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Javdani-Mallak A, Salahshoori I. Environmental pollutants and exosomes: A new paradigm in environmental health and disease. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171774. [PMID: 38508246 DOI: 10.1016/j.scitotenv.2024.171774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/16/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
This study investigates the intricate interplay between environmental pollutants and exosomes, shedding light on a novel paradigm in environmental health and disease. Cellular stress, induced by environmental toxicants or disease, significantly impacts the production and composition of exosomes, crucial mediators of intercellular communication. The heat shock response (HSR) and unfolded protein response (UPR) pathways, activated during cellular stress, profoundly influence exosome generation, cargo sorting, and function, shaping intercellular communication and stress responses. Environmental pollutants, particularly lipophilic ones, directly interact with exosome lipid bilayers, potentially affecting membrane stability, release, and cellular uptake. The study reveals that exposure to environmental contaminants induces significant changes in exosomal proteins, miRNAs, and lipids, impacting cellular function and health. Understanding the impact of environmental pollutants on exosomal cargo holds promise for biomarkers of exposure, enabling non-invasive sample collection and real-time insights into ongoing cellular responses. This research explores the potential of exosomal biomarkers for early detection of health effects, assessing treatment efficacy, and population-wide screening. Overcoming challenges requires advanced isolation techniques, standardized protocols, and machine learning for data analysis. Integration with omics technologies enhances comprehensive molecular analysis, offering a holistic understanding of the complex regulatory network influenced by environmental pollutants. The study underscores the capability of exosomes in circulation as promising biomarkers for assessing environmental exposure and systemic health effects, contributing to advancements in environmental health research and disease prevention.
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Affiliation(s)
- Afsaneh Javdani-Mallak
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Iman Salahshoori
- Department of Polymer Processing, Iran Polymer and Petrochemical Institute, Tehran, Iran; Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran.
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2
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Szczepanek J, Tretyn A. MicroRNA-Mediated Regulation of Histone-Modifying Enzymes in Cancer: Mechanisms and Therapeutic Implications. Biomolecules 2023; 13:1590. [PMID: 38002272 PMCID: PMC10669115 DOI: 10.3390/biom13111590] [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: 09/21/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
In the past decade, significant advances in molecular research have provided a deeper understanding of the intricate regulatory mechanisms involved in carcinogenesis. MicroRNAs, short non-coding RNA sequences, exert substantial influence on gene expression by repressing translation or inducing mRNA degradation. In the context of cancer, miRNA dysregulation is prevalent and closely associated with various stages of carcinogenesis, including initiation, progression, and metastasis. One crucial aspect of the cancer phenotype is the activity of histone-modifying enzymes that govern chromatin accessibility for transcription factors, thus impacting gene expression. Recent studies have revealed that miRNAs play a significant role in modulating these histone-modifying enzymes, leading to significant implications for genes related to proliferation, differentiation, and apoptosis in cancer cells. This article provides an overview of current research on the mechanisms by which miRNAs regulate the activity of histone-modifying enzymes in the context of cancer. Both direct and indirect mechanisms through which miRNAs influence enzyme expression are discussed. Additionally, potential therapeutic implications arising from miRNA manipulation to selectively impact histone-modifying enzyme activity are presented. The insights from this analysis hold significant therapeutic promise, suggesting the utility of miRNAs as tools for the precise regulation of chromatin-related processes and gene expression. A contemporary focus on molecular regulatory mechanisms opens therapeutic pathways that can effectively influence the control of tumor cell growth and dissemination.
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Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, ul. Wilenska 4, 87-100 Torun, Poland
| | - Andrzej Tretyn
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, ul. Lwowska 1, 87-100 Torun, Poland;
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3
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Asl ER, Sarabandi S, Shademan B, Dalvandi K, sheikhansari G, Nourazarian A. MicroRNA targeting: A novel therapeutic intervention for ovarian cancer. Biochem Biophys Rep 2023; 35:101519. [PMID: 37521375 PMCID: PMC10382632 DOI: 10.1016/j.bbrep.2023.101519] [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: 06/13/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
Ovarian cancer, a perilous form of cancer affecting the female reproductive system, exhibits intricate communication networks that contribute to its progression. This study aims to identify crucial molecular abnormalities linked to the disease to enhance diagnostic and therapeutic strategies. In particular, we investigate the role of microRNAs (miRNAs) as diagnostic biomarkers and explore their potential in treating ovarian cancer. By targeting miRNAs, which can influence multiple pathways and genes, substantial therapeutic benefits can be attained. In this review we want to shed light on the promising application of miRNA-based interventions and provide insights into the specific miRNAs implicated in ovarian cancer pathogenesis.
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Affiliation(s)
- Elmira Roshani Asl
- Social Determinants of Health Research Center, Saveh University of Medical Sciences, Saveh, Iran
| | - Sajed Sarabandi
- Department of Veterinary, Faculty of Medicine Sciences, Islamic Azad University of Karaj, Karaj, Iran
| | - Behrouz Shademan
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kourosh Dalvandi
- Ministry of Health and Medical Education, Health Department, Tehran, Iran
| | | | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
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4
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Duisenbek A, Lopez-Armas GC, Pérez M, Avilés Pérez MD, Aguilar Benitez JM, Pereira Pérez VR, Gorts Ortega J, Yessenbekova A, Ablaikhanova N, Escames G, Acuña-Castroviejo D, Rusanova I. Insights into the Role of Plasmatic and Exosomal microRNAs in Oxidative Stress-Related Metabolic Diseases. Antioxidants (Basel) 2023; 12:1290. [PMID: 37372020 DOI: 10.3390/antiox12061290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/05/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
A common denominator of metabolic diseases, including type 2 diabetes Mellitus, dyslipidemia, and atherosclerosis, are elevated oxidative stress and chronic inflammation. These complex, multi-factorial diseases are caused by the detrimental interaction between the individual genetic background and multiple environmental stimuli. The cells, including the endothelial ones, acquire a preactivated phenotype and metabolic memory, exhibiting increased oxidative stress, inflammatory gene expression, endothelial vascular activation, and prothrombotic events, leading to vascular complications. There are different pathways involved in the pathogenesis of metabolic diseases, and increased knowledge suggests a role of the activation of the NF-kB pathway and NLRP3 inflammasome as key mediators of metabolic inflammation. Epigenetic-wide associated studies provide new insight into the role of microRNAs in the phenomenon of metabolic memory and the development consequences of vessel damage. In this review, we will focus on the microRNAs related to the control of anti-oxidative enzymes, as well as microRNAs related to the control of mitochondrial functions and inflammation. The objective is the search for new therapeutic targets to improve the functioning of mitochondria and reduce oxidative stress and inflammation, despite the acquired metabolic memory.
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Affiliation(s)
- Ayauly Duisenbek
- Department of Biophysics, Biomedicine and Neuroscience, Al-Farabi Kazakh National University, Al-Farabi Av. 71, Almaty 050040, Kazakhstan
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, 18019 Granada, Spain
| | - Gabriela C Lopez-Armas
- Departamento de Investigación y Extensión, Centro de Enseñanza Técnica Industrial, C. Nueva Escocia 1885, Guadalajara 44638, Mexico
| | - Miguel Pérez
- Hospital de Alta Resolución de Alcalá la Real, 23680 Jaén, Spain
| | - María D Avilés Pérez
- Endocrinology and Nutrition Unit, Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), University Hospital Clínico San Cecilio, 18016 Granada, Spain
| | | | - Víctor Roger Pereira Pérez
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, 18019 Granada, Spain
| | - Juan Gorts Ortega
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, 18019 Granada, Spain
| | - Arailym Yessenbekova
- Department of Biophysics, Biomedicine and Neuroscience, Al-Farabi Kazakh National University, Al-Farabi Av. 71, Almaty 050040, Kazakhstan
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, 18019 Granada, Spain
| | - Nurzhanyat Ablaikhanova
- Department of Biophysics, Biomedicine and Neuroscience, Al-Farabi Kazakh National University, Al-Farabi Av. 71, Almaty 050040, Kazakhstan
| | - Germaine Escames
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), San Cecilio University Hospital Clínico, 18016 Granada, Spain
- Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
- Department of Physiology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Darío Acuña-Castroviejo
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), San Cecilio University Hospital Clínico, 18016 Granada, Spain
- Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
- Department of Physiology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Iryna Rusanova
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, 18019 Granada, Spain
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), San Cecilio University Hospital Clínico, 18016 Granada, Spain
- Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
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Radhakrishna U, Nath SK, Uppala LV, Veerappa A, Forray A, Muvvala SB, Metpally RP, Crist RC, Berrettini WH, Mausi LM, Vishweswaraiah S, Bahado-Singh RO. Placental microRNA methylome signatures may serve as biomarkers and therapeutic targets for prenatally opioid-exposed infants with neonatal opioid withdrawal syndrome. Front Genet 2023; 14:1215472. [PMID: 37434949 PMCID: PMC10332887 DOI: 10.3389/fgene.2023.1215472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction: The neonate exposed to opioids in utero faces a constellation of withdrawal symptoms postpartum commonly called neonatal opioid withdrawal syndrome (NOWS). The incidence of NOWS has increased in recent years due to the opioid epidemic. MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. Epigenetic variations in microRNAs (miRNAs) and their impact on addiction-related processes is a rapidly evolving area of research. Methods: The Illumina Infinium Methylation EPIC BeadChip was used to analyze DNA methylation levels of miRNA-encoding genes in 96 human placental tissues to identify miRNA gene methylation profiles as-sociated with NOWS: 32 from mothers whose prenatally opioid-exposed infants required pharmacologic management for NOWS, 32 from mothers whose prenatally opioid-exposed infants did not require treat-ment for NOWS, and 32 unexposed controls. Results: The study identified 46 significantly differentially methylated (FDR p-value ≤ 0.05) CpGs associated with 47 unique miRNAs, with a receiver operating characteristic (ROC) area under the curve (AUC) ≥0.75 including 28 hypomethylated and 18 hypermethylated CpGs as potentially associated with NOWS. These dysregulated microRNA methylation patterns may be a contributing factor to NOWS pathogenesis. Conclusion: This is the first study to analyze miRNA methylation profiles in NOWS infants and illustrates the unique role miRNAs might have in diagnosing and treating the disease. Furthermore, these data may provide a step toward feasible precision medicine for NOWS babies as well.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Lavanya V. Uppala
- College of Information Science and Technology, Peter Kiewit Institute, The University of Nebraska at Omaha, Omaha, NE, United States
| | - Avinash Veerappa
- Department of Genetics, Cell Biology and Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Srinivas B. Muvvala
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Danville, PA, United States
| | - Richard C. Crist
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Wade H. Berrettini
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
- Geisinger Clinic, Danville, PA, United States
| | - Lori M. Mausi
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
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Pathania AS. Crosstalk between Noncoding RNAs and the Epigenetics Machinery in Pediatric Tumors and Their Microenvironment. Cancers (Basel) 2023; 15:2833. [PMID: 37345170 DOI: 10.3390/cancers15102833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
According to the World Health Organization, every year, an estimated 400,000+ new cancer cases affect children under the age of 20 worldwide. Unlike adult cancers, pediatric cancers develop very early in life due to alterations in signaling pathways that regulate embryonic development, and environmental factors do not contribute much to cancer development. The highly organized complex microenvironment controlled by synchronized gene expression patterns plays an essential role in the embryonic stages of development. Dysregulated development can lead to tumor initiation and growth. The low mutational burden in pediatric tumors suggests the predominant role of epigenetic changes in driving the cancer phenotype. However, one more upstream layer of regulation driven by ncRNAs regulates gene expression and signaling pathways involved in the development. Deregulation of ncRNAs can alter the epigenetic machinery of a cell, affecting the transcription and translation profiles of gene regulatory networks required for cellular proliferation and differentiation during embryonic development. Therefore, it is essential to understand the role of ncRNAs in pediatric tumor development to accelerate translational research to discover new treatments for childhood cancers. This review focuses on the role of ncRNA in regulating the epigenetics of pediatric tumors and their tumor microenvironment, the impact of their deregulation on driving pediatric tumor progress, and their potential as effective therapeutic targets.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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7
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Alvanou M, Lysandrou M, Christophi P, Psatha N, Spyridonidis A, Papadopoulou A, Yannaki E. Empowering the Potential of CAR-T Cell Immunotherapies by Epigenetic Reprogramming. Cancers (Basel) 2023; 15:cancers15071935. [PMID: 37046597 PMCID: PMC10093039 DOI: 10.3390/cancers15071935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
T-cell-based, personalized immunotherapy can nowadays be considered the mainstream treatment for certain blood cancers, with a high potential for expanding indications. Chimeric antigen receptor T cells (CAR-Ts), an ex vivo genetically modified T-cell therapy product redirected to target an antigen of interest, have achieved unforeseen successes in patients with B-cell hematologic malignancies. Frequently, however, CAR-T cell therapies fail to provide durable responses while they have met with only limited success in treating solid cancers because unique, unaddressed challenges, including poor persistence, impaired trafficking to the tumor, and site penetration through a hostile microenvironment, impede their efficacy. Increasing evidence suggests that CAR-Ts' in vivo performance is associated with T-cell intrinsic features that may be epigenetically altered or dysregulated. In this review, we focus on the impact of epigenetic regulation on T-cell differentiation, exhaustion, and tumor infiltration and discuss how epigenetic reprogramming may enhance CAR-Ts' memory phenotype, trafficking, and fitness, contributing to the development of a new generation of potent CAR-T immunotherapies.
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Affiliation(s)
- Maria Alvanou
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Memnon Lysandrou
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Panayota Christophi
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Nikoleta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 570 10 Thessaloniki, Greece
| | - Alexandros Spyridonidis
- Bone Marrow Transplantation Unit, Institute of Cell Therapy, University of Patras, 265 04 Rio, Greece
| | - Anastasia Papadopoulou
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
| | - Evangelia Yannaki
- Hematology Department-Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, 570 10 Thessaloniki, Greece
- Department of Medicine, University of Washington, Seattle, WA 98195-2100, USA
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8
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Singh NP, Yang X, Bam M, Nagarkatti M, Nagarkatti P. 2,3,7,8-Tetrachlorodibenzo-p-dioxin induces multigenerational alterations in the expression of microRNA in the thymus through epigenetic modifications. PNAS NEXUS 2023; 2:pgac290. [PMID: 36712935 PMCID: PMC9833045 DOI: 10.1093/pnasnexus/pgac290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/07/2022] [Indexed: 05/11/2023]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a potent AhR ligand, is an environmental contaminant that is known for mediating toxicity across generations. However, whether TCDD can induce multigenerational changes in the expression of microRNAs (miRs) has not been previously studied. In the current study, we investigated the effect of administration of TCDD in pregnant mice (F0) on gestational day 14, on the expression of miRs in the thymus of F0 and subsequent generations (F1 and F2). Of the 3200 miRs screened, 160 miRs were dysregulated similarly in F0, F1, and F2 generations, while 46 miRs were differentially altered in F0 to F2 generations. Pathway analysis revealed that the changes in miR signature profile mediated by TCDD affected the genes that regulate cell signaling, apoptosis, thymic atrophy, cancer, immunosuppression, and other physiological pathways. A significant number of miRs that showed altered expression exhibited dioxin response elements (DRE) on their promoters. Focusing on one such miR, namely miR-203 that expressed DREs and was induced across F0 to F2 by TCDD, promoter analysis showed that one of the DREs expressed by miR-203 was functional to TCDD-mediated upregulation. Also, the histone methylation status of H3K4me3 in the miR-203 promoter was significantly increased near the transcriptional start site in TCDD-treated thymocytes across F0 to F2 generations. Genome-wide chromatin immunoprecipitation sequencing study suggested that TCDD may cause alterations in histone methylation in certain genes across the three generations. Together, the current study demonstrates that gestational exposure to TCDD can alter the expression of miRs in F0 through direct activation of DREs as well as across F0, F1, and F2 generations through epigenetic pathways.
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Affiliation(s)
- Narendra P Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Marpe Bam
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
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9
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García-Giménez JL, García-Trevijano ER, Avilés-Alía AI, Ibañez-Cabellos JS, Bovea-Marco M, Bas T, Pallardó FV, Viña JR, Zaragozá R. Identification of circulating miRNAs differentially expressed in patients with Limb-girdle, Duchenne or facioscapulohumeral muscular dystrophies. Orphanet J Rare Dis 2022; 17:450. [PMID: 36575500 PMCID: PMC9793535 DOI: 10.1186/s13023-022-02603-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Limb-girdle muscular dystrophy (LGMD) is a rare neuromuscular disease including a growing and heterogeneous number of subtypes with variable phenotype. Their clinical and histopathological characteristics frequently overlap with other neuromuscular dystrophies. Our goal was to identify, by a non-invasive method, a molecular signature including biochemical and epigenetic parameters with potential value for patient prognosis and stratification. RESULTS Circulating miRNome was obtained by smallRNA-seq in plasma from LGMD patients (n = 6) and matched-controls (n = 6). Data, validated by qPCR in LGMD samples, were also examined in other common muscular dystrophies: Duchenne (DMD) (n = 5) and facioscapulohumeral muscular dystrophy (FSHD) (n = 4). Additionally, biochemical and clinical parameters were analyzed. miRNome analysis showed that thirteen differentially expressed miRs could separate LGMD vs control group by hierarchical clustering. Most of differentially expressed miRs in LGMD patients were up-regulated (miR-122-5p, miR-122b-3p, miR-6511a-3p, miR-192-5p, miR-574-3p, mir-885-3p, miR-29a-3p, miR-4646-3p, miR-203a-3p and miR-203b-5p) whilst only three of sequenced miRs were significantly down-regulated (miR-19b-3p, miR-7706, miR-323b-3p) when compared to matched controls. Bioinformatic analysis of target genes revealed cell cycle, muscle tissue development, regeneration and senescence as the most affected pathways. Four of these circulating miRs (miR-122-5p, miR-192-5p, miR-19b-3p and miR-323b-3p), together with the myomiR miR-206, were further analysed by qPCR in LGMD, DMD and FSHD. The receiver operating characteristic curves (ROC) revealed high area under the curve (AUC) values for selected miRs in all groups, indicating that these miRs have good sensitivity and specificity to distinguish LGMD, DMD and FSHD patients from healthy controls. miR-122-5p, miR-192-5p and miR-323-3p were differentially expressed compared to matched-controls in all groups but apparently, each type of muscular dystrophy showed a specific pattern of miR expression. Finally, a strong correlation between miRs and biochemical data was only found in LGMD patients: while miR-192-5p and miR-122-5p negatively correlated with CK, miR-192-5p positively correlated with vitamin D3 and ALP. CONCLUSIONS Although limited by the small number of patients included in this study, we propose here a specific combination of circulating miR-122-5p/miR-192-5p/miR-323-3 and biochemical parameters as a potential molecular signature whose clinical value for LGMD patient prognosis and stratification should be further confirmed in a larger cohort of patients.
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Affiliation(s)
- José Luis García-Giménez
- grid.413448.e0000 0000 9314 1427Center for Biomedical Network Research On Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain ,grid.429003.c0000 0004 7413 8491INCLIVA Health Research Institute, Valencia, Spain ,grid.5338.d0000 0001 2173 938XDepartment of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain ,EpiDisease S.L. (Spin-Off CIBERER), Valencia, Spain
| | - Elena R. García-Trevijano
- grid.429003.c0000 0004 7413 8491INCLIVA Health Research Institute, Valencia, Spain ,grid.5338.d0000 0001 2173 938XDepartment of Biochemistry and Molecular Biology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Ana I. Avilés-Alía
- grid.5338.d0000 0001 2173 938XDepartment of Biochemistry and Molecular Biology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | | | | | - Teresa Bas
- Institute for Health Research La Fe, IISLaFe, Valencia, Spain ,grid.84393.350000 0001 0360 9602Spine Surgery Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Federico V. Pallardó
- grid.413448.e0000 0000 9314 1427Center for Biomedical Network Research On Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain ,grid.429003.c0000 0004 7413 8491INCLIVA Health Research Institute, Valencia, Spain ,grid.5338.d0000 0001 2173 938XDepartment of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Juan R. Viña
- grid.429003.c0000 0004 7413 8491INCLIVA Health Research Institute, Valencia, Spain ,grid.5338.d0000 0001 2173 938XDepartment of Biochemistry and Molecular Biology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Rosa Zaragozá
- INCLIVA Health Research Institute, Valencia, Spain. .,Department of Human Anatomy and Embryology, Faculty of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibañez 15, 46010, Valencia, Spain.
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10
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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11
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Identification of Epigenetic Interactions between MicroRNA-30c-5p and DNA Methyltransferases in Neuropathic Pain. Int J Mol Sci 2022; 23:ijms232213994. [PMID: 36430472 PMCID: PMC9694031 DOI: 10.3390/ijms232213994] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Neuropathic pain is a prevalent and severe chronic syndrome, often refractory to treatment, whose development and maintenance may involve epigenetic mechanisms. We previously demonstrated a causal relationship between miR-30c-5p upregulation in nociception-related neural structures and neuropathic pain in rats subjected to sciatic nerve injury. Furthermore, a short course of an miR-30c-5p inhibitor administered into the cisterna magna exerts long-lasting antiallodynic effects via a TGF-β1-mediated mechanism. Herein, we show that miR-30c-5p inhibition leads to global DNA hyper-methylation of neurons in the lumbar dorsal root ganglia and spinal dorsal horn in rats subjected to sciatic nerve injury. Specifically, the inhibition of miR-30-5p significantly increased the expression of the novo DNA methyltransferases DNMT3a and DNMT3b in those structures. Furthermore, we identified the mechanism and found that miR-30c-5p targets the mRNAs of DNMT3a and DNMT3b. Quantitative methylation analysis revealed that the promoter region of the antiallodynic cytokine TGF-β1 was hypomethylated in the spinal dorsal horn of nerve-injured rats treated with the miR-30c-5p inhibitor, while the promoter of Nfyc, the host gene of miR-30c-5p, was hypermethylated. These results are consistent with long-term protection against neuropathic pain development after nerve injury. Altogether, our results highlight the key role of miR-30c-5p in the epigenetic mechanisms' underlying neuropathic pain and provide the basis for miR-30c-5p as a therapeutic target.
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12
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Marano N, Holaska JM. Emerin interacts with histone methyltransferases to regulate repressive chromatin at the nuclear periphery. Front Cell Dev Biol 2022; 10:1007120. [PMID: 36274837 PMCID: PMC9583931 DOI: 10.3389/fcell.2022.1007120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
X-Linked Emery-Dreifuss muscular dystrophy is caused by mutations in the gene encoding emerin. Emerin is an inner nuclear membrane protein important for repressive chromatin organization at the nuclear periphery. Myogenic differentiation is a tightly regulated process characterized by genomic reorganization leading to coordinated temporal expression of key transcription factors, including MyoD, Pax7, and Myf5. Emerin was shown to interact with repressive histone modification machinery, including HDAC3 and EZH2. Using emerin-null myogenic progenitor cells we established several EDMD-causing emerin mutant lines in the effort to understand how the functional interaction of emerin with HDAC3 regulates histone methyltransferase localization or function to organize repressive chromatin at the nuclear periphery. We found that, in addition to its interaction with HDAC3, emerin interacts with the histone methyltransferases EZH2 and G9a in myogenic progenitor cells. Further, we show enhanced binding of emerin HDAC3-binding mutants S54F and Q133H to EZH2 and G9a. Treatment with small molecule inhibitors of EZH2 and G9a reduced H3K9me2 or H3K27me3 throughout differentiation. EZH2 and G9a inhibitors impaired cell cycle withdrawal, differentiation commitment, and myotube formation in wildtype progenitors, while they had no effect on emerin-null progenitors. Interestingly, these inhibitors exacerbated the impaired differentiation of emerin S54F and Q133H mutant progenitors. Collectively, these results suggest the functional interaction between emerin and HDAC3, EZH2, and G9a are important for myogenic differentiation.
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Affiliation(s)
| | - James M. Holaska
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
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13
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Hatmal MM, Al-Hatamleh MAI, Olaimat AN, Alshaer W, Hasan H, Albakri KA, Alkhafaji E, Issa NN, Al-Holy MA, Abderrahman SM, Abdallah AM, Mohamud R. Immunomodulatory Properties of Human Breast Milk: MicroRNA Contents and Potential Epigenetic Effects. Biomedicines 2022; 10:biomedicines10061219. [PMID: 35740242 PMCID: PMC9219990 DOI: 10.3390/biomedicines10061219] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Infants who are exclusively breastfed in the first six months of age receive adequate nutrients, achieving optimal immune protection and growth. In addition to the known nutritional components of human breast milk (HBM), i.e., water, carbohydrates, fats and proteins, it is also a rich source of microRNAs, which impact epigenetic mechanisms. This comprehensive work presents an up-to-date overview of the immunomodulatory constituents of HBM, highlighting its content of circulating microRNAs. The epigenetic effects of HBM are discussed, especially those regulated by miRNAs. HBM contains more than 1400 microRNAs. The majority of these microRNAs originate from the lactating gland and are based on the remodeling of cells in the gland during breastfeeding. These miRNAs can affect epigenetic patterns by several mechanisms, including DNA methylation, histone modifications and RNA regulation, which could ultimately result in alterations in gene expressions. Therefore, the unique microRNA profile of HBM, including exosomal microRNAs, is implicated in the regulation of the genes responsible for a variety of immunological and physiological functions, such as FTO, INS, IGF1, NRF2, GLUT1 and FOXP3 genes. Hence, studying the HBM miRNA composition is important for improving the nutritional approaches for pregnancy and infant's early life and preventing diseases that could occur in the future. Interestingly, the composition of miRNAs in HBM is affected by multiple factors, including diet, environmental and genetic factors.
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Affiliation(s)
- Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
- Correspondence: (M.M.H.); (R.M.)
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
| | - Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Walhan Alshaer
- Cell Therapy Center (CTC), The University of Jordan, Amman 11942, Jordan;
| | - Hanan Hasan
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Khaled A. Albakri
- Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Enas Alkhafaji
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan;
| | - Nada N. Issa
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Murad A. Al-Holy
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Salim M. Abderrahman
- Department of Biology and Biotechnology, Faculty of Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Atiyeh M. Abdallah
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha 2713, Qatar;
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
- Correspondence: (M.M.H.); (R.M.)
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14
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Khan SU, Khan MU, Kalsoom F, Khan MI, Gao S, Unar A, Zubair M, Bilal M. Mechanisms of gene regulation by histone degradation in adaptation of yeast: an overview of recent advances. Arch Microbiol 2022; 204:287. [PMID: 35482104 DOI: 10.1007/s00203-022-02897-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/12/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023]
Abstract
Histones are important component of eukaryotic cells chromatin and consist of arginine and lysine residues. Histones play an important role in the protection of DNA. Their contents significantly affect high-level chromatin structure formation, gene expression, DNA replication, and other important life activities. Protein degradation is an important regulatory mechanism of histone content. Recent studies have revealed that modification of amino acid sequence is directly related to histone breakdown. In addition, histone degradation is closely related to covalent modifications, such as ubiquitination and acetylation, which are considered to be driving factors in gene regulation. Gene regulation is an important mechanism in adaptation to the environment and survival of species. With the introduction of highly efficient technology, various mutations in histones have been identified in yeast. In the field of epigenetics and the transmission of chromatin states, two widely used model organisms are the budding yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe. Higher eukaryotes can use their silent loci to maintain their epigenetic states and providing the base to investigate mechanisms underlying development. Therfore, both species have contributed a plethora of information on these mechanisms in both yeast and higher eukaryotes. This study focuses on the role of histone modifications in controlling telomeric silencing in Saccharomyces cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that demonstrate epigenetic inheritance. In view of recent advances, this review focuses on the post-translational modification of histone amino acid residues and reviews the relationship between histone degradation and amino acid residue modification.
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Affiliation(s)
- Safir Ullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Munir Ullah Khan
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Fadia Kalsoom
- Department of Microbiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Muhammad Imran Khan
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Hefei National Laboratory for Physical Sciences at Microscale and the Center for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Department of Pathology, District headquarters hospital, Jhang, 35200, Punjab Province, Islamic Republic of Pakistan.
| | - Shuang Gao
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Ahsanullah Unar
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Zubair
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, People's Republic of China.
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15
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Renzini A, D’Onghia M, Coletti D, Moresi V. Histone Deacetylases as Modulators of the Crosstalk Between Skeletal Muscle and Other Organs. Front Physiol 2022; 13:706003. [PMID: 35250605 PMCID: PMC8895239 DOI: 10.3389/fphys.2022.706003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 01/31/2022] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle plays a major role in controlling body mass and metabolism: it is the most abundant tissue of the body and a major source of humoral factors; in addition, it is primarily responsible for glucose uptake and storage, as well as for protein metabolism. Muscle acts as a metabolic hub, in a crosstalk with other organs and tissues, such as the liver, the brain, and fat tissue. Cytokines, adipokines, and myokines are pivotal mediators of such crosstalk. Many of these circulating factors modulate histone deacetylase (HDAC) expression and/or activity. HDACs form a numerous family of enzymes, divided into four classes based on their homology to their orthologs in yeast. Eleven family members are considered classic HDACs, with a highly conserved deacetylase domain, and fall into Classes I, II, and IV, while class III members are named Sirtuins and are structurally and mechanistically distinct from the members of the other classes. HDACs are key regulators of skeletal muscle metabolism, both in physiological conditions and following metabolic stress, participating in the highly dynamic adaptative responses of the muscle to external stimuli. In turn, HDAC expression and activity are closely regulated by the metabolic demands of the skeletal muscle. For instance, NAD+ levels link Class III (Sirtuin) enzymatic activity to the energy status of the cell, and starvation or exercise affect Class II HDAC stability and intracellular localization. SUMOylation or phosphorylation of Class II HDACs are modulated by circulating factors, thus establishing a bidirectional link between HDAC activity and endocrine, paracrine, and autocrine factors. Indeed, besides being targets of adipo-myokines, HDACs affect the synthesis of myokines by skeletal muscle, altering the composition of the humoral milieu and ultimately contributing to the muscle functioning as an endocrine organ. In this review, we discuss recent findings on the interplay between HDACs and circulating factors, in relation to skeletal muscle metabolism and its adaptative response to energy demand. We believe that enhancing knowledge on the specific functions of HDACs may have clinical implications leading to the use of improved HDAC inhibitors for the treatment of metabolic syndromes or aging.
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Affiliation(s)
- Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Sapienza University of Rome, Rome, Italy
| | - Marco D’Onghia
- Unit of Histology and Medical Embryology, Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Sapienza University of Rome, Rome, Italy
| | - Dario Coletti
- Unit of Histology and Medical Embryology, Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Sapienza University of Rome, Rome, Italy
- Biological Adaptation and Ageing, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
- *Correspondence: Dario Coletti,
| | - Viviana Moresi
- Unit of Histology and Medical Embryology, Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Sapienza University of Rome, Rome, Italy
- Institute of Nanotechnology (Nanotec), National Research Council, Rome, Italy
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16
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miR172 Regulates WUS during Somatic Embryogenesis in Arabidopsis via AP2. Cells 2022; 11:cells11040718. [PMID: 35203367 PMCID: PMC8869827 DOI: 10.3390/cells11040718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
In plants, the embryogenic transition of somatic cells requires the reprogramming of the cell transcriptome, which is under the control of genetic and epigenetic factors. Correspondingly, the extensive modulation of genes encoding transcription factors and miRNAs has been indicated as controlling the induction of somatic embryogenesis in Arabidopsis and other plants. Among the MIRNAs that have a differential expression during somatic embryogenesis, members of the MIRNA172 gene family have been identified, which implies a role of miR172 in controlling the embryogenic transition in Arabidopsis. In the present study, we found a disturbed expression of both MIRNA172 and candidate miR172-target genes, including AP2, TOE1, TOE2, TOE3, SMZ and SNZ, that negatively affected the embryogenic response of transgenic explants. Next, we examined the role of AP2 in the miR172-mediated mechanism that controls the embryogenic response. We found some evidence that by controlling AP2, miR172 might repress the WUS that has an important function in embryogenic induction. We showed that the mechanism of the miR172-AP2-controlled repression of WUS involves histone acetylation. We observed the upregulation of the WUS transcripts in an embryogenic culture that was overexpressing AP2 and treated with trichostatin A (TSA), which is an inhibitor of HDAC histone deacetylases. The increased expression of the WUS gene in the embryogenic culture of the hdac mutants further confirmed the role of histone acetylation in WUS control during somatic embryogenesis. A chromatin-immunoprecipitation analysis provided evidence about the contribution of HDA6/19-mediated histone deacetylation to AP2-controlled WUS repression during embryogenic induction. The upstream regulatory elements of the miR172-AP2-WUS pathway might involve the miR156-controlled SPL9/SPL10, which control the level of mature miR172 in an embryogenic culture.
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17
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Kraczkowska W, Stachowiak L, Pławski A, Jagodziński PP. Circulating miRNA as potential biomarkers for diabetes mellitus type 2: should we focus on searching for sex differences? J Appl Genet 2022; 63:293-303. [PMID: 34984663 PMCID: PMC8979931 DOI: 10.1007/s13353-021-00678-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022]
Abstract
microRNAs are non-coding molecules, approximately 22 nucleotides in length, that regulate various cellular processes. A growing body of evidence has suggested that their dysregulated expression is involved in the pathogenesis of diverse diseases, including diabetes mellitus type 2 (DM2). Early onset of this chronic and complex metabolic disorder is frequently undiagnosed, leading to the development of severe diabetic complications. Notably, DM2 prevalence is rising globally and an increasing number of articles demonstrate that DM2 susceptibility, development, and progression differ between males and females. Therefore, this paper discusses the role of microRNAs as a source of novel diagnostic biomarkers for DM2 and aims to underline the importance of sex disparity in biomarkers research. Taking into account an urgent need for the development of sex-specific diagnostic strategies in DM2, recent results have shown that circulating miRNAs are promising candidates for sex-biased biomarkers.
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Affiliation(s)
- Weronika Kraczkowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland
| | - Lucyna Stachowiak
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland
| | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland.
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18
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Regenerative rehabilitation of skeletal muscle damages. КЛИНИЧЕСКАЯ ПРАКТИКА 2021. [DOI: 10.17816/clinpract70873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The article is devoted to the analysis of the current state of regenerative and rehabilitative treatments of skeletal muscles, the possibilities of restoring the functioning of tissue lost due to aging, injuries or diseases. The study of the molecular genetic basis of mechanotransduction and mechanotherapy will allow the identification of genes and molecules, the expression levels of which can serve as biomarkers of the effectiveness of regenerative-rehabilitation measures. These mechanisms are potential therapeutic targets for stimulating of regeneration of skeletal muscles. The focus of the article is on the choice of an individual approach, both when conducting basic scientific research and developing rehabilitation programs. All this will significantly improve patient outcomes.
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19
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Cañas JA, Núñez R, Cruz-Amaya A, Gómez F, Torres MJ, Palomares F, Mayorga C. Epigenetics in Food Allergy and Immunomodulation. Nutrients 2021; 13:4345. [PMID: 34959895 PMCID: PMC8708211 DOI: 10.3390/nu13124345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022] Open
Abstract
Food allergy (FA) is an increasing problem worldwide and, over recent years, its prevalence is rising in developed countries. Nowadays, the immunological and cellular processes that occur in the allergic reactions are not fully understood, which hampers the development of in vitro diagnostic tools and further treatment options. Moreover, allergic diseases could be reinforced by environmental exposure and genetic modifications. Gene expression can be controlled by different epigenetic mechanisms like DNA methylation, histone modifications, and microRNAs. In addition, several environmental factors such as dietary components (vitamin D, butyrate, folic acid) are able to regulate this epigenetic mechanism. All these factors produce modifications in immune genes that could alter the development and function of immune cells, and therefore the etiology of the disease. Furthermore, these epigenetic mechanisms have also an influence on immunomodulation, which could explain sustained responsiveness or unresponsiveness during immunotherapy due to epigenetic modifications in key genes that induce tolerance in several FA. Thus, in this review we focus on the different epigenetic mechanisms that occur in FA and on the influence of several dietary components in these gene modifications.
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Affiliation(s)
- José A. Cañas
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
| | - Rafael Núñez
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
| | - Anyith Cruz-Amaya
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
| | - Francisca Gómez
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, 29009 Málaga, Spain;
| | - María J. Torres
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, 29009 Málaga, Spain;
- Medicine Department, Universidad de Málaga-UMA, 29010 Málaga, Spain
| | - Francisca Palomares
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
| | - Cristobalina Mayorga
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, 29009 Málaga, Spain;
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20
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Varghese RS, Barefoot ME, Jain S, Chen Y, Zhang Y, Alley A, Kroemer AH, Tadesse MG, Kumar D, Sherif ZA, Ressom HW. Integrative Analysis of DNA Methylation and microRNA Expression Reveals Mechanisms of Racial Heterogeneity in Hepatocellular Carcinoma. Front Genet 2021; 12:708326. [PMID: 34557219 PMCID: PMC8453167 DOI: 10.3389/fgene.2021.708326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Pathologic alterations in epigenetic regulation have long been considered a hallmark of many cancers, including hepatocellular carcinoma (HCC). In a healthy individual, the relationship between DNA methylation and microRNA (miRNA) expression maintains a fine balance; however, disruptions in this harmony can aid in the genesis of cancer or the propagation of existing cancers. The balance between DNA methylation and microRNA expression and its potential disturbance in HCC can vary by race. There is emerging evidence linking epigenetic events including DNA methylation and miRNA expression to cancer disparities. In this paper, we evaluate the epigenetic mechanisms of racial heterogenity in HCC through an integrated analysis of DNA methylation, miRNA, and combined regulation of gene expression. Specifically, we generated DNA methylation, mRNA-seq, and miRNA-seq data through the analysis of tumor and adjacent non-tumor liver tissues from African Americans (AA) and European Americans (EA) with HCC. Using mixed ANOVA, we identified cytosine-phosphate-guanine (CpG) sites, mRNAs, and miRNAs that are significantly altered in HCC vs. adjacent non-tumor tissue in a race-specific manner. We observed that the methylome was drastically changed in EA with a significantly larger number of differentially methylated and differentially expressed genes than in AA. On the other hand, the miRNA expression was altered to a larger extent in AA than in EA. Pathway analysis functionally linked epigenetic regulation in EA to processes involved in immune cell maturation, inflammation, and vascular remodeling. In contrast, cellular proliferation, metabolism, and growth pathways are found to predominate in AA as a result of this epigenetic analysis. Furthermore, through integrative analysis, we identified significantly differentially expressed genes in HCC with disparate epigenetic regulation, associated with changes in miRNA expression for AA and DNA methylation for EA.
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Affiliation(s)
- Rency S. Varghese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Sidharth Jain
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Yifan Chen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Yunxi Zhang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Amber Alley
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | | | - Mahlet G. Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, United States
| | - Deepak Kumar
- Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC, United States
| | - Zaki A. Sherif
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, United States
| | - Habtom W. Ressom
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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21
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HIV-1 Tat and cocaine impact astrocytic energy reservoir influence on miRNA epigenetic regulation. Genomics 2021; 113:3461-3475. [PMID: 34418497 DOI: 10.1016/j.ygeno.2021.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
Astrocytes are the primary regulator of energy metabolism in the central nervous system (CNS), and impairment of astrocyte's energy resource may trigger neurodegeneration. HIV infections and cocaine use are known to alter epigenetic modification, including miRNAs, which can target gene expression post-transcriptionally. However, miRNA-mediated astrocyte energy metabolism has not been delineated in HIV infection and cocaine abuse. Using next-generation sequencing (NGS), we identified a total of 1900 miRNAs, 64 were upregulated and 68 miRNAs were downregulated in the astrocytes by HIV-1 Tat with cocaine exposure. Moreover, miR-4727-3p, miR-5189-5p, miR-5090, and miR-6810-5p expressions were significantly impacted, and their gene targets were identified as VAMP2, NFIB, PPM1H, MEIS1, and PSD93 through the bioinformatic approach. In addition, the astrocytes treated with the nootropic drug piracetam protects these miRNAs. These findings provide evidence that the miRNAs in the astrocytes may be a potential biomarker and therapeutic target for HIV and cocaine abuse-induced neurodegeneration.
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22
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The Impact of Melatonin and NLRP3 Inflammasome on the Expression of microRNAs in Aged Muscle. Antioxidants (Basel) 2021; 10:antiox10040524. [PMID: 33801675 PMCID: PMC8066875 DOI: 10.3390/antiox10040524] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
Muscular aging is a complex process and underlying physiological mechanisms are not fully clear. In recent years, the participation of the NF-kB pathway and the NLRP3 inflammasome in the chronic inflammation process that accompanies the skeletal muscle's aging has been confirmed. microRNAs (miRs) form part of a gene regulatory machinery, and they control numerous biological processes including inflammatory pathways. In this work, we studied the expression of four miRs; three of them are considered as inflammatory-related miRs (miR-21, miR-146a, and miR-223), and miR-483, which is related to the regulation of melatonin synthesis, among other targets. To investigate the changes of miRs expression in muscle along aging, the impact of inflammation, and the role of melatonin in aged skeletal muscle, we used the gastrocnemius muscle of wild type (WT) and NLRP3-knockout (NLRP3-) mice of 3, 12, and 24 months-old, with and without melatonin supplementation. The expression of miRs and pro-caspase-1, caspase-3, pro-IL-1β, bax, bcl-2, and p53, was investigated by qRT-PCR analysis. Histological examination of the gastrocnemius muscle was also done. The results showed that age increased the expression of miR-21 (p < 0.01), miR-146a, and miR-223 (p < 0.05, for both miRs) in WT mice, whereas the 24-months-old mutant mice revealed decline of miR-21 and miR-223 (p < 0.05), compared to WT age. The lack of NLRP3 inflammasome also improved the skeletal muscle fibers arrangement and reduced the collagen deposits compared with WT muscle during aging. For the first time, we showed that melatonin significantly reduced the expression of miR-21, miR-146a, and miR-223 (p < 0.05 for all ones, and p < 0.01 for miR-21 at 24 months old) in aged WT mice, increased miR-223 in NLRP3- mice (p < 0.05), and induced miR-483 expression in both mice strains, this increase being significant at 24 months of age.
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23
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Chhabra R, Rockfield S, Guergues J, Nadeau OW, Hill R, Stevens SM, Nanjundan M. Global miRNA/proteomic analyses identify miRNAs at 14q32 and 3p21, which contribute to features of chronic iron-exposed fallopian tube epithelial cells. Sci Rep 2021; 11:6270. [PMID: 33737539 PMCID: PMC7973504 DOI: 10.1038/s41598-021-85342-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
Malignant transformation of fallopian tube secretory epithelial cells (FTSECs) is a key contributing event to the development of high-grade serous ovarian carcinoma (HGSOC). Our recent findings implicate oncogenic transformative events in chronic iron-exposed FTSECs, including increased expression of oncogenic mediators, increased telomerase transcripts, and increased growth/migratory potential. Herein, we extend these studies by implementing an integrated transcriptomic and mass spectrometry-based proteomics approach to identify global miRNA and protein alterations, for which we also investigate a subset of these targets to iron-induced functional alterations. Proteomic analysis identified > 4500 proteins, of which 243 targets were differentially expressed. Sixty-five differentially expressed miRNAs were identified, of which 35 were associated with the “top” proteomic molecules (> fourfold change) identified by Ingenuity Pathway Analysis. Twenty of these 35 miRNAs are at the 14q32 locus (encoding a cluster of 54 miRNAs) with potential to be regulated by DNA methylation and histone deacetylation. At 14q32, miR-432-5p and miR-127-3p were ~ 100-fold downregulated whereas miR-138-5p was 16-fold downregulated at 3p21 in chronic iron-exposed FTSECs. Combinatorial treatment with methyltransferase and deacetylation inhibitors reversed expression of these miRNAs, suggesting chronic iron exposure alters miRNA expression via epigenetic alterations. In addition, PAX8, an important target in HGSOC and a potential miRNA target (from IPA) was epigenetically deregulated in iron-exposed FTSECs. However, both PAX8 and ALDH1A2 (another IPA-predicted target) were experimentally identified to be independently regulated by these miRNAs although TERT RNA was partially regulated by miR-138-5p. Interestingly, overexpression of miR-432-5p diminished cell numbers induced by long-term iron exposure in FTSECs. Collectively, our global profiling approaches uncovered patterns of miRNA and proteomic alterations that may be regulated by genome-wide epigenetic alterations and contribute to functional alterations induced by chronic iron exposure in FTSECs. This study may provide a platform to identify future biomarkers for early ovarian cancer detection and new targets for therapy.
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Affiliation(s)
- Ravneet Chhabra
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Stephanie Rockfield
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.,Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jennifer Guergues
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.,Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, VT, 05446, USA
| | - Owen W Nadeau
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, VT, 05446, USA
| | - Robert Hill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Stanley M Stevens
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.,Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, VT, 05446, USA
| | - Meera Nanjundan
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.
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24
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Mirra P, Desiderio A, Spinelli R, Nigro C, Longo M, Parrillo L, D'Esposito V, Carissimo A, Hedjazifar S, Smith U, Formisano P, Miele C, Raciti GA, Beguinot F. Adipocyte precursor cells from first degree relatives of type 2 diabetic patients feature changes in hsa-mir-23a-5p, -193a-5p, and -193b-5p and insulin-like growth factor 2 expression. FASEB J 2021; 35:e21357. [PMID: 33710685 DOI: 10.1096/fj.202002156rrr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022]
Abstract
First-degree relatives (FDRs) of type 2 diabetics (T2D) feature dysfunction of subcutaneous adipose tissue (SAT) long before T2D onset. miRNAs have a role in adipocyte precursor cells (APC) differentiation and in adipocyte identity. Thus, impaired miRNA expression may contribute to SAT dysfunction in FDRs. In the present work, we have explored changes in miRNA expression associated with T2D family history which may affect gene expression in SAT APCs from FDRs. Small RNA-seq was performed in APCs from healthy FDRs and matched controls and omics data were validated by qPCR. Integrative analyses of APC miRNome and transcriptome from FDRs revealed down-regulated hsa-miR-23a-5p, -193a-5p and -193b-5p accompanied by up-regulated Insulin-like Growth Factor 2 (IGF2) gene which proved to be their direct target. The expression changes in these marks were associated with SAT adipocyte hypertrophy in FDRs. APCs from FDRs further demonstrated reduced capability to differentiate into adipocytes. Treatment with IGF2 protein decreased APC adipogenesis, while over-expression of hsa-miR-23a-5p, -193a-5p and -193b-5p enhanced adipogenesis by IGF2 targeting. Indeed, IGF2 increased the Wnt Family Member 10B gene expression in APCs. Down-regulation of the three miRNAs and IGF2 up-regulation was also observed in Peripheral Blood Leukocytes (PBLs) from FDRs. In conclusion, APCs from FDRs feature a specific miRNA/gene profile, which associates with SAT adipocyte hypertrophy and appears to contribute to impaired adipogenesis. PBL detection of this profile may help in identifying adipocyte hypertrophy in individuals at high risk of T2D.
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Affiliation(s)
- Paola Mirra
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Antonella Desiderio
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Rosa Spinelli
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Cecilia Nigro
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Michele Longo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Luca Parrillo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Vittoria D'Esposito
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | | | - Shahram Hedjazifar
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pietro Formisano
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Claudia Miele
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Gregory A Raciti
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Francesco Beguinot
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
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25
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Zhu H, Sun B, Zhu L, Zou G, Shen Q. N6-Methyladenosine Induced miR-34a-5p Promotes TNF-α-Induced Nucleus Pulposus Cell Senescence by Targeting SIRT1. Front Cell Dev Biol 2021; 9:642437. [PMID: 33763423 PMCID: PMC7982913 DOI: 10.3389/fcell.2021.642437] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/15/2021] [Indexed: 12/14/2022] Open
Abstract
Low back pain is tightly associated with intervertebral disc degeneration (IVDD) and aberrant nucleus pulposus (NP) is a critical cause. miRNAs N6-methyladenosine (m6A) modification accounts for the TNF-α-induced senescence of NP cells. The aim of this study was to investigate whether m6A modification regulates TNF-α-mediated cell viability, cell cycle arrest, and cell senescence and how it works. The results showed that METTL14 expression positively correlated with m6A and TNF-α expression in HNPCs. The knockdown of METTL14 led to the inhibition of the TNF-α-induced cell senescence. METTL14 overexpression promoted cell senescence. METTL14 regulated the m6A modification of miR-34a-5p and interacted with DGCR8 to process miR-34a-5p. The miR-34a-5p inhibitor inhibited the cell cycle senescence of HNPCs. miR-34a-5p was predicted to interact with the SIRT1 mRNA. SIRT1 overexpression counteracted the miR-34a-5p-promoted cell senescence. METTL14 participates in the TNF-α-induced m6A modification of miR-34a-5p to promote cell senescence in HNPCs and NP cells of IVDD patients. Downregulation of either METTL14 expression or miR-34a-5p leads to the inhibition of cell cycle arrest and senescence. SIRT1 mRNA is an effective binding target of miR-34a-5p, and SIRT1 overexpression mitigates the cell cycle arrest and senescence caused by miR-34a-5p.
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Affiliation(s)
- Hao Zhu
- Department of Orthopaedics, The Affiliated Shanghai General Hospital of Nanjing Medical University, Shanghai, China.,Department of Orthopaedics, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, Yancheng, China
| | - Bao Sun
- Department of Orthopaedics, The Affiliated Shanghai General Hospital of Nanjing Medical University, Shanghai, China
| | - Liang Zhu
- Department of Orthopaedics, The Affiliated Shanghai General Hospital of Nanjing Medical University, Shanghai, China
| | - Guoyou Zou
- Department of Orthopaedics, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, Yancheng, China
| | - Qiang Shen
- Department of Orthopaedics, The Affiliated Shanghai General Hospital of Nanjing Medical University, Shanghai, China
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26
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Li D, Knox B, Gong B, Chen S, Guo L, Liu Z, Tong W, Ning B. Identification of Translational microRNA Biomarker Candidates for Ketoconazole-Induced Liver Injury Using Next-Generation Sequencing. Toxicol Sci 2021; 179:31-43. [PMID: 33078836 PMCID: PMC7855383 DOI: 10.1093/toxsci/kfaa162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Drug-induced liver injury (DILI) is a leading cause of acute liver failure. Reliable and translational biomarkers are needed for early detection of DILI. microRNAs (miRNAs) have received wide attention as a novel class of potential DILI biomarkers. However, it is unclear how DILI drugs other than acetaminophen may influence miRNA expression or which miRNAs could serve as useful biomarkers in humans. We selected ketoconazole (KCZ), a classic hepatotoxin, to study miRNA biomarkers for DILI as a proof of concept for a workflow that integrated in vivo, in vitro, and bioinformatics analyses. We examined hepatic miRNA expression in KCZ-treated rats at multiple doses and durations using miRNA-sequencing and correlated our results with conventional DILI biomarkers such as liver histology. Significant dysregulation of rno-miR-34a-5p, rno-miR-331-3p, rno-miR-15b-3p, and rno-miR-676 was associated with cytoplasmic vacuolization, a phenotype in rat livers with KCZ-induced injury, which preceded the elevation of serum liver transaminases (ALT and AST). Between rats and humans, miR-34a-5p, miR-331-3p, and miR-15b-3p were evolutionarily conserved with identical sequences, whereas miR-676 showed 73% sequence similarity. Using quantitative PCR, we found that the levels of hsa-miR-34a-5p, hsa-miR-331-3p, and hsa-miR-15b-3p were significantly elevated in the culture media of HepaRG cells treated with 100 µM KCZ (a concentration that induced cytotoxicity). Additionally, we computationally characterized the miRNA candidates for their gene targeting, target functions, and miRNA/target evolutionary conservation. In conclusion, we identified miR-34a-5p, miR-331-3p, and miR-15b-3p as translational biomarker candidates for early detection of KCZ-induced liver injury with a workflow applicable to computational toxicology studies.
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Affiliation(s)
- Dongying Li
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
| | - Bridgett Knox
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
| | - Binsheng Gong
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
| | - Si Chen
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
| | - Lei Guo
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
| | - Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079
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27
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Kumar S, Gonzalez EA, Rameshwar P, Etchegaray JP. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers (Basel) 2020; 12:E3657. [PMID: 33291485 PMCID: PMC7762117 DOI: 10.3390/cancers12123657] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that regulate gene expressions. NcRNAs include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), circular RNAs (cRNAs) and piwi-interacting RNAs (piRNAs). This review focuses on two types of ncRNAs: microRNAs (miRNAs) or short interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs). We highlight the mechanisms by which miRNAs and lncRNAs impact the epigenome in the context of cancer. Both miRNAs and lncRNAs have the ability to interact with numerous epigenetic modifiers and transcription factors to influence gene expression. The aberrant expression of these ncRNAs is associated with the development and progression of tumors. The primary reason for their deregulated expression can be attributed to epigenetic alterations. Epigenetic alterations can cause the misregulation of ncRNAs. The experimental evidence indicated that most abnormally expressed ncRNAs impact cellular proliferation and apoptotic pathways, and such changes are cancer-dependent. In vitro and in vivo experiments show that, depending on the cancer type, either the upregulation or downregulation of ncRNAs can prevent the proliferation and progression of cancer. Therefore, a better understanding on how ncRNAs impact tumorigenesis could serve to develop new therapeutic treatments. Here, we review the involvement of ncRNAs in cancer epigenetics and highlight their use in clinical therapy.
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Affiliation(s)
- Subhasree Kumar
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Edward A. Gonzalez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Pranela Rameshwar
- Department of Medicine, Hematology/Oncology, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Jean-Pierre Etchegaray
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
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28
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Marceca GP, Nigita G, Calore F, Croce CM. MicroRNAs in Skeletal Muscle and Hints on Their Potential Role in Muscle Wasting During Cancer Cachexia. Front Oncol 2020; 10:607196. [PMID: 33330108 PMCID: PMC7732629 DOI: 10.3389/fonc.2020.607196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer-associated cachexia is a heterogeneous, multifactorial syndrome characterized by systemic inflammation, unintentional weight loss, and profound alteration in body composition. The main feature of cancer cachexia is represented by the loss of skeletal muscle tissue, which may or may not be accompanied by significant adipose tissue wasting. Such phenotypic alteration occurs as the result of concomitant increased myofibril breakdown and reduced muscle protein synthesis, actively contributing to fatigue, worsening of quality of life, and refractoriness to chemotherapy. According to the classical view, this condition is primarily triggered by interactions between specific tumor-induced pro-inflammatory cytokines and their cognate receptors expressed on the myocyte membrane. This causes a shift in gene expression of muscle cells, eventually leading to a pronounced catabolic condition and cell death. More recent studies, however, have shown the involvement of regulatory non-coding RNAs in the outbreak of cancer cachexia. In particular, the role exerted by microRNAs is being widely addressed, and several mechanistic studies are in progress. In this review, we discuss the most recent findings concerning the role of microRNAs in triggering or exacerbating muscle wasting in cancer cachexia, while mentioning about possible roles played by long non-coding RNAs and ADAR-mediated miRNA modifications.
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Affiliation(s)
- Gioacchino P Marceca
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Federica Calore
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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29
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Lee HT, Oh S, Ro DH, Yoo H, Kwon YW. The Key Role of DNA Methylation and Histone Acetylation in Epigenetics of Atherosclerosis. J Lipid Atheroscler 2020; 9:419-434. [PMID: 33024734 PMCID: PMC7521974 DOI: 10.12997/jla.2020.9.3.419] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Atherosclerosis, which is the most common chronic disease of the coronary artery, constitutes a vascular pathology induced by inflammation and plaque accumulation within arterial vessel walls. Both DNA methylation and histone modifications are epigenetic changes relevant for atherosclerosis. Recent studies have shown that the DNA methylation and histone modification systems are closely interrelated and mechanically dependent on each other. Herein, we explore the functional linkage between these systems, with a particular emphasis on several recent findings suggesting that histone acetylation can help in targeting DNA methylation and that DNA methylation may control gene expression during atherosclerosis.
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Affiliation(s)
- Han-Teo Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul, Korea.,Interdisciplinary Program in Stem Cell Biology, Graduate School of Medicine, Seoul National University, Seoul, Korea
| | - Sanghyeon Oh
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul, Korea.,Interdisciplinary Program in Stem Cell Biology, Graduate School of Medicine, Seoul National University, Seoul, Korea
| | - Du Hyun Ro
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul, Korea.,Interdisciplinary Program in Stem Cell Biology, Graduate School of Medicine, Seoul National University, Seoul, Korea.,Department of Orthopedic Surgery, Seoul National University Hospital, Seoul, Korea
| | - Hyerin Yoo
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul, Korea.,Interdisciplinary Program in Stem Cell Biology, Graduate School of Medicine, Seoul National University, Seoul, Korea
| | - Yoo-Wook Kwon
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes & Cancer, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.,Department of Medicine, College of Medicine, Seoul National University, Seoul, Korea
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30
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Primorac D, Molnar V, Rod E, Jeleč Ž, Čukelj F, Matišić V, Vrdoljak T, Hudetz D, Hajsok H, Borić I. Knee Osteoarthritis: A Review of Pathogenesis and State-Of-The-Art Non-Operative Therapeutic Considerations. Genes (Basel) 2020; 11:E854. [PMID: 32722615 PMCID: PMC7464436 DOI: 10.3390/genes11080854] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/11/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Being the most common musculoskeletal progressive condition, osteoarthritis is an interesting target for research. It is estimated that the prevalence of knee osteoarthritis (OA) among adults 60 years of age or older is approximately 10% in men and 13% in women, making knee OA one of the leading causes of disability in elderly population. Today, we know that osteoarthritis is not a disease characterized by loss of cartilage due to mechanical loading only, but a condition that affects all of the tissues in the joint, causing detectable changes in tissue architecture, its metabolism and function. All of these changes are mediated by a complex and not yet fully researched interplay of proinflammatory and anti-inflammatory cytokines, chemokines, growth factors and adipokines, all of which can be measured in the serum, synovium and histological samples, potentially serving as biomarkers of disease stage and progression. Another key aspect of disease progression is the epigenome that regulates all the genetic expression through DNA methylation, histone modifications, and mRNA interference. A lot of work has been put into developing non-surgical treatment options to slow down the natural course of osteoarthritis to postpone, or maybe even replace extensive surgeries such as total knee arthroplasty. At the moment, biological treatments such as platelet-rich plasma, bone marrow mesenchymal stem cells and autologous microfragmented adipose tissue containing stromal vascular fraction are ordinarily used. Furthermore, the latter two mentioned cell-based treatment options seem to be the only methods so far that increase the quality of cartilage in osteoarthritis patients. Yet, in the future, gene therapy could potentially become an option for orthopedic patients. In the following review, we summarized all of the latest and most important research in basic sciences, pathogenesis, and non-operative treatment.
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Affiliation(s)
- Dragan Primorac
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- Eberly College of Science, The Pennsylvania State University, University Park, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- Medical School, University of Split, 21000 Split, Croatia
- School of Medicine, Faculty of Dental Medicine and Health, University “Josip Juraj Strossmayer”, 31000 Osijek, Croatia
- School of Medicine, JJ Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Medical School REGIOMED, 96 450 Coburg, Germany
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
| | - Vilim Molnar
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- School of Medicine, JJ Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Eduard Rod
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- School of Medicine, JJ Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Željko Jeleč
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- School of Medicine, JJ Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Nursing, University North, 48 000 Varaždin, Croatia
| | - Fabijan Čukelj
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- Medical School, University of Split, 21000 Split, Croatia
| | - Vid Matišić
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
| | - Trpimir Vrdoljak
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- Department of Orthopedics, Clinical Hospital “Sveti Duh”, 10000 Zagreb, Croatia
| | - Damir Hudetz
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- School of Medicine, JJ Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Orthopedics, Clinical Hospital “Sveti Duh”, 10000 Zagreb, Croatia
| | - Hana Hajsok
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- Medical School, University of Zagreb, 10000 Zagreb, Croatia
| | - Igor Borić
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia; (V.M.); (E.R.); (Ž.J.); (F.Č.); (V.M.); (T.V.); (D.H.); (H.H.); (I.B.)
- Medical School, University of Split, 21000 Split, Croatia
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
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Abstract
Being the most common musculoskeletal progressive condition, osteoarthritis is an interesting target for research. It is estimated that the prevalence of knee osteoarthritis (OA) among adults 60 years of age or older is approximately 10% in men and 13% in women, making knee OA one of the leading causes of disability in elderly population. Today, we know that osteoarthritis is not a disease characterized by loss of cartilage due to mechanical loading only, but a condition that affects all of the tissues in the joint, causing detectable changes in tissue architecture, its metabolism and function. All of these changes are mediated by a complex and not yet fully researched interplay of proinflammatory and anti-inflammatory cytokines, chemokines, growth factors and adipokines, all of which can be measured in the serum, synovium and histological samples, potentially serving as biomarkers of disease stage and progression. Another key aspect of disease progression is the epigenome that regulates all the genetic expression through DNA methylation, histone modifications, and mRNA interference. A lot of work has been put into developing non-surgical treatment options to slow down the natural course of osteoarthritis to postpone, or maybe even replace extensive surgeries such as total knee arthroplasty. At the moment, biological treatments such as platelet-rich plasma, bone marrow mesenchymal stem cells and autologous microfragmented adipose tissue containing stromal vascular fraction are ordinarily used. Furthermore, the latter two mentioned cell-based treatment options seem to be the only methods so far that increase the quality of cartilage in osteoarthritis patients. Yet, in the future, gene therapy could potentially become an option for orthopedic patients. In the following review, we summarized all of the latest and most important research in basic sciences, pathogenesis, and non-operative treatment.
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Jiang Y, Ji X, Liu K, Shi Y, Wang C, Li Y, Zhang T, He Y, Xiang M, Zhao R. Exosomal miR-200c-3p negatively regulates the migraion and invasion of lipopolysaccharide (LPS)-stimulated colorectal cancer (CRC). BMC Mol Cell Biol 2020; 21:48. [PMID: 32600257 PMCID: PMC7325272 DOI: 10.1186/s12860-020-00291-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 06/16/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a leading cancer and a major cause of death. Lipopolysaccharide (LPS), an abundant component in gut microbiome, is involved in CRC progression and metastasis, potentially through regulating the miRNA composition of CRC-derived exosomes. In this study, we aimed to identify miRNA species in exosome which regulates CRC progression after LPS stimulation. RESULTS Firstly, we discovered a shift of miRNA profile in CRC exosome after LPS stimulation. Among the differentially expressed miRNAs, we identified miR-200c-3p as a potential key regulator of CRC progression and metastasis. Retrospective analysis revealed that miR-200c-3p was elevated in CRC tumor tissues, but decreased in the serum exosome in CRC patients. In vitro experiments demonstrated that exosomal miR-200c-3p expression did not influence CRC cell proliferation, but negatively regulated their capacity of migration and invasion in the presence of LPS. miR-200c-3p level in exosome influenced exosomal expression of Zinc finger E-box-binding homeobox-1 (ZEB-1) mRNA, one of the miR-200c targets which affects migration and invasion capacity, and further altered ZEB-1 protein expression in CRC cell. In addition, exosomal miR-200c-3p promotes apoptosis of HCT-116 cells. CONCLUSIONS Our findings indicate that exosomal miR-200c-3p inhibits CRC migration and invasion, and promotes their apoptosis after LPS stimulation. It is suggested as a potential diagnostic marker and therapeutic target of CRC.
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Affiliation(s)
- Yimei Jiang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xiaopin Ji
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Kun Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yiqing Shi
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Changgang Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - You Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Tao Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yonggang He
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Ming Xiang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
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Boukelia A, Boucheham A, Belguidoum M, Batouche M, Zehraoui F, Tahi F. A Novel Integrative Approach for Non-coding RNA Classification Based on Deep Learning. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191105160633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background:
Molecular biomarkers show new ways to understand many disease
processes. Noncoding RNAs as biomarkers play a crucial role in several cellular activities, which
are highly correlated to many human diseases especially cancer. The classification and the
identification of ncRNAs have become a critical issue due to their application, such as biomarkers
in many human diseases.
Objective:
Most existing computational tools for ncRNA classification are mainly used for
classifying only one type of ncRNA. They are based on structural information or specific known
features. Furthermore, these tools suffer from a lack of significant and validated features.
Therefore, the performance of these methods is not always satisfactory.
Methods:
We propose a novel approach named imCnC for ncRNA classification based on
multisource deep learning, which integrates several data sources such as genomic and epigenomic
data to identify several ncRNA types. Also, we propose an optimization technique to visualize the
extracted features pattern from the multisource CNN model to measure the epigenomics features
of each ncRNA type.
Results:
The computational results using a dataset of 16 human ncRNA classes downloaded from
RFAM show that imCnC outperforms the existing tools. Indeed, imCnC achieved an accuracy of
94,18%. In addition, our method enables to discover new ncRNA features using an optimization
technique to measure and visualize the features pattern of the imCnC classifier.
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Affiliation(s)
- Abdelbasset Boukelia
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Anouar Boucheham
- University Salah Boubnider Constantine 3, Constantine 25000, Algeria
| | - Meriem Belguidoum
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Mohamed Batouche
- IT Department, CCIS - RC, Princess Nourah University, Riyadh, Saudi Arabia
| | - Farida Zehraoui
- IBISC, University Evry, University Paris-Saclay, Evry, France
| | - Fariza Tahi
- IBISC, University Evry, University Paris-Saclay, Evry, France
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Xu YJ, Liu PP, Ng SC, Teng ZQ, Liu CM. Regulatory networks between Polycomb complexes and non-coding RNAs in the central nervous system. J Mol Cell Biol 2020; 12:327-336. [PMID: 31291646 PMCID: PMC7288736 DOI: 10.1093/jmcb/mjz058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/26/2019] [Accepted: 06/11/2019] [Indexed: 01/29/2023] Open
Abstract
High-throughput sequencing has facilitated the identification of many types of non-coding RNAs (ncRNAs) involved in diverse cellular processes. NcRNAs as epigenetic mediators play key roles in neuronal development, maintenance, and dysfunction by controlling gene expression at multiple levels. NcRNAs may not only target specific DNA or RNA for gene silence but may also directly interact with chromatin-modifying proteins like Polycomb group (PcG) proteins to drive orchestrated transcriptional programs. Recent significant progress has been made in characterizing ncRNAs and PcG proteins involved in transcriptional, post-transcriptional, and epigenetic regulation. More importantly, dysregulation of ncRNAs, PcG proteins, and interplay among them is closely associated with the pathogenesis of central nervous system (CNS) disorders. In this review, we focus on the interplay between ncRNAs and PcG proteins in the CNS and highlight the functional roles of the partnership during neural development and diseases.
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Affiliation(s)
- Ya-Jie Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shyh-Chang Ng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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35
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MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella. Sci Rep 2020; 10:2570. [PMID: 32054914 PMCID: PMC7018962 DOI: 10.1038/s41598-020-59407-3] [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: 04/14/2019] [Accepted: 01/15/2020] [Indexed: 12/23/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) strains cause symptomatic urinary tract infections in humans whereas commensal-like E. coli strains in the urinary bladder cause long-term asymptomatic bacteriuria (ABU). We previously reported that UPEC and ABU strains differentially regulate key DNA methylation and histone acetylation components in the surrogate insect host Galleria mellonella to epigenetically modulate innate immunity-related gene expression, which in turn controls bacterial growth. In this follow-up study, we infected G. mellonella larvae with UPEC strain CFT073 or ABU strain 83972 to identify differences in the expression of microRNAs (miRNAs), a class of non-coding RNAs that regulate gene expression at the post-transcriptional level. Our small RNA sequencing analysis showed that UPEC and ABU infections caused significant changes in the abundance of miRNAs in the larvae, and highlighted the differential expression of 147 conserved miRNAs and 95 novel miRNA candidates. We annotated the G. mellonella genome sequence to investigate the miRNA-regulated expression of genes encoding antimicrobial peptides, signaling proteins, and enzymatic regulators of DNA methylation and histone acetylation in infected larvae. Our results indicate that miRNAs play a role in the epigenetic reprograming of innate immunity in G. mellonella larvae to distinguish between pathogenic and commensal strains of E. coli.
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Iannone F, Montesanto A, Cione E, Crocco P, Caroleo MC, Dato S, Rose G, Passarino G. Expression Patterns of Muscle-Specific miR-133b and miR-206 Correlate with Nutritional Status and Sarcopenia. Nutrients 2020; 12:E297. [PMID: 31979011 PMCID: PMC7071413 DOI: 10.3390/nu12020297] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 12/23/2022] Open
Abstract
Sarcopenia and malnutrition are commonly occurring conditions in the elderly that frequently coexist, leading to substantial effects on morbidity/mortality. Evidence established muscle-specific microRNAs (miRNAs) or myomiRs as essential regulators of skeletal muscle processes, from myogenesis to muscle homeostasis. This study aimed to evaluate the association between myomiRs and sarcopenia and explore the potential of nutrition in mediating this association. qPCR was employed to characterize the myomiR-1, -133a/b, -206, -208b, and -499 expression profiles of 109 non-sarcopenic and 109 sarcopenic subjects. In our sample, the proportion malnourished or at-risk subjects was higher in sarcopenia (p < 0.001). Among the detected myomiRs (miR-133a/b and miR-206), lower levels of miR-133b was significantly associated with the presence of sarcopenia (p = 0.006); however, this relationship was not independent from nutritional status in multivariate analysis, suggesting a mediating effect of nutrition on the relationship between miR-133b and sarcopenia. Correlation analyses showed that lower miR-133b levels were associated with poor nutritional status (Mini Nutritional Assessment Long Form (MNA-LF) score, p = 0.005); furthermore, correlations with albumin, ferritin, and iron were found. Similar results were obtained for miR-206. Statistically more significant correlations were observed in subjects with sarcopenia. In conclusion, our findings highlight a nutrient-miR-133b/miR-206 pathway having a potential role in the age-related muscle decline.
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Affiliation(s)
- Francesca Iannone
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (F.I.); (A.M.); (P.C.); (S.D.); (G.P.)
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (F.I.); (A.M.); (P.C.); (S.D.); (G.P.)
| | - Erika Cione
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (E.C.); (M.C.C.)
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (F.I.); (A.M.); (P.C.); (S.D.); (G.P.)
| | - Maria Cristina Caroleo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (E.C.); (M.C.C.)
| | - Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (F.I.); (A.M.); (P.C.); (S.D.); (G.P.)
| | - Giuseppina Rose
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (F.I.); (A.M.); (P.C.); (S.D.); (G.P.)
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (F.I.); (A.M.); (P.C.); (S.D.); (G.P.)
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Ibrahim AA, Ramadan A, Wahby AA, Hassan M, Soliman HM, Abdel Hamid TA. Micro-RNA 196a2 expression and miR-196a2 (rs11614913) polymorphism in T1DM: a pilot study. J Pediatr Endocrinol Metab 2019; 32:1171-1179. [PMID: 31472066 DOI: 10.1515/jpem-2019-0226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/02/2019] [Indexed: 12/28/2022]
Abstract
Background Recent emerging evidence supports the role of miR-196a2 in various human diseases. However, its role in type 1 diabetes mellitus (T1DM) is still underestimated. We aimed, for the first time, to investigate the expression of miR-196a2 in T1DM and the association of miR-196a2 (rs11614913) polymorphism with susceptibility of T1DM in a sample of patients from Cairo, Egypt. Methods The study included 150 patients and 150 healthy subjects. Evaluation of rs11614913 genotypes and miR-196a2 expression was done using the allelic discrimination and quantitative reverse transcriptase polymerase chain reaction (PCR) method, respectively. Results The Hardy-Weinberg equilibrium of single nucleotide polymorphism(SNP) was detected among controls (p = 0.2). Our results revealed that the TT genotype was more frequent in patients (22.6%) than controls (10%) while the CC genotype was more frequent in controls (47.3%) than patients (39.3%) (p = 0.01). The frequency of the T allele was significantly higher in patients than in controls (41.7 vs. 31.3%), while the C allele was more frequent in controls (p = 0.008). After adjustment for traditional risk factors, the association of the TT genotype with T1DM remained significant (TT vs. CC, odds ration [OR] = 3.2, 95% confidence interval [CI]: 1.4-7.4, p = 0.005). Power analysis of the data yielded a statistical power of 80% for the miR-196a2 rs11614913 with T1DM. Relative expression of miR-196a2 showed significant decrease in patients compared to controls (median = 0.09, 0.5, interquartile range [IQR] = 0.03-1.6, 0.1-2.1). However, miR-196a2 expression showed no significant difference between different rs11614913 genotypes (p = 0.5). Conclusions Our findings demonstrated that miR-196a rs11614913 is associated with T1DM and decreased expression of miR-196a2 may play a role in pathogenesis of T1DM.
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Affiliation(s)
- Alshaymaa A Ibrahim
- Clinical and Chemical Pathology Department, National Research Centre, El Buhouth St, Dokki, Cairo 12311, Egypt, Phone: 00201006193988, Fax: +20233370931
| | - Abeer Ramadan
- Molecular Genetics and Enzymology Department, Human Genetic and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Aliaa Ahmed Wahby
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt
| | - Mirhane Hassan
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt
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Bhargava A, Shukla A, Bunkar N, Shandilya R, Lodhi L, Kumari R, Gupta PK, Rahman A, Chaudhury K, Tiwari R, Goryacheva IY, Mishra PK. Exposure to ultrafine particulate matter induces NF-κβ mediated epigenetic modifications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:39-50. [PMID: 31146237 DOI: 10.1016/j.envpol.2019.05.065] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
Exposure to ultrafine particulate matter (PM0.1) is positively associated with the etiology of different acute and chronic disorders; however, the in-depth biological imprints that link these submicron particles with the disturbances in the epigenomic machinery are not well defined. Earlier, we showed that exposure to these particles causes significant disturbances in the mitochondrial machinery and triggers PI-3-kinase mediated DNA damage responses. In the present study, we aimed to further understand the epigenomic insights of the ultrafine PM exposure. The higher levels of intracellular reactive oxygen species and depleted Nrf-2 in ultrafine PM exposed cells reconfirmed its potential to induce oxidative stress. Importantly, the observed increase in the levels of NF-κβ and associated cytokines among exposed cells suggested the activation of NF-κβ mediated inflammatory loop which potentially serves as a platform for initiating epigenetic insinuations. This fact was strongly supported by the altered miRNA expression profile of the ultrafine PM exposed cells. These NF-κβ induced miRNA alterations were also found to be associated with other epigenetic targets as the exposed cells showed higher expression levels of DNA methyltransferases which positively corresponded with the global changes in DNA methylation levels. Upon further analysis, significant alterations in histone code were also reported in ultrafine PM exposed cells. Conclusively our results suggested that NF-κβ acts as an inflammatory switch that possesses the potential to induce genome-wide epigenetic modification upon ultrafine PM exposure.
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Affiliation(s)
- Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Anushi Shukla
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Neha Bunkar
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Lalit Lodhi
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pushpendra Kumar Gupta
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Akhlaqur Rahman
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Koel Chaudhury
- School of Medical Science & Technology, Indian Institute of Technology, Kharagpur, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Irina Yu Goryacheva
- Department of General and Inorganic Chemistry, Saratov State University, Saratov, Russia
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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Maurus I, Hasan A, Röh A, Takahashi S, Rauchmann B, Keeser D, Malchow B, Schmitt A, Falkai P. Neurobiological effects of aerobic exercise, with a focus on patients with schizophrenia. Eur Arch Psychiatry Clin Neurosci 2019; 269:499-515. [PMID: 31115660 DOI: 10.1007/s00406-019-01025-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/15/2019] [Indexed: 02/08/2023]
Abstract
Schizophrenia is a severe neuropsychiatric disease that is associated with neurobiological alterations in multiple brain regions and peripheral organs. Negative symptoms and cognitive deficits are present in about half of patients and are difficult to treat, leading to an unfavorable functional outcome. To investigate the impact of aerobic exercise on various neurobiological parameters, we conducted a narrative review. Add-on aerobic exercise was shown to be effective in improving negative and general symptoms, cognition, global functioning, and quality of life in schizophrenia patients. Based on findings in healthy individuals and animal models, this qualitative review gives an overview of different lines of evidence on how aerobic exercise impacts brain structure and function and molecular mechanisms in patients with schizophrenia and how its effects could be related to clinical and functional outcomes. Structural magnetic resonance imaging studies showed a volume increase in the hippocampus and cortical regions in schizophrenia patients and healthy controls after endurance training. However, results are inconsistent and individual risk factors may influence neuroplastic processes. Animal studies indicate that alterations in epigenetic mechanisms and synaptic plasticity are possible underlying mechanisms, but that differentiation of glial cells, angiogenesis, and possibly neurogenesis may also be involved. Clinical and animal studies also revealed effects of aerobic exercise on the hypothalamus-pituitary-adrenal axis, growth factors, and immune-related mechanisms. Some findings indicate effects on neurotransmitters and the endocannabinoid system. Further research is required to clarify how individual risk factors in schizophrenia patients mediate or moderate the neurobiological effects of exercise on brain and cognition. Altogether, aerobic exercise is a promising candidate in the search for pathophysiology-based add-on interventions in schizophrenia.
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Affiliation(s)
- Isabel Maurus
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany.
| | - Alkomiet Hasan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany
| | - Astrid Röh
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany
| | - Shun Takahashi
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany.,Department of Neuropsychiatry, Wakayama Medical University, Wakayama, Japan
| | - Boris Rauchmann
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany
| | - Daniel Keeser
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany.,Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Berend Malchow
- Department of Psychiatry and Psychotherapy, University Hospital Jena, Jena, Germany
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany.,Laboratory of Neuroscience (LIM27), Institute of Psychiatry, University of Sao Paulo, São Paulo, Brazil
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336, Munich, Germany
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Polli A, Ickmans K, Godderis L, Nijs J. When Environment Meets Genetics: A Clinical Review of the Epigenetics of Pain, Psychological Factors, and Physical Activity. Arch Phys Med Rehabil 2019; 100:1153-1161. [DOI: 10.1016/j.apmr.2018.09.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023]
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Xu EG, Khursigara AJ, Li S, Esbaugh AJ, Dasgupta S, Volz DC, Schlenk D. mRNA-miRNA-Seq Reveals Neuro-Cardio Mechanisms of Crude Oil Toxicity in Red Drum ( Sciaenops ocellatus). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3296-3305. [PMID: 30816040 DOI: 10.1021/acs.est.9b00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) present in crude oil can cause global gene dysregulation and developmental impairment in fish. However, the mechanisms that alter gene regulation are not well understood. In this study, larval red drum ( Sciaenops ocellatus) were exposed to water accommodated fractions of source oil (6.8, 13.7, and 35.9 μg/L total PAHs) and weathered slick oil (4.7, 8.1, and 18.0 μg/L total PAHs) from the Deepwater Horizon (DWH) oil spill. The global mRNA-microRNA functional networks associated with the toxicity of DWH oil were explored by next-generation sequencing and in-depth bioinformatics analyses. Both source and slick oil significantly altered the expression of miR-18a, miR-27b, and miR-203a across all exposure concentrations. Consistent with the observed concentration-dependent morphological changes, the target mRNAs of these microRNAs were predominantly involved in neuro-cardio system development processes and associated key signaling pathways such as axonal guidance signaling, cAMP-response-element-binding protein signaling in neurons, calcium signaling, and nuclear-factor-of-activated T cells signaling in cardiac hypertrophy. The results indicated that the developmental toxicity of crude oil may result from the abnormal expression of microRNAs and associated target genes, especially for the nervous system. Moreover, we provide a case study for systematic toxicity evaluation leveraging mRNA-microRNA-seq data using nonmodel species.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
- Department of Chemical Engineering , McGill University , Montreal , Quebec H3A 0C5 , Canada
| | - Alexis J Khursigara
- Marine Science Institute , University of Texas at Austin , Austin , Texas 78373 , United States
| | - Shuying Li
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
- Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , P. R. China
| | - Andrew J Esbaugh
- Marine Science Institute , University of Texas at Austin , Austin , Texas 78373 , United States
| | - Subham Dasgupta
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
| | - David C Volz
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
| | - Daniel Schlenk
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
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Gasiūnienė M, Zentelytė A, Treigytė G, Baronaitė S, Savickienė J, Utkus A, Navakauskienė R. Epigenetic alterations in amniotic fluid mesenchymal stem cells derived from normal and fetus-affected gestations: A focus on myogenic and neural differentiations. Cell Biol Int 2019; 43:299-312. [PMID: 30635962 DOI: 10.1002/cbin.11099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/05/2019] [Indexed: 12/21/2022]
Abstract
Amniotic fluid-derived mesenchymal stem cells (AF-MSCs) are autologous to the fetus and represent a potential alternative source for the regenerative medicine and treatment of perinatal disorders. To date, AF-MSCs differentiation capacity to non-mesodermal lineages and epigenetic regulation are still poorly characterized. The present study investigated the differentiation potential of AF-MSCs toward neural-like cells in comparison to the mesodermal myogenic lineage and assessed epigenetic factors involved in tissue-specific differentiation. Myogenic and neural differentiation assays were performed by the incubation with specific induction media. Typical MSCs markers were determined by flow cytometry, the expression of lineage-specific genes, microRNAs and chromatin modifying proteins were examined by RT-qPCR and Western blot, respectively. AF-MSCs of normal and fetus-affected gestations had similar stem cells characteristics and two-lineage potential, as characterized by cell morphology and the expression of myogenic and neural markers. Two-lineage differentiation process was associated with the down-regulation of miR-17 and miR-21, the up-regulation of miR-34a, miR-146a and DNMT3a/DNMT3b along with the gradual decrease in the levels of DNMT1, HDAC1, active marks of chromatin (H4hyperAc, H3K9ac, H3K4me3) and the repressive H3K9me3 mark. Differentiation was accompanied by the down-regulation of PRC1/2 proteins (BMI1/SUZ12, EZH2) and the retention of the repressive H3K27me3 mark. We report that both AF-MSCs of normal and fetus-affected gestations possess differentiation capacity toward myogenic and neural lineages through rather similar epigenetic mechanisms that may provide potential applications for further investigation of the molecular basis of prenatal diseases and for the future autologous therapy.
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Affiliation(s)
- Monika Gasiūnienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Aistė Zentelytė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Gražina Treigytė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Sandra Baronaitė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Jūratė Savickienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, M. K. Ciurlionio st. 21, Vilnius, LT-03101, Lithuania
| | - Rūta Navakauskienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
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Sankrityayan H, Kulkarni YA, Gaikwad AB. Diabetic nephropathy: The regulatory interplay between epigenetics and microRNAs. Pharmacol Res 2019; 141:574-585. [PMID: 30695734 DOI: 10.1016/j.phrs.2019.01.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/20/2022]
Abstract
Diabetic nephropathy (DN) is still one of the leading causes of end-stage renal disease despite the emergence of different therapies to counter the metabolic, hemodynamic and fibrotic pathways, implicating a prominent role of genetic and epigenetic factors in its progression. Epigenetics is the study of changes in the expression of genes which may be inheritable and does not involve a change in the genome sequence. Thrust areas of epigenetic research are DNA methylation and histone modifications. Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) control the expression of genes via post-transcriptional mechanisms. However, the regulation by epigenetic mechanisms and miRNAs are not completely distinct. A number of emerging reports have revealed the interplay between epigenetic machinery and miRNA expression, particularly in cancer. Further research has proved that a feedback loop exists between miRNA expression and epigenetic regulation in disorders including DN. Studies showed that different miRNAs (miR-200, miR-29 etc.) were found to be regulated by epigenetic mechanisms viz. DNA methylation and histone modifications. Conversely, miRNAs (miR-301, miR-449 etc.) themselves modulated levels of DNA methyltranferases (DNMTs) and Histone deacetylases (HDACs), enzymes vital to epigenetic modifications. With already few FDA approved epigenetic -modulating drugs (Vorinostat, Decitabine) in the market and miRNA therapeutic drugs under clinical trial it becomes imperative to analyze the possible interaction between the two classes of drugs in the modulation of a disease process. The purpose of this review is to articulate the interplay between miRNA expression and epigenetic modifications with a particular focus on its impact on the development and progression of DN.
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Affiliation(s)
- Himanshu Sankrityayan
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Yogesh A Kulkarni
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai 400056, India
| | - Anil Bhanudas Gaikwad
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India.
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Fathollahi A, Aslani S, Jamshidi A, Mahmoudi M. Epigenetics in osteoarthritis: Novel spotlight. J Cell Physiol 2019; 234:12309-12324. [DOI: 10.1002/jcp.28020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/30/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Anwar Fathollahi
- Department of Immunology School of Medicine, Shahid Beheshti University of Medical Sciences Tehran Iran
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
| | - Saeed Aslani
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
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Saxena S, Gupta A, Shukla V, Rani V. Functional annotation of differentially expressed fetal cardiac microRNA targets: implication for microRNA-based cardiovascular therapeutics. 3 Biotech 2018; 8:494. [PMID: 30498667 DOI: 10.1007/s13205-018-1520-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/17/2018] [Indexed: 01/23/2023] Open
Abstract
Gene expression pattern of a failing heart depicts remarkable similarity with developing fetal heart. Elucidating genetic as well as epigenetic mechanisms regulating the gene expression during cardiac development will improve our understanding of cardiovascular diseases. In the present study, we aimed to validate and characterize differentially expressed known microRNAs (miRNA) obtained from next generation sequencing data of two fetal cardiac developmental stages (days 4th and 14th) from chicken (G. gallus domesticus) using bioinformatic approaches. Potential mRNA targets of individual miRNA were identified and classified according to their biological, cellular, and molecular functions. Functional annotation of putative target genes was performed to predict their association with cardiovascular diseases. We identified a total of 19 differentially expressed miRNAs between 4th and 14th day sample from the data sets obtained by next generation sequencing. A total of nearly 1522 potential targets ranging from 15 to 270 for each miRNA were predicted out of which 1221 were unique, while 301 were overlapping. Gene ontology and KEGG analysis revealed that majority of these target genes regulate critical cellular and molecular processes including transcriptional regulation, protein transport, signal transduction, matrix remodeling, Ras signaling, MAPK signaling, and TGF-beta signaling pathways indicating the complex nature of microRNA-mediated gene regulation during cardiogenesis. We found a significant association between potential target genes and cardiovascular diseases validating a link between fetal cardiac miRNAs and regulation of cardiovascular disease-related genes. These important findings may lay a foundation for further understanding the regulatory mechanisms operative in gene re-programming in the failing heart.
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Xu EG, Magnuson JT, Diamante G, Mager E, Pasparakis C, Grosell M, Roberts AP, Schlenk D. Changes in microRNA-mRNA Signatures Agree with Morphological, Physiological, and Behavioral Changes in Larval Mahi-Mahi Treated with Deepwater Horizon Oil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13501-13510. [PMID: 30376307 DOI: 10.1021/acs.est.8b04169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we performed a systematic evaluation of global microRNA-mRNA interactions associated with the developmental toxicity of Deepwater Horizon oil using a combination of integrated mRNA and microRNA deep sequencing, expression profiling, gene ontology enrichment, and functional predictions by a series of advanced bioinformatic tools. After exposure to water accommodated fraction (WAF) of both weathered slick oil (0.5%, 1%, and 2%) and source oil (0.125%, 0.25%, and 0.5%) from the Deep Water Horizon oil spill, four dose-dependent miRNAs were identified, including three up-regulated (miR-23b, miR-34b, and miR-181b) and one down-regulated miRNAs (miR-203a) in mahi-mahi hatchings exposed from 6 h postfertilization (hpf) to 48 hpf. Consistent with morphological, physiological, and behavioral changes, the target genes of these miRNAs were largely involved in the development of the cardiovascular, visual, nervous system and associated toxicity pathways, suggesting that miRNAs play an essential role in regulating the responses to oil exposure. The results obtained from this study improve our understanding of the role of miRNAs and their target genes in relation to dose-dependent oil toxicity and provide the potential of using miRNAs as novel biomarkers in future oil studies.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
| | - Jason T Magnuson
- Department of Biological Sciences & Advanced Environmental Research Institute , University of North Texas in Denton , Denton , Texas 76203 , United States
| | - Graciel Diamante
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
| | - Edward Mager
- Department of Biological Sciences & Advanced Environmental Research Institute , University of North Texas in Denton , Denton , Texas 76203 , United States
| | - Christina Pasparakis
- Department of Marine Biology and Ecology, RSMAS , University of Miami , Miami , Florida 33149 , United States
| | - Martin Grosell
- Department of Marine Biology and Ecology, RSMAS , University of Miami , Miami , Florida 33149 , United States
| | - Aaron P Roberts
- Department of Biological Sciences & Advanced Environmental Research Institute , University of North Texas in Denton , Denton , Texas 76203 , United States
| | - Daniel Schlenk
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
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47
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Role of microRNAs in inner ear development and hearing loss. Gene 2018; 686:49-55. [PMID: 30389561 DOI: 10.1016/j.gene.2018.10.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/12/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023]
Abstract
The etiology of hearing loss tends to be multi-factorial and affects a significant proportion of the global population. Despite the differences in etiology, a common physical pathological change that leads to hearing loss is damage to the mechanosensory hair cells of the inner ear. MicroRNAs (miRNAs) have been shown to play a role in inner ear development and thus, may play a role in the development or prevention of hearing loss. In this paper, we review the mechanism of action of miRNAs in the auditory system. We present an overview about the role of miRNAs in inner ear development, summarize the current research on the role of miRNAs in gene regulation, and discuss the effects of both miRNA mutations as well as overexpression. We discuss the crucial role of miRNAs in ensuring normal physiological development of the inner ear. Any deviation from the proper function of miRNA in the cochlea seems to contribute to deleterious damage to the structure of the auditory system and subsequently results in hearing loss. As interest for miRNA research increases, this paper serves as a platform to review current understandings and postulate future avenues for research. A better knowledge about the role of miRNA in the auditory system will help in developing novel treatment modalities for restoring hearing function based on regeneration of damaged inner ear hair cells.
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48
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Fan B, Luk AOY, Chan JCN, Ma RCW. MicroRNA and Diabetic Complications: A Clinical Perspective. Antioxid Redox Signal 2018; 29:1041-1063. [PMID: 28950710 DOI: 10.1089/ars.2017.7318] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE The rising global prevalence of diabetes and its debilitating complications give rise to significant disability and premature mortality. Due to the silent nature of diabetes and its vascular complications, and limitations in current methods for detection, there is a need for novel biomarkers for early detection and prognosis. Recent Advances: Metabolic memory and epigenetic factors are important in the pathogenesis of diabetic complications and interact with genetic variants, metabolic factors, and clinical risk factors. Micro(mi)RNAs interact with epigenetic mechanisms and pleiotropically mediate the effects of hyperglycemia on the vasculature. Utilizing mature profiling techniques and platforms, an increasing number of miRNA signatures and interaction networks have been identified for diabetes and its related cardiorenal complications. As a result, these short, single-stranded molecules are emerging as potential diagnostic and predictive tools in human studies, and may function as disease biomarkers, as well as treatment targets. CRITICAL ISSUES However, there is complex interaction between the genome and epigenome. The regulation of miRNAs may differ across species and tissues. Most profiling studies to date lack validation, often requiring large, well-characterized cohorts and reliable normalization strategies. Furthermore, the incremental benefits of miRNAs as biomarkers, beyond prediction provided by traditional risk factors, are critical issues to consider, yet often neglected in published studies. FUTURE DIRECTIONS All in all, the future for miRNA-based diagnostics and therapeutics for diabetic complications appears promising. Improved understanding of the complex mechanisms underlying miRNA dysregulation, and more well-designed studies utilizing prospective samples would facilitate the translation to clinical use.
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Affiliation(s)
- Baoqi Fan
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China
| | - Andrea On Yan Luk
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China .,2 Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, China
| | - Juliana Chung Ngor Chan
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China .,2 Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, China .,3 Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong , Prince of Wales Hospital, Shatin, China .,4 The Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine , Shatin, China
| | - Ronald Ching Wan Ma
- 1 Department of Medicine and Therapeutics, The Chinese University of Hong Kong , Shatin, China .,2 Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, China .,3 Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong , Prince of Wales Hospital, Shatin, China .,4 The Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine , Shatin, China
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Ariza-Nieto M, Alley JB, Samy S, Fitzgerald L, Vermeylen F, Shuler ML, Alemán JO. Circulating MIR148A associates with sensitivity to adiponectin levels in human metabolic surgery for weight loss. Endocr Connect 2018; 7:975-982. [PMID: 30300537 PMCID: PMC6176280 DOI: 10.1530/ec-18-0205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE We sought to discover secreted biomarkers to monitor the recovery of physiological adiponectin levels with metabolic surgery, focusing on epigenetic changes that might predict adiponectin function. DESIGN We conducted a prospective observational study of patients undergoing metabolic surgery by Roux-en-Y Gastric Bypass (RYGB) for weight loss in a single center (IRB GHS # 1207-27). METHODS All patients (n = 33; 27 females; 6 males) signed informed consent. Metabolites, adiponectin and MIR148A were measured in fasting plasma. We followed MIQE for transcript profiles. RESULTS Patients lost on average 47 ± 12% excess BMI (%EBMI) after 12 weeks. Adiponectin pre, post or delta (post minus pre) did not correlate with %EBMIL. A decrease in adiponectin following weight loss surgery was observed in a subset of patients, chi-square test of independence rejects the null hypotheses that the liver DNA methyltransferase 1 (DNMT1) and delta adiponectin are independent (chi-square statistics χ2 = 6.9205, P = 0.00852, n = 33), as well as MIR148A and delta adiponectin are independent (chi-square statistics χ2 = 9.6823, P = 0.00186, n = 33). The presence of plasma MIR148A allows identification of patients that appear to be adiponectin insensitive at baseline. CONCLUSION We combined the presence of plasma MIR148A, the concentration of total adiponectin and the expression of DNA methyltransferase 1 (DNMT1) in liver biopsy tissue to identify patients with non-physiological adiponectin. Weight loss and physical activity interventions complemented with the new method presented here could serve to monitor the physiological levels of adiponectin, thought to be important for long-term weight loss maintenance.
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Affiliation(s)
- Magnolia Ariza-Nieto
- Cornell UniversityMeinig School of Biomedical Engineering, Ithaca, New York, USA
- epiWELLLLC, Ithaca, New York, USA
- Correspondence should be addressed to M Ariza-Nieto:
| | - Joshua B Alley
- Donald Guthrie Foundation for Education and ResearchGuthrie Clinic, Sayre, Pennsylvania, USA
| | - Sanjay Samy
- Donald Guthrie Foundation for Education and ResearchGuthrie Clinic, Sayre, Pennsylvania, USA
| | - Laura Fitzgerald
- Donald Guthrie Foundation for Education and ResearchGuthrie Clinic, Sayre, Pennsylvania, USA
| | - Francoise Vermeylen
- Cornell UniversityCornell Statistical Consulting Unit, Ithaca, New York, USA
| | - Michael L Shuler
- Cornell UniversityMeinig School of Biomedical Engineering, Ithaca, New York, USA
| | - José O Alemán
- New York University Langone Medical CenterNew York, New York, USA
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50
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Lardenoije R, Pishva E, Lunnon K, van den Hove DL. Neuroepigenetics of Aging and Age-Related Neurodegenerative Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:49-82. [PMID: 30072060 DOI: 10.1016/bs.pmbts.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases are complex, progressive disorders and affect millions of people worldwide, contributing significantly to the global burden of disease. In recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we describe the current state of play for epigenetic research into neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. We focus on the recent evidence for a potential role of DNA modifications, histone modifications and non-coding RNA in the etiology of these disorders. Finally, we discuss how new technological and bioinformatics advances in the field of epigenetics could further progress our understanding about the underlying mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Roy Lardenoije
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands; University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Daniel L van den Hove
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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