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Coppedè F. DNA methylation in amyotrophic lateral sclerosis: where do we stand and what is next? Epigenomics 2024; 16:1185-1196. [PMID: 39258797 DOI: 10.1080/17501911.2024.2394380] [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: 05/28/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Genes involved in immune response, inflammation and metabolism are among those most likely affected by changes in DNA methylation (DNAm) and expression levels in amyotrophic lateral sclerosis (ALS) tissues. Unfortunately, it is still largely unclear whether any of these changes precede the onset of disease symptoms or whether most of them are the result of the muscular and metabolic changes that follow symptoms onset. In this article the author discusses the strengths and limitations of the available studies of DNAm in ALS and provides some suggestions on what, in his opinion, could be done in the near future for a better understanding of the DNAm changes occurring in ALS, their link with environmental exposures and their potential clinical utility.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Pisa, 56126, Italy
- Interdepartmental Research Center of Biology & Pathology of Aging, University of Pisa, Pisa, 56126, Italy
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2
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Faheem A, Masud R, Nasir R, Awan ZK, Nasir HA, Khan ZK, Fayyaz H, Raza SI. Exome sequencing revealed variants in SGCA and SIL1 genes underlying limb girdle muscular dystrophy and Marinesco-Sjögren syndrome patients. Mol Biol Rep 2024; 51:853. [PMID: 39060875 DOI: 10.1007/s11033-024-09746-5] [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: 03/19/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND Inherited neuromuscular (NMD) and neurodegenerative diseases (NDD) belong to two distinct categories that disturb different components of the nervous system, leading to a variety of different symptoms and clinical manifestations. Both NMD and NDD are a heterogeneous group of genetic conditions. Genetic variations in the SGCA and SIL1 genes have been implicated in causing Limb Girdle Muscular Dystrophy (LGMD), a type of neuromuscular disorder, and Marinesco-Sjögren Syndrome (MSS) which is a neurodegenerative disorder. METHODS In the present study, we have investigated four patients presenting LGMD and five patients with MSS features. After collecting detailed clinical and family history, necessary laboratory investigations, including estimation of a skeletal muscle marker enzyme serum creatine kinase (CK), nerve conduction study (NCS), electromyography (EMG), echocardiography (Echo), Magnetic resonance imaging (MRI -brain), CT-brain and X-rays were performed. Whole exome followed by Sanger sequencing was employed to search for the disease-causing variants. RESULTS Physical examination in LGMD patients revealed poor muscle tone and facing difficulty in straightening up from the floor. Clinical history revealed frequent falls and strenuousness in climbing stairs. They started toe-walking in early childhood. Laboratory investigations confirmed elevated CK levels and abnormal NCS and EMG. The MSS patients showed abnormalities in gate and jerking movement, abnormal speech, and strabismus with cataract. MRI-brain showed cerebral atrophy in some MSS patients with elevated CK levels. Whole exome sequencing revealed a nonsense variant [c.C574T, p.(Arg192*)] in the SGCA gene and a frameshift [c.936dupG, p.(Leu313AlaFs*39)] in the SIL1 gene in LGMD and MSS patients, respectively. CONCLUSION Our study emphasizes the significance of integrating clinical and genetic analyses for precise diagnosis and tailored management strategies in inherited NMD and NDD disorders. To the best of our knowledge, this is the first study documenting SGCA and SIL1 recurrent variants in subcontinent populations with few rare clinical features. The recurrent mutations expanding the global understanding of the mutation's geographic and ethnic distribution and contributing valuable epidemiological data. The study will facilitate genetic counseling for families experiencing similar clinical features, both within Pakistani populations and in other regions.
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Affiliation(s)
- Ali Faheem
- Department of Biochemistry, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Rizwan Masud
- Department of Physiology, Rai Medical College, Sargodha, Punjab, Pakistan
| | - Rabea Nasir
- Department of Physiology, M. Islam Medical College, Gujranwala, Pakistan
| | - Zeeshan Khalid Awan
- Department of Pathology, Rawal Institute of Health Sciences, Islamabad, Pakistan
| | - Hammad Ali Nasir
- Department of Paediatrics, Khalida Safdar Memorial Hospital, Rawalpindi, Pakistan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zara Khalid Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Department of Biochemistry, Shaheed Zulfiqar Ali Bhutto Medical University,, Rawal Institute of Health Sciences, Islamabad, Pakistan
| | - Hajra Fayyaz
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
- Department of Biochemistry, HBS Medical College, Islamabad, Pakistan.
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3
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Bittel AJ, Chen YW. DNA Methylation in the Adaptive Response to Exercise. Sports Med 2024; 54:1419-1458. [PMID: 38561436 DOI: 10.1007/s40279-024-02011-6] [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] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Emerging evidence published over the past decade has highlighted the role of DNA methylation in skeletal muscle function and health, including as an epigenetic transducer of the adaptive response to exercise. In this review, we aim to synthesize the latest findings in this field to highlight: (1) the shifting understanding of the genomic localization of altered DNA methylation in response to acute and chronic aerobic and resistance exercise in skeletal muscle (e.g., promoter, gene bodies, enhancers, intergenic regions, un-annotated regions, and genome-wide methylation); (2) how these global/regional methylation changes relate to transcriptional activity following exercise; and (3) the factors (e.g., individual demographic or genetic features, dietary, training history, exercise parameters, local epigenetic characteristics, circulating hormones) demonstrated to alter both the pattern of DNA methylation after exercise, and the relationship between DNA methylation and gene expression. Finally, we discuss the changes in non-CpG methylation and 5-hydroxymethylation after exercise, as well as the importance of emerging single-cell analyses to future studies-areas of increasing focus in the field of epigenetics. We anticipate that this review will help generate a framework for clinicians and researchers to begin developing and testing exercise interventions designed to generate targeted changes in DNA methylation as part of a personalized exercise regimen.
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Affiliation(s)
- Adam J Bittel
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.
| | - Yi-Wen Chen
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Science, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Integrative Systems Biology, Institute for Biomedical Sciences, The George Washington University, 2121 I St NW, Washington, DC, 20052, USA
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4
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Hu S, Feng L, Yang Z, Fan X, Gao H, Yang T. A recognition of exosomes as regulators of epigenetic mechanisms in central nervous system diseases. Front Mol Neurosci 2024; 17:1370449. [PMID: 38528957 PMCID: PMC10962328 DOI: 10.3389/fnmol.2024.1370449] [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: 01/14/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
Exosomes, vesicular structures originating from cells, participate in the conveyance of proteins and nucleic acids. Presently, the centrality of epigenetic modifications in neurological disorders is widely acknowledged. Exosomes exert influence over various epigenetic phenomena, thereby modulating post-transcriptional regulatory processes contingent upon their constituent makeup. Consequently, the heightened attention directed toward exosomes as instigators of epigenetic alterations has burgeoned in recent years. Notably, exosomes serve as vehicles for delivering methyltransferases to recipient cells. More significantly, non-coding RNAs, particularly microRNAs (miRNAs), represent pivotal contents within exosomes, wielding the capacity to influence the expression of diverse factors within the cerebral milieu. The transfer of these exosomal contents amidst brain cells, encompassing neuronal cells and microglia, assumes a critical role in the genesis and progression of neurological disorders, also, this role is not limited to neurological disorders, it may deal with any human disease, such as cancer, and cardiovascular diseases. This review will concentrate on elucidating the regulation of exosome-induced epigenetic events and its subsequent ramifications for neurological diseases. A more profound comprehension of the involvement of exosome-mediated epigenetic regulation in neurological disorders contributes to a heightened awareness of the etiology and advancement of cerebral afflictions.
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Affiliation(s)
- Shunxin Hu
- Shandong First Medical University, Tai'an, China
| | - Lei Feng
- Jining First People's Hospital, Jining, China
| | | | - Xuechen Fan
- Jining First People's Hospital, Jining, China
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Megalizzi D, Trastulli G, Caputo V, Colantoni L, Caltagirone C, Strafella C, Cascella R, Giardina E. Epigenetic profiling of the D4Z4 locus: Optimization of the protocol for studying DNA methylation at single CpG site level. Electrophoresis 2023; 44:1588-1594. [PMID: 37565369 DOI: 10.1002/elps.202300058] [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: 03/21/2023] [Revised: 06/27/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
The alteration of epigenetic modifications, including DNA methylation, can contribute to the etiopathogenesis and progression of many diseases. Among them, facioscapulohumeral dystrophy (FSHD) is a muscular disorder characterized by the loss of repressive epigenetic features affecting the D4Z4 locus (4q35). As a consequence, these alterations are responsible for DNA hypomethylation and a transcriptional-active chromatin conformation change that, in turn, lead to the aberrant expression of DUX4 in muscle cells. In the present study, methylation levels of 29 CpG sites of the DR1 region (within each repeat unit of the D4Z4 macrosatellite) were assessed on 335 subjects by employing primers designed for enhancing the performance of the assay. First, the DR1 original primers were optimized by adding M13 oligonucleotide tails. Moreover, the DR1 reverse primer was replaced with a degenerate one. As a result, the protocol optimization allowed a better sequencing resolution and a more accurate evaluation of DR1 methylation levels. Moreover, the assessment of the repeatability of measurements proved the reliability and robustness of the assay. The optimized protocol emerges as an excellent method to detect methylation levels compatible with FSHD.
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Affiliation(s)
- Domenica Megalizzi
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Giulia Trastulli
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Emiliano Giardina
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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Coppedè F. Special Issue "Genetics and Epigenetics of Neuromuscular Diseases". Genes (Basel) 2023; 14:1522. [PMID: 37628574 PMCID: PMC10454685 DOI: 10.3390/genes14081522] [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: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 08/27/2023] Open
Abstract
Neuromuscular disorders (NMDs) include several hereditary or acquired conditions that impair the neuromuscular system and muscle function [...].
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
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Coppedè F, Franzago M, Giardina E, Nigro CL, Matullo G, Moltrasio C, Nacmias B, Pileggi S, Sirchia SM, Stoccoro A, Storlazzi CT, Stuppia L, Tricarico R, Merla G. A perspective on diet, epigenetics and complex diseases: where is the field headed next? Epigenomics 2022; 14:1281-1304. [DOI: 10.2217/epi-2022-0239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dietary factors can regulate epigenetic processes during life, modulating the intracellular pools of metabolites necessary for epigenetic reactions and regulating the activity of epigenetic enzymes. Their effects are strong during the prenatal life, when epigenetic patterns are written, allowing organogenesis. However, interactions between diet and the epigenome continue throughout life and likely contribute to the onset and progression of various complex diseases. Here, we review the contribution of dietary factors to the epigenetic changes observed in complex diseases and suggest future steps to better address this issue, focusing on neurobehavioral, neuropsychiatric and neurodegenerative disorders, cardiovascular diseases, obesity and Type 2 diabetes, cancer and inflammatory skin diseases.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Pisa, 56126, Italy
| | - Marica Franzago
- Department of Medicine & Aging, School of Medicine & Health Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, 66100, Italy
- Center for Advanced Studies & Technology, “G. d'Annunzio” University of Chieti–Pescara, Chieti, 66100, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, 00179, Italy
- Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome, 00133, Italy
| | | | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, 10126, Italy
| | - Chiara Moltrasio
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
- Department of Medical Surgical & Health Sciences, University of Trieste, Trieste, 34137, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research & Child Health, University of Florence, Florence, 50139, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, 50143, Italy
| | - Silvana Pileggi
- Department of Health Sciences, Medical Genetics, University of Milan, Milan, 20142, Italy
| | - Silvia Maria Sirchia
- Department of Health Sciences, Medical Genetics, University of Milan, Milan, 20142, Italy
| | - Andrea Stoccoro
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Pisa, 56126, Italy
| | | | - Liborio Stuppia
- Center for Advanced Studies & Technology, “G. d'Annunzio” University of Chieti–Pescara, Chieti, 66100, Italy
- Department of Psychological, Health & Territorial Sciences, School of Medicine & Health Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, 66100, Italy
| | - Rossella Tricarico
- Department of Biology & Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, 71013, Italy
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
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8
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Ruffo P, De Amicis F, Giardina E, Conforti FL. Long-noncoding RNAs as epigenetic regulators in neurodegenerative diseases. Neural Regen Res 2022; 18:1243-1248. [PMID: 36453400 PMCID: PMC9838156 DOI: 10.4103/1673-5374.358615] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The growing and rapid development of high-throughput sequencing technologies have allowed a greater understanding of the mechanisms underlying gene expression regulation. Editing the epigenome and epitranscriptome directs the fate of the transcript influencing the functional outcome of each mRNA. In this context, non-coding RNAs play a decisive role in addressing the expression regulation at the gene and chromosomal levels. Long-noncoding RNAs, consisting of more than 200 nucleotides, have been shown to act as epigenetic regulators in several key molecular processes involving neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Long-noncoding RNAs are abundantly expressed in the central nervous system, suggesting that their deregulation could trigger neuronal degeneration through RNA modifications. The evaluation of their diagnostic significance and therapeutic potential could lead to new treatments for these diseases for which there is no cure.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Francesca De Amicis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy,Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy,Correspondence to: Francesca Luisa Conforti, .
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9
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Coppedè F, Cereda C, Lintas C, Stoccoro A. Editorial: Epigenetics of Neurodevelopmental, Neuromuscular and Neurodegenerative Disorders. Front Mol Neurosci 2022; 15:948827. [PMID: 35754706 PMCID: PMC9231183 DOI: 10.3389/fnmol.2022.948827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Cristina Cereda
- Department of Women, Mothers and Neonatal Care, Children's Hospital V. Buzzi, Milan, Italy
| | - Carla Lintas
- Laboratory of Medical Genetics, University Campus Bio-Medico of Rome, Rome, Italy
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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10
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Dobrowolny G, Scicchitano BM. The Role of Skeletal Muscle in Neuromuscular Diseases: From Cellular and Molecular Players to Therapeutic Interventions. Cells 2022; 11:cells11071207. [PMID: 35406771 PMCID: PMC8997919 DOI: 10.3390/cells11071207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- Gabriella Dobrowolny
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, DAHFMO-Unità di Istologia ed Embriologia Medica, Sapienza Università di Roma, 00161 Roma, Italy
- Correspondence: (G.D.); (B.M.S.)
| | - Bianca Maria Scicchitano
- Sezione di Istologia ed Embriologia, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
- Correspondence: (G.D.); (B.M.S.)
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Johnson MA, Klickstein JA, Khanna R, Gou Y, Raman M. The Cure VCP Scientific Conference 2021: Molecular and clinical insights into neurodegeneration and myopathy linked to multisystem proteinopathy-1 (MSP-1). Neurobiol Dis 2022; 169:105722. [PMID: 35405261 PMCID: PMC9169230 DOI: 10.1016/j.nbd.2022.105722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/08/2022] [Accepted: 04/05/2022] [Indexed: 12/17/2022] Open
Abstract
The 2021 VCP Scientific Conference took place virtually from September 9–10, 2021. This conference, planned and organized by the nonprofit patient advocacy group Cure VCP Disease, Inc. (https://www.curevcp.org), was the first VCP focused meeting since the 215th ENMC International Workshop VCP-related multi-system proteinopathy in 2016 (Evangelista et al., 2016). Mutations in VCP cause a complex and heterogenous disease termed inclusion body myopathy (IBM) with Paget’s disease of the bone (PDB) and frontotemporal dementia (FTD) (IBMPFD), or multisystem proteinopathy 1 (MSP-1) Kimonis (n.d.), Kovach et al. (2001), Kimonis et al. (2000). In addition, VCP mutations also cause other age-related neurodegenerative disorders including amyptrophic lateral sclerosis (ALS), Parkinsonism, Charcot-Marie type II-B, vacuolar tauopathy among others (Korb et al., 2022). The objectives of this conference were as follows: (1) to provide a forum that facilitates sharing of published and unpublished information on physiological roles of p97/VCP, and on how mutations of VCP lead to diseases; (2) to bolster understanding of mechanisms involved in p97/VCP-relevant diseases and to enable identification of therapeutics to treat these conditions; (3) to identify gaps and barriers of further discoveries and translational research in the p97/VCP field; (4) to set a concrete basic and translational research agenda for future studies including crucial discussions on biomarker discoveries and patient longitudinal studies to facilitate near-term clinical trials; (5) to accelerate cross-disciplinary research collaborations among p97/VCP researchers; (6) to enable attendees to learn about new tools and reagents with the potential to facilitate p97/VCP research; (7) to assist trainees in propelling their research and to foster mentorship from leaders in the field; and (8) to promote diversity and inclusion of under-represented minorities in p97/VCP research as diversity is critically important for strong scientific research. Given the range of topics, the VCP Scientific Conference brought together over one hundred and forty individuals representing a diverse group of research scientists, trainees, medical practitioners, industry representatives, and patient advocates. Twenty-five institutions with individuals from thirteen countries attended this virtual meeting. In this report, we summarize the major topics presented at this conference by a range of experts.
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Affiliation(s)
- Michelle A Johnson
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Jacob A Klickstein
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Richa Khanna
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Yunzi Gou
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, United States of America
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States of America.
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12
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Coppede F. Targeting the epigenome to treat neurodegenerative diseases or delay their onset: a perspective. Neural Regen Res 2022; 17:1745-1747. [PMID: 35017429 PMCID: PMC8820689 DOI: 10.4103/1673-5374.332145] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Fabio Coppede
- Department of Translational Research and of New Surgical and Medical Technologies, Interdepartmental Research Center Nutrafood "Nutraceuticals and Food for Health", University of Pisa, Pisa, Italy
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13
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Visconti VV, Centofanti F, Fittipaldi S, Macrì E, Novelli G, Botta A. Epigenetics of Myotonic Dystrophies: A Minireview. Int J Mol Sci 2021; 22:ijms222212594. [PMID: 34830473 PMCID: PMC8623789 DOI: 10.3390/ijms222212594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 12/14/2022] Open
Abstract
Myotonic dystrophy type 1 and 2 (DM1 and DM2) are two multisystemic autosomal dominant disorders with clinical and genetic similarities. The prevailing paradigm for DMs is that they are mediated by an in trans toxic RNA mechanism, triggered by untranslated CTG and CCTG repeat expansions in the DMPK and CNBP genes for DM1 and DM2, respectively. Nevertheless, increasing evidences suggest that epigenetics can also play a role in the pathogenesis of both diseases. In this review, we discuss the available information on epigenetic mechanisms that could contribute to the DMs outcome and progression. Changes in DNA cytosine methylation, chromatin remodeling and expression of regulatory noncoding RNAs are described, with the intent of depicting an epigenetic signature of DMs. Epigenetic biomarkers have a strong potential for clinical application since they could be used as targets for therapeutic interventions avoiding changes in DNA sequences. Moreover, understanding their clinical significance may serve as a diagnostic indicator in genetic counselling in order to improve genotype–phenotype correlations in DM patients.
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Affiliation(s)
- Virginia Veronica Visconti
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Federica Centofanti
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Simona Fittipaldi
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Elisa Macrì
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
- IRCCS (Institute for Treatment and Research) Neuromed, 86077 Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Annalisa Botta
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
- Correspondence: ; Tel.: +39-6-7259-6078
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Morales F, Corrales E, Zhang B, Vásquez M, Santamaría-Ulloa C, Quesada H, Sirito M, Estecio MR, Monckton DG, Krahe R. Myotonic dystrophy type 1 (DM1) clinical sub-types and CTCF site methylation status flanking the CTG expansion are mutant allele length-dependent. Hum Mol Genet 2021; 31:262-274. [PMID: 34432028 DOI: 10.1093/hmg/ddab243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a complex disease with a wide spectrum of symptoms. The exact relationship between mutant CTG repeat expansion size and clinical outcome remains unclear. DM1 congenital patients (CDM) inherit the largest expanded alleles, which are associated with abnormal and increased DNA methylation flanking the CTG repeat. However, DNA methylation at the DMPK locus remains understudied. Its relationship to DM1 clinical subtypes, expansion size and age-at-onset is not yet completely understood. Using pyrosequencing-based methylation analysis on 225 blood DNA samples from Costa Rican DM1 patients, we determined that the size of the estimated progenitor allele length (ePAL) is not only a good discriminator between CDM and non-CDM cases (with an estimated threshold at 653 CTG repeats), but also for all DM1 clinical subtypes. Secondly, increased methylation at both CTCF sites upstream and downstream of the expansion was almost exclusively present in CDM cases. Thirdly, levels of abnormal methylation were associated with clinical subtype, age and ePAL, with strong correlations between these variables. Fourthly, both ePAL and the intergenerational expansion size were significantly associated with methylation status. Finally, methylation status was associated with ePAL and maternal inheritance, with almost exclusively maternal transmission of CDM. In conclusion, increased DNA methylation at the CTCF sites flanking the DM1 expansion could be linked to ePAL, and both increased methylation and the ePAL could be considered biomarkers for the CDM phenotype.
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Affiliation(s)
- Fernando Morales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Eyleen Corrales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Baili Zhang
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Melissa Vásquez
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Carolina Santamaría-Ulloa
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Hazel Quesada
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Mario Sirito
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Marcos R Estecio
- Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Ralf Krahe
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
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15
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Dobrowolny G, Barbiera A, Sica G, Scicchitano BM. Age-Related Alterations at Neuromuscular Junction: Role of Oxidative Stress and Epigenetic Modifications. Cells 2021; 10:1307. [PMID: 34074012 PMCID: PMC8225025 DOI: 10.3390/cells10061307] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/19/2021] [Accepted: 05/22/2021] [Indexed: 12/11/2022] Open
Abstract
With advancing aging, a decline in physical abilities occurs, leading to reduced mobility and loss of independence. Although many factors contribute to the physio-pathological effects of aging, an important event seems to be related to the compromised integrity of the neuromuscular system, which connects the brain and skeletal muscles via motoneurons and the neuromuscular junctions (NMJs). NMJs undergo severe functional, morphological, and molecular alterations during aging and ultimately degenerate. The effect of this decline is an inexorable decrease in skeletal muscle mass and strength, a condition generally known as sarcopenia. Moreover, several studies have highlighted how the age-related alteration of reactive oxygen species (ROS) homeostasis can contribute to changes in the neuromuscular junction morphology and stability, leading to the reduction in fiber number and innervation. Increasing evidence supports the involvement of epigenetic modifications in age-dependent alterations of the NMJ. In particular, DNA methylation, histone modifications, and miRNA-dependent gene expression represent the major epigenetic mechanisms that play a crucial role in NMJ remodeling. It is established that environmental and lifestyle factors, such as physical exercise and nutrition that are susceptible to change during aging, can modulate epigenetic phenomena and attenuate the age-related NMJs changes. This review aims to highlight the recent epigenetic findings related to the NMJ dysregulation during aging and the role of physical activity and nutrition as possible interventions to attenuate or delay the age-related decline in the neuromuscular system.
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Affiliation(s)
- Gabriella Dobrowolny
- Department of Anatomy, Histology, Forensic Medicine and Orthopaedics (DAHFMO)-Unit of Histology and Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy;
| | - Alessandra Barbiera
- Department of Life Sciences and Public Health, Histology and Embryology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (A.B.); (G.S.)
| | - Gigliola Sica
- Department of Life Sciences and Public Health, Histology and Embryology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (A.B.); (G.S.)
| | - Bianca Maria Scicchitano
- Department of Life Sciences and Public Health, Histology and Embryology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (A.B.); (G.S.)
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