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Risha KS, Rasal KD, Reang D, Iquebal MA, Sonwane A, Brahmane M, Chaudhari A, Nagpure N. DNA Methylation Profiling in Genetically Selected Clarias magur (Hamilton, 1822) Provides Insights into the Epigenetic Regulation of Growth and Development. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:776-789. [PMID: 39037491 DOI: 10.1007/s10126-024-10346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
DNA methylation is an epigenetic alteration that impacts gene expression without changing the DNA sequence affecting an organism's phenotype. This study utilized a reduced representation bisulfite sequencing (RRBS) approach to investigate the patterns of DNA methylation in genetically selected Clarias magur stocks. RRBS generated 249.22 million reads, with an average of 490,120 methylation sites detected in various parts of genes, including exons, introns, and intergenic regions. A total of 896 differentially methylated regions (DMRs) were identified; 356 and 540 were detected as hyper-methylated and hypo-methylated regions, respectively. The DMRs and their association with overlapping genes were explored using whole genome data of magur, which revealed 205 genes in exonic, 210 in intronic, and 480 in intergenic regions. The analysis identified the maximum number of genes enriched in biological processes such as RNA biosynthetic process, response to growth factors, nervous system development, neurogenesis, and anatomical structure morphogenesis. Differentially methylated genes (DMGs) such as myrip, mylk3, mafb, egr3, ndnf, meis2a, foxn3, bmp1a, plxna3, fgf6, sipa1l1, mcu, cnot8, trim55b, and myof were associated with growth and development. The selected DMGs were analyzed using real-time PCR, which showed altered mRNA expression levels. This work offers insights into the epigenetic mechanisms governing growth performance regulation in magur stocks. This work provides a valuable resource of epigenetic data that could be integrated into breeding programs to select high-performing individuals.
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Affiliation(s)
- K Shasti Risha
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India.
| | - Dhalongsaih Reang
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Arvind Sonwane
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Manoj Brahmane
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Naresh Nagpure
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
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Lopes-Fatturi A, Fonseca-Souza G, Wambier LM, Brancher JA, Küchler EC, Feltrin-Souza J. Genetic polymorphisms associated with developmental defects of enamel: A systematic review. Int J Paediatr Dent 2024. [PMID: 38949474 DOI: 10.1111/ipd.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/20/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND Polymorphisms in genes related to enamel formation and mineralization may increase the risk of developmental defects of enamel (DDE). AIM To evaluate the existing literature on genetic polymorphisms associated with DDE. DESIGN This systematic review was registered in the PROSPERO (CRD42018115270). The literature search was performed in PubMed, Scopus, Web of Science, LILACS, BBO, Cochrane Library, and in the gray literature. Observational studies assessing the association between DDE and genetic polymorphism were included. The Newcastle-Ottawa Scale was used to assess the risk of bias. RESULTS One thousand one hundred and forty-six articles were identified, and 28 met the inclusion criteria. Five studies presented a low risk of bias. Ninety-two genes related to enamel development, craniofacial patterning morphogenesis, immune response, and hormone transcription/reception were included. Molar-incisor hypomineralization (MIH) and/or hypomineralization of primary second molars (HPSM) were associated with 80 polymorphisms of genes responsible for enamel development, immune response, morphogenesis, and xenobiotic detoxication. A significant association was found between the different clinical manifestations of dental fluorosis (DF) with nine polymorphisms of genes responsible for enamel development, craniofacial development, hormonal transcription/reception, and oxidative stress. Hypoplasia was associated with polymorphisms located in intronic regions. CONCLUSION MIH, HPSM, DF, and hypoplasia reported as having a complex etiology are significantly associated with genetic polymorphisms of several genes.
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Kawaf RR, Ramadan WS, El-Awady R. Deciphering the interplay of histone post-translational modifications in cancer: Co-targeting histone modulators for precision therapy. Life Sci 2024; 346:122639. [PMID: 38615747 DOI: 10.1016/j.lfs.2024.122639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
Chromatin undergoes dynamic regulation through reversible histone post-translational modifications (PTMs), orchestrated by "writers," "erasers," and "readers" enzymes. Dysregulation of these histone modulators is well implicated in shaping the cancer epigenome and providing avenues for precision therapies. The approval of six drugs for cancer therapy targeting histone modulators, along with the ongoing clinical trials of numerous candidates, represents a significant advancement in the field of precision medicine. Recently, it became apparent that histone PTMs act together in a coordinated manner to control gene expression. The intricate crosstalk of histone PTMs has been reported to be dysregulated in cancer, thus emerging as a critical factor in the complex landscape of cancer development. This formed the foundation of the swift emergence of co-targeting different histone modulators as a new strategy in cancer therapy. This review dissects how histone PTMs, encompassing acetylation, phosphorylation, methylation, SUMOylation and ubiquitination, collaboratively influence the chromatin states and impact cellular processes. Furthermore, we explore the significance of histone modification crosstalk in cancer and discuss the potential of targeting histone modification crosstalk in cancer management. Moreover, we underscore the significant strides made in developing dual epigenetic inhibitors, which hold promise as emerging candidates for effective cancer therapy.
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Affiliation(s)
- Rawan R Kawaf
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Wafaa S Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
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Zhang J, Yang A, Cui W, Zhang J, Niu A, Hu X, Li Q. Tracing toxic path of antimony: From bioaccumulation to DNA hypomethylation in zebrafish (Danio rerio). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116351. [PMID: 38653027 DOI: 10.1016/j.ecoenv.2024.116351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
The increasing concentration of Antimony (Sb) in ecological environments has raised serious concerns about its potential biotoxicological impact. This study investigated the toxicokinetics, Global DNA Methylation (GDM), biomarker expression, and Integrated Biological Response (IBR) of Sb at different concentrations in zebrafish. The toxic mechanism of Sb exposure was simulated using molecular dynamics (MD). The results showed that significant differences effect existed (BCFk: liver > ovary > gut > brain) and uptake saturation phenomenon of Sb among zebrafish tissues. Over a 54-day exposure period, the liver emerged as the main target site for Sb-induced GDM, and the restoration was slower than in other tissues during the 54-day recovery period. Moreover, the concentration of Sb had a significant impact on the normally expression of biomarkers, with GSTM1 inhibited and MTF2, MT1, TET3, and p53 showing varying degrees of activation at different Sb concentrations. This could be attributed to Sb3+ potentially occupying the active site or tightly binding to the deep cavity of these genes. The IBR and MD results highlighted DNMT1 as the most sensitive biomarker among those assessed. This heightened sensitivity can be attributed to the stable binding of Sb3+ to DNMT1, resulting in alterations in the conformation of DNMT1's catalytic domain and inhibition of its activity. Consequently, this disruption leads to damage to the integrity of GDM. The study suggests that DNA methylation could serve as a valuable biomarker for assessing the ecotoxicological impact of Sb exposure. It contributes to a better understanding of the toxicity mechanisms in aquatic environments caused potential pollutants.
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Affiliation(s)
- Jingyun Zhang
- The College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, PR China
| | - Aijiang Yang
- The College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, PR China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, PR China; Institute of Environmental Engineering Planning and Designing, Guizhou University, Guiyang 550025, PR China.
| | - Wen Cui
- The College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, PR China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, PR China
| | - Jian Zhang
- The College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, PR China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, PR China
| | - Apin Niu
- The College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, PR China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, PR China; Institute of Environmental Engineering Planning and Designing, Guizhou University, Guiyang 550025, PR China
| | - Xia Hu
- The College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, PR China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, PR China; Institute of Environmental Engineering Planning and Designing, Guizhou University, Guiyang 550025, PR China
| | - Qing Li
- The College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, PR China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, PR China; Institute of Environmental Engineering Planning and Designing, Guizhou University, Guiyang 550025, PR China
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Frazer LC, Yamaguchi Y, Singh DK, Akopyants NS, Good M. DNA methylation in necrotizing enterocolitis. Expert Rev Mol Med 2024; 26:e16. [PMID: 38557638 PMCID: PMC11140546 DOI: 10.1017/erm.2024.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Epigenetic modifications, such as DNA methylation, are enzymatically regulated processes that directly impact gene expression patterns. In early life, they are central to developmental programming and have also been implicated in regulating inflammatory responses. Research into the role of epigenetics in neonatal health is limited, but there is a growing body of literature related to the role of DNA methylation patterns and diseases of prematurity, such as the intestinal disease necrotizing enterocolitis (NEC). NEC is a severe intestinal inflammatory disease, but the key factors that precede disease development remain to be determined. This knowledge gap has led to a failure to design effective targeted therapies and identify specific biomarkers of disease. Recent literature has identified altered DNA methylation patterns in the stool and intestinal tissue of neonates with NEC. These findings provide the foundation for a new avenue in NEC research. In this review, we will provide a general overview of DNA methylation and then specifically discuss the recent literature related to methylation patterns in neonates with NEC. We will also discuss how DNA methylation is used as a biomarker for other disease states and how, with further research, methylation patterns may serve as potential biomarkers for NEC.
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Affiliation(s)
- Lauren C. Frazer
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yukihiro Yamaguchi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dhirendra K. Singh
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalia S. Akopyants
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Misty Good
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Nabil Salama A, Badr EAEF, Holah NS, El Barbary AA, Hessien M. Conservative Hypomethylation of Mesenchymal Stem Cells and Their Secretome Restored the Follicular Development in Cisplatin-Induced Premature Ovarian Failure Mice. Reprod Sci 2024; 31:1053-1068. [PMID: 37957472 PMCID: PMC10959784 DOI: 10.1007/s43032-023-01389-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
Premature ovarian failure (POF) is one of the main causes of infertility in women under the age of 40 years. Recently, epigenetic reprogramming, particularly DNA hypomethylation, has emerged as a promising strategy to enhance the therapeutic potential of mesenchymal stem cells (MSCs). Thus, it is crucial to elucidate how far global hypomethylation of MSCs genome can maintain their pluripotency and viability and improve their therapeutic effect in chemotherapy-induced POF mice. Herein, the genomic DNA of bone marrow-derived MSCs (BM-MSCs) was hypomethylated by the DNA methyltransferase inhibitor (5-Aza-dC), and the degree of global hypomethylation was assessed by methylation-sensitive HepII/MspI restriction analysis. Next, mildly hypomethylated cells and their secretome were independently transplanted (or infused) in POF mice, established via cisplatin-mediated gonadotoxicity. We found that conservative global hypomethylation of BM-MSCs genome with low doses of 5-Aza-dC (≤0.5 μM) has maintained cell viability and MSCs-specific clusters of differentiation (CD). Engraftment of mildly hypomethylated cells in POF mice, or infusion of their secretome, improved the concentrations of estradiol (E2), follicle-stimulating hormone (FSH), and anti-Mullerian hormone (AMH). Furthermore, mice restored their normal body weight, ovarian size, and ovarian follicle count. This was associated with improved follicular development, where the populations of healthy primordial, primary, secondary, and tertiary follicles were significantly ameliorated, relative to mice transplanted with normally methylated cells. This observational study suggests that transplantation of mildly hypomethylated BM-MSCs cells and their secretome can restore the structural and functional integrity of the damaged ovaries in POF mice. Also, it presents conservative hypomethylation of BM-MSCs and their secretome as a promising alternative to MSCs transplantation.
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Affiliation(s)
- Amira Nabil Salama
- Directorate of Health Affairs, Joint Regional Laboratories, Shebin El-Koum, Menoufia, 32511, Egypt
| | - Eman Abd El-Fatah Badr
- Department of Medical Biochemistry, Faculty of Medicine, Menoufia University, Shebin El-Koum City, 32511, Egypt
| | - Nanis Shawky Holah
- Department of Pathology, Faculty of Medicine, Menoufia University, Shebin El-Koum City, 32511, Egypt
| | - Ahmed A El Barbary
- Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed Hessien
- Directorate of Health Affairs, Joint Regional Laboratories, Shebin El-Koum, Menoufia, 32511, Egypt.
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
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7
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Hubers N, Hagenbeek FA, Pool R, Déjean S, Harms AC, Roetman PJ, van Beijsterveldt CEM, Fanos V, Ehli EA, Vermeiren RRJM, Bartels M, Hottenga JJ, Hankemeier T, van Dongen J, Boomsma DI. Integrative multi-omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention-Deficit/Hyperactivity Disorder. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32955. [PMID: 37534875 DOI: 10.1002/ajmg.b.32955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The evolving field of multi-omics combines data and provides methods for simultaneous analysis across several omics levels. Here, we integrated genomics (transmitted and non-transmitted polygenic scores [PGSs]), epigenomics, and metabolomics data in a multi-omics framework to identify biomarkers for Attention-Deficit/Hyperactivity Disorder (ADHD) and investigated the connections among the three omics levels. We first trained single- and next multi-omics models to differentiate between cases and controls in 596 twins (cases = 14.8%) from the Netherlands Twin Register (NTR) demonstrating reasonable in-sample prediction through cross-validation. The multi-omics model selected 30 PGSs, 143 CpGs, and 90 metabolites. We confirmed previous associations of ADHD with glucocorticoid exposure and the transmembrane protein family TMEM, show that the DNA methylation of the MAD1L1 gene associated with ADHD has a relation with parental smoking behavior, and present novel findings including associations between indirect genetic effects and CpGs of the STAP2 gene. However, out-of-sample prediction in NTR participants (N = 258, cases = 14.3%) and in a clinical sample (N = 145, cases = 51%) did not perform well (range misclassification was [0.40, 0.57]). The results highlighted connections between omics levels, with the strongest connections between non-transmitted PGSs, CpGs, and amino acid levels and show that multi-omics designs considering interrelated omics levels can help unravel the complex biology underlying ADHD.
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Affiliation(s)
- Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219, University of Toulouse, CNRS, Toulouse, France
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Peter J Roetman
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, USA
| | - Robert R J M Vermeiren
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
- Youz, Parnassia Group, the Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
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He X, Zhang S, Zhong Y, Huang X, Liu F, He J, Mai S. A low-shrinkage-stress and anti-bacterial adherent dental resin composite: physicochemical properties and biocompatibility. J Mater Chem B 2024; 12:814-827. [PMID: 38189164 DOI: 10.1039/d3tb01556d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Polymerisation shrinkage and biofilm accumulation are the two main problems associated with dental resin composites (DRCs) that induce secondary caries, which can cause restoration failure. Polymerisation shrinkage can lead to microleakage gaps between the tooth and the DRCs, causing the aggregation of bacteria and development of secondary caries. Reducing the shrinkage stress (SS) and improving the resistance to bacterial adhesion have always been the focus of this field in modifying DRCs. A thiol-ene resin system can effectively reduce the polymerisation SS via its step-growth mechanism for delaying the gel point. Fluorinated compounds can reduce the surface free energies, thereby reducing bacterial adhesion. Thus, in this study, a range of mass fractions (0, 10, 20, 30, and 40 wt%) of a fluorinated thiol-ene resin system were added to a fluorinated dimethacrylate resin system/tricyclo decanedimethanol diacrylate to create a fluorinated methacrylate-thiol-ene ternary resin matrix. DRCs were prepared using the obtained ternary resin matrix, and their physical and chemical properties, effect on bacterial adhesion, and biocompatibility were investigated. The results demonstrated that the volumetric shrinkage and SS of the DRCs were reduced with no reduction in conversion degree even after the thiol-ene resin system was added. All DRC-based fluorinated resin systems exhibited an excellent anti-bacterial adhesion effect, as evidenced by the colony-forming unit counts, live/dead bacterial staining, and crystal violet staining tests against Streptococcus mutans (S. mutans). The genetic expressions associated with the bacterial adhesion of S. mutans were substantially affected after being cultured with fluorinated DRCs. All fluorinated DRCs demonstrated good biocompatibility through the in vitro cytotoxicity test and live/dead staining images of the L-929 cells. The above results illustrate that the DRCs based on the fluorinated methacrylate-thiol-ene resin matrix can be potentially applied in clinical practice due to their low SS and anti-bacterial adhesion effect.
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Affiliation(s)
- Xinlin He
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China.
- Guanghua School of Stomatology, Sun Yat-sen University, Guangdong, 510055, People's Republic of China
- Institute of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China
| | - Shengcan Zhang
- College of Materials Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China.
| | - Yewen Zhong
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China.
- Guanghua School of Stomatology, Sun Yat-sen University, Guangdong, 510055, People's Republic of China
- Institute of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China
| | - Xiangya Huang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China.
- Guanghua School of Stomatology, Sun Yat-sen University, Guangdong, 510055, People's Republic of China
- Institute of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China
| | - Fang Liu
- College of Materials Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China.
| | - Jingwei He
- College of Materials Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China.
| | - Sui Mai
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China.
- Guanghua School of Stomatology, Sun Yat-sen University, Guangdong, 510055, People's Republic of China
- Institute of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, 510055, People's Republic of China
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9
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Bou Ghanem A, Hussayni Y, Kadbey R, Ratel Y, Yehya S, Khouzami L, Ghadieh HE, Kanaan A, Azar S, Harb F. Exploring the complexities of 1C metabolism: implications in aging and neurodegenerative diseases. Front Aging Neurosci 2024; 15:1322419. [PMID: 38239489 PMCID: PMC10794399 DOI: 10.3389/fnagi.2023.1322419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
The intricate interplay of one-carbon metabolism (OCM) with various cellular processes has garnered substantial attention due to its fundamental implications in several biological processes. OCM serves as a pivotal hub for methyl group donation in vital biochemical reactions, influencing DNA methylation, protein synthesis, and redox balance. In the context of aging, OCM dysregulation can contribute to epigenetic modifications and aberrant redox states, accentuating cellular senescence and age-associated pathologies. Furthermore, OCM's intricate involvement in cancer progression is evident through its capacity to provide essential one-carbon units crucial for nucleotide synthesis and DNA methylation, thereby fueling uncontrolled cell proliferation and tumor development. In neurodegenerative disorders like Alzheimer's and Parkinson's, perturbations in OCM pathways are implicated in the dysregulation of neurotransmitter synthesis and mitochondrial dysfunction, contributing to disease pathophysiology. This review underscores the profound impact of OCM in diverse disease contexts, reinforcing the need for a comprehensive understanding of its molecular complexities to pave the way for targeted therapeutic interventions across inflammation, aging and neurodegenerative disorders.
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Affiliation(s)
- Ayman Bou Ghanem
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Yaman Hussayni
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Raghid Kadbey
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Yara Ratel
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Shereen Yehya
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Lara Khouzami
- College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
- AUB Diabetes, American University of Beirut Medical Center, Beirut, Lebanon
| | - Amjad Kanaan
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Frederic Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
- AUB Diabetes, American University of Beirut Medical Center, Beirut, Lebanon
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Gao J, Feng Y, Yang Y, Shi Y, Liu J, Lin H, Zhang L. Identification of Key DNA methylation sites related to differentially expressed genes in Lung squamous cell carcinoma. Comput Biol Med 2023; 167:107615. [PMID: 37918267 DOI: 10.1016/j.compbiomed.2023.107615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/24/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Changes in DNA methylation level at some CpG locus are closely associated with the occurrence of lung squamous cell carcinoma (LUSC). However, its specific regulatory mechanism is still unclear. Therefore, it is necessary to systematically identify and analyze those key CpG sites whose DNA methylation levels are closely related to the differential expression of up- and down-regulated genes in LUSC. Due to the dispersion of DNA methylation sites in different regions of genome, to study the correlation between gene expression level and DNA methylation, we divided gene into 6 non-overlapping functional regions and proposed a two-step correlation analysis method to identify differential DNA methylation sites and matched differential expression genes. As a results, we obtained 39 key CpG sites scattered in 27 genes. Through comparative analysis of LUSC-normal sample pairs, we found that these sites and genes can accurately cluster LUSC samples and normal samples. Finally, we used these sites and genes to distinguish LUSC from normal samples. The results suggest that they can be used as effective biomarkers for identifying LUSC. In addition, the proposed two-step correlation analysis method can also be extended to the identification of biomarkers of other cancers and diseases.
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Affiliation(s)
- Jie Gao
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Yongxian Feng
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Yan Yang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Yuetong Shi
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Junjie Liu
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hao Lin
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Lirong Zhang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
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11
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Zhao Y, Xiong W, Li C, Zhao R, Lu H, Song S, Zhou Y, Hu Y, Shi B, Ge J. Hypoxia-induced signaling in the cardiovascular system: pathogenesis and therapeutic targets. Signal Transduct Target Ther 2023; 8:431. [PMID: 37981648 PMCID: PMC10658171 DOI: 10.1038/s41392-023-01652-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 11/21/2023] Open
Abstract
Hypoxia, characterized by reduced oxygen concentration, is a significant stressor that affects the survival of aerobic species and plays a prominent role in cardiovascular diseases. From the research history and milestone events related to hypoxia in cardiovascular development and diseases, The "hypoxia-inducible factors (HIFs) switch" can be observed from both temporal and spatial perspectives, encompassing the occurrence and progression of hypoxia (gradual decline in oxygen concentration), the acute and chronic manifestations of hypoxia, and the geographical characteristics of hypoxia (natural selection at high altitudes). Furthermore, hypoxia signaling pathways are associated with natural rhythms, such as diurnal and hibernation processes. In addition to innate factors and natural selection, it has been found that epigenetics, as a postnatal factor, profoundly influences the hypoxic response and progression within the cardiovascular system. Within this intricate process, interactions between different tissues and organs within the cardiovascular system and other systems in the context of hypoxia signaling pathways have been established. Thus, it is the time to summarize and to construct a multi-level regulatory framework of hypoxia signaling and mechanisms in cardiovascular diseases for developing more therapeutic targets and make reasonable advancements in clinical research, including FDA-approved drugs and ongoing clinical trials, to guide future clinical practice in the field of hypoxia signaling in cardiovascular diseases.
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Affiliation(s)
- Yongchao Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Weidong Xiong
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China
| | - Chaofu Li
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Ranzun Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Hao Lu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - You Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Yiqing Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
| | - Bei Shi
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - Junbo Ge
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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12
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Pang WQ, Lai CS, Mad' Atari MF, Pandian BR, Mohamad Ibrahim MN, Tan ST, Yoong ICK, Subramaniam S. Effect of graphene oxide nanoparticles on in vitro growth of Fragaria x ananassa (Cameron Highlands white Strawberry) and evaluation of genetic stability using DAMD and ISSR markers. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108104. [PMID: 37862933 DOI: 10.1016/j.plaphy.2023.108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Graphene oxide (GO) is a novel nanomaterial with distinct physical properties and significant biological applications. The use of GO in plant tissue culture offers several new properties and potential applications. This research is vital due to the growing need for innovative techniques to promote plant growth, improve plant productivity and mitigate challenges posed by environmental stressors. This study focused on the rare Cameron Highlands white strawberry plants (Fragaria x ananassa) and addressed issues such as callus production during direct shoot induction and hyperhydricity. The research aimed to investigate the effects of GO on the regeneration process and genetic stability of white strawberry plants and to use molecular markers to ensure that plants propagated in vitro are true to type. For this purpose, shoot tip explants were used and different concentrations of GO (0, 2.5, 5.0, 7.5, 10 mg/L) were added to the Murashige and Skoog (MS) medium for six weeks. The results showed that the optimum concentration for promoting the development of white strawberry seedlings was 7.5 mg/L of GO. The study also revealed that the addition of 7.5 mg/L GO in combination with 8 μM TDZ to the MS medium facilitated the induction of multiple shoots. Moreover, the clonal fidelity of the in vitro plants treated with GO showed a genetic similarity of over 97%. These results confirm that lower GO concentrations improve plant development and stability. Consequently, this nanomaterial has a positive effect on the growth of strawberry plants and is therefore well suited for strawberry tissue culture.
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Affiliation(s)
- Wei Quan Pang
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, 11800, Penang, Malaysia
| | - Chern Shun Lai
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, 11800, Penang, Malaysia
| | | | - Bothi Raja Pandian
- School of Chemical Sciences, Universiti Sains Malaysia (USM), Georgetown, Penang, 11800, Malaysia
| | | | - Swee Tiam Tan
- Kelip-kelip! Center of Excellence for Light Enabling Technologies, School of Energy and Chemical Engineering, Xiamen University Malaysia, Jalan Sunsuria, Bandar Sunsuria, 43900, Sepang, Selangor, Malaysia
| | - Ivan Chew Ken Yoong
- Seedlab Technologies Sdn Bhd, 5-3-16, The Promenade, Persiaran Mahsuri 1, 11950, Bayan Lepas, Penang, Malaysia
| | - Sreeramanan Subramaniam
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, 11800, Penang, Malaysia; Chemical Centre Biology (CCB), Universiti Sains Malaysia (USM), Bayan Lepas, 11900, Penang, Malaysia; Institute of Nano Optoelectronics Research and Technology, Universiti Sains Malaysia (USM), 11900, Bayan Lepas, Penang, Malaysia.
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13
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Akhtar MS, Alavudeen SS, Raza A, Imam MT, Almalki ZS, Tabassum F, Iqbal MJ. Current understanding of structural and molecular changes in diabetic cardiomyopathy. Life Sci 2023; 332:122087. [PMID: 37714373 DOI: 10.1016/j.lfs.2023.122087] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Diabetic Mellitus has been characterized as the most prevalent disease throughout the globe associated with the serious morbidity and mortality of vital organs. Cardiomyopathy is the major leading complication of diabetes and within this, myocardial dysfunction or failure is the leading cause of the emergency hospital admission. The review is aimed to comprehend the perspectives associated with diabetes-induced cardiovascular complications. The data was collected from several electronic databases such as Google Scholar, Science Direct, ACS publication, PubMed, Springer, etc. using the keywords such as diabetes and its associated complication, the prevalence of diabetes, the anatomical and physiological mechanism of diabetes-induced cardiomyopathy, the molecular mechanism of diabetes-induced cardiomyopathy, oxidative stress, and inflammatory stress, etc. The collected scientific data was screened by different experts based on the inclusion and exclusion criteria of the study. This review findings revealed that diabetes is associated with inefficient substrate utilization, inability to increase glucose metabolism and advanced glycation end products within the diabetic heart resulting in mitochondrial uncoupling, glucotoxicity, lipotoxicity, and initially subclinical cardiac dysfunction and finally in overt heart failure. Furthermore, several factors such as hypertension, overexpression of renin angiotensin system, hypertrophic obesity, etc. have been seen as majorly associated with cardiomyopathy. The molecular examination showed biochemical disability and generation of the varieties of free radicals and inflammatory cytokines and becomes are the substantial causes of cardiomyopathy. This review provides a better understanding of the involved pathophysiology and offers an open platform for discussing and targeting therapy in alleviating diabetes-induced early heart failure or cardiomyopathy.
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Affiliation(s)
- Md Sayeed Akhtar
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Al-Fara, Abha 62223, Saudi Arabia.
| | - Sirajudeen S Alavudeen
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Al-Fara, Abha 62223, Saudi Arabia
| | - Asif Raza
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine, Penn State Milton S. Hershey Medical Center, 500 University Drive, Hershey, PA 17033, USA
| | - Mohammad Tarique Imam
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 16273, Saudi Arabia
| | - Ziad Saeed Almalki
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 16273, Saudi Arabia
| | - Fauzia Tabassum
- Department of Pharmacology, College of Dentistry and Pharmacy, Buraydah Private College, Al Qassim 51418, Saudi Arabia; Department of Pharmacology, Vision College, Ishbilia, Riyadh 13226-3830, Saudi Arabia
| | - Mir Javid Iqbal
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
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14
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Zavafer A, Bates H, Mancilla C, Ralph PJ. Phenomics: conceptualization and importance for plant physiology. TRENDS IN PLANT SCIENCE 2023; 28:1004-1013. [PMID: 37137749 DOI: 10.1016/j.tplants.2023.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Phenomics is a relatively new discipline of biology that has been widely applied in several fields, mainly in crop sciences. We reviewed the concepts used in this discipline (particularly for plants) and found a lack of consensus on what defines a phenomic study. Furthermore, phenomics has been primarily developed around its technical aspects (operationalization), while the conceptual framework of the actual research lags behind. Each research group has given its own interpretation of this 'omic' and thus unwittingly created a 'conceptual controversy'. Addressing this issue is of particular importance, as the experimental designs and concepts of phenomics are so diverse that it is difficult to compare studies. In this opinion article, we evaluate the conceptual framework of phenomics.
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Affiliation(s)
- Alonso Zavafer
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia; Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada; Department of Engineering, Brock University, St. Catharines, Ontario, Canada.
| | - Harvey Bates
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Cristian Mancilla
- Department of Engineering, Brock University, St. Catharines, Ontario, Canada
| | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia
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15
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Mullakkalparambil Velayudhan S, Sejian V, Devaraj C, Manjunathareddy GB, Ruban W, Kadam V, König S, Bhatta R. Novel Insights to Assess Climate Resilience in Goats Using a Holistic Approach of Skin-Based Advanced NGS Technologies. Int J Mol Sci 2023; 24:10319. [PMID: 37373465 DOI: 10.3390/ijms241210319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
A novel study was conducted to elucidate heat-stress responses on a number of hair- and skin-based traits in two indigenous goat breeds using a holistic approach that considered a number of phenotypic and genomic variables. The two goat breeds, Kanni Aadu and Kodi Aadu, were subjected to a simulated heat-stress study using the climate chambers. Four groups consisting of six goats each (KAC, Kaani Aadu control; KAH, Kanni Aadu heat stress; KOC, Kodi Aadu control; and KOH, Kodi Aadu heat stress) were considered for the study. The impact of heat stress on caprine skin tissue along with a comparative assessment of the thermal resilience of the two goat breeds was assessed. The variables considered were hair characteristics, hair cortisol, hair follicle quantitative PCR (qPCR), sweating (sweating rate and active sweat gland measurement), skin histometry, skin-surface infrared thermography (IRT), skin 16S rRNA V3-V4 metagenomics, skin transcriptomics, and skin bisulfite sequencing. Heat stress significantly influenced the hair fiber characteristics (fiber length) and hair follicle qPCR profile (Heat-shock protein 70 (HSP70), HSP90, and HSP110). Significantly higher sweating rate, activated sweat gland number, skin epithelium, and sweat gland number (histometry) were observed in heat stressed goats. The skin microbiota was also observed to be significantly altered due to heat stress, with a relatively higher alteration being noticed in Kanni Aadu goats than in Kodi Aadi goats. Furthermore, the transcriptomics and epigenetics analysis also pointed towards the significant impact of heat stress at the cellular and molecular levels in caprine skin tissue. The higher proportion of differentially expressed genes (DEGs) along with higher differentially methylated regions (DMRs) in Kanni Aadu goats due to heat stress when compared to Kodi Aadu goats pointed towards the better resilience of the latter breed. A number of established skin, adaptation, and immune-response genes were also observed to be significantly expressed/methylated. Additionally, the influence of heat stress at the genomic level was also predicted to result in significant functional alterations. This novel study thereby highlights the impact of heat stress on the caprine skin tissue and also the difference in thermal resilience exhibited by the two indigenous goat breeds, with Kodi Aadu goats being more resilient.
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Affiliation(s)
| | - Veerasamy Sejian
- Rajiv Gandhi Institute of Veterinary Education and Research, Kurumbapet, Pondicherry 605008, India
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
| | - Chinnasamy Devaraj
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
| | | | - Wilfred Ruban
- Department of Livestock Product Technology, Hebbal Veterinary College, Karnataka Veterinary Animal and Fishery Sciences University, Hebbal, Bangalore 560024, India
| | - Vinod Kadam
- Textile Manufacturing and Textile Chemistry Division, Central Sheep and Wool Research Institute, Avikanagar, Malpura 304501, India
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstr. 21b, 35390 Giessen, Germany
| | - Raghavendra Bhatta
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
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16
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Hajishengallis G. Illuminating the oral microbiome and its host interactions: animal models of disease. FEMS Microbiol Rev 2023; 47:fuad018. [PMID: 37113021 PMCID: PMC10198557 DOI: 10.1093/femsre/fuad018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023] Open
Abstract
Periodontitis and caries are driven by complex interactions between the oral microbiome and host factors, i.e. inflammation and dietary sugars, respectively. Animal models have been instrumental in our mechanistic understanding of these oral diseases, although no single model can faithfully reproduce all aspects of a given human disease. This review discusses evidence that the utility of an animal model lies in its capacity to address a specific hypothesis and, therefore, different aspects of a disease can be investigated using distinct and complementary models. As in vitro systems cannot replicate the complexity of in vivo host-microbe interactions and human research is typically correlative, model organisms-their limitations notwithstanding-remain essential in proving causality, identifying therapeutic targets, and evaluating the safety and efficacy of novel treatments. To achieve broader and deeper insights into oral disease pathogenesis, animal model-derived findings can be synthesized with data from in vitro and clinical research. In the absence of better mechanistic alternatives, dismissal of animal models on fidelity issues would impede further progress to understand and treat oral disease.
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Affiliation(s)
- George Hajishengallis
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, 240 S. 40th Street, Philadelphia, PA 19104-6030, USA
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17
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Chianese U, Papulino C, Megchelenbrink W, Tambaro FP, Ciardiello F, Benedetti R, Altucci L. Epigenomic machinery regulating pediatric AML: clonal expansion mechanisms, therapies, and future perspectives. Semin Cancer Biol 2023; 92:84-101. [PMID: 37003397 DOI: 10.1016/j.semcancer.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with a genetic, epigenetic, and transcriptional etiology mainly presenting somatic and germline abnormalities. AML incidence rises with age but can also occur during childhood. Pediatric AML (pAML) accounts for 15-20% of all pediatric leukemias and differs considerably from adult AML. Next-generation sequencing technologies have enabled the research community to "paint" the genomic and epigenomic landscape in order to identify pathology-associated mutations and other prognostic biomarkers in pAML. Although current treatments have improved the prognosis for pAML, chemoresistance, recurrence, and refractory disease remain major challenges. In particular, pAML relapse is commonly caused by leukemia stem cells that resist therapy. Marked patient-to-patient heterogeneity is likely the primary reason why the same treatment is successful for some patients but, at best, only partially effective for others. Accumulating evidence indicates that patient-specific clonal composition impinges significantly on cellular processes, such as gene regulation and metabolism. Although our understanding of metabolism in pAML is still in its infancy, greater insights into these processes and their (epigenetic) modulation may pave the way toward novel treatment options. In this review, we summarize current knowledge on the function of genetic and epigenetic (mis)regulation in pAML, including metabolic features observed in the disease. Specifically, we describe how (epi)genetic machinery can affect chromatin status during hematopoiesis, leading to an altered metabolic profile, and focus on the potential value of targeting epigenetic abnormalities in precision and combination therapy for pAML. We also discuss the possibility of using alternative epidrug-based therapeutic approaches that are already in clinical practice, either alone as adjuvant treatments and/or in combination with other drugs.
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Affiliation(s)
- Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Chiara Papulino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Wout Megchelenbrink
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Princess Máxima Center, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands.
| | - Francesco Paolo Tambaro
- Bone Marrow Transplant Unit, Pediatric Oncology Department AORN Santobono Pausilipon, 80129, Naples Italy.
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Biogem Institute of Molecular and Genetic Biology, 83031 Ariano Irpino, Italy; IEOS, Institute for Endocrinology and Oncology "Gaetano Salvatore" (IEOS), 80131 Naples, Italy.
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18
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Targeting emerging cancer hallmarks by transition metal complexes: Epigenetic reprogramming and epitherapies. Part II. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Khan AQ, Thielen L, Le Pen G, Krebs MO, Kebir O, Groh A, Deest M, Bleich S, Frieling H, Jahn K. Methylation pattern and mRNA expression of synapse-relevant genes in the MAM model of schizophrenia in the time-course of adolescence. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:110. [PMID: 36481661 PMCID: PMC9732294 DOI: 10.1038/s41537-022-00319-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022]
Abstract
Schizophrenia is highly heritable and aggregating in families, but genetics alone does not exclusively explain the pathogenesis. Many risk factors, including childhood trauma, viral infections, migration, and the use of cannabis, are associated with schizophrenia. Adolescence seems to be the critical period where symptoms of the disease manifest. This work focuses on studying an epigenetic regulatory mechanism (the role of DNA methylation) and its interaction with mRNA expression during development, with a particular emphasis on adolescence. The presumptions regarding the role of aberrant neurodevelopment in schizophrenia were tested in the Methyl-Azoxy-Methanol (MAM) animal model. MAM treatment induces neurodevelopmental disruptions and behavioral deficits in off-springs of the treated animals reminiscent of those observed in schizophrenia and is thus considered a promising model for studying this pathology. On a gestational day-17, adult pregnant rats were treated with the antimitotic agent MAM. Experimental animals were divided into groups and subgroups according to substance treatment (MAM and vehicle agent [Sham]) and age of analysis (pre-adolescent and post-adolescent). Methylation and mRNA expression analysis of four candidate genes, which are often implicated in schizophrenia, with special emphasis on the Dopamine hypothesis i.e., Dopamine receptor D2 (Drd2), and the "co-factors" Disrupted in schizophrenia 1 (DISC1), Synaptophysin (Syp), and Dystrobrevin-binding protein 1 (Dtnbp1), was performed in the Gyrus cingulum (CING) and prefrontal cortex (PFC). Data were analyzed to observe the effect of substance treatment between groups and the impact of adolescence within-group. We found reduced pre-adolescent expression levels of Drd2 in both brain areas under the application of MAM. The "co-factor genes" did not show high deviations in mRNA expression levels but high alterations of methylation rates under the application of MAM (up to ~20%), which diminished in the further time course, reaching a comparable level like in Sham control animals after adolescence. The pre-adolescent reduction in DRD2 expression might be interpreted as downregulation of the receptor due to hyperdopaminergic signaling from the ventral tegmental area (VTA), eventually even to both investigated brain regions. The notable alterations of methylation rates in the three analyzed co-factor genes might be interpreted as attempt to compensate for the altered dopaminergic neurotransmission.
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Affiliation(s)
- Abdul Qayyum Khan
- grid.10423.340000 0000 9529 9877Laboratory for Molecular Neurosciences (LMN), Department of Psychiatry, Social Psychiatry and Psychotherapy, Medical School Hannover (MHH), Carl-Neuberg-Str. 1, 30625 Hannover, Germany ,grid.444940.9University of Management and Technology—School of Pharmacy, 72-A Raiwind Rd, Dubai Town, Lahore Pakistan
| | - Lukas Thielen
- grid.10423.340000 0000 9529 9877Laboratory for Molecular Neurosciences (LMN), Department of Psychiatry, Social Psychiatry and Psychotherapy, Medical School Hannover (MHH), Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Gwenaëlle Le Pen
- grid.512035.0Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Pathophysiology of Psychiatric disorders: Development and Vulnerability, U1266, 102-108 Rue de la Santé, 75014 Paris, France
| | - Marie-Odile Krebs
- grid.512035.0Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Pathophysiology of Psychiatric disorders: Development and Vulnerability, U1266, 102-108 Rue de la Santé, 75014 Paris, France ,GHU Paris Psychiatrie et Neurosciences, 1 Rue Cabanis, 75014 Paris, France
| | - Oussama Kebir
- grid.512035.0Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Pathophysiology of Psychiatric disorders: Development and Vulnerability, U1266, 102-108 Rue de la Santé, 75014 Paris, France ,GHU Paris Psychiatrie et Neurosciences, 1 Rue Cabanis, 75014 Paris, France
| | - Adrian Groh
- grid.10423.340000 0000 9529 9877Laboratory for Molecular Neurosciences (LMN), Department of Psychiatry, Social Psychiatry and Psychotherapy, Medical School Hannover (MHH), Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Maximilian Deest
- grid.10423.340000 0000 9529 9877Laboratory for Molecular Neurosciences (LMN), Department of Psychiatry, Social Psychiatry and Psychotherapy, Medical School Hannover (MHH), Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Stefan Bleich
- grid.10423.340000 0000 9529 9877Laboratory for Molecular Neurosciences (LMN), Department of Psychiatry, Social Psychiatry and Psychotherapy, Medical School Hannover (MHH), Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Helge Frieling
- grid.10423.340000 0000 9529 9877Laboratory for Molecular Neurosciences (LMN), Department of Psychiatry, Social Psychiatry and Psychotherapy, Medical School Hannover (MHH), Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Kirsten Jahn
- grid.10423.340000 0000 9529 9877Laboratory for Molecular Neurosciences (LMN), Department of Psychiatry, Social Psychiatry and Psychotherapy, Medical School Hannover (MHH), Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Adelipour M, Cheraghzadeh M, Rashidi M. Polyphenols as epigenetic modulators in treating or preventing of cancers. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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21
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Smyth LK, Balme GA, Tyzack-Pitman R, Bishop JM, Justin O’Riain M. Like mother like daughter: quantifying the relationship between relatedness and phenotypic similarity in leopard pelage patterns. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00308-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Rump K, Spellenberg T, von Busch A, Wolf A, Ziehe D, Thon P, Rahmel T, Adamzik M, Koos B, Unterberg M. AQP5-1364A/C Polymorphism Affects AQP5 Promoter Methylation. Int J Mol Sci 2022; 23:ijms231911813. [PMID: 36233114 PMCID: PMC9570216 DOI: 10.3390/ijms231911813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
The quantity of aquaporin 5 protein in neutrophil granulocytes is associated with human sepsis-survival. The C-allele of the aquaporin (AQP5)-1364A/C polymorphism was shown to be associated with decreased AQP5 expression, which was shown to be relevant in this context leading towards improved outcomes in sepsis. To date, the underlying mechanism of the C-allele—leading to lower AQP5 expression—has been unknown. Knowing the detailed mechanism depicts a crucial step with a target to further interventions. Genotype-dependent regulation of AQP5 expression might be mediated by the epigenetic mechanism of promoter methylation and treatment with epigenetic-drugs could maybe provide benefit. Hence, we tested the hypothesis that AQP5 promoter methylation differs between genotypes in specific types of immune cells.: AQP5 promoter methylation was quantified in cells of septic patients and controls by methylation-specific polymerase chain reaction and quantified by a standard curve. In cell-line models, AQP5 expression was analyzed after demethylation to determine the impact of promoter methylation on AQP5 expression. C-allele of AQP5-1364 A/C promoter polymorphism is associated with a five-fold increased promoter methylation in neutrophils (p = 0.0055) and a four-fold increase in monocytes (p = 0.0005) and lymphocytes (p = 0.0184) in septic patients and healthy controls as well. In addition, a decreased AQP5 promoter methylation was accompanied by an increased AQP5 expression in HL-60 (p = 0.0102) and REH cells (p = 0.0102). The C-allele which is associated with lower gene expression in sepsis is accompanied by a higher methylation level of the AQP5 promoter. Hence, AQP5 promoter methylation could depict a key mechanism in genotype-dependent expression.
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Wojciech Tynior, Joanna Katarzyna Strzelczyk. A Brief Landscape of Epigenetic Mechanisms in Dental Pathologies. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722050115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Hosseini S, Trakooljul N, Hirschfeld M, Wimmers K, Simianer H, Tetens J, Sharifi AR, Brenig B. Epigenetic Regulation of Phenotypic Sexual Plasticity Inducing Skewed Sex Ratio in Zebrafish. Front Cell Dev Biol 2022; 10:880779. [PMID: 35912111 PMCID: PMC9334531 DOI: 10.3389/fcell.2022.880779] [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: 02/21/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
The plasticity of sexual phenotype in response to environmental conditions results in biased sex ratios, and their variation has an effect on population dynamics. Epigenetic modifications can modulate sex ratio variation in species, where sex is determined by genetic and environmental factors. However, the role of epigenetic mechanisms underlying skewed sex ratios is far from being clear and is still an object of debate in evolutionary developmental biology. In this study, we used zebrafish as a model animal to investigate the effect of DNA methylation on sex ratio variation in sex-biased families in response to environmental temperature. Two sex-biased families with a significant difference in sex ratio were selected for genome-wide DNA methylation analysis using reduced representation bisulfite sequencing (RRBS). The results showed significant genome-wide methylation differences between male-biased and female-biased families, with a greater number of methylated CpG sites in testes than ovaries. Likewise, pronounced differences between testes and ovaries were identified within both families, where the male-biased family exhibited a higher number of methylated sites than the female-biased family. The effect of temperature showed more methylated positions in the high incubation temperature than the control temperature. We found differential methylation of many reproduction-related genes (e.g., sox9a, nr5a2, lhx8a, gata4) and genes involved in epigenetic mechanisms (e.g., dnmt3bb.1, dimt1l, hdac11, h1m) in both families. We conclude that epigenetic modifications can influence the sex ratio variation in zebrafish families and may generate skewed sex ratios, which could have a negative consequence for population fitness in species with genotype-environment interaction sex-determining system under rapid environmental changes.
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Affiliation(s)
- Shahrbanou Hosseini
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Functional Breeding Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- *Correspondence: Shahrbanou Hosseini, ; Nares Trakooljul,
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany
- *Correspondence: Shahrbanou Hosseini, ; Nares Trakooljul,
| | - Marc Hirschfeld
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany
| | - Henner Simianer
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
| | - Jens Tetens
- Functional Breeding Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
| | - Ahmad Reza Sharifi
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
| | - Bertram Brenig
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
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25
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Yao Z, Zhu G, Too J, Duan M, Wang Z. Feature Selection of OMIC Data by Ensemble Swarm Intelligence Based Approaches. Front Genet 2022; 12:793629. [PMID: 35350819 PMCID: PMC8957794 DOI: 10.3389/fgene.2021.793629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 12/28/2022] Open
Abstract
OMIC datasets have high dimensions, and the connection among OMIC features is very complicated. It is difficult to establish linkages among these features and certain biological traits of significance. The proposed ensemble swarm intelligence-based approaches can identify key biomarkers and reduce feature dimension efficiently. It is an end-to-end method that only relies on the rules of the algorithm itself, without presets such as the number of filtering features. Additionally, this method achieves good classification accuracy without excessive consumption of computing resources.
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Affiliation(s)
- Zhaomin Yao
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
| | - Gancheng Zhu
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Jingwei Too
- Faculty of Electrical Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, Melaka, Malaysia
| | - Meiyu Duan
- Key Laboratory of Symbolic Computation, College of Computer Science and Technology, Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Zhiguo Wang
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, China.,College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
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Sui J, Qiao W, Xiang X, Luo Y. Epigenetic Changes in Mycobacterium tuberculosis and its Host Provide Potential Targets or Biomarkers for Drug Discovery and Clinical Diagnosis. Pharmacol Res 2022; 179:106195. [DOI: 10.1016/j.phrs.2022.106195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 11/26/2022]
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Starzyńska A, Wychowański P, Nowak M, Sobocki BK, Jereczek-Fossa BA, Słupecka-Ziemilska M. Association between Maternal Periodontitis and Development of Systematic Diseases in Offspring. Int J Mol Sci 2022; 23:2473. [PMID: 35269617 PMCID: PMC8910384 DOI: 10.3390/ijms23052473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 12/24/2022] Open
Abstract
Periodontal disease (PD) is one of the most common oral conditions affecting both youths and adults. There are some research works suggesting a high incidence of PD in pregnant women. As an inflammatory disease of bacterial origin, PD may result in the activation of the pathways affecting the course and the pregnancy outcome. The authors, based on the literature review, try to answer the PICO question: Does maternal periodontitis (exposure) influence the incidence of complications rates in pregnancy and the development of systemic diseases in childhood and adult offspring (outcome) in the humans of any race (population) compared to the offspring of mothers with healthy periodontium (comparison)? The authors try to describe the molecular pathways and mechanisms of these interdependencies. There is some evidence that maternal periodontitis may affect the pregnancy course and outcome, resulting in preeclampsia, preterm delivery, vulvovaginitis and low birth weight. It can be suggested that maternal periodontitis may affect offspring epigenome and result in some health consequences in their adult life.
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Affiliation(s)
- Anna Starzyńska
- Department of Oral Surgery, Medical University of Gdańsk, 7 Dębinki Street, 80-211 Gdańsk, Poland;
| | - Piotr Wychowański
- Department of Oral Surgery, Medical University of Warsaw, 6 Binieckiego Street, 02-097 Warsaw, Poland;
- Specialized Private Implantology Clinic Wychowanski Stomatologia, 9/33 Rakowiecka Street, 02-517 Warsaw, Poland
| | - Maciej Nowak
- Department of Periodontology and Oral Diseases, Medical University of Warsaw, 6 Binieckiego Street, 02-097 Warsaw, Poland;
| | - Bartosz Kamil Sobocki
- Department of Oral Surgery, Medical University of Gdańsk, 7 Dębinki Street, 80-211 Gdańsk, Poland;
| | - Barbara Alicja Jereczek-Fossa
- Department of Oncology and Hemato-Oncology, University of Milan, 7 Festa del Perdono Street, 20-112 Milan, Italy;
- Division of Radiotherapy, IEO European Institute of Oncology, IRCCS, 435 Ripamonti Street, 20-141 Milan, Italy
| | - Monika Słupecka-Ziemilska
- Department of Human Epigenetics, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, 02-106 Warsaw, Poland;
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Dholariya S, Singh RD, Radadiya M, Parchwani D, Sharma G, Mir R. Role of the Tumor Microenvironment and the Influence of Epigenetics on the Tumor Microenvironment in Oral Carcinogenesis: Potential Implications. Crit Rev Oncog 2022; 27:47-64. [PMID: 37199302 DOI: 10.1615/critrevoncog.2022047088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Oral cancer has become a significant problem throughout the world, particularly in countries that are still developing. Recent literature supports the contribution of components of the tumor microenvironment (TME) and the effect of epigenetic changes happening in the cells of the TME on oral cancer development and progression. In this review, we comprehensively examine the significance of TME in the development of OC along with the current understanding of the epigenetic modifications that regulate the TME and their cohesive impact on tumor traits and their potential as therapeutic targets.
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Affiliation(s)
- Sagar Dholariya
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Ragini D Singh
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | | | | | | | - Rashid Mir
- Department of Medical Lab Technology, University of Tabuk, Kingdom of Saudi Arabia, Tabuk, India
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Smoking and XPC Gene Polymorphism Interact to Modulate the Risk of Oral Cancer. J Maxillofac Oral Surg 2021; 20:607-611. [PMID: 34776693 DOI: 10.1007/s12663-020-01340-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/16/2020] [Indexed: 10/25/2022] Open
Abstract
Purpose Oral cancer is the most common cancer among the Indian men and the second most common cancer among the Indian women. Such high incidence of oral cancer in India is due to consumption of tobacco in different form including smoking of cigarette. Smoke of tobacco contains different carcinogens which causes DNA damage. Such DNA damage if remain unrepaired due to faulty DNA repair system can cause mutation and eventual development of cancer. Methodology In the present study, we aimed to check the role of smoking as well as interaction of smoking and XPC polymorphism in risk modulation of oral cancer. Total of 372 subjects including 300 healthy controls and 72 patients of oral cancers been genotyped for the XPC PAT D/I, A/C and C/T polymorphisms with PCR based or PCR-RFLP based method. Genotype frequency was analyzed by chi-square test and strength of associations by odds ratio with 95% confidence intervals. Results The present study showed that compared to nonsmokers, smokers are at five times higher risk to develop oral cancer (p value= 0.001, OR= 5.03, 95% CI 2.91-8.69) and three times higher risk to develop node-positive (p value= 0.01, OR= 3.66, 95% CI 1.34-9.95) oral cancer. It has also been observed that individuals who were smokers and carrier of variant allele genotypes (AC and CC) for XPC A/C polymorphism were at threefold higher risk (p value= 0.01, OR=2.97, 95% CI 1.29-6.86) to develop oral cancer compared to individual who were smokers but do not carry the C allele (AA genotype). This observation indicates that C allele of XPC A/C polymorphism interacts with smoking and significantly increases the risk of oral cancer. Conclusion This study demonstrates a possible role of smoking and gene-smoking interaction in risk enhancement of oral cancer.
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Li X, Lyu C, Luo Z, Zhao J, Wang Z, Yang C, Dai Q, Li H, Zhou Y, Li Z, Chen F, Gao Y. The roles of IGF2 and DNMT methylation and elongase6 related fatty acids in metabolic syndrome. Food Funct 2021; 12:10253-10262. [PMID: 34549217 DOI: 10.1039/d1fo00502b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: The prevalence of metabolic syndrome (MetS) has increased along with rapid socio-economic development in China in recent decades, aggravating the burden of the health care system. Both plasma levels of fatty acids (FAs) and aberrant DNA methylation profiles are associated with MetS risk. However, studies exploring the role of DNA methylation and FAs simultaneously in MetS etiology are sparse. Objective: We aimed to explore the association between the gene methylation levels of insulin-like growth factor II (IGF2), H19, DNA methyltransferases 1 (DNMT1), DNA methyltransferases 3a (DNMT3a), and DNA methyltransferases 3b (DNMT3b) and MetS risk, and the etiological role of elongation of very-long-chain fatty acid elongase 6 (ELOVL6) related fatty acids. Method: Plasma levels of FAs were measured using a Gas Chromatography-Flame Ionization Detector (GC-FID) after organic extraction, and gene methylation was quantified using a real-time Quantitative Polymerase Chain Reaction (Q-PCR) detecting system after bisulfite treatment. The C18/C16 ratio was used as the indicator of ELOVL6 activity. Odds Ratio (OR) and 95% Confidence Interval (CI) were estimated with logistic regression. Results: Methylation levels in IGF2 and DNMT3a were not significantly associated with MetS risk. However, when stratified by C18/C16 ratio (high vs. low), positive associations were observed between the risk of MetS and methylation levels (>median) of IGF2a3 (OR = 3.1, 95% CI = 1.3-7.5) and DNMT3a (OR = 2.5, 95% CI = 1.1-5.8) genes, in individuals with lower C18/C16 ratios, while no significant associations were observed in subjects with high C18/C16 ratios. Conclusion: Methylation levels in IGF2 and DNMT3a genes may affect the risk of MetS in an ELOVL6 activity-dependent way among Chinese adults. Further studies in other populations are needed to validate this finding.
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Affiliation(s)
- Xiang Li
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health-Bloomington, Indiana University, Bloomington, USA
| | - ZhongCheng Luo
- Lunenfeld-Tanenbaum Research Institute, Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Jing Zhao
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Zhongli Wang
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Jiaxing University, The Second Hospital of Jiaxing, Jiaxing, China
| | - Chun Yang
- School of Public Health, Capital Medical University, Beijing, China
| | - Qi Dai
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Hui Li
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Yunhua Zhou
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Zi Li
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Fuxue Chen
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Ying Gao
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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Kim H, Momen-Heravi F, Chen S, Hoffmann P, Kebschull M, Papapanou PN. Differential DNA methylation and mRNA transcription in gingival tissues in periodontal health and disease. J Clin Periodontol 2021; 48:1152-1164. [PMID: 34101221 DOI: 10.1111/jcpe.13504] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/13/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
AIM We investigated differential DNA methylation in gingival tissues in periodontal health, gingivitis, and periodontitis, and its association with differential mRNA expression. MATERIALS AND METHODS Gingival tissues were harvested from individuals and sites with clinically healthy and intact periodontium, gingivitis, and periodontitis. Samples were processed for differential DNA methylation and mRNA expression using the IlluminaEPIC (850 K) and the IlluminaHiSeq2000 platforms, respectively. Across the three phenotypes, we identified differentially methylated CpG sites and regions, differentially expressed genes (DEGs), and genes with concomitant differential methylation at their promoters and expression were identified. The findings were validated using our earlier databases using HG-U133Plus2.0Affymetrix microarrays and Illumina (450 K) methylation arrays. RESULTS We observed 43,631 differentially methylated positions (DMPs) between periodontitis and health, and 536 DMPs between gingivitis and health (FDR < 0.05). On the mRNA level, statistically significant DEGs were observed only between periodontitis and health (n = 126). Twelve DEGs between periodontitis and health (DCC, KCNA3, KCNA2, RIMS2, HOXB7, PNOC, IRX1, JSRP1, TBX1, OPCML, CECR1, SCN4B) were also differentially methylated between the two phenotypes. Spearman correlations between methylation and expression in the EPIC/mRNAseq dataset were largely replicated in the 450 K/Affymetrix datasets. CONCLUSIONS Concomitant study of DNA methylation and gene expression patterns may identify genes whose expression is epigenetically regulated in periodontitis.
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Affiliation(s)
- Hyunjin Kim
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center and Department of Systems Biology, Columbia University, New York, New York, USA.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Fatemeh Momen-Heravi
- Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
| | - Steven Chen
- Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Moritz Kebschull
- Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA.,School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Panos N Papapanou
- Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
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32
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Li T, Wei Y, Qu M, Mou L, Miao J, Xi M, Liu Y, He R. Formaldehyde and De/Methylation in Age-Related Cognitive Impairment. Genes (Basel) 2021; 12:genes12060913. [PMID: 34199279 PMCID: PMC8231798 DOI: 10.3390/genes12060913] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/31/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
Formaldehyde (FA) is a highly reactive substance that is ubiquitous in the environment and is usually considered as a pollutant. In the human body, FA is a product of various metabolic pathways and participates in one-carbon cycle, which provides carbon for the synthesis and modification of bio-compounds, such as DNA, RNA, and amino acids. Endogenous FA plays a role in epigenetic regulation, especially in the methylation and demethylation of DNA, histones, and RNA. Recently, epigenetic alterations associated with FA dysmetabolism have been considered as one of the important features in age-related cognitive impairment (ARCI), suggesting the potential of using FA as a diagnostic biomarker of ARCI. Notably, FA plays multifaceted roles, and, at certain concentrations, it promotes cell proliferation, enhances memory formation, and elongates life span, effects that could also be involved in the aetiology of ARCI. Further investigation of and the regulation of the epigenetics landscape may provide new insights about the aetiology of ARCI and provide novel therapeutic targets.
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Affiliation(s)
- Ting Li
- Bayannur Hospital, Bayannur 015000, China;
| | - Yan Wei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Meihua Qu
- Translational Medical Center, Weifang Second People’s Hospital, The Second Affiliated Hospital of Weifang Medical University, Weifang 261041, China;
| | - Lixian Mou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Junye Miao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Mengqi Xi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China; (M.X.); (Y.L.)
| | - Ying Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China; (M.X.); (Y.L.)
| | - Rongqiao He
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
- Correspondence:
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33
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Chilunga FP, Henneman P, Venema A, Meeks KAC, Requena-Méndez A, Beune E, Mockenhaupt FP, Smeeth L, Bahendeka S, Danquah I, Klipstein-Grobusch K, Adeyemo A, Mannens MMAM, Agyemang C. Genome-wide DNA methylation analysis on C-reactive protein among Ghanaians suggests molecular links to the emerging risk of cardiovascular diseases. NPJ Genom Med 2021; 6:46. [PMID: 34117263 PMCID: PMC8196035 DOI: 10.1038/s41525-021-00213-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/20/2021] [Indexed: 12/28/2022] Open
Abstract
Molecular mechanisms at the intersection of inflammation and cardiovascular diseases (CVD) among Africans are still unknown. We performed an epigenome-wide association study to identify loci associated with serum C-reactive protein (marker of inflammation) among Ghanaians and further assessed whether differentially methylated positions (DMPs) were linked to CVD in previous reports, or to estimated CVD risk in the same population. We used the Illumina Infinium® HumanMethylation450 BeadChip to obtain DNAm profiles of blood samples in 589 Ghanaians from the RODAM study (without acute infections, not taking anti-inflammatory medications, CRP levels < 40 mg/L). We then used linear models to identify DMPs associated with CRP concentrations. Post-hoc, we evaluated associations of identified DMPs with elevated CVD risk estimated via ASCVD risk score. We also performed subset analyses at CRP levels ≤10 mg/L and replication analyses on candidate probes. Finally, we assessed for biological relevance of our findings in public databases. We subsequently identified 14 novel DMPs associated with CRP. In post-hoc evaluations, we found that DMPs in PC, BTG4 and PADI1 showed trends of associations with estimated CVD risk, we identified a separate DMP in MORC2 that was associated with CRP levels ≤10 mg/L, and we successfully replicated 65 (24%) of previously reported DMPs. All DMPs with gene annotations (13) were biologically linked to inflammation or CVD traits. We have identified epigenetic loci that may play a role in the intersection between inflammation and CVD among Ghanaians. Further studies among other Africans are needed to confirm our findings.
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Affiliation(s)
- Felix P Chilunga
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ana Requena-Méndez
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Global Public Health, Karolinska Institutet, Solna, Sweden
| | - Erik Beune
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank P Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Silver Bahendeka
- Department of Medicine, MKPGMS-Uganda Martyrs University, Kampala, Uganda
| | - Ina Danquah
- Heidelberg Institute of Global Health (HIGH), Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Kerstin Klipstein-Grobusch
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Amsterdam Reproduction & Development research institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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Bisserier M, Mathiyalagan P, Zhang S, Elmastour F, Dorfmüller P, Humbert M, David G, Tarzami S, Weber T, Perros F, Sassi Y, Sahoo S, Hadri L. Regulation of the Methylation and Expression Levels of the BMPR2 Gene by SIN3a as a Novel Therapeutic Mechanism in Pulmonary Arterial Hypertension. Circulation 2021; 144:52-73. [PMID: 34078089 DOI: 10.1161/circulationaha.120.047978] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Epigenetic mechanisms are critical in the pathogenesis of pulmonary arterial hypertension (PAH). Previous studies have suggested that hypermethylation of the BMPR2 (bone morphogenetic protein receptor type 2) promoter is associated with BMPR2 downregulation and progression of PAH. Here, we investigated for the first time the role of SIN3a (switch-independent 3a), a transcriptional regulator, in the epigenetic mechanisms underlying hypermethylation of BMPR2 in the pathogenesis of PAH. METHODS We used lung samples from PAH patients and non-PAH controls, preclinical mouse and rat PAH models, and human pulmonary arterial smooth muscle cells. Expression of SIN3a was modulated using a lentiviral vector or a siRNA in vitro and a specific adeno-associated virus serotype 1 or a lentivirus encoding for human SIN3a in vivo. RESULTS SIN3a is a known transcriptional regulator; however, its role in cardiovascular diseases, especially PAH, is unknown. It is interesting that we detected a dysregulation of SIN3 expression in patients and in rodent models, which is strongly associated with decreased BMPR2 expression. SIN3a is known to regulate epigenetic changes. Therefore, we tested its role in the regulation of BMPR2 and found that BMPR2 is regulated by SIN3a. It is interesting that SIN3a overexpression inhibited human pulmonary arterial smooth muscle cells proliferation and upregulated BMPR2 expression by preventing the methylation of the BMPR2 promoter region. RNA-sequencing analysis suggested that SIN3a downregulated the expression of DNA and histone methyltransferases such as DNMT1 (DNA methyltransferase 1) and EZH2 (enhancer of zeste 2 polycomb repressive complex 2) while promoting the expression of the DNA demethylase TET1 (ten-eleven translocation methylcytosine dioxygenase 1). Mechanistically, SIN3a promoted BMPR2 expression by decreasing CTCF (CCCTC-binding factor) binding to the BMPR2 promoter. Last, we identified intratracheal delivery of adeno-associated virus serotype human SIN3a to be a beneficial therapeutic approach in PAH by attenuating pulmonary vascular and right ventricle remodeling, decreasing right ventricle systolic pressure and mean pulmonary arterial pressure, and restoring BMPR2 expression in rodent models of PAH. CONCLUSIONS All together, our study unveiled the protective and beneficial role of SIN3a in pulmonary hypertension. We also identified a novel and distinct molecular mechanism by which SIN3a regulates BMPR2 in human pulmonary arterial smooth muscle cells. Our study also identified lung-targeted SIN3a gene therapy using adeno-associated virus serotype 1 as a new promising therapeutic strategy for treating patients with PAH.
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Affiliation(s)
- Malik Bisserier
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
| | - Prabhu Mathiyalagan
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
| | - Shihong Zhang
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
| | - Firas Elmastour
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
| | - Peter Dorfmüller
- Hôpital Marie Lannelongue, Department of Pathology, Le Plessis Robinson, France (P.D.)
| | - Marc Humbert
- Université Paris-Sud, and Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin-Bicêtre, Paris, France (M.H.).,Service de Pneumologie et Soins Intensifs Respiratoires and INSERM U999, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre, Paris, France (M.H., F.P.)
| | | | - Sima Tarzami
- Department of Physiology and Biophysics, College of Medicine, Howard University, Washington, DC (S.T.)
| | - Thomas Weber
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
| | - Frederic Perros
- Service de Pneumologie et Soins Intensifs Respiratoires and INSERM U999, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre, Paris, France (M.H., F.P.)
| | - Yassine Sassi
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
| | - Susmita Sahoo
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
| | - Lahouaria Hadri
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY (M.B., P.M., S.Z., F.E., Y.S., T.W., S.S., L.H.)
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Menini M, Dellepiane E, Pera F, Izzotti A, Baldi D, Delucchi F, Bagnasco F, Pesce P. MicroRNA in Implant Dentistry: From Basic Science to Clinical Application. Microrna 2021; 10:14-28. [PMID: 33970853 DOI: 10.2174/2211536610666210506123240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 11/22/2022]
Abstract
Specific microRNA (miRNA) expression profiles have been reported to be predictive of specific clinical outcomes of dental implants and might be used as biomarkers in implant dentistry with diagnostic and prognostic purposes. The aim of the present narrative review was to summarize current knowledge regarding the use of miRNAs in implant dentistry. The authors attempted to identify all available evidence on the topic and critically appraise it in order to lay the foundation for the development of further research oriented towards the clinical application of miRNAs in implant dentistry.
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Affiliation(s)
- Maria Menini
- Division of Fixed and Implant Prosthodontics, Department of Surgical Sciences (DISC), University of Genoa, Genova, Italy
| | - Elena Dellepiane
- Division of Fixed and Implant Prosthodontics, Department of Surgical Sciences (DISC), University of Genoa, Genova, Italy
| | - Francesco Pera
- Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Alberto Izzotti
- Department of Health Sciences, University of Genoa, Genova, Italy
| | - Domenico Baldi
- Division of Fixed and Implant Prosthodontics, Department of Surgical Sciences (DISC), University of Genoa, Genova, Italy
| | - Francesca Delucchi
- Division of Fixed and Implant Prosthodontics, Department of Surgical Sciences (DISC), University of Genoa, Genova, Italy
| | - Francesco Bagnasco
- Division of Fixed and Implant Prosthodontics, Department of Surgical Sciences (DISC), University of Genoa, Genova, Italy
| | - Paolo Pesce
- Division of Fixed and Implant Prosthodontics, Department of Surgical Sciences (DISC), University of Genoa, Genova, Italy
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Chilunga FP, Henneman P, Venema A, Meeks KAC, Gonzalez JR, Ruiz-Arenas C, Requena-Méndez A, Beune E, Spranger J, Smeeth L, Bahendeka S, Owusu-Dabo E, Klipstein-Grobusch K, Adeyemo A, Mannens MMAM, Agyemang C. DNA methylation as the link between migration and the major noncommunicable diseases: the RODAM study. Epigenomics 2021; 13:653-666. [PMID: 33890479 PMCID: PMC8173498 DOI: 10.2217/epi-2020-0329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/29/2021] [Indexed: 01/19/2023] Open
Abstract
Aim: We assessed epigenome-wide DNA methylation (DNAm) differences between migrant and non-migrant Ghanaians. Materials & methods: We used the Illumina Infinium® HumanMethylation450 BeadChip to profile DNAm of 712 Ghanaians in whole blood. We used linear models to detect differentially methylated positions (DMPs) associated with migration. We performed multiple post hoc analyses to validate our findings. Results: We identified 13 DMPs associated with migration (delta-beta values: 0.2-4.5%). Seven DMPs in CPLX2, EIF4E3, MEF2D, TLX3, ST8SIA1, ANG and CHRM3 were independent of extrinsic genomic influences in public databases. Two DMPs in NLRC5 were associated with duration of stay in Europe among migrants. All DMPs were biologically linked to migration-related factors. Conclusion: Our findings provide the first insights into DNAm differences between migrants and non-migrants.
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Affiliation(s)
- Felix P Chilunga
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Karlijn AC Meeks
- Center for Research on Genomics & Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Juan R Gonzalez
- Barcelona Institute for Global Health (ISGlobal, University of Barcelona), 08003 Barcelona, Spain
| | - Carlos Ruiz-Arenas
- Barcelona Institute for Global Health (ISGlobal, University of Barcelona), 08003 Barcelona, Spain
| | - Ana Requena-Méndez
- Barcelona Institute for Global Health (ISGlobal, University of Barcelona), 08003 Barcelona, Spain
- Department of Global Public Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Erik Beune
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Joachim Spranger
- Department of Endocrinology, Diabetes & Metabolism, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, 1E 7HT, UK
| | - Silver Bahendeka
- Department of Medicine, MKPGMS-Uganda Martyrs University, 8H33+5M Kampala, Uganda
| | - Ellis Owusu-Dabo
- School of Public Health, Kwame Nkrumah University of Science & Technology, MCFH+R9 Kumasi, Ghana
| | - Kerstin Klipstein-Grobusch
- Julius Global Health, Julius Center for Health Sciences & Primary Care, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of The Witwatersrand, 2193 Johannesburg, South Africa
| | - Adebowale Adeyemo
- Center for Research on Genomics & Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Marcel MAM Mannens
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Reszka E, Jabłońska E, Wieczorek E, Valent P, Arock M, Nilsson G, Nedoszytko B, Niedoszytko M. Epigenetic Changes in Neoplastic Mast Cells and Potential Impact in Mastocytosis. Int J Mol Sci 2021; 22:2964. [PMID: 33803981 PMCID: PMC7999363 DOI: 10.3390/ijms22062964] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/23/2022] Open
Abstract
Systemic mastocytosis (SM) is a hematologic neoplasm with abnormal accumulation of mast cells in various organ systems such as the bone marrow, other visceral organs and skin. So far, only little is known about epigenetic changes contributing to the pathogenesis of SM. In the current article, we provide an overview of epigenetic changes that may occur and be relevant to mastocytosis, including mutations in genes involved in epigenetic processes, such as TET2, DNMT3A and ASXL1, and global and gene-specific methylation patterns in neoplastic cells. Moreover, we discuss methylation-specific pathways and other epigenetic events that may trigger disease progression in mast cell neoplasms. Finally, we discuss epigenetic targets and the effects of epigenetic drugs, such as demethylating agents and BET-targeting drugs, on growth and viability of neoplastic mast cells. The definitive impact of these targets and the efficacy of epigenetic therapies in advanced SM need to be explored in future preclinical studies and clinical trials.
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Affiliation(s)
- Edyta Reszka
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, 91-348 Lodz, Poland; (E.J.); (E.W.)
| | - Ewa Jabłońska
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, 91-348 Lodz, Poland; (E.J.); (E.W.)
| | - Edyta Wieczorek
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, 91-348 Lodz, Poland; (E.J.); (E.W.)
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria;
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria
| | - Michel Arock
- Department of Hematological Biology, Pitié-Sapêtrière Hospital, Sorbonne University, 75013 Paris, France;
| | - Gunnar Nilsson
- Division of Immunology and Allergy, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden;
| | - Bogusław Nedoszytko
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-211 Gdansk, Poland;
- Invicta Fertility and Reproductive Center, Molecular Laboratory, Polna 64, 81-740 Sopot, Poland
| | - Marek Niedoszytko
- Department of Allergology, Medical University of Gdansk, 80-211 Gdansk, Poland
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Abstract
Acquisition and establishment of the oral microbiota occur in a dynamic process over various stages and involve close and continuous interactions with the host and its environment. In the present review, we discuss the stages of this process in chronological order. We start with the prenatal period and address the following questions: ‘Is the fetus exposed to maternal microbiota during pregnancy?’ and ‘If so, what is the potential role of this exposure?’ We comment on recent reports of finding bacterial DNA in placenta during pregnancies, and provide current views on the potential functions of prenatal microbial encounters. Next, we discuss the physiological adaptations that take place in the newborn during the birth process and the effect of this phase of life on the acquisition of the oral microbiota. Is it really just exposure to maternal vaginal microbes that results in the difference between vaginally and Cesarian section‐born infants? Then, we review the postnatal phase, in which we focus on transmission of microbes, the intraoral niche specificity, the effects of the host behavior and environment, as well as the role of genetic background of the host on shaping the oral microbial ecosystem. We discuss the changes in oral microbiota during the transition from deciduous to permanent dentition and during puberty. We also address the finite knowledge on colonization of the oral cavity by microbes other than the bacterial component. Finally, we identify the main outstanding questions that limit our understanding of the acquisition and establishment of a healthy microbiome at an individual level.
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Affiliation(s)
- A M Marije Kaan
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Dono Kahharova
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
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Han Y, Huang L, Zhou F. A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers. Bioinformatics 2021; 37:2183-2189. [PMID: 33515240 DOI: 10.1093/bioinformatics/btab055] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/25/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION A feature selection algorithm may select the subset of features with the best associations with the class labels. The recursive feature elimination (RFE) is a heuristic feature screening framework and has been widely used to select the biological OMIC biomarkers. This study proposed a dynamic recursive feature elimination (dRFE) framework with more flexible feature elimination operations. The proposed dRFE was comprehensively compared with 11 existing feature selection algorithms and five classifiers on the eight difficult transcriptome datasets from a previous study, the ten newly collected transcriptome datasets and the five methylome datasets. RESULTS The experimental data suggested that the regular RFE framework did not perform well, and dRFE outperformed the existing feature selection algorithms in most cases. The dRFE-detected features achieved Acc=1.0000 for the two methylome datasets GSE53045 and GSE66695. The best prediction accuracies of the dRFE-detected features were 0.9259, 0.9424, and 0.8601 for the other three methylome datasets GSE74845, GSE103186, and GSE80970, respectively. Four transcriptome datasets received Acc=1.0000 using the dRFE-detected features, and the prediction accuracies for the other six newly collected transcriptome datasets were between 0.6301 and 0.9917. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuanyuan Han
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
| | - Fengfeng Zhou
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
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Interaction of tobacco chewing and smoking habit with interleukin 6 promoter polymorphism in oral precancerous lesions and oral cancer. Eur Arch Otorhinolaryngol 2021; 278:4011-4019. [PMID: 33501560 DOI: 10.1007/s00405-021-06620-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
OBJECTIVE Our study aims to determine the influence of smoking or tobacco chewing and the association of Interleukin 6 (IL-6) polymorphism, where G is substituted by A at the position - 596 (IL-6 - 596 G/A) and substitution of G by cytosine (C) at position - 572 (IL-6 - 572 G/C) on the susceptibility of precancerous oral lesions and oral cancer. MATERIALS AND METHODS The participants consisted of 250 subjects among which 75 were suffering from oral cancer, 75 subjects with precancerous oral lesions and 100 were healthy controls. Single-nucleotide polymorphism study (SNP) was done by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP). RESULTS IL-6 - 596 G/A SNP revealed genotypes, GG, and GA in subjects with precancerous oral lesions and oral cancer, and AA genotype was not found in any subject. IL-6 - 596 G/A was strongly associated with oral precancerous lesions but not with oral cancer. The present study reports that smokers carrying GA for IL-6 - 596 G/A were at several folds higher risk of developing oral precancerous lesions. Smokers with GC and CC for IL-6 - 572 G/C were at higher risk of developing oral precancerous lesions. No significant interaction was observed between these habits and IL-6 - 596 G/A and IL-6 - 572 G/C SNP with oral cancer. CONCLUSION The interaction of variant A allele of IL-6 - 596 G/A and C allele of IL-6 - 572 G/C polymorphism with smoking and increases the risk of oral precancerous lesions. Tobacco chewing was not related with IL-6 - 596 G/A or IL-6 - 572 G/C in oral precancerous lesions or oral cancer. CLINICAL RELEVANCE The study will help to determine the susceptibility of individuals with smoking or chewing habits to the development of oral precancerous lesion and oral cancer by monitoring the IL-6 SNPs which can be used as a biomarker for risk determination.
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Nwanaji-Enwerem JC, Colicino E. DNA Methylation-Based Biomarkers of Environmental Exposures for Human Population Studies. Curr Environ Health Rep 2021; 7:121-128. [PMID: 32062850 DOI: 10.1007/s40572-020-00269-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW This manuscript orients the reader to the underlying motivations of environmental biomarker development for human population studies and provides the foundation for applying these novel biomarkers in future research. In this review, we focus our attention on the DNA methylation-based biomarkers of (i) smoking, among adults and pregnant women, (ii) lifetime cannabis use, (iii) alcohol consumption, and (iv) cumulative exposure to lead. RECENT FINDINGS Prior environmental exposures and lifestyle modulate DNA methylation levels. Exposure-related DNA methylation changes can either be persistent or reversible once the exposure is no longer present, and this combination of both persistent and reversible changes has essential value for biomarker development. Here, we present available biomarkers representing past and cumulative exposures using individual DNA methylation profiles. In the present work, we describe how the field of environmental epigenetics can leverage machine learning algorithms to develop exposure biomarkers and reduce problems of misreporting exposures or limited access technology. We emphasize the crucial role of the individual DNA methylation profiles in those predictions, providing a summary of each biomarker, and highlighting their advantages, and limitations. Future research can cautiously leverage these DNA methylation-based biomarkers to understand the onset and progression of diseases.
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Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Belfer Center for Science and International Affairs, Harvard Kennedy School of Government, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 17 E 102nd St. West 3rd Floor, New York, NY, 10029, USA.
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Carmel M, Michaelovsky E, Weinberger R, Frisch A, Mekori-Domachevsky E, Gothelf D, Weizman A. Differential methylation of imprinting genes and MHC locus in 22q11.2 deletion syndrome-related schizophrenia spectrum disorders. World J Biol Psychiatry 2021; 22:46-57. [PMID: 32212948 DOI: 10.1080/15622975.2020.1747113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVES 22q11.2 deletion syndrome (DS) is the strongest known genetic risk for schizophrenia. Methylome screening was conducted to elucidate possible involvement of epigenetic alterations in the emergence of schizophrenia spectrum disorders (SZ-SD) in 22q11.2DS. METHODS Sixteen adult men with/without SZ-SD were recruited from a 22q11.2DS cohort and underwent genome-wide DNA methylation profile analysis. Differentially methylated probes (DMPs) and regions (DMRs) were analysed using the ChAMP software. RESULTS The DMPs (p-value <10-6) and DMRs (p-valueArea <0.01) were enriched in two gene sets, 'imprinting genes' and 'chr6p21', a region overlapping the MHC locus. Most of the identified imprinting genes are involved in neurodevelopment and located in clusters under imprinting control region (ICR) regulation, including PEG10, SGCE (7q21.3), GNAS, GNAS-AS1 (20q13.32) and SNHG14, SNURF-SNRPN, SNORD115 (15q11.2). The differentially methylated genes from the MHC locus included immune HLA-genes and non-immune genes, RNF39, PPP1R18 and NOTCH4, implicated in neurodevelopment and synaptic plasticity. The most significant DMR is located in MHC locus and covered the transcription regulator ZFP57 that is required for control and maintenance of gene imprinting at multiple ICRs. CONCLUSIONS The differential methylation in imprinting genes and in chr6p21-22 indicate the neurodevelopmental nature of 22q11.2DS-related SZ and the major role of MHC locus in the risk to develop SZ.
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Affiliation(s)
- Miri Carmel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Elena Michaelovsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ronnie Weinberger
- The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel
| | - Amos Frisch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ehud Mekori-Domachevsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Weizman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Geha Mental Health Center, Petach Tikva, Israel
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Alghamdi MA, AL-Eitan LN, Tarkhan AH, Al-Qarqaz FA. Global gene methylation profiling of common warts caused by human papillomaviruses infection. Saudi J Biol Sci 2021; 28:612-622. [PMID: 33424347 PMCID: PMC7783806 DOI: 10.1016/j.sjbs.2020.10.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
Infection with the human papillomaviruses (HPV) often involves the epigenetic modification of the host genome. Despite its prevalence among the population, host genome methylation in HPV-induced warts is not clearly understood. In this study, genome-wide methylation profiling was carried out on paired healthy skin and wart samples in order to investigate the effects that benign HPV infection has on gene methylation status. To overcome this gap in knowledge, paired wart (n = 12) and normal skin (n = 12) samples were obtained from Arab males in order to perform DNA extraction and subsequent genome-wide methylation profiling on the Infinium Methylation EPIC Bead Chip microarray. Analysis of differential methylation revealed a clear pattern of discrimination between the wart and normal skin samples. In warts, the most differentially methylated (DM) genes included long non-coding RNAs (AC005884, AL049646.2, AC126121.2, AP001790.1, and AC107959.3), microRNAs (MIR374B, MIR596, MIR1255B1, MIR26B, and MIR196A2),snoRNAs (SNORD114-22, SNORD70, and SNORD114-31), pseudogenes (AC069366.1, RNU4ATAC11P, AC120057.1, NANOGP3, AC106038.2, TPT1P2, SDC4P, PKMP3, and VN2R3P), and protein-coding genes (AREG, GJB2, C12orf71, AC020909.2, S100A8, ZBED2, FABP7, and CYSLTR1). In addition, pathway analysis revealed that, among the most differentially methylated genes, STAT5A, RARA, MEF2D, MAP3K8, and THRA were the common regulators. It can be observed that HPV-induced warts involve a clear and unique epigenetic alteration to the host genome.
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Affiliation(s)
- Mansour A. Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
- Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
| | - Laith N. AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Amneh H. Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Firas A. Al-Qarqaz
- Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
- Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital Jordan University of Science and Technology, Irbid 22110, Jordan
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The Role of Epigenetic Functionalization of Implants and Biomaterials in Osseointegration and Bone Regeneration-A Review. Molecules 2020; 25:molecules25245879. [PMID: 33322654 PMCID: PMC7763898 DOI: 10.3390/molecules25245879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
The contribution of epigenetic mechanisms as a potential treatment model has been observed in cancer and autoimmune/inflammatory diseases. This review aims to put forward the epigenetic mechanisms as a promising strategy in implant surface functionalization and modification of biomaterials, to promote better osseointegration and bone regeneration, and could be applicable for alveolar bone regeneration and osseointegration in the future. Materials and Methods: Electronic and manual searches of the literature in PubMed, MEDLINE, and EMBASE were conducted, using a specific search strategy limited to publications in the last 5 years to identify preclinical studies in order to address the following focused questions: (i) Which, if any, are the epigenetic mechanisms used to functionalize implant surfaces to achieve better osseointegration? (ii) Which, if any, are the epigenetic mechanisms used to functionalize biomaterials to achieve better tissue regeneration? Findings from several studies have emphasized the role of miRNAs in functionalizing implants surfaces and biomaterials to promote osseointegration and bone regeneration, respectively. However, there are scarce data on the role of DNA methylation and histone modifications for these specific applications, despite being commonly applied in cancer research. Studies over the past few years have demonstrated that biomaterials are immunomodulatory rather than inert materials. In this context, epigenetics can act as next generation of advanced treatment tools for future regenerative techniques. Yet, there is a need to evaluate the efficacy/cost effectiveness of these techniques in comparison to current standards of care.
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Bernardini L, Barbosa E, Charão MF, Goethel G, Muller D, Bau C, Steffens NA, Santos Stein C, Moresco RN, Garcia SC, Souza Vencato M, Brucker N. Oxidative damage, inflammation, genotoxic effect, and global DNA methylation caused by inhalation of formaldehyde and the purpose of melatonin. Toxicol Res (Camb) 2020; 9:778-789. [PMID: 33447362 PMCID: PMC7786178 DOI: 10.1093/toxres/tfaa079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/09/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Formaldehyde (FA) exposure has been proven to increase the risk of asthma and cancer. This study aimed to evaluate for 28 days the FA inhalation effects on oxidative stress, inflammation process, genotoxicity, and global DNA methylation in mice as well as to investigate the potential protective effects of melatonin. For that, analyses were performed on lung, liver and kidney tissues, blood, and bone marrow. Bronchoalveolar lavage was used to measure inflammatory parameters. Lipid peroxidation (TBARS), protein carbonyl (PCO), non-protein thiols (NPSH), catalase activity (CAT), comet assay, micronuclei (MN), and global methylation were determined. The exposure to 5-ppm FA resulted in oxidative damage to the lung, presenting a significant increase in TBARS and NO levels and a decrease in NPSH levels, besides an increase in inflammatory cells recruited for bronchoalveolar lavage. Likewise, in the liver tissue, the exposure to 5-ppm FA increased TBARS and PCO levels and decreased NPSH levels. In addition, FA significantly induced DNA damage, evidenced by the increase of % tail moment and MN frequency. The pretreatment of mice exposed to FA applying melatonin improved inflammatory and oxidative damage in lung and liver tissues and attenuated MN formation in bone marrow cells. The pulmonary histological study reinforced the results observed in biochemical parameters, demonstrating the potential beneficial role of melatonin. Therefore, our results demonstrated that FA exposure with repeated doses might induce oxidative damage, inflammatory, and genotoxic effects, and melatonin minimized the toxic effects caused by FA inhalation in mice.
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Affiliation(s)
- Letícia Bernardini
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Eduardo Barbosa
- Graduate Program on Toxicology and Analytical Toxicology, University Feevale, Novo Hamburgo, RS 93525-075, Brazil
| | - Mariele Feiffer Charão
- Graduate Program on Toxicology and Analytical Toxicology, University Feevale, Novo Hamburgo, RS 93525-075, Brazil
| | - Gabriela Goethel
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS 90610-000, Brazil
| | - Diana Muller
- Department of Genetics, Instituto de Biociências, Federal University of Rio Grande do Sul, Porto Alegre, RS 90610-000, Brazil
| | - Claiton Bau
- Department of Genetics, Instituto de Biociências, Federal University of Rio Grande do Sul, Porto Alegre, RS 90610-000, Brazil
| | - Nadine Arnold Steffens
- Graduate Program in Pharmaceutical Sciences, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Carolina Santos Stein
- Graduate Program in Pharmaceutical Sciences, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Rafael Noal Moresco
- Graduate Program in Pharmaceutical Sciences, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Solange Cristina Garcia
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS 90610-000, Brazil
| | - Marina Souza Vencato
- Departament of Morphology, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Natália Brucker
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
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Iyer GR, Hasan Q. Alteration of methylation status in archival DNA samples: A qualitative assessment by methylation specific polymerase chain reaction. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:837-842. [PMID: 32649027 DOI: 10.1002/em.22398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/25/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is an epigenetic mechanism that regulates gene expression, which also facilitates genomic imprinting. Genomic imprinting is responsible for differential expression of genes based on parent of origin. Altered methylation of parental alleles results in imprinting disorders diagnosed by methylation specific polymerase chain reaction (MS-PCR) technique. With increasing evidence of genes under epigenetic influence, methylation studies are extensively performed on archival samples. To evaluate effect of storage and storage conditions on DNA methylation, a systematic MS-PCR based analysis was planned on an imprinted gene, SNRPN, located on chromosome 15q11.2. It was assessed by MS-PCR on fresh, 4 -20, and -80°C stored DNA samples for different time periods for systematic evaluation of methylation status. Technical factors like type of sample processing, method of DNA isolation, primer region polymorphism, sample heterogeneity were also evaluated. DNA methylation was observed to be altered for SNRPN gene after storage at -80°C from 2 months onwards. Long-term storage of DNA at -80°C results in altered DNA methylation status. This may lead to false MS-PCR diagnosis of imprinting disorders. Our proof of concept study should be followed with quantitative validation since the findings have critical implications in the present era of biobanking.
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Affiliation(s)
- Gayatri Rangarajan Iyer
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
- Department of Genetics, Osmania University, Tarnaka, Hyderabad, India
| | - Qurratulain Hasan
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
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Barros SP, Hefni E, Fahimipour F, Kim S, Arora P. Maintaining barrier function of infected gingival epithelial cells by inhibition of DNA methylation. J Periodontol 2020; 91 Suppl 1:S68-S78. [PMID: 32633810 DOI: 10.1002/jper.20-0262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/14/2020] [Accepted: 06/20/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Infection and inflammation induce epigenetic changes that alter gene expression. In periodontal disease, inflammation, and microbial dysbiosis occur, which can lead to compromised barrier function of the gingival epithelia. Here, we tested the hypotheses that infection of cultured human gingival epithelial (HGEp) cells with Porphyromonas gingivalis disrupts barrier function by inducing epigenetic alterations and that these effects can be blocked by inhibitors of DNA methylation. METHODS Primary HGEp cells were infected with P. gingivalis either in the presence or absence of the non-nucleoside DNA methyltransferase (DNMT) inhibitors RG108, (-) epigallocatechin-3-gallate (EGCG), or curcumin. Barrier function was assessed as transepithelial electrical resistance (TEER). DNA methylation and mRNA abundance were quantified for genes encoding components of three cell-cell junction complexes, CDH1, PKP2, and TJP1. Cell morphology and the abundance of cell-cell junction proteins were evaluated by confocal microscopy. RESULTS Compared to non-infected cells, P. gingivalis infection decreased TEER (P < 0.0001) of HGEp cells; increased methylation of the CDH1, PKP2, and TJP1 (P < 0.0001); and reduced their expression (mRNA abundance) (P < 0.005). Pretreatment with DNMT inhibitors prevented these infection-induced changes in HGEp cells, as well as the altered morphology associated with infection. CONCLUSION Pathogenic infection induced changes in DNA methylation and impaired the barrier function of cultured primary gingival epithelial cells, which suggests a mechanism for systemic consequences of periodontal disease. Inhibition of these events by non-nucleoside DNMT inhibitors represents a potential strategy to treat periodontal disease.
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Affiliation(s)
- Silvana P Barros
- Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Eman Hefni
- Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Farahnaz Fahimipour
- Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Steven Kim
- Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Barbato-Ferreira DA, Costa SFDS, Gomez RS, Bastos JV. DNA Methylation patterns of immune response-related genes in inflammatory external root resorption. Braz Oral Res 2020; 34:e087. [PMID: 32785479 DOI: 10.1590/1807-3107bor-2020.vol34.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/28/2020] [Indexed: 11/22/2022] Open
Abstract
Inflammatory external root resorption (IERR) is a pathological process defined by the progressive loss of dental hard tissue, dentin, and cementum, resulting from the combination of the loss of external root protective apparatus and root canal infection. It has been suggested that healing patterns after tooth replantation may be influenced by the genetic and immunological profiles of the patients. The purpose of the present investigation was to evaluate the DNA methylation patterns of 22 immune response-related genes in extracted human teeth presenting with IERR. Methylation assays were performed on samples of root fragments showing IERR and compared with healthy bone tissue collected during the surgical extraction of impacted teeth. The methylation patterns were quantified using EpiTect Methyl II Signature Human Cytokine Production PCR Array. The results revealed significantly higher hypermethylation of the FOXP3 gene promoter in IERR (65.95%) than in the bone group (23.43%) (p < 0.001). The ELANE gene was also highly methylated in the pooled IERR sample, although the difference was not statistically significant (p= 0.054). Our study suggests that the differential methylation patterns of immune response-related genes, such as FOXP3 and ELANE, may be involved in IERR modulation, and this could be related to the presence of root canal infection. However, further studies are needed to corroborate these findings to determine the functional relevance of these alterations and their role in the pathogenesis of IERR.
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Affiliation(s)
| | - Sara Ferreira Dos Santos Costa
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Juliana Vilela Bastos
- Department of Restorative Dentistry, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Beck JD, Van Dyke TE. Steven Offenbacher, DDS, PhD, MMSc: The gifts of a giant in science and the father of periodontal medicine. J Periodontol 2020; 91 Suppl 1:S1-S3. [PMID: 32619038 DOI: 10.1002/jper.20-0494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Shin Y, Kim M, Won J, Kim J, Oh SB, Lee JH, Park K. Epigenetic Modification of CFTR in Head and Neck Cancer. J Clin Med 2020; 9:jcm9030734. [PMID: 32182826 PMCID: PMC7141320 DOI: 10.3390/jcm9030734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR), a cyclic AMP (cAMP)-regulated chloride channel, is critical for secretion and absorption across diverse epithelia. Mutations or absence of CFTR result in pathogeneses, including cancer. While CFTR has been proposed as a tumor suppressing gene in tumors of the intestine, lung, and breast cancers, its effects in head and neck cancer (HNC) have yet to be investigated. This study aimed to define expression patterns and epigenetic modifications of CFTR in HNC. CFTR was expressed in normal but not in HNC cells and tissues. Treatment with 5-aza-2'-deoxycytidine (5-Aza-CdR) was associated with rescued expression of CFTR, whose function was confirmed by patch clamp technique. Further experiments demonstrated that CFTR CpG islands were hypermethylated in cancer cells and tissues and hypomethylated in normal cells and tissue. Our results suggest that CFTR epigenetic modifications are critical in both down-regulation and up-regulation of CFTR expression in HNC and normal cells respectively. We then investigated the impact of CFTR on expressions and functions of cancer-related genes. CFTR silencing was closely associated with changes to other cancer-related genes, suppressing apoptosis while enhancing proliferation, cell motility, and invasion in HNC. Our findings demonstrate that hypermethylation of CFTR CpG islands and CFTR deficiency is closely related to HNC.
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Affiliation(s)
- Yonghwan Shin
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
| | - Minkyoung Kim
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
| | - Jonghwa Won
- Department of Neurobiology and Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (J.W.); (S.B.O.)
| | - Junchul Kim
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
| | - Seog Bae Oh
- Department of Neurobiology and Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (J.W.); (S.B.O.)
| | - Jong-Ho Lee
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Seoul National University, Seoul 110-749, Korea;
| | - Kyungpyo Park
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
- Correspondence: ; Tel.: +82-02-740-8658
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