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Ruiz-De La Cruz M, Martínez-Gregorio H, Estela Díaz-Velásquez C, Ambriz-Barrera F, Resendiz-Flores NG, Gitler-Weingarten R, Rojo-Castillo MP, Pradda D, Oliver J, Perdomo S, Gómez-García EM, De La Cruz-Montoya AH, Terrazas LI, Torres-Mejía G, Hernández-Hernández FDLC, Vaca-Paniagua F. Methylation marks in blood DNA reveal breast cancer risk in patients fulfilling hereditary disease criteria. NPJ Precis Oncol 2024; 8:136. [PMID: 38898118 PMCID: PMC11187128 DOI: 10.1038/s41698-024-00611-z] [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: 08/25/2023] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
Less than 15-20% of patients who meet the criteria for hereditary breast and ovarian cancer (HBOC) carry pathogenic coding genetic mutations, implying that other molecular mechanisms may contribute to the increased risk of this condition. DNA methylation in peripheral blood has been suggested as a potential epigenetic marker for the risk of breast cancer (BC). We aimed to discover methylation marks in peripheral blood associated with BC in 231 pre-treatment BC patients meeting HBOC criteria, testing negative for coding pathogenic variants, and 156 healthy controls, through methylation analysis by targeted bisulfite sequencing on 18 tumor suppressor gene promoters (330 CpG sites). We found i) hypermethylation in EPCAM (17 CpG sites; p = 0.017) and RAD51C (27 CpG sites; p = 0.048); ii) hypermethylation in 36 CpG-specific sites (FDR q < 0.05) in the BC patients; iii) four specific CpG sites were associated with a higher risk of BC (FDR q < 0.01, Bonferroni p < 0.001): cg89786999-FANCI (OR = 1.65; 95% CI:1.2-2.2), cg23652916-PALB2 (OR = 2.83; 95% CI:1.7-4.7), cg47630224-MSH2 (OR = 4.17; 95% CI:2.1-8.5), and cg47596828-EPCAM (OR = 1.84; 95% CI:1.5-2.3). Validation of cg47630224-MSH2 methylation in one Australian cohort showed an association with 3-fold increased BC risk (AUC: 0.929; 95% CI: 0.904-0.955). Our findings suggest that four DNA methylation CpG sites may be associated with a higher risk of BC, potentially serving as biomarkers in patients without detectable coding mutations.
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Affiliation(s)
- Miguel Ruiz-De La Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
- Centro de Investigación y de Estudios Avanzados IPN (CINVESTAV). Avenida Instituto Politécnico Nacional #2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Departamento de Infectómica y Patogénesis Molecular, Ciudad de México, Mexico
| | - Héctor Martínez-Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | - Clara Estela Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
| | - Fernando Ambriz-Barrera
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | - Norma Gabriela Resendiz-Flores
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | | | | | - Didier Pradda
- Institute for Health Equity Research, Department of Health Science and Policy and Department of Environmental Medicine and Public Health at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Javier Oliver
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, 29010, Málaga, Spain
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), 150 Cours Albert Thomas, 69372, Lyon, France
| | | | | | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | | | - Fidel de la Cruz Hernández-Hernández
- Centro de Investigación y de Estudios Avanzados IPN (CINVESTAV). Avenida Instituto Politécnico Nacional #2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Departamento de Infectómica y Patogénesis Molecular, Ciudad de México, Mexico.
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico.
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico.
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Immunoprofiles and DNA Methylation of Inflammatory Marker Genes in Ulcerative Colitis-Associated Colorectal Tumorigenesis. Biomolecules 2021; 11:biom11101440. [PMID: 34680073 PMCID: PMC8533626 DOI: 10.3390/biom11101440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Immunological and epigenetic changes are interconnected and contribute to tumorigenesis. We determined the immunoprofiles and promoter methylation of inflammation-related genes for colitis-associated colorectal carcinomas (CA-CRC). The results were compared with Lynch syndrome (LS)-associated colorectal tumors, which are characterized by an active immune environment through inherited mismatch repair defects. CA-CRCs (n = 31) were immunohistochemically evaluated for immune cell scores (ICSs) and PDCD1 and CD274 expression. Seven inflammation-associated genes (CD274, NTSR1, PPARG, PTGS2, PYCARD, SOCS1, and SOCS2), the repair gene MGMT, and eight standard marker genes for the CpG Island Methylator Phenotype (CIMP) were investigated for promoter methylation in CA-CRCs, LS tumors (n = 29), and paired normal mucosae by multiplex ligation-dependent probe amplification. All but one CA-CRCs were microsatellite-stable and all LS tumors were microsatellite-unstable. Most CA-CRCs had a high ICS (55%) and a positive CD274 expression in immune cells (52%). NTSR1 revealed frequent tumor-specific hypermethylation in CA-CRC and LS. When compared to LS mucosae, normal mucosae from patients with CA-CRC showed significantly higher methylation of NTSR1 and most CIMP markers. In conclusion, CA-CRCs share a frequent ICShigh/CD274pos expression pattern with LS tumors. Elevated methylation in normal mucosa may indicate field cancerization as a feature of CA-CRC-associated tumorigenesis.
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Rajamäki K, Taira A, Katainen R, Välimäki N, Kuosmanen A, Plaketti RM, Seppälä TT, Ahtiainen M, Wirta EV, Vartiainen E, Sulo P, Ravantti J, Lehtipuro S, Granberg KJ, Nykter M, Tanskanen T, Ristimäki A, Koskensalo S, Renkonen-Sinisalo L, Lepistö A, Böhm J, Taipale J, Mecklin JP, Aavikko M, Palin K, Aaltonen LA. Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease-Associated Colorectal Cancer. Gastroenterology 2021; 161:592-607. [PMID: 33930428 DOI: 10.1053/j.gastro.2021.04.042] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. METHODS Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. RESULTS Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNT-induced epithelial-mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4α binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 5'untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. CONCLUSIONS Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.
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Affiliation(s)
- Kristiina Rajamäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.
| | - Aurora Taira
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Riku Katainen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anna Kuosmanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Roosa-Maria Plaketti
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Toni T Seppälä
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Surgery, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland; Department of Surgical Oncology, Johns Hopkins University, Baltimore, Maryland
| | - Maarit Ahtiainen
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | - Erkki-Ville Wirta
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Emilia Vartiainen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Päivi Sulo
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Janne Ravantti
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Suvi Lehtipuro
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tomas Tanskanen
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Selja Koskensalo
- Department of Gastrointestinal Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Gastrointestinal Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Anna Lepistö
- Department of Gastrointestinal Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jukka-Pekka Mecklin
- Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland; Department of Education and Research, Central Finland Central Hospital, Jyväskylä, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.
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Liu C, Yuan ZY, Yuan H, Wu KX, Cao B, Ren KY, Cui MJ, Liu JH, Chen HX, Pang YW. Status of Gene Methylation and Polymorphism in Different Courses of Ulcerative Colitis and Their Comparison with Sporadic Colorectal Cancer. Inflamm Bowel Dis 2021; 27:522-529. [PMID: 32793962 DOI: 10.1093/ibd/izaa203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Indexed: 12/09/2022]
Abstract
BACKGROUND The objective of this study is to explore the common genetic and epigenetic mechanism of ulcerative colitis (UC) and sporadic colorectal cancer (SCRC) by observing genes methylation level and single nucleotide polymorphisms (SNPs) of different disease courses in UC and SCRC. METHODS Two hundred subjects were enrolled, including 40 in the healthy control (HC) group, 50 in the short disease course UC group (SUC), 52 in the long disease course UC group (LUC), and 58 in the SCRC group. Methylation-specific polymerase chain reaction was used to detect the methylation of MINT1 and cyclooxygenase 2 (COX-2) gene. Single nucleotide polymorphisms of interleukin (IL)-23R rs10889677 and IL-1β rs1143627 were detected by Sanger sequencing. RESULTS Compared with HCs (32.5%), methylation level of MINT1 was significantly increased in SCRC (67.2%; P = 0.001) and was a risk factor for CRC (odds ratio, [OR] 4.26). The methylation ratios of COX-2 were 95.0%, 58.0%, 23.1%, and 24.1% in HC, SUC, LUC, and SCRC, respectively, which were negatively correlated with the disease course of UC (r = -0.290). Hypermethylation of COX-2 was a protective factor for SUC (OR, 0.11), LUC (OR, 0.02), and SCRC (OR, 0.03; P < 0.05). Compared with HCs, rs10889677 allele A was a risk factor for SUC and LUC, and rs1143627 allele T was a protective factor for SUC and LUC. Genotype TT was a protective factor for SUC. CONCLUSION The hypomethylation of COX-2 gene was a common risk factor and epigenetic modification for UC and SCRC, which might be one of the mechanisms through which UC patients were susceptible to CRC. The hypermethylation of MINT1 was a risk factor for SCRC but not for UC; alleles of IL-23Rrs10889677 and IL-1βrs1143627 were related to UC but not to SCRC.
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Affiliation(s)
- Chen Liu
- Departments of School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Zi-Ying Yuan
- Department of Gastroenterology, Peking University Third Hospital, Haidian District, Beijing, China
| | - Hao Yuan
- Department of Gastroenterology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ke-Xiang Wu
- Department of Electrophysiology, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Bin Cao
- Department of Gastroenterology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ke-Yu Ren
- Department of Gastroenterology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ming-Juan Cui
- Department of Gastroenterology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jun-Heng Liu
- Department of Gastroenterology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Hai-Xing Chen
- Departments of School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Yao-Wei Pang
- Departments of School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
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Rosa I, Silva P, da Mata S, Magro F, Carneiro F, Peixoto A, Silva M, Sousa HT, Roseira J, Parra J, Barosa R, Vieira A, Brito MJ, Lago P, Coelho A, Moleiro J, Pereira da Silva J, Fonseca R, Albuquerque C, Dias Pereira A. Methylation patterns in dysplasia in inflammatory bowel disease patients. Scand J Gastroenterol 2020; 55:646-655. [PMID: 32456486 DOI: 10.1080/00365521.2020.1766552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background and aims: Inflammatory Bowel Disease (IBD) with colonic involvement increases colorectal cancer risk. However, the distinction between IBD related and sporadic dysplasia in IBD patients is difficult. Some data favors the importance of abnormal DNA methylation in IBD-related carcinogenesis. We aimed to define methylation patterns in patients with colonic cancer or dysplasia diagnosis following an IBD diagnosis.Methods: Multicentric cross-sectional study-91 samples from colonic mucosa with/without dysplasia from 9 patients with IBD-related dysplasia/cancer and 26 patients with IBD and sporadic dysplasia/cancer were included. Methylation patterns of CpG islands in the promoter regions of 67 genes were studied by Methylation-specific Multiplex Ligation-dependent Probe Amplification.Results: Mean age at IBD diagnosis: 42 ± 16 years;at dysplasia diagnosis: 56 ± 14 years. Twenty-ninepatients had ulcerative colitis. Twenty-five patients had at least 1 lesion endoscopically described as adenoma-like, 4 at least 1 non-adenoma like, 3 had cancer and 3 had dysplasia in flat mucosa. No patient had both adenoma-like and non-adenoma-like lesions. Patients with an IBD-related lesion were significantly younger at IBD diagnosis (p = .003) and at dysplasia/cancer diagnosis (p = .039). Promoter methylation of IGF2, RARB, ESR1, CHFR, CDH13, WT1, GATA5, WIF1genes was significantly associated to dysplasia/cancer; methylation of MSH6, TIMP3 was significantly associated to IBD-related dysplasia/cancer. Promoter methylation of MSH6, MSH3, RUNX3, CRABP1, TP73, RARB, CDH13, PAX5, WT1, THBS1, TP53, SFRP1, WIF1, APAF1, BCL2 genes was significantly associated to active IBD.Conclusions: Methylation analysis, namely of MSH6, may contribute to the classification of dysplastic lesions in IBD- to be further tested in prospective studies.
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Affiliation(s)
- Isadora Rosa
- Gastroenterology Department, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
| | - Patrícia Silva
- Molecular Pathobiology Investigation Unit, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
| | - Sara da Mata
- Pathology Department, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
| | - Fernando Magro
- Gastroenterology Department, Centro Hospitalar de São João, EPE, Porto, Portugal
| | - Fátima Carneiro
- Pathology Department, Centro Hospitalar de São João, EPE, Porto, Portugal
| | - Armando Peixoto
- Gastroenterology Department, Centro Hospitalar de São João, EPE, Porto, Portugal
| | - Marco Silva
- Gastroenterology Department, Centro Hospitalar de São João, EPE, Porto, Portugal
| | - Helena T Sousa
- Gastroenterology Department, Centro Hospitalar Universitário do Algarve, EPE, Unidade de Portimão, Portimão, Portugal.,Algarve Biomedical Center, Campus Gambelas - Universidade do Algarve, Faro, Portugal
| | - Joana Roseira
- Gastroenterology Department, Centro Hospitalar Universitário do Algarve, EPE, Unidade de Portimão, Portimão, Portugal.,Algarve Biomedical Center, Campus Gambelas - Universidade do Algarve, Faro, Portugal
| | - José Parra
- Pathology Department, Centro Hospitalar Universitário do Algarve, EPE, Unidade de Portimão, Portimão, Portugal
| | - Rita Barosa
- Gastroenterology Department, Hospital Garcia de Orta, EPE, Almada, Portugal
| | - Ana Vieira
- Gastroenterology Department, Hospital Garcia de Orta, EPE, Almada, Portugal
| | - Maria José Brito
- Pathology Department, Hospital Garcia de Orta, EPE, Almada, Portugal
| | - Paula Lago
- Gastroenterology Department, Centro Hospitalar do Porto, EPE - Hospital de Santo António, Porto, Portugal
| | - André Coelho
- Portuguese Inflammatory Bowel Diseases Study Group, Porto, Portugal
| | - Joana Moleiro
- Gastroenterology Department, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
| | - João Pereira da Silva
- Gastroenterology Department, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
| | - Ricardo Fonseca
- Pathology Department, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
| | - Cristina Albuquerque
- Molecular Pathobiology Investigation Unit, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
| | - A Dias Pereira
- Gastroenterology Department, Instituto Português de Oncologia de Lisboa, Francisco Gentil, EPE, Lisboa, Portugal
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- Portuguese Inflammatory Bowel Diseases Study Group, Porto, Portugal
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Burke KE, Nayor J, Campbell EJ, Ananthakrishnan AN, Khalili H, Richter JM. Interval Colorectal Cancer in Inflammatory Bowel Disease: The Role of Guideline Adherence. Dig Dis Sci 2020; 65:111-118. [PMID: 31367882 PMCID: PMC6946853 DOI: 10.1007/s10620-019-05754-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/19/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Factors associated with interval colorectal cancer (CRC) development in the inflammatory bowel disease (IBD) population remain unclear. AIMS Among a cohort of patients with interval CRC, we aimed to evaluate IBD characteristics, colonoscopy quality indicators, and surveillance guideline adherence. METHODS We performed a retrospective review of IBD- and non-IBD-associated interval CRCs diagnosed between January 2007 and December 2014 within a large US healthcare system. We evaluated risk factors for CRC among patients with IBD. We assessed adherence to surveillance guidelines according to the American Society for Gastrointestinal Endoscopy (IBD surveillance) and the US Multi-Society Task Force on Colorectal Cancer (polyp surveillance). We compared colonoscopy quality measures between patients with and without IBD. RESULTS Among 5345 cases of colonic adenocarcinoma, we detected 15 IBD-associated cases of interval CRC and 230 non-IBD-associated cases of interval CRC. Compared to patients without IBD, IBD patients were younger (54.5 vs. 70.4 years; p < 0.0001) and experienced a shorter interval between index colonoscopy and CRC diagnosis (20.7 vs. 35.1 months; p = 0.0009). Fifty three percent (8/15) of interval CRCs in IBD patients were detected within surveillance guidelines. All IBD patients with interval CRC detected after guideline surveillance interval had high-risk features, including active inflammation, previous low-grade or indefinite dysplasia, multiple pseudopolyps on index colonoscopy, or a first-degree relative with CRC. There were no differences in colonoscopy quality measures between patients with and without IBD. CONCLUSIONS This study stresses the importance of strict short-interval surveillance for IBD patients with high-risk features, including active inflammation on index colonoscopy.
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Affiliation(s)
- Kristin E Burke
- Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Jennifer Nayor
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Emily J Campbell
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, USA
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, USA
| | - James M Richter
- Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, USA
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Pekow J, Hernandez K, Meckel K, Deng Z, Haider HI, Khalil A, Zhang C, Talisila N, Siva S, Jasmine F, Li YC, Rubin DT, Hyman N, Bissonnette M, Weber C, Kibriya MG. IBD-associated Colon Cancers Differ in DNA Methylation and Gene Expression Profiles Compared With Sporadic Colon Cancers. J Crohns Colitis 2019; 13:884-893. [PMID: 30753380 PMCID: PMC7327274 DOI: 10.1093/ecco-jcc/jjz014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS As ulcerative colitis [UC]-associated colorectal cancer [CRC] and sporadic CRC differ in presentation and molecular features, we sought to evaluate differences in the impact of DNA methylation on gene expression. METHODS DNA methylation was assessed in 11 UC-CRCs and adjacent tissue and 11 sporadic CRCs and adjacent tissue, using Illumina arrays. RNA sequencing was performed on 10 UC-CRCs and adjacent tissue and eight sporadic CRCs and adjacent tissues. Differences in DNA methylation and transcript expression, as well as their correlation in the same tissues, were assessed. Immunohistochemistry was performed for three proteins, ANPEP, FAM92A1, and STK31, all of which exhibited an inverse correlation between DNA methylation and transcript expression in UC. RESULTS Thirty three loci demonstrated differences in DNA methylation between UC-CRC and adjacent tissue. In contrast, there were 4204 differentially methylated loci between sporadic colon cancer and adjacent tissue. Eight hundred eighty six genes as well as 10 long non-coding RNAs [lncRNA] were differentially expressed between UC-CRC and adjacent tissues. Although there were no differentially methylated loci between UC and sporadic CRC, 997 genes and 38 lncRNAs were differentially expressed between UC-CRC and sporadic CRC. In UC, 18 genes demonstrated a negative correlation between DNA methylation and transcript expression. Evaluation of protein expression related to three genes, ANPEP, FAM92A1, and STK31, confirmed down-regulation of ANPEP and up-regulation of STK31 in UC-CRC. CONCLUSIONS Regulation of transcript expression by DNA methylation involves genes key to colon carcinogenesis and may account for differences in presentation and outcomes between inflammatory bowel disease and sporadic colon cancer.
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Affiliation(s)
- Joel Pekow
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition,Corresponding author: Joel Pekow, MD, 900 East 57th St, MB #9, University of Chicago Medicine, Section of Gastroenterology, Hepatology, and Nutrition, Chicago, IL 60637, USA. Tel: 773-702-2774; Fax: 773-702-2281;
| | - Kyle Hernandez
- University of Chicago, Center for Research Informatics,University of Chicago, Department of Pediatrics
| | - Katherine Meckel
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | - Zifeng Deng
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | - Haider I Haider
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | - Abdurahman Khalil
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | | | - Nitya Talisila
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | - Shivi Siva
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | | | - Yan Chun Li
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | - David T Rubin
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
| | - Neil Hyman
- University of Chicago, Department of Surgery
| | - Marc Bissonnette
- University of Chicago, Section of Gastroenterology, Hepatology, and Nutrition
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8
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Whyte JM, Ellis JJ, Brown MA, Kenna TJ. Best practices in DNA methylation: lessons from inflammatory bowel disease, psoriasis and ankylosing spondylitis. Arthritis Res Ther 2019; 21:133. [PMID: 31159831 PMCID: PMC6547594 DOI: 10.1186/s13075-019-1922-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic technology have enabled a greater understanding of the genetics of common immune-mediated diseases such as ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. The substantial overlap in genetically identified pathogenic pathways has been demonstrated between these diseases. However, to date, gene discovery approaches have only mapped a minority of the heritability of these common diseases, and most disease-associated variants have been found to be non-coding, suggesting mechanisms of disease-association through transcriptional regulatory effects. Epigenetics is a major interface between genetic and environmental modifiers of disease and strongly influence transcription. DNA methylation is a well-characterised epigenetic mechanism, and a highly stable epigenetic marker, that is implicated in disease pathogenesis. DNA methylation is an under-investigated area in immune-mediated diseases, and many studies in the field are affected by experimental design limitations, related to study design, technical limitations of the methylation typing methods employed, and statistical issues. This has resulted in both sparsity of investigations into disease-related changes in DNA methylation, a paucity of robust findings, and difficulties comparing studies in the same disease. In this review, we cover the basics of DNA methylation establishment and control, and the methods used to examine it. We examine the current state of DNA methylation studies in AS, IBD and psoriasis; the limitations of previous studies; and the best practices for DNA methylation studies. The purpose of this review is to assist with proper experimental design and consistency of approach in future studies to enable a better understanding of the functional role of DNA methylation in immune-mediated disease.
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Affiliation(s)
- Jessica M Whyte
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Jonathan J Ellis
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia. .,Translational Research Institute, Princess Alexandra Hospital, 37 Kent Street, Woolloongabba, Queensland, 4102, Australia.
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
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Xue M, Shi L, Wang W, Chen S, Wang L. An Overview of Molecular Profiles in Ulcerative Colitis-Related Cancer. Inflamm Bowel Dis 2018; 24:1883-1894. [PMID: 29945208 DOI: 10.1093/ibd/izy221] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Indexed: 12/16/2022]
Abstract
Ulcerative colitis (UC) is an independent risk factor of colorectal cancer (CRC). Both genetic and epigentic events induce a unique molecular profile during the development from UC to UC-related CRC (UCRC). These molecular changes play varied roles in DNA repair, immune response, cell metabolism, and interaction with the microbiota during the carcinogenesis process. This review will systmatically discuss the molecular characteristics of UCRC and point out the future perspectives in this research field.
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Affiliation(s)
- Meng Xue
- Department of Gastroenterology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liuhong Shi
- Department of Ultrasound, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weijia Wang
- Department of Cardiology, School of Medicine, the Johns Hopkins Hospital, Baltimore, Maryland
| | - Shujie Chen
- Department of Gastroenterology, Sir Runrun Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liangjing Wang
- Department of Gastroenterology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
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10
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PARP-1 protects against colorectal tumor induction, but promotes inflammation-driven colorectal tumor progression. Proc Natl Acad Sci U S A 2018; 115:E4061-E4070. [PMID: 29632181 DOI: 10.1073/pnas.1712345115] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common tumor entities, which is causally linked to DNA repair defects and inflammatory bowel disease (IBD). Here, we studied the role of the DNA repair protein poly(ADP-ribose) polymerase-1 (PARP-1) in CRC. Tissue microarray analysis revealed PARP-1 overexpression in human CRC, correlating with disease progression. To elucidate its function in CRC, PARP-1 deficient (PARP-1-/-) and wild-type animals (WT) were subjected to azoxymethane (AOM)/ dextran sodium sulfate (DSS)-induced colorectal carcinogenesis. Miniendoscopy showed significantly more tumors in WT than in PARP-1-/- mice. Although the lack of PARP-1 moderately increased DNA damage, both genotypes exhibited comparable levels of AOM-induced autophagy and cell death. Interestingly, miniendoscopy revealed a higher AOM/DSS-triggered intestinal inflammation in WT animals, which was associated with increased levels of innate immune cells and proinflammatory cytokines. Tumors in WT animals were more aggressive, showing higher levels of STAT3 activation and cyclin D1 up-regulation. PARP-1-/- animals were then crossed with O6-methylguanine-DNA methyltransferase (MGMT)-deficient animals hypersensitive to AOM. Intriguingly, PARP-1-/-/MGMT-/- double knockout (DKO) mice developed more, but much smaller tumors than MGMT-/- animals. In contrast to MGMT-deficient mice, DKO animals showed strongly reduced AOM-dependent colonic cell death despite similar O6-methylguanine levels. Studies with PARP-1-/- cells provided evidence for increased alkylation-induced DNA strand break formation when MGMT was inhibited, suggesting a role of PARP-1 in the response to O6-methylguanine adducts. Our findings reveal PARP-1 as a double-edged sword in colorectal carcinogenesis, which suppresses tumor initiation following DNA alkylation in a MGMT-dependent manner, but promotes inflammation-driven tumor progression.
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11
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Sepulveda AR, J. Del Portillo A. Molecular Basis of Diseases of the Gastrointestinal Tract. MOLECULAR PATHOLOGY 2018:387-415. [DOI: 10.1016/b978-0-12-802761-5.00019-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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12
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Emmett RA, Davidson KL, Gould NJ, Arasaradnam RP. DNA methylation patterns in ulcerative colitis-associated cancer: a systematic review. Epigenomics 2017; 9:1029-1042. [PMID: 28621161 DOI: 10.2217/epi-2017-0025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/19/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Evidence points to the role of DNA methylation in ulcerative colitis (UC)-associated cancer (UCC), the most serious complication of ulcerative colitis. A better understanding of the etiology of UCC may facilitate the development of new therapeutic targets and help to identify biomarkers of the disease risk. METHODS A search was performed in three databases following PRISMA protocol. DNA methylation in UCC was compared with sporadic colorectal cancer (SCRC), and individual genes differently methylated in UCC identified. RESULTS While there were some similarities in the methylation patterns of UCC compared with SCRC, generally lower levels of hypermethylation in promoter regions of individual genes was evident in UCC. Certain individual genes are, however, highly methylated in colitis-associated cancer: RUNX3, MINT1, MYOD and p16 exon1 and the promoter regions of EYA4 and ESR. CONCLUSION Patterns of DNA methylation differ between UCC and SCRC. Seven genes appear to be promising putative biomarkers.
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Affiliation(s)
- Ruth A Emmett
- Warwick Medical School, University of Warwick, Coventry, UK
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13
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Tahara T, Hirata I, Nakano N, Tahara S, Horiguchi N, Kawamura T, Okubo M, Ishizuka T, Yamada H, Yoshida D, Ohmori T, Maeda K, Komura N, Ikuno H, Jodai Y, Kamano T, Nagasaka M, Nakagawa Y, Tuskamoto T, Urano M, Shibata T, Kuroda M, Ohmiya N. Potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in ulcerative colitis. Oncotarget 2017; 8:61917-61926. [PMID: 28977914 PMCID: PMC5617474 DOI: 10.18632/oncotarget.18716] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/23/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND AIM Fusobacterium enrichment has been associated with colorectal cancer development. Ulcerative colitis (UC) associated tumorigenesis is characterized as high degree of methylation accumulation through continuous colonic inflammation. The aim of this study was to investigate a potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in UC. METHODS In the candidate analysis, inflamed colonic mucosa from 86 UC patients were characterized the methylation status of colorectal a panel of cancer related 24 genes. In the genome-wide analysis, an Infinium HumanMethylation450 BeadChip array was utilized to characterize the methylation status of >450,000 CpG sites for fourteen UC patients. Results were correlated with Fusobacterium status. RESULTS UC with Fusobacterium enrichment (FB-high) was characterized as high degree of type C (for cancer-specific) methylation compared to other (FB-low/neg) samples (P<0.01). Genes hypermethylated in FB-high samples included well-known type C genes in colorectal cancer, such as MINT2 and 31, P16 and NEUROG1. Multivariate analysis demonstrated that the FB high status held an increased likelihood for methylation high as an independent factor (odds ratio: 16.18, 95% confidence interval: 1.94-135.2, P=0.01). Genome-wide methylation analysis demonstrated a unique methylome signature of FB-high cases irrespective of promoter, outside promoter, CpG and non-CpG sites. Group of promoter CpG sites that were exclusively hypermethylated in FB-high cases significantly codified the genes related to the catalytic activity (P=0.039). CONCLUSION Our findings suggest that Fusobacterium accelerates DNA methylation in specific groups of genes in the inflammatory colonic mucosa in UC.
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Affiliation(s)
- Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Ichiro Hirata
- Department of Gastroenterology, Kenporen Osaka Central Hospital Japan, Osaka, Japan
| | - Naoko Nakano
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Sayumi Tahara
- Department of Diagnostic Pathology I, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Noriyuki Horiguchi
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomohiko Kawamura
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masaaki Okubo
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takamitsu Ishizuka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hyuga Yamada
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Dai Yoshida
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takafumi Ohmori
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kohei Maeda
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naruomi Komura
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hirokazu Ikuno
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yasutaka Jodai
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Toshiaki Kamano
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Mitsuo Nagasaka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tetsuya Tuskamoto
- Department of Diagnostic Pathology I, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Makoto Urano
- Department of Diagnostic Pathology I, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Makoto Kuroda
- Department of Diagnostic Pathology I, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Naoki Ohmiya
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
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14
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Targeted sequencing-based analyses of candidate gene variants in ulcerative colitis-associated colorectal neoplasia. Br J Cancer 2017; 117:136-143. [PMID: 28524162 PMCID: PMC5520210 DOI: 10.1038/bjc.2017.148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Long-standing ulcerative colitis (UC) leading to colorectal cancer (CRC) is one of the most serious and life-threatening consequences acknowledged globally. Ulcerative colitis-associated colorectal carcinogenesis showed distinct molecular alterations when compared with sporadic colorectal carcinoma. METHODS Targeted sequencing of 409 genes in tissue samples of 18 long-standing UC subjects at high risk of colorectal carcinoma (UCHR) was performed to identify somatic driver mutations, which may be involved in the molecular changes during the transformation of non-dysplastic mucosa to high-grade dysplasia. Findings from the study are also compared with previously published genome wide and exome sequencing data in inflammatory bowel disease-associated and sporadic colorectal carcinoma. RESULTS Next-generation sequencing analysis identified 1107 mutations in 275 genes in UCHR subjects. In addition to TP53 (17%) and KRAS (22%) mutations, recurrent mutations in APC (33%), ACVR2A (61%), ARID1A (44%), RAF1 (39%) and MTOR (61%) were observed in UCHR subjects. In addition, APC, FGFR3, FGFR2 and PIK3CA driver mutations were identified in UCHR subjects. Recurrent mutations in ARID1A (44%), SMARCA4 (17%), MLL2 (44%), MLL3 (67%), SETD2 (17%) and TET2 (50%) genes involved in histone modification and chromatin remodelling were identified in UCHR subjects. CONCLUSIONS Our study identifies new oncogenic driver mutations which may be involved in the transition of non-dysplastic cells to dysplastic phenotype in the subjects with long-standing UC with high risk of progression into colorectal neoplasia.
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15
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Saraggi D, Fassan M, Mescoli C, Scarpa M, Valeri N, Michielan A, D'Incá R, Rugge M. The molecular landscape of colitis-associated carcinogenesis. Dig Liver Dis 2017; 49:326-330. [PMID: 28089111 DOI: 10.1016/j.dld.2016.12.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 12/11/2022]
Abstract
In spite of the well-established histopathological phenotyping of IBD-associated preneoplastic and neoplastic lesions, their molecular landscape remains to be fully elucidated. Several studies have pinpointed the initiating role of longstanding/relapsing inflammatory insult on the intestinal mucosa, with the activation of different pro-inflammatory cytokines (TNF-α, IL-6, IL-10, IFN-γ), chemokines and metabolites of arachidonic acid resulting in the activation of key transcription factors such as NF-κB. Longstanding inflammation may also modify the intestinal microbiota, prompting the overgrowth of genotoxic microorganisms, which may act as further cancer promoters. Most of the molecular dysregulation occurring in sporadic colorectal carcinogenesis is documented in colitis-associated adenocarcinoma too, but marked differences have been established in both their timing and prevalence. Unlike sporadic cancers, TP53 alterations occur early in IBD-related carcinogenesis, while APC dysregulation emerges mainly in the most advanced stages of the oncogenic cascade. From the therapeutic standpoint, colitis-associated cancers are associated with a lower prevalence of KRAS mutations than the sporadic variant. Epigenetic changes, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs, are significantly involved in colitis-associated cancer development and progression. The focus now is on identifying diagnostic and prognostic biomarkers, with a view to ultimately designing patient-tailored therapies.
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Affiliation(s)
- Deborah Saraggi
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Claudia Mescoli
- Department of Surgical Oncology and Gastroenterology (DiSCOG), Gastroenterology Unit, University of Padua, Padua, Italy
| | - Marco Scarpa
- Istituto Oncologico Veneto, IOV-IRCCS, Surgical Oncology Unit, Padua, Italy
| | - Nicola Valeri
- Department of Molecular Pathology, The Institute of Cancer Research, London, UK; Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Andrea Michielan
- Department of Surgical Oncology and Gastroenterology (DiSCOG), Gastroenterology Unit, University of Padua, Padua, Italy
| | - Renata D'Incá
- Department of Surgical Oncology and Gastroenterology (DiSCOG), Gastroenterology Unit, University of Padua, Padua, Italy
| | - Massimo Rugge
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy.
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Abstract
INTRODUCTION Aberrant DNA methylation frequently occurs in the inflammatory mucosa in ulcerative colitis (UC) and is involved in UC-related tumorigenesis. We performed comprehensive DNA methylation profiling of the promoter regions of the inflamed rectal mucosae of patients with UC. DESIGN The methylation status of the promoter CpG islands (CGIs) of 45 cancer/inflammation or age-related candidate genes and the LINE1 repetitive element were examined in the colonic mucosae of 84 cancer-free patients with UC by bisulfite pyrosequencing. Methylation status of selected genes (DPYS, N33, MIR1247, GSTP1, and SOX11) was also determined in 14 neoplastic lesions (5 with high-grade dysplasia and 9 with carcinoma) and 8 adjacent tissues derived from 12 patients. An Infinium HumanMethylation450 BeadChip array was used to characterize the methylation status of >450,000 CpG sites for 10 patients with UC. RESULTS Clustering analysis based on the methylation status of the candidate genes clearly distinguished the inflammatory samples from the noninflammatory samples. The hypermethylation of the promoter CGIs strongly correlated with increased disease duration, which is a known risk factor for the development of colon cancer. Genome-wide methylation analyses revealed a high rate of hypermethylation in the severe phenotype of UC, particularly at the CGIs. Exclusively hypermethylated promoter CGIs in the severe phenotypes were significantly related to genes involved in biosynthetic processes, the regulation of metabolic processes, and nitrogen compound metabolic processes. CONCLUSION Our findings suggest the potential utility of DNA methylation as a molecular marker and therapeutic target for UC-related tumorigenesis.
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Suehiro Y, Sakai K, Nishioka M, Hashimoto S, Takami T, Higaki S, Shindo Y, Hazama S, Oka M, Nagano H, Sakaida I, Yamasaki T. Highly sensitive stool DNA testing of Fusobacterium nucleatum as a marker for detection of colorectal tumours in a Japanese population. Ann Clin Biochem 2016; 54:86-91. [PMID: 27126270 DOI: 10.1177/0004563216643970] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Accumulating evidence shows an over-abundance of Fusobacterium nucleatum in colorectal tumour tissues. Although stool DNA testing of Fusobacterium nucleatum might be a potential marker for the detection of colorectal tumours, the difficulty in detecting Fusobacterium nucleatum in stool by conventional methods prevented further explorations. Therefore, we developed a droplet digital polymerase chain reaction (PCR) assay for detecting Fusobacterium nucleatum in stool and investigated its clinical utility in the management of colorectal tumours in a Japanese population. Methods Feces were collected from 60 healthy subjects (control group) and from 11 patients with colorectal non-advanced adenomas (non-advanced adenoma group), 19 patients with colorectal advanced adenoma/carcinoma in situ (advanced adenoma/carcinoma in situ (CIS) group) and 158 patients with colorectal cancer of stages I to IV (colorectal cancer group). Absolute copy numbers of Fusobacterium nucleatum were measured by droplet digital PCR. Results The median copy number of Fusobacterium nucleatum was 17.5 in the control group, 311 in the non-advanced adenoma group, 122 in the advanced adenoma/CIS group, and 317 in the colorectal cancer group. In comparison with that in the control group, the Fusobacterium nucleatum level was significantly higher in the non-advanced adenoma group, the advanced adenoma/CIS group and the colorectal cancer group. Conclusions This study illustrates the potential of stool DNA testing of Fusobacterium nucleatum by droplet digital PCR to detect individuals with colorectal tumours in a Japanese population.
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Affiliation(s)
- Yutaka Suehiro
- 1 Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Kouhei Sakai
- 1 Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Mitsuaki Nishioka
- 2 Division of Laboratory, Yamaguchi University Hospital, Ube, Yamaguchi, Japan
| | - Shinichi Hashimoto
- 3 Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Taro Takami
- 3 Department of Gastroenterology and Hepatology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shingo Higaki
- 4 Department of Gastroenterology, Sentohiru Hospital, Ube, Japan
| | - Yoshitaro Shindo
- 5 Department of Digestive Surgery and Surgical Oncology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shoichi Hazama
- 5 Department of Digestive Surgery and Surgical Oncology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Masaaki Oka
- 5 Department of Digestive Surgery and Surgical Oncology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroaki Nagano
- 5 Department of Digestive Surgery and Surgical Oncology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Isao Sakaida
- 2 Division of Laboratory, Yamaguchi University Hospital, Ube, Yamaguchi, Japan
| | - Takahiro Yamasaki
- 1 Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube, Japan
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A Biomarker Panel to Detect Synchronous Neoplasm in Non-neoplastic Surveillance Biopsies from Patients with Ulcerative Colitis. Inflamm Bowel Dis 2016; 22:1568-74. [PMID: 27135485 DOI: 10.1097/mib.0000000000000789] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Patients with ulcerative colitis (UC) are at risk for colorectal neoplasia. Challenges associated with surveillance colonoscopy with random biopsies for detection of dysplasia/cancer are well-documented. This study extended our findings in UC-associated colorectal cancer to include low-grade dysplasia (LGD) patients, testing whether our biomarker panel detects any UC-associated neoplasm. METHODS DNA from the LGD area and the corresponding nonadjacent, non-dysplastic section from 171 UC-LGD patients was extracted. TaqMan SNP Genotyping Assays for TNF-α, IL-1β, and IL23R were used to evaluate polymorphisms for each gene. Bisulfite-treated DNA was used for methylation testing of RUNX3, COX2, and MINT1. LGD data were combined with UC-cancer patient data for statistical testing. Logistic regression analyses determined associations between genetic/epigenetic/clinical variables and UC-associated neoplasia. Receiver operating characteristic analyses were performed to determine the final synchronous neoplasm detection panel. RESULTS Comparison of nonadjacent, non-dysplastic DNA from UC-neoplasm patients versus UC-controls indicated that TNF-α, IL-1β, and methylation of RUNX3, MINT1, and COX2 were significantly different (P < 0.0001). In multivariable analysis, all remained significant with an area under the curve of 0.85, exceeding the clinical variable panel area under the curve. Combining clinical and experimental variables yielded a neoplasm biomarker panel with an area under the curve of 0.95 (sensitivity and specificity of 82% and 91%, respectively). Analysis of DNA from LGD with known progression compared with LGD without progression indicated a significant difference in RUNX3 methylation. CONCLUSIONS A combined clinical, genetic, and epigenetic model for detecting synchronous neoplasm by testing of non-neoplastic colonic tissue had favorable operating characteristics and could complement current patient care.
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Robles AI, Traverso G, Zhang M, Roberts NJ, Khan MA, Joseph C, Lauwers GY, Selaru FM, Popoli M, Pittman ME, Ke X, Hruban RH, Meltzer SJ, Kinzler KW, Vogelstein B, Harris CC, Papadopoulos N. Whole-Exome Sequencing Analyses of Inflammatory Bowel Disease-Associated Colorectal Cancers. Gastroenterology 2016; 150:931-43. [PMID: 26764183 PMCID: PMC5270616 DOI: 10.1053/j.gastro.2015.12.036] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 12/06/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS A long duration of inflammatory bowel disease (IBD) increases the risk for colorectal cancer. Mutation analysis of limited numbers of genes has indicated that colorectal tumors that develop in patients with IBD differ from those of patients without IBD. We performed whole-exome sequencing analyses to characterize the genetic landscape of these tumors. METHODS We collected colorectal tumor and non-neoplastic tissues from 31 patients with IBD and colorectal cancer (15 with ulcerative colitis, 14 with Crohn's disease, and 2 with indeterminate colitis) and performed whole-exome sequencing analyses of the microdissected tumor and matched nontumor tissues. We identified somatic alterations by comparing matched specimens. The prevalence of mutations in sporadic colorectal tumors was obtained from previously published exome-sequencing studies. RESULTS Two specimens had somatic mutations in the DNA proofreading or mismatch repair genes POLE, MLH1, and MSH6 and the tumor cells had a hypermutable phenotype. The remaining tumors had, on average, 71 alterations per sample. TP53 was the most commonly mutated gene, with prevalence similar to that of sporadic colorectal tumors (63% of cases). However, tumors from the patients with IBD had a different mutation spectrum. APC and KRAS were mutated at significantly lower rates in tumors from patients with IBD than in sporadic colorectal tumors (13% and 20% of cases, respectively). Several genes were mutated more frequently or uniquely in tumors from patients with IBD, including SOX9 and EP300 (which encode proteins in the WNT pathway), NRG1 (which encodes an ERBB ligand), and IL16 (which encodes a cytokine). Our study also revealed recurrent mutations in components of the Rho and Rac GTPase network, indicating a role for noncanonical WNT signaling in development of colorectal tumors in patients with IBD. CONCLUSIONS Colorectal tumors that develop in patients with IBD have distinct genetic features from sporadic colorectal tumors. These findings could be used to develop disease-specific markers for diagnosis and treatment of patients with IBD and colorectal cancer.
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Affiliation(s)
- Ana I. Robles
- Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD, USA
| | - Giovanni Traverso
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Department of Chemical Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ming Zhang
- Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J. Roberts
- Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mohammed A. Khan
- Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD, USA
| | - Christine Joseph
- Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gregory Y. Lauwers
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Florin M. Selaru
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maria Popoli
- Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Meredith E. Pittman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiquan Ke
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H. Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen J. Meltzer
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W. Kinzler
- Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center at Johns Hopkins, Baltimore, Maryland; Howard Hughes Medical Institute, Chevy Chase, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Curtis C. Harris
- Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD, USA
| | - Nickolas Papadopoulos
- Ludwig Center at Johns Hopkins, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Oxidative Stress and Carbonyl Lesions in Ulcerative Colitis and Associated Colorectal Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2016:9875298. [PMID: 26823956 PMCID: PMC4707327 DOI: 10.1155/2016/9875298] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/14/2015] [Accepted: 10/25/2015] [Indexed: 12/15/2022]
Abstract
Oxidative stress has long been known as a pathogenic factor of ulcerative colitis (UC) and colitis-associated colorectal cancer (CAC), but the effects of secondary carbonyl lesions receive less emphasis. In inflammatory conditions, reactive oxygen species (ROS), such as superoxide anion free radical (O2 (∙-)), hydrogen peroxide (H2O2), and hydroxyl radical (HO(∙)), are produced at high levels and accumulated to cause oxidative stress (OS). In oxidative status, accumulated ROS can cause protein dysfunction and DNA damage, leading to gene mutations and cell death. Accumulated ROS could also act as chemical messengers to activate signaling pathways, such as NF-κB and p38 MAPK, to affect cell proliferation, differentiation, and apoptosis. More importantly, electrophilic carbonyl compounds produced by lipid peroxidation may function as secondary pathogenic factors, causing further protein and membrane lesions. This may in turn exaggerate oxidative stress, forming a vicious cycle. Electrophilic carbonyls could also cause DNA mutations and breaks, driving malignant progression of UC. The secondary lesions caused by carbonyl compounds may be exceptionally important in the case of host carbonyl defensive system deficit, such as aldo-keto reductase 1B10 deficiency. This review article updates the current understanding of oxidative stress and carbonyl lesions in the development and progression of UC and CAC.
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Mokarram P, Kavousipour S, Sarabi MM, Mehrabani G, Fahmidehkar MA, Shamsdin SA, Alipour A, Naini MA. MGMT-B gene promoter hypermethylation in patients with inflammatory bowel disease - a novel finding. Asian Pac J Cancer Prev 2015; 16:1945-52. [PMID: 25773792 DOI: 10.7314/apjcp.2015.16.5.1945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a disease strongly associated with colorectal cancer (CRC) as a well-known precancerous condition. Alterations in DNA methylation and mutation in K-ras are believed to play an early etiopathogenic role in CRC and may also an initiating event through deregulation of molecular signaling. Epigenetic silencing of APC and SFRP2 in the WNT signaling pathway may also be involved in IBD-CRC. The role of aberrant DNA methylation in precancerous state of colorectal cancer (CRC) is under intensive investigation worldwide. The aim of this study was to investigate the status of promoter methylation of MGMT-B, APC1A and SFRP2 genes, in inflamed and normal colon tissues of patients with IBD compared with control normal tissues. A total of 52 IBD tissues as well as corresponding normal tissues and 30 samples from healthy participants were obtained. We determined promoter methylation status of MGMT-B, SFRP2 and APC1A genes by chemical treatment with sodium bisulfite and subsequent MSP. The most frequently methylated locus was MGMT-B (71%; 34 of 48), followed by SFRP2 (66.6 %; 32 of 48), and APC1A (43.7%; 21 of 48). Our study demonstrated for the first time that hypermethylation of the MGMT-B and the SFRP2 gene promoter regions might be involved in IBD development. Methylation of MGMT-B and SFRP2 in IBD patients may provide a method for early detection of IBD-associated neoplasia.
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Affiliation(s)
- Pooneh Mokarram
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran E-mail : ,
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22
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Yashiro M. Molecular Alterations of Colorectal Cancer with Inflammatory Bowel Disease. Dig Dis Sci 2015; 60:2251-63. [PMID: 25840920 DOI: 10.1007/s10620-015-3646-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/26/2015] [Indexed: 12/18/2022]
Abstract
Inflammatory bowel disease (IBD) is an important etiologic factor in the development of colorectal cancer (CRC). The risk of CRC begins to increase 8 or 10 years after the diagnosis of IBD. This type of cancer is called colitis-associated CRC (CA-CRC). The molecular pathogenesis of inflammatory epithelium might play a critical role in the development of CA-CRC. Genetic alterations detected in CA-CRC such as genetic mutations, microsatellite instability, and DNA hypermethylation are also recognized in sporadic CRC; however, there are differences in the timing and frequency of molecular events between CA-CRC and sporadic CRC. Interaction between gene-environmental factors, including inflammation, lifestyle, psychological stress, and prior appendectomy, might be associated with the etiopathology of IBD. The mucosal inflammatory mediators, such as oxidant stress, free radicals, and chemokines, may cause the genetic alterations. Understanding the molecular mechanisms of CA-CRC might be important to develop clinical efficacies for patients with IBD. This review discusses the molecular characteristics of CA-CRC, especially ulcerative colitis-associated CRC, including clinical features, signaling pathways, and interactions between genetic alterations and environment involved in inflammatory carcinogenesis.
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Affiliation(s)
- Masakazu Yashiro
- Department of Surgical Oncology, Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan,
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Mokarram P, Estiar MA, Ashktorab H. Methylation in Colorectal Cancer. EPIGENETICS TERRITORY AND CANCER 2015:373-455. [DOI: 10.1007/978-94-017-9639-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Tahara T, Shibata T, Okubo M, Ishizuka T, Nakamura M, Nagasaka M, Nakagawa Y, Ohmiya N, Arisawa T, Hirata I. DNA methylation status of epithelial-mesenchymal transition (EMT)--related genes is associated with severe clinical phenotypes in ulcerative colitis (UC). PLoS One 2014; 9:e107947. [PMID: 25303049 PMCID: PMC4193736 DOI: 10.1371/journal.pone.0107947] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022] Open
Abstract
Background Epithelial-to-mesenchymal transition (EMT) is a phenomenon that allows the conversion of adherent epithelial cells to a mesenchymal cell phenotype, which enhances migratory capacity and invasiveness. Recent studies have suggested that EMT contributes to the pathogenesis of ulcerative colitis (UC). We investigated the promoter DNA methylation status of EMT-related genes in the colonic mucosa in UC. Methods Colonic biopsies were obtained from the rectal inflammatory mucosa of 86 UC patients and the non-inflammatory proximal colonic mucosa of 10 paired patients. Bisulfite pyrosequencing was used to quantify the methylation of 5 candidate CpG island promoters (NEUROG1, CDX1, miR-1247, CDH1, and CDH13) and LINE1. Results Using an unsupervised hierarchical clustering analysis, inflamed rectal mucosa was well separated from mucosa that appeared normal. The CDH1 and CDH13 promoters were significantly associated with patient age (p = 0.04, 0.03, respectively). A similar trend was found between those genes and the duration of disease (CDH1: p = 0.07, CDH13: p = 0.0002, mean of both: p<0.00001). Several positive associations were found between hypermethylation and severe clinical phenotypes (CDX1 and miR-1247 and a refractory phenotype: p = 0.04 and 0.006, respectively. miR-1247 and CDH1 hyper methylation and a more severe Mayo endoscopic subscore: miR-1247: p = 0.0008, CDH1: p = 0.03, mean of both: p = 0.003). When the severe clinical phenotype was defined as having any of five phenotypes (hospitalized more than twice, highest Mayo endoscopic subscore, steroid dependence, refractory, or a history of surgery) miR-1247 hypermethylation was associated with the same phenotype (p = 0.008). Conclusions Our data suggest that variability in the methylation status of EMT-related genes is associated with more severe clinical phenotypes in UC.
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Affiliation(s)
- Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
- * E-mail:
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masaaki Okubo
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takamitsu Ishizuka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masakatsu Nakamura
- Department of Gastroenterology, Kanazawa Medical University, Ishikawa, Japan
| | - Mitsuo Nagasaka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naoki Ohmiya
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomiyasu Arisawa
- Department of Gastroenterology, Kanazawa Medical University, Ishikawa, Japan
| | - Ichiro Hirata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
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Shinmura K, Konishi K, Yamochi T, Kubota Y, Yano Y, Katagiri A, Muramoto T, Kihara T, Tojo M, Konda K, Tagawa T, Yanagisawa F, Kogo M, Makino R, Takimoto M, Yoshida H. Molecular features of colorectal polyps presenting Kudo's type II mucosal crypt pattern: are they based on the same mechanism of tumorigenesis? Endosc Int Open 2014; 2:E171-7. [PMID: 26134964 PMCID: PMC4423326 DOI: 10.1055/s-0034-1377518] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/10/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND AND STUDY AIMS The molecular features of serrated polyps (SPs) with hyperplastic crypt pattern, also called Kudo's type II observed by chromoendoscopy, were evaluated. METHODS The clinicopathological and molecular features of 114 SPs with a hyperplastic pit pattern detected under chromoendoscopy (five dysplastic SPs, 63 sessile serrated adenoma/polyps (SSA/Ps), 36 microvesicular hyperplastic polyps (MVHPs), and 10 goblet cell-rich hyperplastic polyps (GCHPs)) were examined. The frequency of KRAS and BRAF mutations and CpG island methylator phenotype (CIMP) were investigated. RESULTS Dysplastic SPs and SSA/Ps were frequently located in the proximal colon compared to others (SSA/Ps vs. MVHPs or GCHPs, P < 0.0001). No significant difference was found in the frequency of BRAF mutation among SPs apart from GCHP (60 % for dysplastic SPs, 44 % for SSA/Ps, 47 % for MVHPs, and 0 % for GCHPs). The frequency of CIMP was higher in dysplastic SPs or SSA/Ps than in MVHPs or GCHPs (60 % for dysplastic SPs, 56 % for SSA/Ps, 32 % for MVHPs, and 10 % for GCHPs) (SSA/Ps vs. GCHP, P = 0.0068). When serrated neoplasias (SNs) and MVHPs were classified into proximal and distal lesions, the frequency of CIMP was significantly higher in the proximal compared to the distal SNs (64 % vs. 11 %, P = 0.0032). Finally, multivariate analysis showed that proximal location and BRAF mutation were significantly associated with an increased risk of CIMP. CONCLUSIONS Distinct molecular features were observed between proximal and distal SPs with hyperplastic crypt pattern. Proximal MVHPs may develop more frequently through SSA/Ps to CIMP cancers than distal MVHPs.
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Affiliation(s)
- Kensuke Shinmura
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Kazuo Konishi
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan,Corresponding author Kazuo Konishi, MD
PhD Division of Gastroenterology, Department of
MedicineShowa University School of
Medicine1-5-8 Hatanodai,
Shinagawa-kuTokyo
142-8666Japan+81-3-37847553
| | - Toshiko Yamochi
- Department of Pathology, Showa University School of Medicine, Tokyo,
Japan
| | - Yutaro Kubota
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Yuichiro Yano
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Atsushi Katagiri
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Takashi Muramoto
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Toshihiro Kihara
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Masayuki Tojo
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Kenichi Konda
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Teppei Tagawa
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Fumito Yanagisawa
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
| | - Mari Kogo
- Department of Hospital Pharmaceutics, Showa University School of
Pharmacy, Tokyo, Japan
| | - Reiko Makino
- Clinical Collaborating Laboratory, Showa University School of Medicine,
Tokyo, Japan
| | - Masafumi Takimoto
- Department of Pathology, Showa University School of Medicine, Tokyo,
Japan
| | - Hitoshi Yoshida
- Division of Gastroenterology, Department of Medicine, Showa University
School of Medicine, Tokyo, Japan
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Abstract
Most of what is known about the pathogenesis of inflammatory bowel disease (IBD) pertains to complex interplay between host genetics, immunity, and environmental factors. Epigenetic modifications play pivotal roles in intestinal immunity and mucosal homeostasis as well as mediating gene-environment interactions. In this article, we provide a historical account of epigenetic research either directly related or pertinent to the pathogenesis and management of IBD. We further collate emerging evidence supporting roles for epigenetic mechanisms in relevant aspects of IBD biology, including deregulated immunity, host-pathogen recognition and mucosal integrity. Finally, we highlight key epigenetic mechanisms that link chronic inflammation to specific IBD comorbidities, including colitis-associated cancer and discuss their potential utility as novel biomarkers or pharmacologic targets in IBD therapy.
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Lobatón T, Azuara D, Rodríguez-Moranta F, Loayza C, Sanjuan X, de Oca J, Fernández-Robles A, Guardiola J, Capellá G. Relationship between methylation and colonic inflammation in inflammatory bowel disease. World J Gastroenterol 2014; 20:10591-10598. [PMID: 25132780 PMCID: PMC4130871 DOI: 10.3748/wjg.v20.i30.10591] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/23/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the relationship between the methylation status in the SLIT2 and TGFB2 promoters and colonic inflammation in inflammatory bowel disease patients.
METHODS: We evaluated the methylation status of 2 genes (SLIT2 and TGFB2) in 226 biopsies taken from 62 colonoscopies of 38 patients (29 ulcerative colitis and 9 Crohn’s colitis) using methylation-specific melting curve analysis. The relationships between methylation status and clinical, biological, endoscopic and histological activities were evaluated. Twenty-three of the 38 patients had a second colonoscopy and were included in a longitudinal analysis. Numerical results were given as the means ± SD of the sample and range, except when specified. Student t analysis, U Mann Whitney and ANOVA factor were used to compare the means. Qualitative results were based on the χ2 test.
RESULTS: SLIT2 methylation was more frequent in samples with endoscopic activity than with endoscopic remission (55% vs 18%, P < 0.001). SLIT2 methylation was also higher in samples with acute inflammation (56.5%) than in samples with chronic (24%) or absent inflammation (15%) (P < 0.001). For TGFB2 methylation, the correlation was only significant with endoscopic activity. Methylation was higher in the distal colon for both genes (P < 0.001 for SLIT2 and P = 0.022 for TGFB2). In the multivariate analysis, only inflammation status (and not disease duration or extension) was independently associated with SLIT2 methylation [OR = 6.6 (95%CI: 1.65-27.36), P = 0.009]. In the longitudinal analysis, the maintenance of endoscopic remission was protective for methylation.
CONCLUSION: Endoscopic and histological inflammation are predictive for SLIT2 methylation.
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Konda K, Konishi K, Yamochi T, Ito YM, Nozawa H, Tojo M, Shinmura K, Kogo M, Katagiri A, Kubota Y, Muramoto T, Yano Y, Kobayashi Y, Kihara T, Tagawa T, Makino R, Takimoto M, Imawari M, Yoshida H. Distinct molecular features of different macroscopic subtypes of colorectal neoplasms. PLoS One 2014; 9:e103822. [PMID: 25093594 PMCID: PMC4122357 DOI: 10.1371/journal.pone.0103822] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 07/01/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Colorectal adenoma develops into cancer with the accumulation of genetic and epigenetic changes. We studied the underlying molecular and clinicopathological features to better understand the heterogeneity of colorectal neoplasms (CRNs). METHODS We evaluated both genetic (mutations of KRAS, BRAF, TP53, and PIK3CA, and microsatellite instability [MSI]) and epigenetic (methylation status of nine genes or sequences, including the CpG island methylator phenotype [CIMP] markers) alterations in 158 CRNs including 56 polypoid neoplasms (PNs), 25 granular type laterally spreading tumors (LST-Gs), 48 non-granular type LSTs (LST-NGs), 19 depressed neoplasms (DNs) and 10 small flat-elevated neoplasms (S-FNs) on the basis of macroscopic appearance. RESULTS S-FNs showed few molecular changes except SFRP1 methylation. Significant differences in the frequency of KRAS mutations were observed among subtypes (68% for LST-Gs, 36% for PNs, 16% for DNs and 6% for LST-NGs) (P<0.001). By contrast, the frequency of TP53 mutation was higher in DNs than PNs or LST-Gs (32% vs. 5% or 0%, respectively) (P<0.007). We also observed significant differences in the frequency of CIMP between LST-Gs and LST-NGs or PNs (32% vs. 6% or 5%, respectively) (P<0.005). Moreover, the methylation level of LINE-1 was significantly lower in DNs or LST-Gs than in PNs (58.3% or 60.5% vs. 63.2%, P<0.05). PIK3CA mutations were detected only in LSTs. Finally, multivariate analyses showed that macroscopic morphologies were significantly associated with an increased risk of molecular changes (PN or LST-G for KRAS mutation, odds ratio [OR] 9.11; LST-NG or DN for TP53 mutation, OR 5.30; LST-G for PIK3CA mutation, OR 26.53; LST-G or DN for LINE-1 hypomethylation, OR 3.41). CONCLUSION We demonstrated that CRNs could be classified into five macroscopic subtypes according to clinicopathological and molecular differences, suggesting that different mechanisms are involved in the pathogenesis of colorectal tumorigenesis.
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Affiliation(s)
- Kenichi Konda
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Kazuo Konishi
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
- * E-mail:
| | - Toshiko Yamochi
- Department of Pathology, Showa University School of Medicine, Tokyo, Japan
| | - Yoichi M. Ito
- Department of Biostatistics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hisako Nozawa
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Masayuki Tojo
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Kensuke Shinmura
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Mari Kogo
- Department of Hospital Pharmaceutics, Showa University School of Pharmacy, Tokyo, Japan
| | - Atsushi Katagiri
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Yutaro Kubota
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Takashi Muramoto
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Yuichiro Yano
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Yoshiya Kobayashi
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Toshihiro Kihara
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Teppei Tagawa
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Reiko Makino
- Clinical Collaborating laboratory, Showa University School of Medicine, Tokyo, Japan
| | - Masafumi Takimoto
- Department of Pathology, Showa University School of Medicine, Tokyo, Japan
| | - Michio Imawari
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Hitoshi Yoshida
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
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Chen YZ, Liu D, Zhao YX, Wang HT, Gao Y, Chen Y. Aberrant promoter methylation of the SFRP1 gene may contribute to colorectal carcinogenesis: a meta-analysis. Tumour Biol 2014; 35:9201-10. [PMID: 24929326 DOI: 10.1007/s13277-014-2180-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/02/2014] [Indexed: 12/15/2022] Open
Abstract
This meta-analysis of published cohort studies was conducted to evaluate whether promoter methylation of the secreted frizzled-related protein 1 (SFRP1) gene contributes to colorectal carcinogenesis. The Web of Science (1945 ~ 2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966 ~ 2013), EMBASE (1980 ~ 2013), CINAHL (1982 ~ 2013), and the Chinese Biomedical Database (CBM) (1982 ~ 2013) were searched without language restrictions. Meta-analysis was conducted using the STATA 12.0 software. We calculated odds ratio (OR) and its 95 % confidence interval (95 % CI) to estimate the correlations between SFRP1 promoter methylation and colorectal carcinogenesis. In the present meta-analysis, 8 cohort studies with a total of 942 patients with colorectal cancer (CRC) were included. The pooled results revealed that the frequency of SFRP1 promoter methylation in cancer tissues were significantly higher than those of normal, adjacent, and benign tissues (cancer tissues vs. normal tissues: OR = 31.49, 95 % CI = 17.57 ~ 56.44, P < 0.001; cancer tissues vs. adjacent tissues: OR = 5.95, 95 % CI 3.12 ~ 10.00, P < 0.001; cancer tissues vs. benign tissues: OR = 3.01, 95 % CI 1.72 ~ 5.27, P < 0.001; respectively). Furthermore, ethnicity-stratified analysis indicated that SFRP1 promoter methylation was strongly correlated with colorectal carcinogenesis among both Asians and Caucasians (all P < 0.05). Our findings provide empirical evidence that SFRP1 promoter methylation may be correlated with the pathogenesis of CRC.
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Affiliation(s)
- Yan-Zhi Chen
- Department of Radiotherapy, The Fourth Affiliated Hospital of China Medical University, Chongshan East No 4, Huanggu District, Liaoning, Shenyang, 110032, People's Republic of China
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Tahara T, Yamamoto E, Suzuki H, Maruyama R, Chung W, Garriga J, Jelinek J, Yamano HO, Sugai T, An B, Shureiqi I, Toyota M, Kondo Y, Estécio MRH, Issa JPJ. Fusobacterium in colonic flora and molecular features of colorectal carcinoma. Cancer Res 2014; 74:1311-8. [PMID: 24385213 DOI: 10.1158/0008-5472.can-13-1865] [Citation(s) in RCA: 357] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fusobacterium species are part of the gut microbiome in humans. Recent studies have identified overrepresentation of Fusobacterium in colorectal cancer tissues, but it is not yet clear whether this is pathogenic or simply an epiphenomenon. In this study, we evaluated the relationship between Fusobacterium status and molecular features in colorectal cancers through quantitative real-time PCR in 149 colorectal cancer tissues, 89 adjacent normal appearing mucosae and 72 colonic mucosae from cancer-free individuals. Results were correlated with CpG island methylator phenotype (CIMP) status, microsatellite instability (MSI), and mutations in BRAF, KRAS, TP53, CHD7, and CHD8. Whole-exome capture sequencing data were also available in 11 cases. Fusobacterium was detectable in 111 of 149 (74%) colorectal cancer tissues and heavily enriched in 9% (14/149) of the cases. As expected, Fusobacterium was also detected in normal appearing mucosae from both cancer and cancer-free individuals, but the amount of bacteria was much lower compared with colorectal cancer tissues (a mean of 250-fold lower for Pan-fusobacterium). We found the Fusobacterium-high colorectal cancer group (FB-high) to be associated with CIMP positivity (P = 0.001), TP53 wild-type (P = 0.015), hMLH1 methylation positivity (P = 0.0028), MSI (P = 0.018), and CHD7/8 mutation positivity (P = 0.002). Among the 11 cases where whole-exome sequencing data were available, two that were FB-high cases also had the highest number of somatic mutations (a mean of 736 per case in FB-high vs. 225 per case in all others). Taken together, our findings show that Fusobacterium enrichment is associated with specific molecular subsets of colorectal cancers, offering support for a pathogenic role in colorectal cancer for this gut microbiome component.
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Affiliation(s)
- Tomomitsu Tahara
- Authors' Affiliations: Fels Institute for Cancer Research & Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania; Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake; First Departments of Internal Medicine and Molecular Biology, Sapporo Medical University, Sapporo; Department of Gastroenterology, Akita Red Cross Hospital, Akita; Department of Pathology, Iwate Medical University, Morioka; Division of Molecular Oncology, Aichi Cancer Center Research Institute, Nagoya, Japan; Division of OVP, Department of Clinical Cancer Prevention, Cancer Prevention and Population Sciences; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston; and Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
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Tahara T, Yamamoto E, Suzuki H, Maruyama R, Chung W, Garriga J, Jelinek J, Yamano HO, Sugai T, An B, Shureiqi I, Toyota M, Kondo Y, Estécio MRH, Issa JPJ. Fusobacterium in colonic flora and molecular features of colorectal carcinoma. Cancer Res 2014. [PMID: 24385213 DOI: 10.1158/0008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fusobacterium species are part of the gut microbiome in humans. Recent studies have identified overrepresentation of Fusobacterium in colorectal cancer tissues, but it is not yet clear whether this is pathogenic or simply an epiphenomenon. In this study, we evaluated the relationship between Fusobacterium status and molecular features in colorectal cancers through quantitative real-time PCR in 149 colorectal cancer tissues, 89 adjacent normal appearing mucosae and 72 colonic mucosae from cancer-free individuals. Results were correlated with CpG island methylator phenotype (CIMP) status, microsatellite instability (MSI), and mutations in BRAF, KRAS, TP53, CHD7, and CHD8. Whole-exome capture sequencing data were also available in 11 cases. Fusobacterium was detectable in 111 of 149 (74%) colorectal cancer tissues and heavily enriched in 9% (14/149) of the cases. As expected, Fusobacterium was also detected in normal appearing mucosae from both cancer and cancer-free individuals, but the amount of bacteria was much lower compared with colorectal cancer tissues (a mean of 250-fold lower for Pan-fusobacterium). We found the Fusobacterium-high colorectal cancer group (FB-high) to be associated with CIMP positivity (P = 0.001), TP53 wild-type (P = 0.015), hMLH1 methylation positivity (P = 0.0028), MSI (P = 0.018), and CHD7/8 mutation positivity (P = 0.002). Among the 11 cases where whole-exome sequencing data were available, two that were FB-high cases also had the highest number of somatic mutations (a mean of 736 per case in FB-high vs. 225 per case in all others). Taken together, our findings show that Fusobacterium enrichment is associated with specific molecular subsets of colorectal cancers, offering support for a pathogenic role in colorectal cancer for this gut microbiome component.
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Affiliation(s)
- Tomomitsu Tahara
- Authors' Affiliations: Fels Institute for Cancer Research & Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania; Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake; First Departments of Internal Medicine and Molecular Biology, Sapporo Medical University, Sapporo; Department of Gastroenterology, Akita Red Cross Hospital, Akita; Department of Pathology, Iwate Medical University, Morioka; Division of Molecular Oncology, Aichi Cancer Center Research Institute, Nagoya, Japan; Division of OVP, Department of Clinical Cancer Prevention, Cancer Prevention and Population Sciences; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston; and Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
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Sebastian S, Hernández V, Myrelid P, Kariv R, Tsianos E, Toruner M, Marti-Gallostra M, Spinelli A, van der Meulen-de Jong AE, Yuksel ES, Gasche C, Ardizzone S, Danese S. Colorectal cancer in inflammatory bowel disease: results of the 3rd ECCO pathogenesis scientific workshop (I). J Crohns Colitis 2014; 8:5-18. [PMID: 23664897 DOI: 10.1016/j.crohns.2013.04.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 04/05/2013] [Indexed: 02/08/2023]
Abstract
Epidemiological studies demonstrate an increased risk of colorectal cancer in patients with inflammatory bowel disease (IBD). A detailed literature review was conducted on epidemiology, risk factors, pathophysiology, chemoprevention and outcomes of colorectal cancer (CRC) in IBD as part of the 3rd ECCO scientific pathogenesis workshop.
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Affiliation(s)
- Shaji Sebastian
- Hull & East Yorkshire Hospitals NHS Trust, Hull York Medical School, Hull, United Kingdom.
| | - Vincent Hernández
- Gastroenterology Department, Complexo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Pär Myrelid
- Division of Surgery, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, County Council of Östergötland, Linköping, Sweden
| | - Revital Kariv
- Service for Gastrointestinal Malignancies, Department of Gastroenterology & Liver Disease, Tel Aviv Sourasky Medical Center, Israel
| | - Epameinondas Tsianos
- University of Ioannina, 1st Division of Internal Medicine and Hepato-Gastroenterology Unit, Greece
| | - Murat Toruner
- Ankara University Medical School, Ibni Sina Hospital, Division of Gastroenterology, Ankara, Turkey
| | - Marc Marti-Gallostra
- Department of Colorectal Surgery, University Hospital of Valle de Hebron, Barcelona, Spain
| | - Antonino Spinelli
- Dipartimento e Cattedra di Chirurgia Generale, Istituto Clinico Humanitas IRCCS, Università degli Studi di Milano, Rozzano, Milano, Italy
| | | | - Elif Sarıtas Yuksel
- Department of Gastroenterology, Katip Celebi University, Ataturk Research and Teaching Hospital, Izmir, Turkey
| | - Christoph Gasche
- Christian Doppler Laboratory on Molecular Cancer Chemoprevention, Division of Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Sandro Ardizzone
- Chair of Gastroenterology, "L. Sacco" University Hospital, Milan, Italy
| | - Silvio Danese
- Department of Gastroenterology, Istituto Clinico Humanitas, Milan, Italy.
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Low D, Mizoguchi A, Mizoguchi E. DNA methylation in inflammatory bowel disease and beyond. World J Gastroenterol 2013; 19:5238-5249. [PMID: 23983426 PMCID: PMC3752557 DOI: 10.3748/wjg.v19.i32.5238] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/13/2013] [Accepted: 07/19/2013] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a consequence of the complex, dysregulated interplay between genetic predisposition, environmental factors, and microbial composition in the intestine. Despite a great advancement in identifying host-susceptibility genes using genome-wide association studies (GWAS), the majority of IBD cases are still underrepresented. The immediate challenge in post-GWAS era is to identify other causative genetic factors of IBD. DNA methylation has received increasing attention for its mechanistical role in IBD pathogenesis. This stable, yet dynamic DNA modification, can directly affect gene expression that have important implications in IBD development. The alterations in DNA methylation associated with IBD are likely to outset as early as embryogenesis all the way until old-age. In this review, we will discuss the recent advancement in understanding how DNA methylation alterations can contribute to the development of IBD.
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Bardhan K, Liu K. Epigenetics and colorectal cancer pathogenesis. Cancers (Basel) 2013; 5:676-713. [PMID: 24216997 PMCID: PMC3730326 DOI: 10.3390/cancers5020676] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) develops through a multistage process that results from the progressive accumulation of genetic mutations, and frequently as a result of mutations in the Wnt signaling pathway. However, it has become evident over the past two decades that epigenetic alterations of the chromatin, particularly the chromatin components in the promoter regions of tumor suppressors and oncogenes, play key roles in CRC pathogenesis. Epigenetic regulation is organized at multiple levels, involving primarily DNA methylation and selective histone modifications in cancer cells. Assessment of the CRC epigenome has revealed that virtually all CRCs have aberrantly methylated genes and that the average CRC methylome has thousands of abnormally methylated genes. Although relatively less is known about the patterns of specific histone modifications in CRC, selective histone modifications and resultant chromatin conformation have been shown to act, in concert with DNA methylation, to regulate gene expression to mediate CRC pathogenesis. Moreover, it is now clear that not only DNA methylation but also histone modifications are reversible processes. The increased understanding of epigenetic regulation of gene expression in the context of CRC pathogenesis has led to development of epigenetic biomarkers for CRC diagnosis and epigenetic drugs for CRC therapy.
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Affiliation(s)
- Kankana Bardhan
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, and Cancer Center, Georgia Regents University, Augusta, GA 30912, USA.
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Azuara D, Rodriguez-Moranta F, de Oca J, Sanjuan X, Guardiola J, Lobaton T, Wang A, Boadas J, Piqueras M, Monfort D, Galter S, Esteller M, Moreno V, Capellá G. Novel methylation panel for the early detection of neoplasia in high-risk ulcerative colitis and Crohn's colitis patients. Inflamm Bowel Dis 2013; 19:165-73. [PMID: 22532293 DOI: 10.1002/ibd.22994] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Patients with ulcerative colitis and Crohn's colonic disease are at increased risk of developing colorectal cancer (CRC). The aim of the study was to analyze the methylation status of selected genes as a risk marker for CRC in inflammatory bowel disease (IBD) patients. METHODS We evaluated the methylation status of four genes (TGFB2, SLIT2, HS3ST2, and TMEFF2) in biopsies of four groups of patients: 60 patients with sporadic CRC, 32 patients with IBD-associated neoplasia, 85 patients with IBD without associated neoplasia (20 at high risk and 65 at low risk), and 28 healthy controls. Methylation-specific melting curve analysis (MS-MCA) was used. Methylation status of these genes was also assessed in stool DNA from 60 IBD patients without neoplasia. RESULTS Methylation of the panel of genes analyzed was a very common phenomenon (78%) in IBD-associated neoplasia. The prevalence of methylation in adjacent nonneoplastic mucosa was also high (12/30). This prevalence was higher than in mucosa from healthy controls (2/28;7.1%; P < 0.05). Methylation of SLIT2 and TMEFF2 was more frequently detected in the mucosa of IBD patients at high risk of dysplasia or cancer (15/20) than patients at low risk (32/63) (P = 0.05 and P = 0.03, respectively). When stool samples were assessed, only SLIT2 gene methylation was more frequently methylated in the group of patients at high risk of dysplasia or cancer (4/16) compared to low risk (0/37) (P = 0.006). CONCLUSIONS Analysis of a panel of methylation markers may help in the early identification of colorectal dysplasia or cancer in high-risk IBD patients.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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Tahara T, Arisawa T. Potential usefulness of DNA methylation as a risk marker for digestive cancer associated with inflammation. Expert Rev Mol Diagn 2012; 12:489-97. [PMID: 22702365 DOI: 10.1586/erm.12.38] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA methylation has been deeply involved in the development and progression of digestive cancer, while aberrant DNA methylation has also often been observed in aged and inflammatory digestive tissues. Helicobacter pylori-related chronic gastritis, ulcerative colitis, and hepatitis B virus- and hepatitis C virus-related chronic hepatitis, are significant risk factors for developing cancer. A number of studies have revealed the specific methylation patterns for specific tissue types. DNA methylation status is stably transmitted to daughter cells. Also, unlike genetic mutations, it is possible to detect very tiny amounts of methylated DNA among tissues. Therefore, the use of aberrant methylation as a marker could be applicable to risk estimation of cancer development. We discuss the potential usefulness of DNA methylation as a risk marker for inflammation-associated digestive cancer, especially with attempts on gastric cancer, ulcerative colitis-associated cancer, and hepatitis B virus- and hepatitis C virus-related hepatocellular carcinoma.
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Affiliation(s)
- Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, 1-98 Dengakugakubo Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
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Relationship between tumor DNA methylation status and patient characteristics in African-American and European-American women with breast cancer. PLoS One 2012; 7:e37928. [PMID: 22701537 PMCID: PMC3365111 DOI: 10.1371/journal.pone.0037928] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/30/2012] [Indexed: 01/06/2023] Open
Abstract
Aberrant DNA methylation is critical for development and progression of breast cancer. We investigated the association of CpG island methylation in candidate genes and clinicopathological features in 65 African-American (AA) and European-American (EA) breast cancer patients. Quantitative methylation analysis was carried out on bisulfite modified genomic DNA and sequencing (pyrosequencing) for promoter CpG islands of p16, ESR1, RASSF1A, RARβ2, CDH13, HIN1, SFRP1 genes and the LINE1 repetitive element using matched paired non-cancerous and breast tumor specimen (32 AA and 33 EA women). Five of the genes, all known tumor suppressor genes (RASSF1A, RARβ2, CDH13, HIN1 and SFRP1), were found to be frequently hypermethylated in breast tumor tissues but not in the adjacent non-cancerous tissues. Significant differences in the CDH13 methylation status were observed by comparing DNA methylation between AA and EA patients, with more obvious CDH13 methylation differences between the two patient groups in the ER- disease and among young patients (age<50). In addition, we observed associations between CDH13, SFRP1, and RASSF1A methylation and breast cancer subtypes and between SFRP1 methylation and patient's age. Furthermore, tumors that received neoadjuvant therapy tended to have reduced RASSF1A methylation when compared with chemotherapy naïve tumors. Finally, Kaplan Meier survival analysis showed a significant association between methylation at 3 loci (RASSF1A, RARβ2 and CDH13) and reduced overall disease survival. In conclusion, the DNA methylation status of breast tumors was found to be significantly associated with clinicopathological features and race/ethnicity of the patients.
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Olaru AV, Cheng Y, Agarwal R, Yang J, David S, Abraham JM, Yu W, Lazarev M, Brant SR, Marohn MR, Hutcheon DF, Harpaz N, Meltzer SJ, Mori Y, Mori Y. Unique patterns of CpG island methylation in inflammatory bowel disease-associated colorectal cancers. Inflamm Bowel Dis 2012; 18:641-8. [PMID: 21830278 PMCID: PMC3214229 DOI: 10.1002/ibd.21826] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 06/20/2011] [Indexed: 12/20/2022]
Abstract
BACKGROUND CpG island (CGI) hypermethylation at discrete loci is a prevalent cancer-promoting abnormality in sporadic colorectal carcinomas (S-CRCs). We investigated genome-wide CGI methylation in inflammatory bowel disease (IBD)-associated CRCs (IBD-CRCs). METHODS Methylation microarray analyses were conducted on seven IBD-CRCs, 17 S-CRCs, and eight normal control colonic tissues from patients without CRC or IBD. CGI methylator phenotype (CIMP), a surrogate marker for widespread cancer-specific CGI hypermethylation, was examined in 30 IBD-CRCs and 43 S-CRCs. RESULTS The genome-wide CGI methylation pattern of IBD-CRCs was CIMP status-dependent. Based on methylation array data profiling of all autosomal loci, CIMP(+) IBD-CRCs grouped together with S-CRCs, while CIMP(-) IBD-CRCs grouped together with control tissues. CIMP(-) IBD-CRCs demonstrated less methylation than did age-matched CIMP(-) S-CRCs at autosomal CGIs (z-score -0.17 vs. 0.09, P = 3 × 10(-3)) and CRC-associated hypermethylation target CGIs (z-score -0.43 vs. 0.68, P = 1 × 10(-4)). Age-associated hypermethylation target CGIs were significantly overrepresented in CGIs that were hypermethylated in S-CRCs (P = 1 × 10(-192)), but not in CGIs that were hypermethylated in IBD-CRCs (P = 0.11). In contrast, KRAS mutation prevalence was similar between IBD-CRCs and S-CRCs. Notably, CIMP(+) prevalence was significantly higher in older than in younger IBD-CRC cases (50.0 vs. 4.2, P = 0.02), but not in S-CRC cases (9.7 vs. 16.7, P = 0.92). CONCLUSIONS Cancer-specific CGI hypermethylation and age-associated CGI hypermethylation are diminished in IBD-CRCs relative to S-CRCs, while the KRAS mutation rate is comparable between these cancers. CGI hypermethylation appears to play only a minor role in IBD-associated carcinogenesis. We speculate that aging, rather than inflammation per se, promotes CIMP(+) CRCs in IBD patients.
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Affiliation(s)
- Alexandru V. Olaru
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Yulan Cheng
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Rachana Agarwal
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Jian Yang
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Stefan David
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - John M. Abraham
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Wayne Yu
- Sidney Kimmel Comprehensive Cancer Center, DNA Microarray Core Facility, Johns Hopkins University School of Medicine; 1503 E. Jefferson Street, Baltimore, Maryland 21287
| | - Mark Lazarev
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Steven R. Brant
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Michael R. Marohn
- Department of Surgery, Johns Hopkins University School of Medicine; 600 N. Wolfe Street, Baltimore MD 21207
| | - David F. Hutcheon
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Noam Harpaz
- Department of Pathology, Mount Sinai School of Medicine; One Gustave L. Levy Place, New York, New York 10029
| | - Stephen J. Meltzer
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205, Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center; 1503 E. Jefferson Street, Baltimore, Maryland 21287
| | - Yuriko Mori
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
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DNA methylation profiles of primary colorectal carcinoma and matched liver metastasis. PLoS One 2011; 6:e27889. [PMID: 22132162 PMCID: PMC3221680 DOI: 10.1371/journal.pone.0027889] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 10/26/2011] [Indexed: 12/31/2022] Open
Abstract
Background The contribution of DNA methylation to the metastatic process in colorectal cancers (CRCs) is unclear. Methods We evaluated the methylation status of 13 genes (MINT1, MINT2, MINT31, MLH1, p16, p14, TIMP3, CDH1, CDH13, THBS1, MGMT, HPP1 and ERα) by bisulfite-pyrosequencing in 79 CRCs comprising 36 CRCs without liver metastasis and 43 CRCs with liver metastasis, including 16 paired primary CRCs and liver metastasis. We also performed methylated CpG island amplification microarrays (MCAM) in three paired primary and metastatic cancers. Results Methylation of p14, TIMP3 and HPP1 in primary CRCs progressively decreased from absence to presence of liver metastasis (13.1% vs. 4.3%; 14.8% vs. 3.7%; 43.9% vs. 35.8%, respectively) (P<.05). When paired primary and metastatic tumors were compared, only MGMT methylation was significantly higher in metastatic cancers (27.4% vs. 13.4%, P = .013), and this difference was due to an increase in methylation density rather than frequency in the majority of cases. MCAM showed an average 7.4% increase in DNA methylated genes in the metastatic samples. The numbers of differentially hypermethylated genes in the liver metastases increased with increasing time between resection of the primary and resection of the liver metastasis. Bisulfite-pyrosequencing validation in 12 paired samples showed that most of these increases were not conserved, and could be explained by differences in methylation density rather than frequency. Conclusions Most DNA methylation differences between primary CRCs and matched liver metastasis are due to random variation and an increase in DNA methylation density rather than de-novo inactivation and silencing. Thus, DNA methylation changes occur for the most part before progression to liver metastasis.
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Sanchez JA, Dejulius KL, Bronner M, Church JM, Kalady MF. Relative role of methylator and tumor suppressor pathways in ulcerative colitis-associated colon cancer. Inflamm Bowel Dis 2011; 17:1966-70. [PMID: 21618350 DOI: 10.1002/ibd.21526] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 09/20/2010] [Indexed: 12/09/2022]
Abstract
BACKGROUND Chronic ulcerative colitis (UC) is associated with an increased colorectal cancer risk which may be secondary to repetitive mucosal injury. Both epigenetic methylation and the classic adenoma-to-carcinoma sequence have been implicated in this malignant transformation, but the underlying molecular mechanisms remain poorly defined. This study compares the molecular characteristics of colitis-associated and common colorectal cancers. METHODS Nineteen patients with colorectal adenocarcinomas arising within UC were matched for age and cancer site with 54 patients with sporadic adenocarcinomas. Tumor tissue was examined for BRAF mutations, CpG island methylator phenotype (CIMP), and MLH1 promoter methylation. Mutations of KRAS and p53 were assessed by sequencing. RESULTS Patient demographics were similar for the two groups. CIMP was observed in 22% of sporadic colorectal cancers and in 5% of UC cancers (P = 0.162). Rates of BRAF mutation (4% vs 5%, P = 1.0), MLH1 methylation (9% versus 5%, P = 0.682), and KRAS mutations (24% versus 32%, P = 0.552) were similar between the groups. However, colitis-associated colorectal cancers were more likely to have a p53 mutation compared to sporadic adenocarcinomas (95% versus 53%, P = 0.001). The dominant mutation for colitis-associated cancers was a mutation in codon 4, representing half of the mutations. Furthermore, colitis-associated cancers had a higher rate of mutation in codon 8 (48% versus 6%, P < 0.001) than sporadic counterparts. CONCLUSIONS Unlike other inflammatory gastrointestinal cancers, colitis-associated colorectal cancers do not preferentially arise via a methylator pathway when compared to sporadic colorectal cancers. Chromosomal instability remains an important etiology, but with a unique p53 frequency and mutation pattern.
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Affiliation(s)
- Julian A Sanchez
- Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio 44195, USA.
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Saito S, Kato J, Hiraoka S, Horii J, Suzuki H, Higashi R, Kaji E, Kondo Y, Yamamoto K. DNA methylation of colon mucosa in ulcerative colitis patients: correlation with inflammatory status. Inflamm Bowel Dis 2011; 17:1955-65. [PMID: 21830274 DOI: 10.1002/ibd.21573] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 10/11/2010] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although DNA methylation of colonic mucosa in ulcerative colitis (UC) has been suggested, the majority of published reports indicate the correlation between methylation of colon mucosa and occurrence of UC-related dysplasia or cancer without considering the mucosal inflammatory status. The aim of this study was to verify whether mucosal inflammation-specific DNA methylation occurs in the colon of UC. METHODS Of 15 gene loci initially screened, six loci (ABCB1, CDH1, ESR1, GDNF, HPP1, and MYOD1) methylated in colon mucosa of UC were analyzed according to inflammatory status using samples from 28 surgically resected UC patients. RESULTS Four of six regions (CDH1, GDNF, HPP1, and MYOD1) were more highly methylated in the active inflamed mucosa than in the quiescent mucosa in each UC patient (P = 0.003, 0.0002, 0.02, and 0.048, respectively). In addition, when the methylation status of all samples taken from examined patients was stratified according to inflammatory status, methylation of CDH1 and GDNF loci was significantly higher in active inflamed mucosa than in quiescent mucosa (P = 0.045 and 0.002, respectively). Multiple linear regression analysis revealed that active inflammation was an independent factor of methylation for CDH1 and GDNF. DNA methyltransferase 1 and 3b were highly expressed in colon epithelial cells with active mucosal inflammation, suggesting their involvement in inflammation-dependent methylation. CONCLUSIONS Methylation in colonic mucosa of UC was correlated with mucosal inflammatory status, suggesting the involvement of methylation due to chronic active inflammation in UC carcinogenesis.
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Affiliation(s)
- Shunsuke Saito
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama Japan
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Yano Y, Konishi K, Yamochi T, Katagiri A, Nozawa H, Suzuki H, Toyota M, Kubota Y, Muramoto T, Kobayashi Y, Tojo M, Konda K, Makino R, Kaneko K, Yoshikawa N, Ota H, Imawari M. Clinicopathological and molecular features of colorectal serrated neoplasias with different mucosal crypt patterns. Am J Gastroenterol 2011; 106:1351-8. [PMID: 21427714 DOI: 10.1038/ajg.2011.76] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Endoscopic examination shows that serrated neoplasias (SNs), such as serrated adenomas and sessile serrated adenomas, exhibit different mucosal crypt patterns. However, it remains unclear whether advanced serrated polyps with different mucosal crypt patterns have different clinicopathological or molecular features. METHODS We classified the mucosal crypt patterns of 86 SNs into three types (hyperplastic, adenomatous, and mixed pattern) and evaluated their clinicopathological and molecular features. RESULTS We found significant differences in the proliferative activity status between SNs with mixed/adenomatous patterns and those with the hyperplastic patterns. SNs with the hyperplastic pattern were frequently located in the proximal colon and had a macroscopically superficial appearance, whereas SNs with the adenomatous pattern were often located in the distal colon and had a protruding appearance. Furthermore, a significant difference was observed in the frequency of the CpG island methylator phenotype (CIMP), involving the methylation of two or more CIMP-related genes (MINT1, MINT2, MINT31, p16, and MLH1), between SNs with the hyperplastic pattern and those with the mixed/adenomatous patterns (18/32 (56%) vs. 8/28 (29%) or 7/26 (27%); P=0.0309 or P=0.0249, respectively). Moreover, the prevalence of KRAS mutations was significantly higher in SNs with the adenomatous pattern than in those with the hyperplastic pattern (7/26 (27%) vs. 1/32 (3%); P=0.0173). In comparison with other patterns, the mixed pattern was detected more frequently in mixed serrated polyps (MSPs), which contain separate histological components. Some MSPs exhibited concordant molecular alterations among the different histological components. CONCLUSIONS The clinicopathological and molecular features of SNs correlated strongly with their mucosal crypt patterns, which were observed using chromoendoscopy.
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Affiliation(s)
- Yuichiro Yano
- Division of Gastroenterology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan.
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Abstract
Patients with inflammatory bowel disease (IBD) have an increased risk of developing colorectal cancer (CRC). Risk factors are extent and severity of colonic inflammation, concurrent primary sclerosing cholangitis, and a positive family history of sporadic CRC. The chromosomal instability, microsatellite instability and hypermethylation pathways form the molecular background of IBD-related carcinogenesis, which is not different from sporadic CRC. The dysplasia-carcinoma sequence of IBD-related colorectal carcinogenesis makes patients suitable for endoscopic surveillance. In the future, new molecular biomarkers and endoscopic techniques may improve early detection of precursor lesions of IBD-related CRC. The potential of aminosalicylates and ursodeoxycholic acid as chemopreventive agents needs to be studied in randomized clinical trials. Patients with IBD who are being treated with thiopurines have a slightly increased risk of developing lymphoproliferative disorders, whereas patients with small bowel Crohn's disease have a high relative risk and a small absolute risk of developing small bowel adenocarcinoma.
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Affiliation(s)
- M M H Claessen
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, the Netherlands
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Rawson JB, Manno M, Mrkonjic M, Daftary D, Dicks E, Buchanan DD, Younghusband HB, Parfrey PS, Young JP, Pollett A, Green RC, Gallinger S, McLaughlin JR, Knight JA, Bapat B. Promoter methylation of Wnt antagonists DKK1 and SFRP1 is associated with opposing tumor subtypes in two large populations of colorectal cancer patients. Carcinogenesis 2011; 32:741-7. [PMID: 21304055 DOI: 10.1093/carcin/bgr020] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Aberrant activation of canonical Wnt signaling is a hallmark event in colorectal carcinogenesis. The Dickkopf-1 (DKK1) and Secreted Frizzled Related Protein 1 (SFRP1) genes encode extracellular inhibitors of Wnt signaling that are frequently silenced by promoter hypermethylation in colorectal cancer (CRC). These methylation events have been identified as prognostic markers of patient outcome and tumor subtype in several cancers but similar roles in CRC have not been comprehensively examined. In CRC, the microsatellite instability (MSI) subtype associates with favorable disease outcome but the molecular events that are responsible remain poorly understood. Consequently, we quantified promoter methylation status of the Wnt antagonist genes DKK1 and SFRP1 in a large population-based cohort of CRCs from Ontario (n = 549) and Newfoundland (n = 696) stratified by MSI status. We examined the association between methylation status and clinicopathological features including tumor MSI status and patient survival. DKK1 and SFRP1 were methylated in 13 and 95% of CRCs, respectively. In Ontario, DKK1 methylation was strongly associated with MSI tumors after adjustment for age, sex and tumor location [odds ratio (OR) = 13.7, 95% confidence interval (CI) = 7.8-24.2, P < 0.001]. Conversely, SFRP1 methylation was inversely associated with MSI tumors after these adjustments (OR = 0.3, 95% CI = 0.1-0.9, P = 0.009). Similar results were obtained in Newfoundland. There were no independent associations with recurrence-free survival. This is the first large study to identify associations between Wnt antagonist promoter hypermethylation and CRC MSI subtype. These events provide insight into subtype-specific epigenetic mediation of Wnt signaling in CRC.
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Affiliation(s)
- James B Rawson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Worthley DL, Whitehall VLJ, Le Leu RK, Irahara N, Buttenshaw RL, Mallitt KA, Greco SA, Ramsnes I, Winter J, Hu Y, Ogino S, Young GP, Leggett BA. DNA methylation in the rectal mucosa is associated with crypt proliferation and fecal short-chain fatty acids. Dig Dis Sci 2011; 56:387-96. [PMID: 20635146 DOI: 10.1007/s10620-010-1312-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/14/2010] [Indexed: 01/29/2023]
Abstract
BACKGROUND DNA methylation varies throughout the normal colorectal mucosa and DNA methylation in normal appearing mucosa is associated with serrated and adenomatous neoplasia elsewhere within the colorectum. AIMS The purpose of this study was to measure luminal chemistry, rectal proliferation and mucosal DNA methylation and thus determine whether regional and pathological patterns of DNA methylation could be explained by luminal and epithelial factors. METHODS Twenty healthy subjects had normal rectal mucosal biopsies and a 24-h fecal collection. Rectal biopsies were analyzed for epithelial proliferation (Ki67 immunohistochemistry) and DNA methylation at 17 different markers, including "type A" markers (ESR1, GATA5, HIC1, HPP1, SFRP1), "type C" markers (MGMT, MLH1, CDKN2A, MINT1, MINT2, MINT31, IGF2, CACNA1G, NEUROG1, SOCS1, RUNX3), and LINE-1. Fecal analysis included short-chain fatty acids (SCFA), pH and ammonia. Mean "type A" and CIMP panel methylation Z-scores were calculated. RESULTS Rectal proliferation was significantly correlated with methylation at ESR1 (ρ = 0.81, P = 0.003) and GATA5 (ρ = 0.78, P = 0.012). LINE-1 methylation was 71.7 vs. 74.1%, in patients with "low" and "high" fecal total SCFA concentration (defined by the median value), respectively (P = 0.0019). On multivariate linear regression "type A" methylation was independently associated with rectal proliferation (P = 0.001). LINE-1 methylation was directly associated with rectal proliferation (P = 0.038) and total fecal SCFA concentration (P = 0.002), and inversely associated with fecal NH(3) concentrations (P = 0.003). CONCLUSIONS DNA methylation in normal rectal mucosa is associated with crypt proliferation and fecal SCFA concentration. These associations may help to explain regional differences in DNA methylation as well as providing a possible link between the colorectal lumen and carcinogenesis.
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Affiliation(s)
- Daniel L Worthley
- Conjoint Gastroenterology Laboratory, Royal Brisbane and Women's Hospital Research Foundation Clinical Research Centre, Brisbane, QLD, Australia.
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46
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Hughes KR, Sablitzky F, Mahida YR. Expression profiling of Wnt family of genes in normal and inflammatory bowel disease primary human intestinal myofibroblasts and normal human colonic crypt epithelial cells. Inflamm Bowel Dis 2011; 17:213-20. [PMID: 20848536 DOI: 10.1002/ibd.21353] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Wnt signaling regulates intestinal epithelial stem cell function. Wnt ligands bind Frizzled (Fz) receptors and low-density lipoprotein-receptor-related protein (LRP) 5 and 6. Secreted Frizzled-related protein (SFRP) and Dickkopf families inhibit Wnt signaling. Our aim was to study expression of Wnt family of genes in isolated intestinal myofibroblasts and crypt epithelial cells. METHODS Myofibroblasts were isolated from normal colonic and small intestinal mucosal samples and those affected by ulcerative colitis (UC) and Crohn's disease. Expression of the Wnt family of genes was studied by polymerase chain reaction (PCR) array. Epithelial proliferation was studied using IEC-6 cells. RESULTS Most of the myofibroblast isolates expressed Wnt2, Wnt5A, Wnt5B, Fzd1, Fzd2, Fzd4, Fzd6, Fzd7, Fzd8, LRP6, Dickkopf1, and SFRP1. Compared to myofibroblasts isolated from normal colonic mucosal samples, real-time reverse transcription-PCR studies (using additional isolates) showed significantly reduced expression of SFRP1 in UC myofibroblasts (3.34-fold reduction, P < 0.01). Recombinant SFRP1 inhibited proliferation of IEC-6 epithelial cells. In colonic crypt epithelial cells, expression of Wnt ligands and their inhibitors was generally either absent or very weak. By contrast, all the crypt epithelial preparations expressed Fzd1, Fzd5, Fzd7, Fzd8, and LRP6. CONCLUSIONS Human intestinal myofibroblasts expressed a number of Wnt ligands, their receptors, and inhibitors. In contrast, colonic crypt epithelial cells predominantly expressed Wnt receptors. Compared to myofibroblasts isolated from normal colonic mucosa, those affected by UC showed significantly reduced expression of SFRP1. Since reduced SFRP1 expression has been associated with malignancy, low myofibroblast expression of this Wnt inhibitor may be implicated in increased risk of cancer in UC.
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Affiliation(s)
- K R Hughes
- Institute of Infection, Immunity and Inflammation, University of Nottingham, Nottingham, UK
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Bediaga NG, Acha-Sagredo A, Guerra I, Viguri A, Albaina C, Ruiz Diaz I, Rezola R, Alberdi MJ, Dopazo J, Montaner D, Renobales M, Fernández AF, Field JK, Fraga MF, Liloglou T, de Pancorbo MM. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res 2010; 12:R77. [PMID: 20920229 PMCID: PMC3096970 DOI: 10.1186/bcr2721] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 09/29/2010] [Indexed: 12/13/2022] Open
Abstract
Introduction Identification of gene expression-based breast cancer subtypes is considered a critical means of prognostication. Genetic mutations along with epigenetic alterations contribute to gene-expression changes occurring in breast cancer. So far, these epigenetic contributions to sporadic breast cancer subtypes have not been well characterized, and only a limited understanding exists of the epigenetic mechanisms affected in those particular breast cancer subtypes. The present study was undertaken to dissect the breast cancer methylome and to deliver specific epigenotypes associated with particular breast cancer subtypes. Methods By using a microarray approach, we analyzed DNA methylation in regulatory regions of 806 cancer-related genes in 28 breast cancer paired samples. We subsequently performed substantial technical and biologic validation by pyrosequencing, investigating the top qualifying 19 CpG regions in independent cohorts encompassing 47 basal-like, 44 ERBB2+ overexpressing, 48 luminal A, and 48 luminal B paired breast cancer/adjacent tissues. With the all-subset selection method, we identified the most subtype-predictive methylation profiles in multivariable logistic regression analysis. Results The approach efficiently recognized 15 individual CpG loci differentially methylated in breast cancer tumor subtypes. We further identified novel subtype-specific epigenotypes that clearly demonstrate the differences in the methylation profiles of basal-like and human epidermal growth factor 2 (HER2)-overexpressing tumors. Conclusions Our results provide evidence that well-defined DNA methylation profiles enable breast cancer subtype prediction and support the utilization of this biomarker for prognostication and therapeutic stratification of patients with breast cancer.
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Affiliation(s)
- Naiara G Bediaga
- BIOMICs Research Group, Centro de Investigacion y Estudios Avanzados ‘Lucio Lascaray’, University of the Basque Country UPV/EHU, Vitoria-Gazteiz, Spain
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Harpaz N, Polydorides AD. Colorectal dysplasia in chronic inflammatory bowel disease: pathology, clinical implications, and pathogenesis. Arch Pathol Lab Med 2010; 134:876-95. [PMID: 20524866 DOI: 10.5858/134.6.876] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
CONTEXT Colorectal cancer, the most lethal long-term complication of chronic inflammatory bowel disease (IBD), is the culmination of a complex sequence of molecular and histologic derangements of the intestinal epithelium that are initiated and at least partially sustained by chronic inflammation. Dysplasia, the earliest histologic manifestation of this process, plays an important role in cancer prevention by providing the first clinical alert that this sequence is underway and serving as an endpoint in colonoscopic surveillance of patients at high risk for colorectal cancer. OBJECTIVE To review the histology, nomenclature, clinical implications, and molecular pathogenesis of dysplasia in IBD. DATA SOURCE Literature review and illustrations from case material. CONCLUSIONS The diagnosis and grading of dysplasia in endoscopic surveillance biopsies play a decisive role in the management of patients with IBD. Although interpathologist variation, endoscopic sampling problems, and incomplete information regarding the natural history of dysplastic lesions are important limiting factors, indirect evidence that surveillance may be an effective means of reducing cancer-related mortality in the population with IBD has helped validate the histologic criteria, nomenclature, and clinical recommendations that are the basis of current practice among pathologists and clinicians. Emerging technologic advances in endoscopy may permit more effective surveillance, but ultimately the greatest promise for cancer prevention in IBD lies in expanding our thus far limited understanding of the molecular pathogenetic relationships between neoplasia and chronic inflammation.
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Affiliation(s)
- Noam Harpaz
- Department of Pathology, The Mount Sinai School of Medicine, New York, New York 10092, USA.
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Abstract
Background: Epigenetic silencing of Wnt antagonists and expression changes in genes associated with Wnt response pathways occur in early sporadic colorectal tumourigenesis, indicating that tumour cells are more sensitive to Wnt growth factors and respond differently. In this study, we have investigated whether similar changes occur in key markers of the Wnt response pathways in the genetic form of the disease, familial adenomatous polyposis (FAP). Methods: We investigated epigenetic and expression changes using pyrosequencing and real-time RT-PCR in samples from seven patients without neoplasia, and matched normal and tumour tissues from 22 sporadic adenoma and 14 FAP patients. Results: We found that 17 out of 24 (71%) FAP adenomas were hypermethylated at sFRP1, compared with 20 out of 22 (91%) of sporadic cases. This was reflected at the level of sFRP1 transcription, where 73% of FAP and 100% of sporadic cases were down-regulated. Increased expression levels of c-myc and FZD3 were less common in FAP (35 and 46% respectively) than sporadic tumours (78 and 67% respectively). Conclusion: Overall, the changes in expression and methylation were comparable, although the degree of change was generally lower in the FAP adenomas. Molecular heterogeneity between multiple adenomas from individual FAP patients may reflect different developmental fates for these premalignant tumours.
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50
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Kuester D, Guenther T, Biesold S, Hartmann A, Bataille F, Ruemmele P, Peters B, Meyer F, Schubert D, Bohr UR, Malfertheiner P, Lippert H, Silver ARJ, Roessner A, Schneider-Stock R. Aberrant methylation of DAPK in long-standing ulcerative colitis and ulcerative colitis-associated carcinoma. Pathol Res Pract 2010; 206:616-24. [PMID: 20630662 DOI: 10.1016/j.prp.2010.05.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 05/19/2010] [Indexed: 02/08/2023]
Abstract
Death-associated protein kinase (DAPK) has pro-apoptotic functions and participates in various apoptotic systems. DAPK acts as a tumor suppressor, and its inactivation by promoter hypermethylation has been frequently observed in various human cancers. As alterations of pro-apoptotic genes might cause instability in the balance of cell-turnover during chronic inflammatory processes, epigenetic silencing of DAPK might be involved in the carcinogenesis of ulcerative colitis-associated carcinoma (UCC). To evaluate the role of DAPK in the inflammation-driven carcinogenesis of ulcerative colitis (UC), we analyzed promoter hypermethylation and protein expression of DAPK using methylation-specific PCR and immunohistochemistry in 43 UCCs and paired UC-background mucosa, as well as in UC-background mucosa of 50 patients without UCC. The frequency of methylation of DAPK in UCCs was low (27.6%) compared to overall non-neoplastic UC-background mucosa (48.3%; p=0.02) and sporadic colorectal carcinoma (57.4%, p=0.019). The difference in the methylation frequency in UC-background mucosa in patients without UCC (54.2%), compared to those with UCC (40.0%), was not significant (p=0.141). Promoter methylation correlated significantly with decreased DAPK protein expression (p<0.001) and severity of inflammatory activity (p=0.024). In unmethylated UC-background mucosa, DAPK protein expression increased with activity of UC-associated inflammation, suggesting a protective role of the pro-apoptotic DAPK during the chronic inflammatory process of UC. Thus, inactivation of DAPK by promoter hypermethylation might be crucial for accumulation of DNA damage in inflamed mucosa of UC, and might therefore contribute to the initiation of the neoplastic process and development of UC-associated carcinoma.
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Affiliation(s)
- Doerthe Kuester
- Department of Pathology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, 39120 Magdeburg, Germany.
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