1
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Zhang R, Liu H, Bai B, Wang H. Quantification of Epigenetic DNA and RNA Modifications by UHPLC-MS/MS Technologies: New Concepts and New Improvements for the Special Collections. J Sep Sci 2025; 48:e70159. [PMID: 40344478 DOI: 10.1002/jssc.70159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2025] [Revised: 03/21/2025] [Accepted: 04/17/2025] [Indexed: 05/11/2025]
Abstract
Dynamic and reversible DNA and RNA modifications are essential for cell differentiation and development. Aberrant epigenetic modifications are closely associated with the occurrence and progression of diseases, serving as potential markers for cancer diagnosis and prognosis. Ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) offers distinct advantages in the qualitative and quantitative analysis of various modifications due to its sensitivity, specificity, and accuracy. This review provides a comprehensive overview of the current knowledge regarding the liquid chromatography-mass spectrometry (LC-MS) analysis of DNA and RNA modifications, including analytical procedures, advancements, and biological applications, with a focus on tracing the source of (N6-2'-deoxy-adenosine) 6mdA in eukaryotes. Additionally, we examine the integration of UHPLC-MS/MS with other separation techniques to achieve accurate quantification of modifications in specific regions, certain fragments, and free nucleosides.
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Affiliation(s)
- Rui Zhang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hailong Liu
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Biao Bai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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2
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Haddadin L, Sun X. Stem Cells in Cancer: From Mechanisms to Therapeutic Strategies. Cells 2025; 14:538. [PMID: 40214491 PMCID: PMC11988674 DOI: 10.3390/cells14070538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Revised: 03/23/2025] [Accepted: 04/01/2025] [Indexed: 04/14/2025] Open
Abstract
Stem cells have emerged as a pivotal area of research in the field of oncology, offering new insights into the mechanisms of cancer initiation, progression, and resistance to therapy. This review provides a comprehensive overview of the role of stem cells in cancer, focusing on cancer stem cells (CSCs), their characteristics, and their implications for cancer therapy. We discuss the origin and identification of CSCs, their role in tumorigenesis, metastasis, and drug resistance, and the potential therapeutic strategies targeting CSCs. Additionally, we explore the use of normal stem cells in cancer therapy, focusing on their role in tissue regeneration and their use as delivery vehicles for anticancer agents. Finally, we highlight the challenges and future directions in stem cell research in cancer.
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Affiliation(s)
| | - Xueqin Sun
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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3
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Pinto R, Vedeld HM, Lind GE, Jeanmougin M. Unraveling epigenetic heterogeneity across gastrointestinal adenocarcinomas through a standardized analytical framework. Mol Oncol 2025; 19:1117-1131. [PMID: 39696831 PMCID: PMC11977639 DOI: 10.1002/1878-0261.13772] [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: 04/19/2024] [Revised: 09/30/2024] [Accepted: 10/31/2024] [Indexed: 12/20/2024] Open
Abstract
In this study, we propose an alternative approach for stratifying genome-scale DNA methylation profiles of gastrointestinal (GI) adenocarcinomas based on a robust analytical framework. A set of 978 GI adenocarcinomas and 120 adjacent normal tissues from public repositories was quality controlled and analyzed. Hierarchical consensus clustering of the tumors, based on differential epigenetic variability between malignant and normal samples, identified six distinct subtypes defined either by a pan-GI or a lower GI-specific phenotype. In addition to methylation levels, aberrant methylation frequencies and the degree of DNA methylation instability contributed to the characterization of each subtype. We found significant differences in the outcome of patients, with the poorest overall survival seen for those belonging to a pan-GI subtype with infrequent aberrant methylation. In conclusion, our standardized approach contributes to a refined characterization of the epigenetic heterogeneity in GI adenocarcinomas, offering insights into subtype-specific methylation with the potential to support prognostication.
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Affiliation(s)
- Rita Pinto
- Department of Molecular Oncology, Institute for Cancer ResearchOslo University Hospital – Norwegian Radium HospitalOsloNorway
| | - Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer ResearchOslo University Hospital – Norwegian Radium HospitalOsloNorway
| | - Guro Elisabeth Lind
- Department of Molecular Oncology, Institute for Cancer ResearchOslo University Hospital – Norwegian Radium HospitalOsloNorway
- Department of Biosciences, The Faculty of Mathematics and Natural SciencesUniversity of OsloNorway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer ResearchOslo University Hospital – Norwegian Radium HospitalOsloNorway
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4
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Fu Y, Timp W, Sedlazeck FJ. Computational analysis of DNA methylation from long-read sequencing. Nat Rev Genet 2025:10.1038/s41576-025-00822-5. [PMID: 40155770 DOI: 10.1038/s41576-025-00822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2025] [Indexed: 04/01/2025]
Abstract
DNA methylation is a critical epigenetic mechanism in numerous biological processes, including gene regulation, development, ageing and the onset of various diseases such as cancer. Studies of methylation are increasingly using single-molecule long-read sequencing technologies to simultaneously measure epigenetic states such as DNA methylation with genomic variation. These long-read data sets have spurred the continuous development of advanced computational methods to gain insights into the roles of methylation in regulating chromatin structure and gene regulation. In this Review, we discuss the computational methods for calling methylation signals, contrasting methylation between samples, analysing cell-type diversity and gaining additional genomic insights, and then further discuss the challenges and future perspectives of tool development for DNA methylation research.
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Affiliation(s)
- Yilei Fu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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5
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Zhou J, Wu Y, Liu H, Tian W, Castanon RG, Bartlett A, Zhang Z, Yao G, Shi D, Clock B, Marcotte S, Nery JR, Liem M, Claffey N, Boggeman L, Barragan C, Drigo RAE, Weimer AK, Shi M, Cooper-Knock J, Zhang S, Snyder MP, Preissl S, Ren B, O’Connor C, Chen S, Luo C, Dixon JR, Ecker JR. Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.23.644697. [PMID: 40196612 PMCID: PMC11974725 DOI: 10.1101/2025.03.23.644697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multi-omic profiling of 3D genome structure and DNA methylation for 86,689 single nuclei across 16 human tissues, identifying 35 major and 206 cell subtypes. We revealed extensive changes in CG and non-CG methylation across almost all cell types and characterized 3D chromatin structure at an unprecedented cellular resolution. Intriguingly, extensive discrepancies exist between cell types delineated by DNA methylation and genome structure, indicating that the role of distinct epigenomic features in maintaining cell identity may vary by lineage. This study expands our understanding of the diversity of DNA methylation and chromatin structure and offers an extensive reference for exploring gene regulation in human health and disease.
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Affiliation(s)
- Jingtian Zhou
- Arc Institute, Palo Alto, CA, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Yue Wu
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Zuolong Zhang
- School of Software, Henan University, Kaifeng, Henan, China
| | - Guocong Yao
- School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China
| | - Dengxiaoyu Shi
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ben Clock
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Samantha Marcotte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Michelle Liem
- Flow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Lara Boggeman
- Flow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cesar Barragan
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rafael Arrojo e Drigo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
- Center for Computational Systems Biology, Vanderbilt University, Nashville, TN
- Diabetes Research and Training Center (DRTC), Vanderbilt University Medical Center, Nashville, TN, 37235
| | - Annika K. Weimer
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Minyi Shi
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Sai Zhang
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Departments of Biostatistics & Biomedical Engineering, Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Pharmaceutical Sciences, Pharmacology & Toxicology, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Bing Ren
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Carolyn O’Connor
- Flow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Shengbo Chen
- School of Software, Nanchang University, Nanchang, Jiangxi, China
| | - Chongyuan Luo
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Jesse R. Dixon
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
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6
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Colemon A, Romney CV, Jones AD, Bagsby C, Jackson R, Ramanathan S. Interplay Between TGFβ1 Signaling and Cancer-Testis Antigen MAGEB2: A New Thorn in Cancer's Side? Int J Mol Sci 2025; 26:2448. [PMID: 40141091 PMCID: PMC11942090 DOI: 10.3390/ijms26062448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2025] [Revised: 03/03/2025] [Accepted: 03/07/2025] [Indexed: 03/28/2025] Open
Abstract
The Melanoma Antigen Gene (MAGE) family of proteins is the largest family of cancer-testis antigens (CTAs) and shares a MAGE homology domain (MHD). MAGE proteins are divided into Type I and Type II MAGEs depending on their chromosomal location and expression patterns. Type I MAGEs are true CTAs. MAGEB2 is a Type I MAGE, belonging to the MAGEB subfamily, and unlike some MAGE proteins, has not been found to bind to and enhance E3 ligase activity. MAGEB2 has been discovered to be an RNA-binding protein that serves to protect spermatogonial cells in the testis from extraneous stressors. We have discovered that MAGEB2 is necessary and sufficient for the proliferation of cells and is expressed by the differential DNA methylation of its gene promoter. Furthermore, we identified JunD as the transcription factor that regulates MAGEB2 expression. When expressed, MAGEB2 suppresses transforming grown factor-β1 (TGFβ1) signaling by decreasing mRNA levels of Thrombospondin-1 (TSP-1). TSP-1 is an anti-angiogenic protein that activates TGFβ1. Restoring levels of TSP-1 or TGFβ1 results in the inability of MAGEB2 to drive proliferation, suggesting that MAGEB2-expressing tumors might be more susceptible to therapies that induce or activate TSP-1 or TGFβ1 signaling.
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Affiliation(s)
- Ashley Colemon
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
- Fisk-Vanderbilt Master’s-to-Ph.D. Bridge Program, Nashville, TN 37208, USA
| | - Carlan V. Romney
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
- Fisk-Vanderbilt Master’s-to-Ph.D. Bridge Program, Nashville, TN 37208, USA
| | - Angelle D. Jones
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
| | - Clarke Bagsby
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
| | - Richala Jackson
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
| | - Saumya Ramanathan
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
- Fisk-Vanderbilt Master’s-to-Ph.D. Bridge Program, Nashville, TN 37208, USA
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7
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Margalit S, Tulpová Z, Michaeli Y, Zur T, Deek J, Louzoun-Zada S, Nifker G, Grunwald A, Scher Y, Schütz L, Weinhold E, Gnatek Y, Omer D, Dekel B, Friedman E, Ebenstein Y. Optical genome and epigenome mapping of clear cell renal cell carcinoma. NAR Cancer 2025; 7:zcaf008. [PMID: 40061565 PMCID: PMC11886815 DOI: 10.1093/narcan/zcaf008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 02/18/2025] [Accepted: 03/05/2025] [Indexed: 04/02/2025] Open
Abstract
Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily captured by short-read sequencing. This study presents a novel approach for simultaneous profiling of long-range genetic and epigenetic changes in matched cancer samples, focusing on clear cell renal cell carcinoma (ccRCC). ccRCC is a common kidney cancer subtype frequently characterized by a 3p deletion and the inactivation of the von Hippel-Lindau (VHL) gene. We performed integrated genetic, cytogenetic, and epigenetic analyses on paired tumor and adjacent nontumorous tissue samples. Optical genome mapping identified genomic aberrations as structural and copy number variations, complementing exome-sequencing findings. Single-molecule methylome and hydroxymethylome mapping revealed a significant global reduction in 5hmC level in both sample pairs, and a correlation between both epigenetic signals and gene expression was observed. The single-molecule epigenetic analysis identified numerous differentially modified regions, some implicated in ccRCC pathogenesis, including the genes VHL, PRCC, and PBRM1. Notably, pathways related to metabolism and cancer development were significantly enriched among these differential regions. This study demonstrates the feasibility of integrating optical genome and epigenome mapping for comprehensive characterization of matched tumor and adjacent tissue, uncovering both established and novel somatic aberrations.
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Affiliation(s)
- Sapir Margalit
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpová
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Institute of Experimental Botany of the Czech Academy of Sciences, 77900, Olomouc, Czech Republic
| | - Yael Michaeli
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Tahir Detinis Zur
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Jasline Deek
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Sivan Louzoun-Zada
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Gil Nifker
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Assaf Grunwald
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yuval Scher
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Yehudit Gnatek
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Dorit Omer
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- Pediatric Nephrology Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- School of Medicine, Faculty of Medical and Health Sciences, Tel-Aviv University, 6997801 Tel Aviv, Israel
| | - Eitan Friedman
- School of Medicine, Faculty of Medical and Health Sciences, Tel-Aviv University, 6997801 Tel Aviv, Israel
- The Susanne Levy Gertner Oncogenetics Unit, The Danek Gertner Institute of Human Genetics, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Yuval Ebenstein
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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8
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Li W, Luo P, Chen Q, Cheng L, Gan L, Zhang F, Zhong H, Zheng L, Qian B. Epigenetic modifications in bladder cancer: crosstalk between DNA methylation and miRNAs. Front Immunol 2025; 16:1518144. [PMID: 39981244 PMCID: PMC11841399 DOI: 10.3389/fimmu.2025.1518144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 01/22/2025] [Indexed: 02/22/2025] Open
Abstract
Bladder cancer (BC) is a malignant tumor characterized by a high incidence of urinary system diseases. The complex pathogenesis of BC has long been a focal point in medical research. With the robust development of epigenetics, the crucial role of epigenetic modifications in the occurrence and progression of BC has been elucidated. These modifications not only affect gene expression but also impact critical biological behaviors of tumor cells, including proliferation, differentiation, apoptosis, invasion, and metastasis. Notably, DNA methylation, an important epigenetic regulatory mechanism, often manifests as global hypomethylation or hypermethylation of specific gene promoter regions in BC. Alterations in this methylation pattern can lead to increased genomic instability, which profoundly influences the expression of proto-oncogenes and tumor suppressor genes. MiRNAs, as noncoding small RNAs, participate in various biological processes of BC by regulating target genes. Consequently, this work aims to explore the interaction mechanisms between DNA methylation and miRNAs in the occurrence and development of BC. Research has demonstrated that DNA methylation not only directly influences the expression of miRNA genes but also indirectly affects the maturation and functionality of miRNAs by modulating the methylation status of miRNA promoter regions. Simultaneously, miRNAs can regulate DNA methylation levels by targeting key enzymes such as DNA methyltransferases (DNMTs), thereby establishing a complex feedback regulatory network. A deeper understanding of the crosstalk mechanisms between DNA methylation and miRNAs in BC will contribute to elucidating the complexity and dynamics of epigenetic modifications in this disease, and may provide new molecular targets and strategies for the early diagnosis, treatment, and prognostic evaluation of BC.
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Affiliation(s)
- Wei Li
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Peiyue Luo
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Qi Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Le Cheng
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Lifeng Gan
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Fangtao Zhang
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Haidong Zhong
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Liying Zheng
- Department of Graduate, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Biao Qian
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
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9
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Furlano K, Keshavarzian T, Biernath N, Fendler A, de Santis M, Weischenfeldt J, Lupien M. Epigenomics-guided precision oncology: Chromatin variants in prostate tumor evolution. Int J Cancer 2025. [PMID: 39853587 DOI: 10.1002/ijc.35327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 12/17/2024] [Accepted: 01/02/2025] [Indexed: 01/26/2025]
Abstract
Prostate cancer is a common malignancy that in 5%-30% leads to treatment-resistant and highly aggressive disease. Metastasis-potential and treatment-resistance is thought to rely on increased plasticity of the cancer cells-a mechanism whereby cancer cells alter their identity to adapt to changing environments or therapeutic pressures to create cellular heterogeneity. To understand the molecular basis of this plasticity, genomic studies have uncovered genetic variants to capture clonal heterogeneity of primary tumors and metastases. As cellular plasticity is largely driven by non-genetic events, complementary studies in cancer epigenomics are now being conducted to identify chromatin variants. These variants, defined as genomic loci in cancer cells that show changes in chromatin state due to the loss or gain of epigenomic marks, inclusive of histone post-translational modifications, DNA methylation and histone variants, are considered the fundamental units of epigenomic heterogeneity. In prostate cancer chromatin variants hold the promise of guiding the new era of precision oncology. In this review, we explore the role of epigenomic heterogeneity in prostate cancer, focusing on how chromatin variants contribute to tumor evolution and therapy resistance. We therefore discuss their impact on cellular plasticity and stochastic events, highlighting the value of single-cell sequencing and liquid biopsy epigenomic assays to uncover new therapeutic targets and biomarkers. Ultimately, this review aims to support a new era of precision oncology, utilizing insights from epigenomics to improve prostate cancer patient outcomes.
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Affiliation(s)
- Kira Furlano
- Department of Urology, Charité- Universitätsmedizin Berlin, Berlin, Germany
| | - Tina Keshavarzian
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Nadine Biernath
- Department of Urology, Charité- Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Fendler
- Department of Urology, Charité- Universitätsmedizin Berlin, Berlin, Germany
| | - Maria de Santis
- Department of Urology, Charité- Universitätsmedizin Berlin, Berlin, Germany
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Joachim Weischenfeldt
- Department of Urology, Charité- Universitätsmedizin Berlin, Berlin, Germany
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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10
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Li JS, Riggins K, Yang L, Chen C, Castro P, Alfarkh W, Zarrin-Khameh N, Scheurer ME, Creighton CJ, Musher B, Li W, Shen L. DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations. Clin Epigenetics 2025; 17:11. [PMID: 39844333 PMCID: PMC11753045 DOI: 10.1186/s13148-025-01817-z] [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: 07/13/2024] [Accepted: 01/10/2025] [Indexed: 01/24/2025] Open
Abstract
BACKGROUND The incidence of early-onset colorectal cancer (EOCRC) has been rising at an alarming rate in the USA, and EOCRC disproportionately affects racial/ethnic minorities. Here, we construct comprehensive profiles of EOCRC DNA methylomes at base-pair resolution for a cohort of Hispanic and African American patients. RESULTS We show the epigenetic landscape of these EOCRC patients differs from that of late-onset colorectal cancer patients, and methylation canyons in EOCRC tumor tissue preferentially overlapped genes in cancer-related pathways. Furthermore, we identify epigenetic alterations in metabolic genes that are specific to our racial/ethnic minority EOCRC cohort but not Caucasian patients from TCGA. Top genes differentially methylated between these cohorts included the obesity-protective MFAP2 gene as well as cancer risk susceptibility genes APOL3 and RNASEL. CONCLUSIONS In this study, we provide to the scientific community high-resolution DNA methylomes for a cohort of EOCRC patients from underrepresented populations. Our exploratory findings in this cohort highlight epigenetic mechanisms underlying the pathogenesis of EOCRC and nominate novel biomarkers for EOCRC in underrepresented populations.
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Affiliation(s)
- Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Karen Riggins
- Department of Medicine, Hematology and Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Li Yang
- Department of Pediatrics, USDA Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chaorong Chen
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Patricia Castro
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wedad Alfarkh
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Neda Zarrin-Khameh
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology, Ben Taub Hospital, 1504 Taub Loop, Houston, TX, 77030, USA
| | - Michael E Scheurer
- Department of Pediatrics, Center for Epidemiology and Population Health, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J Creighton
- Department of Medicine and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benjamin Musher
- Department of Medicine, Gastrointestinal Medical Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA.
| | - Lanlan Shen
- Department of Pediatrics, USDA Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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11
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Liu Y, Hrit JA, Chomiak AA, Stransky S, Hoffman JR, Tiedemann RL, Wiseman AK, Kariapper LS, Dickson BM, Worden EJ, Fry CJ, Sidoli S, Rothbart SB. DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states. Mol Cell 2025; 85:394-412.e12. [PMID: 39631394 PMCID: PMC11741932 DOI: 10.1016/j.molcel.2024.11.009] [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: 03/20/2024] [Revised: 09/17/2024] [Accepted: 11/07/2024] [Indexed: 12/07/2024]
Abstract
Mono-ubiquitination of lysine 18 on histone H3 (H3K18ub), catalyzed by UHRF1, is a DNMT1 docking site that facilitates replication-coupled DNA methylation maintenance. Its functions beyond this are unknown. Here, we genomically map simultaneous increases in UHRF1-dependent H3K18ub and SUV39H1/H2-dependent H3K9me3 following DNMT1 inhibition. Mechanistically, transient accumulation of hemi-methylated DNA at CpG islands facilitates UHRF1 recruitment and E3 ligase activity toward H3K18. Notably, H3K18ub enhances SUV39H1/H2 methyltransferase activity and, in colon cancer cells, nucleates new H3K9me3 domains at CpG island promoters of DNA methylation-silenced tumor suppressor genes (TSGs). Disrupting UHRF1 enzyme activity prevents H3K9me3 accumulation while promoting PRC2-dependent H3K27me3 as a tertiary layer of gene repression in these regions. By contrast, disrupting H3K18ub-dependent SUV39H1/H2 activity enhances the transcriptional activating and antiproliferative effects of DNMT1 inhibition. Collectively, these findings reveal roles for UHRF1 and H3K18ub in regulating a hierarchy of repressive histone methylation signaling and rationalize a combination strategy for epigenetic cancer therapy.
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Affiliation(s)
- Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Joel A Hrit
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Alison A Chomiak
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | - Ashley K Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Leena S Kariapper
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bradley M Dickson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Evan J Worden
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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12
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Laisné M, Lupien M, Vallot C. Epigenomic heterogeneity as a source of tumour evolution. Nat Rev Cancer 2025; 25:7-26. [PMID: 39414948 DOI: 10.1038/s41568-024-00757-9] [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] [Accepted: 09/16/2024] [Indexed: 10/18/2024]
Abstract
In the past decade, remarkable progress in cancer medicine has been achieved by the development of treatments that target DNA sequence variants. However, a purely genetic approach to treatment selection is hampered by the fact that diverse cell states can emerge from the same genotype. In multicellular organisms, cell-state heterogeneity is driven by epigenetic processes that regulate DNA-based functions such as transcription; disruption of these processes is a hallmark of cancer that enables the emergence of defective cell states. Advances in single-cell technologies have unlocked our ability to quantify the epigenomic heterogeneity of tumours and understand its mechanisms, thereby transforming our appreciation of how epigenomic changes drive cancer evolution. This Review explores the idea that epigenomic heterogeneity and plasticity act as a reservoir of cell states and therefore as a source of tumour evolution. Best practices to quantify epigenomic heterogeneity and explore its various causes and consequences are discussed, including epigenomic reprogramming, stochastic changes and lasting memory. The design of new therapeutic approaches to restrict epigenomic heterogeneity, with the long-term objective of limiting cancer development and progression, is also addressed.
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Affiliation(s)
- Marthe Laisné
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontorio, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontorio, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontorio, Canada.
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France.
- Translational Research Department, Institut Curie, PSL University, Paris, France.
- Single Cell Initiative, Institut Curie, PSL University, Paris, France.
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13
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Smith ZD, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nat Rev Genet 2025; 26:7-30. [PMID: 39134824 DOI: 10.1038/s41576-024-00760-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2024] [Indexed: 12/15/2024]
Abstract
The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan and discuss how they interact with other regulatory layers to support diverse genomic functions. We then review the rising interest in alternative patterns found during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype.
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Affiliation(s)
- Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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14
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Magnani E, Macchi F, Randic T, Chen C, Madakashira B, Ranjan S, Eski SE, Singh SP, Sadler KC. Epigenetic Disordering Drives Stemness, Senescence Escape and Tumor Heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.29.629346. [PMID: 39763773 PMCID: PMC11703240 DOI: 10.1101/2024.12.29.629346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
Abstract
Tumor heterogeneity is the substrate for tumor evolution and the linchpin of treatment resistance. Cancer cell heterogeneity is largely attributed to distinct genetic changes within each cell population. However, the widespread epigenome repatterning that characterizes most cancers is also highly heterogenous within tumors and could generate cells with diverse identities and malignant features. We show that high levels of the epigenetic regulator and oncogene, UHRF1, in zebrafish hepatocytes rapidly induced methylome disordering, loss of heterochromatin, and DNA damage, resulting in cell cycle arrest, senescence, and acquisition of stemness. Reducing UHRF1 expression transitions these cells from senescent to proliferation-competent. The expansion of these damaged cells results in hepatocellular carcinomas (HCC) that have immature cancer cells intermingled with fibroblasts, immune and senescent cells expressing high UHRF1 levels, which serve as reservoirs for new cancer cells. This defines a distinct and heterogenous HCC subtype resulting from epigenetic changes, stemness and senescence escape.
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Affiliation(s)
- Elena Magnani
- Program in Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Tijana Randic
- Program in Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Charlene Chen
- Program in Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Bhavani Madakashira
- Program in Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Shashi Ranjan
- Program in Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Sema Elif Eski
- Laboratory of Regeneration and Stress Biology, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM-Jacques E. Dumont), Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Sumeet P. Singh
- Laboratory of Regeneration and Stress Biology, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM-Jacques E. Dumont), Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Kirsten C. Sadler
- Program in Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, NYU Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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15
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Chu WT, Wang J. Uncovering the lung cancer mechanisms through the chromosome structural ensemble characteristics and nucleation seeds. J Chem Phys 2024; 161:225101. [PMID: 39660659 DOI: 10.1063/5.0238929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 11/25/2024] [Indexed: 12/12/2024] Open
Abstract
Lung cancer is one of the most common cancers in humans. However, there is still a need to understand the underlying mechanisms of a normal cell developing into a cancer cell. Here, we develop the chromosome dynamic structural model and quantify the important characteristics of the chromosome structural ensemble of the normal lung cell and the lung cancer A549 cell. Our results demonstrate the essential relationship among the chromosome ensemble, the epigenetic marks, and the gene expressions, which suggests the linkage between chromosome structure and function. The analysis reveals that the lung cancer cell may have a higher level of relative ensemble fluctuation (micro CFI) and a higher degree of phase separation between the two compartments than the normal lung cell. In addition, the significant conformational "switching off" events (from compartment A to B) are more than the significant conformational "switching on" events during the lung cancerization. We identify "nucleation seeds" or hot spots in chromosomes, which initiate the transitions and determine the mechanisms. The hot spots and interaction network results reveal that the lung cancerization process (from normal lung to A549) and the reversion process have different mechanisms. These investigations have revealed the cell fate determination mechanism of the lung cancer process, which will be helpful for the further prevention and control of cancers.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jin Wang
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
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16
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Liapodimitri A, Tetens AR, Craig-Schwartz J, Lunsford K, Skalitzky KO, Koldobskiy MA. Progress Toward Epigenetic Targeted Therapies for Childhood Cancer. Cancers (Basel) 2024; 16:4149. [PMID: 39766049 PMCID: PMC11674401 DOI: 10.3390/cancers16244149] [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: 11/08/2024] [Revised: 12/09/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025] Open
Abstract
Among the most significant discoveries from cancer genomics efforts has been the critical role of epigenetic dysregulation in cancer development and progression. Studies across diverse cancer types have revealed frequent mutations in genes encoding epigenetic regulators, alterations in DNA methylation and histone modifications, and a dramatic reorganization of chromatin structure. Epigenetic changes are especially relevant to pediatric cancers, which are often characterized by a low rate of genetic mutations. The inherent reversibility of epigenetic lesions has led to an intense interest in the development of epigenetic targeted therapies. Additionally, the recent appreciation of the interplay between the epigenome and immune regulation has sparked interest in combination therapies and synergistic immunotherapy approaches. Further, the recent appreciation of epigenetic variability as a driving force in cancer evolution has suggested new roles for epigenetic therapies in limiting plasticity and resistance. Here, we review recent progress and emerging directions in the development of epigenetic targeted therapeutics and their promise across the landscape of childhood cancers.
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Affiliation(s)
- Athanasia Liapodimitri
- Division of Pediatric Oncology, Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (A.L.); (A.R.T.); (J.C.-S.); (K.L.); (K.O.S.)
| | - Ashley R. Tetens
- Division of Pediatric Oncology, Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (A.L.); (A.R.T.); (J.C.-S.); (K.L.); (K.O.S.)
| | - Jordyn Craig-Schwartz
- Division of Pediatric Oncology, Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (A.L.); (A.R.T.); (J.C.-S.); (K.L.); (K.O.S.)
| | - Kayleigh Lunsford
- Division of Pediatric Oncology, Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (A.L.); (A.R.T.); (J.C.-S.); (K.L.); (K.O.S.)
| | - Kegan O. Skalitzky
- Division of Pediatric Oncology, Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (A.L.); (A.R.T.); (J.C.-S.); (K.L.); (K.O.S.)
| | - Michael A. Koldobskiy
- Division of Pediatric Oncology, Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (A.L.); (A.R.T.); (J.C.-S.); (K.L.); (K.O.S.)
- Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
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17
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Tiedemann R, Hrit J, Du Q, Wiseman A, Eden H, Dickson B, Kong X, Chomiak A, Vaughan R, Tibben B, Hebert J, David Y, Zhou W, Baylin S, Jones P, Clark S, Rothbart S. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. Nucleic Acids Res 2024; 52:13733-13756. [PMID: 39607687 PMCID: PMC11662662 DOI: 10.1093/nar/gkae1105] [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: 03/07/2024] [Revised: 10/04/2024] [Accepted: 10/25/2024] [Indexed: 11/29/2024] Open
Abstract
The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. The model posits that nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites for DNMT1 through ubiquitin interacting motifs (UIM1 and UIM2). However, the extent to which DNMT1 relies on ubiquitin signaling through UHRF1 in support of DNA methylation maintenance remains unclear. Here, with integrative epigenomic and biochemical analyses, we reveal that DNA methylation maintenance at low-density cytosine-guanine dinucleotides (CpGs) is particularly vulnerable to disruption of UHRF1 ubiquitin ligase activity and DNMT1 ubiquitin reading activity through UIM1. Hypomethylation of low-density CpGs in this manner induces formation of partially methylated domains (PMDs), a methylation signature observed across human cancers. In contrast, UIM2 disruption completely abolishes the DNA methylation maintenance function of DNMT1 in a CpG density-independent manner. In the context of DNA methylation recovery following acute DNMT1 depletion, we further reveal a 'bookmarking' function for UHRF1 ubiquitin ligase activity in support of DNA re-methylation. Collectively, these studies show that DNMT1-dependent DNA methylation inheritance is a ubiquitin-regulated process that is partially reliant on UHRF1 and suggest a disrupted UHRF1-DNMT1 ubiquitin signaling axis contributes to PMD formation in cancers.
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Affiliation(s)
- Rochelle L Tiedemann
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Joel Hrit
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Qian Du
- Epigenetics Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Ashley K Wiseman
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Hope E Eden
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Bradley M Dickson
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Xiangqian Kong
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 401 N Broadway, Baltimore, MD, USA
| | - Alison A Chomiak
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Robert M Vaughan
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Jakob M Hebert
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, NY, NY 10065, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, NY, NY 10065, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA19104, USA
| | - Stephen B Baylin
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 401 N Broadway, Baltimore, MD, USA
| | - Peter A Jones
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Susan J Clark
- Epigenetics Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
- St. Vincent's Clinical School, University of New South Wales, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
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18
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Kelly K, Scherer M, Braun MM, Lutsik P, Plass C. EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data. Genome Biol 2024; 25:305. [PMID: 39623476 PMCID: PMC11613708 DOI: 10.1186/s13059-024-03446-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 11/26/2024] [Indexed: 12/06/2024] Open
Abstract
Epigenetic heterogeneity is a fundamental property of biological systems and is recognized as a potential driver of tumor plasticity and therapy resistance. Single-cell epigenomics technologies have been widely employed to study epigenetic variation between-but not within-cellular clusters. We introduce epiCHAOS: a quantitative metric of cell-to-cell heterogeneity, applicable to any single-cell epigenomics data type. After validation in synthetic datasets, we apply epiCHAOS to investigate global and region-specific patterns of epigenetic heterogeneity across diverse biological systems. EpiCHAOS provides an excellent approximation of stemness and plasticity in development and malignancy, making it a valuable addition to single-cell cancer epigenomics analyses.
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Affiliation(s)
- Katherine Kelly
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Michael Scherer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Martina Maria Braun
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona, Institute of Science and Technology (BIST), Barcelona, 08003, Spain
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Department of Oncology, KU Leuven, Leuven, Belgium.
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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19
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Zhou J, Li D, Xu M, Zhu T, Li Z, Fu Z, Wang M, Li S, Gu D. Interactions between polycyclic aromatic hydrocarbons and genetic variants in the cGAS-STING pathway affect the risk of colorectal cancer. Arch Toxicol 2024; 98:4117-4129. [PMID: 39287666 DOI: 10.1007/s00204-024-03862-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024]
Abstract
The cGAS-STING pathway plays an essential role in the activation of tumor immune cells. Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants with potential carcinogenicity, and their exposure is associated with the development of colorectal cancer. However, the impacts of genetic factors in the cGAS‒STING pathway and gene‒environment interactions on colorectal cancer remain understudied. We used logistic regression models and interaction analysis to evaluate the impact of genetic variants on colorectal cancer risk and gene‒environment interactions. We analysed the expression patterns of candidate genes based on the RNA-seq data. Molecular biology experiments were performed to investigate the impact of PAHs exposure on candidate gene expression and the progression of colorectal cancer. We identified the susceptibility locus rs3750511 in the cGAS‒STING pathway, which is associated with colorectal cancer risk. A negative interaction between TRAF2 rs3750511 and PAHs exposure was also identified. Single-cell RNA-seq analysis revealed significantly elevated expression of TRAF2 in colorectal cancer tissues compared with normal tissues, especially in T cells. BPDE exposure increased TRAF2 expression and the malignant phenotype of colorectal cancer cells. The treatment also further increased the expression of the TRAF2 downstream gene NF-κB and decreased the expression of Caspase8. Our results suggest that the genetic variant of rs3750511 affects the expression of TRAF2, thereby increasing the risk of colorectal cancer through interaction with PAHs. Our study provides new insights into the influence of gene‒environment interactions on the risk of developing colorectal cancer.
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Affiliation(s)
- Jieyu Zhou
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Dongzheng Li
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Menghuan Xu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tianru Zhu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zhengyi Li
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China.
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Shuwei Li
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China.
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20
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Lu S, Zheng Z, Zhu C. Histone methyltransferase WHSC1 cooperate with YBX1 promote glioblastoma progression via regulating PLK1 expression. Cell Signal 2024; 124:111471. [PMID: 39406278 DOI: 10.1016/j.cellsig.2024.111471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 10/03/2024] [Accepted: 10/12/2024] [Indexed: 10/22/2024]
Abstract
Wolf-Hirschhorn syndrome candidate gene 1 (WHSC1), a histone methyltransferase, has been implicated in various tumor development processes by regulating target gene expression. However, the role of WHSC1 in glioblastoma remains unexplored. This study investigates the impact of WHSC1 in glioblastoma and its association with prognosis. Our findings reveal that WHSC1 is overexpressed in glioblastoma and correlates with poor patient outcomes. Functional assays demonstrate that the reduction of WHSC1 significantly impairs cell proliferation and tumorigenicity. Mechanistically, WHSC1 modulates PLK1 expression by binding to its promoter region, leading to the activation of the PLK1-AKT pathway, and regulating H3K36 dimethylation levels. Furthermore, YBX1 can cooperate with WHSC1 to activate PLK1 transcription. These results shed light on the potential significance of WHSC1 in glioblastoma and offer a promising avenue for future therapeutic approaches targeting this molecule in glioblastoma treatment.
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Affiliation(s)
- Shuaijun Lu
- The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Zhibo Zheng
- The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Changling Zhu
- The First Affiliated Hospital of Ningbo University, Ningbo 315020, China.
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21
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Balaramane D, Spill Y, Weber M, Bardet A. MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets. Nucleic Acids Res 2024; 52:e98. [PMID: 39420630 PMCID: PMC11602171 DOI: 10.1093/nar/gkae880] [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: 07/21/2023] [Revised: 09/13/2024] [Accepted: 09/30/2024] [Indexed: 10/19/2024] Open
Abstract
DNA methylation is an epigenetic mark involved in the regulation of gene expression, and patterns of DNA methylation anticorrelate with chromatin accessibility and transcription factor binding. DNA methylation can be profiled at the single cytosine resolution in the whole genome and has been performed in many cell types and conditions. Computational approaches are then essential to study DNA methylation patterns in a single condition or capture dynamic changes of DNA methylation levels across conditions. Toward this goal, we developed MethyLasso, a new approach to segment DNA methylation data. We use it as an all-in-one tool to perform the identification of low-methylated regions, unmethylated regions, DNA methylation valleys and partially methylated domains in a single condition as well as differentially methylated regions between two conditions. We performed a rigorous benchmarking comparing existing approaches by evaluating the agreement of the regions across tools, their number, size, level of DNA methylation, boundaries, cytosine-guanine content and coverage using several real datasets as well as the sensitivity and precision of the approaches using simulated data and show that MethyLasso performs best overall. MethyLasso is freely available at https://github.com/bardetlab/methylasso.
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Affiliation(s)
- Delphine Balaramane
- CNRS UMR7242 Biotechnologie et signalisation cellulaire, Université de Strasbourg, 300 Bd Sébastien Brant, 67412 Illkirch Cedex, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Cedex, France
- Centre National de Recherche scientifique (CNRS) UMR7104, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
- Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
- Institut National de santé et de Recherche Médicale (INSERM) U1258, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Yannick G Spill
- CNRS UMR7242 Biotechnologie et signalisation cellulaire, Université de Strasbourg, 300 Bd Sébastien Brant, 67412 Illkirch Cedex, France
| | - Michaël Weber
- CNRS UMR7242 Biotechnologie et signalisation cellulaire, Université de Strasbourg, 300 Bd Sébastien Brant, 67412 Illkirch Cedex, France
| | - Anaïs Flore Bardet
- CNRS UMR7242 Biotechnologie et signalisation cellulaire, Université de Strasbourg, 300 Bd Sébastien Brant, 67412 Illkirch Cedex, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Cedex, France
- Centre National de Recherche scientifique (CNRS) UMR7104, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
- Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
- Institut National de santé et de Recherche Médicale (INSERM) U1258, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
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22
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Köhnke T, Karigane D, Hilgart E, Fan AC, Kayamori K, Miyauchi M, Collins CT, Suchy FP, Rangavajhula A, Feng Y, Nakauchi Y, Martinez-Montes E, Fowler JL, Loh KM, Nakauchi H, Koldobskiy MA, Feinberg AP, Majeti R. DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.26.620318. [PMID: 39553934 PMCID: PMC11565803 DOI: 10.1101/2024.10.26.620318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3A R882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3A R882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3A R882 mutations were largely dispensable for disease maintenance. Replacing DNMT3A R882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3A R882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy.
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Affiliation(s)
- Thomas Köhnke
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Daiki Karigane
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Eleanor Hilgart
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Amy C. Fan
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Kensuke Kayamori
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Masashi Miyauchi
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Cailin T. Collins
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Fabian P. Suchy
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Athreya Rangavajhula
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Yang Feng
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Yusuke Nakauchi
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Eduardo Martinez-Montes
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Jonas L. Fowler
- Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Kyle M. Loh
- Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Hiromitsu Nakauchi
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
| | - Michael A. Koldobskiy
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Andrew P. Feinberg
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University; Stanford, CA, 94305, USA
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23
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Grisolia P, Tufano R, Iannarone C, De Falco A, Carlino F, Graziano C, Addeo R, Scrima M, Caraglia F, Ceccarelli A, Nuzzo PV, Cossu AM, Forte S, Giuffrida R, Orditura M, Caraglia M, Ceccarelli M. Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation. J Transl Med 2024; 22:938. [PMID: 39407254 PMCID: PMC11476115 DOI: 10.1186/s12967-024-05734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 10/05/2024] [Indexed: 10/20/2024] Open
Abstract
BACKGROUND Recent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Sequencing (cfMeDIP-seq), may be informative in characterizing breast cancer in patients with BRCA1/2 germline mutations for early cancer detection and response to therapy. METHODS We enrolled 23 BC patients with germline mutation of BRCA1 and BRCA2 genes, 19 healthy controls without BRCA1/2 mutation, and two healthy individuals who carried BRCA1/2 mutations. Blood samples were collected for all study subjects at the diagnosis, and plasma was isolated by centrifugation. Cell-free DNA was extracted from 1 mL of plasma, and cfMeDIP-seq was performed for each sample. Shallow whole genome sequencing was performed on the immuno-precipitated samples. Then, the differentially methylated 300-bp regions (DMRs) between 25 BRCA germline mutation carriers and 19 non-carriers were identified. DMRs were compared with tumor-specific regions from public datasets to perform an unbiased analysis. Finally, two statistical classifiers were trained based on the GLMnet and random forest model to evaluate if the identified DMRs could discriminate BRCA-positive from healthy samples. RESULTS We identified 7,095 hypermethylated and 212 hypomethylated regions in 25 BRCA germline mutation carriers compared to 19 controls. These regions discriminate tumors from healthy samples with high accuracy and sensitivity. We show that the circulating tumor DNA of BRCA1/2 mutant breast cancers is characterized by the hypomethylation of genes involved in DNA repair and cell cycle. We uncovered the TFs associated with these DRMs and identified that proteins of the Erythroblast Transformation Specific (ETS) family are particularly active in the hypermethylated regions. Finally, we assessed that these regions could discriminate between BRCA positives from healthy samples with an AUC of 0.95, a sensitivity of 88%, and a specificity of 94.74%. CONCLUSIONS Our study emphasizes the importance of tumor cell-derived DNA methylation in BC, reporting a different methylation profile between patients carrying mutations in BRCA1, BRCA2, and wild-type controls. Our minimally invasive approach could allow early cancer diagnosis, assessment of minimal residual disease, and monitoring of response to therapy.
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Affiliation(s)
- Piera Grisolia
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
- Laboratory of Molecular and Precision Oncology, Biogem, IRGS, Ariano Irpino, Italy
| | - Rossella Tufano
- Laboratory of Computational Biology, IRGS, Ariano Irpino, Italy
| | - Clara Iannarone
- Laboratory of Molecular and Precision Oncology, Biogem, IRGS, Ariano Irpino, Italy
| | | | - Francesca Carlino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138, Naples, Italy
- Oncology Unit, San Felice a Cancello Hospital, ASL Caserta, Sanfelice a Cancello, Italy
| | - Cinzia Graziano
- Laboratory of Molecular and Precision Oncology, Biogem, IRGS, Ariano Irpino, Italy
| | - Raffaele Addeo
- Oncology Unit, S. Giovanni di Dio Hospital, ASL Napoli2 Nord, Frattamaggiore, Italy
| | - Marianna Scrima
- Laboratory of Molecular and Precision Oncology, Biogem, IRGS, Ariano Irpino, Italy
| | - Francesco Caraglia
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138, Naples, Italy
| | - Anna Ceccarelli
- Medical Oncology, Catholic University of the Sacred Heart, 00168, Rome, RM, Italy
| | - Pier Vitale Nuzzo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Alessia Maria Cossu
- Laboratory of Molecular and Precision Oncology, Biogem, IRGS, Ariano Irpino, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138, Naples, Italy
| | | | | | - Michele Orditura
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138, Naples, Italy
| | - Michele Caraglia
- Laboratory of Molecular and Precision Oncology, Biogem, IRGS, Ariano Irpino, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138, Naples, Italy
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA.
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24
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Li Y, Li W, Deng J, Yin M. PER3 promoter hypermethylation correlates to the progression of pan-cancer. Clin Epigenetics 2024; 16:140. [PMID: 39402618 PMCID: PMC11476066 DOI: 10.1186/s13148-024-01760-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 10/07/2024] [Indexed: 10/19/2024] Open
Abstract
BACKGROUND Malignant cells exhibit reduced period circadian regulator 3 (PER3) expression. However, the underlying mechanisms of variations in PER3 expression in cancers and the specific function of PER3 in tumor progression remain poorly understood. RESULTS We explored multiple public databases, conducted bioinformatics analyses, and performed in vitro and in vivo experiments for validation. We found PER3 expression was decreased in most types of cancers, and PER3 downregulation was associated with a poor prognosis in 8 types of cancer. PER3 promoter methylation levels were increased in 11 types of cancer. Promoter hypermethylation (CpG islands [CGIs] cg12258811 and cg14204433) correlated with decreased PER3 expression in six cancers (breast invasive carcinoma, colon adenocarcinoma, head and neck squamous cell carcinoma, kidney renal papillary cell carcinoma [KIRP], lung adenocarcinoma [LUAD], and uterine corpus endometrial carcinoma). CGI cg12258811 hypermethylation was associated with reduced survival time and advanced cancer stages. Moreover, the bisulfite pyrosequencing assay confirmed CGI cg12258811 hypermethylation and its negative correlation with PER3 expression. In vitro and in vivo experiments demonstrated that PER3 inhibited KIRP and LUAD progression. Decitabine enhanced PER3 expression and inhibited KIRP cell functions by reducing promoter (cg12258811) methylation level. CONCLUSIONS Our findings advanced the mechanistic understanding of variations in PER3 expression in cancers and confirmed the tumor-associated function of PER3 hypermethylation and downregulation.
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Affiliation(s)
- Yaoxu Li
- Department of Stomatology, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China
| | - Wenjuan Li
- Department of Emergency and Critical Care Medicine, The First Afliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jinhai Deng
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China
| | - Mingzhu Yin
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China.
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Wanzhou District, Chongqing, 404100, China.
- Three Gorges Hospital & Academy for Advanced Interdisciplinary Technology, CQU-Ferenc Krausz Nobel Laureate Scientific Workstation, Chongqing University, Chongqing, China.
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25
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Tokairin K, Ito M, Lee AG, Teo M, He S, Cheng MY, Steinberg GK. Genome-Wide DNA Methylation Profiling Reveals Low Methylation Variability in Moyamoya Disease. Transl Stroke Res 2024:10.1007/s12975-024-01299-w. [PMID: 39356405 DOI: 10.1007/s12975-024-01299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/13/2024] [Accepted: 09/09/2024] [Indexed: 10/03/2024]
Abstract
Moyamoya disease (MMD) is a chronic cerebrovascular disorder that can lead to stroke and neurological dysfunctions. Given the largely sporadic nature and the role of gene-environment interactions in various diseases, we examined epigenetic modifications in MMD. We performed genome-wide DNA methylation using Illumina 850 K Methylation EPIC BeadChip, in two racially distinct adult female cohorts: a non-Asian cohort (13 MMD patients and 7 healthy controls) and an Asian cohort (14 MMD patients and 3 healthy controls). An additional external cohort with both sexes (females: 5 MMD patients and 5 healthy controls, males: 5 MMD patients and 5 healthy controls) was included for validation. Our findings revealed strikingly low DNA methylation variability between MMD patients and healthy controls, in both MMD female cohorts. In the non-Asian cohort, only 6 probes showed increased variability versus 647 probes that showed decreased variability. Similarly, in the Asian cohort, the MMD group also displayed a reduced methylation variability across all 2845 probes. Subsequent analysis showed that these differentially variable probes are located on genes involved in key biological processes such as methylation and transcription, DNA repair, cytoskeletal remodeling, natural killer cell signaling, cellular growth, and migration. These findings mark the first observation of low methylation variability in any disease, contrasting with the high variability observed in other disorders. This reduced methylation variability in MMD may hinder patients' adaptability to environmental shifts, such as hemodynamic stress, thereby influencing vascular homeostasis and contributing to MMD pathology. These findings offer new insights into the mechanisms of MMD and potential treatment strategies.
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Affiliation(s)
- Kikutaro Tokairin
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA, 94305, USA
- Stanford Stroke Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Masaki Ito
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA, 94305, USA
- Stanford Stroke Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex G Lee
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Mario Teo
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA, 94305, USA
- Stanford Stroke Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Shihao He
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking, China
| | - Michelle Y Cheng
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA, 94305, USA.
- Stanford Stroke Center, Stanford University School of Medicine, Stanford, CA, USA.
| | - Gary K Steinberg
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA, 94305, USA.
- Stanford Stroke Center, Stanford University School of Medicine, Stanford, CA, USA.
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26
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Zhao K, Oualkacha K, Zeng Y, Shen C, Klein K, Lakhal-Chaieb L, Labbe A, Pastinen T, Hudson M, Colmegna I, Bernatsky S, Greenwood CMT. Addressing dispersion in mis-measured multivariate binomial outcomes: A novel statistical approach for detecting differentially methylated regions in bisulfite sequencing data. Stat Med 2024; 43:3899-3920. [PMID: 38932470 DOI: 10.1002/sim.10149] [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: 07/18/2023] [Revised: 04/13/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Motivated by a DNA methylation application, this article addresses the problem of fitting and inferring a multivariate binomial regression model for outcomes that are contaminated by errors and exhibit extra-parametric variations, also known as dispersion. While dispersion in univariate binomial regression has been extensively studied, addressing dispersion in the context of multivariate outcomes remains a complex and relatively unexplored task. The complexity arises from a noteworthy data characteristic observed in our motivating dataset: non-constant yet correlated dispersion across outcomes. To address this challenge and account for possible measurement error, we propose a novel hierarchical quasi-binomial varying coefficient mixed model, which enables flexible dispersion patterns through a combination of additive and multiplicative dispersion components. To maximize the Laplace-approximated quasi-likelihood of our model, we further develop a specialized two-stage expectation-maximization (EM) algorithm, where a plug-in estimate for the multiplicative scale parameter enhances the speed and stability of the EM iterations. Simulations demonstrated that our approach yields accurate inference for smooth covariate effects and exhibits excellent power in detecting non-zero effects. Additionally, we applied our proposed method to investigate the association between DNA methylation, measured across the genome through targeted custom capture sequencing of whole blood, and levels of anti-citrullinated protein antibodies (ACPA), a preclinical marker for rheumatoid arthritis (RA) risk. Our analysis revealed 23 significant genes that potentially contribute to ACPA-related differential methylation, highlighting the relevance of cell signaling and collagen metabolism in RA. We implemented our method in the R Bioconductor package called "SOMNiBUS."
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Affiliation(s)
- Kaiqiong Zhao
- Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada
| | - Karim Oualkacha
- Département de Mathématiques, Université du Québec à Montréal, Montreal, Quebec, Canada
| | - Yixiao Zeng
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Cathy Shen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Kathleen Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Lajmi Lakhal-Chaieb
- Département de Mathématiques et de Statistique, Université Laval, Quebec, Quebec, Canada
| | - Aurélie Labbe
- Département de Sciences de la Décision, HEC Montrèal, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy, Independence, Missouri, USA
| | - Marie Hudson
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Inés Colmegna
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Sasha Bernatsky
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics and Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
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27
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Zhang J, Xu L, Yan X, Hu J, Gao X, Zhao H, Geng M, Wang N, Hu S. Multiomics and machine learning-based analysis of pancancer pseudouridine modifications. Discov Oncol 2024; 15:361. [PMID: 39162904 PMCID: PMC11335713 DOI: 10.1007/s12672-024-01093-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/12/2024] [Indexed: 08/21/2024] Open
Abstract
Pseudouridine widely affects the stability and function of RNA. However, our knowledge of pseudouridine properties in tumors is incomplete. We systematically analyzed pseudouridine synthases (PUSs) expression, genomic aberrations, and prognostic features in 10907 samples from 33 tumors. We found that the pseudouridine-associated pathway was abnormal in tumors and affected patient prognosis. Dysregulation of the PUSs expression pattern may arise from copy number variation (CNV) mutations and aberrant DNA methylation. Functional enrichment analyses determined that the PUSs expression was closely associated with the MYC, E2F, and MTORC1 signaling pathways. In addition, PUSs are involved in the remodeling of the tumor microenvironment (TME) in solid tumors, such as kidney and lung cancers. Particularly in lung cancer, increased expression of PUSs is accompanied by increased immune checkpoint expression and Treg infiltration. The best signature model based on more than 112 machine learning combinations had good prognostic ability in ACC, DLBC, GBM, KICH, MESO, THYM, TGCT, and PRAD tumors, and is expected to guide immunotherapy for 19 tumor types. The model was also effective in identifying patients with tumors amenable to etoposide, camptothecin, cisplatin, or bexarotene treatment. In conclusion, our work highlights the dysregulated features of PUSs and their role in the TME and patient prognosis, providing an initial molecular basis for future exploration of pseudouridine. Studies targeting pseudouridine are expected to lead to the development of potential diagnostic strategies and the evaluation and improvement of antitumor therapies.
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Affiliation(s)
- Jiheng Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lei Xu
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Xiuwei Yan
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jiahe Hu
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Xin Gao
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Hongtao Zhao
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Mo Geng
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Nan Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Shaoshan Hu
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China.
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Górczak K, Burzykowski T, Claesen J. A varying-coefficient model for the analysis of methylation sequencing data. Comput Biol Chem 2024; 111:108094. [PMID: 38781748 DOI: 10.1016/j.compbiolchem.2024.108094] [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: 03/06/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
DNA methylation is an important epigenetic modification involved in gene regulation. Advances in the next generation sequencing technology have enabled the retrieval of DNA methylation information at single-base-resolution. However, due to the sequencing process and the limited amount of isolated DNA, DNA-methylation-data are often noisy and sparse, which complicates the identification of differentially methylated regions (DMRs), especially when few replicates are available. We present a varying-coefficient model for detecting DMRs by using single-base-resolved methylation information. The model simultaneously smooths the methylation profiles and allows detection of DMRs, while accounting for additional covariates. The proposed model takes into account possible overdispersion by using a beta-binomial distribution. The overdispersion itself can be modeled as a function of the genomic region and explanatory variables. We illustrate the properties of the proposed model by applying it to two real-life case studies.
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Affiliation(s)
- Katarzyna Górczak
- Data Science Institute, Hasselt University, Belgium; Open Analytics NV, Antwerp, Belgium
| | - Tomasz Burzykowski
- Data Science Institute, Hasselt University, Belgium; Department of Biostatistics and Medical Informatics, Medical University of Bialystok, Poland; International Drug Development Institute (IDDI), Belgium
| | - Jürgen Claesen
- Data Science Institute, Hasselt University, Belgium; Department of Epidemiology and Data Science, Amsterdam UMC, VU Amsterdam, The Netherlands.
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29
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Xiong HY, Wyns A, Campenhout JV, Hendrix J, De Bruyne E, Godderis L, Schabrun S, Nijs J, Polli A. Epigenetic Landscapes of Pain: DNA Methylation Dynamics in Chronic Pain. Int J Mol Sci 2024; 25:8324. [PMID: 39125894 PMCID: PMC11312850 DOI: 10.3390/ijms25158324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Chronic pain is a prevalent condition with a multifaceted pathogenesis, where epigenetic modifications, particularly DNA methylation, might play an important role. This review delves into the intricate mechanisms by which DNA methylation and demethylation regulate genes associated with nociception and pain perception in nociceptive pathways. We explore the dynamic nature of these epigenetic processes, mediated by DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) enzymes, which modulate the expression of pro- and anti-nociceptive genes. Aberrant DNA methylation profiles have been observed in patients with various chronic pain syndromes, correlating with hypersensitivity to painful stimuli, neuronal hyperexcitability, and inflammatory responses. Genome-wide analyses shed light on differentially methylated regions and genes that could serve as potential biomarkers for chronic pain in the epigenetic landscape. The transition from acute to chronic pain is marked by rapid DNA methylation reprogramming, suggesting its potential role in pain chronicity. This review highlights the importance of understanding the temporal dynamics of DNA methylation during this transition to develop targeted therapeutic interventions. Reversing pathological DNA methylation patterns through epigenetic therapies emerges as a promising strategy for pain management.
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Affiliation(s)
- Huan-Yu Xiong
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
| | - Arne Wyns
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
| | - Jente Van Campenhout
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
| | - Jolien Hendrix
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
- Department of Public Health and Primary Care, Centre for Environment & Health, KU Leuven, 3000 Leuven, Belgium;
- Research Foundation—Flanders (FWO), 1000 Brussels, Belgium
| | - Elke De Bruyne
- Translational Oncology Research Center (TORC), Team Hematology and Immunology (HEIM), Vrije Universiteit Brussel, 1090 Brussels, Belgium;
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment & Health, KU Leuven, 3000 Leuven, Belgium;
| | - Siobhan Schabrun
- The School of Physical Therapy, University of Western Ontario, London, ON N6A 3K7, Canada;
- The Gray Centre for Mobility and Activity, Parkwood Institute, St. Joseph’s Healthcare, London, ON N6A 4V2, Canada
| | - Jo Nijs
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
- Chronic Pain Rehabilitation, Department of Physical Medicine and Physiotherapy, University Hospital Brussels, 1090 Brussels, Belgium
- Department of Health and Rehabilitation, Unit of Physiotherapy, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 41390 Göterbog, Sweden
| | - Andrea Polli
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
- Department of Public Health and Primary Care, Centre for Environment & Health, KU Leuven, 3000 Leuven, Belgium;
- Research Foundation—Flanders (FWO), 1000 Brussels, Belgium
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30
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Bai X, Yao HC, Wu B, Liu LR, Ding YY, Xiao CL. DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing. Brief Bioinform 2024; 25:bbae413. [PMID: 39177264 PMCID: PMC11342253 DOI: 10.1093/bib/bbae413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 08/24/2024] Open
Abstract
Recent nanopore sequencing system (R10.4) has enhanced base calling accuracy and is being increasingly utilized for detecting CpG methylation state. However, the robustness and universality of the methylation calling model in officially supplied Dorado remains poorly tested. In this study, we obtained heterogeneous datasets from human and plant sources to carry out comprehensive evaluations, which showed that Dorado performed significantly different across datasets. We therefore developed deep neural networks and implemented several optimizations in training a new model called DeepBAM. DeepBAM achieved superior and more stable performances compared with Dorado, including higher area under the ROC curves (98.47% on average and up to 7.36% improvement) and F1 scores (94.97% on average and up to 16.24% improvement) across the datasets. DeepBAM-based whole genome methylation frequencies have achieved >0.95 correlations with BS-seq on four of five datasets, outperforming Dorado in all instances. It enables unraveling allele-specific methylation patterns, including regions of transposable elements. The enhanced performance of DeepBAM paves the way for broader applications of nanopore sequencing in CpG methylation studies.
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Affiliation(s)
- Xin Bai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Hui-Cong Yao
- School of Artificial Intelligence, Sun Yat-Sen University, Gaoxin District, Zhuhai 519000, China
| | - Bo Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Luo-Ran Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Yu-Ying Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
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31
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Cucoreanu C, Tigu AB, Nistor M, Moldovan RC, Pralea IE, Iacobescu M, Iuga CA, Szabo R, Dindelegan GC, Ciuce C. Epigenetic and Molecular Alterations in Obesity: Linking CRP and DNA Methylation to Systemic Inflammation. Curr Issues Mol Biol 2024; 46:7430-7446. [PMID: 39057082 PMCID: PMC11275580 DOI: 10.3390/cimb46070441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Obesity is marked by excessive fat accumulation in the adipose tissue, which disrupts metabolic processes and causes chronic systemic inflammation. Commonly, body mass index (BMI) is used to assess obesity-related risks, predicting potential metabolic disorders. However, for a better clustering of obese patients, we must consider molecular and epigenetic changes which may be responsible for inflammation and metabolic changes. Our study involved two groups of patients, obese and healthy donors, on which routine analysis were performed, focused on BMI, leukocytes count, and C-reactive protein (CRP) and completed with global DNA methylation and gene expression analysis for genes involved in inflammation and adipogenesis. Our results indicate that obese patients exhibited elevated leukocytes levels, along with increased BMI and CRP. The obese group revealed a global hypomethylation and upregulation of proinflammatory genes, with adipogenesis genes following the same trend of being overexpressed. The study confirms that obesity is linked to systematic inflammation and metabolic dysfunction through epigenetic and molecular alterations. The CRP was correlated with the hypomethylation status in obese patients, and this fact may contribute to a better understanding of the roles of specific genes in adipogenesis and inflammation, leading to a better personalized therapy.
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Affiliation(s)
- Ciprian Cucoreanu
- Department of General Surgery, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Adrian-Bogdan Tigu
- Department of Translational Medicine, Research Center for Advance Medicine—MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
| | - Madalina Nistor
- Department of Translational Medicine, Research Center for Advance Medicine—MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
| | - Radu-Cristian Moldovan
- Department of Proteomics and Metabolomics, Research Center for Advance Medicine—MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
| | - Ioana-Ecaterina Pralea
- Department of Proteomics and Metabolomics, Research Center for Advance Medicine—MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
| | - Maria Iacobescu
- Department of Proteomics and Metabolomics, Research Center for Advance Medicine—MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
| | - Cristina-Adela Iuga
- Department of Proteomics and Metabolomics, Research Center for Advance Medicine—MEDFUTURE, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
| | - Robert Szabo
- Department of Anesthesia and Intensive Care, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania
| | - George-Calin Dindelegan
- Department of General Surgery, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Constatin Ciuce
- Department of General Surgery, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
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32
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Ao X, Parisien M, Fillingim RB, Ohrbach R, Slade GD, Diatchenko L, Smith SB. Whole-genome methylation profiling reveals regions associated with painful temporomandibular disorders and active recovery processes. Pain 2024; 165:1060-1073. [PMID: 38015635 PMCID: PMC11018476 DOI: 10.1097/j.pain.0000000000003104] [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: 05/07/2023] [Accepted: 08/24/2023] [Indexed: 11/30/2023]
Abstract
ABSTRACT Temporomandibular disorders (TMDs), collectively representing one of the most common chronic pain conditions, have a substantial genetic component, but genetic variation alone has not fully explained the heritability of TMD risk. Reasoning that the unexplained heritability may be because of DNA methylation, an epigenetic phenomenon, we measured genome-wide DNA methylation using the Illumina MethylationEPIC platform with blood samples from participants in the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) study. Associations with chronic TMD used methylation data from 496 chronic painful TMD cases and 452 TMD-free controls. Changes in methylation between enrollment and a 6-month follow-up visit were determined for a separate sample of 62 people with recent-onset painful TMD. More than 750,000 individual CpG sites were examined for association with chronic painful TMD. Six differentially methylated regions were significantly ( P < 5 × 10 -8 ) associated with chronic painful TMD, including loci near genes involved in the regulation of inflammatory and neuronal response. A majority of loci were similarly differentially methylated in acute TMD consistent with observed transience or persistence of symptoms at follow-up. Functional characterization of the identified regions found relationships between methylation at these loci and nearby genetic variation contributing to chronic painful TMD and with gene expression of proximal genes. These findings reveal epigenetic contributions to chronic painful TMD through methylation of the genes FMOD , PM20D1 , ZNF718 , ZFP57 , and RNF39 , following the development of acute painful TMD. Epigenetic regulation of these genes likely contributes to the trajectory of transcriptional events in affected tissues leading to resolution or chronicity of pain.
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Affiliation(s)
- Xiang Ao
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Marc Parisien
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Roger B. Fillingim
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, Florida; Pain Research and Intervention Center of Excellence, Department of Community Dentistry and Behavioral Science, College of Dentistry, University of Florida, Gainesville, Florida
| | - Richard Ohrbach
- Department of Oral Diagnostic Sciences, University at Buffalo, Buffalo, New York
| | - Gary D. Slade
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Luda Diatchenko
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Shad B. Smith
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University, Durham, North Carolina, USA
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33
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Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors. Nat Commun 2024; 15:3635. [PMID: 38688903 PMCID: PMC11061294 DOI: 10.1038/s41467-024-47943-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors, we utilize a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition. In the progenitor-like cell types of tumors, we identify a preponderance differential Cytosine-phosphate-Guanine site hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like histone deacetylase 4 and insulin-like growth factor 1 receptor, are associated with cell type-specific changes in gene expression in tumors. Our results highlight the importance of epigenomic alterations in the progenitor-like cell types and its role in cell type-specific transcriptional regulation in pediatric central nervous system tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Medical Center, New York, NY, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Laurent Perreard
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - George J Zanazzi
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 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.
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Teschendorff AE. On epigenetic stochasticity, entropy and cancer risk. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230054. [PMID: 38432318 PMCID: PMC10909509 DOI: 10.1098/rstb.2023.0054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/26/2023] [Indexed: 03/05/2024] Open
Abstract
Epigenetic changes are known to accrue in normal cells as a result of ageing and cumulative exposure to cancer risk factors. Increasing evidence points towards age-related epigenetic changes being acquired in a quasi-stochastic manner, and that they may play a causal role in cancer development. Here, I describe the quasi-stochastic nature of DNA methylation (DNAm) changes in ageing cells as well as in normal cells at risk of neoplastic transformation, discussing the implications of this stochasticity for developing cancer risk prediction strategies, and in particular, how it may require a conceptual paradigm shift in how we select cancer risk markers. I also describe the mounting evidence that a significant proportion of DNAm changes in ageing and cancer development are related to cell proliferation, reflecting tissue-turnover and the opportunity this offers for predicting cancer risk via the development of epigenetic mitotic-like clocks. Finally, I describe how age-associated DNAm changes may be causally implicated in cancer development via an irreversible suppression of tissue-specific transcription factors that increases epigenetic and transcriptomic entropy, promoting a more plastic yet aberrant cancer stem-cell state. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, People's Republic of China
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Toh H, Sasaki H. Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes. Life Sci Alliance 2024; 7:e202302403. [PMID: 38233073 PMCID: PMC10794778 DOI: 10.26508/lsa.202302403] [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: 09/28/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
DNA methylation is an essential epigenetic mechanism that regulates cellular reprogramming and development. Studies using whole-genome bisulfite sequencing have revealed distinct DNA methylome landscapes in human and mouse cells and tissues. However, the factors responsible for the differences in megabase-scale methylome patterns between cell types remain poorly understood. By analyzing publicly available 258 human and 301 mouse whole-genome bisulfite sequencing datasets, we reveal that genomic regions rich in guanine and cytosine, when located near the nuclear center, are highly susceptible to both global DNA demethylation and methylation events during embryonic and germline reprogramming. Furthermore, we found that regions that generate partially methylated domains during global DNA methylation are more likely to resist global DNA demethylation, contain high levels of adenine and thymine, and are adjacent to the nuclear lamina. The spatial properties of genomic regions, influenced by their guanine-cytosine content, are likely to affect the accessibility of molecules involved in DNA (de)methylation. These properties shape megabase-scale DNA methylation patterns and change as cells differentiate, leading to the emergence of different megabase-scale methylome patterns across cell types.
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Affiliation(s)
- Hidehiro Toh
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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36
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Zhang S, Ma B, Liu Y, Shen Y, Li D, Liu S, Song F. Predicting locus-specific DNA methylation levels in cancer and paracancer tissues. Epigenomics 2024; 16:549-570. [PMID: 38477028 PMCID: PMC11158003 DOI: 10.2217/epi-2023-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Aim: To predict base-resolution DNA methylation in cancerous and paracancerous tissues. Material & methods: We collected six cancer DNA methylation datasets from The Cancer Genome Atlas and five cancer datasets from Gene Expression Omnibus and established machine learning models using paired cancerous and paracancerous tissues. Tenfold cross-validation and independent validation were performed to demonstrate the effectiveness of the proposed method. Results: The developed cross-tissue prediction models can substantially increase the accuracy at more than 68% of CpG sites and contribute to enhancing the statistical power of differential methylation analyses. An XGBoost model leveraging multiple correlating CpGs may elevate the prediction accuracy. Conclusion: This study provides a powerful tool for DNA methylation analysis and has the potential to gain new insights into cancer research from epigenetics.
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Affiliation(s)
- Shuzheng Zhang
- School of Information Science & Technology, Dalian Maritime University, Dalian, 116026, China
| | - Baoshan Ma
- School of Information Science & Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yu Liu
- School of Information Science & Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yiwen Shen
- School of Information Science & Technology, Dalian Maritime University, Dalian, 116026, China
| | - Di Li
- Department of Neuro Intervention, Dalian Medical University affiliated Dalian Municipal Central Hospital, Dalian, 116033, China
| | - Shuxin Liu
- Department of Nephrology, Dalian Medical University affiliated Dalian Municipal Central Hospital, Dalian, 116033, China
| | - Fengju Song
- Department of Epidemiology & Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
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37
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Taglini F, Kafetzopoulos I, Rolls W, Musialik KI, Lee HY, Zhang Y, Marenda M, Kerr L, Finan H, Rubio-Ramon C, Gautier P, Wapenaar H, Kumar D, Davidson-Smith H, Wills J, Murphy LC, Wheeler A, Wilson MD, Sproul D. DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Rep 2024; 25:1130-1155. [PMID: 38291337 PMCID: PMC7615734 DOI: 10.1038/s44319-024-00061-5] [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: 04/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here, we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1α and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3-marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.
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Affiliation(s)
- Francesca Taglini
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Altos Labs, Cambridge Institute, Cambridge, UK
| | - Willow Rolls
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kamila Irena Musialik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, Imperial College London, London, UK
| | - Heng Yang Lee
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Endocrine Oncology Research Group, Department of Surgery, The Royal College of Surgeons RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Yujie Zhang
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Mattia Marenda
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hannah Finan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Swiss Federal Institute of Technology, ETH Zürich, Institute of Molecular Health Sciences, Zürich, Switzerland
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Dhananjay Kumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Hazel Davidson-Smith
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ann Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, Dickson BM, Kong X, Chomiak AA, Vaughan RM, Hebert JM, David Y, Zhou W, Baylin SB, Jones PA, Clark SJ, Rothbart SB. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580169. [PMID: 38405904 PMCID: PMC10888769 DOI: 10.1101/2024.02.13.580169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. Nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites for DNMT1 through ubiquitin interacting motifs (UIM1 and UIM2). Here, we profile contributions of UHRF1 and DNMT1 to genome-wide DNA methylation inheritance and dissect specific roles for ubiquitin signaling in this process. We reveal DNA methylation maintenance at low-density CpGs is vulnerable to disruption of UHRF1 ubiquitin ligase activity and DNMT1 ubiquitin reading activity through UIM1. Hypomethylation of low-density CpGs in this manner induces formation of partially methylated domains (PMD), a methylation signature observed across human cancers. Furthermore, disrupting DNMT1 UIM2 function abolishes DNA methylation maintenance. Collectively, we show DNMT1-dependent DNA methylation inheritance is a ubiquitin-regulated process and suggest a disrupted UHRF1-DNMT1 ubiquitin signaling axis contributes to the development of PMDs in human cancers.
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Gu M, Ren B, Fang Y, Ren J, Liu X, Wang X, Zhou F, Xiao R, Luo X, You L, Zhao Y. Epigenetic regulation in cancer. MedComm (Beijing) 2024; 5:e495. [PMID: 38374872 PMCID: PMC10876210 DOI: 10.1002/mco2.495] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Epigenetic modifications are defined as heritable changes in gene activity that do not involve changes in the underlying DNA sequence. The oncogenic process is driven by the accumulation of alterations that impact genome's structure and function. Genetic mutations, which directly disrupt the DNA sequence, are complemented by epigenetic modifications that modulate gene expression, thereby facilitating the acquisition of malignant characteristics. Principals among these epigenetic changes are shifts in DNA methylation and histone mark patterns, which promote tumor development and metastasis. Notably, the reversible nature of epigenetic alterations, as opposed to the permanence of genetic changes, positions the epigenetic machinery as a prime target in the discovery of novel therapeutics. Our review delves into the complexities of epigenetic regulation, exploring its profound effects on tumor initiation, metastatic behavior, metabolic pathways, and the tumor microenvironment. We place a particular emphasis on the dysregulation at each level of epigenetic modulation, including but not limited to, the aberrations in enzymes responsible for DNA methylation and histone modification, subunit loss or fusions in chromatin remodeling complexes, and the disturbances in higher-order chromatin structure. Finally, we also evaluate therapeutic approaches that leverage the growing understanding of chromatin dysregulation, offering new avenues for cancer treatment.
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Affiliation(s)
- Minzhi Gu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Bo Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yuan Fang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Jie Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiaohong Liu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xing Wang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Feihan Zhou
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Ruiling Xiao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiyuan Luo
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Lei You
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yupei Zhao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
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Gao Y, Zhou N, Liu J. Ovarian Cancer Diagnosis and Prognosis Based on Cell-Free DNA Methylation. Cancer Control 2024; 31:10732748241255548. [PMID: 38764160 PMCID: PMC11104031 DOI: 10.1177/10732748241255548] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Background: Ovarian cancer stands as the deadliest malignant tumor within the female reproductive tract. As a result of the absence of effective diagnostic and monitoring markers, 75% of ovarian cancer cases are diagnosed at a late stage, leading to a mere 50% survival rate within five years. The advancement of molecular biology is essential for accurate diagnosis and treatment of ovarian cancer. Methods: A review of several randomized clinical trials, focusing on the ovarian cancer, was undertaken. The advancement of molecular biology and diagnostic methods related to accurate diagnosis and treatment of ovarian cancer were examined. Results: Liquid biopsy is an innovative method of detecting malignant tumors that has gained increasing attention over the past few years. Cell-free DNA assay-based liquid biopsies show potential in delineating tumor status heterogeneity and tracking tumor recurrence. DNA methylation influences a multitude of biological functions and diseases, especially during the initial phases of cancer. The cell-free DNA methylation profiling system has emerged as a sensitive and non-invasive technique for identifying and detecting the biological origins of cancer. It holds promise as a biomarker, enabling early screening, recurrence monitoring, and prognostic evaluation of cancer. Conclusions: This review evaluates recent advancements and challenges associated with cell-free DNA methylation analysis for the diagnosis, prognosis monitoring, and assessment of therapeutic responses in the management of ovarian cancers, aiming to offer guidance for precise diagnosis and treatment of this disease.
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Affiliation(s)
- Yajuan Gao
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Nanyang Zhou
- Department of Traditional Chinese Medicine, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Jie Liu
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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41
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Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024; 98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [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: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is intrinsic to tumours and contributes to malignancy and metastasis while hindering the efficiency of existing treatments. Epigenetic mechanisms play a crucial role in the regulation of hypoxic cancer cell programs, both in the initial phases of sensing the decrease in oxygen levels and during adaptation to chronic lack of oxygen. During the latter, the epigenetic regulation of tumour biology intersects with hypoxia-sensitive transcription factors in a complex network of gene regulation that also involves metabolic reprogramming. Here, we review the current literature on the epigenetic control of gene programs in hypoxic cancer cells. We highlight common themes and features of such epigenetic remodelling and discuss their relevance for the development of therapeutic strategies.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium; KU Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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42
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Guo J, Zhao M, Chen C, Wang F, Chen Z. A laser-induced graphene-based electrochemical immunosensor for nucleic acid methylation detection. Analyst 2023; 149:137-147. [PMID: 37986634 DOI: 10.1039/d3an01628e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The detection of methylation in DNA and RNA is essential for the diagnosis and treatment of a wide range of diseases. A one-step fabricated laser-induced graphene (LIG) electrode has received increasing attention due to its good electrical conductivity, large specific surface area, ease of miniaturization, low cost and flexibility. Herein, a potential biosensor for N6-methyladenosine (m6A-RNA) and 5-methylcystosine-single strand DNA (5mC-ssDNA) detection was designed. The aim of this paper is to address the problem of detecting the m6A-RNA and 5mC-ssDNA content in cells. By stepwise modification of gold nanoparticles (AuNPs), sulfhydryl-modified nucleic acid chains, biotin-modified antibodies, and streptavidin-modified horseradish peroxidase (SA-HRP) at the LIG electrode, the peak current responses exhibited an increase proportional to the concentration of m6A-RNA and 5mC-ssDNA in the hydrogen peroxide-hydroquinone (H2O2-HQ) system. This method demonstrated a low detection limit of 2.81 pM for m6A-RNA and 9.53 pM for 5mC-ssDNA, with a linear detection range of 0.01 nM to 10 nM for both targets. The regression equation was determined as ΔI = 4.83 log c + 12.32 (R2 = 0.9980) for m6A-RNA and ΔI = 9.82 log c + 22.09 (R2 = 0.9903) for 5mC-ssDNA. Our method has good selectivity toward different detection targets of nucleic acid chains, stability for long-term storage and consecutive scanning (RSD of 9.42% and 2.08%, respectively) and reproducibility of 5 electrodes (RSD of 6.85%). This method utilizes gold-sulfur bonding to immobilize the detection target, which improves the conductivity of the LIG electrode and introduces an amplified portion of the signal by taking advantage of antigen-antibody specific binding. Thus, dual detection of m6A-RNA and 5mC-ssDNA was realized. Importantly, this approach is successfully applied for the detection of targets in spiked samples extracted from HeLa cells, suggesting its potential for clinical applications and providing a new perspective for the development of point-of care testing (POCT) techniques.
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Affiliation(s)
- Jingyi Guo
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
| | - Mei Zhao
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
| | - Chen Chen
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
| | - Fang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
| | - Zilin Chen
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
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Xue X, Wang Z, Wang Y, Zhou X. Disease Diagnosis Based on Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2114-2127. [PMID: 37527510 DOI: 10.1021/acschembio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid modifications include a wide range of epigenetic and epitranscriptomic factors and impact a wide range of nucleic acids due to their profound influence on biological inheritance, growth, and metabolism. The recently developed methods of mapping and characterizing these modifications have promoted their discovery as well as large-scale studies in eukaryotes, especially in humans. Because of these pioneering strategies, nucleic acid modifications have been shown to have a great impact on human disorders such as cancer. Therefore, whether nucleic acid modifications could become a new type of biomarker remains an open question. In this review, we briefly look back at classical nucleic acid modifications and then focus on the progress made in investigating these modifications as diagnostic biomarkers in clinical therapy and present our perspective on their development prospects.
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Affiliation(s)
- Xiaochen Xue
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiying Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Department of Chemistry, College of Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
- Cross Research Institute of Zhongnan Hospital, Wuhan University, Wuhan 430071, China
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44
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Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [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: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
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Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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45
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Liang WW, Lu RJH, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, Payne SH, Fenyö D, Rodriguez H, Wiznerowicz M, Shen H, Mani DR, Rodland KD, Lazar AJ, Robles AI, Ding L. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin. Cancer Cell 2023; 41:1567-1585.e7. [PMID: 37582362 PMCID: PMC11613269 DOI: 10.1016/j.ccell.2023.07.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. Here, we leveraged multi-omic profiling of 687 tumors and matched non-involved adjacent tissues from the kidney, brain, pancreas, lung, head and neck, and endometrium to identify aberrant methylation associated with RNA and protein abundance changes and build a Pan-Cancer catalog. We uncovered lineage-specific epigenetic drivers including hypomethylated FGFR2 in endometrial cancer. We showed that hypermethylated STAT5A is associated with pervasive regulon downregulation and immune cell depletion, suggesting that epigenetic regulation of STAT5A expression constitutes a molecular switch for immunosuppression in squamous tumors. We further demonstrated that methylation subtype-enrichment information can explain cell-of-origin, intra-tumor heterogeneity, and tumor phenotypes. Overall, we identified cis-acting DNA methylation events that drive transcriptional and translational changes, shedding light on the tumor's epigenetic landscape and the role of its cell-of-origin.
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Affiliation(s)
- Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Steven M Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rossana Lazcano
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Iga Kolodziejczak
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Yizhe Song
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Akshay Govindan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xiang Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Sunantha Sethuraman
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Heliodor Swiecicki Clinical Hospital in Poznań, Ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Okletey J, Angelis D, Jones TM, Montagna C, Spiliotis ET. An oncogenic isoform of septin 9 promotes the formation of juxtanuclear invadopodia by reducing nuclear deformability. Cell Rep 2023; 42:112893. [PMID: 37516960 PMCID: PMC10530659 DOI: 10.1016/j.celrep.2023.112893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/17/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Invadopodia are extracellular matrix (ECM) degrading structures, which promote cancer cell invasion. The nucleus is increasingly viewed as a mechanosensory organelle that determines migratory strategies. However, how the nucleus crosstalks with invadopodia is little known. Here, we report that the oncogenic septin 9 isoform 1 (SEPT9_i1) is a component of breast cancer invadopodia. SEPT9_i1 depletion diminishes invadopodium formation and the clustering of the invadopodium precursor components TKS5 and cortactin. This phenotype is characterized by deformed nuclei and nuclear envelopes with folds and grooves. We show that SEPT9_i1 localizes to the nuclear envelope and juxtanuclear invadopodia. Moreover, exogenous lamin A rescues nuclear morphology and juxtanuclear TKS5 clusters. Importantly, SEPT9_i1 is required for the amplification of juxtanuclear invadopodia, which is induced by the epidermal growth factor. We posit that nuclei of low deformability favor the formation of juxtanuclear invadopodia in a SEPT9_i1-dependent manner, which functions as a tunable mechanism for overcoming ECM impenetrability.
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Affiliation(s)
- Joshua Okletey
- Department of Biology, Drexel University, 3245 Chestnut Street, Philadelphia, PA 19104, USA
| | - Dimitrios Angelis
- Department of Biology, Drexel University, 3245 Chestnut Street, Philadelphia, PA 19104, USA
| | - Tia M Jones
- Department of Biology, Drexel University, 3245 Chestnut Street, Philadelphia, PA 19104, USA
| | - Cristina Montagna
- Department of Radiology and Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Elias T Spiliotis
- Department of Biology, Drexel University, 3245 Chestnut Street, Philadelphia, PA 19104, USA.
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Zheng Y, Ziman B, Ho AS, Sinha UK, Xu LY, Li EM, Koeffler HP, Berman BP, Lin DC. Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation. Genome Biol 2023; 24:193. [PMID: 37620896 PMCID: PMC10463844 DOI: 10.1186/s13059-023-03035-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND As one of the most common malignancies, esophageal cancer has two subtypes, squamous cell carcinoma and adenocarcinoma, arising from distinct cells-of-origin. Distinguishing cell-type-specific molecular features from cancer-specific characteristics is challenging. RESULTS We analyze whole-genome bisulfite sequencing data on 45 esophageal tumor and nonmalignant samples from both subtypes. We develop a novel sequence-aware method to identify large partially methylated domains (PMDs), revealing profound heterogeneity at both methylation level and genomic distribution of PMDs across tumor samples. We identify subtype-specific PMDs that are associated with repressive transcription, chromatin B compartments and high somatic mutation rate. While genomic locations of these PMDs are pre-established in normal cells, the degree of loss is significantly higher in tumors. We find that cell-type-specific deposition of H3K36me2 may underlie genomic distribution of PMDs. At a smaller genomic scale, both cell-type- and cancer-specific differentially methylated regions (DMRs) are identified for each subtype. Using binding motif analysis within these DMRs, we show that a cell-type-specific transcription factor HNF4A maintains the binding sites that it generates in normal cells, while establishing new binding sites cooperatively with novel partners such as FOSL1 in esophageal adenocarcinoma. Finally, leveraging pan-tissue single-cell and pan-cancer epigenomic datasets, we demonstrate that a substantial fraction of cell-type-specific PMDs and DMRs identified here in esophageal cancer are actually markers that co-occur in other cancers originating from related cell types. CONCLUSIONS These findings advance our understanding of DNA methylation dynamics at various genomic scales in normal and malignant states, providing novel mechanistic insights into cell-type- and cancer-specific epigenetic regulations.
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Affiliation(s)
- Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Benjamin Ziman
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, 2250 Alcazar Street - CSA 207D, Los Angeles, CA, 90033, USA
| | - Allen S Ho
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Uttam K Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Guangdong, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Guangdong, China
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Benjamin P Berman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - De-Chen Lin
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA.
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, 2250 Alcazar Street - CSA 207D, Los Angeles, CA, 90033, USA.
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48
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Jeong S, Cho S, Yang SK, Oh SA, Kang YK. Parallel shift of DNA methylation and gene expression toward the mean in mouse spleen with aging. Aging (Albany NY) 2023; 15:6690-6709. [PMID: 37494662 PMCID: PMC10415566 DOI: 10.18632/aging.204903] [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: 04/19/2023] [Accepted: 07/06/2023] [Indexed: 07/28/2023]
Abstract
Age-associated DNA-methylation drift (AMD) manifests itself in two ways in mammals: global decrease (hypomethylation) and local increase of DNA methylation (hypermethylation). To comprehend the principle behind this bidirectional AMD, we studied methylation states of spatially clustered CpG dinucleotides in mouse splenic DNA using reduced-representation-bisulfite-sequencing (RRBS). The mean methylation levels of whole CpGs declined with age. Promoter-resident CpGs, generally weakly methylated (<5%) in young mice, became hypermethylated in old mice, whereas CpGs in gene-body and intergenic regions, initially moderately (~33%) and extensively (>80%) methylated, respectively, were hypomethylated in the old. Chromosome-wise analysis of methylation revealed that inter-individual heterogeneities increase with age. The density of nearby CpGs was used to classify individual CpGs, which found hypermethylation in CpG-rich regions and hypomethylation in CpG-poor regions. When genomic regions were grouped by methylation level, high-methylation regions tended to become hypomethylated whereas low-methylation regions tended to become hypermethylated, regardless of genomic structure/function. Data analysis revealed that while methylation level and CpG density were interdependent, methylation level was a better predictor of the AMD pattern representing a shift toward the mean. Further analysis of gene-expression data showed a decrease in the expression of highly-expressed genes and an increase in the expression of lowly-expressed genes with age. This shift towards the mean in gene-expression changes was correlated with that of methylation changes, indicating a potential link between the two age-associated changes. Our findings suggest that age-associated hyper- and hypomethylation events are stochastic and attributed to malfunctioning intrinsic mechanisms for methylation maintenance in low- and high-methylation regions, respectively.
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Affiliation(s)
- Sangkyun Jeong
- Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Yuseong-gu, Daejeon 34054, South Korea
- Genomics Department, Keyomics Co. Ltd., Yuseong-gu, Daejeon 34013, South Korea
| | - Sunwha Cho
- Genomics Department, Keyomics Co. Ltd., Yuseong-gu, Daejeon 34013, South Korea
| | - Seung Kyoung Yang
- Genomics Department, Keyomics Co. Ltd., Yuseong-gu, Daejeon 34013, South Korea
| | - Soo A. Oh
- Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Yuseong-gu, Daejeon 34054, South Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, South Korea
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49
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Guo H, Vuille JA, Wittner BS, Lachtara EM, Hou Y, Lin M, Zhao T, Raman AT, Russell HC, Reeves BA, Pleskow HM, Wu CL, Gnirke A, Meissner A, Efstathiou JA, Lee RJ, Toner M, Aryee MJ, Lawrence MS, Miyamoto DT, Maheswaran S, Haber DA. DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs. Cell 2023; 186:2765-2782.e28. [PMID: 37327786 PMCID: PMC10436379 DOI: 10.1016/j.cell.2023.05.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/09/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
Abstract
Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution genome-wide single-cell DNA methylation sequencing, we identify 40 core domains that are uniformly hypomethylated from the earliest detectable stages of prostate malignancy through metastatic circulating tumor cells (CTCs). Nested among these repressive domains are smaller loci with preserved methylation that escape silencing and are enriched for cell proliferation genes. Transcriptionally silenced genes within the core hypomethylated domains are enriched for immune-related genes; prominent among these is a single gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells and four IFI16-related interferon-inducible genes implicated in innate immunity. The re-expression of CD1 or IFI16 murine orthologs in immuno-competent mice abrogates tumorigenesis, accompanied by the activation of anti-tumor immunity. Thus, early epigenetic changes may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for CTCs.
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Affiliation(s)
- Hongshan Guo
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Joanna A Vuille
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Emily M Lachtara
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yu Hou
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maoxuan Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ting Zhao
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ayush T Raman
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hunter C Russell
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Brittany A Reeves
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Haley M Pleskow
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Chin-Lee Wu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Jason A Efstathiou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Richard J Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mehmet Toner
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Engineering in Medicine and Shriners Hospital for Children, Harvard Medical School, Boston, MA 02114, USA
| | - Martin J Aryee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David T Miyamoto
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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Okletey J, Angelis D, Jones TM, Montagna C, Spiliotis ET. An oncogenic isoform of septin 9 promotes the formation of juxtanuclear invadopodia by reducing nuclear deformability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.18.545473. [PMID: 37398172 PMCID: PMC10312791 DOI: 10.1101/2023.06.18.545473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Invadopodia are extracellular matrix (ECM) degrading structures, which promote cancer cell invasion. The nucleus is increasingly viewed as a mechanosensory organelle that determines migratory strategies. However, how the nucleus crosstalks with invadopodia is little known. Here, we report that the oncogenic septin 9 isoform 1 (SEPT9_i1) is a component of breast cancer invadopodia. SEPT9_i1 depletion diminishes invadopodia formation and the clustering of invadopodia precursor components TKS5 and cortactin. This phenotype is characterized by deformed nuclei, and nuclear envelopes with folds and grooves. We show that SEPT9_i1 localizes to the nuclear envelope and juxtanuclear invadopodia. Moreover, exogenous lamin A rescues nuclear morphology and juxtanuclear TKS5 clusters. Importantly, SEPT9_i1 is required for the amplification of juxtanuclear invadopodia, which is induced by the epidermal growth factor. We posit that nuclei of low deformability favor the formation of juxtanuclear invadopodia in a SEPT9_i1-dependent manner, which functions as a tunable mechanism for overcoming ECM impenetrability. Highlights The oncogenic SEPT9_i1 is enriched in breast cancer invadopodia in 2D and 3D ECMSEPT9_i1 promotes invadopodia precursor clustering and invadopodia elongationSEPT9_i1 localizes to the nuclear envelope and reduces nuclear deformabilitySEPT9_i1 is required for EGF-induced amplification of juxtanuclear invadopodia. eTOC Blurb Invadopodia promote the invasion of metastatic cancers. The nucleus is a mechanosensory organelle that determines migratory strategies, but how it crosstalks with invadopodia is unknown. Okletey et al show that the oncogenic isoform SEPT9_i1 promotes nuclear envelope stability and the formation of invadopodia at juxtanuclear areas of the plasma membrane.
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