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Stein RA, Riber L. Epigenetic effects of short-chain fatty acids from the large intestine on host cells. MICROLIFE 2023; 4:uqad032. [PMID: 37441522 PMCID: PMC10335734 DOI: 10.1093/femsml/uqad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.
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Affiliation(s)
- Richard A Stein
- Corresponding author. Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA. Tel: +1-917-684-9438; E-mail: ;
| | - Leise Riber
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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52
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Affandi T, Haas A, Ohm AM, Wright GM, Black JC, Reyland ME. PKCδ regulates chromatin remodeling and DNA repair through SIRT6. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.541991. [PMID: 37292592 PMCID: PMC10245827 DOI: 10.1101/2023.05.24.541991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein kinase C delta (PKCδ) is a ubiquitous kinase whose function is defined in part by localization to specific cellular compartments. Nuclear PKCδ is both necessary and sufficient for IR-induced apoptosis, while inhibition of PKCδ activity provides radioprotection in vivo. How nuclear PKCδ regulates DNA-damage induced cell death is poorly understood. Here we show that PKCδ regulates histone modification, chromatin accessibility, and double stranded break (DSB) repair through a mechanism that requires SIRT6. Overexpression of PKCδ promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKCδ increases DNA repair via non-homologous end joining (NHEJ) and homologous recombination (HR) as evidenced by more rapid formation of NHEJ (DNA-PK) and HR (Rad51) DNA damage foci, increased expression of repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKCδ depletion is associated with more open chromatin, while overexpression of PKCδ reduces chromatin accessibility. Epiproteome analysis revealed that PKCδ depletion increases chromatin associated H3K36me2, and reduces ribosylation of KDM2A and chromatin bound KDM2A. We identify SIRT6 as a downstream mediator of PKCδ. PKCδ-depleted cells have increased expression of SIRT6, and depletion of SIRT6 reverses the changes in chromatin accessibility, histone modification and NHEJ and HR DNA repair seen with PKCδ-depletion. Furthermore, depletion of SIRT6 reverses radioprotection in PKCδ-depleted cells. Our studies describe a novel pathway whereby PKCδ orchestrates SIRT6-dependent changes in chromatin accessibility to increase DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKCδ.
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Affiliation(s)
- Trisiani Affandi
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ami Haas
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angela M. Ohm
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Gregory M. Wright
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joshua C. Black
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary E. Reyland
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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53
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Saviana M, Le P, Micalo L, Del Valle-Morales D, Romano G, Acunzo M, Li H, Nana-Sinkam P. Crosstalk between miRNAs and DNA Methylation in Cancer. Genes (Basel) 2023; 14:1075. [PMID: 37239435 PMCID: PMC10217889 DOI: 10.3390/genes14051075] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
miRNAs are some of the most well-characterized regulators of gene expression. Integral to several physiological processes, their aberrant expression often drives the pathogenesis of both benign and malignant diseases. Similarly, DNA methylation represents an epigenetic modification influencing transcription and playing a critical role in silencing numerous genes. The silencing of tumor suppressor genes through DNA methylation has been reported in many types of cancer and is associated with tumor development and progression. A growing body of literature has described the crosstalk between DNA methylation and miRNAs as an additional layer in the regulation of gene expression. Methylation in miRNA promoter regions inhibits its transcription, while miRNAs can target transcripts and subsequently regulate the proteins responsible for DNA methylation. Such relationships between miRNA and DNA methylation serve an important regulatory role in several tumor types and highlight a novel avenue for potential therapeutic targets. In this review, we discuss the crosstalk between DNA methylation and miRNA expression in the pathogenesis of cancer and describe how miRNAs influence DNA methylation and, conversely, how methylation impacts the expression of miRNAs. Finally, we address how these epigenetic modifications may be leveraged as biomarkers in cancer.
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Affiliation(s)
| | | | | | | | | | | | | | - Patrick Nana-Sinkam
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, 1250 E. Marshall Street, Richmond, VA 23298, USA
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54
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Aakula A, Sharma M, Tabaro F, Nätkin R, Kamila J, Honkanen H, Schapira M, Arrowsmith C, Nykter M, Westermarck J. RAS and PP2A activities converge on epigenetic gene regulation. Life Sci Alliance 2023; 6:e202301928. [PMID: 36858798 PMCID: PMC9979842 DOI: 10.26508/lsa.202301928] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Abstract
RAS-mediated human cell transformation requires inhibition of the tumor suppressor protein phosphatase 2A (PP2A). However, the phosphoprotein targets and cellular processes in which RAS and PP2A activities converge in human cancers have not been systematically analyzed. Here, we discover that phosphosites co-regulated by RAS and PP2A are enriched on proteins involved in epigenetic gene regulation. As examples, RAS and PP2A co-regulate the same phosphorylation sites on HDAC1/2, KDM1A, MTA1/2, RNF168, and TP53BP1. We validate RAS- and PP2A-elicited regulation of HDAC1/2 chromatin recruitment, of RNF168-TP53BP1 interaction, and of gene expression. Consistent with their known synergistic effects in cancer, RAS activation and PP2A inhibition resulted in epigenetic reporter derepression and activation of oncogenic transcription. Transcriptional derepression by PP2A inhibition was associated with an increase in euchromatin and a decrease in global DNA methylation. Collectively, the results indicate that epigenetic protein complexes constitute a significant point of convergence for RAS hyperactivity and PP2A inhibition in cancer. Furthermore, the work provides an important resource for future studies focusing on phosphoregulation of epigenetic gene regulation in cancer and in other RAS/PP2A-regulated cellular processes.
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Affiliation(s)
- Anna Aakula
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mukund Sharma
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Francesco Tabaro
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Reetta Nätkin
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Jesse Kamila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Henrik Honkanen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Matti Nykter
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
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55
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la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [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: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
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Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
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56
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Moshi JM, Ummelen M, Broers JLV, Ramaekers FCS, Hopman AHN. Impact of antigen retrieval protocols on the immunohistochemical detection of epigenetic DNA modifications. Histochem Cell Biol 2023:10.1007/s00418-023-02187-4. [PMID: 37010548 DOI: 10.1007/s00418-023-02187-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2023] [Indexed: 04/04/2023]
Abstract
This study compares three different pretreatment protocols for the immunohistochemical detection of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in nuclear DNA. The human biological samples analyzed included formalin-fixed and paraffin-embedded (FFPE) normal squamous epithelium, ethanol-fixed cultured cells, and metaphase chromosomes. The antigen retrieval methods included low pH Citrate and high pH Tris-ethylenediaminetetraacetic acid (EDTA) protocols, as well as a method using Pepsin pretreatment combined with HCl for DNA denaturation. A gradual increase in the detection levels of 5-mC and 5-hmC was observed when going from Citrate via Tris/EDTA to Pepsin/HCl retrieval. While the Citrate retrieval protocol was the least efficient for the detection of 5-mC and 5-hmC, it did preserve nuclear morphology and enabled visualization of differences in intra- and internuclear distribution patterns in tissue and cell culture samples by single- and double-fluorescence detection. Quantification of (hydroxy)methylation levels in FFPE material demonstrated a significant heterogeneity and differences in 5-mC and 5-hmC levels within and between nuclei in the different compartments of normal squamous epithelium. It was concluded that immunohistochemical detection of 5-mC and 5-hmC enables the correlation of these DNA modifications with histomorphological features in heterogeneous tissues, but this is influenced by different pretreatment protocols that must be carefully chosen to allow an appropriate interpretation of these epigenetic switches.
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Affiliation(s)
- Jobran M Moshi
- Department of Molecular Cell Biology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Monique Ummelen
- Department of Molecular Cell Biology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Jos L V Broers
- Department of Molecular Cell Biology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Frans C S Ramaekers
- Department of Molecular Cell Biology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Anton H N Hopman
- Department of Molecular Cell Biology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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57
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Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
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58
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Orchard KJA, Akbar M, Crowe LAN, Cole J, Millar NL, Raleigh SM. Characterization of Histone Modifications in Late-Stage Rotator Cuff Tendinopathy. Genes (Basel) 2023; 14:496. [PMID: 36833423 PMCID: PMC9956879 DOI: 10.3390/genes14020496] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
The development and progression of rotator cuff tendinopathy (RCT) is multifactorial and likely to manifest through a combination of extrinsic, intrinsic, and environmental factors, including genetics and epigenetics. However, the role of epigenetics in RCT, including the role of histone modification, is not well established. Using chromatin immunoprecipitation sequencing, differences in the trimethylation status of H3K4 and H3K27 histones in late-stage RCT compared to control were investigated in this study. For H3K4, 24 genomic loci were found to be significantly more trimethylated in RCT compared to control (p < 0.05), implicating genes such as DKK2, JAG2, and SMOC2 in RCT. For H3K27, 31 loci were shown to be more trimethylated (p < 0.05) in RCT compared to control, inferring a role for EPHA3, ROCK1, and DEFβ115. Furthermore, 14 loci were significantly less trimethylated (p < 0.05) in control compared to RCT, implicating EFNA5, GDF6, and GDF7. Finally, the TGFβ signaling, axon guidance, and regulation of focal adhesion assembly pathways were found to be enriched in RCT. These findings suggest that the development and progression of RCT is, at least in part, under epigenetic control, highlighting the influence of histone modifications in this disorder and paving the way to further understand the role of epigenome in RCT.
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Affiliation(s)
- Kayleigh J. A. Orchard
- Centre for Sports, Exercise and Life Sciences, Coventry University, Coventry CV1 5FB, UK
| | - Moeed Akbar
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Lindsay A. N. Crowe
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - John Cole
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Neal L. Millar
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Stuart M. Raleigh
- Centre for Sports, Exercise and Life Sciences, Coventry University, Coventry CV1 5FB, UK
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59
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Ramatchandirin B, Pearah A, He L. Regulation of Liver Glucose and Lipid Metabolism by Transcriptional Factors and Coactivators. Life (Basel) 2023; 13:life13020515. [PMID: 36836874 PMCID: PMC9962321 DOI: 10.3390/life13020515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
The prevalence of nonalcoholic fatty liver disease (NAFLD) worldwide is on the rise and NAFLD is becoming the most common cause of chronic liver disease. In the USA, NAFLD affects over 30% of the population, with similar occurrence rates reported from Europe and Asia. This is due to the global increase in obesity and type 2 diabetes mellitus (T2DM) because patients with obesity and T2DM commonly have NAFLD, and patients with NAFLD are often obese and have T2DM with insulin resistance and dyslipidemia as well as hypertriglyceridemia. Excessive accumulation of triglycerides is a hallmark of NAFLD and NAFLD is now recognized as the liver disease component of metabolic syndrome. Liver glucose and lipid metabolisms are intertwined and carbon flux can be used to generate glucose or lipids; therefore, in this review we discuss the important transcription factors and coactivators that regulate glucose and lipid metabolism.
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Affiliation(s)
| | - Alexia Pearah
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ling He
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 600 N. Wolfe St, Baltimore, MD 21287, USA
- Correspondence: ; Tel.: +1-410-502-5765; Fax: +1-410-502-5779
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60
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Meyer BS, Moiron M, Caswara C, Chow W, Fedrigo O, Formenti G, Haase B, Howe K, Mountcastle J, Uliano-Silva M, Wood J, Jarvis ED, Liedvogel M, Bouwhuis S. Sex-specific changes in autosomal methylation rate in ageing common terns. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.982443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Senescence, an age-related decline in survival and/or reproductive performance, occurs in species across the tree of life. Molecular mechanisms underlying this within-individual phenomenon are still largely unknown, but DNA methylation changes with age are among the candidates. Using a longitudinal approach, we investigated age-specific changes in autosomal methylation of common terns, relatively long-lived migratory seabirds known to show senescence. We collected blood at 1-, 3- and/or 4-year intervals, extracted DNA from the erythrocytes and estimated autosomal DNA methylation by mapping Reduced Representative Bisulfite Sequencing reads to a de novo assembled reference genome. We found autosomal methylation levels to decrease with age within females, but not males, and no evidence for selective (dis)appearance of birds of either sex in relation to their methylation level. Moreover, although we found positions in the genome to consistently vary in their methylation levels, individuals did not show such strong consistent variance. These results pave the way for studies at the level of genome features or specific positions, which should elucidate the functional consequences of the patterns observed, and how they translate to the ageing phenotype.
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61
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Barbero G, de Sousa Serro MG, Perez Lujan C, Vitullo AD, González CR, González B. Transcriptome profiling of histone writers/erasers enzymes across spermatogenesis, mature sperm and pre-cleavage embryo: Implications in paternal epigenome transitions and inheritance mechanisms. Front Cell Dev Biol 2023; 11:1086573. [PMID: 36776561 PMCID: PMC9911891 DOI: 10.3389/fcell.2023.1086573] [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: 11/01/2022] [Accepted: 01/04/2023] [Indexed: 01/28/2023] Open
Abstract
Accumulating evidence points out that sperm carry epigenetic instructions to embryo in the form of retained histones marks and RNA cargo that can transmit metabolic and behavioral traits to offspring. However, the mechanisms behind epigenetic inheritance of paternal environment are still poorly understood. Here, we curated male germ cells RNA-seq data and analyzed the expression profile of all known histone lysine writers and erasers enzymes across spermatogenesis, unraveling the developmental windows at which they are upregulated, and the specific activity related to canonical and non-canonical histone marks deposition and removal. We also characterized the epigenetic enzymes signature in the mature sperm RNA cargo, showing most of them positive translation at pre-cleavage zygote, suggesting that paternally-derived enzymes mRNA cooperate with maternal factors to embryo chromatin assembly. Our study shows several histone modifying enzymes not described yet in spermatogenesis and even more, important mechanistic aspects behind transgenerational epigenetics. Epigenetic enzymes not only can respond to environmental stressors, but could function as vectors of epigenetic information and participate in chromatin organization during maternal-to-zygote transition.
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Affiliation(s)
- Gastón Barbero
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Maximiliano G. de Sousa Serro
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Camila Perez Lujan
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Alfredo D. Vitullo
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Candela R. González
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Betina González
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina,*Correspondence: Betina González,
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62
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Puris E, Fricker G, Gynther M. The Role of Solute Carrier Transporters in Efficient Anticancer Drug Delivery and Therapy. Pharmaceutics 2023; 15:pharmaceutics15020364. [PMID: 36839686 PMCID: PMC9966068 DOI: 10.3390/pharmaceutics15020364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Transporter-mediated drug resistance is a major obstacle in anticancer drug delivery and a key reason for cancer drug therapy failure. Membrane solute carrier (SLC) transporters play a crucial role in the cellular uptake of drugs. The expression and function of the SLC transporters can be down-regulated in cancer cells, which limits the uptake of drugs into the tumor cells, resulting in the inefficiency of the drug therapy. In this review, we summarize the current understanding of low-SLC-transporter-expression-mediated drug resistance in different types of cancers. Recent advances in SLC-transporter-targeting strategies include the development of transporter-utilizing prodrugs and nanocarriers and the modulation of SLC transporter expression in cancer cells. These strategies will play an important role in the future development of anticancer drug therapies by enabling the efficient delivery of drugs into cancer cells.
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63
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Vitullo AD, Roldan ERS, González CR. Editorial: Environmental factors affecting the germ line epigenome. Front Endocrinol (Lausanne) 2023; 13:1126967. [PMID: 36686465 PMCID: PMC9850218 DOI: 10.3389/fendo.2022.1126967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Affiliation(s)
- Alfredo D. Vitullo
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eduardo R. S. Roldan
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Candela R. González
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Liu M, Mai JW, Luo DX, Liu GX, Xu T, Xin WJ, Lin SY, Li ZY. NFATc2-dependent epigenetic downregulation of the TSC2/Beclin-1 pathway is involved in neuropathic pain induced by oxaliplatin. Mol Pain 2023; 19:17448069231158289. [PMID: 36733258 PMCID: PMC9941598 DOI: 10.1177/17448069231158289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Neuropathic pain is a common dose-limiting side effect of oxaliplatin, which hampers the effective treatment of tumors. Here, we found that upregulation of transcription factor NFATc2 decreased the expression of Beclin-1, a critical molecule in autophagy, in the spinal dorsal horn, and contributed to neuropathic pain following oxaliplatin treatment. Meanwhile, manipulating autophagy levels by intrathecal injection of rapamycin (RAPA) or 3-methyladenine (3-MA) differentially altered mechanical allodynia in oxaliplatin-treated or naïve rats. Utilizing chromatin immunoprecipitation-sequencing (ChIP-seq) assay combined with bioinformatics analysis, we found that NFATc2 negatively regulated the transcription of tuberous sclerosis complex protein 2 (TSC2), which contributed to the oxaliplatin-induced Beclin-1 downregulation. Further assays revealed that NFATc2 regulated histone H4 acetylation and methylation in the TSC2 promoter site 1 in rats' dorsal horns with oxaliplatin treatment. These results suggested that NFATc2 mediated the epigenetic downregulation of the TSC2/Beclin-1 autophagy pathway and contributed to oxaliplatin-induced mechanical allodynia, which provided a new therapeutic insight for chemotherapy-induced neuropathic pain.
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Affiliation(s)
- Meng Liu
- Department of Anesthesia and Pain Medicine, 74668Guangzhou First People's Hospital, Guangzhou, China
| | - Jing-Wen Mai
- Department of Anesthesiology, 598838Huizhou Central People's Hospital, Huizhou, China
| | - De-Xing Luo
- Department of Anesthesiology, 598838Huizhou Central People's Hospital, Huizhou, China
| | - Guan-Xi Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.,The Affiliated Brain Hospital of Guangzhou Medical University, 159357Guangzhou Huiai Hospital, Guangzhou, China
| | - Ting Xu
- Department of Emergency Medicine, The First Affiliated Hospital of Sun Yat-Sen University and Zhongshan Medical School, 26469Sun Yat-Sen University, China
| | - Wen-Jun Xin
- Department of Emergency Medicine, The First Affiliated Hospital of Sun Yat-Sen University and Zhongshan Medical School, 26469Sun Yat-Sen University, China
| | - Su-Yan Lin
- Department of Neurology, 220741The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhen-Yu Li
- Department of Emergency Medicine, The First Affiliated Hospital of Sun Yat-Sen University and Zhongshan Medical School, 26469Sun Yat-Sen University, China
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CRISPR-dCas9 system for epigenetic editing towards therapeutic applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:15-24. [DOI: 10.1016/bs.pmbts.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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66
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Das U, Gangisetty O, Chaudhary S, Tarale P, Rousseau B, Price J, Frazier I, Sarkar DK. Epigenetic insight into effects of prenatal alcohol exposure on stress axis development: Systematic review with meta-analytic approaches. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2023; 47:18-35. [PMID: 36341762 DOI: 10.1111/acer.14972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
We conducted a systematic review with meta-analytic elements using publicly available Gene Expression Omnibus (GEO) datasets to determine the role of epigenetic mechanisms in prenatal alcohol exposure (PAE)-induced hypothalamic-pituitary-adrenal (HPA) axis dysfunctions in offspring. Several studies have demonstrated that PAE has long-term consequences on HPA axis functions in offspring. Some studies determined that alcohol-induced epigenetic alterations during fetal development persist in adulthood. However, additional research is needed to understand the major epigenetic events leading to alcohol-induced teratogenesis of the HPA axis. Our network analysis of GEO datasets identified key pathways relevant to alcohol-mediated histone modifications, DNA methylation, and miRNA involvement associated with PAE-induced alterations of the HPA axis. Our analysis indicated that PAE perturbated the epigenetic machinery to activate corticotrophin-releasing hormone, while it suppressed opioid, glucocorticoid receptor, and circadian clock genes. These results help to further our understanding of the epigenetic basis of alcohol's effects on HPA axis development.
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Affiliation(s)
- Ujjal Das
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Omkaram Gangisetty
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Shaista Chaudhary
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Prashant Tarale
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Bénédicte Rousseau
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Julianne Price
- Molecular Neuroscience of Alcohol and Drug Abuse Research Training, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center of Alcohol & Substance Use Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Department of Kinesiology & Health, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Ian Frazier
- Molecular Neuroscience of Alcohol and Drug Abuse Research Training, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center of Alcohol & Substance Use Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Department of Kinesiology & Health, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Dipak K Sarkar
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Molecular Neuroscience of Alcohol and Drug Abuse Research Training, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center of Alcohol & Substance Use Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Rutgers Endocrinology Program, Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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67
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Maheshwari A. Innate Immune Memory in Macrophages. NEWBORN (CLARKSVILLE, MD.) 2023; 2:60-79. [PMID: 37206580 PMCID: PMC10193650 DOI: 10.5005/jp-journals-11002-0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Macrophages have been recognized as the primary mediators of innate immunity starting from embryonic/fetal development. Macrophage-mediated defenses may not be as antigen-specific as adaptive immunity, but increasing information suggests that these responses do strengthen with repeated immunological triggers. The concept of innate memory in macrophages has been described as "trained immunity" or "innate immune memory (IIM)." As currently understood, this cellular memory is rooted in epigenetic and metabolic reprogramming. The recognition of IIM may be particularly important in the fetus and the young neonate who are yet to develop protective levels of adaptive immunity, and could even be of preventive/therapeutic importance in many disorders. There may also be a possibility of therapeutic enhancement with targeted vaccination. This article presents a review of the properties, mechanisms, and possible clinical significance of macrophage-mediated IIM.
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Affiliation(s)
- Akhil Maheshwari
- Founding Chairman, Global Newborn Society, Clarksville, Maryland, United States of America
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68
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Chu DT, Thi YVN, Chew NW. Histone modifications in fat metabolism and obesity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:135-152. [PMID: 37019590 DOI: 10.1016/bs.pmbts.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The World Health Organization (WHO) has identified the obesity epidemic as one of the leading causes of overall morbidity and mortality. Obesity affects individual health, and quality of life and has negative long-term economic implications on society and the entire country. In recent years, studies on histone modifications in fat metabolism and obesity have received great attention. Processes such as methylation, histone modification, chromatin remodeling, and microRNA expression are mechanisms in epigenetic regulation. These processes play a particularly important role in cell development and differentiation through gene regulation. In this chapter, we discuss the types of histone modifications in adipose tissue under different conditions, the role of histone modifications in adipose tissue development, and the relationship between histone modifications and biosynthesis in the body. In addition, the chapter provides detailed information on histone modifications in obesity, the relationship between histone modifications and food consumption status, and the role of histone modifications in overweight and obesity.
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69
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Early epigenetic markers for precision medicine. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:153-164. [DOI: 10.1016/bs.pmbts.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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70
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Nawaz K, Cziesielski MJ, Mariappan KG, Cui G, Aranda M. Histone modifications and DNA methylation act cooperatively in regulating symbiosis genes in the sea anemone Aiptasia. BMC Biol 2022; 20:265. [DOI: 10.1186/s12915-022-01469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Abstract
Background
The symbiotic relationship between cnidarians and dinoflagellates is one of the most widespread endosymbiosis in our oceans and provides the ecological basis of coral reef ecosystems. Although many studies have been undertaken to unravel the molecular mechanisms underlying these symbioses, we still know little about the epigenetic mechanisms that control the transcriptional responses to symbiosis.
Results
Here, we used the model organism Exaiptasia diaphana to study the genome-wide patterns and putative functions of the histone modifications H3K27ac, H3K4me3, H3K9ac, H3K36me3, and H3K27me3 in symbiosis. While we find that their functions are generally conserved, we observed that colocalization of more than one modification and or DNA methylation correlated with significantly higher gene expression, suggesting a cooperative action of histone modifications and DNA methylation in promoting gene expression. Analysis of symbiosis genes revealed that activating histone modifications predominantly associated with symbiosis-induced genes involved in glucose metabolism, nitrogen transport, amino acid biosynthesis, and organism growth while symbiosis-suppressed genes were involved in catabolic processes.
Conclusions
Our results provide new insights into the mechanisms of prominent histone modifications and their interaction with DNA methylation in regulating symbiosis in cnidarians.
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71
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Das DN, Ravi N. Influences of polycyclic aromatic hydrocarbon on the epigenome toxicity and its applicability in human health risk assessment. ENVIRONMENTAL RESEARCH 2022; 213:113677. [PMID: 35714684 DOI: 10.1016/j.envres.2022.113677] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The existence of polycyclic aromatic hydrocarbons (PAHs) in ambient air is an escalating concern worldwide because of their ability to cause cancer and induce permanent changes in the genetic material. Growing evidence implies that during early life-sensitive stages, the risk of progression of acute and chronic diseases depends on epigenetic changes initiated by the influence of environmental cues. Several reports deciphered the relationship between exposure to environmental chemicals and epigenetics, and have known toxicants that alter the epigenetic states. Amongst PAHs, benzo[a]pyrene (B[a]P) is accepted as a group 1 cancer-causing agent by the International Agency for the Research on Cancer (IARC). B[a]P is a well-studied pro-carcinogen that is metabolically activated by the aryl hydrocarbon receptor (AhR)/cytochrome P450 pathway. Cytochrome P450 plays a pivotal role in the stimulation step, which is essential for DNA adduct formation. Accruing evidence suggests that epigenetic alterations assume a fundamental part in PAH-promoted carcinogenesis. This interaction between PAHs and epigenetic factors results in an altered profile of these marks, globally and locus-specific. Some of the epigenetic changes due to exposure to PAHs lead to increased disease susceptibility and progression. It is well understood that exposure to environmental carcinogens, such as PAH triggers disease pathways through changes in the genome. Several evidence reported due to the epigenome-wide association studies, that early life adverse environmental events may trigger widespread and persistent variations in transcriptional profiling. Moreover, these variations respond to DNA damage and/or a consequence of epigenetic modifications that need further investigation. Growing evidence has associated PAHs with epigenetic variations involving alterations in DNA methylation, histone modification, and micro RNA (miRNA) regulation. Epigenetic alterations to PAH exposure were related to chronic diseases, such as pulmonary disease, cardiovascular disease, endocrine disruptor, nervous system disorder, and cancer. This hormetic response gives a novel perception concerning the toxicity of PAHs and the biological reaction that may be a distinct reliance on exposure. This review sheds light on understanding the latest evidence about how PAHs can alter epigenetic patterns and human health. In conclusion, as several epigenetic change mechanisms remain unclear yet, further analyses derived from PAHs exposure must be performed to find new targets and disease biomarkers. In spite of the current limitations, numerous evidence supports the perception that epigenetics grips substantial potential for advancing our knowledge about the molecular mechanisms of environmental toxicants, also for predicting health-associated risks due to environmental circumstances exposure and individual susceptibility.
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Affiliation(s)
- Durgesh Nandini Das
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Nathan Ravi
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, 63110, USA; Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA; Institute for Public Health, Washington University in St. Louis, St. Louis, MO, 63110, USA; Veterans Affairs St. Louis Hospital, St. Louis, MO, 63106, USA.
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72
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Anne A, Saxena S, Mohan KN. Genome-wide methylation analysis of post-mortem cerebellum samples supports the role of peroxisomes in autism spectrum disorder. Epigenomics 2022; 14:1015-1027. [PMID: 36154275 DOI: 10.2217/epi-2022-0184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We tested the hypothesis that a subset of patients with autism spectrum disorder (ASD) contains candidate genes with high DNA methylation differences (effective values) that potentially affect one of the two alleles. Materials & methods: Genome-wide DNA methylation comparisons were made on cerebellum samples from 30 patients and 45 controls. Results: 12 genes with high effective values, including GSDMD, MMACHC, SLC6A5 and NKX6-2, implicated in ASD and other neuropsychiatric disorders were identified. Monoallelic promoter methylation and downregulation were observed for SERHL (serine hydrolase-like) and CAT (catalase) genes associated with peroxisome function. Conclusion: These data are consistent with the hypothesis implicating impaired peroxisome function/biogenesis for ASD. A similar approach holds promise for identifying rare epimutations in ASD and other complex disorders.
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Affiliation(s)
- Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Sonal Saxena
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
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73
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Mumtaz I, Ayaz MO, Khan MS, Manzoor U, Ganayee MA, Bhat AQ, Dar GH, Alghamdi BS, Hashem AM, Dar MJ, Ashraf GM, Maqbool T. Clinical relevance of biomarkers, new therapeutic approaches, and role of post-translational modifications in the pathogenesis of Alzheimer's disease. Front Aging Neurosci 2022; 14:977411. [PMID: 36158539 PMCID: PMC9490081 DOI: 10.3389/fnagi.2022.977411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that causes progressive loss of cognitive functions like thinking, memory, reasoning, behavioral abilities, and social skills thus affecting the ability of a person to perform normal daily functions independently. There is no definitive cure for this disease, and treatment options available for the management of the disease are not very effective as well. Based on histopathology, AD is characterized by the accumulation of insoluble deposits of amyloid beta (Aβ) plaques and neurofibrillary tangles (NFTs). Although several molecular events contribute to the formation of these insoluble deposits, the aberrant post-translational modifications (PTMs) of AD-related proteins (like APP, Aβ, tau, and BACE1) are also known to be involved in the onset and progression of this disease. However, early diagnosis of the disease as well as the development of effective therapeutic approaches is impeded by lack of proper clinical biomarkers. In this review, we summarized the current status and clinical relevance of biomarkers from cerebrospinal fluid (CSF), blood and extracellular vesicles involved in onset and progression of AD. Moreover, we highlight the effects of several PTMs on the AD-related proteins, and provide an insight how these modifications impact the structure and function of proteins leading to AD pathology. Finally, for disease-modifying therapeutics, novel approaches, and targets are discussed for the successful treatment and management of AD.
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Affiliation(s)
- Ibtisam Mumtaz
- Laboratory of Nanotherapeutics and Regenerative Medicine, Department of Nanotechnology, University of Kashmir, Srinagar, India
| | - Mir Owais Ayaz
- Laboratory of Cell and Molecular Biology, Department of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
- Centre for Scientific and Innovative Research, Ghaziabad, Utter Pradesh, India
| | - Mohamad Sultan Khan
- Neurobiology and Molecular Chronobiology Laboratory, Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Umar Manzoor
- Laboratory of Immune and Inflammatory Disease, Jeju Research Institute of Pharmaceutical Sciences, Jeju National University, Jeju, South Korea
| | - Mohd Azhardin Ganayee
- Laboratory of Nanotherapeutics and Regenerative Medicine, Department of Nanotechnology, University of Kashmir, Srinagar, India
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
| | - Aadil Qadir Bhat
- Laboratory of Cell and Molecular Biology, Department of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
- Centre for Scientific and Innovative Research, Ghaziabad, Utter Pradesh, India
| | - Ghulam Hassan Dar
- Sri Pratap College, Cluster University Srinagar, Jammu and Kashmir, India
| | - Badrah S. Alghamdi
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pre-clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M. Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Jamal Dar
- Laboratory of Cell and Molecular Biology, Department of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
- Centre for Scientific and Innovative Research, Ghaziabad, Utter Pradesh, India
| | - Gulam Md. Ashraf
- Pre-clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tariq Maqbool
- Laboratory of Nanotherapeutics and Regenerative Medicine, Department of Nanotechnology, University of Kashmir, Srinagar, India
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74
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Varma SJ, Calvani E, Grüning NM, Messner CB, Grayson N, Capuano F, Mülleder M, Ralser M. Global analysis of cytosine and adenine DNA modifications across the tree of life. eLife 2022; 11:81002. [PMID: 35900202 PMCID: PMC9333990 DOI: 10.7554/elife.81002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022] Open
Abstract
Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global quantification of DNA modifications have thus far been applied mostly to individual problems. We established a mass spectrometric method for the sensitive and accurate quantification of multiple enzymatic DNA modifications. Then, we isolated DNA from 124 archean, bacterial, fungal, plant, and mammalian species, and several tissues and created a resource of global DNA modification quantities. Our dataset provides insights into the general nature of enzymatic DNA modifications, reveals unique biological cases, and provides complementary quantitative information to normalize and assess the accuracy of sequencing-based detection of DNA modifications. We report that only three of the studied DNA modifications, methylcytosine (5mdC), methyladenine (N6mdA) and hydroxymethylcytosine (5hmdC), were detected above a picomolar detection limit across species, and dominated in higher eukaryotes (5mdC), in bacteria (N6mdA), or the vertebrate central nervous systems (5hmdC). All three modifications were detected simultaneously in only one of the tested species, Raphanus sativus. In contrast, these modifications were either absent or detected only at trace quantities, across all yeasts and insect genomes studied. Further, we reveal interesting biological cases. For instance, in Allium cepa, Helianthus annuus, or Andropogon gerardi, more than 35% of cytosines were methylated. Additionally, next to the mammlian CNS, 5hmdC was also detected in plants like Lepidium sativum and was found on 8% of cytosines in the Garra barreimiae brain samples. Thus, identifying unexpected levels of DNA modifications in several wild species, our resource underscores the need to address biological diversity for studying DNA modifications.
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Affiliation(s)
| | - Enrica Calvani
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nana-Maria Grüning
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Grayson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Michael Mülleder
- Core Facility-High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany.,The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
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75
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Agborbesong E, Li LX, Li L, Li X. Molecular Mechanisms of Epigenetic Regulation, Inflammation, and Cell Death in ADPKD. Front Mol Biosci 2022; 9:922428. [PMID: 35847973 PMCID: PMC9277309 DOI: 10.3389/fmolb.2022.922428] [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: 04/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder, which is caused by mutations in the PKD1 and PKD2 genes, characterizing by progressive growth of multiple cysts in the kidneys, eventually leading to end-stage kidney disease (ESKD) and requiring renal replacement therapy. In addition, studies indicate that disease progression is as a result of a combination of factors. Understanding the molecular mechanisms, therefore, should facilitate the development of precise therapeutic strategies for ADPKD treatment. The roles of epigenetic modulation, interstitial inflammation, and regulated cell death have recently become the focuses in ADPKD. Different epigenetic regulators, and the presence of inflammatory markers detectable even before cyst growth, have been linked to cyst progression. Moreover, the infiltration of inflammatory cells, such as macrophages and T cells, have been associated with cyst growth and deteriorating renal function in humans and PKD animal models. There is evidence supporting a direct role of the PKD gene mutations to the regulation of epigenetic mechanisms and inflammatory response in ADPKD. In addition, the role of regulated cell death, including apoptosis, autophagy and ferroptosis, have been investigated in ADPKD. However, there is no consensus whether cell death promotes or delays cyst growth in ADPKD. It is therefore necessary to develop an interactive picture between PKD gene mutations, the epigenome, inflammation, and cell death to understand why inherited PKD gene mutations in patients may result in the dysregulation of these processes that increase the progression of renal cyst formation.
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Affiliation(s)
- Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Linda Xiaoyan Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Lu Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
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76
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Rooney K, Sadikovic B. DNA Methylation Episignatures in Neurodevelopmental Disorders Associated with Large Structural Copy Number Variants: Clinical Implications. Int J Mol Sci 2022; 23:ijms23147862. [PMID: 35887210 PMCID: PMC9324454 DOI: 10.3390/ijms23147862] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Large structural chromosomal deletions and duplications, referred to as copy number variants (CNVs), play a role in the pathogenesis of neurodevelopmental disorders (NDDs) through effects on gene dosage. This review focuses on our current understanding of genomic disorders that arise from large structural chromosome rearrangements in patients with NDDs, as well as difficulties in overlap of clinical presentation and molecular diagnosis. We discuss the implications of epigenetics, specifically DNA methylation (DNAm), in NDDs and genomic disorders, and consider the implications and clinical impact of copy number and genomic DNAm testing in patients with suspected genetic NDDs. We summarize evidence of global methylation episignatures in CNV-associated disorders that can be used in the diagnostic pathway and may provide insights into the molecular pathogenesis of genomic disorders. Finally, we discuss the potential for combining CNV and DNAm assessment into a single diagnostic assay.
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Affiliation(s)
- Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Correspondence: ; Tel.: +1-519-685-8500 (ext. 53074)
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Improvement of Sleeping Beauty Transposon System Enabling Efficient and Stable Protein Production. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-021-0231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bisserier M, Brojakowska A, Saffran N, Rai AK, Lee B, Coleman M, Sebastian A, Evans A, Mills PJ, Addya S, Arakelyan A, Garikipati VNS, Hadri L, Goukassian DA. Astronauts Plasma-Derived Exosomes Induced Aberrant EZH2-Mediated H3K27me3 Epigenetic Regulation of the Vitamin D Receptor. Front Cardiovasc Med 2022; 9:855181. [PMID: 35783863 PMCID: PMC9243458 DOI: 10.3389/fcvm.2022.855181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
There are unique stressors in the spaceflight environment. Exposure to such stressors may be associated with adverse effects on astronauts' health, including increased cancer and cardiovascular disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. AC16 cells (human cardiomyocyte cell line) were treated with L-10 and R+3 astronauts-derived exosomes for 24 h. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Transcription factor (TF) enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3–chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes by promoting the activation of the PRC2 complex and H3K27me3 levels.
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Affiliation(s)
- Malik Bisserier
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
| | - Agnieszka Brojakowska
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
| | - Nathaniel Saffran
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
| | - Amit Kumar Rai
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Brooke Lee
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Matthew Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Aimy Sebastian
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Angela Evans
- Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Paul J. Mills
- Center of Excellence for Research and Training in Integrative Health, University of California, San Diego, La Jolla, CA, United States
| | - Sankar Addya
- Kimmel Cancer Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Arsen Arakelyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA), Yerevan, Armenia
- Department of Bioengineering, Bioinformatics, and Molecular Biology, Russian-Armenian University, Yerevan, Armenia
| | - Venkata Naga Srikanth Garikipati
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Lahouaria Hadri
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
- Lahouaria Hadri
| | - David A. Goukassian
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
- *Correspondence: David A. Goukassian
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Epigenetic Studies for Evaluation of NPS Toxicity: Focus on Synthetic Cannabinoids and Cathinones. Biomedicines 2022; 10:biomedicines10061398. [PMID: 35740419 PMCID: PMC9219842 DOI: 10.3390/biomedicines10061398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
In the recent decade, numerous new psychoactive substances (NPSs) have been added to the illicit drug market. These are synthetized to mimic the effects of classic drugs of abuse (i.e., cannabis, cocaine, etc.), with the purpose of bypassing substance legislations and increasing the pharmacotoxicological effects. To date, research into the acute pharmacological effects of new NPSs is ongoing and necessary in order to provide an appropriate contribution to public health. In fact, multiple examples of NPS-related acute intoxication and mortality have been recorded in the literature. Accordingly, several in vitro and in vivo studies have investigated the pharmacotoxicological profiles of these compounds, revealing that they can cause adverse effects involving various organ systems (i.e., cardiovascular, respiratory effects) and highlighting their potential increased consumption risks. In this sense, NPSs should be regarded as a complex issue that requires continuous monitoring. Moreover, knowledge of long-term NPS effects is lacking. Because genetic and environmental variables may impact NPS responses, epigenetics may aid in understanding the processes behind the harmful events induced by long-term NPS usage. Taken together, “pharmacoepigenomics” may provide a new field of combined study on genetic differences and epigenetic changes in drug reactions that might be predictive in forensic implications.
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80
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Zhou S, Shu Y. Transcriptional Regulation of Solute Carrier (SLC) Drug Transporters. Drug Metab Dispos 2022; 50:DMD-MR-2021-000704. [PMID: 35644529 PMCID: PMC9488976 DOI: 10.1124/dmd.121.000704] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 05/02/2022] [Accepted: 05/16/2022] [Indexed: 09/03/2023] Open
Abstract
Facilitated transport is necessitated for large size, charged, and/or hydrophilic drugs to move across the membrane. The drug transporters in the solute carrier (SLC) superfamily, mainly including organic anion-transporting polypeptides (OATPs), organic anion transporters (OATs), organic cation transporters (OCTs), organic cation/carnitine transporters (OCTNs), peptide transporters (PEPTs), and multidrug and toxin extrusion proteins (MATEs), are critical facilitators of drug transport and distribution in human body. The expression of these SLC drug transporters is found in tissues throughout the body, with high abundance in the epithelial cells of major organs for drug disposition, such as intestine, liver, and kidney. These SLC drug transporters are clinically important in drug absorption, metabolism, distribution, and excretion. The mechanisms underlying their regulation have been revealing in recent years. Epigenetic and nuclear receptor-mediated transcriptional regulation of SLC drug transporters have particularly attracted much attention. This review focuses on the transcriptional regulation of major SLC drug transporter genes. Revealing the mechanisms underlying the transcription of those critical drug transporters will help us understand pharmacokinetics and pharmacodynamics, ultimately improving drug therapeutic effectiveness while minimizing drug toxicity. Significance Statement It has become increasingly recognized that solute carrier (SLC) drug transporters play a crucial, and sometimes determinative, role in drug disposition and response, which is reflected in decision-making during not only clinical drug therapy but also drug development. Understanding the mechanisms accounting for the transcription of these transporters is critical to interpret their abundance in various tissues under different conditions, which is necessary to clarify the pharmacological response, adverse effects, and drug-drug interactions for clinically used drugs.
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Affiliation(s)
- Shiwei Zhou
- Pharmaceutical Sciences, University of Maryland, United States
| | - Yan Shu
- Pharmaceutical Sciences, University of Maryland, United States
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81
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Xiang Q, Zhao Y, Lin J, Jiang S, Li W. Epigenetic modifications in spinal ligament aging. Ageing Res Rev 2022; 77:101598. [PMID: 35218968 DOI: 10.1016/j.arr.2022.101598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 02/07/2023]
Abstract
Spinal stenosis is a common degenerative spine disorder in the aged population and the spinal ligament aging is a main contributor to this chronic disease. However, the underlying mechanisms of spinal ligament aging remain unclear. Epigenetics is the study of heritable and reversible changes in the function of a gene or genome that occur without any alteration in the primary DNA sequence. Epigenetic alterations have been demonstrated to play crucial roles in age-related diseases and conditions, and they are recently studied as biomarkers and therapeutic targets in the field of cancer research. The main epigenetic modifications, including DNA methylation alteration, histone modifications as well as dysregulated noncoding RNA modulation, have all been implicated in spinal ligament aging diseases. DNA methylation modulates the expression of critical genes including WNT5A, GDNF, ACSM5, miR-497 and miR-195 during spinal ligament degeneration. Histone modifications widely affect gene expression and obvious histone modification abnormalities have been found in spinal ligament aging. MicroRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) exert crucial regulating effects on spinal ligament aging conditions via targeting various osteogenic or fibrogenic differentiation related genes. To our knowledge, there is no systematic review yet to summarize the involvement of epigenetic mechanisms of spinal ligament aging in degenerative spinal diseases. In this study, we systematically discussed the different epigenetic modifications and their potential functions in spinal ligament aging process.
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82
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Accurate and highly interpretable prediction of gene expression from histone modifications. BMC Bioinformatics 2022; 23:151. [PMID: 35473556 PMCID: PMC9040271 DOI: 10.1186/s12859-022-04687-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Histone Mark Modifications (HMs) are crucial actors in gene regulation, as they actively remodel chromatin to modulate transcriptional activity: aberrant combinatorial patterns of HMs have been connected with several diseases, including cancer. HMs are, however, reversible modifications: understanding their role in disease would allow the design of ‘epigenetic drugs’ for specific, non-invasive treatments. Standard statistical techniques were not entirely successful in extracting representative features from raw HM signals over gene locations. On the other hand, deep learning approaches allow for effective automatic feature extraction, but at the expense of model interpretation. Results Here, we propose ShallowChrome, a novel computational pipeline to model transcriptional regulation via HMs in both an accurate and interpretable way. We attain state-of-the-art results on the binary classification of gene transcriptional states over 56 cell-types from the REMC database, largely outperforming recent deep learning approaches. We interpret our models by extracting insightful gene-specific regulative patterns, and we analyse them for the specific case of the PAX5 gene over three differentiated blood cell lines. Finally, we compare the patterns we obtained with the characteristic emission patterns of ChromHMM, and show that ShallowChrome is able to coherently rank groups of chromatin states w.r.t. their transcriptional activity. Conclusions In this work we demonstrate that it is possible to model HM-modulated gene expression regulation in a highly accurate, yet interpretable way. Our feature extraction algorithm leverages on data downstream the identification of enriched regions to retrieve gene-wise, statistically significant and dynamically located features for each HM. These features are highly predictive of gene transcriptional state, and allow for accurate modeling by computationally efficient logistic regression models. These models allow a direct inspection and a rigorous interpretation, helping to formulate quantifiable hypotheses.
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83
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Houschyar KS, Borrelli MR, Rein S, Tapking C, Popp D, Palackic A, Puladi B, Ooms M, Houschyar M, Branski LK, Schmitt L, Modabber A, Rübben A, Hölzle F, Yazdi AS. Head and neck squamous cell carcinoma: a potential therapeutic target for the Wnt signaling pathway. EUROPEAN JOURNAL OF PLASTIC SURGERY 2022. [DOI: 10.1007/s00238-022-01958-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Abstract
Squamous cell carcinoma (SCC) of the head and neck region accounts for 3% of all tumors worldwide. The incidence is higher in men, with most carcinomas found in the oral cavity. At the point of initial diagnosis, distant metastases are rare. The Wnt signaling pathway is critically involved in cell development and stemness and has been associated with SCC. Understanding precisely how Wnt signaling regulates SCC progression and how it can, therefore, be modulated for the therapeutic benefit has enormous potential in the treatment of head and neck SCC. In this review, we will describe the underlying mechanisms of Wnt signaling and outline how Wnt signaling controls cellular processes both in homeostasis and in the development and progression of SCC.Level of evidence: Not gradable.
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84
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Halawa S, Latif N, Tseng YT, Ibrahim AM, Chester AH, Moustafa A, Aguib Y, Yacoub MH. Profiling Genome-Wide DNA Methylation Patterns in Human Aortic and Mitral Valves. Front Cardiovasc Med 2022; 9:840647. [PMID: 35463757 PMCID: PMC9019152 DOI: 10.3389/fcvm.2022.840647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/11/2022] [Indexed: 12/05/2022] Open
Abstract
Cardiac valves exhibit highly complex structures and specialized functions that include dynamic interactions between cells, extracellular matrix (ECM) and their hemodynamic environment. Valvular gene expression is tightly regulated by a variety of mechanisms including epigenetic factors such as histone modifications, RNA-based mechanisms and DNA methylation. To date, methylation fingerprints of non-diseased human aortic and mitral valves have not been studied. In this work we analyzed the differential methylation profiles of 12 non-diseased aortic and mitral valve tissue samples (in matched pairs). Analysis of methylation data [reduced representation bisulfite sequencing (RRBS)] of 16,101 promoters genome-wide revealed 584 differentially methylated (DM) promoters, of which 13 were reported in endothelial mesenchymal trans-differentiation (EMT), 37 in aortic and mitral valve disease and 7 in ECM remodeling. Both functional classification as well as network analysis showed that the genes associated with the DM promoters were enriched for WNT-, Cadherin-, Endothelin-, PDGF-, HIF-1 and VEGF- signaling implicated in valvular physiology and pathophysiology. Additional enrichment was detected for TGFB-, NOTCH- and Integrin- signaling involved in EMT as well as ECM remodeling. This data provides the first insight into differential regulation of human aortic and mitral valve tissue and identifies candidate genes linked to DM promoters. Our work will improve the understanding of valve biology, valve tissue engineering approaches and contributes to the identification of relevant drug targets.
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Affiliation(s)
- Sarah Halawa
- Aswan Heart Centre, Aswan, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
- Sarah Halawa
| | - Najma Latif
- Heart Science Centre, Magdi Yacoub Institute, Harefield, United Kingdom
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom
| | - Yuan-Tsan Tseng
- Heart Science Centre, Magdi Yacoub Institute, Harefield, United Kingdom
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom
| | - Ayman M. Ibrahim
- Aswan Heart Centre, Aswan, Egypt
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Adrian H. Chester
- Heart Science Centre, Magdi Yacoub Institute, Harefield, United Kingdom
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom
| | - Ahmed Moustafa
- Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
- Department of Biology, American University in Cairo, New Cairo, Egypt
| | - Yasmine Aguib
- Aswan Heart Centre, Aswan, Egypt
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom
- Yasmine Aguib
| | - Magdi H. Yacoub
- Aswan Heart Centre, Aswan, Egypt
- Heart Science Centre, Magdi Yacoub Institute, Harefield, United Kingdom
- National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom
- *Correspondence: Magdi H. Yacoub
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85
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Connacher J, von Grüning H, Birkholtz L. Histone Modification Landscapes as a Roadmap for Malaria Parasite Development. Front Cell Dev Biol 2022; 10:848797. [PMID: 35433676 PMCID: PMC9010790 DOI: 10.3389/fcell.2022.848797] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/04/2022] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum remains the deadliest parasite species in the world, responsible for 229 million cases of human malaria in 2019. The ability of the P. falciparum parasite to progress through multiple life cycle stages and thrive in diverse host and vector species hinges on sophisticated mechanisms of epigenetic regulation of gene expression. Emerging evidence indicates such epigenetic control exists in concentric layers, revolving around core histone post-translational modification (PTM) landscapes. Here, we provide a necessary update of recent epigenome research in malaria parasites, focusing specifically on the ability of dynamic histone PTM landscapes to orchestrate the divergent development and differentiation pathways in P. falciparum parasites. In addition to individual histone PTMs, we discuss recent findings that imply functional importance for combinatorial PTMs in P. falciparum parasites, representing an operational histone code. Finally, this review highlights the remaining gaps and provides strategies to address these to obtain a more thorough understanding of the histone modification landscapes that are at the center of epigenetic regulation in human malaria parasites.
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86
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Du Y, Zhang P, Liu W, Tian J. Optical Imaging of Epigenetic Modifications in Cancer: A Systematic Review. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:88-101. [PMID: 36939779 PMCID: PMC9590553 DOI: 10.1007/s43657-021-00041-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023]
Abstract
Increasing evidence has demonstrated that abnormal epigenetic modifications are strongly related to cancer initiation. Thus, sensitive and specific detection of epigenetic modifications could markedly improve biological investigations and cancer precision medicine. A rapid development of molecular imaging approaches for the diagnosis and prognosis of cancer has been observed during the past few years. Various biomarkers unique to epigenetic modifications and targeted imaging probes have been characterized and used to discriminate cancer from healthy tissues, as well as evaluate therapeutic responses. In this study, we summarize the latest studies associated with optical molecular imaging of epigenetic modification targets, such as those involving DNA methylation, histone modification, noncoding RNA regulation, and chromosome remodeling, and further review their clinical application on cancer diagnosis and treatment. Lastly, we further propose the future directions for precision imaging of epigenetic modification in cancer. Supported by promising clinical and preclinical studies associated with optical molecular imaging technology and epigenetic drugs, the central role of epigenetics in cancer should be increasingly recognized and accepted.
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Affiliation(s)
- Yang Du
- grid.9227.e0000000119573309CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190 China
- grid.410726.60000 0004 1797 8419The University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Pei Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190 China
- grid.412474.00000 0001 0027 0586Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Supportive Care Center and Day Oncology Unit, Peking University Cancer Hospital and Institute, Beijing, 100142 China
| | - Wei Liu
- grid.412474.00000 0001 0027 0586Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Supportive Care Center and Day Oncology Unit, Peking University Cancer Hospital and Institute, Beijing, 100142 China
| | - Jie Tian
- grid.9227.e0000000119573309CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190 China
- grid.64939.310000 0000 9999 1211Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine, Beihang University, Beijing, 100191 China
- grid.440736.20000 0001 0707 115XSchool of Life Science and Technology, Xidian University, Xi’an, 710071 Shaanxi China
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Borosha S, Ratri A, Ghosh S, Malcom CA, Chakravarthi VP, Vivian JL, Fields TA, Rumi MAK, Fields PE. DOT1L Mediated Gene Repression in Extensively Self-Renewing Erythroblasts. Front Genet 2022; 13:828086. [PMID: 35401699 PMCID: PMC8984088 DOI: 10.3389/fgene.2022.828086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
DOT1L is essential for embryonic hematopoiesis but the precise mechanisms of its action remain unclear. The only recognized function of DOT1L is histone H3 lysine 79 (H3K79) methylation, which has been implicated in both transcriptional activation and repression. We observed that deletion of the mouse Dot1L gene (Dot1L-KO) or selective mutation of its methyltransferase domain (Dot1L-MM) can differentially affect early embryonic erythropoiesis. However, both mutations result in embryonic lethality by mid-gestation and growth of hematopoietic progenitor cells (HPCs) is similarly affected in extensively self-renewing erythroblast (ESRE) cultures established from yolk sac cells. To understand DOT1L-mediated gene regulation and to clarify the role of H3K79 methylation, we analyzed whole transcriptomes of wildtype and Dot1L-mutant ESRE cells. We observed that more than 80% of the differentially expressed genes (DEGs) were upregulated in the mutant ESRE cells either lacking the DOT1L protein or the DOT1L methyltransferase activity. However, approximately 45% of the DEGs were unique to either mutant group, indicating that DOT1L possesses both methyltransferase-dependent and -independent gene regulatory functions. Analyses of Gene Ontology and signaling pathways for the DEGs were consistent, with DEGs that were found to be common or unique to either mutant group. Genes related to proliferation of HPCs were primarily impacted in Dot1L-KO cells, while genes related to HPC development were affected in the Dot1L-MM cells. A subset of genes related to differentiation of HPCs were affected in both mutant groups of ESREs. Our findings suggest that DOT1L primarily acts to repress gene expression in HPCs, and this function can be independent of its methyltransferase activity.
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88
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Montjean D, Neyroud AS, Yefimova MG, Benkhalifa M, Cabry R, Ravel C. Impact of Endocrine Disruptors upon Non-Genetic Inheritance. Int J Mol Sci 2022; 23:ijms23063350. [PMID: 35328771 PMCID: PMC8950994 DOI: 10.3390/ijms23063350] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023] Open
Abstract
Similar to environmental factors, EDCs (endocrine-disrupting chemicals) can influence gene expression without modifying the DNA sequence. It is commonly accepted that the transgenerational inheritance of parentally acquired traits is conveyed by epigenetic alterations also known as “epimutations”. DNA methylation, acetylation, histone modification, RNA-mediated effects and extracellular vesicle effects are the mechanisms that have been described so far to be responsible for these epimutations. They may lead to the transgenerational inheritance of diverse phenotypes in the progeny when they occur in the germ cells of an affected individual. While EDC-induced health effects have dramatically increased over the past decade, limited effects on sperm epigenetics have been described. However, there has been a gain of interest in this issue in recent years. The gametes (sperm and oocyte) represent targets for EDCs and thus a route for environmentally induced changes over several generations. This review aims at providing an overview of the epigenetic mechanisms that might be implicated in this transgenerational inheritance.
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Affiliation(s)
- Debbie Montjean
- Fertilys Fertility Center, 1950 Rue Maurice-Gauvin #103, Laval, QC H7S 1Z5, Canada;
- Correspondence: (D.M.); (C.R.)
| | - Anne-Sophie Neyroud
- CHU de Rennes, Département de Gynécologie Obstétrique et Reproduction Humaine-CECOS, Hôpital Sud, 16 Boulevard de Bulgarie, 35000 Rennes, France;
| | - Marina G. Yefimova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St-Petersburg, Russia;
| | - Moncef Benkhalifa
- Fertilys Fertility Center, 1950 Rue Maurice-Gauvin #103, Laval, QC H7S 1Z5, Canada;
- Médecine et Biologie de la Reproduction, CECOS de Picardie, CHU Amiens, 80054 Amiens, France;
- UFR de Médecine, Université de Picardie Jules Verne, 80054 Amiens, France
- Peritox, Centre Universitaire de Recherche en Santé, Université de Picardie Jules Verne, 80054 Amiens, France
| | - Rosalie Cabry
- Médecine et Biologie de la Reproduction, CECOS de Picardie, CHU Amiens, 80054 Amiens, France;
- UFR de Médecine, Université de Picardie Jules Verne, 80054 Amiens, France
- Peritox, Centre Universitaire de Recherche en Santé, Université de Picardie Jules Verne, 80054 Amiens, France
| | - Célia Ravel
- CHU de Rennes, Département de Gynécologie Obstétrique et Reproduction Humaine-CECOS, Hôpital Sud, 16 Boulevard de Bulgarie, 35000 Rennes, France;
- CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR_S 1085, University Rennes, 35000 Rennes, France
- Correspondence: (D.M.); (C.R.)
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Holubekova V, Kolkova Z, Kasubova I, Samec M, Mazurakova A, Koklesova L, Kubatka P, Rokos T, Kozubik E, Biringer K, Kudela E. Interaction of cervical microbiome with epigenome of epithelial cells: Significance of inflammation to primary healthcare. Biomol Concepts 2022; 13:61-80. [PMID: 35245973 DOI: 10.1515/bmc-2022-0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
One pillar of the predictive, preventive, and personalized medicine framework strategies is the female health. The evaluation of women's lifestyle and dietary habits in context with genetic and modifiable risk factors may reflect the prevention of cervical cancer before the occurrence of clinical symptoms and prediction of cervical lesion behavior. The main aim of this review is to analyze publications in the field of precision medicine that allow the use of research knowledge of cervical microbiome, epigenetic modifications, and inflammation in potential application in clinical practice. Personalized approach in evaluating patient's risk of future development of cervical abnormality should consider the biomarkers of the local microenvironment characterized by the microbial composition, epigenetic pattern of cervical epithelium, and presence of chronic inflammation. Novel sequencing techniques enable a more detailed characterization of actual state in cervical epithelium. Better understanding of all changes in multiomics level enables a better assessment of disease prognosis and selects the eligible targeted therapy in personalized medicine. Restoring of healthy vaginal microflora and reversing the outbreak of cervical abnormality can be also achieved by dietary habits as well as uptake of prebiotics, probiotics, synbiotics, microbial transplantation, and others.
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Affiliation(s)
- Veronika Holubekova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Zuzana Kolkova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Ivana Kasubova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Marek Samec
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Alena Mazurakova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Tomas Rokos
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kozubik
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Kamil Biringer
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kudela
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
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Dey A, Kundu M, Das S, Jena BC, Mandal M. Understanding the function and regulation of Sox2 for its therapeutic potential in breast cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188692. [PMID: 35122882 DOI: 10.1016/j.bbcan.2022.188692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/11/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022]
Abstract
Sox family of transcriptional factors play essential functions in development and are implicated in multiple clinical disorders, including cancer. Sox2 being their most prominent member and performing a critical role in reprogramming differentiated adult cells to an embryonic phenotype is frequently upregulated in multiple cancers. High Sox2 levels are detected in breast tumor tissues and correlate with a worse prognosis. In addition, Sox2 expression is connected with resistance to conventional anticancer therapy. Together, it can be said that inhibiting Sox2 expression can reduce the malignant features associated with breast cancer, including invasion, migration, proliferation, stemness, and chemoresistance. This review highlights the critical roles played by the Sox gene family members in initiating or suppressing breast tumor development, while primarily focusing on Sox2 and its role in breast tumor initiation, maintenance, and progression, elucidates the probable mechanisms that control its activity, and puts forward potential therapeutic strategies to inhibit its expression.
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Affiliation(s)
- Ankita Dey
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Moumita Kundu
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Subhayan Das
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Bikash Chandra Jena
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
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91
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Manz XD, Szulcek R, Pan X, Symersky P, Dickhoff C, Majolée J, Kremer V, Michielon E, Jordanova ES, Radonic T, Bijnsdorp IV, Piersma SR, Pham TV, Jimenez CR, Vonk Noordegraaf A, de Man FS, Boon RA, Voorberg J, Hordijk PL, Aman J, Bogaard HJ. Epigenetic Modification of the VWF Promotor Drives Platelet Aggregation on the Pulmonary Endothelium in Chronic Thromboembolic Pulmonary Hypertension. Am J Respir Crit Care Med 2022; 205:806-818. [PMID: 35081007 DOI: 10.1164/rccm.202109-2075oc] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Von Willebrand Factor (VWF) mediates platelet adhesion during thrombosis. While chronic thromboembolic pulmonary hypertension (CTEPH) is associated with increased plasma levels of VWF, the role of this protein in CTEPH has remained enigmatic. OBJECTIVE To identify the role of VWF in CTEPH. METHODS CTEPH-specific patient plasma and pulmonary endarterectomy material from CTEPH patients were used to study the relationship between inflammation, VWF expression and pulmonary thrombosis. Cell culture findings were validated in human tissue and proteomics and chromatin immunoprecipitation were used to investigate the underlying mechanism of CTEPH. MEASUREMENTS AND MAIN RESULTS VWF is increased in plasma and in the pulmonary endothelium of CTEPH patients. In vitro, the increase in VWF gene expression and the higher release of VWF protein upon endothelial activation resulted in elevated platelet adhesion to CTEPH endothelium. Proteomic analysis revealed that Nuclear Factor κB 2 (NFκB2) was significantly increased in CTEPH. We demonstrate reduced histone tri-methylation and increased histone acetylation of the VWF promotor in CTEPH endothelium, facilitating binding of NFκB2 to the VWF promotor and driving VWF transcription. Genetic interference of NFκB2 normalized the high VWF RNA expression levels and reversed the pro-thrombotic phenotype observed in CTEPH-PAEC. CONCLUSION Epigenetic regulation of the VWF promotor contributes to the creation of a local environment that favors in situ thrombosis in the pulmonary arteries. It reveals a direct molecular link between inflammatory pathways and platelet adhesion in the pulmonary vascular wall, emphasizing a possible role of in situ thrombosis in the development or progression of CTEPH.
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Affiliation(s)
- Xue D Manz
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam, Netherlands
| | - Robert Szulcek
- Charite Universitatsmedizin Berlin, 14903, Physiology, Berlin, Germany
| | - Xiaoke Pan
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam, Netherlands
| | - Petr Symersky
- Amsterdam UMC Locatie VUmc, 1209, Cardio-thoracic Surgery, Amsterdam, Netherlands
| | - Chris Dickhoff
- Amsterdam UMC Locatie VUmc, 1209, Cardio-thoracic Surgery, Amsterdam, Netherlands
| | - Jisca Majolée
- Amsterdam UMC Locatie VUmc, 1209, Physiology, Amsterdam, Netherlands
| | - Veerle Kremer
- Amsterdam UMC Locatie VUmc, 1209, Physiology, Amsterdam, Netherlands
| | - Elisabetta Michielon
- Amsterdam UMC Locatie VUmc, 1209, Molecular Cell Biology and Immunology, Amsterdam, Netherlands
| | - Ekaterina S Jordanova
- Amsterdam UMC Locatie VUmc, 1209, Center for Gynecologic Oncology Amsterdam, Amsterdam, Netherlands
| | - Teodora Radonic
- Amsterdam UMC Locatie VUmc, 1209, Pathology, Amsterdam, Netherlands
| | - Irene V Bijnsdorp
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Sander R Piersma
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Thang V Pham
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Connie R Jimenez
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Anton Vonk Noordegraaf
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Frances S de Man
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Reinier A Boon
- Amsterdam UMC Locatie VUmc, 1209, Physiology, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Jan Voorberg
- Sanquin Research, 159217, Molecular Hematology, Amsterdam, Netherlands
| | | | - Jurjan Aman
- Amsterdam UMC - Locatie VUMC, 1209, Pulmonary Diseases, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Harm Jan Bogaard
- Vrije Universiteit Amsterdam, 1190, Pulmonary Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands;
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92
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von Grüning H, Coradin M, Mendoza MR, Reader J, Sidoli S, Garcia BA, Birkholtz LM. A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development. Mol Cell Proteomics 2022; 21:100199. [PMID: 35051657 PMCID: PMC8941266 DOI: 10.1016/j.mcpro.2022.100199] [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: 08/06/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/07/2023] Open
Abstract
Histone posttranslational modifications (PTMs) frequently co-occur on the same chromatin domains or even in the same molecule. It is now established that these “histone codes” are the result of cross talk between enzymes that catalyze multiple PTMs with univocal readout as compared with these PTMs in isolation. Here, we performed a comprehensive identification and quantification of histone codes of the malaria parasite, Plasmodium falciparum. We used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P. falciparum. We provide an updated, high-resolution compendium of 77 PTMs on H3 and H3.3, of which 34 are newly identified in P. falciparum. Coexisting PTMs with unique stage distinctions were identified, indicating that many of these combinatorial PTMs are associated with specific stages of the parasite life cycle. We focused on the code H3R17me2K18acK23ac for its unique presence in mature gametocytes; chromatin proteomics identified a gametocyte-specific SAGA-like effector complex including the transcription factor AP2-G2, which we tied to this specific histone code, as involved in regulating gene expression in mature gametocytes. Ultimately, this study unveils previously undiscovered histone PTMs and their functional relationship with coexisting partners. These results highlight that investigating chromatin regulation in the parasite using single histone PTM assays might overlook higher-order gene regulation for distinct proliferation and differentiation processes. First middle-down chromatin proteomics compendium of the malaria parasite, Plasmodium falciparum. Novel histone PTMs (including arginine methylation) in both asexual parasites and transmissible gametocytes. Histone PTM cross talk is dynamic life cycle stage stratified. Gametocytes rely on histone PTM connectivity to allow onward transmission. AP2-G2 is an important effector of H3K18acK23ac in mature gametocytes.
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Affiliation(s)
- Hilde von Grüning
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa; Institute for Sustainable Malaria Control, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa
| | - Mariel Coradin
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariel R Mendoza
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa; Institute for Sustainable Malaria Control, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa.
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93
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Haghighijoo Z, Zamani L, Moosavi F, Emami S. Therapeutic potential of quinazoline derivatives for Alzheimer's disease: A comprehensive review. Eur J Med Chem 2022; 227:113949. [PMID: 34742016 DOI: 10.1016/j.ejmech.2021.113949] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/02/2021] [Accepted: 10/22/2021] [Indexed: 12/24/2022]
Abstract
Quinazolines are considered as a promising class of bioactive heterocyclic compounds with broad properties. Particularly, the quinazoline scaffold has an impressive role in the design and synthesis of new CNS-active drugs. The drug-like properties and pharmacological characteristics of quinazoline could lead to different drugs with various targets. Among CNS disorders, Alzheimer's disease (AD) is a progressive neurodegenerative disorder with memory loss, cognitive decline and language dysfunction. AD is a complex and multifactorial disease therefore, the need for finding multi-target drugs against this devastative disease is urgent. A literature survey revealed that quinazoline derivatives have diverse therapeutic potential for AD as modulators/inhibitors of β-amyloid, tau protein, cholinesterases, monoamine oxidases, and phosphodiesterases as well as other protective effects. Thus, we describe here the most relevant and recent studies about anti-AD agents with quinazoline structure which can further aid the development and discovery of new anti-AD agents.
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Affiliation(s)
- Zahra Haghighijoo
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA
| | - Leila Zamani
- Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - Fatemeh Moosavi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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94
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Sahu RK, Verma VV, Kumar A, Tandon S, Chandra Das B, Hedau ST. In silico prediction and interaction of resveratrol on methyl-CpG binding proteins by molecular docking and MD simulations study. RSC Adv 2022; 12:11493-11504. [PMID: 35425086 PMCID: PMC9006347 DOI: 10.1039/d2ra00432a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022] Open
Abstract
Resveratrol enhances the BRCA1 gene expression and the MBD family of proteins bind to the promoter region of the BRCA1 gene. However, the molecular interaction is not yet reported. Here we have analyzed the binding affinity of resveratrol with MBD proteins. Our results suggest that resveratrol binds to the MBD proteins with higher binding affinity toward MeCP2 protein (ΔG = −6.5) by sharing four hydrogen bonds as predicted by molecular docking studies. Further, the molecular dynamics simulations outcomes showed that the backbones of all three protein–ligand complexes are stabilized after the period of 75 ns, constantly fluctuating around the deviations of 0.4 Å, 0.5 Å and 0.7 Å for MBD1, MBD2 and MeCP2, respectively. The inter-molecular hydrogen bonding trajectory analysis for protein–ligand complexes also support the strong binding between MeCP2–resveratrol complex. Further, binding free energy calculations showed binding energy of −94.764 kJ mol−1, −53.826 kJ mol−1 and −36.735 kJ mol−1 for MeCP2–resveratrol, MBD2–resveratrol and MBD1–resveratrol complexes, respectively, which also supported our docking results. Our study also highlighted that the MBD family of proteins forms a binding interaction with other signaling proteins that are involved in various cancer initiation pathways. Resveratrol enhances the BRCA1 gene expression and the MBD family of proteins bind to the promoter region of the BRCA1 gene.![]()
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Affiliation(s)
- Ram Krishna Sahu
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, ICMR, I – 7, Sector – 39, Noida – 201 301, Utter Pradesh, India
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Ved Vrat Verma
- Information System for Research Management Division, ICMR, Aruna Asif Ali Marg, New Delhi – 110029, India
| | - Amit Kumar
- Information System for Research Management Division, ICMR, Aruna Asif Ali Marg, New Delhi – 110029, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Bhudev Chandra Das
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Suresh T. Hedau
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, ICMR, I – 7, Sector – 39, Noida – 201 301, Utter Pradesh, India
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95
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Histone H3 lysine-trimethylation markers are decreased by recombinant methioninase and increased by methotrexate at concentrations which inhibit methionine-addicted osteosarcoma cell proliferation. Biochem Biophys Rep 2021; 28:101177. [PMID: 34877414 PMCID: PMC8633566 DOI: 10.1016/j.bbrep.2021.101177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 11/26/2022] Open
Abstract
Methionine addiction is a fundamental and general hallmark of cancer cells, which require exogenous methionine, despite their ability to synthesize normal amounts of methionine from homocysteine. In contrast, methionine-independent normal cells do not require exogenous methionine in the presence of a methionine precursor. The methionine addiction of cancer cells is due to excess transmethylation reactions. We have previously shown that histone H3 lysine marks are over-methylated in cancer cells and the over-methylation is unstable when the cancer cells are restricted of methionine. In the present study, we show that methionine-addicted osteosarcoma cells are sensitive to both methotrexate (MTX) and recombinant methioninase (rMETase), but they affect histone H3 lysine-methylation in the opposite direction. Concentrations of MTX and rMETase, which inhibit osteosarcoma cells viability to 20%, had opposing effects on the status of histone methylation of H3K9me3 and H3K27me3. rMETase significantly decreased the amount of H3K9me3 and H3K27me3. In contrast, MTX significantly increased the amount of H3K9me and H3K27me3. The results suggest that increase or decrease in these methylated histone lysine marks is associated with proliferation arrest of methionine-addicted osteosarcoma. Osteosarcoma cells are sensitive to both methotrexate and recombinant methioninase. MTX increased the amount of H3K9me and H3K27me3. RMETase decreased the amount of H3K9me3 and H3K27me3. Increase/decrease in H3K9me3 and H3K27me3 is associated with proliferation arrest.
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96
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Albulescu A, Plesa A, Fudulu A, Iancu IV, Anton G, Botezatu A. Epigenetic approaches for cervical neoplasia screening (Review). Exp Ther Med 2021; 22:1481. [PMID: 34765022 PMCID: PMC8576616 DOI: 10.3892/etm.2021.10916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Human papillomavirus (HPV) infection is the leading cause of cervical cancer. The Papanicolaou cytology test is the usually employed type of screening for this infection; however, its sensibility is limited. Only a small percentage of women infected with high-risk HPV develop cervical cancer with an array of genetic and epigenetic modifications. Thus, it is necessary to develop rapid, reproducible and minimally invasive technologies for screening. DNA methylation has gained attention as an alternative method for molecular diagnosis and prognosis in HPV infection. The aim of the present review was to highlight the potential of DNA methylation in cervical neoplasia screening for clinical applications. It was observed that the methylation human and viral genes was correlated with high-grade lesions and cancer. Methylation biomarkers have shown a good capacity to discriminate between high-grade lesions with a transformative potential and cervical cancer, being able to detect these modifications at an early stage. With further research, the epigenetic profiles and subtypes of the tumors could be elaborated, which would aid in therapy selection by opening avenues in personalized precision medicine. Response to therapy could also be evaluated through such methods and the accessibility of liquid biopsies would allow a constant monitoring of the patient's status without invasive sampling techniques.
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Affiliation(s)
- Adrian Albulescu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania.,Pharmacology Department, National Institute for Chemical Pharmaceutical Research and Development, Bucharest 031299, Romania
| | - Adriana Plesa
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Alina Fudulu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Iulia Virginia Iancu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Gabriela Anton
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Anca Botezatu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
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97
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Hwang SY, Lee YH, Kuk MU, Kim JW, Oh S, Park JT. Improvement of Tol2 Transposon System Enabling Efficient Protein Production in CHO Cells. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0310-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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98
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Zhang J, Han B, Zheng W, Lin S, Li H, Gao Y, Sun D. Genome-Wide DNA Methylation Profile in Jejunum Reveals the Potential Genes Associated With Paratuberculosis in Dairy Cattle. Front Genet 2021; 12:735147. [PMID: 34721525 PMCID: PMC8554095 DOI: 10.3389/fgene.2021.735147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/23/2021] [Indexed: 12/04/2022] Open
Abstract
Paratuberculosis in cattle causes substantial economic losses to the dairy industry. Exploring functional genes and corresponding regulatory pathways related to resistance or susceptibility to paratuberculosis is essential to the breeding of disease resistance in cattle. Co-analysis of genome-wide DNA methylation and transcriptome profiles is a critically important approach to understand potential regulatory mechanism underlying the development of diseases. In this study, we characterized the profiles of DNA methylation of jejunum from nine Holstein cows in clinical, subclinical, and healthy groups using whole-genome bisulfite sequencing (WGBS). The average methylation level in functional regions was 29.95% in the promoter, 29.65% in the 5’ untranslated region (UTR), 68.24% in exons, 71.55% in introns, and 72.81% in the 3’ UTR. A total of 3,911, 4,336, and 4,094 differentially methylated genes (DMGs) were detected in clinical vs. subclinical, clinical vs. healthy, and subclinical vs. healthy comparative group, respectively. Gene ontology (GO) and analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these DMGs were significantly enriched in specific biological processes related to immune response, such as Th1 and Th2 cell differentiation, wnt, TNF, MAPK, ECM-receptor interaction, cellular senescence, calcium, and chemokine signaling pathways (q value <0.05). The integration of information about DMGs, differentially expressed genes (DEGs), and biological functions suggested nine genes CALCRL, TNC, GATA4, CD44, TGM3, CXCL9, CXCL10, PPARG, and NFATC1 as promising candidates related to resistance/susceptibility to Mycobacterium avium subspecies paratuberculosis (MAP). This study reports on the high-resolution DNA methylation landscapes of the jejunum methylome across three conditions (clinical, subclinical, and healthy) in dairy cows. Our investigations integrated different sources of information about DMGs, DEGs, and pathways, enabling us to find nine functional genes that might have potential application in resisting paratuberculosis in dairy cattle.
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Affiliation(s)
- Junnan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bo Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Weijie Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shan Lin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Houcheng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yahui Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
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99
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Engdahl E, Svensson K, Lin PID, Alavian-Ghavanini A, Lindh C, Rüegg J, Bornehag CG. DNA methylation at GRIN2B partially mediates the association between prenatal bisphenol F exposure and cognitive functions in 7-year-old children in the SELMA study. ENVIRONMENT INTERNATIONAL 2021; 156:106617. [PMID: 34015668 DOI: 10.1016/j.envint.2021.106617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Accumulating evidence suggests that prenatal chemical exposure triggers epigenetic modifications that could influence health outcomes later in life. In this study, we investigated whether DNA methylation (DNAm) levels at the glutamate ionotropic receptor NMDA type subunit 2B (GRIN2B) gene underlies the association between prenatal exposure to an endocrine disrupting chemical (EDC), bisphenol F (BPF), and lower cognitive functions in 7-year-old children. METHODS Data from 799 children participating in the Swedish Environmental Longitudinal Mother and child Asthma and allergy (SELMA) pregnancy cohort was analyzed. Prenatal BPF exposure was assessed by measuring BPF levels in maternal urine. At age 7, DNAm of three CpG sites in a regulatory region of the GRIN2B gene was analyzed from buccal swabs using bisulfite-Pyrosequencing. Cognitive functions, including full-scale IQ and four subscales, were evaluated using the Wechsler Intelligence Scale for Children (WISC-IV). Associations between prenatal BPF exposure and GRIN2B DNAm, as well as between GRIN2B DNAm and cognitive functions, were determined using regression models adjusted for potential confounders. Generalized structural equation models (gSEM) were used to evaluate if GRIN2B DNAm mediates the association between prenatal BPF exposure and cognitive functions at 7 years of age. RESULTS Prenatal BPF exposure was positively associated with GRIN2B DNAm levels at the third CpG site (CpG3), while CpG3 methylation was inversely associated with cognitive test scores. Mediation analyses showed that CpG3 methylation exerted 6-9% of the association between BPF exposure and full-scale IQ, as well as verbal comprehension and perceptual reasoning in boys, while not significant in girls. CONCLUSIONS This study is the first to identify locus-specific DNAm as a mediating factor underlying an epidemiological association between prenatal EDC exposure and cognitive functions in childhood. It also confirms previous findings, that GRIN2B DNAm is responsive to environmental exposures.
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Affiliation(s)
- Elin Engdahl
- Uppsala University, Department of Organismal Biology, 752 36 Uppsala, Sweden.
| | - Katherine Svensson
- Karlstad University, Department of Health Sciences, 651 88 Karlstad, Sweden
| | - Ping-I Daniel Lin
- Karlstad University, Department of Health Sciences, 651 88 Karlstad, Sweden
| | - Ali Alavian-Ghavanini
- Karolinska Institutet, Swetox, Unit of Toxicology Sciences, 151 36 Södertälje, Sweden
| | - Christian Lindh
- Lund University, Division of Occupational and Environmental Medicine, 223 81 Lund, Sweden
| | - Joëlle Rüegg
- Uppsala University, Department of Organismal Biology, 752 36 Uppsala, Sweden; Karlstad University, Department of Health Sciences, 651 88 Karlstad, Sweden
| | - Carl-Gustaf Bornehag
- Karlstad University, Department of Health Sciences, 651 88 Karlstad, Sweden; Icahn School of Medicine at Mount Sinai, NY 10029, USA
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Saxena S, Choudhury S, Maroju PA, Anne A, Kumar L, Mohan KN. Dysregulation of schizophrenia-associated genes and genome-wide hypomethylation in neurons overexpressing DNMT1. Epigenomics 2021; 13:1539-1555. [PMID: 34647491 DOI: 10.2217/epi-2021-0133] [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] [Indexed: 11/21/2022] Open
Abstract
Aim: To study the effects of DNMT1 overexpression on transcript levels of genes dysregulated in schizophrenia and on genome-wide methylation patterns. Materials & methods: Transcriptome and DNA methylome comparisons were made between R1 (wild-type) and Dnmt1tet/tet mouse embryonic stem cells and neurons overexpressing DNMT1. Genes dysregulated in both Dnmt1tet/tet cells and schizophrenia patients were studied further. Results & conclusions: About 50% of dysregulated genes in patients also showed altered transcript levels in Tet/Tet neurons in a DNA methylation-independent manner. These neurons unexpectedly showed genome-wide hypomethylation, increased transcript levels of Tet1 and Apobec 1-3 genes and increased activity and copy number of LINE-1 elements. The observed similarities between Tet/Tet neurons and schizophrenia brain samples reinforce DNMT1 overexpression as a risk factor.
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Affiliation(s)
- Sonal Saxena
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Sumana Choudhury
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Pranay Amruth Maroju
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Anuhya Anne
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Lov Kumar
- Computer Science & Information Systems, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Kommu Naga Mohan
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
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