite instability group, and CIBERSORT was used to assess the immune cell infiltration characteristics. After identifying the differentially methylated genes and differentially expression genes using R packages, the methylation-driven genes were further identified. Prognostic genes that were used to establish the methylation-related risk score model were generated by the univariate and multivariate Cox regression model. Finally, we established and evaluated the methylation-related prognostic model for CRC patients. A total of 69 MDGs were obtained and three of these genes (MIOX, TH, DKFZP434K028) were selected to construct the prognostic model. Patients in the low-risk score group had a conspicuously better overall survival than those in the high-risk score group (p < .0001). The area under the receiver operating characteristic curve for this model was 0.689 at 3 years, 0.674 at 4 years, and 0.658 at 5 years. The Wilcoxon test showed that higher risk score was associated with higher T stage (p = .01), N stages (p = .0028), metastasis (p = .013), and advanced pathological stage (p = .0013). However, the more instability of microsatellite status, the lower risk score of CRC patients (p = .0048). Our constructed methylation-related prognostic model based on microsatellite status presents potential significance in assessing recurrence risk stratification, tumor staging, and immunotherapy for CRC patients.
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Affiliation(s)
- Lichao Cao
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Erfei Chen
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Hezi Zhang
- Shenzhen Nuclear Gene Technology Co., Ltd., Shenzhen, China
| | - Ying Ba
- Shenzhen Nuclear Gene Technology Co., Ltd., Shenzhen, China
| | - Bianbian Yan
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Tong Li
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
| | - Jin Yang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, China
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19
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Ren C, Tang X, Lan H. Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer. PeerJ 2021; 9:e11377. [PMID: 33987034 PMCID: PMC8103922 DOI: 10.7717/peerj.11377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 11/20/2022] Open
Abstract
Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using STITCH. Higher infiltration rates of CD8 T cells, plasma cells, and monocytes were found in the lower quartile WT1 group and the favorable 6-gene signature group. In conclusion, we demonstrated that WT1 is hypermethylated and up-regulated in the four BC molecular subtypes and a 6-gene signature may predict BC prognosis.
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Affiliation(s)
- Chongyang Ren
- Department of Breast Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaojiang Tang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Haitao Lan
- Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
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20
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Rousselle T, Bardhi E, Maluf DG, Mas VR. Epigenetic modifications and the development of kidney graft fibrosis. Curr Opin Organ Transplant 2021; 26:1-9. [PMID: 33315766 PMCID: PMC8059991 DOI: 10.1097/mot.0000000000000839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW To outline recent discoveries in epigenetic regulatory mechanisms that have potential implications in the development of renal fibrosis following kidney transplantation. RECENT FINDINGS The characterization of renal fibrosis following kidney transplantation has shown TGFβ/Smad signaling to play a major role in the progression to chronic allograft dysfunction. The onset of unregulated proinflammatory pathways are only exacerbated by the decline in regulatory mechanisms lost with progressive patient age and comorbidities such as hypertension and diabetes. However, significant developments in the recognition of epigenetic regulatory markers upstream of aberrant TGFβ-signaling has significant clinical potential to provide therapeutic targets for the treatment of renal fibrosis. In addition, discoveries in extracellular vesicles and the characterization of their cargo has laid new framework for the potential to evaluate patient outcomes independent of invasive biopsies. SUMMARY The current review summarizes the main findings in epigenetic machinery specific to the development of renal fibrosis and highlights therapeutic options that have significant potential to translate into clinical practice.
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Affiliation(s)
- Thomas Rousselle
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
| | - Elissa Bardhi
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
| | - Daniel G. Maluf
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
- Program in Transplantation, School of Medicine, University
of Maryland
| | - Valeria R. Mas
- Division of Transplant, Department of Surgery, School of
Medicine, University of Maryland
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21
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Novel Epigenetic Eight-Gene Signature Predictive of Poor Prognosis and MSI-Like Phenotype in Human Metastatic Colorectal Carcinomas. Cancers (Basel) 2021; 13:cancers13010158. [PMID: 33466447 PMCID: PMC7796477 DOI: 10.3390/cancers13010158] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The global methylation profile of two human metastatic colorectal carcinoma subgroups with significantly different outcomes (primary-resistant versus drug-sensitive tumors) was analyzed and compared with the gene expression and methylation data from The Cancer Genome Atlas COlon ADenocarcinoma (TCGA COAD) metastatic colorectal carcinoma dataset with the aim to identify a prognostic signature of functionally methylated genes. A novel epigenetic eight-gene signature, with hypermethylation of the promoter regions, was identified and validated for its capacity to predict poor outcome, which had a CpG-island methylator phenotype (CIMP)-high status and microsatellite instability (MSI)-like phenotype. Abstract Epigenetics is involved in tumor progression and drug resistance in human colorectal carcinoma (CRC). This study addressed the hypothesis that the DNA methylation profiling may predict the clinical behavior of metastatic CRCs (mCRCs). The global methylation profile of two human mCRC subgroups with significantly different outcome was analyzed and compared with gene expression and methylation data from The Cancer Genome Atlas COlon ADenocarcinoma (TCGA COAD) and the NCBI GENE expression Omnibus repository (GEO) GSE48684 mCRCs datasets to identify a prognostic signature of functionally methylated genes. A novel epigenetic signature of eight hypermethylated genes was characterized that was able to identify mCRCs with poor prognosis, which had a CpG-island methylator phenotype (CIMP)-high and microsatellite instability (MSI)-like phenotype. Interestingly, methylation events were enriched in genes located on the q-arm of chromosomes 13 and 20, two chromosomal regions with gain/loss alterations associated with adenoma-to-carcinoma progression. Finally, the expression of the eight-genes signature and MSI-enriching genes was confirmed in oxaliplatin- and irinotecan-resistant CRC cell lines. These data reveal that the hypermethylation of specific genes may provide prognostic information that is able to identify a subgroup of mCRCs with poor prognosis.
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22
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Riasat K, Bardell D, Goljanek-Whysall K, Clegg PD, Peffers MJ. Epigenetic mechanisms in Tendon Ageing. Br Med Bull 2020; 135:90-107. [PMID: 32827252 PMCID: PMC7585832 DOI: 10.1093/bmb/ldaa023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Tendon is a composite material with a well-ordered hierarchical structure exhibiting viscoelastic properties designed to transfer force. It is recognized that the incidence of tendon injury increases with age, suggesting a deterioration in homeostatic mechanisms or reparative processes. This review summarizes epigenetic mechanisms identified in ageing healthy tendon. SOURCES OF DATA We searched multiple databases to produce a systematic review on the role of epigenetic mechanisms in tendon ageing. AREAS OF AGREEMENT Epigenetic mechanisms are important in predisposing ageing tendon to injury. AREAS OF CONTROVERSY The relative importance of epigenetic mechanisms are unknown in terms of promoting healthy ageing. It is also unknown whether these changes represent protective mechanisms to function or predispose to pathology. GROWING POINT Epigenetic markers in ageing tendon, which are under-researched including genome-wide chromatin accessibility, should be investigated. AREAS TIMELY FOR DEVELOPING RESEARCH Metanalysis through integration of multiple datasets and platforms will enable a holistic understanding of the epigenome in ageing and its relevance to disease.
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Affiliation(s)
- Kiran Riasat
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - David Bardell
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK.,Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE, UK
| | - Katarzyna Goljanek-Whysall
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Peter D Clegg
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Mandy J Peffers
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
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23
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Zhang E, Zhang M, Shi C, Sun L, Shan L, Zhang H, Song Y. An overview of advances in multi-omics analysis in prostate cancer. Life Sci 2020; 260:118376. [PMID: 32898525 DOI: 10.1016/j.lfs.2020.118376] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 02/09/2023]
Abstract
Prostate cancer (PCa) is a deadly disease for men, and studies of all types of omics data are necessary to promote precision medicine. The maturity of sequencing technology, the improvements of computer processing power, and the progress achieved in omics analysis methods have improved research efficiency and saved research costs. The occurrence and development of PCa is due to multisystem and multilevel pathological changes. Although omics research at a single level is important, this approach often has limitations. In contrast, the combined analysis of multiple types of omics data can better analyze PCa changes as a whole, thus ensuring the validity of research results to the greatest extent. This paper introduces the applications of single omics in PCa and then summarizes research progress in the combined analysis of two or more types of omics data, so as to systematically and comprehensively analyze the necessity of combined analysis of multiple omics data in PCa.
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Affiliation(s)
- Enchong Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Mo Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Changlong Shi
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Li Sun
- Department of Breast Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Liping Shan
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Hui Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China.
| | - Yongsheng Song
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China.
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24
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Gao H, He X, Li Q, Wang Y, Tian Y, Chen X, Wang J, Guo Y, Wang W, Li X. Genome-wide DNA methylome analysis reveals methylation subtypes with different clinical outcomes for acute myeloid leukemia patients. Cancer Med 2020; 9:6296-6305. [PMID: 32628355 PMCID: PMC7476826 DOI: 10.1002/cam4.3291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/11/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
Leukemia is the second common blood cancer after lymphoma, and its incidence rate has an increasing trend in recent years. Acute myeloid leukemia (AML) is one of the prevalent forms of leukemia. Although previous studies have investigated the methylation profile for AML patients, the AML methylation subtypes based on the genome‐wide methylome are still unclear. In the present study, we identified three methylation subtypes for AML samples based on the methylation profiles at CGI, CGI shore, CGI shelf, and opensea genomic contexts. Analyzing the molecular characteristics and clinical factors of the three subtypes revealed different methylation patterns and clinical outcomes between them. Further analysis revealed subtype dependent marker genes and their promoter CpG sites with regulatory function. Finally, we found that combining the AML patient age and methylation pattern brought better clinical outcome classification. In conclusion, we identified AML methylation subtypes and their marker genes, these results may help to excavate potential targets for clinical therapy and the development of precision medicine for AML patients.
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Affiliation(s)
- Haiyan Gao
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xin He
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Qiang Li
- Department of Paediatrics, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ying Wang
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yaoyao Tian
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xi Chen
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jinghua Wang
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yan Guo
- Assessment Admittance Section, Heilongjiang Hospital Service Management Evaluation Center, Harbin, China
| | - Wei Wang
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xiaoyun Li
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
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25
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Wan ML, Wang Y, Zeng Z, Deng B, Zhu BS, Cao T, Li YK, Xiao J, Han Q, Wu Q. Colorectal cancer (CRC) as a multifactorial disease and its causal correlations with multiple signaling pathways. Biosci Rep 2020; 40:BSR20200265. [PMID: 32149326 PMCID: PMC7087324 DOI: 10.1042/bsr20200265] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancy and one of the leading causes of cancer-related death among men worldwide. CRC is a multifactor digestive pathology, which is a huge problem faced not only by clinicians but also by researchers. Importantly, a unique feature of CRC is the dysregulation of molecular signaling pathways. To date, a series of reviews have indicated that different signaling pathways are disordered and have potential as therapeutic targets in CRC. Nevertheless, an overview of the function and interaction of multiple signaling pathways in CRC is needed. Therefore, we summarized the pathways, biological functions and important interactions involved in CRC. First, we investigated the involvement of signaling pathways, including Wnt, PI3K/Akt, Hedgehog, ErbB, RHOA, Notch, BMP, Hippo, AMPK, NF-κB, MAPK and JNK. Subsequently, we discussed the biological function of these pathways in pathophysiological aspects of CRC, such as proliferation, apoptosis and metastasis. Finally, we summarized important interactions among these pathways in CRC. We believe that the interaction of these pathways could provide new strategies for the treatment of CRC.
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Affiliation(s)
- Mao-lin Wan
- Department of Hepatobiliary and Pancreatic Surgery, Xianning Central Hospital, the First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437000, P.R. China
| | - Yu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of University of South China, Hengyang, 421001, P.R. China
| | - Zhi Zeng
- Department of Pathology, Xianning Central Hospital, the First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437000, P.R. China
| | - Bo Deng
- Department of Oncology, Xianning Central Hospital, the First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437000, P.R. China
| | - Bi-sheng Zhu
- Department of Oncology, Xianning Central Hospital, the First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437000, P.R. China
| | - Ting Cao
- Department of Digestive Medical, The Affiliated Nanhua Hospital, University of South China, Hengyang, 421002, P.R. China
| | - Yu-kun Li
- Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, Hengyang, Hunan, 421001, P.R. China
| | - Jiao Xiao
- Department of Endocrinology, The Affiliated Nanhua Hospital, University of South China, Hengyang, 421002, P.R. China
| | - Qi Han
- Department of Oncology, Xianning Central Hospital, the First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437000, P.R. China
| | - Qing Wu
- Department of Digestive Medical, The Affiliated Nanhua Hospital, University of South China, Hengyang, 421002, P.R. China
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Borchiellini M, Ummarino S, Di Ruscio A. The Bright and Dark Side of DNA Methylation: A Matter of Balance. Cells 2019; 8:cells8101243. [PMID: 31614870 PMCID: PMC6830319 DOI: 10.3390/cells8101243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/06/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to disease transition. As a result, minimal DNA methylation changes during developmental stages drive severe phenotypes, as observed in germ-line imprinting disorders, while genome-wide alterations occurring in somatic cells are linked to cancer onset and progression. By summarizing the molecular events governing DNA methylation, we focus on the methods that have facilitated mapping and understanding of this epigenetic mark in healthy conditions and diseases. Overall, we review the bright (health-related) and dark (disease-related) side of DNA methylation changes, outlining how bulk and single-cell genomic analyses are moving toward the identification of new molecular targets and driving the development of more specific and less toxic demethylating agents.
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Affiliation(s)
- Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy.
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
| | - Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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