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Nikolaienko O, Lønning PE, Knappskog S. ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions. Bioinformatics 2021; 38:133-140. [PMID: 34383893 PMCID: PMC8696093 DOI: 10.1093/bioinformatics/btab586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/26/2021] [Accepted: 08/11/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION With recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyze such events. RESULTS We have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs). ramr can be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics of ramr and confirmed its applicability for analysis of large public datasets. Using ramr we identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages. AVAILABILITY AND IMPLEMENTATION The R package is freely available at https://github.com/BBCG/ramr and https://bioconductor.org/packages/ramr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Per Eystein Lønning
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
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Degtyareva AO, Antontseva EV, Merkulova TI. Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. Int J Mol Sci 2021; 22:6454. [PMID: 34208629 PMCID: PMC8235176 DOI: 10.3390/ijms22126454] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
The vast majority of the genetic variants (mainly SNPs) associated with various human traits and diseases map to a noncoding part of the genome and are enriched in its regulatory compartment, suggesting that many causal variants may affect gene expression. The leading mechanism of action of these SNPs consists in the alterations in the transcription factor binding via creation or disruption of transcription factor binding sites (TFBSs) or some change in the affinity of these regulatory proteins to their cognate sites. In this review, we first focus on the history of the discovery of regulatory SNPs (rSNPs) and systematized description of the existing methodical approaches to their study. Then, we brief the recent comprehensive examples of rSNPs studied from the discovery of the changes in the TFBS sequence as a result of a nucleotide substitution to identification of its effect on the target gene expression and, eventually, to phenotype. We also describe state-of-the-art genome-wide approaches to identification of regulatory variants, including both making molecular sense of genome-wide association studies (GWAS) and the alternative approaches the primary goal of which is to determine the functionality of genetic variants. Among these approaches, special attention is paid to expression quantitative trait loci (eQTLs) analysis and the search for allele-specific events in RNA-seq (ASE events) as well as in ChIP-seq, DNase-seq, and ATAC-seq (ASB events) data.
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Affiliation(s)
- Arina O. Degtyareva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Elena V. Antontseva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Tatiana I. Merkulova
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Villicaña S, Bell JT. Genetic impacts on DNA methylation: research findings and future perspectives. Genome Biol 2021; 22:127. [PMID: 33931130 PMCID: PMC8086086 DOI: 10.1186/s13059-021-02347-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple recent studies highlight that genetic variants can have strong impacts on a significant proportion of the human DNA methylome. Methylation quantitative trait loci, or meQTLs, allow for the exploration of biological mechanisms that underlie complex human phenotypes, with potential insights for human disease onset and progression. In this review, we summarize recent milestones in characterizing the human genetic basis of DNA methylation variation over the last decade, including heritability findings and genome-wide identification of meQTLs. We also discuss challenges in this field and future areas of research geared to generate insights into molecular processes underlying human complex traits.
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Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
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Transcription Factor AP4 Mediates Cell Fate Decisions: To Divide, Age, or Die. Cancers (Basel) 2021; 13:cancers13040676. [PMID: 33567514 PMCID: PMC7914591 DOI: 10.3390/cancers13040676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Here, we review the literature on Activating Enhancer-Binding Protein 4 (AP4)/transcription factor AP4 (TFAP4) function and regulation and its role in cancer. Elevated expression of AP4 was detected in tumors of various organs and is associated with poor patient survival. AP4 is encoded by a Myc target gene and mediates cell fate decisions by regulating multiple processes, such as cell proliferation, epithelial-mesenchymal transition, stemness, apoptosis, and cellular senescence. Thereby, AP4 may be critical for tumor initiation and progression. In this review article, we summarize published evidence showing how AP4 functions as a transcriptional activator and repressor of a plethora of direct target genes in various physiological and pathological conditions. We also highlight the complex interactions of AP4 with c-Myc, N-Myc, p53, lncRNAs, and miRNAs in feed-back loops, which control AP4 levels and mediate AP4 functions. In the future, a better understanding of AP4 may contribute to improved prognosis and therapy of cancer. Abstract Activating Enhancer-Binding Protein 4 (AP4)/transcription factor AP4 (TFAP4) is a basic-helix-loop-helix-leucine-zipper transcription factor that was first identified as a protein bound to SV40 promoters more than 30 years ago. Almost 15 years later, AP4 was characterized as a target of the c-Myc transcription factor, which is the product of a prototypic oncogene that is activated in the majority of tumors. Interestingly, AP4 seems to represent a central hub downstream of c-Myc and N-Myc that mediates some of their functions, such as proliferation and epithelial-mesenchymal transition (EMT). Elevated AP4 expression is associated with progression of cancer and poor patient prognosis in multiple tumor types. Deletion of AP4 in mice points to roles of AP4 in the control of stemness, tumor initiation and adaptive immunity. Interestingly, ex vivo AP4 inactivation results in increased DNA damage, senescence, and apoptosis, which may be caused by defective cell cycle progression. Here, we will summarize the roles of AP4 as a transcriptional repressor and activator of target genes and the contribution of protein and non-coding RNAs encoded by these genes, in regulating the above mentioned processes. In addition, proteins interacting with or regulating AP4 and the cellular signaling pathways altered after AP4 dysregulation in tumor cells will be discussed.
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Russell H, Kedzierska K, Buchanan DD, Thomas R, Tham E, Mints M, Keränen A, Giles GG, Southey MC, Milne RL, Tomlinson I, Church D, Spurdle AB, O'Mara TA, Lewis A. The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability. Clin Epigenetics 2020; 12:102. [PMID: 32641106 PMCID: PMC7346630 DOI: 10.1186/s13148-020-00889-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Both colorectal (CRC, 15%) and endometrial cancers (EC, 30%) exhibit microsatellite instability (MSI) due to MLH1 hypermethylation and silencing. The MLH1 promoter polymorphism, rs1800734 is associated with MSI CRC risk, increased methylation and reduced MLH1 expression. In EC samples, we investigated rs1800734 risk using MSI and MSS cases and controls. We found no evidence that rs1800734 or other MLH1 SNPs were associated with the risk of MSI EC. We found the rs1800734 risk allele had no effect on MLH1 methylation or expression in ECs. We propose that MLH1 hypermethylation occurs by different mechanisms in CRC and EC.
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Affiliation(s)
- Holly Russell
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Katarzyna Kedzierska
- Cancer Genomics and Immunology Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, 3010, Australia
| | - Rachael Thomas
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Miriam Mints
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Anne Keränen
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
| | - Melissa C Southey
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
| | - Ian Tomlinson
- Cancer Genetics and Evolution Laboratory, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - David Church
- Cancer Genomics and Immunology Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, QLD, Brisbane, 4006, Australia
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, QLD, Brisbane, 4006, Australia
| | - Annabelle Lewis
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University, Kingston Lane, Uxbridge, UB8 3PH, UK.
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