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Rinaldi M, Pezone A, Quadrini GI, Abbadessa G, Laezza MP, Passaro ML, Porcellini A, Costagliola C. Targeting shared pathways in tauopathies and age-related macular degeneration: implications for novel therapies. Front Aging Neurosci 2024; 16:1371745. [PMID: 38633983 PMCID: PMC11021713 DOI: 10.3389/fnagi.2024.1371745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
The intricate parallels in structure and function between the human retina and the central nervous system designate the retina as a prospective avenue for understanding brain-related processes. This review extensively explores the shared physiopathological mechanisms connecting age-related macular degeneration (AMD) and proteinopathies, with a specific focus on tauopathies. The pivotal involvement of oxidative stress and cellular senescence emerges as key drivers of pathogenesis in both conditions. Uncovering these shared elements not only has the potential to enhance our understanding of intricate neurodegenerative diseases but also sets the stage for pioneering therapeutic approaches in AMD.
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Affiliation(s)
- Michele Rinaldi
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
| | - Antonio Pezone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Gaia Italia Quadrini
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
| | - Gianmarco Abbadessa
- Division of Neurology, Department of Advanced Medical and Surgical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Maria Paola Laezza
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso, Italy
| | - Maria Laura Passaro
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso, Italy
| | | | - Ciro Costagliola
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
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2
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Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.569638. [PMID: 38106096 PMCID: PMC10723383 DOI: 10.1101/2023.12.08.569638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
DNA methylation marks have recently been used to build models known as "epigenetic clocks" which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In analysis of multimodal data from 9,331 human individuals, we find that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but also with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping enables mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging faster or slower than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.
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Affiliation(s)
- Zane Koch
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Adam Li
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Steven Cummings
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Trey Ideker
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla California, 92093, USA
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3
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Pagliara D, Ciolfi A, Pedace L, Haghshenas S, Ferilli M, Levy MA, Miele E, Nardini C, Cappelletti C, Relator R, Pitisci A, De Vito R, Pizzi S, Kerkhof J, McConkey H, Nazio F, Kant SG, Di Donato M, Agolini E, Matraxia M, Pasini B, Pelle A, Galluccio T, Novelli A, Barakat TS, Andreani M, Rossi F, Mecucci C, Savoia A, Sadikovic B, Locatelli F, Tartaglia M. Identification of a robust DNA methylation signature for Fanconi anemia. Am J Hum Genet 2023; 110:1938-1949. [PMID: 37865086 PMCID: PMC10645556 DOI: 10.1016/j.ajhg.2023.09.014] [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: 06/29/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/23/2023] Open
Abstract
Fanconi anemia (FA) is a clinically variable and genetically heterogeneous cancer-predisposing disorder representing the most common bone marrow failure syndrome. It is caused by inactivating predominantly biallelic mutations involving >20 genes encoding proteins with roles in the FA/BRCA DNA repair pathway. Molecular diagnosis of FA is challenging due to the wide spectrum of the contributing gene mutations and structural rearrangements. The assessment of chromosomal fragility after exposure to DNA cross-linking agents is generally required to definitively confirm diagnosis. We assessed peripheral blood genome-wide DNA methylation (DNAm) profiles in 25 subjects with molecularly confirmed clinical diagnosis of FA (FANCA complementation group) using Illumina's Infinium EPIC array. We identified 82 differentially methylated CpG sites that allow to distinguish subjects with FA from healthy individuals and subjects with other genetic disorders, defining an FA-specific DNAm signature. The episignature was validated using a second cohort of subjects with FA involving different complementation groups, documenting broader genetic sensitivity and demonstrating its specificity using the EpiSign Knowledge Database. The episignature properly classified DNA samples obtained from bone marrow aspirates, demonstrating robustness. Using the selected probes, we trained a machine-learning model able to classify EPIC DNAm profiles in molecularly unsolved cases. Finally, we show that the generated episignature includes CpG sites that do not undergo functional selective pressure, allowing diagnosis of FA in individuals with reverted phenotype due to gene conversion. These findings provide a tool to accelerate diagnostic testing in FA and broaden the clinical utility of DNAm profiling in the diagnostic setting.
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Affiliation(s)
- Daria Pagliara
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Lucia Pedace
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Marco Ferilli
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Evelina Miele
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Claudia Nardini
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Camilla Cappelletti
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Angela Pitisci
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Rita De Vito
- Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Francesca Nazio
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Sarina G Kant
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 Rotterdam, the Netherlands
| | - Maddalena Di Donato
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Marta Matraxia
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Barbara Pasini
- AOU Città della salute e della scienza di Torino, Molinette's Hospital, 10126 Torino, Italy
| | - Alessandra Pelle
- AOU Città della salute e della scienza di Torino, Molinette's Hospital, 10126 Torino, Italy
| | - Tiziana Galluccio
- Laboratory of Transplant Immunogenetics, Department of Hematology/Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC University Medical Center, 3015 Rotterdam, the Netherlands
| | - Marco Andreani
- Laboratory of Transplant Immunogenetics, Department of Hematology/Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Francesca Rossi
- Department of Woman, Child and of General and Specialist Surgery, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Cristina Mecucci
- Institute of Hematology and Center for Hemato-Oncology Research, University and Hospital of Perugia, 06123 Perugia, Italy
| | - Anna Savoia
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Franco Locatelli
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy; Department of Pediatrics, Catholic University of the Sacred Hearth, 00168 Rome, Italy.
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
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4
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Craddock J, Jiang J, Patrick SM, Mutambirwa SBA, Stricker PD, Bornman MSR, Jaratlerdsiri W, Hayes VM. Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers (Basel) 2023; 15:3462. [PMID: 37444571 DOI: 10.3390/cancers15133462] [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: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer is driven by acquired genetic alterations, including those impacting the epigenetic machinery. With African ancestry as a significant risk factor for aggressive disease, we hypothesize that dysregulation among the roughly 656 epigenetic genes may contribute to prostate cancer health disparities. Investigating prostate tumor genomic data from 109 men of southern African and 56 men of European Australian ancestry, we found that African-derived tumors present with a longer tail of epigenetic driver gene candidates (72 versus 10). Biased towards African-specific drivers (63 versus 9 shared), many are novel to prostate cancer (18/63), including several putative therapeutic targets (CHD7, DPF3, POLR1B, SETD1B, UBTF, and VPS72). Through clustering of all variant types and copy number alterations, we describe two epigenetic PCa taxonomies capable of differentiating patients by ancestry and predicted clinical outcomes. We identified the top genes in African- and European-derived tumors representing a multifunctional "generic machinery", the alteration of which may be instrumental in epigenetic dysregulation and prostate tumorigenesis. In conclusion, numerous somatic alterations in the epigenetic machinery drive prostate carcinogenesis, but African-derived tumors appear to achieve this state with greater diversity among such alterations. The greater novelty observed in African-derived tumors illustrates the significant clinical benefit to be derived from a much needed African-tailored approach to prostate cancer healthcare aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Jenna Craddock
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa 0208, South Africa
| | - Phillip D Stricker
- Department of Urology, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Vanessa M Hayes
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
- Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
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5
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Improda T, Morgera V, Vitale M, Chiariotti L, Passaro F, Feola A, Porcellini A, Cuomo M, Pezone A. Specific Methyl-CpG Configurations Define Cell Identity through Gene Expression Regulation. Int J Mol Sci 2023; 24:9951. [PMID: 37373098 DOI: 10.3390/ijms24129951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Cell identity is determined by the chromatin structure and profiles of gene expression, which are dependent on chromatin accessibility and DNA methylation of the regions critical for gene expression, such as enhancers and promoters. These epigenetic modifications are required for mammalian development and are essential for the establishment and maintenance of the cellular identity. DNA methylation was once thought to be a permanent repressive epigenetic mark, but systematic analyses in various genomic contexts have revealed a more dynamic regulation than previously thought. In fact, both active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. To link methylation signatures of specific genes to their expression profiles, we determined the methyl-CpG configurations of the promoters of five genes switched on and off during murine postnatal brain differentiation by bisulfite-targeted sequencing. Here, we report the structure of significant, dynamic, and stable methyl-CpG profiles associated with silencing or activation of the expression of genes during neural stem cell and brain postnatal differentiation. Strikingly, these methylation cores mark different mouse brain areas and cell types derived from the same areas during differentiation.
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Affiliation(s)
- Teresa Improda
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Valentina Morgera
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Maria Vitale
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Lorenzo Chiariotti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Napoli, Italy
| | - Fabiana Passaro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Napoli, Italy
| | - Antonia Feola
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Antonio Porcellini
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Mariella Cuomo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Napoli, Italy
| | - Antonio Pezone
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
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6
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Pezone A, Olivieri F, Napoli MV, Procopio A, Avvedimento EV, Gabrielli A. Inflammation and DNA damage: cause, effect or both. Nat Rev Rheumatol 2023; 19:200-211. [PMID: 36750681 DOI: 10.1038/s41584-022-00905-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Inflammation is a biological response involving immune cells, blood vessels and mediators induced by endogenous and exogenous stimuli, such as pathogens, damaged cells or chemicals. Unresolved (chronic) inflammation is characterized by the secretion of cytokines that maintain inflammation and redox stress. Mitochondrial or nuclear redox imbalance induces DNA damage, which triggers the DNA damage response (DDR) that is orchestrated by ATM and ATR kinases, which modify gene expression and metabolism and, eventually, establish the senescent phenotype. DDR-mediated senescence is induced by the signalling proteins p53, p16 and p21, which arrest the cell cycle in G1 or G2 and promote cytokine secretion, producing the senescence-associated secretory phenotype. Senescence and inflammation phenotypes are intimately associated, but highly heterogeneous because they vary according to the cell type that is involved. The vicious cycle of inflammation, DNA damage and DDR-mediated senescence, along with the constitutive activation of the immune system, is the core of an evolutionarily conserved circuitry, which arrests the cell cycle to reduce the accumulation of mutations generated by DNA replication during redox stress caused by infection or inflammation. Evidence suggests that specific organ dysfunctions in apparently unrelated diseases of autoimmune, rheumatic, degenerative and vascular origins are caused by inflammation resulting from DNA damage-induced senescence.
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Affiliation(s)
- Antonio Pezone
- Dipartimento di Biologia, Università Federico II, Napoli, Italy.
| | - Fabiola Olivieri
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Maria Vittoria Napoli
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Antonio Procopio
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Enrico Vittorio Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, Napoli, Italy.
| | - Armando Gabrielli
- Fondazione di Medicina Molecolare e Terapia Cellulare, Università Politecnica delle Marche, Ancona, Italy.
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7
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McCarthy-Leo C, Darwiche F, Tainsky MA. DNA Repair Mechanisms, Protein Interactions and Therapeutic Targeting of the MRN Complex. Cancers (Basel) 2022; 14:5278. [PMID: 36358700 PMCID: PMC9656488 DOI: 10.3390/cancers14215278] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
Repair of a DNA double-strand break relies upon a pathway of proteins to identify damage, regulate cell cycle checkpoints, and repair the damage. This process is initiated by a sensor protein complex, the MRN complex, comprised of three proteins-MRE11, RAD50, and NBS1. After a double-stranded break, the MRN complex recruits and activates ATM, in-turn activating other proteins such as BRCA1/2, ATR, CHEK1/2, PALB2 and RAD51. These proteins have been the focus of many studies for their individual roles in hereditary cancer syndromes and are included on several genetic testing panels. These panels have enabled us to acquire large amounts of genetic data, much of which remains a challenge to interpret due to the presence of variants of uncertain significance (VUS). While the primary aim of clinical testing is to accurately and confidently classify variants in order to inform medical management, the presence of VUSs has led to ambiguity in genetic counseling. Pathogenic variants within MRN complex genes have been implicated in breast, ovarian, prostate, colon cancers and gliomas; however, the hundreds of VUSs within MRE11, RAD50, and NBS1 precludes the application of these data in genetic guidance of carriers. In this review, we discuss the MRN complex's role in DNA double-strand break repair, its interactions with other cancer predisposing genes, the variants that can be found within the three MRN complex genes, and the MRN complex's potential as an anti-cancer therapeutic target.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Fatima Darwiche
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael A. Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Karmanos Cancer Institute at Wayne State University School of Medicine, Detroit, MI 48201, USA
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8
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Wang J, Li D, Yang J, Chang L, Zhang R, Li J. CRISPR/Cas9-mediated epigenetic editing tool: An optimized strategy for targeting de novo DNA methylation with stable status via homology directed repair pathway. Biochimie 2022; 202:190-205. [DOI: 10.1016/j.biochi.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022]
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9
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Zimmer-Bensch G, Zempel H. DNA Methylation in Genetic and Sporadic Forms of Neurodegeneration: Lessons from Alzheimer's, Related Tauopathies and Genetic Tauopathies. Cells 2021; 10:3064. [PMID: 34831288 PMCID: PMC8624300 DOI: 10.3390/cells10113064] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022] Open
Abstract
Genetic and sporadic forms of tauopathies, the most prevalent of which is Alzheimer's Disease, are a scourge of the aging society, and in the case of genetic forms, can also affect children and young adults. All tauopathies share ectopic expression, mislocalization, or aggregation of the microtubule associated protein TAU, encoded by the MAPT gene. As TAU is a neuronal protein widely expressed in the CNS, the overwhelming majority of tauopathies are neurological disorders. They are characterized by cognitive dysfunction often leading to dementia, and are frequently accompanied by movement abnormalities such as parkinsonism. Tauopathies can lead to severe neurological deficits and premature death. For some tauopathies there is a clear genetic cause and/or an epigenetic contribution. However, for several others the disease etiology is unclear, with few tauopathies being environmentally triggered. Here, we review current knowledge of tauopathies listing known genetic and important sporadic forms of these disease. Further, we discuss how DNA methylation as a major epigenetic mechanism emerges to be involved in the disease pathophysiology of Alzheimer's, and related genetic and non-genetic tauopathies. Finally, we debate the application of epigenetic signatures in peripheral blood samples as diagnostic tools and usages of epigenetic therapy strategies for these diseases.
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Affiliation(s)
- Geraldine Zimmer-Bensch
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, 52074 Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, 52074 Aachen, Germany
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
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10
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Sapozhnikov DM, Szyf M. Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9. Nat Commun 2021; 12:5711. [PMID: 34588447 PMCID: PMC8481236 DOI: 10.1038/s41467-021-25991-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
Despite four decades of research to support the association between DNA methylation and gene expression, the causality of this relationship remains unresolved. Here, we reaffirm that experimental confounds preclude resolution of this question with existing strategies, including recently developed CRISPR/dCas9 and TET-based epigenetic editors. Instead, we demonstrate a highly effective method using only nuclease-dead Cas9 and guide RNA to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzyme, thereby enabling the examination of the role of DNA demethylation per se in living cells, with no evidence of off-target activity. Using this method, we probe a small number of inducible promoters and find the effect of DNA demethylation to be small, while demethylation of CpG-rich FMR1 produces larger changes in gene expression. This method could be used to reveal the extent and nature of the contribution of DNA methylation to gene regulation.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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11
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Epigenome Chaos: Stochastic and Deterministic DNA Methylation Events Drive Cancer Evolution. Cancers (Basel) 2021; 13:cancers13081800. [PMID: 33918773 PMCID: PMC8069666 DOI: 10.3390/cancers13081800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Cancer is a group of diseases characterized by abnormal cell growth with a high potential to invade other tissues. Genetic abnormalities and epigenetic alterations found in tumors can be due to high levels of DNA damage and repair. These can be transmitted to daughter cells, which assuming other alterations as well, will generate heterogeneous and complex populations. Deciphering this complexity represents a central point for understanding the molecular mechanisms of cancer and its therapy. Here, we summarize the genomic and epigenomic events that occur in cancer and discuss novel approaches to analyze the epigenetic complexity of cancer cell populations. Abstract Cancer evolution is associated with genomic instability and epigenetic alterations, which contribute to the inter and intra tumor heterogeneity, making genetic markers not accurate to monitor tumor evolution. Epigenetic changes, aberrant DNA methylation and modifications of chromatin proteins, determine the “epigenome chaos”, which means that the changes of epigenetic traits are randomly generated, but strongly selected by deterministic events. Disordered changes of DNA methylation profiles are the hallmarks of all cancer types, but it is not clear if aberrant methylation is the cause or the consequence of cancer evolution. Critical points to address are the profound epigenetic intra- and inter-tumor heterogeneity and the nature of the heterogeneity of the methylation patterns in each single cell in the tumor population. To analyze the methylation heterogeneity of tumors, new technological and informatic tools have been developed. This review discusses the state of the art of DNA methylation analysis and new approaches to reduce or solve the complexity of methylated alleles in DNA or cell populations.
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Chen F, Zhang Y, Creighton CJ. Systematic identification of non-coding somatic single nucleotide variants associated with altered transcription and DNA methylation in adult and pediatric cancers. NAR Cancer 2021; 3:zcab001. [PMID: 33554123 PMCID: PMC7849833 DOI: 10.1093/narcan/zcab001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 01/12/2023] Open
Abstract
Whole-genome sequencing combined with transcriptomics can reveal impactful non-coding single nucleotide variants (SNVs) in cancer. Here, we developed an integrative analytical approach that, as a first step, identifies genes altered in expression or DNA methylation in association with nearby somatic SNVs, in contrast to alternative approaches that first identify mutational hotspots. Using genomic datasets from the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium and the Children's Brain Tumor Tissue Consortium (CBTTC), we identified hundreds of genes and associated CpG islands for which the nearby presence of a non-coding somatic SNV recurrently associated with altered expression or DNA methylation, respectively. Genomic regions upstream or downstream of genes, gene introns and gene untranslated regions were all involved. The PCAWG adult cancer cohort yielded different significant SNV-expression associations from the CBTTC pediatric brain tumor cohort. The SNV-expression associations involved a wide range of cancer types and histologies, as well as potential gain or loss of transcription factor binding sites. Notable genes with SNV-associated increased expression include TERT, COPS3, POLE2 and HDAC2—involving multiple cancer types—MYC, BCL2, PIM1 and IGLL5—involving lymphomas—and CYHR1—involving pediatric low-grade gliomas. Non-coding somatic SNVs show a major role in shaping the cancer transcriptome, not limited to mutational hotspots.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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Pezone A, Tramontano A, Scala G, Cuomo M, Riccio P, De Nicola S, Porcellini A, Chiariotti L, Avvedimento E. Tracing and tracking epiallele families in complex DNA populations. NAR Genom Bioinform 2020; 2:lqaa096. [PMID: 33575640 PMCID: PMC7671405 DOI: 10.1093/nargab/lqaa096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/14/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a stable epigenetic modification, extremely polymorphic and driven by stochastic and deterministic events. Most of the current techniques used to analyse methylated sequences identify methylated cytosines (mCpGs) at a single-nucleotide level and compute the average methylation of CpGs in the population of molecules. Stable epialleles, i.e. CpG strings with the same DNA sequence containing a discrete linear succession of phased methylated/non-methylated CpGs in the same DNA molecule, cannot be identified due to the heterogeneity of the 5'-3' ends of the molecules. Moreover, these are diluted by random unstable methylated CpGs and escape detection. We present here MethCoresProfiler, an R-based tool that provides a simple method to extract and identify combinations of methylated phased CpGs shared by all components of epiallele families in complex DNA populations. The methylated cores are stable over time, evolve by acquiring or losing new methyl sites and, ultimately, display high information content and low stochasticity. We have validated this method by identifying and tracing rare epialleles and their families in synthetic or in vivo complex cell populations derived from mouse brain areas and cells during postnatal differentiation. MethCoresProfiler is written in R language. The software is freely available at https://github.com/84AP/MethCoresProfiler/.
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Affiliation(s)
- Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Alfonso Tramontano
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy
| | - Giovanni Scala
- Department of Biology, Università Federico II Napoli, 80126 Naples, Italy
| | - Mariella Cuomo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Patrizia Riccio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Sergio De Nicola
- Department of Physics, Università Federico II Napoli, 80126 Naples, Italy
| | - Antonio Porcellini
- Department of Biology, Università Federico II Napoli, 80126 Naples, Italy
| | - Lorenzo Chiariotti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Enrico V Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
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Wang WJ, Li LY, Cui JW. Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis. Epigenetics Chromatin 2020; 13:49. [PMID: 33168103 PMCID: PMC7654176 DOI: 10.1186/s13072-020-00371-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
With the rapid development of next-generation sequencing technology, chromosome structural variation has gradually gained increased clinical significance in tumorigenesis. However, the molecular mechanism(s) underlying this structural variation remain poorly understood. A search of the literature shows that a three-dimensional chromatin state plays a vital role in inducing structural variation and in the gene expression profiles in tumorigenesis. Structural variants may result in changes in copy number or deletions of coding sequences, as well as the perturbation of structural chromatin features, especially topological domains, and disruption of interactions between genes and their regulatory elements. This review focuses recent work aiming at elucidating how structural variations develop and misregulate oncogenes and tumor suppressors, to provide general insights into tumor formation mechanisms and to provide potential targets for future anticancer therapies.
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Affiliation(s)
- Wen-Jun Wang
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China
| | - Ling-Yu Li
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China
| | - Jiu-Wei Cui
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China.
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Tramontano A, Boffo FL, Russo G, De Rosa M, Iodice I, Pezone A. Methylation of the Suppressor Gene p16INK4a: Mechanism and Consequences. Biomolecules 2020; 10:biom10030446. [PMID: 32183138 PMCID: PMC7175352 DOI: 10.3390/biom10030446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
Tumor suppressor genes in the CDKN2A/B locus (p15INK4b, p16INK4a, and p14ARF) function as biological barriers to transformation and are the most frequently silenced or deleted genes in human cancers. This gene silencing frequently occurs due to DNA methylation of the promoter regions, although the underlying mechanism is currently unknown. We present evidence that methylation of p16INK4a promoter is associated with DNA damage caused by interference between transcription and replication processes. Inhibition of replication or transcription significantly reduces the DNA damage and CpGs methylation of the p16INK4a promoter. We conclude that de novo methylation of the promoter regions is dependent on local DNA damage. DNA methylation reduces the expression of p16INK4a and ultimately removes this barrier to oncogene-induced senescence.
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Affiliation(s)
- Alfonso Tramontano
- Department of Precision Medicine University of Campania “L. Vanvitelli”, 80131 Naples, Italy;
| | - Francesca Ludovica Boffo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Giusi Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Mariarosaria De Rosa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Ilaria Iodice
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Antonio Pezone
- Department of Precision Medicine University of Campania “L. Vanvitelli”, 80131 Naples, Italy;
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
- Correspondence: or ; Tel.: +39-0817-463-614
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Association of glomerular DNA damage and DNA methylation with one-year eGFR decline in IgA nephropathy. Sci Rep 2020; 10:237. [PMID: 31937846 PMCID: PMC6959244 DOI: 10.1038/s41598-019-57140-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/03/2019] [Indexed: 12/03/2022] Open
Abstract
Accumulation of DNA double-strand breaks (DSBs) is linked to aging and age-related diseases. We recently reported the possible association of DNA DSBs with altered DNA methylation in murine models of kidney disease. However, DSBs and DNA methylation in human kidneys was not adequately investigated. This study was a cross-sectional observational study to evaluate the glomerular DNA DSB marker γH2AX and phosphorylated Ataxia Telangiectasia Mutated (pATM), and the DNA methylation marker 5-methyl cytosine (5mC) by immunostaining, and investigated the association with pathological features and clinical parameters in 29 patients with IgA nephropathy. To evaluate podocyte DSBs, quantitative long-distance PCR of the nephrin gene using laser-microdissected glomerular samples and immunofluorescent double-staining with WT1 and γH2AX were performed. Glomerular γH2AX level was associated with glomerular DNA methylation level in IgA nephropathy. Podocytopathic features were associated with increased number of WT1(+)γH2AX(+) cells and reduced amount of PCR product of the nephrin gene, which indicate podocyte DNA DSBs. Glomerular γH2AX and 5mC levels were significantly associated with the slope of eGFR decline over one year in IgA nephropathy patients using multiple regression analysis adjusted for age, baseline eGFR, amount of proteinuria at biopsy and immunosuppressive therapy after biopsy. Glomerular γH2AX level was associated with DNA methylation level, both of which may be a good predictor of renal outcome in IgA nephropathy.
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Cali CP, Park DS, Lee EB. Targeted DNA methylation of neurodegenerative disease genes via homology directed repair. Nucleic Acids Res 2019; 47:11609-11622. [PMID: 31680172 PMCID: PMC7145628 DOI: 10.1093/nar/gkz979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/18/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022] Open
Abstract
DNA methyltransferases (DNMTs) are thought to be involved in the cellular response to DNA damage, thus linking DNA repair mechanisms with DNA methylation. In this study we present Homology Assisted Repair Dependent Epigenetic eNgineering (HARDEN), a novel method of targeted DNA methylation that utilizes endogenous DNA double strand break repair pathways. This method allows for stable targeted DNA methylation through the process of homology directed repair (HDR) via an in vitro methylated exogenous repair template. We demonstrate that HARDEN can be applied to the neurodegenerative disease genes C9orf72 and APP, and methylation can be induced via HDR with both single and double stranded methylated repair templates. HARDEN allows for higher targeted DNA methylation levels than a dCas9-DNMT3a fusion protein construct at C9orf72, and genome-wide methylation analysis reveals no significant off-target methylation changes when inducing methylation via HARDEN, whereas the dCas9-DNMT3a fusion construct causes global off-target methylation. HARDEN is applied to generate a patient derived iPSC model of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) that recapitulates DNA methylation patterns seen in patients, demonstrating that DNA methylation of the 5' regulatory region directly reduces C9orf72 expression and increases histone H3K9 tri-methylation levels.
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Affiliation(s)
- Christopher P Cali
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel S Park
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol 2019; 20:209. [PMID: 31610796 PMCID: PMC6792267 DOI: 10.1186/s13059-019-1818-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored. Results By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration. Conclusion Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lixing Yang
- Ben May Department for Cancer Research and Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Melanie Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angela Hadjipanayis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angeliki Pantazi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Christopher A Bristow
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Harshad S Mahadeshwar
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jiabin Tang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sahil Seth
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Semin Lee
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaojia Ren
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xingzhi Song
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huandong Sun
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lovelace J Luquette
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ruibin Xi
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lynda Chin
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Eli and Edythe L. Broad Institute of Massachusetts Institute Of Technology and Harvard University, Cambridge, MA, 02142, USA
| | | | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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Bai G, Song J, Yuan Y, Chen Z, Tian Y, Yin X, Niu Y, Liu J. Systematic analysis of differentially methylated expressed genes and site-specific methylation as potential prognostic markers in head and neck cancer. J Cell Physiol 2019; 234:22687-22702. [PMID: 31131446 PMCID: PMC6772109 DOI: 10.1002/jcp.28835] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Head and neck cancer (HNC) remains one of the most malignant tumors with a significantly high mortality. DNA methylation exerts a vital role in the prognosis of HNC. In this study, we try to screen abnormal differential methylation genes (DMGs) and pathways in Head-Neck Squamous Cell Carcinoma via integral bioinformatics analysis. Data of gene expression microarrays and gene methylation microarrays were obtained from the Cancer Genome Atlas database. Aberrant DMGs were identified by the R Limma package. We conducted the Cox regression analysis to select the prognostic aberrant DMGs and site-specific methylation. Five aberrant DMGs were recognized that significantly correlated with overall survival. The prognostic model was constructed based on five DMGs (PAX9, STK33, GPR150, INSM1, and EPHX3). The five DMG models acted as prognostic biomarkers for HNC. The area under the curve based on the five DMGs predicting 5-year survival is 0.665. Moreover, the correlation between the DMGs/site-specific methylation and gene expression was also explored. The findings demonstrated that the five DMGs can be used as independent prognostic biomarkers for predicting the prognosis of patients with HNC. Our study might lay the groundwork for further mechanism exploration in HNC and may help identify diagnostic biomarkers for early stage HNC.
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Affiliation(s)
- Guohui Bai
- Zunyi Medical University, Zunyi, Guizhou, China.,Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Guizhou, China
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guizhou, China
| | - Yiwen Yuan
- Guizhou Medical Univerisity, Guizhou, China
| | - Zhu Chen
- Guiyang Hospital of Stomatology, Guizhou, China
| | - Yuan Tian
- Stomatology Colledge Affiliated to Zunyi Medical University, Zunyi, Guizhou, China
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guizhou, China
| | - Yuming Niu
- Department of Stomatology and Center for Evidence-Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jianguo Liu
- Zunyi Medical University, Zunyi, Guizhou, China.,Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Guizhou, China
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