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Zuccato JA, Mamatjan Y, Nassiri F, Ajisebutu A, Liu JC, Muazzam A, Singh O, Zhang W, Voisin M, Mirhadi S, Suppiah S, Wybenga-Groot L, Tajik A, Simpson C, Saarela O, Tsao MS, Kislinger T, Aldape KD, Moran MF, Patil V, Zadeh G. Prediction of brain metastasis development with DNA methylation signatures. Nat Med 2024:10.1038/s41591-024-03286-y. [PMID: 39379704 DOI: 10.1038/s41591-024-03286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/05/2024] [Indexed: 10/10/2024]
Abstract
Brain metastases (BMs) are the most common and among the deadliest brain tumors. Currently, there are no reliable predictors of BM development from primary cancer, which limits early intervention. Lung adenocarcinoma (LUAD) is the most common BM source and here we obtained 402 tumor and plasma samples from a large cohort of patients with LUAD with or without BM (n = 346). LUAD DNA methylation signatures were evaluated to build and validate an accurate model predicting BM development from LUAD, which was integrated with clinical factors to provide comprehensive patient-specific BM risk probabilities in a nomogram. Additionally, immune and cell interaction gene sets were differentially methylated at promoters in BM versus paired primary LUAD and had aligning dysregulation in the proteome. Immune cells were differentially abundant in BM versus LUAD. Finally, liquid biomarkers identified from methylated cell-free DNA sequenced in plasma were used to generate and validate accurate classifiers for early BM detection. Overall, LUAD methylomes can be leveraged to predict and noninvasively identify BM, moving toward improved patient outcomes with personalized treatment.
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Affiliation(s)
- Jeffrey A Zuccato
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- The Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Farshad Nassiri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Ajisebutu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey C Liu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ammara Muazzam
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olivia Singh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Wen Zhang
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mathew Voisin
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Shideh Mirhadi
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Suganth Suppiah
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Leanne Wybenga-Groot
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Tajik
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- School of Medicine, St. George's University, Grenada, Grenada
| | - Craig Simpson
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olli Saarela
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Ming S Tsao
- Department of Pathology, The Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Michael F Moran
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.
| | - Gelareh Zadeh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [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: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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3
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Delgado D, Gillard M, Tong L, Demanelis K, Oliva M, Gleason KJ, Chernoff M, Chen L, Paner GP, Vander Griend D, Pierce BL. The Impact of Inherited Genetic Variation on DNA Methylation in Prostate Cancer and Benign Tissues of African American and European American Men. Cancer Epidemiol Biomarkers Prev 2024; 33:557-566. [PMID: 38294689 PMCID: PMC10990789 DOI: 10.1158/1055-9965.epi-23-0849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/29/2023] [Accepted: 01/29/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND American men of African ancestry (AA) have higher prostate cancer incidence and mortality rates compared with American men of European ancestry (EA). Differences in genetic susceptibility mechanisms may contribute to this disparity. METHODS To gain insights into the regulatory mechanisms of prostate cancer susceptibility variants, we tested the association between SNPs and DNA methylation (DNAm) at nearby CpG sites across the genome in benign and cancer prostate tissue from 74 AA and 74 EA men. Genome-wide SNP data (from benign tissue) and DNAm were generated using Illumina arrays. RESULTS Among AA men, we identified 6,298 and 2,641 cis-methylation QTLs (meQTL; FDR of 0.05) in benign and tumor tissue, respectively, with 6,960 and 1,700 detected in EA men. We leveraged genome-wide association study (GWAS) summary statistics to identify previously reported prostate cancer GWAS signals likely to share a common causal variant with a detected meQTL. We identified nine GWAS-meQTL pairs with strong evidence of colocalization (four in EA benign, three in EA tumor, two in AA benign, and three in AA tumor). Among these colocalized GWAS-meQTL pairs, we identified colocalizing expression quantitative trait loci (eQTL) impacting four eGenes with known roles in tumorigenesis. CONCLUSIONS These findings highlight epigenetic regulatory mechanisms by which prostate cancer-risk SNPs can modify local DNAm and/or gene expression in prostate tissue. IMPACT Overall, our findings showed general consistency in the meQTL landscape of AA and EA men, but meQTLs often differ by tissue type (normal vs. cancer). Ancestry-based linkage disequilibrium differences and lack of AA representation in GWAS decrease statistical power to detect colocalization for some regions.
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Affiliation(s)
- Dayana Delgado
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637
| | - Marc Gillard
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637
- Genomics Research Center, AbbVie, North Chicago, IL 60064
| | | | - Meytal Chernoff
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL, USA
- University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Lin Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637
| | - Gladell P. Paner
- Department of Pathology, University of Chicago, Chicago, IL 60637
| | - Donald Vander Griend
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60607
- The University of Illinois Cancer Center, Chicago, IL
| | - Brandon L. Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60615
- Comprehensive Cancer Center, University of Chicago, Chicago, IL 60637
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Shi Z, Guo X, Hu X, Li R, Li X, Lu J, Jin M, Jiang X. DNA methylation profiling identifies epigenetic signatures of early gastric cancer. Virchows Arch 2024; 484:687-695. [PMID: 38507065 DOI: 10.1007/s00428-024-03765-0] [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: 08/20/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Research on the DNA methylation status of gastric cancer (GC) has primarily focused on identifying invasive GC to develop biomarkers for diagnostic. However, DNA methylation in noninvasive GC remains unclear. We conducted a comprehensive DNA methylation profiling study of differentiated-type intramucosal GCs (IMCs). Illumina 850K microarrays were utilized to assess the DNA methylation profiles of formalin-fixed paraffin-embedded tissues from eight patients who were Epstein-Barr virus-negative and DNA mismatch repair proficient, including IMCs and paired adjacent nontumor mucosa. Gene expression profiling microarray data from the GEO database were analyzed via bioinformatics to identify candidate methylation genes. The final validation was conducted using quantitative real-time PCR, the TCGA methylation database, and single-sample gene set enrichment analysis (GSEA). Genome-wide DNA methylation profiling revealed a global decrease in methylation in IMCs compared with nontumor tissues. Differential methylation analysis between IMCs and nontumor tissues identified 449 differentially methylated probes, with a majority of sites showing hypomethylation in IMCs compared with nontumor tissues (66.1% vs 33.9%). Integrating two RNA-seq microarray datasets, we found one hypomethylation-upregulated gene: eEF1A2, overlapped with our DNA methylation data. The mRNA expression of eEF1A2 was higher in twenty-four IMC tissues than in their paired adjacent nontumor tissues. GSEA indicated that the functions of eEF1A2 were associated with the development of IMCs. Furthermore, TCGA data indicated that eEF1A2 is hypomethylated in advanced GC. Our study illustrates the implications of DNA methylation alterations in IMCs and suggests that aberrant hypomethylation and high mRNA expression of eEF1A2 might play a role in IMCs development.
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Affiliation(s)
- Zhongyue Shi
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xinmeng Guo
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xiumei Hu
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ruiqi Li
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xue Li
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jun Lu
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Mulan Jin
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
| | - Xingran Jiang
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
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5
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Youssef O, Loukola A, Zidi-Mouaffak YHS, Tamlander M, Ruotsalainen S, Kilpeläinen E, Mars N, Ripatti S, Palotie A, Donner K, Carpén O. High-Resolution Genotyping of Formalin-Fixed Tissue Accurately Estimates Polygenic Risk Scores in Human Diseases. J Transl Med 2024; 104:100325. [PMID: 38220043 DOI: 10.1016/j.labinv.2024.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues stored in biobanks and pathology archives are a vast but underutilized source for molecular studies on different diseases. Beyond being the "gold standard" for preservation of diagnostic human tissues, FFPE samples retain similar genetic information as matching blood samples, which could make FFPE samples an ideal resource for genomic analysis. However, research on this resource has been hindered by the perception that DNA extracted from FFPE samples is of poor quality. Here, we show that germline disease-predisposing variants and polygenic risk scores (PRS) can be identified from FFPE normal tissue (FFPE-NT) DNA with high accuracy. We optimized the performance of FFPE-NT DNA on a genome-wide array containing 657,675 variants. Via a series of testing and validation phases, we established a protocol for FFPE-NT genotyping with results comparable with blood genotyping. The median call rate of FFPE-NT samples in the validation phase was 99.85% (range 98.26%-99.94%) and median concordance with matching blood samples was 99.79% (range 98.85%-99.9%). We also demonstrated that a rare pathogenic PALB2 genetic variant predisposing to cancer can be correctly identified in FFPE-NT samples. We further imputed the FFPE-NT genotype data and calculated the FFPE-NT genome-wide PRS in 3 diseases and 4 disease risk variables. In all cases, FFPE-NT and matching blood PRS were highly concordant (all Pearson's r > 0.95). The ability to precisely genotype FFPE-NT on a genome-wide array enables translational genomics applications of archived FFPE-NT samples with the possibility to link to corresponding phenotypes and longitudinal health data.
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Affiliation(s)
- Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland; Clinical and Chemical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Anu Loukola
- Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Yossra H S Zidi-Mouaffak
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Max Tamlander
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Analytic and Translational Genetics Unit, Department of Medicine, and the Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kati Donner
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
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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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Zhao Z, Song Z, Wang Z, Zhang F, Ding Z, Fan T. Advances in Molecular Pathology, Diagnosis and Treatment of Spinal Cord Astrocytomas. Technol Cancer Res Treat 2024; 23:15330338241262483. [PMID: 39043042 PMCID: PMC11271101 DOI: 10.1177/15330338241262483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 07/25/2024] Open
Abstract
Spinal cord astrocytoma (SCA) is a rare subtype of astrocytoma, posing challenges in diagnosis and treatment. Low-grade SCA can achieve long-term survival solely through surgery, while high-grade has a disappointing prognosis even with comprehensive treatment. Diagnostic criteria and standard treatment of intracranial astrocytoma have shown obvious limitations in SCA. Research on the molecular mechanism in SCA is lagging far behind that on intracranial astrocytoma. In recent years, huge breakthroughs have been made in molecular pathology of astrocytoma, and novel techniques have emerged, including DNA methylation analysis and radiomics. These advances are now making it possible to provide a precise diagnosis and develop corresponding treatment strategies in SCA. Our aim is to review the current status of diagnosis and treatment of SCA, and summarize the latest research advancement, including tumor subtype, molecular characteristics, diagnostic technology, and potential therapy strategies, thus deepening our understanding of this uncommon tumor type and providing guidance for accurate diagnosis and treatment.
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Affiliation(s)
- Zijun Zhao
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Zihan Song
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zairan Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fan Zhang
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Ze Ding
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Tao Fan
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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8
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Meyer OS, Andersen MM, Børsting C, Morling N, Wulf HC, Philipsen PA, Lerche CM, Dyrberg Andersen J. Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis. Epigenetics 2023; 18:2144574. [PMID: 36373380 PMCID: PMC9980693 DOI: 10.1080/15592294.2022.2144574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory.
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Affiliation(s)
- Olivia Strunge Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,CONTACT Olivia Strunge Meyer Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Heafth and Medical Sciences, University of Copenhagen. Frederik V's vej 11, 2100 Copenhagen, Denmark
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,Department of Mathematical Sciences, Aalborg University, 9220Aalborg, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,Department of Mathematical Sciences, Aalborg University, 9220Aalborg, Denmark
| | - Hans Christian Wulf
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark
| | - Peter Alshede Philipsen
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark
| | - Catharina Margrethe Lerche
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark,Department of Pharmacy, University of Copenhagen, 2100Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark
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Li M, Yin Y, Zhang M, Jiang C, Li H, Yang R. DNA Methylation Status of HYAL1 in Malignant and Benign Thyroid Nodules. Horm Metab Res 2023; 55:869-875. [PMID: 38040022 DOI: 10.1055/a-2188-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
Differentiation between benign and malignant thyroid nodules has been a challenge in clinical practice. Exploring a novel biomarker to determine the malignancy of thyroid nodules has important implications. We semi-quantitatively determined the DNA methylation levels of four CpG sites located at the gene body of HYAL1 in formalin-fixed paraffin-embedded (FFPE) tissue samples from 190 early-stage papillary thyroid cancer (PTC) cases and 190 age- and gender-matched subjects with benign thyroid nodule (BTN). HYAL1 expression was evaluated by immunohistochemical (IHC) staining in another cohort of 55 PTC and 55 matched BTN cases. Covariates-adjusted odds ratios (ORs) for 10% increased methylation were calculated by binary logistic regression. A 165 bp amplicon covering four CpG sites at the second exon of HYAL1 gene was designed. After adjusted for all covariates, higher methylation level of HYAL1_CpG_3,4 in the FFPE tissue was associated with PTC (OR per 10% increased methylation=1.53, p=0.025), even with stage І PTC (OR per 10% increased methylation=1.58, p=0.021). Hypermethylation of HYAL1_CpG_3,4 had a significant association with early-stage PTC in the females (OR per 10% increased methylation=1.60, p=0.028) rather than in the males. Besides, we found the higher expression of HYAL1 protein in PTC than that in BTN patients (IHC score: 2.3 vs. 0.5, p=1.00E-06). Our study suggested altered methylation and expression of HYAL1 could be a novel and potential biomarker in distinguishing malignant and benign thyroid nodules.
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Affiliation(s)
- Mengxia Li
- Department of Epidemiology and Biostatistics, Nanjing Medical University, Nanjing, China
| | - Yifei Yin
- Department of Thyroid and Breast Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China
| | - Minmin Zhang
- Department of Thyroid and Breast Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China
| | - Chenxia Jiang
- Department of Pathology, Nantong University Affiliated Hospital, Nantong, China
| | - Hong Li
- Department of Pathology, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, Nanjing Medical University, Nanjing, China
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10
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Dupont ME, Jacobsen SB, Christiansen SNN, Tfelt-Hansen J, Smerup MH, Andersen JD, Morling N. Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels. Sci Rep 2023; 13:16381. [PMID: 37773256 PMCID: PMC10541404 DOI: 10.1038/s41598-023-43788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/28/2023] [Indexed: 10/01/2023] Open
Abstract
Untreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.
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Affiliation(s)
- Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steffan Noe Niikanoff Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Holdgaard Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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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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12
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Wah NW, Mok Y, Omar N, Chang KTE, Tay TKY, Hue SSS, Lee VKM. Clinicopathologic and Molecular Characteristics of Epstein-Barr Virus-Associated Smooth Muscle Tumor Compared With Those of Leiomyoma and Leiomyosarcoma. Mod Pathol 2023; 36:100127. [PMID: 36965331 DOI: 10.1016/j.modpat.2023.100127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/28/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Epstein-Barr virus (EBV)-associated smooth muscle tumors (EBV-SMTs) are rare smooth muscle neoplasms exclusively associated with immunosuppression, such as in patients with HIV/AIDS, posttransplant, and congenital immunodeficiency. However, the genomic landscape of EBV-SMTs is poorly understood. Leiomyosarcomas harbor genomic instability and multiple recurrent DNA copy number alterations, whereas leiomyomas lack such changes. Thus, this study aimed to fill this knowledge gap by characterizing copy number alterations in EBV-SMTs and correlating this information with clinicopathologic characteristics. Our study investigated and compared the pathologic characteristics and copy number profiles of 9 EBV-SMTs (from 7 post-transplant and AIDS patients), 6 leiomyomas, and 7 leiomyosarcomas, using chromosomal microarray platforms. Our results showed a lower copy number alteration burden in EBV-SMTs and leiomyoma than in leiomyosarcoma. This contrast in the molecular profile between EBV-SMTs and leiomyosarcoma is concordant with the different clinical behaviors and pathologic characteristics exhibited by these tumors. Despite having an overall copy number alteration profile closer to leiomyoma, recurrent copy number gain of oncogenes, such as RUNX1, CCND2, and ETS2, was found in EBV-SMTs. Epigenetic alterations may play an important role in tumorigenesis as recurrent copy number gains were found in histone deacetylases. A gene enrichment analysis also demonstrated enrichment of genes involved in the host response to viral infection, suggesting that the tumor immune microenvironment may play an important role in EBV-SMT tumorigenesis.
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Affiliation(s)
- Naw Wah Wah
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yingting Mok
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Pathology, National University Hospital, National University Health System, Singapore; Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | | | - Kenneth Tou En Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | | | - Susan Swee-Shan Hue
- Department of Pathology, National University Hospital, National University Health System, Singapore
| | - Victor Kwan Min Lee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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13
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Sommerer Y, Dobricic V, Schilling M, Ohlei O, Sabet SS, Wesse T, Fuß J, Franzenburg S, Franke A, Parkkinen L, Lill CM, Bertram L. Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer's disease. Alzheimers Res Ther 2023; 15:92. [PMID: 37149695 PMCID: PMC10163801 DOI: 10.1186/s13195-023-01232-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/15/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND Studies on DNA methylation (DNAm) in Alzheimer's disease (AD) have recently highlighted several genomic loci showing association with disease onset and progression. METHODS Here, we conducted an epigenome-wide association study (EWAS) using DNAm profiles in entorhinal cortex (EC) from 149 AD patients and control brains and combined these with two previously published EC datasets by meta-analysis (total n = 337). RESULTS We identified 12 cytosine-phosphate-guanine (CpG) sites showing epigenome-wide significant association with either case-control status or Braak's tau-staging. Four of these CpGs, located in proximity to CNFN/LIPE, TENT5A, PALD1/PRF1, and DIRAS1, represent novel findings. Integrating DNAm levels with RNA sequencing-based mRNA expression data generated in the same individuals showed significant DNAm-mRNA correlations for 6 of the 12 significant CpGs. Lastly, by calculating rates of epigenetic age acceleration using two recently proposed "epigenetic clock" estimators we found a significant association with accelerated epigenetic aging in the brains of AD patients vs. controls. CONCLUSION In summary, our study represents the hitherto most comprehensive EWAS in AD using EC and highlights several novel differentially methylated loci with potential effects on gene expression.
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Affiliation(s)
- Yasmine Sommerer
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Marcel Schilling
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tanja Wesse
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Janina Fuß
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Christina M Lill
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
- Ageing Epidemiology Unit (AGE), School of Public Health, Imperial College London, London, UK
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany.
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway.
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14
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Wenger A, Carén H. Methylation Profiling in Diffuse Gliomas: Diagnostic Value and Considerations. Cancers (Basel) 2022; 14:cancers14225679. [PMID: 36428772 PMCID: PMC9688075 DOI: 10.3390/cancers14225679] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Diffuse gliomas cause significant morbidity across all age groups, despite decades of intensive research efforts. Here, we review the differences in diffuse gliomas in adults and children, as well as the World Health Organisation (WHO) 2021 classification of these tumours. We explain how DNA methylation-based classification works and list the methylation-based tumour types and subclasses for adult and paediatric diffuse gliomas. The benefits and utility of methylation-based classification in diffuse gliomas demonstrated to date are described. This entails the identification of novel tumour types/subclasses, patient stratification and targeted treatment/clinical management, and alterations in the clinical diagnosis in favour of the methylation-based over the histopathological diagnosis. Finally, we address several considerations regarding the use of DNA methylation profiling as a diagnostic tool, e.g., the threshold of the classifier, the calibrated score, tumour cell content and intratumour heterogeneity.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90 Gothenburg, Sweden
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90 Gothenburg, Sweden
- Correspondence:
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15
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Bücker L, Lehmann U. CDH1 (E-cadherin) Gene Methylation in Human Breast Cancer: Critical Appraisal of a Long and Twisted Story. Cancers (Basel) 2022; 14:cancers14184377. [PMID: 36139537 PMCID: PMC9497067 DOI: 10.3390/cancers14184377] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Genes can be inactivated by specific modifications of DNA bases, most often by adding a methyl group to the DNA base cytosine if it is followed by guanosine (CG methylation). This modification prevents gene expression and has been reported for many different genes in nearly all types of cancer. A prominent example is the gene CDH1, which encodes the cell-adhesion molecule E-cadherin. This is an important player in the spreading of tumor cells within the body (metastasis). Particularly in human breast cancer, many different research groups have studied the inactivation of the CDH1 gene via DNA methylation using various methods. Over the last 20 years, different, in part, even contradicting results have been published for the CDH1 gene in breast cancer. This review summarizes the most important publications and explains the bewildering heterogeneity of results through careful analysis of the methods which have been used. Abstract Epigenetic inactivation of a tumor suppressor gene by aberrant DNA methylation is a well-established defect in human tumor cells, complementing genetic inactivation by mutation (germline or somatic). In human breast cancer, aberrant gene methylation has diagnostic, prognostic, and predictive potential. A prominent example is the hypermethylation of the CDH1 gene, encoding the adhesion protein E-Cadherin (“epithelial cadherin”). In numerous publications, it is reported as frequently affected by gene methylation in human breast cancer. However, over more than two decades of research, contradictory results concerning CDH1 gene methylation in human breast cancer accumulated. Therefore, we review the available evidence for and against the role of DNA methylation of the CDH1 gene in human breast cancer and discuss in detail the methodological reasons for conflicting results, which are of general importance for the analysis of aberrant DNA methylation in human cancer specimens. Since the loss of E-cadherin protein expression is a hallmark of invasive lobular breast cancer (ILBC), special attention is paid to CDH1 gene methylation as a potential mechanism for loss of expression in this special subtype of human breast cancer. Proper understanding of the methodological basis is of utmost importance for the correct interpretation of results supposed to demonstrate the presence and clinical relevance of aberrant DNA methylation in cancer specimens.
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Affiliation(s)
| | - Ulrich Lehmann
- Correspondence: ; Tel.: +49-(0)511-532-4501; Fax: +49-(0)511-532-5799
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16
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Wenger A, Ferreyra Vega S, Schepke E, Löfgren M, Olsson Bontell T, Tisell M, Nilsson D, Kling T, Carén H. DNA methylation alterations across time and space in paediatric brain tumours. Acta Neuropathol Commun 2022; 10:105. [PMID: 35842717 PMCID: PMC9287974 DOI: 10.1186/s40478-022-01406-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
DNA methylation is increasingly used for tumour classification and has expanded upon the > 100 currently known brain tumour entities. A correct diagnosis is the basis for suitable treatment for patients with brain tumours, which is the leading cause of cancer-related death in children. DNA methylation profiling is required for diagnosis of certain tumours, and used clinically for paediatric brain tumours in several countries. We therefore evaluated if the methylation-based classification is robust in different locations of the same tumour, and determined how the methylation pattern changed over time to relapse. We sampled 3-7 spatially separated biopsies per patient, and collected samples from paired primary and relapse brain tumours from children. Altogether, 121 samples from 46 paediatric patients with brain tumours were profiled with EPIC methylation arrays. The methylation-based classification was mainly homogeneous for all included tumour types that were successfully classified, which is promising for clinical diagnostics. There were indications of multiple subclasses within tumours and switches in the relapse setting, but not confirmed as the classification scores were below the threshold. Site-specific methylation alterations did occur within the tumours and varied significantly between tumour types for the temporal samples, and as a trend in spatial samples. More alterations were present in high-grade tumours compared to low-grade, and significantly more alterations with longer relapse times. The alterations in the spatial and temporal samples were significantly depleted in CpG islands, exons and transcription start sites, while enriched in OpenSea and regions not affiliated with a gene, suggesting a random location of the alterations in less conserved regions. In conclusion, more DNA methylation changes accumulated over time and more alterations occurred in high-grade tumours. The alterations mainly occurred in regions without gene affiliation, and did not affect the methylation-based classification, which largely remained homogeneous in paediatric brain tumours.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
| | - Sandra Ferreyra Vega
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Elizabeth Schepke
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
- Childhood Cancer Centre, Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maja Löfgren
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Magnus Tisell
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Daniel Nilsson
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
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17
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Hallén T, Johannsson G, Dahlén R, Glad CAM, Örndal C, Engvall A, Carén H, Skoglund T, Olsson DS. Genome-wide DNA Methylation Differences in Nonfunctioning Pituitary Adenomas With and Without Postsurgical Progression. J Clin Endocrinol Metab 2022; 107:2318-2328. [PMID: 35485764 PMCID: PMC9282265 DOI: 10.1210/clinem/dgac266] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Indexed: 12/26/2022]
Abstract
CONTEXT Tumor progression in surgically treated patients with nonfunctioning pituitary adenomas (NFPAs) is associated with excess mortality. Reliable biomarkers allowing early identification of tumor progression are missing. OBJECTIVE To explore DNA methylation patterns associated with tumor progression in NFPA patients. METHODS This case-controlled exploratory trial at a university hospital studied patients who underwent surgery for NFPA that had immunohistochemical characteristics of a gonadotropinoma. Cases included patients requiring reintervention due to tumor progression (reintervention group, n = 26) and controls who had a postoperative residual tumor without tumor progression for at least 5 years (radiologically stable group, n = 17). Genome-wide methylation data from each tumor sample were analyzed using the Infinium MethylationEPIC BeadChip platform. RESULTS The analysis showed that 605 CpG positions were significantly differently methylated (differently methylated positions, DMPs) between the patient groups (false discovery rate adjusted P value < 0.05, beta value > 0.2), mapping to 389 genes. The largest number of DMPs were detected in the genes NUP93 and LGALS1. The 3 hypomethylated DMPs and the 3 hypermethylated DMPs with the lowest P values were all significantly (P < 0.05) and individually associated with reintervention-free survival. One of the hypermethylated DMPs with the lowest P value was located in the gene GABRA1. CONCLUSION In this exploratory study, DNA methylation patterns in NFPA patients were associated with postoperative tumor progression requiring reintervention. The DMPs included genes that have been previously associated with tumor development. Our study is a step toward finding epigenetic signatures to predict tumor progression in patients with NFPA.
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Affiliation(s)
- Tobias Hallén
- Department of Neurosurgery, Sahlgrenska University Hospital, 413 45 Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gudmundur Johannsson
- Department of Medicine, Sahlgrenska University Hospital, 413 45 Gothenburg, Sweden
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Rahil Dahlén
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Camilla A M Glad
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Charlotte Örndal
- Unilabs Pathology Sweden AB, Department of Pathology and Cytology, Skaraborgs Hospital, 541 85 Skövde
| | - Angelica Engvall
- Department of Neuroradiology, Sahlgrenska University Hospital, 413 46 Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Thomas Skoglund
- Department of Neurosurgery, Sahlgrenska University Hospital, 413 45 Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Daniel S Olsson
- Correspondence: Assoc. Prof. Daniel S. Olsson, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Box 428, SE-405 30, Sweden.
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Di Lena P, Sala C, Nardini C. Evaluation of different computational methods for DNA methylation-based biological age. Brief Bioinform 2022; 23:6632619. [PMID: 35794713 DOI: 10.1093/bib/bbac274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years there has been a widespread interest in researching biomarkers of aging that could predict physiological vulnerability better than chronological age. Aging, in fact, is one of the most relevant risk factors for a wide range of maladies, and molecular surrogates of this phenotype could enable better patients stratification. Among the most promising of such biomarkers is DNA methylation-based biological age. Given the potential and variety of computational implementations (epigenetic clocks), we here present a systematic review of such clocks. Furthermore, we provide a large-scale performance comparison across different tissues and diseases in terms of age prediction accuracy and age acceleration, a measure of deviance from physiology. Our analysis offers both a state-of-the-art overview of the computational techniques developed so far and a heterogeneous picture of performances, which can be helpful in orienting future research.
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Affiliation(s)
- Pietro Di Lena
- Department of Computer Science and Engineering, University of Bologna, Mura Anteo Zamboni 7, 40126 Bologna, Italy
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
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19
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Giesche J, Mellert K, Geißler S, Arndt S, Seeling C, von Baer A, Schultheiss M, Marienfeld R, Möller P, Barth TF. Epigenetic lockdown of CDKN1A (p21) and CDKN2A (p16) characterises the neoplastic spindle cell component of giant cell tumours of bone. J Pathol 2022; 257:687-696. [PMID: 35522566 DOI: 10.1002/path.5925] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/16/2022] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
Giant cell tumour of bone (GCTB) comprises the eponymous osteoclastic multinucleated giant cells eliciting bone lysis, a H3F3A-mutated neoplastic mononucleated fibroblast-like cell population and H3F3A-wild type mononucleated stromal cells. In this study, we characterised four new cell lines from GCTB. Furthermore, we compared the genome-wide DNA methylation profile of 13 such tumours and three further cell lines with giant cell rich lesions comprising three H3F3B-mutated chondroblastomas, three USP6-rearranged aneurysmal bone cysts, three non-ossifying fibromas, two hyperparathyroidism-associated brown tumours as well as mesenchymal stem cells, osteoblasts, and osteoclasts. In an unsupervised analysis, we delineated GCTB and chondroblastomas from the other analysed tumour entities. Using comparative methylation analysis, we demonstrated that the methylation pattern of the cell lines approximately equals that of H3F3A-mutated stromal cells in tissue. These patterns more resemble that of osteoblasts than that of mesenchymal stem cells, which argues for the osteoblast as the cell of origin of giant cell tumours of bone. Using enrichment analysis, we detected distinct hypermethylated clusters containing histone and collagen genes as well as target genes of the tumour suppressor p53. We found that the promotor regions of CDKN1A, CDKN2A and IGFBP3 are methylated more strongly in GCTB than in the other giant cell containing lesions, mesenchymal stem cells, osteoblasts, and osteoclasts (p<0.001). This hypermethylation correlates with the lower gene expression at the mRNA level for these three genes in the cell lines, the lack of p16 and p21 in these cell lines and the lower expression of p16 and p21 in GCTB. Overall, our analysis reveals characteristic DNA methylation patterns of giant cell tumours of bone and chondroblastomas and shows that cell lines of giant cell tumours of bone are a valid model for further analysis of H3F3A-mutated tumour cells. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Julian Giesche
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Kevin Mellert
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Sven Geißler
- Centre for Regenerative Therapies, Berlin Institute of Health, Charité University Hospital Berlin, Berlin, Germany
| | - Sophia Arndt
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Carolin Seeling
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | | | | | - Ralf Marienfeld
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Peter Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Thomas Fe Barth
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
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20
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Christiansen SN, Andersen JD, Kampmann ML, Liu J, Andersen MM, Tfelt-Hansen J, Morling N. Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts. Epigenetics 2022; 17:1636-1645. [PMID: 35356867 PMCID: PMC9621037 DOI: 10.1080/15592294.2022.2051861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Infinium MethylationEPIC BeadChip (EPIC) is a reliable method for measuring the DNA methylation of more than 850,000 CpG positions. In clinical and forensic settings, it is critical to be able to work with low DNA amounts without risking reduced reproducibility. We evaluated the EPIC for a range of DNA amounts using two-fold serial dilutions investigated on two different days. While the β-value distributions were generally unaffected by decreasing DNA amounts, the median squared Pearson’s correlation coefficient (R2) of between-days β-value comparisons decreased from 0.994 (500 ng DNA) to 0.957 (16 ng DNA). The median standard deviation of the β-values was 0.005 and up to 0.017 (median of medians: 0.014) for β-values around 0.6–0.7. With decreasing amounts of DNA from 500 ng to 16 ng, the percentage of probes with standard deviations ≤ 0.1 decreased from 99.9% to 99.4%. This study showed that high reproducibility results are obtained with DNA amounts in the range 125–500 ng DNA, while DNA amounts equal to 63 ng or below gave less reproducible results.
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Affiliation(s)
- Steffan Noe Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Denmark
| | - Jing Liu
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Denmark.,Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Denmark.,Department of Mathematical Sciences, Aalborg University, Aalborg Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Denmark.,The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Denmark
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21
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Epigenome-Wide Association Study Reveals Differential Methylation Sites and Association of Gene Expression Regulation with Ischemic Moyamoya Disease in Adults. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7192060. [PMID: 35368875 PMCID: PMC8970806 DOI: 10.1155/2022/7192060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/28/2022] [Indexed: 12/12/2022]
Abstract
Background The association of DNA methylation with the pathogenesis of adult ischemic moyamoya disease (MMD) is unknown. Here, we investigated the genome-wide DNA methylation profiles in patients with MMD and identified the genes related to the pathogenesis of MMD. Methods Whole blood samples were collected from 20 individuals, including 10 patients with ischemic moyamoya disease without any underlying disease and 10 healthy individuals. Genome-wide DNA methylation analysis was performed using Illumina 850K microarrays. Transcriptional correlation was verified using quantitative reverse transcription-polymerase chain reaction. In vitro experiments were used to analyze the association of functional defects with candidate epigenetic markers. Results The genome-wide methylation level in the whole blood of adults with ischemic MMD was higher than that in the healthy individuals. In total, 759 methylation probes differed significantly between the case and control. The hypermethylated regions were mostly concentrated in the gene spacer regions. Among genes with the highest degree of the differential expression, KCNMA1 and GALNT2 were upregulated, whereas SOX6 and RBM33 were downregulated. Conclusions This is the first study showing that the low expression of genes associated with epigenetic regulation, such as SOX6 and RBM33, may be related to vascular occlusion in MMD, whereas the overexpression of KCNMA1 and GALNT2 may be related to the vascular hyperplasia. The results suggest that DNA methylation was involved in the pathogenesis of MMD, and new pathogenic genes were proposed as biological markers.
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22
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Kyung Lee M, Armstrong DA, Hazlett HF, Dessaint JA, Mellinger DL, Aridgides DS, Christensen BC, Ashare A. Exposure to extracellular vesicles from Pseudomonas aeruginosa result in loss of DNA methylation at enhancer and DNase hypersensitive site regions in lung macrophages. Epigenetics 2021; 16:1187-1200. [PMID: 33380271 PMCID: PMC8813072 DOI: 10.1080/15592294.2020.1853318] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/11/2020] [Accepted: 10/23/2020] [Indexed: 02/08/2023] Open
Abstract
Various pathogens use differing strategies to evade host immune response including modulating the host's epigenome. Here, we investigate if EVs secreted from P. aeruginosa alter DNA methylation in human lung macrophages, thereby potentially contributing to a dysfunctional innate immune response. Using a genome-wide DNA methylation approach, we demonstrate that P. aeruginosa EVs alter certain host cell DNA methylation patterns. We identified 1,185 differentially methylated CpGs (FDR < 0.05), which were significantly enriched for distal DNA regulatory elements including enhancer regions and DNase hypersensitive sites. Notably, all but one of the 1,185 differentially methylated CpGs were hypomethylated in association with EV exposure. Significantly hypomethylated CpGs tracked to genes including AXL, CFB and CCL23. Gene expression analysis identified 310 genes exhibiting significantly altered expression 48 hours post P. aeruginosa EV treatment, with 75 different genes upregulated and 235 genes downregulated. Some CpGs associated with cytokines such as CSF3 displayed strong negative correlations between DNA methylation and gene expression. Our infection model illustrates how secreted products (EVs) from bacteria can alter DNA methylation of the host epigenome. Changes in DNA methylation in distal DNA regulatory regions in turn can modulate cellular gene expression and potential downstream cellular processes.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - David A. Armstrong
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Haley F. Hazlett
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - John A. Dessaint
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Diane L. Mellinger
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | | | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Alix Ashare
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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23
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Singh O, Pratt D, Aldape K. Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors. Acta Neuropathol Commun 2021; 9:148. [PMID: 34496929 PMCID: PMC8425010 DOI: 10.1186/s40478-021-01249-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
It is recognized that the tumor microenvironment (TME) plays a critical role in the biology of cancer. To better understand the role of immune cell components in CNS tumors, we applied a deconvolution approach to bulk DNA methylation array data in a large set of newly profiled samples (n = 741) as well as samples from external data sources (n = 3311) of methylation-defined glial and glioneuronal tumors. Using the cell-type proportion data as input, we used dimensionality reduction to visualize sample-wise patterns that emerge from the cell type proportion estimations. In IDH-wildtype glioblastomas (n = 2,072), we identified distinct tumor clusters based on immune cell proportion and demonstrated an association with oncogenic alterations such as EGFR amplification and CDKN2A/B homozygous deletion. We also investigated the immune cluster-specific distribution of four malignant cellular states (AC-like, OPC-like, MES-like and NPC-like) in the IDH-wildtype cohort. We identified two major immune-based subgroups of IDH-mutant gliomas, which largely aligned with 1p/19q co-deletion status. Non-codeleted gliomas showed distinct proportions of a key genomic aberration (CDKN2A/B loss) among immune cell-based groups. We also observed significant positive correlations between monocyte proportion and expression of PD-L1 and PD-L2 (R = 0.54 and 0.68, respectively). Overall, the findings highlight specific roles of the TME in biology and classification of CNS tumors, where specific immune cell admixtures correlate with tumor types and genomic alterations.
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Affiliation(s)
- Omkar Singh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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24
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Lehmann U, Jung A. [Next generation sequencing in histopathology : Applications and methodological challenges]. DER PATHOLOGE 2021; 42:363-368. [PMID: 34170385 DOI: 10.1007/s00292-021-00953-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 10/21/2022]
Abstract
The enormous increase in sequencing capacity due to the development of next generation sequencing technologies opens up new opportunities in the fields of histopathology, research, and diagnostics, but also poses huge challenges.The identification of genomic aberrations (point mutations, small insertions and deletions, fusion transcripts, and tumor mutation burden (TMB)) have already become a reliable part of routine molecular diagnostics. This will be supplemented by additional applications, namely gene amplifications, microsatellite instability, genomic signatures like homologous recombination deficiency (HRD), mRNA expression patterns, B‑ and T‑cell clonality, and DNA methylation. Challenges in preanalytics and the evaluation of assay sensitivity and specificity as well as proper curation of identified aberrations, which requires a new type of specialist, are presented and discussed.
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Affiliation(s)
- Ulrich Lehmann
- Institut für Pathologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland.
| | - Andreas Jung
- Pathologisches Institut, Medizinische Fakultät, LMU München, Thalkirchner Str. 36, 80337, München, Deutschland
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25
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Talukdar FR, Soares Lima SC, Khoueiry R, Laskar RS, Cuenin C, Sorroche BP, Boisson AC, Abedi-Ardekani B, Carreira C, Menya D, Dzamalala CP, Assefa M, Aseffa A, Miranda-Gonçalves V, Jerónimo C, Henrique RM, Shakeri R, Malekzadeh R, Gasmelseed N, Ellaithi M, Gangane N, Middleton DRS, Le Calvez-Kelm F, Ghantous A, Roux ML, Schüz J, McCormack V, Parker MI, Pinto LFR, Herceg Z. Genome-Wide DNA Methylation Profiling of Esophageal Squamous Cell Carcinoma from Global High-Incidence Regions Identifies Crucial Genes and Potential Cancer Markers. Cancer Res 2021; 81:2612-2624. [PMID: 33741694 DOI: 10.1158/0008-5472.can-20-3445] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/04/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
Epigenetic mechanisms such as aberrant DNA methylation (DNAme) are known to drive esophageal squamous cell carcinoma (ESCC), yet they remain poorly understood. Here, we studied tumor-specific DNAme in ESCC cases from nine high-incidence countries of Africa, Asia, and South America. Infinium MethylationEPIC array was performed on 108 tumors and 51 normal tissues adjacent to the tumors (NAT) in the discovery phase, and targeted pyrosequencing was performed on 132 tumors and 36 NAT in the replication phase. Top genes for replication were prioritized by weighting methylation results using RNA-sequencing data from The Cancer Genome Atlas and GTEx and validated by qPCR. Methylome analysis comparing tumor and NAT identified 6,796 differentially methylated positions (DMP) and 866 differential methylated regions (DMR), with a 30% methylation (Δβ) difference. The majority of identified DMPs and DMRs were hypermethylated in tumors, particularly in promoters and gene-body regions of genes involved in transcription activation. The top three prioritized genes for replication, PAX9, SIM2, and THSD4, had similar methylation differences in the discovery and replication sets. These genes were exclusively expressed in normal esophageal tissues in GTEx and downregulated in tumors. The specificity and sensitivity of these DNAme events in discriminating tumors from NAT were assessed. Our study identified novel, robust, and crucial tumor-specific DNAme events in ESCC tumors across several high-incidence populations of the world. Methylome changes identified in this study may serve as potential targets for biomarker discovery and warrant further functional characterization. SIGNIFICANCE: This largest genome-wide DNA methylation study on ESCC from high-incidence populations of the world identifies functionally relevant and robust DNAme events that could serve as potential tumor-specific markers. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2612/F1.large.jpg.
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Affiliation(s)
| | - Sheila C Soares Lima
- Department of Molecular Carcinogenesis, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Rita Khoueiry
- International Agency for Research on Cancer, Lyon, France
| | | | - Cyrille Cuenin
- International Agency for Research on Cancer, Lyon, France
| | - Bruna Pereira Sorroche
- International Agency for Research on Cancer, Lyon, France
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | | | | | | | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Vera Miranda-Gonçalves
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Rui M Henrique
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Ramin Shakeri
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Nagla Gasmelseed
- Department of Molecular Biology, National Cancer Institute, University of Gezira, Gezira, Sudan
| | - Mona Ellaithi
- Department of Histopathology and Cytology, Al-Neelain University, Khartoum, Sudan
| | - Nitin Gangane
- Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | | | | | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France
| | | | - Joachim Schüz
- International Agency for Research on Cancer, Lyon, France
| | | | - M Iqbal Parker
- Integrative Biomedical Sciences and IDM, University of Cape Town, Cape Town, South Africa
| | | | - Zdenko Herceg
- International Agency for Research on Cancer, Lyon, France.
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26
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Ferreyra Vega S, Olsson Bontell T, Corell A, Smits A, Jakola AS, Carén H. DNA methylation profiling for molecular classification of adult diffuse lower-grade gliomas. Clin Epigenetics 2021; 13:102. [PMID: 33941250 PMCID: PMC8091784 DOI: 10.1186/s13148-021-01085-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/20/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND DNA methylation profiling has facilitated and improved the classification of a wide variety of tumors of the central nervous system. In this study, we investigated the potential utility of DNA methylation profiling to achieve molecular diagnosis in adult primary diffuse lower-grade glioma (dLGG) according to WHO 2016 classification system. We also evaluated whether methylation profiling could provide improved molecular characterization and identify prognostic differences beyond the classical histological WHO grade together with IDH mutation status and 1p/19q codeletion status. All patients diagnosed with dLGG in the period 2007-2016 from the Västra Götaland region in Sweden were assessed for inclusion in the study. RESULTS A total of 166 dLGG cases were subjected for genome-wide DNA methylation analysis. Of these, 126 (76%) were assigned a defined diagnostic methylation class with a class prediction score ≥ 0.84 and subclass score ≥ 0.50. The assigned methylation classes were highly associated with their IDH mutation status and 1p/19q codeletion status. IDH-wildtype gliomas were further divided into subgroups with distinct molecular features. CONCLUSION The stratification of the patients by methylation profiling was as effective as the integrated WHO 2016 molecular reclassification at predicting the clinical outcome of the patients. Our study shows that DNA methylation profiling is a reliable and robust approach for the classification of dLGG into molecular defined subgroups, providing accurate detection of molecular markers according to WHO 2016 classification.
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Affiliation(s)
- Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alba Corell
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anja Smits
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neuroscience, Neurology, Uppsala University, Uppsala, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Neurosurgery, St. Olavs University Hospital, Trondheim, Norway
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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27
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Oliveira DVNP, Hentze J, O'Rourke CJ, Andersen JB, Høgdall C, Høgdall EV. DNA Methylation in Ovarian Tumors-a Comparison Between Fresh Tissue and FFPE Samples. Reprod Sci 2021; 28:3212-3218. [PMID: 33891290 PMCID: PMC8526488 DOI: 10.1007/s43032-021-00589-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/15/2021] [Indexed: 01/14/2023]
Abstract
Among women, ovarian cancer (OC) is one of the most severe forms of malignancy, accounting for a low 5-year survival rate, of approximately 52%. Early symptoms are unspecific and hence hard to detect. The origin of OC and its subtypes are still unclear, underlying the need for efficient diagnostic biomarkers. In that regard, epigenetics studies are emerging in cancer diagnostics, with encouraging outcomes. Among them, DNA methylation profiling has shown that the origins of the cancer epigenome are associated with molecular factors that are crucial to carcinogenesis, such as regulation of oncogenes and tumor suppressors. Furthermore, those events have been detected in abnormal cell morphology before neoplastic formation, indicating its potential crucial use in the OC diagnostics in the future. Nonetheless, studies are limited, and whether methylation analysis can be performed optimally in formalin-fixed paraffin-embedded (FFPE) preparations of OC cases is still elusive. In the present report, we investigated the performance of DNA methylation analysis in FFPE samples, compared to their matched fresh frozen tissue in a small cohort of OC samples. We found that the overall DNA methylation profile in FFPE tissue showed high concordance to that found in fresh frozen tissue, and accounting for the small cohort size, the differentially methylated sites found primarily in frozen tissue, compared to benign samples, were also reproducible in FFPE. Overall, by using samples from our current clinical setting of tissue preservation, these preliminary observations might provide insights into the clinical use of FFPE tissues in methylation studies without critically compromising the outcome.
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Affiliation(s)
| | - Julie Hentze
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Colm J O'Rourke
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Jesper B Andersen
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Claus Høgdall
- Department of Gynecology, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark.
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28
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Maden SK, Thompson RF, Hansen KD, Nellore A. Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. NAR Genom Bioinform 2021; 3:lqab025. [PMID: 33937763 PMCID: PMC8061458 DOI: 10.1093/nargab/lqab025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
While DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35 360 Illumina Infinium HumanMethylation450K DNAm array samples published on the Gene Expression Omnibus. We learned a controlled vocabulary of sample labels by applying regular expressions to metadata and used existing models to predict various sample properties including epigenetic age. We found approximately two-thirds of samples were from blood, one-quarter were from brain and one-third were from cancer patients. About 19% of samples failed at least one of Illumina's 17 prescribed quality assessments; signal distributions across samples suggest modifying manufacturer-recommended thresholds for failure would make these assessments more informative. We further analyzed DNAm variances in seven tissues (adipose, nasal, blood, brain, buccal, sperm and liver) and characterized specific probes distinguishing them. Finally, we compiled DNAm array data and metadata, including our learned and predicted sample labels, into database files accessible via the recountmethylation R/Bioconductor companion package. Its vignettes walk the user through some analyses contained in this paper.
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Affiliation(s)
- Sean K Maden
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
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29
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Ueda S, Yamashita S, Watanabe SI, Wakabayashi M, Motoi N, Noguchi M, Sekine S, Sato Y, Ushijima T. Influence of degree of DNA degradation in formalin-fixed and paraffin-embedded tissue samples on accuracy of genome-wide DNA methylation analysis. Epigenomics 2021; 13:565-576. [PMID: 33820444 DOI: 10.2217/epi-2020-0431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Depending upon the degree of DNA degradation of formalin-fixed and paraffin-embedded tissue samples, accuracy of measurement by Infinium MethylationEPIC BeadChip assay (Illumina, CA, USA) was assessed. Materials & methods: DNA quality of six formalin-fixed and paraffin-embedded lung tissue samples with different formalin fixation periods was assessed by Illumina quality control, DNA copy number and DNA integrity number value. Infinium data from restored bisulfite treated DNA were compared with datum from a fresh-frozen sample. Results: The correlation coefficient decreased from 0.993 to 0.970 depending upon DNA degradation, even if the Illumina quality control was met. Exclusion of specific probes improved the correlation regardless of tissue. Conclusion: Poor DNA quality can be assessed as an amplifiable DNA copy number and DNA integrity number value. Probe filtering has the potential to improve assay accuracy.
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Affiliation(s)
- Sho Ueda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104 0045, Japan.,Department of Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki 305 8575, Japan.,Department of Thoracic Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki 305 8575, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104 0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo 104 0045, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104 0045, Japan
| | - Noriko Motoi
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104 0045, Japan
| | - Masayuki Noguchi
- Department of Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki 305 8575, Japan
| | - Shigeki Sekine
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104 0045, Japan
| | - Yukio Sato
- Department of Thoracic Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki 305 8575, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104 0045, Japan
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Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy. Int J Mol Sci 2021; 22:ijms22062790. [PMID: 33801838 PMCID: PMC7999472 DOI: 10.3390/ijms22062790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Sudden cardiac death (SCD) is a diagnostic challenge in forensic medicine. In a relatively large proportion of the SCDs, the deaths remain unexplained after autopsy. This challenge is likely caused by unknown disease mechanisms. Changes in DNA methylation have been associated with several heart diseases, but the role of DNA methylation in SCD is unknown. In this study, we investigated DNA methylation in two SCD subtypes, sudden unexplained death (SUD) and sudden unexpected death in epilepsy (SUDEP). We assessed DNA methylation of more than 850,000 positions in cardiac tissue from nine SUD and 14 SUDEP cases using the Illumina Infinium MethylationEPIC BeadChip. In total, six differently methylated regions (DMRs) between the SUD and SUDEP cases were identified. The DMRs were located in proximity to or overlapping genes encoding proteins that are a part of the glutathione S-transferase (GST) superfamily. Whole genome sequencing (WGS) showed that the DNA methylation alterations were not caused by genetic changes, while whole transcriptome sequencing (WTS) showed that DNA methylation was associated with expression levels of the GSTT1 gene. In conclusion, our results indicate that cardiac DNA methylation is similar in SUD and SUDEP, but with regional differential methylation in proximity to GST genes.
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Salo-Mullen EE, Maio A, Mukherjee S, Bandlamudi C, Shia J, Kemel Y, Cadoo KA, Liu Y, Carlo M, Ranganathan M, Kane S, Srinivasan P, Chavan SS, Donoghue MTA, Bourque C, Sheehan M, Tejada PR, Patel Z, Arnold AG, Kennedy JA, Amoroso K, Breen K, Catchings A, Sacca R, Marcell V, Markowitz AJ, Latham A, Walsh M, Misyura M, Ceyhan-Birsoy O, Solit DB, Berger MF, Robson ME, Taylor BS, Offit K, Mandelker D, Stadler ZK. Prevalence and Characterization of Biallelic and Monoallelic NTHL1 and MSH3 Variant Carriers From a Pan-Cancer Patient Population. JCO Precis Oncol 2021; 5:PO.20.00443. [PMID: 34250384 PMCID: PMC8232072 DOI: 10.1200/po.20.00443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
NTHL1 and MSH3 have been implicated as autosomal recessive cancer predisposition genes. Although individuals with biallelic NTHL1 and MSH3 pathogenic variants (PVs) have increased cancer and polyposis risk, risks for monoallelic carriers are uncertain. We sought to assess the prevalence and characterize NTHL1 and MSH3 from a large pan-cancer patient population. MATERIALS AND METHODS Patients with pan-cancer (n = 11,081) underwent matched tumor-normal sequencing with consent for germline analysis. Medical records and tumors were reviewed and analyzed. Prevalence of PVs was compared with reference controls (Genome Aggregation Database). RESULTS NTHL1-PVs were identified in 40 patients including 39 monoallelic carriers (39/11,081 = 0.35%) and one with biallelic variants (1/11,081 = 0.009%) and a diagnosis of isolated early-onset breast cancer. NTHL1-associated mutational signature 30 was identified in the tumors of the biallelic patient and two carriers. Colonic polyposis was not identified in any NTHL1 patient. MSH3-PVs were identified in 13 patients, including 12 monoallelic carriers (12/11,081 = 0.11%) and one with biallelic MSH3 variants (1/11,081 = 0.009%) and diagnoses of later-onset cancers, attenuated polyposis, and abnormal MSH3-protein expression. Of the 12 MSH3 carriers, two had early-onset cancer diagnoses with tumor loss of heterozygosity of the wild-type MSH3 allele. Ancestry-specific burden tests demonstrated that NTHL1 and MSH3 prevalence was not significantly different in this pan-cancer population versus controls. CONCLUSION NTHL1 and MSH3 germline alterations were not enriched in this pan-cancer patient population. However, tumor-specific findings, such as mutational signature 30 and loss of heterozygosity of the wild-type allele, suggest the potential contribution of monoallelic variants to tumorigenesis in a subset of patients.
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Affiliation(s)
- Erin E. Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena Kemel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karen A. Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Megha Ranganathan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarah Kane
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shweta S. Chavan
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark T. A. Donoghue
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caitlin Bourque
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Zalak Patel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angela G. Arnold
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer A. Kennedy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kimberly Amoroso
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kelsey Breen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amanda Catchings
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rosalba Sacca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vanessa Marcell
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Arnold J. Markowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maksym Misyura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B. Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry S. Taylor
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K. Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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32
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Lehmann U, Stark H, Bartels S, Schlue J, Büsche G, Kreipe H. Genome-wide DNA methylation profiling is able to identify prefibrotic PMF cases at risk for progression to myelofibrosis. Clin Epigenetics 2021; 13:28. [PMID: 33541399 PMCID: PMC7860011 DOI: 10.1186/s13148-021-01010-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Patients suffering from the BCR-ABL1-negative myeloproliferative disease prefibrotic primary myelofibrosis (pre-PMF) have a certain risk for progression to myelofibrosis. Accurate risk estimation for this fibrotic progression is of prognostic importance and clinically relevant. Commonly applied risk scores are based on clinical, cytogenetic, and genetic data but do not include epigenetic modifications. Therefore, we evaluated the assessment of genome-wide DNA methylation patterns for their ability to predict fibrotic progression in PMF patients. RESULTS For this purpose, the DNA methylation profile was analyzed genome-wide in a training set of 22 bone marrow trephines from patients with either fibrotic progression (n = 12) or stable disease over several years (n = 10) using the 850 k EPIC array from Illumina. The DNA methylation classifier constructed from this data set was validated in an independently measured test set of additional 11 bone marrow trephines (7 with stable disease, 4 with fibrotic progress). Hierarchical clustering of methylation β-values and linear discriminant classification yielded very good discrimination between both patient groups. By gene ontology analysis, the most differentially methylated CpG sites are primarily associated with genes involved in cell-cell and cell-matrix interactions. CONCLUSIONS In conclusion, we could show that genome-wide DNA methylation profiling of bone marrow trephines is feasible under routine diagnostic conditions and, more importantly, is able to predict fibrotic progression in pre-fibrotic primary myelofibrosis with high accuracy.
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Affiliation(s)
- Ulrich Lehmann
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Helge Stark
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Stephan Bartels
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jerome Schlue
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Guntram Büsche
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
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33
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Cell lineage-specific methylome and genome alterations in gout. Aging (Albany NY) 2021; 13:3843-3865. [PMID: 33493135 PMCID: PMC7906142 DOI: 10.18632/aging.202353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/05/2020] [Indexed: 12/14/2022]
Abstract
In this study, we examined data from 69 gout patients and 1,455 non-gout controls using a MethylationEPIC BeadChip assay and Illumina HiSeq platform to identify lineage-specific epigenetic alterations and associated genetic factors that contributed to gouty inflammation. Cell lineage-specific differentially methylated sites were identified using CellDMC after adjusting for sex, age, alcohol drinking, smoking status, and smoking history (total pack-years). Different cell lineages displayed distinct differential methylation. Ingenuity Pathway Analysis and NetworkAnalyst indicated that many differential methylated sites were associated with interleukin-1β expression in monocytes. On the UCSC Genome Browser and WashU Epigenome Browser, metabolic trait, cis-methylation quantitative trait loci, genetic, and functional annotation analyses identified nine methylation loci located in interleukin-1β-regulating genes (PRKCZ, CIDEC, VDAC1, CPT1A, BIRC2, BRCA1, STK11, and NLRP12) that were associated specifically with gouty inflammation. All nine sites mapped to active regulatory elements in monocytes. MoLoTool and ReMap analyses indicated that the nine methylation loci overlapped with binding sites of several transcription factors that regulated interleukin-1β production and gouty inflammation. Decreases in PRKCZ and STK11 methylation were also associated with higher numbers of first-degree relatives who also had gout. The gouty-inflammation specific methylome and genome alterations could potentially aid in the identification of novel therapeutic targets.
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34
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Genome wide methylation profiling of selected matched soft tissue sarcomas identifies methylation changes in metastatic and recurrent disease. Sci Rep 2021; 11:667. [PMID: 33436720 PMCID: PMC7804318 DOI: 10.1038/s41598-020-79648-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
In this study we used the Illumina Infinium Methylation array to investigate in a cohort of matched archival human tissue samples (n = 32) from 14 individuals with soft tissue sarcomas if genome-wide methylation changes occur during metastatic and recurrent (Met/Rec) disease. A range of sarcoma types were selected for this study: leiomyosarcoma (LMS), myxofibrosarcoma (MFS), rhabdomyosarcoma (RMS) and synovial sarcoma (SS). We identified differential methylation in all Met/Rec matched samples, demonstrating that epigenomic differences develop during the clonal evolution of sarcomas. Differentially methylated regions and genes were detected, not been previously implicated in sarcoma progression, including at PTPRN2 and DAXX in LMS, WT1-AS and TNXB in SS, VENTX and NTRK3 in pleomorphic RMS and MEST and the C14MC / miR-379/miR-656 in MFS. Our overall findings indicate the presence of objective epigenetic differences across primary and Met/Rec human tissue samples not previously reported.
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35
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Ohmomo H, Komaki S, Ono K, Sutoh Y, Hachiya T, Arai E, Fujimoto H, Yoshida T, Kanai Y, Sasaki M, Shimizu A. Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing. Pathol Int 2020; 71:135-140. [PMID: 33333623 PMCID: PMC7898333 DOI: 10.1111/pin.13054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/28/2020] [Accepted: 11/16/2020] [Indexed: 11/29/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE-derived DNA for targeted-bisulfite sequencing (TB-seq) is lacking. Here, we evaluated the suitability of FFPE-derived DNA for TB-seq. We conducted TB-seq using FFPE-derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB-seq statistics between the two preservation methods. The approximately 600-bp average fragment size of the FFPE-derived DNA was significantly shorter than that of the FF-derived DNA. The sequencing libraries constructed using FFPE-derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF-derived DNA. In the mapped data of FFPE-derived DNA, duplicated reads accounted for > 60% of the obtained sequence reads, with lower mean on-target coverage. Therefore, the standard TB-seq protocol is inadequate for obtaining high-quality data for epigenetic analysis from FFPE-derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.
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Affiliation(s)
- Hideki Ohmomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Shohei Komaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Kanako Ono
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Yoichi Sutoh
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Teruhiko Yoshida
- Department of Clinical Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.,Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
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36
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Kling T, Wenger A, Carén H. DNA methylation-based age estimation in pediatric healthy tissues and brain tumors. Aging (Albany NY) 2020; 12:21037-21056. [PMID: 33168783 PMCID: PMC7695434 DOI: 10.18632/aging.202145] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Several DNA methylation clocks have been developed to reflect chronological age of human tissues, but most clocks have been trained on adult samples. The rapid methylome changes in children and the role of epigenetics in pediatric tumors calls for tools accurately estimating methylation age in children. We aimed to evaluate seven methylation clocks in multiple tissues from healthy children to inform future studies on the optimal clock for pediatric cohorts, and analyzed the methylation age in brain tumors. We found that clocks trained on pediatric samples were the best in all tested tissues, highlighting the need for dedicated clocks. For blood samples, the Skin and blood clock had the best correlation with chronological age, while PedBE was the most accurate for saliva and buccal samples, and Horvath for brain tissue. Horvath methylation age was accelerated in pediatric brain tumors and the acceleration was subtype-specific for atypical teratoid rhabdoid tumor (ATRT), ependymoma, medulloblastoma and glioma. The subtypes with the highest acceleration corresponded to the worst prognostic categories in ATRT, ependymoma and glioma, whereas the relationship was reversed in medulloblastoma. This suggests that methylation age has potential as a prognostic biomarker in pediatric brain tumors and should be further explored.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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37
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Xia D, Leon AJ, Cabanero M, Pugh TJ, Tsao MS, Rath P, Siu LLY, Yu C, Bedard PL, Shepherd FA, Zadeh G, Chetty R, Aldape K. Minimalist approaches to cancer tissue-of-origin classification by DNA methylation. Mod Pathol 2020; 33:1874-1888. [PMID: 32415265 PMCID: PMC8808378 DOI: 10.1038/s41379-020-0547-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 11/09/2022]
Abstract
Classification of cancers by tissue-of-origin is fundamental to diagnostic pathology. While the combination of clinical data, tissue histology, and immunohistochemistry is usually sufficient, there remains a small but not insignificant proportion of difficult-to-classify cases. These challenging cases provide justification for ancillary molecular testing, including high-throughput DNA methylation array profiling, which promises cell-of-origin information and compatibility with formalin-fixed specimens. While diagnostically powerful, methylation profiling platforms are costly and technically challenging to implement, particularly for less well-resourced laboratories. To address this, we simulated the performance of "minimalist" methylation-based tests for cancer classification using publicly-available and internal institutional profiling data. These analyses showed that small and focused sets of the most informative CpG biomarkers from the arrays are sufficient for accurate diagnoses. As an illustrative example, one classifier, using information from just 53 out of about 450,000 available CpG probes, achieved an accuracy of 94.5% on 2575 fresh primary validation cases across 28 cancer types from The Cancer Genome Atlas Network. By training minimalist classifiers on formalin-fixed primary and metastatic cases, generally high accuracies were also achieved on additional datasets. These results support the potential of minimalist methylation testing, possibly via quantitative PCR and targeted next-generation sequencing platforms, in cancer classification.
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Affiliation(s)
- Daniel Xia
- Division of Hematopathology and Transfusion Medicine, University Health Network, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | | | - Michael Cabanero
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Division of Anatomical Pathology, University Health Network, Toronto, ON, Canada
| | | | - Ming Sound Tsao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Division of Anatomical Pathology, University Health Network, Toronto, ON, Canada
| | - Prisni Rath
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Lillian Lai-Yun Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Celeste Yu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | | | - Gelareh Zadeh
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Runjan Chetty
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Division of Anatomical Pathology, University Health Network, Toronto, ON, Canada
| | - Kenneth Aldape
- Laboratory of Pathology, Center of Cancer Research, National Cancer Institute, Bethesda, MD, USA
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38
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Armstrong DA, Lee MK, Hazlett HF, Dessaint JA, Mellinger DL, Aridgides DS, Hendricks GM, Abdalla MAK, Christensen BC, Ashare A. Extracellular Vesicles from Pseudomonas aeruginosa Suppress MHC-Related Molecules in Human Lung Macrophages. Immunohorizons 2020; 4:508-519. [PMID: 32819967 DOI: 10.4049/immunohorizons.2000026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/01/2020] [Indexed: 12/18/2022] Open
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is one of the most common pathogens colonizing the lungs of cystic fibrosis patients. P. aeruginosa secrete extracellular vesicles (EVs) that contain LPS and other virulence factors that modulate the host's innate immune response, leading to an increased local proinflammatory response and reduced pathogen clearance, resulting in chronic infection and ultimately poor patient outcomes. Lung macrophages are the first line of defense in the airway innate immune response to pathogens. Proper host response to bacterial infection requires communication between APC and T cells, ultimately leading to pathogen clearance. In this study, we investigate whether EVs secreted from P. aeruginosa alter MHC Ag expression in lung macrophages, thereby potentially contributing to decreased pathogen clearance. Primary lung macrophages from human subjects were collected via bronchoalveolar lavage and exposed to EVs isolated from P. aeruginosa in vitro. Gene expression was measured with the NanoString nCounter gene expression assay. DNA methylation was measured with the EPIC array platform to assess changes in methylation. P. aeruginosa EVs suppress the expression of 11 different MHC-associated molecules in lung macrophages. Additionally, we show reduced DNA methylation in a regulatory region of gene complement factor B (CFB) as the possible driving mechanism of widespread MHC gene suppression. Our results demonstrate MHC molecule downregulation by P. aeruginosa-derived EVs in lung macrophages, which is consistent with an immune evasion strategy employed by a prokaryote in a host-pathogen interaction, potentially leading to decreased pulmonary bacterial clearance.
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Affiliation(s)
- David A Armstrong
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756;
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
| | - Haley F Hazlett
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - John A Dessaint
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756
| | - Diane L Mellinger
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756
| | - Daniel S Aridgides
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756
| | - Gregory M Hendricks
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Moemen A K Abdalla
- Department of Biochemistry, Faculty of Science, Alexandria University, Alexandria 21526, Egypt; and
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
| | - Alix Ashare
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
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Wenger A, Ferreyra Vega S, Kling T, Bontell TO, Jakola AS, Carén H. Intratumor DNA methylation heterogeneity in glioblastoma: implications for DNA methylation-based classification. Neuro Oncol 2020; 21:616-627. [PMID: 30668814 PMCID: PMC6502500 DOI: 10.1093/neuonc/noz011] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND A feature of glioblastoma (GBM) is cellular and molecular heterogeneity, both within and between tumors. This variability causes a risk for sampling bias and potential tumor escape from future targeted therapy. Heterogeneous intratumor gene expression in GBM is well documented, but little is known regarding the epigenetic heterogeneity. Variability in DNA methylation within tumors would have implications for diagnostics, as methylation can be used for tumor classification, subtyping, and determination of the clinically used biomarker O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation. We therefore aimed to profile the intratumor DNA methylation heterogeneity in GBM and its effect on diagnostic properties. METHODS Three to 4 spatially separated biopsies per tumor were collected from 12 GBM patients. We performed genome-wide DNA methylation analysis and investigated intratumor variation. RESULTS All samples were classified as GBM isocitrate dehydrogenase (IDH) wild type (wt)/mutated by methylation profiling, but the subclass differed within 5 tumors. Some GBM samples exhibited higher DNA methylation differences within tumors than between, and many cytosine-phosphate-guanine (CpG) sites (mean: 17 000) had different methylation levels within the tumors. MGMT methylation status differed in IDH mutated patients (1/1). CONCLUSIONS We demonstrated that intratumor DNA methylation heterogeneity is a feature of GBM. Although all biopsies were classified as GBM IDH wt/mutated by methylation analysis, the assigned subclass differed in samples from the same patient. The observed heterogeneity within tumors is important to consider for methylation-based biomarkers and future improvements in stratification of GBM patients.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Neurosurgery, St Olavs University Hospital, Trondheim, Norway
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Cheung K, Burgers MJ, Young DA, Cockell S, Reynard LN. Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage. Epigenetics 2019; 15:594-603. [PMID: 31833794 PMCID: PMC7574380 DOI: 10.1080/15592294.2019.1700003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying almost double the number of sites than the 450K array. In this study, we compare DNA methylation values of shared CpGs of the same human cartilage samples assayed using both platforms. DNA methylation was measured in 21 human cartilage samples using the both 450K and EPIC arrays. Additional matched 450K and EPIC data in whole tumour and whole blood were downloaded from GEO GSE92580 and GSE86833, respectively. Data were processed using the Bioconductor package Minfi. DNA methylation of six CpG sites was validated for the same 21 cartilage samples by pyrosequencing. In cartilage samples, overall sample correlations of methylation values between arrays were high (Pearson’s r > 0.96). However, 50.5% of CpG sites showed poor correlation (r < 0.2) between arrays. Sites with limited variance and with either very high or very low methylation levels in cartilage exhibited lower correlation values, corroborating prior studies in whole blood. Bisulphite pyrosequencing did not highlight one array as generating more accurate methylation values. For a specific CpG site, the array methylation correlation coefficient differed between cartilage, tumour, and whole blood, reflecting the difference in methylation variance between cell types. Researchers should be cautious when analysing methylation of CpG sites that show low methylation variance within the cell type of interest, regardless of the method used to assay methylation.
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Affiliation(s)
- Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne, UK
| | - Marjolein J Burgers
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne, UK
| | - Louise N Reynard
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK
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Shimada M, Miyagawa T, Takeshima A, Kakita A, Toyoda H, Niizato K, Oshima K, Tokunaga K, Honda M. Epigenome-wide association study of narcolepsy-affected lateral hypothalamic brains, and overlapping DNA methylation profiles between narcolepsy and multiple sclerosis. Sleep 2019; 43:5574506. [DOI: 10.1093/sleep/zsz198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/07/2019] [Indexed: 01/05/2023] Open
Abstract
Abstract
Narcolepsy with cataplexy is a sleep disorder caused by a deficiency in hypocretin neurons in the lateral hypothalamus (LH). Here we performed an epigenome-wide association study (EWAS) of DNA methylation for narcolepsy and replication analyses using DNA samples extracted from two brain regions: LH (Cases: N = 4; Controls: N = 4) and temporal cortex (Cases: N = 7; Controls: N = 7). Seventy-seven differentially methylated regions (DMRs) were identified in the LH analysis, with the top association of a DMR in the myelin basic protein (MBP) region. Only five DMRs were detected in the temporal cortex analysis. Genes annotated to LH DMRs were significantly associated with pathways related to fatty acid response or metabolism. Two additional analyses applying the EWAS data were performed: (1) investigation of methylation profiles shared between narcolepsy and other disorders and (2) an integrative analysis of DNA methylation data and a genome-wide association study for narcolepsy. The results of the two approaches, which included significant overlap of methylated positions associated with narcolepsy and multiple sclerosis, indicated that the two diseases may partly share their pathogenesis. In conclusion, DNA methylation in LH where loss of orexin-producing neurons occurs may play a role in the pathophysiology of the disease.
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Affiliation(s)
- Mihoko Shimada
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Taku Miyagawa
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Akari Takeshima
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiromi Toyoda
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kazuhiro Niizato
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Kenichi Oshima
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Makoto Honda
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Seiwa Hospital, Institute of Neuropsychiatry, Tokyo, Japan
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Armstrong DA, Chen Y, Dessaint JA, Aridgides DS, Channon JY, Mellinger DL, Christensen BC, Ashare A. DNA Methylation Changes in Regional Lung Macrophages Are Associated with Metabolic Differences. Immunohorizons 2019; 3:274-281. [PMID: 31356157 PMCID: PMC6686200 DOI: 10.4049/immunohorizons.1900042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022] Open
Abstract
A number of pulmonary diseases occur with upper lobe predominance, including cystic fibrosis and smoking-related chronic obstructive pulmonary disease. In the healthy lung, several physiologic and metabolic factors exhibit disparity when comparing the upper lobe of the lung to lower lobe, including differences in oxygenation, ventilation, lymphatic flow, pH, and blood flow. In this study, we asked whether these regional differences in the lung are associated with DNA methylation changes in lung macrophages that could potentially lead to altered cell responsiveness upon subsequent environmental challenge. All analyses were performed using primary lung macrophages collected via bronchoalveolar lavage from healthy human subjects with normal pulmonary function. Epigenome-wide DNA methylation was examined via Infinium MethylationEPIC (850K) array and validated by targeted next-generation bisulfite sequencing. We observed 95 CpG loci with significant differential methylation in lung macrophages, comparing upper lobe to lower lobe (all false discovery rate < 0.05). Several of these genes, including CLIP4, HSH2D, NR4A1, SNX10, and TYK2, have been implicated as participants in inflammatory/immune-related biological processes. Functionally, we identified phenotypic differences in oxygen use, comparing upper versus lower lung macrophages. Our results support a hypothesis that epigenetic changes, specifically DNA methylation, at a multitude of gene loci in lung macrophages are associated with metabolic differences regionally in lung.
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Affiliation(s)
- David A Armstrong
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756;
| | - Youdinghuan Chen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
| | - John A Dessaint
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756
| | - Daniel S Aridgides
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756
| | - Jacqueline Y Channon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756; and
| | - Diane L Mellinger
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
| | - Alix Ashare
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756; .,Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756; and
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Larsson S, Wenger A, Dósa S, Sabel M, Kling T, Carén H. Cell line-based xenograft mouse model of paediatric glioma stem cells mirrors the clinical course of the patient. Carcinogenesis 2019; 39:1304-1309. [PMID: 29982329 PMCID: PMC6175027 DOI: 10.1093/carcin/bgy091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
The leading cause of cancer-related mortality among children is brain tumour, and glioblastoma multiforme (GBM) has the worst prognosis. New treatments are urgently needed, but with few cases and clinical trials in children, pre-clinical models such as patient-derived tumour xenografts (PDTX) are important. To generate these, tumour tissue is transplanted into mice, but this yields highly variable results and requires serial passaging in mice, which is time-consuming and expensive. We therefore aimed to establish a cell line-based orthotopic mouse model representative of the patient tumour. Glioma stem cell (GSC) lines derived from paediatric GBM were orthotopically transplanted into immunodeficient mice. Overall survival data were collected and histological analysis of the resulting neoplasias was performed. Genome-wide DNA methylation arrays were used for methylation and copy-number alterations (CNA) profiling. All GSC lines initiated tumours on transplantation and the survival of the mice correlated well with the survival of the patients. Xenograft tumours presented histological hallmarks of GBM, and were also classified as GBM by methylation profiling. Each xenograft tumour clustered together with its respective injected GSC line and patient tumour based on the methylation data. We have established a robust and reproducible cell line-based xenograft paediatric GBM model. The xenograft tumours accurately reflected the patient tumours and mirrored the clinical course of the patient. This model can therefore be used to assess patient response in pre-clinical studies.
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Affiliation(s)
- Susanna Larsson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Anna Wenger
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Sándor Dósa
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg.,The Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
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Gu S, Lin S, Ye D, Qian S, Jiang D, Zhang X, Li Q, Yang J, Ying X, Li Z, Tang M, Wang J, Jin M, Chen K. Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer. Clin Epigenetics 2019; 11:41. [PMID: 30846004 PMCID: PMC6407227 DOI: 10.1186/s13148-019-0628-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/04/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Epigenetic alternation is a common contributing factor to neoplastic transformation. Although previous studies have reported a cluster of aberrant promoter methylation changes associated with silencing of tumor suppressor genes, little is known concerning their sequential DNA methylation changes during the carcinogenetic process. The aim of the present study was to address a genome-wide search for identifying potentially important methylated changes and investigate the onset and pattern of methylation changes during the progression of colorectal neoplasia. METHODS A three-phase design was employed in this study. In the screening phase, DNA methylation profile of 12 pairs of colorectal cancer (CRC) and adjacent normal tissues was analyzed by using the Illumina MethylationEPIC BeadChip. Significant CpG sites were selected based on a cross-validation analysis from The Cancer Genome Atlas (TCGA) database. Methylation levels of candidate CpGs were assessed using pyrosequencing in the training dataset (tumor lesions and adjacent normal tissues from 46 CRCs) and the validation dataset (tumor lesions and paired normal tissues from 13 hyperplastic polyps, 129 adenomas, and 256 CRCs). A linear mixed-effects model was used to examine the incremental changes of DNA methylation during the progression of colorectal neoplasia. RESULTS The comparisons between normal and tumor samples in the screening phase revealed an extensive CRC-specific methylomic pattern with 174,006 (21%) methylated CpG sites, of which 22,232 (13%) were hyermethylated and 151,774 (87%) were hypomethylated. Hypermethylation mostly occurred in CpG islands with an overlap of gene promoters, while hypomethylation tended to be mapped far away from functional regions. Further cross validation analysis from TCGA dataset confirmed 265 hypermethylated promoters coupling with downregulated gene expression. Among which, hypermethylated changes in MEEPD2 promoter was successfully replicated in both training and validation phase. Significant hypermethylation appeared since precursor lesions with an extensive modification in CRCs. The linear mixed-effects modeling analysis found that a cumulative pattern of MPPED2 methylation changes from normal mucosa to hyperplastic polyp to adenoma, and to carcinoma (P < 0.001). CONCLUSIONS Our findings indicate that epigenetic alterations of MPPED2 promoter region appear sequentially during the colorectal neoplastic progression. It might be able to serve as a promising biomarker for early diagnosis and stage surveillance of colorectal tumorigenesis.
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Affiliation(s)
- Simeng Gu
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Shujuan Lin
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Ding Ye
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China.,Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University School of Public Health, 548 Binwen Road, Hangzhou, 310053, China
| | - Sangni Qian
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Danjie Jiang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xiaocong Zhang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qilong Li
- Jiashan Institute of Cancer Prevention and Treatment, 345 Jiefangdong Road, Jiashan, 314100, China
| | - Jinhua Yang
- Jiashan Institute of Cancer Prevention and Treatment, 345 Jiefangdong Road, Jiashan, 314100, China
| | - Xiaojiang Ying
- Department of Anorectal Surgery, Shaoxing People's Hospital, 568 Zhongxingbei Road, Shaoxing, 312000, China
| | - Zhenjun Li
- Department of Anorectal Surgery, Shaoxing People's Hospital, 568 Zhongxingbei Road, Shaoxing, 312000, China
| | - Mengling Tang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jianbing Wang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mingjuan Jin
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China.
| | - Kun Chen
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China. .,Cancer Institute, the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.
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Morrison FG, Miller MW, Logue MW, Assef M, Wolf EJ. DNA methylation correlates of PTSD: Recent findings and technical challenges. Prog Neuropsychopharmacol Biol Psychiatry 2019; 90:223-234. [PMID: 30503303 PMCID: PMC6314898 DOI: 10.1016/j.pnpbp.2018.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022]
Abstract
There is increasing evidence that epigenetic factors play a critical role in posttraumatic stress disorder (PTSD), by mediating the impact of environmental exposures to trauma on the regulation of gene expression. DNA methylation is one epigenetic process that has been highly studied in PTSD. This review will begin by providing an overview of DNA methylation (DNAm) methods, and will then highlight two major biological systems that have been identified in the epigenetic regulation in PTSD: (a) the immune system and (b) the stress response system. In addition to candidate gene approaches, we will review novel strategies to study epigenome-wide PTSD-related effects, including epigenome-wide algorithms that distill information from many loci into a single summary score (e.g., measures of "epigenetic age" which have been associated with PTSD). This review will also cover recent epigenome wide association studies (EWAS) of PTSD, and biological pathway models used to identify gene sets enriched in PTSD. Finally, we address technical and methodological advances and challenges to the field, and highlight exciting directions for future research.
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Affiliation(s)
- Filomene G Morrison
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA.
| | - Mark W Miller
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA
| | - Mark W Logue
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA; Biomedical Genetics, Boston University School of Medicine, USA; Department of Biostatistics, Boston University School of Public Health, USA
| | - Michele Assef
- Boston University, College of Health & Rehabilitation Sciences: Sargent College, USA
| | - Erika J Wolf
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA
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46
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Abstract
This chapter discusses analysis and interpretation of large-scale Illumina DNA methylation microarray data, used in the context of cancer studies. We outline commonly used normalization procedures and list issues to consider regarding data preprocessing. Focusing on software packages for R, we describe methods for finding features in the methylation data that are of importance for generating and testing hypotheses in cancer research, like differentially methylated positions or regions and global methylation trends.
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Affiliation(s)
- Teresia Kling
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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47
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Chen Y, Armstrong DA, Salas LA, Hazlett HF, Nymon AB, Dessaint JA, Aridgides DS, Mellinger DL, Liu X, Christensen BC, Ashare A. Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis. Clin Epigenetics 2018; 10:152. [PMID: 30526669 PMCID: PMC6288922 DOI: 10.1186/s13148-018-0580-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/06/2018] [Indexed: 11/10/2022] Open
Abstract
Background Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. All analyses were performed using primary alveolar macrophages from human subjects collected via bronchoalveolar lavage. Epigenome-wide DNA methylation was examined via Illumina MethylationEPIC (850 K) array. Targeted next-generation bisulfite sequencing was used to validate selected differentially methylated CpGs. Methylation-based sample classification was performed using the recursively partitioned mixture model (RPMM) and was tested against sample case-control status. Differentially methylated loci were identified by fitting linear models with adjustment of age, sex, estimated cell type proportions, and repeat measurement. Results RPMM class membership was significantly associated with the CF disease status (P = 0.026). One hundred nine CpG loci were differentially methylated in CF BAL cells (all FDR ≤ 0.1). The majority of differentially methylated loci in CF were hypo-methylated and found within non-promoter CpG islands as well as in putative enhancer regions and DNase hyper-sensitive regions. Conclusions These results support a hypothesis that epigenetic changes, specifically DNA methylation at a multitude of gene loci in lung macrophages, may participate, at least in part, in driving dysfunctional innate immune cells in the CF lung. Electronic supplementary material The online version of this article (10.1186/s13148-018-0580-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youdinghuan Chen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - David A Armstrong
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Haley F Hazlett
- Program in Experimental and Molecular Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Amanda B Nymon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - John A Dessaint
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Daniel S Aridgides
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Diane L Mellinger
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Xiaoying Liu
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Alix Ashare
- Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Program in Experimental and Molecular Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, Samet Y, Maoz M, Druid H, Arner P, Fu KY, Kiss E, Spalding KL, Landesberg G, Zick A, Grinshpun A, Shapiro AMJ, Grompe M, Wittenberg AD, Glaser B, Shemer R, Kaplan T, Dor Y. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun 2018; 9:5068. [PMID: 30498206 PMCID: PMC6265251 DOI: 10.1038/s41467-018-07466-6] [Citation(s) in RCA: 553] [Impact Index Per Article: 92.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/05/2018] [Indexed: 01/12/2023] Open
Abstract
Methylation patterns of circulating cell-free DNA (cfDNA) contain rich information about recent cell death events in the body. Here, we present an approach for unbiased determination of the tissue origins of cfDNA, using a reference methylation atlas of 25 human tissues and cell types. The method is validated using in silico simulations as well as in vitro mixes of DNA from different tissue sources at known proportions. We show that plasma cfDNA of healthy donors originates from white blood cells (55%), erythrocyte progenitors (30%), vascular endothelial cells (10%) and hepatocytes (1%). Deconvolution of cfDNA from patients reveals tissue contributions that agree with clinical findings in sepsis, islet transplantation, cancer of the colon, lung, breast and prostate, and cancer of unknown primary. We propose a procedure which can be easily adapted to study the cellular contributors to cfDNA in many settings, opening a broad window into healthy and pathologic human tissue dynamics. The methylation status of circulating cell-free DNA (cfDNA) can be informative about recent cell death events. Here the authors present an approach to determine the tissue origins of cfDNA, using a reference methylation atlas of 25 human tissues and cell types, and find that cfDNA from patients reveals tissue contributions that agree with clinical findings.
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Affiliation(s)
- Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Daniel Neiman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Hai Zemmour
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Amit Korach
- Department of Cardio-Thoracic Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Yaacov Samet
- Department of Vascular Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Myriam Maoz
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, SE17177, Stockholm, Sweden.,Dept of Forensic Medicine, The National Board of Forensic Medicine, SE11120, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE17176, Stockholm, Sweden
| | - Keng-Yeh Fu
- Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Endre Kiss
- Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Kirsty L Spalding
- Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE17176, Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Giora Landesberg
- Dept of Anesthesiology and Critical Care Medicine, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Aviad Zick
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Albert Grinshpun
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - A M James Shapiro
- Department of Surgery and the Clinical Islet Transplant Program, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Avigail Dreazan Wittenberg
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Benjamin Glaser
- Dept of Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
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49
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van Dongen J, Ehli EA, Jansen R, van Beijsterveldt CEM, Willemsen G, Hottenga JJ, Kallsen NA, Peyton SA, Breeze CE, Kluft C, Heijmans BT, Bartels M, Davies GE, Boomsma DI. Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs. Epigenetics Chromatin 2018; 11:54. [PMID: 30253792 PMCID: PMC6156977 DOI: 10.1186/s13072-018-0225-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND DNA methylation arrays are widely used in epigenome-wide association studies and methylation quantitative trait locus (mQTL) studies. Here, we performed the first genome-wide analysis of monozygotic (MZ) twin correlations and mQTLs on data obtained with the Illumina MethylationEPIC BeadChip (EPIC array) and compared the performance of the EPIC array to the Illumina HumanMethylation450 BeadChip (HM450 array) for buccal-derived DNA. RESULTS Good-quality EPIC data were obtained for 102 buccal-derived DNA samples from 49 MZ twin pairs (mean age = 7.5 years, range = 1-10). Differences between MZ twins in the cellular content of buccal swabs were a major driver for differences in their DNA methylation profiles, highlighting the importance to adjust for cellular composition in DNA methylation studies of buccal-derived DNA. After adjusting for cellular composition, the genome-wide mean correlation (r) between MZ twins was 0.21 for the EPIC array, and cis mQTL analysis in 84 twins identified 1,296,323 significant associations (FDR 5%), encompassing 33,749 methylation sites and 616,029 genetic variants. MZ twin correlations were slightly larger (p < 2.2 × 10-16) for novel EPIC probes (N = 383,066, mean r = 0.22) compared to probes that are also present on HM450 (N = 406,822, mean r = 0.20). In line with this observation, a larger percentage of novel EPIC probes was associated with genetic variants (novel EPIC probes with significant mQTL 4.7%, HM450 probes with mQTL 3.9%, p < 2.2 × 10-16). Methylation sites with a large MZ correlation and sites associated with mQTLs were most strongly enriched in epithelial cell DNase I hypersensitive sites (DHSs), enhancers, and histone mark H3K4me3. CONCLUSIONS We conclude that the contribution of familial factors to individual differences in DNA methylation and the effect of mQTLs are larger for novel EPIC probes, especially those within regulatory elements connected to active regions specific to the investigated tissue.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Erik A. Ehli
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Oldenaller 1, 1081 HJ Amsterdam, The Netherlands
| | - Catharina E. M. van Beijsterveldt
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Jouke J. Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Noah A. Kallsen
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Shanna A. Peyton
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Charles E. Breeze
- Altius Institute for Biomedical Sciences, 2211 Elliott Ave, Seattle, WA 98121 USA
| | - Cornelis Kluft
- Good Biomarker Sciences, Zernikedreef 8, 2333 CL Leiden, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology Section, Leiden University Medical Center, Postal Zone S-05-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gareth E. Davies
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
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50
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Ohara K, Arai E, Takahashi Y, Fukamachi Y, Ito N, Maeshima AM, Fujimoto H, Yoshida T, Kanai Y. Feasibility of methylome analysis using small amounts of genomic DNA from formalin-fixed paraffin-embedded tissue. Pathol Int 2018; 68:633-635. [PMID: 30239063 DOI: 10.1111/pin.12716] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/13/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Kentaro Ohara
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yoriko Takahashi
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo 105-6215, Japan
| | - Yukihiro Fukamachi
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo 105-6215, Japan
| | - Nanako Ito
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Akiko Miyagi Maeshima
- Department of Pathology and Clinical Laboratories, Pathology Division, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
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