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van Toledo DEFWM, Bleijenberg AGC, Venema A, de Wit MJ, van Eeden S, Meijer GA, Carvalho B, Dekker E, Henneman P, IJspeert JEG, van Noesel CJM. Aberrant PRDM2 methylation as an early event in serrated lesions destined to evolve into microsatellite-instable colorectal cancers. J Pathol Clin Res 2024; 10:e348. [PMID: 38380944 PMCID: PMC10880511 DOI: 10.1002/cjp2.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/17/2023] [Accepted: 10/15/2023] [Indexed: 02/22/2024]
Abstract
Up to 30% of colorectal cancers (CRCs) develop from sessile serrated lesions (SSLs). Within the serrated neoplasia pathway, at least two principally distinct oncogenetic routes exist generating microsatellite-stable and microsatellite-instable CRCs, respectively. Aberrant DNA methylation (DNAm) is found early in the serrated pathway and might play a role in both oncogenetic routes. We studied a cohort of 23 SSLs with a small focus (<10 mm) of dysplasia or cancer, 10 of which were MLH1 deficient and 13 MLH1 proficient. By comparing, for each SSL, the methylation status of (1) the region of dysplasia or cancer (SSL-D), (2) the nondysplastic SSL (SSL), and (3) adjacent normal mucosa, differentially methylated probes (DMPs) and regions (DMRs) were assessed both genome-wide as well as in a tumor-suppressor gene-focused approach. By comparing DNAm of MLH1-deficient SSL-Ds with their corresponding SSLs, we identified five DMRs, including those annotating for PRDM2 and, not unexpectedly, MLH1. PRDM2 gene promotor methylation was associated with MLH1 expression status, as it was largely hypermethylated in MLH1-deficient SSL-Ds and hypomethylated in MLH1-proficient SSL-Ds. Significantly increased DNAm levels of PRDM2 and MLH1, in particular at 'critical' MLH1 probe sites, were to some extent already visible in SSLs as compared to normal mucosa (p = 0.02, p = 0.01, p < 0.0001, respectively). No DMRs, nor DMPs, were identified for SSLs destined to evolve into MLH1-proficient SSL-Ds. Our data indicate that, within both arms of the serrated CRC pathway, the majority of the epigenetic alterations are introduced early during SSL formation. Promoter hypermethylation of PRDM2 and MLH1 on the other hand specifically initiates in SSLs destined to transform into MLH1-deficient CRCs suggesting that the fate of SSLs may not necessarily result from a stochastic process but possibly is already imprinted and predisposed.
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Affiliation(s)
- David EFWM van Toledo
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Arne GC Bleijenberg
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Andrea Venema
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Mireille J de Wit
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Susanne van Eeden
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Gerrit A Meijer
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Beatrice Carvalho
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Peter Henneman
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Joep EG IJspeert
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Carel JM van Noesel
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
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2
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Musulen E, Gené M, Cuatrecasas M, Amat I, Veiga JA, Fernández-Aceñero MJ, Chimisana VF, Tarragona J, Jurado I, Fernández-Victoria R, Martínez-Ciarpaglini C, Alenda González C, Zac C, Fernández-Figueras MT, Esteller M. Gastric metaplasia as a precursor of nonconventional dysplasia in inflammatory bowel disease. Hum Pathol 2024; 143:50-61. [PMID: 38000679 DOI: 10.1016/j.humpath.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/18/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Gastric metaplasia in colonic mucosa with inflammatory bowel disease (IBD) develops as an adaptation mechanism. The association between gastric metaplasia and nonconventional and/or conventional dysplasia as precursors of colitis-associated colorectal cancer is unknown. To address this question, we retrospectively reviewed a series of 33 IBD colectomies to identify gastric metaplasia in 76 precursor lesions. We obtained 61 nonconventional and 15 conventional dysplasias. Among nonconventional dysplasia, 31 (50.8 %) were low-grade (LGD), 4 (6.5 %) were high-grade (HGD), 9 (14.8 %) had both LGD and HGD, and 17 (27.9 %) had no dysplasia (ND), while 14 (93 %) conventional dysplasias had LGD, and 1 (7 %) had LGD and HGD. Gastric metaplasia was assessed by concomitant immunoexpression of MUC5AC and loss of CDX2 staining. Expression of a p53-mut pattern was considered as a surrogate for gene mutation, and complete loss of MLH1 staining as presence of MLH1 hypermethylation. In nonconventional dysplasia, MUC5AC immunoexpression decreased as the degree of dysplasia increased, being 78 % in LGD and 39 % in HGD (p = 0.006). CDX2 was lost in epithelial glands with high expression of MUC5AC (p < 0.001). The p53-mut pattern was observed in 77 % HGD, 45 % LGD, and in 6 % with ND (p < 0.001). Neither nonconventional nor conventional dysplasia showed complete loss of MLH1 staining. Gastric metaplasia was also present in mucosa adjacent to nonconventional dysplasia with chronic changes or active inflammation. Our results show that gastric metaplasia appears in IBD-inflamed colon mucosa, it is the substrate of most nonconventional dysplasia and occurs prior to p53 alterations.
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Affiliation(s)
- Eva Musulen
- Pathology Department, Hospital Universitari General de Catalunya-Grupo QuironSalud, 08915 Sant Cugat Del Vallès, Barcelona, Spain; Institut de Recerca Contra La Leucèmia Josep Carreras (IJC), 08916 Badalona, Barcelona, Spain.
| | - Míriam Gené
- Pathology Department, Hospital Universitari Joan XXIII, 43005 Tarragona, Spain; Surgery Department, Programme of Surgery and Morphological Sciences, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola Del Vallès, Spain
| | - Míriam Cuatrecasas
- Pathology Department, Hospital Clínic, 08036 Barcelona, Spain; Department of Basic Clinical Practice, University of Barcelona (UB), 08036 Barcelona, Spain
| | - Irene Amat
- Pathology Department, Complejo Hospitalario de Navarra, 31008 Navarra, Spain
| | - Jesús Alberto Veiga
- Pathology Department, Complejo Hospitalario Universitario de Ferrol, 15405 Ferrol, Spain
| | | | | | - Jordi Tarragona
- Pathology Department, Hospital Universitari Arnau de Vilanova, 25198 Lleida, Spain
| | - Ismael Jurado
- Pathology Department, Consorci Sanitari de Terrassa, 08227 Terrassa, Spain
| | | | - Carolina Martínez-Ciarpaglini
- Pathology Department, Hospital Clínico Universitario de Valencia, INCLIVA- Instituto de Investigación Sanitaria, Universidad de Valencia, 46010 Valencia, Spain
| | - Cristina Alenda González
- Pathology Department, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 031010 Alicante, Spain
| | - Carlos Zac
- Pathology Department, Hospital Universitari I Politècnic La Fe, 46026 Valencia, Spain
| | - María Teresa Fernández-Figueras
- Pathology Department, Hospital Universitari General de Catalunya-Grupo QuironSalud, 08915 Sant Cugat Del Vallès, Barcelona, Spain; School of Medicine, Campus Sant Cugat Del Vallès, Universitat Internacional de Catalunya (UIC), 08917 Sant Cugat Del Vallès, Spain
| | - Manel Esteller
- Institut de Recerca Contra La Leucèmia Josep Carreras (IJC), 08916 Badalona, Barcelona, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain; Faculty of Medicine and Health Sciences, Department of Physiological Sciences, Universitat de Barcelona (UB), 08007 Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
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3
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Gallardo-Gómez M, Costas-Ríos L, Garcia-Prieto CA, Álvarez-Rodríguez L, Bujanda L, Barrero M, Castells A, Balaguer F, Jover R, Esteller M, Tardío Baiges A, González-Carreró Fojón J, Cubiella J, De Chiara L. Serum DNA methylome of the colorectal cancer serrated pathway enables non-invasive detection. Mol Oncol 2023. [PMID: 38129291 DOI: 10.1002/1878-0261.13573] [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: 09/27/2023] [Revised: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
The clinical relevance of the colorectal cancer serrated pathway is evident, but the screening of serrated lesions remains challenging. We aimed to characterize the serum methylome of the serrated pathway and to evaluate circulating cell-free DNA (cfDNA) methylomes as a potential source of biomarkers for the non-invasive detection of serrated lesions. We collected serum samples from individuals with serrated adenocarcinoma (SAC), traditional serrated adenomas, sessile serrated lesions, hyperplastic polyps and individuals with no colorectal findings. First, we quantified cfDNA methylation with the MethylationEPIC array. Then, we compared the methylation profiles with tissue and serum datasets. Finally, we evaluated the utility of serum cfDNA methylation biomarkers. We identified a differential methylation profile able to distinguish high-risk serrated lesions from no serrated neoplasia, showing concordance with tissue methylation from SAC and sessile serrated lesions. Serum methylation profiles are pathway-specific, clearly separating serrated lesions from conventional adenomas. The combination of ninjurin 2 (NINJ2) and glutamate-rich 1 (ERICH1) methylation discriminated high-risk serrated lesions and SAC with 91.4% sensitivity (64.4% specificity), while zinc finger protein 718 (ZNF718) methylation reported 100% sensitivity for the detection of SAC (96% specificity). This is the first study exploring the serum methylome of serrated lesions. Differential methylation of cfDNA can be used for the non-invasive detection of colorectal serrated lesions.
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Affiliation(s)
- María Gallardo-Gómez
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Lara Costas-Ríos
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
| | - Carlos A Garcia-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Spain
| | - Lara Álvarez-Rodríguez
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Maialen Barrero
- Department of Oncology, Hospital Universitario Donostia, San Sebastián, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Spain
| | - Rodrigo Jover
- Servicio de Medicina Digestiva, Hospital General Universitario Dr. Balmis ISABIAL, Universidad Miguel Hernández, Alicante, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Spain
| | - Antoni Tardío Baiges
- Department of Pathology, Hospital Álvaro Cunqueiro, Instituto de Investigación Biomédica Galicia Sur, Vigo, Spain
| | | | - Joaquín Cubiella
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Loretta De Chiara
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
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Bhandari YR, Krishna V, Powers R, Parmar S, Thursby SJ, Gupta E, Kulak O, Gokare P, Reumers J, Van Wesenbeeck L, Bachman KE, Baylin SB, Easwaran H. Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers. Proc Natl Acad Sci U S A 2023; 120:e2301536120. [PMID: 37487069 PMCID: PMC10401032 DOI: 10.1073/pnas.2301536120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Colorectal cancers (CRCs) form a heterogenous group classified into epigenetic and transcriptional subtypes. The basis for the epigenetic subtypes, exemplified by varying degrees of promoter DNA hypermethylation, and its relation to the transcriptional subtypes is not well understood. We link cancer-specific transcription factor (TF) expression alterations to methylation alterations near TF-binding sites at promoter and enhancer regions in CRCs and their premalignant precursor lesions to provide mechanistic insights into the origins and evolution of the CRC molecular subtypes. A gradient of TF expression changes forms a basis for the subtypes of abnormal DNA methylation, termed CpG-island promoter DNA methylation phenotypes (CIMPs), in CRCs and other cancers. CIMP is tightly correlated with cancer-specific hypermethylation at enhancers, which we term CpG-enhancer methylation phenotype (CEMP). Coordinated promoter and enhancer methylation appears to be driven by downregulation of TFs with common binding sites at the hypermethylated enhancers and promoters. The altered expression of TFs related to hypermethylator subtypes occurs early during CRC development, detectable in premalignant adenomas. TF-based profiling further identifies patients with worse overall survival. Importantly, altered expression of these TFs discriminates the transcriptome-based consensus molecular subtypes (CMS), thus providing a common basis for CIMP and CMS subtypes.
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Affiliation(s)
- Yuba R. Bhandari
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Vinod Krishna
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Rachael Powers
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sehej Parmar
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ekta Gupta
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ozlem Kulak
- Division of Gastrointestinal and Liver Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Prashanth Gokare
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Joke Reumers
- Discovery Technologies and Molecular Pharmacology, Therapeutics Discovery, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgiumg
| | - Liesbeth Van Wesenbeeck
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgium
| | - Kurtis E. Bachman
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Stephen B. Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
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Janssens K, Neefs I, Ibrahim J, Schepers A, Pauwels P, Peeters M, Van Camp G, Op de Beeck K. Epigenome-wide methylation analysis of colorectal carcinoma, adenoma and normal tissue reveals novel biomarkers addressing unmet clinical needs. Clin Epigenetics 2023; 15:111. [PMID: 37415235 PMCID: PMC10327366 DOI: 10.1186/s13148-023-01516-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Biomarker discovery in colorectal cancer has mostly focused on methylation patterns in normal and colorectal tumor tissue, but adenomas remain understudied. Therefore, we performed the first epigenome-wide study to profile methylation of all three tissue types combined and to identify discriminatory biomarkers. RESULTS Public methylation array data (Illumina EPIC and 450K) were collected from a total of 1 892 colorectal samples. Pairwise differential methylation analyses between tissue types were performed for both array types to "double evidence" differentially methylated probes (DE DMPs). Subsequently, the identified DMPs were filtered on methylation level and used to build a binary logistic regression prediction model. Focusing on the clinically most interesting group (adenoma vs carcinoma), we identified 13 DE DMPs that could effectively discriminate between them (AUC = 0.996). We validated this model in an in-house experimental methylation dataset of 13 adenomas and 9 carcinomas. It reached a sensitivity and specificity of 96% and 95%, respectively, with an overall accuracy of 96%. Our findings raise the possibility that the 13 DE DMPs identified in this study can be used as molecular biomarkers in the clinic. CONCLUSIONS Our analyses show that methylation biomarkers have the potential to discriminate between normal, precursor and carcinoma tissues of the colorectum. More importantly, we highlight the power of the methylome as a source of markers for discriminating between colorectal adenomas and carcinomas, which currently remains an unmet clinical need.
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Affiliation(s)
- Katleen Janssens
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
- Centre for Oncological Research Antwerp (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Isabelle Neefs
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
- Centre for Oncological Research Antwerp (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Joe Ibrahim
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
- Centre for Oncological Research Antwerp (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anne Schepers
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
| | - Patrick Pauwels
- Centre for Oncological Research Antwerp (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Marc Peeters
- Centre for Oncological Research Antwerp (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Guy Van Camp
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
- Centre for Oncological Research Antwerp (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Ken Op de Beeck
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium.
- Centre for Oncological Research Antwerp (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium.
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Zheng R, Pan Y, Liu X, Liu F, Li A, Zheng D, Luo Y. Comprehensive analysis of REST corepressors ( RCORs) in pan-cancer. Front Cell Dev Biol 2023; 11:1162344. [PMID: 37342230 PMCID: PMC10277624 DOI: 10.3389/fcell.2023.1162344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
REST corepressors (RCORs) are the core component of the LSD1/CoREST/HDACs transcriptional repressor complex, which have been revealed differently expressed in various cancers, but the therapeutic and prognostic mechanisms in cancer are still poorly understood. In this study, we analyzed expression, prognostic value, molecular subtypes, genetic alteration, immunotherapy response and drug sensitivity of RCORs in pan-cancer. Clinical correlation, stemness index, immune infiltration and regulatory networks of RCORs in hepatocellular carcinoma (HCC) were detected through TCGA and GSCA database. In-vitro experiments were conducted to explore the role of RCOR1 in HCC cells. The expression of RCORs varied among different cancers, and have prognostic values in several cancers. Cancer subtypes were categorized according to the expression of RCORs with clinical information. RCORs were significantly correlated with immunotherapy response, MSI, drug sensitivity and genetic alteration in pan-cancer. In HCC, RCORs were considered as potential predictor of stemness and also had association with immune infiltration. The ceRNA-TF-kinase regulatory networks of RCORs were constructed. Besides, RCOR1 acts as an oncogene in HCC and promotes the proliferation of HCC cells by inhibiting cell cycle arrest and cell apoptosis. Taken together, our study revealed the potential molecular mechanisms of RCORs in pan-cancer, offering a benchmark for disease-related research.
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Affiliation(s)
- Rong Zheng
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Yingying Pan
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Xinhui Liu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Feiye Liu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Aimin Li
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Dayong Zheng
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Yue Luo
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
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7
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Fennell LJ, Hartel G, McKeone DM, Bond CE, Kane A, Leggett BA, Patch AM, Whitehall VL. Comparative analysis of Illumina Mouse Methylation BeadChip and reduced-representation bisulfite sequencing for routine DNA methylation analysis. CELL REPORTS METHODS 2022; 2:100323. [PMID: 36452869 PMCID: PMC9701610 DOI: 10.1016/j.crmeth.2022.100323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/14/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
Researching the murine epigenome in disease models has been hampered by the lack of appropriate and cost-effective DNA methylation arrays. Here we perform a comprehensive, comparative analysis between the Mouse Methylation BeadChip (MMB) and reduced-representation bisulfite sequencing (RRBS) in two murine models of colorectal carcinogenesis. We evaluate the coverage, variability, and ability to identify differential DNA methylation of RRBS and MMB. We show that MMB is an effective tool for profiling the murine methylome that performs comparably with RRBS, identifying similar differentially methylated pathways. Although choice of technology is experiment dependent and will be predicated on the underlying biology being probed, these analyses provide insights into the relative strengths and weaknesses of each approach.
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Affiliation(s)
- Lochlan J. Fennell
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Science, Monash University, 19 Innovation Walk, Clayton, VIC, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
| | - Gunter Hartel
- Statistics Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Diane M. McKeone
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Catherine E. Bond
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
| | - Alexandra Kane
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
- Conjoint Internal Medical Laboratories, Pathology Queensland, Brisbane, QLD, Australia
| | - Barbara A. Leggett
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
- Department of Gastroenterology and Hepatology, Royal Brisbane and Womens’ Hospital, Brisbane, QLD, Australia
| | - Ann-Marie Patch
- Clinical Genomics Laboratory, Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Vicki L.J. Whitehall
- Conjoint Gastroenterology Laboratory, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
- Conjoint Internal Medical Laboratories, Pathology Queensland, Brisbane, QLD, Australia
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Fennell L, Kane A, Liu C, McKeone D, Hartel G, Su C, Bond C, Bettington M, Leggett B, Whitehall V. Braf mutation induces rapid neoplastic transformation in the aged and aberrantly methylated intestinal epithelium. Gut 2022; 71:1127-1140. [PMID: 34230216 PMCID: PMC9120393 DOI: 10.1136/gutjnl-2020-322166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/30/2021] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Sessile serrated lesions (SSLs) are common across the age spectrum, but the BRAF mutant cancers arising occur predominantly in the elderly. Aberrant DNA methylation is uncommon in SSL from young patients. Here, we interrogate the role of ageing and DNA methylation in SSL initiation and progression. DESIGN We used an inducible model of Braf mutation to direct recombination of the oncogenic Braf V637E allele to the murine intestine. BRAF mutation was activated after periods of ageing, and tissue was assessed for histological, DNA methylation and gene expression changes thereafter. We also investigated DNA methylation alterations in human SSLs. RESULTS Inducing Braf mutation in aged mice was associated with a 10-fold relative risk of serrated lesions compared with young mice. There were extensive differences in age-associated DNA methylation between animals induced at 9 months versus wean, with relatively little differential Braf-specific methylation. DNA methylation at WNT pathway genes scales with age and Braf mutation accelerated age-associated DNA methylation. In human SSLs, increased epigenetic age was associated with high-risk serrated colorectal neoplasia. CONCLUSIONS SSLs arising in the aged intestine are at a significantly higher risk of spontaneous neoplastic progression. These findings provide support for a new conceptual model for serrated colorectal carcinogenesis, whereby risk of Braf-induced neoplastic transformation is dependent on age and may be related to age-associated molecular alterations that accumulate in the ageing intestine, including DNA methylation. This may have implications for surveillance and chemopreventive strategies targeting the epigenome.
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Affiliation(s)
- Lochlan Fennell
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Alexandra Kane
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
- Conjoint Internal Medical Laboratory, Chemical Pathology, Health Support Queensland Pathology Queensland, Herston, Queensland, Australia
| | - Cheng Liu
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Diane McKeone
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Gunter Hartel
- Statistics Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chang Su
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Catherine Bond
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Mark Bettington
- Envoi Specialist Pathologists, Brisbane, Queensland, Australia
| | - Barbara Leggett
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
- Department of Gastroenterology and Hepatology, The Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vicki Whitehall
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
- Conjoint Internal Medical Laboratory, Chemical Pathology, Health Support Queensland Pathology Queensland, Herston, Queensland, Australia
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9
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Batts KP, Cinnor B, Kim A, Stickney E, Burgart LJ. Sessile Serrated Adenoma With Dysplasia of the Colon. Am J Clin Pathol 2022; 157:180-195. [PMID: 34542560 DOI: 10.1093/ajcp/aqab112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Sessile serrated adenomas with dysplasia (SSADs) of the colon are transitional lesions between sessile serrated adenomas (SSAs) and a subset of colorectal adenocarcinomas. We wished to gain insight into the relative percentages and significance of SSAD subtypes. METHODS Retrospective (2007-2012) clinicopathologic review of colorectal polyps initially regarded as having mixed serrated and dysplastic elements. SSADs were subdivided into those with cap-like adenomatous dysplasia (ad1), non-cap-like adenomatous dysplasia (ad2), serrated dysplasia (ser), minimal dysplasia (min), and dysplasia not otherwise specified (nos). MLH1 immunostaining was performed on many. RESULTS SSADser (7.7%) had a greater propensity for right colon, women, and MLH1 loss vs the entire cohort. SSAad1 (11.6%) had the least female preponderance, was least likely to have MLH1 loss, and was most likely to affect the left colorectum. SSAD with MLH1 loss was associated with an increased burden of SSAs in the background colon (P = .0003) but not tubular adenomas or hyperplastic polyps. Most SSADs (ad2 and nos groups, 80% combined) showed difficult-to-classify dysplasia, intermediate MLH1 loss rates, and intermediate clinical features. CONCLUSIONS While some trends exist, morphologically subclassifying SSADs is probably not justified in routine clinical practice. MLH1 loss portends a greater burden of SSAs in the background colon.
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Affiliation(s)
| | | | - Adam Kim
- MNGI Digestive Health, Minneapolis, MN, USA
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10
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van Toledo DEFWM, IJspeert JEG, Dekker E. Current Approaches in Managing Colonic Serrated Polyps and Serrated Polyposis. Annu Rev Med 2022; 73:293-306. [PMID: 35084990 DOI: 10.1146/annurev-med-042220-024703] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For decades, conventional adenomas were the only known precursor lesions of colorectal cancer (CRC). Accordingly, education and research regarding CRC prevention were mainly focused on adenomas. The groundbreaking discovery that serrated polyps (SPs) also have the potential to develop into CRCs, and seem to account for a considerable proportion of sporadic CRCs, has led to a paradigm shift in the prevention, diagnosis, and treatment of CRC. Studies in recent years have led to our current understanding of SPs and associated CRC, but a lot of work is still to be done to further improve knowledge about this serrated neoplasia pathway and the clinical management of SPs and serrated polyposis syndrome (SPS). In this review, we reflect on the current understanding of SPs with respect to terminology, detection, resection, and surveillance and reflect on the management of SPS.
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Affiliation(s)
- David E F W M van Toledo
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; , ,
| | - Joep E G IJspeert
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; , ,
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; , ,
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11
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Turpín-Sevilla MDC, Pérez-Sanz F, García-Solano J, Sebastián-León P, Trujillo-Santos J, Carbonell P, Estrada E, Tuomisto A, Herruzo I, Fennell LJ, Mäkinen MJ, Rodríguez-Braun E, Whitehall VLJ, Conesa A, Conesa-Zamora P. Global Methylome Scores Correlate with Histological Subtypes of Colorectal Carcinoma and Show Different Associations with Common Clinical and Molecular Features. Cancers (Basel) 2021; 13:cancers13205165. [PMID: 34680315 PMCID: PMC8533997 DOI: 10.3390/cancers13205165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The typical methylation patterns associated with cancer are hypermethylation at gene promoters and global genome hypomethylation. Aberrant CpG island hypermethylation at promoter regions and global genome hypomethylation have not been associated with histological colorectal carcinomas (CRC) subsets. Using Illumina's 450 k Infinium Human Methylation beadchip, the methylome of 82 CRCs were analyzed, comprising different histological subtypes: 40 serrated adenocarcinomas (SAC), 32 conventional carcinomas (CC) and 10 CRCs showing histological and molecular features of microsatellite instability (hmMSI-H), and, additionally, 35 normal adjacent mucosae. Scores reflecting the overall methylation at 250 bp, 1 kb and 2 kb from the transcription starting site (TSS) were studied. RESULTS SAC has an intermediate methylation pattern between CC and hmMSI-H for the three genome locations. In addition, the shift from promoter hypermethylation to genomic hypomethylation occurs at a small sequence between 250 bp and 1 Kb from the gene TSS, and an asymmetric distribution of methylation was observed between both sides of the CpG islands (N vs. S shores). CONCLUSION These findings show that different histological subtypes of CRC have a particular global methylation pattern depending on sequence distance to TSS and highlight the so far underestimated importance of CpGs aberrantly hypomethylated in the clinical phenotype of CRCs.
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Affiliation(s)
- María del Carmen Turpín-Sevilla
- Facultad de Medicina, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda, Km 1800, Pozuelo de Alarcón, 28223 Madrid, Spain; (M.d.C.T.-S.); (I.H.)
| | - Fernando Pérez-Sanz
- Biomedical Informatics & Bioinformatics Platform, Institute for Biomedical Research of Murcia (IMIB)/Foundation for Healthcare Training & Research of the Region of Murcia (FFIS), Calle Luis Fontes Pagán 9, 30003 Murcia, Spain;
| | - José García-Solano
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain;
- Facultad de Ciencias de la Salud, Universidad Católica de Murcia (UCAM), Campus Los Jerónimos, 30107 Guadalupe, Spain
- Group of Molecular Pathology and Pharmacogenetics, Institute for Biomedical Research from Murcia (IMIB), HGUSL, 30202 Cartagena, Spain
| | - Patricia Sebastián-León
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain;
| | - Javier Trujillo-Santos
- Department of Internal Medicine, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain;
| | - Pablo Carbonell
- Biochemistry and Clinical Genetic Center, Virgen de la Arrixaca University Hospital, 30100 Murcia, Spain;
| | - Eduardo Estrada
- Department of Social Psychology and Methodology, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - Anne Tuomisto
- Cancer and Translational Medicine Research Unit, Department of Pathology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.T.); (M.J.M.)
| | - Irene Herruzo
- Facultad de Medicina, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda, Km 1800, Pozuelo de Alarcón, 28223 Madrid, Spain; (M.d.C.T.-S.); (I.H.)
| | - Lochlan J. Fennell
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (L.J.F.); (V.L.J.W.)
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4072, Australia
| | - Markus J. Mäkinen
- Cancer and Translational Medicine Research Unit, Department of Pathology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.T.); (M.J.M.)
| | - Edith Rodríguez-Braun
- Clinical Oncology Department, Santa Lucía General University Hospital (HGUSL). C/Mezquita s/n, 30202 Cartagena, Spain;
| | - Vicki L. J. Whitehall
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (L.J.F.); (V.L.J.W.)
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4072, Australia
| | - Ana Conesa
- Microbiology and Cell Sciences Department, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, FL 32611, USA;
| | - Pablo Conesa-Zamora
- Facultad de Ciencias de la Salud, Universidad Católica de Murcia (UCAM), Campus Los Jerónimos, 30107 Guadalupe, Spain
- Group of Molecular Pathology and Pharmacogenetics, Institute for Biomedical Research from Murcia (IMIB), HGUSL, 30202 Cartagena, Spain
- Clinical Oncology Department, Santa Lucía General University Hospital (HGUSL). C/Mezquita s/n, 30202 Cartagena, Spain;
- Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain
- Correspondence: ; Tel.: +34-968128600 (ext. 951615)
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12
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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13
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Takahashi S, Okamoto K, Tanahashi T, Fujimoto S, Nakagawa T, Bando M, Ma B, Kawaguchi T, Fujino Y, Mitsui Y, Kitamura S, Miyamoto H, Sato Y, Muguruma N, Bando Y, Sato T, Fujimori T, Takayama T. S100P Expression via DNA Hypomethylation Promotes Cell Growth in the Sessile Serrated Adenoma/Polyp-Cancer Sequence. Digestion 2021; 102:789-802. [PMID: 33395688 DOI: 10.1159/000512575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 10/26/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND/AIMS Sessile serrated adenomas/polyps (SSA/Ps) are a putative precursor lesion of colon cancer. Although the relevance of DNA hypermethylation in the SSA/P-cancer sequence is well documented, the role of DNA hypomethylation is unknown. We investigated the biological relevance of DNA hypomethylation in the SSA/P-cancer sequence by using 3-dimensional organoids of SSA/P. METHODS We first analyzed hypomethylated genes using datasets from our previous DNA methylation array analysis on 7 SSA/P and 2 cancer in SSA/P specimens. Expression levels of hypomethylated genes in SSA/P specimens were determined by RT-PCR and immunohistochemistry. We established 3-dimensional SSA/P organoids and performed knockdown experiments using a lentiviral shRNA vector. DNA hypomethylation at CpG sites of the gene was quantitated by MassARRAY analysis. RESULTS The mean number of hypomethylated genes in SSA/P and cancer in SSA/P was 41.6 ± 27.5 and 214 ± 19.8, respectively, showing a stepwise increment in hypomethylation during the SSA/P-cancer sequence. S100P, S100α2, PKP3, and MUC2 were most commonly hypomethylated in SSA/P specimens. The mRNA and protein expression levels of S100P, S100α2, and MUC2 were significantly elevated in SSA/P compared with normal colon tissues, as revealed by RT-PCR and immunohistochemistry, respectively. Among these, mRNA and protein levels were highest for S100P. Knockdown of the S100P gene using a lentiviral shRNA vector in 3-dimensional SSA/P organoids inhibited cell growth by >50% (p < 0.01). The mean diameter of SSA/P organoids with S100P gene knockdown was significantly smaller compared with control organoids. MassARRAY analysis of DNA hypomethylation in the S100P gene revealed significant hypomethylation at specific CpG sites in intron 1, exon 1, and the 5'-flanking promoter region. CONCLUSION These results suggest that DNA hypomethylation, including S100P hypomethylation, is supposedly associated with the SSA/P-cancer sequence. S100P overexpression via DNA hypomethylation plays an important role in promoting cell growth in the SSA/P-cancer sequence.
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Affiliation(s)
- Sayo Takahashi
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Koichi Okamoto
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Toshihito Tanahashi
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Shota Fujimoto
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Tadahiko Nakagawa
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Masahiro Bando
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Beibei Ma
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Tomoyuki Kawaguchi
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yasuteru Fujino
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yasuhiro Mitsui
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Shinji Kitamura
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hiroshi Miyamoto
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yasushi Sato
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Naoki Muguruma
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yoshimi Bando
- Division of Pathology, Tokushima University Hospital, Tokushima, Japan
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | | | - Tetsuji Takayama
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan,
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Genome-wide DNA methylation profiling and gut flora analysis in intestinal polyps patients. Eur J Gastroenterol Hepatol 2021; 33:1071-1081. [PMID: 34213504 DOI: 10.1097/meg.0000000000002181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The intestinal polyp is the precancerous lesion of colorectal cancer. DNA methylation and intestinal microbiota may play an important role in the development of intestinal polyp. MATERIALS AND METHODS In this study, we included 10 patients with intestinal polyps who received the colonoscopy examination. We applied the Illumina Human Methylation 850K array to investigate the epigenome-wide DNA methylation patterns. Then, we filtered out the hub genes in the protein-protein interaction networks using functional epigenetic modules analysis. We also analyzed the colonizing bacteria on the surface of polyps compared with those in normal colonic mucosal epithelium with 16S ribosomal DNA sequencing. RESULTS We identified 323 hypermethylated sites and 7992 hypomethylated sites between intestinal polyps and normal samples. Five hub genes, including CREB1, LPA, SVIL and KRT18, were identified in five modules. Hypomethylation of CREB1 is a candidate marker of colorectal adenoma. Gut microbiota analysis showed that Butyricicoccus was significantly decreased in the intestinal polyp groups. CONCLUSION In conclusion, we identified DNA methylation disparities in intestinal polyps compared with normal tissue, of which methylation of CREB1 may hold clinical significance in colorectal cancer progress. Colonizing bacteria in the colonic epithelium might be related to the formation of intestinal polyps.
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Variation Over Time and Factors Associated With Detection Rates of Sessile Serrated Lesion Across the United States: Results Form a National Sample Using the GIQuIC Registry. Am J Gastroenterol 2021; 116:95-99. [PMID: 32833735 DOI: 10.14309/ajg.0000000000000824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Sessile serrated lesions (SSLs) are important precursor lesions for the CpG island-methylated pathway to colorectal cancer. The reported detection rates of SSL are highly variable, and national or population-based estimates are not available. Patient-, provider-, and procedure-level factors associated with the detection rates of SSL have not been well described. The aim of our study was to study the detection rates of SSL, variability of rates over time, and factors associated with detection rates of SSL in a national sample of patients undergoing colonoscopy using the GIQuIC registry. METHODS We used colonoscopies submitted to the GIQuIC registry from 2014 to 2017 on adults, aged 18-89 years. Only the first colonoscopy record per patient was included. Indications for colonoscopy were categorized as screening, diagnostic, and surveillance. We used the hierarchical logistic models to study the factors associated with the detection rates of SSL. The Cochrane-Armitage test was used to study the significance of trend over time. RESULTS There were a total of 5,173,211 colonoscopies performed by 3,934 endoscopists during the study period. Among the 2,101,082 screening colonoscopies over the study period in adults older than or equal to 50 years that were complete to the cecum, the average detection rate per endoscopist for SSL was 6.43% (SD 5.18) and 6.25% standardized for the 2010 US population. There was a significant increase in the detection rates of SSLs from screening colonoscopies over the study period from 4.99% in 2014 to 7.09% in 2017 (P trend <0.001). Clinically significant factors associated with higher detection rates of SSL were longer withdrawal times (>11 minutes vs ≤6 minutes) (odds ratio [OR] 9.61; 9.03-10.24), adequate preparation (OR 1.25; 1.22-1.28), female sex (OR 1.17; 1.16-1.18), and use of a specialized gastrointestinal pathology group (OR 1.12; 95% confidence interval 1.04, 1.19). DISCUSSION Population-based estimates of the detection rates of SSL are 6% and have increased over time.
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16
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Yang D, Holsten T, Börnigen D, Frank S, Mawrin C, Glatzel M, Schüller U. Ependymoma relapse goes along with a relatively stable epigenome, but a severely altered tumor morphology. Brain Pathol 2020; 31:33-44. [PMID: 32633004 PMCID: PMC8018105 DOI: 10.1111/bpa.12875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 11/30/2022] Open
Abstract
The molecular biology of ependymomas is not well understood and this is particularly true for ependymoma relapses. We aimed at finding out if and to which extent, relapses differ from their corresponding primary tumors on the morphological, chromosomal and epigenetic level. We investigated 24 matched ependymoma primary and relapsed tumor samples and, as a first step, compared cell density, necrosis, vessel proliferation, Ki67 proliferative index, trimethylation at H3K27 and expression of CXorf67. For the investigation of global methylation profiles, we used public data in order to analyze copy number variation profiles, differential methylation, methylation status and fractions of hypo‐ and hypermethylated CpGs in different epigenomic substructures. Morphologically, we found a significant increase with relapse in cell density and proliferation. H3K27 trimethylation and CXorf67 expression remained stable between primary and relapse tumor samples, and the analysis of DNA methylation profiles neither revealed significant differences in copy number variations nor differentially methylated regions. Significant differences in the methylation status were found for CpG islands, but also in N Shelves or S Shelves, depending on the molecular subgroup. The fraction of probes changing their methylation in the epigenomic substructures appeared subgroup‐specific. Most changes occur in CpG islands, for which relapsed tumors demonstrate higher methylation values than primary tumors. The morphological differences reflect increased aggressiveness upon ependymoma relapse, but, despite slight changes, this observation does not appear to be sufficiently explained by epigenetic changes.
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Affiliation(s)
- Denise Yang
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Till Holsten
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Daniela Börnigen
- Bioinformatics Core Unit, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Frank
- Division for Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Christian Mawrin
- Institute for Neuropathology, University of Magdeburg, Magdeburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Hua X, Newcomb PA, Chubak J, Malen RC, Ziebell R, Kamineni A, Zhu LC, Upton MP, Wurscher MA, Thomas SS, Newman H, Hardikar S, Burnett-Hartman AN. Associations between molecular characteristics of colorectal serrated polyps and subsequent advanced colorectal neoplasia. Cancer Causes Control 2020; 31:631-640. [PMID: 32358694 DOI: 10.1007/s10552-020-01304-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/24/2020] [Indexed: 02/08/2023]
Abstract
PURPOSE BRAF mutation and DNA hypermethylation have linked sessile serrated adenomas/polyps (SSA/Ps) to serrated colorectal cancer (CRC) in cross-sectional studies, but they have not been evaluated in a longitudinal study. We aimed to evaluate the associations between molecular markers of serrated polyps and subsequent advanced colorectal neoplasia. METHODS Study subjects included Kaiser Permanente Washington members aged 20-75 years who received an index colonoscopy between 1/1/1998 and 12/31/2007 and had hyperplastic polyps (HPs) or SSA/Ps according to study pathology review. Polyps from index colonoscopies were removed and assayed for BRAF mutation, CpG island methylator phenotype (CIMP), and MLH1 methylation. Pathology reports and biopsies from the subsequent lower gastrointestinal endoscopy through 1/1/2013 were reviewed for advanced colorectal neoplasia. We identified additional incident CRC cases through linkage to the Seattle-Puget Sound Surveillance Epidemiology and End Results registry. We used generalized estimating equations to calculate adjusted odds ratios (OR) and 95% confidence intervals (CI) for subsequent advanced colorectal neoplasia, comparing index serrated polyps with different molecular markers. RESULTS We included 553 individuals with index serrated polyps (420 HPs and 133 SSA/Ps) and 795 subsequent endoscopies. The prevalence of BRAF-mutant, CIMP-high, and MLH1-methylated serrated polyps were 51%, 4%, and 2%, respectively. BRAF and CIMP were not associated with subsequent advanced colorectal neoplasia. MLH1-methylated SSP/As were significantly more likely to have subsequent advanced neoplasia (OR = 4.66, 95% CI 1.06-20.51). CONCLUSION Our results suggest that BRAF-mutant and CIMP-high serrated polyps are not associated with subsequent advanced colorectal neoplasia. Among SSA/Ps, MLH1 methylation may be an important marker to identify high-risk CRC precursors.
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Affiliation(s)
- Xinwei Hua
- School of Public Health, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Polly A Newcomb
- School of Public Health, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jessica Chubak
- School of Public Health, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Rachel C Malen
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rebecca Ziebell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Aruna Kamineni
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Lee-Ching Zhu
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Melissa P Upton
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Hana Newman
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sheetal Hardikar
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Andrea N Burnett-Hartman
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Kaiser Permanente Colorado, Institute for Health Research, 2550 S Parker Rd, Suite 200, Waterpark III, 2nd floor, Aurora, CO, 80014, USA.
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