1
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Doi S, Suzuki T, Soeda S, Miyata N, Inazu T. Role of plant homeodomain finger protein 8 in P19 embryonic carcinoma cells revealed by genome editing and specific inhibitor. Biochem Biophys Rep 2024; 38:101670. [PMID: 38463639 PMCID: PMC10923654 DOI: 10.1016/j.bbrep.2024.101670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/01/2024] [Accepted: 02/16/2024] [Indexed: 03/12/2024] Open
Abstract
Plant homeodomain finger protein 8 (PHF8) is a histone demethylase that regulates the expression of various genes. PHF8 targets repressor histone markers and activates gene expression. Although PHF8 has been involved in X-linked mental retardation and certain types of cancers, the role of PHF8 remains largely unknown, and its relevance to the pathogenesis of these diseases is also uncertain. In the present study, we aimed to clarify the cellular function of PHF8 in P19 cells using Phf8 knockout (KO) cells generated via the CRISPR-Cas9 system and by performing PHF8 specific inhibitor experiments, instead of using PHF8 small interfering RNA transfection. After establishing Phf8 KO cells, we analyzed the effects of PHF8 on neuronal differentiation and cell proliferation. Both PHF8 deficiency and inhibition of its activity did not considerably affect neuronal differentiation, however, they showed an increased trend of promoted neurite outgrowth. Moreover, we found that PHF8 regulated cell proliferation via the MEK/ERK pathway. PHF8 deficiency and activity inhibition reduced the phosphorylation of ERK and MEK. The MEK expression level was associated with PHF8 expression, as revealed by chromatin immunoprecipitation analysis. These results suggested that PHF8 regulates cell proliferation via the MEK/ERK pathway in P19 embryonic carcinoma cells.
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Affiliation(s)
- Shusuke Doi
- Graduate School of Pharmacy, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | | | - Shuhei Soeda
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Naoki Miyata
- Institute of Dug Discovery Science, Nagoya City University, Mizuho, Nagoya, 467-8603, Japan
| | - Tetsuya Inazu
- Graduate School of Pharmacy, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
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2
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Nava AA, Arboleda VA. The omics era: a nexus of untapped potential for Mendelian chromatinopathies. Hum Genet 2024; 143:475-495. [PMID: 37115317 PMCID: PMC11078811 DOI: 10.1007/s00439-023-02560-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The OMICs cascade describes the hierarchical flow of information through biological systems. The epigenome sits at the apex of the cascade, thereby regulating the RNA and protein expression of the human genome and governs cellular identity and function. Genes that regulate the epigenome, termed epigenes, orchestrate complex biological signaling programs that drive human development. The broad expression patterns of epigenes during human development mean that pathogenic germline mutations in epigenes can lead to clinically significant multi-system malformations, developmental delay, intellectual disabilities, and stem cell dysfunction. In this review, we refer to germline developmental disorders caused by epigene mutation as "chromatinopathies". We curated the largest number of human chromatinopathies to date and our expanded approach more than doubled the number of established chromatinopathies to 179 disorders caused by 148 epigenes. Our study revealed that 20.6% (148/720) of epigenes cause at least one chromatinopathy. In this review, we highlight key examples in which OMICs approaches have been applied to chromatinopathy patient biospecimens to identify underlying disease pathogenesis. The rapidly evolving OMICs technologies that couple molecular biology with high-throughput sequencing or proteomics allow us to dissect out the causal mechanisms driving temporal-, cellular-, and tissue-specific expression. Using the full repertoire of data generated by the OMICs cascade to study chromatinopathies will provide invaluable insight into the developmental impact of these epigenes and point toward future precision targets for these rare disorders.
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Affiliation(s)
- Aileen A Nava
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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3
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Bryant L, Sangree A, Clark K, Bhoj E. Histone 3.3-related chromatinopathy: missense variants throughout H3-3A and H3-3B cause a range of functional consequences across species. Hum Genet 2024; 143:497-510. [PMID: 36867246 DOI: 10.1007/s00439-023-02536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Abstract
There has been considerable recent interest in the role that germline variants in histone genes play in Mendelian syndromes. Specifically, missense variants in H3-3A and H3-3B, which both encode Histone 3.3, were discovered to cause a novel neurodevelopmental disorder, Bryant-Li-Bhoj syndrome. Most of the causative variants are private and scattered throughout the protein, but all seem to have either a gain-of-function or dominant negative effect on protein function. This is highly unusual and not well understood. However, there is extensive literature about the effects of Histone 3.3 mutations in model organisms. Here, we collate the previous data to provide insight into the elusive pathogenesis of missense variants in Histone 3.3.
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Affiliation(s)
- Laura Bryant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Annabel Sangree
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Clark
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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4
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Silveira HG, Steiner CE, Toccoli G, Angeloni LL, Heleno JL, Spineli-Silva S, dos Santos AM, Vieira TP, Melaragno MI, Gil-da-Silva-Lopes VL. Variants in KMT2A in Three Individuals with Previous Suspicion of 22q11.2 Deletion Syndrome. Genes (Basel) 2024; 15:211. [PMID: 38397201 PMCID: PMC10888166 DOI: 10.3390/genes15020211] [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: 12/25/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The condition known as 22q11.2 deletion syndrome (MIM #188400) is a rare disease with a highly variable clinical presentation including more than 180 features; specific guidelines for screening individuals have been used to support clinical suspicion before confirmatory tests by Brazil's Craniofacial Project. Of the 2568 patients listed in the Brazilian Database on Craniofacial Anomalies, 43 individuals negative for the 22q11.2 deletion syndrome were further investigated through whole-exome sequencing. Three patients (6.7%) presented with heterozygous pathogenic variants in the KMT2A gene, including a novel variant (c.6158+1del) and two that had been previously reported (c.173dup and c.3241C>T); reverse phenotyping concluded that all three patients presented features of Wiedemann-Steiner syndrome, such as neurodevelopmental disorders and dysmorphic facial features (n = 3), hyperactivity and anxiety (n = 2), thick eyebrows and lower-limb hypertrichosis (n = 2), congenital heart disease (n = 1), short stature (n = 1), and velopharyngeal insufficiency (n = 2). Overlapping features between 22q11.2 deletion syndrome and Wiedemann-Steiner syndrome comprised neuropsychiatric disorders and dysmorphic characteristics involving the eyes and nose region; velopharyngeal insufficiency was seen in two patients and is an unreported finding in WDSTS. Therefore, we suggest that both conditions should be included in each other's differential diagnoses.
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Affiliation(s)
- Henrique Garcia Silveira
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (Unifesp), São Paulo 04023-062, Brazil; (H.G.S.); (G.T.); (M.I.M.)
| | - Carlos Eduardo Steiner
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Giovana Toccoli
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (Unifesp), São Paulo 04023-062, Brazil; (H.G.S.); (G.T.); (M.I.M.)
| | - Luise Longo Angeloni
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Júlia Lôndero Heleno
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Samira Spineli-Silva
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Ana Mondadori dos Santos
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
- Faculdade São Leopoldo Mandic (SLMandic), Campinas 13045-755, Brazil
| | - Társis Paiva Vieira
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Maria Isabel Melaragno
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (Unifesp), São Paulo 04023-062, Brazil; (H.G.S.); (G.T.); (M.I.M.)
| | - Vera Lúcia Gil-da-Silva-Lopes
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
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5
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Geiger M, Gorica E, Mohammed SA, Mongelli A, Mengozi A, Delfine V, Ruschitzka F, Costantino S, Paneni F. Epigenetic Network in Immunometabolic Disease. Adv Biol (Weinh) 2024; 8:e2300211. [PMID: 37794610 DOI: 10.1002/adbi.202300211] [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: 06/08/2023] [Revised: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Although a large amount of data consistently shows that genes affect immunometabolic characteristics and outcomes, epigenetic mechanisms are also heavily implicated. Epigenetic changes, including DNA methylation, histone modification, and noncoding RNA, determine gene activity by altering the accessibility of chromatin to transcription factors. Various factors influence these alterations, including genetics, lifestyle, and environmental cues. Moreover, acquired epigenetic signals can be transmitted across generations, thus contributing to early disease traits in the offspring. A closer investigation is critical in this aspect as it can help to understand the underlying molecular mechanisms further and gain insights into potential therapeutic targets for preventing and treating diseases arising from immuno-metabolic dysregulation. In this review, the role of chromatin alterations in the transcriptional modulation of genes involved in insulin resistance, systemic inflammation, macrophage polarization, endothelial dysfunction, metabolic cardiomyopathy, and nonalcoholic fatty liver disease (NAFLD), is discussed. An overview of emerging chromatin-modifying drugs and the importance of the individual epigenetic profile for personalized therapeutic approaches in patients with immuno-metabolic disorders is also presented.
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Affiliation(s)
- Martin Geiger
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Era Gorica
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Shafeeq Ahmed Mohammed
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Alessia Mongelli
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Alessandro Mengozi
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Valentina Delfine
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Frank Ruschitzka
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Sarah Costantino
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- University Heart Center, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Francesco Paneni
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- University Heart Center, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- Department of Research and Education, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
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6
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Ren Z, Tang H, Zhang W, Guo M, Cui J, Wang H, Xie B, Yu J, Chen Y, Zhang M, Han C, Chu T, Liang Q, Zhao S, Huang Y, He X, Liu K, Liu C, Chen C. The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling During Neurodevelopment. Neurosci Bull 2023:10.1007/s12264-023-01161-3. [PMID: 38060137 DOI: 10.1007/s12264-023-01161-3] [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: 07/06/2023] [Accepted: 09/13/2023] [Indexed: 12/08/2023] Open
Abstract
Intellectual disability (ID) is a condition characterized by cognitive impairment and difficulties in adaptive functioning. In our research, we identified two de novo mutations (c.955C>T and c.732C>A) at the KDM2A locus in individuals with varying degrees of ID. In addition, by using the Gene4Denovo database, we discovered five additional cases of de novo mutations in KDM2A. The mutations we identified significantly decreased the expression of the KDM2A protein. To investigate the role of KDM2A in neural development, we used both 2D neural stem cell models and 3D cerebral organoids. Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells (NPCs), increases apoptosis, induces premature neuronal differentiation, and affects synapse maturation. Through ChIP-Seq analysis, we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis. In addition, the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes. By integrating ChIP-Seq and RNA-Seq data, we made a significant discovery of the core genes' remarkable enrichment in the MAPK signaling pathway. Importantly, this enrichment was specifically linked to the p38 MAPK pathway. Furthermore, disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID, autism spectrum disorder, and schizophrenia. Overall, our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes, thereby modulating the MAPK signaling pathway and potentially impacting early brain development.
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Affiliation(s)
- Zongyao Ren
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Haiyan Tang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Wendiao Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Minghui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jingjie Cui
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, Changsha, 410007, China
| | - Bin Xie
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jing Yu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yonghao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Ming Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Cong Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Tianyao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Qiuman Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Shunan Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yingjie Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Xuelian He
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430014, China.
| | - Kefu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410011, China.
- Furong Laboratory, Changsha, 410000, China.
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7
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Rajaselvi ND, Jida MD, Ajeeshkumar KK, Nair SN, John P, Aziz Z, Nisha AR. Antineoplastic activity of plant-derived compounds mediated through inhibition of histone deacetylase: a review. Amino Acids 2023; 55:1803-1817. [PMID: 37389730 DOI: 10.1007/s00726-023-03298-x] [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: 04/13/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
In the combat of treating cancer recent therapeutic approaches are focused towards enzymatic targets as they occupy a pivotal participation in the cascade of oncogenesis and malignancy. There are several enzymes that modulate the epigenetic pathways and chromatin structure related to cancer mutation. Among several epigenetic mechanisms such as methylation, phosphorylation, and sumoylation, acetylation status of histones is crucial and is governed by counteracting enzymes like histone acetyl transferase (HAT) and histone deacetylases (HDAC) which have contradictory effects on the histone acetylation. HDAC inhibition induces chromatin relaxation which forms euchromatin and thereby initiates the expression of certain transcription factors attributed with apoptosis, which are mostly correlated with the expression of the p21 gene and acetylation of H3 and H4 histones. Most of the synthetic and natural HDAC inhibitors elicit antineoplastic effect through activation of various apoptotic pathways and promoting cell cycle arrest at various phases. Due to their promising chemo preventive action and low cytotoxicity against normal host cells, bioactive substances like flavonoids, alkaloids, and polyphenolic compounds from plants have recently gained importance. Even though all bioactive compounds mentioned have an HDAC inhibitory action, some of them have a direct effect and others enhance the effects of the standard well known HDAC inhibitors. In this review, the action of plant derived compounds against histone deacetylases in a variety of in vitro cancer cell lines and in vivo animal models are articulated.
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Affiliation(s)
- N Divya Rajaselvi
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, 680 651, India
| | - M D Jida
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, 680 651, India
| | - K K Ajeeshkumar
- Tumor Biology Lab, ICMR-National Institute of Pathology, New Delhi, India
| | - Suresh N Nair
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, 680 651, India
| | - Preethy John
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Pookode, Wayanad, 673 576, India
| | - Zarina Aziz
- Department of Veterinary Physiology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, 680 651, India
| | - A R Nisha
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, 680 651, India.
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8
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van Eyk CL, Fahey MC, Gecz J. Redefining cerebral palsies as a diverse group of neurodevelopmental disorders with genetic aetiology. Nat Rev Neurol 2023; 19:542-555. [PMID: 37537278 DOI: 10.1038/s41582-023-00847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Cerebral palsy is a clinical descriptor covering a diverse group of permanent, non-degenerative disorders of motor function. Around one-third of cases have now been shown to have an underlying genetic aetiology, with the genetic landscape overlapping with those of neurodevelopmental disorders including intellectual disability, epilepsy, speech and language disorders and autism. Here we review the current state of genomic testing in cerebral palsy, highlighting the benefits for personalized medicine and the imperative to consider aetiology during clinical diagnosis. With earlier clinical diagnosis now possible, we emphasize the opportunity for comprehensive and early genomic testing as a crucial component of the routine diagnostic work-up in people with cerebral palsy.
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Affiliation(s)
- Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Michael C Fahey
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia.
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
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9
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da Fonseca Junior AM, Ispada J, Dos Santos EC, de Lima CB, da Silva JVA, Paulson E, Goszczynski DE, Goissis MD, Ross PJ, Milazzotto MP. Adaptative response to changes in pyruvate metabolism on the epigenetic landscapes and transcriptomics of bovine embryos. Sci Rep 2023; 13:11504. [PMID: 37460590 DOI: 10.1038/s41598-023-38686-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
The epigenetic reprogramming that occurs during the earliest stages of embryonic development has been described as crucial for the initial events of cell specification and differentiation. Recently, the metabolic status of the embryo has gained attention as one of the main factors coordinating epigenetic events. In this work, we investigate the link between pyruvate metabolism and epigenetic regulation by culturing bovine embryos from day 5 in the presence of dichloroacetate (DCA), a pyruvate analog that increases the pyruvate to acetyl-CoA conversion, and iodoacetate (IA), which inhibits the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), leading to glycolysis inhibition. After 8 h of incubation, both DCA and IA-derived embryos presented higher mitochondrial membrane potential. Nevertheless, in both cases, lower levels of acetyl-CoA, ATP-citrate lyase and mitochondrial membrane potential were found in blastocysts, suggesting an adaptative metabolic response, especially in the DCA group. The metabolic alteration found in blastocysts led to changes in the global pattern of H3K9 and H3K27 acetylation and H3K27 trimethylation. Transcriptome analysis revealed that such alterations resulted in molecular differences mainly associated to metabolic processes, establishment of epigenetic marks, control of gene expression and cell cycle. The latter was further confirmed by the alteration of total cell number and cell differentiation in both groups when compared to the control. These results corroborate previous evidence of the relationship between the energy metabolism and the epigenetic reprogramming in preimplantation bovine embryos, reinforcing that the culture system is decisive for precise epigenetic reprogramming, with consequences for the molecular control and differentiation of cells.
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Affiliation(s)
- Aldcejam Martins da Fonseca Junior
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | - Jessica Ispada
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | - Erika Cristina Dos Santos
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | | | - João Vitor Alcantara da Silva
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | - Erika Paulson
- Department of Animal Science, University of California, UC - Davis, Davis, USA
| | | | | | - Pablo Juan Ross
- Department of Animal Science, University of California, UC - Davis, Davis, USA
| | - Marcella Pecora Milazzotto
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil.
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10
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Sheppard SE, Bryant L, Wickramasekara RN, Vaccaro C, Robertson B, Hallgren J, Hulen J, Watson CJ, Faundes V, Duffourd Y, Lee P, Simon MC, de la Cruz X, Padilla N, Flores-Mendez M, Akizu N, Smiler J, Pellegrino Da Silva R, Li D, March M, Diaz-Rosado A, Peixoto de Barcelos I, Choa ZX, Lim CY, Dubourg C, Journel H, Demurger F, Mulhern M, Akman C, Lippa N, Andrews M, Baldridge D, Constantino J, van Haeringen A, Snoeck-Streef I, Chow P, Hing A, Graham JM, Au M, Faivre L, Shen W, Mao R, Palumbos J, Viskochil D, Gahl W, Tifft C, Macnamara E, Hauser N, Miller R, Maffeo J, Afenjar A, Doummar D, Keren B, Arn P, Macklin-Mantia S, Meerschaut I, Callewaert B, Reis A, Zweier C, Brewer C, Saggar A, Smeland MF, Kumar A, Elmslie F, Deshpande C, Nizon M, Cogne B, van Ierland Y, Wilke M, van Slegtenhorst M, Koudijs S, Chen JY, Dredge D, Pier D, Wortmann S, Kamsteeg EJ, Koch J, Haynes D, Pollack L, Titheradge H, Ranguin K, Denommé-Pichon AS, Weber S, Pérez de la Fuente R, Sánchez del Pozo J, Lezana Rosales JM, Joset P, Steindl K, Rauch A, Mei D, Mari F, Guerrini R, Lespinasse J, Tran Mau-Them F, Philippe C, Dauriat B, Raymond L, Moutton S, Cueto-González AM, Tan TY, Mignot C, Grotto S, Renaldo F, Drivas TG, Hennessy L, Raper A, Parenti I, Kaiser FJ, Kuechler A, Busk ØL, Islam L, Siedlik JA, Henderson LB, Juusola J, Person R, Schnur RE, Vitobello A, Banka S, Bhoj EJ, Stessman HA. Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice. SCIENCE ADVANCES 2023; 9:eade1463. [PMID: 36897941 PMCID: PMC10005179 DOI: 10.1126/sciadv.ade1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Pathogenic variants in KMT5B, a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM# 617788). Given the relatively recent discovery of this disorder, it has not been fully characterized. Deep phenotyping of the largest (n = 43) patient cohort to date identified that hypotonia and congenital heart defects are prominent features that were previously not associated with this syndrome. Both missense variants and putative loss-of-function variants resulted in slow growth in patient-derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wild-type littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA sequencing of patient lymphoblasts and Kmt5b haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified additional pathogenic variants and clinical features in KMT5B-related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems.
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Affiliation(s)
- Sarah E. Sheppard
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Unit on Vascular Malformations, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Laura Bryant
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rochelle N. Wickramasekara
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
- Molecular Diagnostic Laboratory, Boys Town National Research Hospital, Omaha, NE, USA
| | - Courtney Vaccaro
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brynn Robertson
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Jodi Hallgren
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Jason Hulen
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Cynthia J. Watson
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Yannis Duffourd
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Pearl Lee
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M. Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xavier de la Cruz
- Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Natália Padilla
- Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marco Flores-Mendez
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Smiler
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- 10x Genomics, Pleasanton, CA, USA
| | | | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael March
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abdias Diaz-Rosado
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Zhao Xiang Choa
- Epithelial Epigenetics and Development Laboratory, A*STAR Skin Research Labs, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chin Yan Lim
- Epithelial Epigenetics and Development Laboratory, A*STAR Skin Research Labs, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Hubert Journel
- Service de Génétique Médicale, Hopital Chubert, Vannes, Bretagne, France
| | - Florence Demurger
- Department of Clinical Genetics, Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Maureen Mulhern
- Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cigdem Akman
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Marisa Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Dustin Baldridge
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - John Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Irina Snoeck-Streef
- Department of Child Neurology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA, USA
| | - Anne Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA, USA
| | - John M. Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - Margaret Au
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Dijon, Bourgogne, France
| | - Wei Shen
- University of Utah, Salt Lake City, UT, USA
- Mayo Clinic, Rochester, MN, USA
| | - Rong Mao
- University of Utah, Salt Lake City, UT, USA
| | | | | | - William Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia Tifft
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ellen Macnamara
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Natalie Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Rebecca Miller
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Jessica Maffeo
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Alexandra Afenjar
- AP-HP, Sorbonne Université, Département de neuropediatrie, Hospital Armand Trousseau, Paris, France
| | - Diane Doummar
- AP-HP, Sorbonne Université, Département de neuropediatrie, Hospital Armand Trousseau, Paris, France
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, Paris, France
| | - Pamela Arn
- Department of Pediatrics, Nemours Children’s Specialty Care, Jacksonville, FL, USA
| | | | - Ilse Meerschaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Carole Brewer
- Clinical Genetics Department, Royal Devon and Exeter Hospital (Heavitree), Exeter EX1 2ED, UK
| | - Anand Saggar
- Clinical Genetics Department, St George’s Hospital, St George’s Healthcare NHS Trust, London SW17 0QT, UK
| | - Marie F. Smeland
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
- Department of Pediatric Rehabilitation, University Hospital of North Norway, Norway
| | - Ajith Kumar
- Northeast Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Frances Elmslie
- South West Thames Centre for Genomics, St George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Charu Deshpande
- Department of Medical Genetics, Guy’s Hospital, London SE1 9RT, UK
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
| | - Benjamin Cogne
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
- Nantes Université, CNRS, INSERM, L’institut du thorax, F-44000 Nantes, France
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Suzanne Koudijs
- Department of Neurology, Erasmus University Medical Center–Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jin Yun Chen
- Neurology Department, Massachusetts General Hospital, Boston, MA, USA
| | - David Dredge
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Danielle Pier
- Neurology Department, Massachusetts General Hospital, Boston, MA, USA
| | - Saskia Wortmann
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
- Amalia Children’s Hospital, RadboudUMC Nijmegen, Nijmegen, Netherlands
| | - Erik-Jan Kamsteeg
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johannes Koch
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children–Orlando Health, Orlando, FL, USA
| | - Lynda Pollack
- Division of Genetics, Arnold Palmer Hospital for Children–Orlando Health, Orlando, FL, USA
| | - Hannah Titheradge
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s NHS Trust, Birmingham B15 2TG, UK
| | - Kara Ranguin
- Department of Genetics, Reference Centre for Rare Diseases and Developmental Anomalies, Caen Hospital, Caen, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Sacha Weber
- Department of Genetics, Reference Centre for Rare Diseases and Developmental Anomalies, Caen Hospital, Caen, France
| | | | - Jaime Sánchez del Pozo
- UDISGEN (Unidad de Dismorfología y Genética) 12 de Octubre University Hospital, Madrid, Spain
| | | | - Pascal Joset
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
| | - Anita Rauch
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
- University of Zurich, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- University of Zurich, URPP Adaptive Brain Circuits in Development and Learning (AdaBD), Zurich, Switzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, Zurich 8006, Switzerland
| | - Davide Mei
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Francesco Mari
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - James Lespinasse
- UF de Génétique Chromosomique, Centre Hospitalier de Chambéry, Hôtel-dieu, France
| | - Frédéric Tran Mau-Them
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Benjamin Dauriat
- Service de cytogénétique et génétique médicale, Centre Hospitalier Universitaire de Limoges, France
| | - Laure Raymond
- Service de génétique, Laboratoire Eurofins Biomnis, Lyon, France
| | | | - Anna M. Cueto-González
- Hospital Vall d'Hebron, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Cyril Mignot
- AP-HP, Sorbonne Université, Département de Génétique, Paris, France
| | - Sarah Grotto
- AP-HP, Sorbonne Université, Département de Génétique, Paris, France
| | - Florence Renaldo
- AP-HP, Sorbonne Université, Département de neuropediatrie, Centre de référence neurogénétique, Hôpital Armand Trousseau, Paris, France
| | - Theodore G. Drivas
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Hennessy
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Raper
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J. Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Øyvind L. Busk
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Lily Islam
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s NHS Trust, Birmingham B15 2TG, UK
| | - Jacob A. Siedlik
- Department of Exercise Science and Pre-Health Professions, Creighton University, Omaha, NE, USA
| | | | | | | | - Rhonda E. Schnur
- GeneDx, Gaithersburg, MD, USA
- Department of Pediatrics, Division of Genetics Cooper Medical School of Rowan University Cooper University Health Care 3, Cooper Plaza, Camden, NJ, USA
| | - Antonio Vitobello
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Elizabeth J. Bhoj
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Holly A. F. Stessman
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
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Gavril EC, Nucă I, Pânzaru MC, Ivanov AV, Mihai CT, Antoci LM, Ciobanu CG, Rusu C, Popescu R. Genotype-Phenotype Correlations in 2q37-Deletion Syndrome: An Update of the Clinical Spectrum and Literature Review. Genes (Basel) 2023; 14:465. [PMID: 36833393 PMCID: PMC9957522 DOI: 10.3390/genes14020465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
2q37 microdeletion/deletion syndrome (2q37DS) is one of the most common subtelomeric deletion disorders, caused by a 2q37 deletion of variable size. The syndrome is characterized by a broad and diverse spectrum of clinical findings: characteristic facial dysmorphism, developmental delay/intellectual disability (ID), brachydactyly type E, short stature, obesity, hypotonia in infancy, and abnormal behavior with autism spectrum disorder. Although numerous cases have been described so far, the exact mapping of the genotype and phenotype have not yet been achieved. MATERIALS AND METHODS In this study we analyzed nine newly diagnosed cases with 2q37 deletion (3 male/6 female, aged between 2 and 30 years old), and followed up at the Iasi Regional Medical Genetics Centre. All patients were tested first with MLPA using combined kits P036/P070 subtelomeric screening mix and follow-up mix P264; after, the deletion size and location were confirmed via CGH-array. We compared our findings with the data of other cases reported in the literature. RESULTS From nine cases, four had pure 2q37 deletions of variable sizes, and five presented deletion/duplication rearrangements (with chromosomes 2q, 9q, and 11p). In most cases, characteristic phenotypic aspects were observed: 9/9 facial dysmorphism, 8/9 global developmental delay and ID, 6/9 hypotonia, 5/9 behavior disorders, and 8/9 skeletal anomalies-especially brachydactyly type E. Two cases had obesity, one case had craniosynostosis, and four had heart defects. Other features found in our cases included translucent skin and telangiectasias (6/9), and a hump of fat on the upper thorax (5/9). CONCLUSIONS Our study enriches the literature data by describing new clinical features associated with 2q37 deletion, and possible genotype-phenotype correlations.
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Affiliation(s)
- Eva-Cristiana Gavril
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Irina Nucă
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Monica-Cristina Pânzaru
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Anca Viorica Ivanov
- Pediatrics Department, Grigore T. Popa University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
| | | | - Lucian-Mihai Antoci
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
| | - Cristian-Gabriel Ciobanu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
| | - Cristina Rusu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Roxana Popescu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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Lodhi N, Singh M, Srivastava R, Sawant SV, Tuli R. Epigenetic malleability at core promoter initiates tobacco PR-1a expression post salicylic acid treatment. Mol Biol Rep 2023; 50:417-431. [PMID: 36335522 DOI: 10.1007/s11033-022-08074-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Tobacco's PR-1a gene is induced by pathogen attack or exogenous application of salicylic acid (SA). Nucleosome mapping and chromatin immunoprecipitation assay were used to delineate the histone modifications on the PR-1a promoter. However, the epigenetic modifications of the inducible promoter of the PR-1a gene are not fully understood yet. METHODS AND RESULTS Southern approach was used to scan the promoter of PR-1a to identify presence of nucleosomes, ChIP assays were performed using anti-histones antibodies of repressive chromatin by di- methylated at H3K9 and H4K20 or active chromatin by acetylated H3K9/14 and H4K16 to find epigenetic malleability of nucleosome over core promoter in uninduced or induced state post SA treatment. Class I and II mammalian histone deacetylase (HDAC) inhibitor TSA treatment was used to enhance the expression of PR-1a by facilitating the histone acetylation post SA treatment. Here, we report correlated consequences of the epigenetic modifications correspond to disassembly of the nucleosome (spans from - 102 to + 55 bp, masks TATA and transcription initiation) and repressor complex from core promoter, eventually initiates the transcription of PR-1a gene post SA treatment. While active chromatin marks di and trimethylation of H3K4, acetylation of H3K9 and H4K16 are increased which are associated to the transcription initiation of PR-1a following SA treatment. However, in uninduced state constitutive expression of a negative regulator (SNI1) of AtPR1, suppresses AtPR1 expression by six-fold in Arabidopsis thaliana. Further, we report 50-to-1000-fold increased expression of AtPR1 in uninduced lsd1 mutant plants, up to threefold increased expression of AtPR1 in uninduced histone acetyl transferases (HATs) mutant plants, SNI1 dependent negative regulation of AtPR1, all together our results suggest that inactive state of PR-1a is indeed maintained by a repressive complex. CONCLUSION The study aimed to reveal the mechanism of transcription initiation of tobacco PR-1a gene in presence or absence of SA. This is the first study that reports nucleosome and repressor complex over core promoter region maintains the inactivation of gene in uninduced state, and upon induction disassembling of both initiates the downstream gene activation process.
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Affiliation(s)
- Niraj Lodhi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India. .,Mirna Analytics, New York, NY, 19047, USA.
| | - Mala Singh
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India
| | - Rakesh Srivastava
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India
| | - Samir V Sawant
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India
| | - Rakesh Tuli
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India.,University Institute of Engineering & Technology (UIET), Sector 25, Panjab University, Chandigarh, 160014, India
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13
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Conte M, Eletto D, Pannetta M, Petrone AM, Monti MC, Cassiano C, Giurato G, Rizzo F, Tessarz P, Petrella A, Tosco A, Porta A. Effects of Hst3p inhibition in Candida albicans: a genome-wide H3K56 acetylation analysis. Front Cell Infect Microbiol 2022; 12:1031814. [PMID: 36389164 PMCID: PMC9647175 DOI: 10.3389/fcimb.2022.1031814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/10/2022] [Indexed: 11/30/2022] Open
Abstract
Candida spp. represent the third most frequent worldwide cause of infection in Intensive Care Units with a mortality rate of almost 40%. The classes of antifungals currently available include azoles, polyenes, echinocandins, pyrimidine derivatives, and allylamines. However, the therapeutical options for the treatment of candidiasis are drastically reduced by the increasing antifungal resistance. The growing need for a more targeted antifungal therapy is limited by the concern of finding molecules that specifically recognize the microbial cell without damaging the host. Epigenetic writers and erasers have emerged as promising targets in different contexts, including the treatment of fungal infections. In C. albicans, Hst3p, a sirtuin that deacetylates H3K56ac, represents an attractive antifungal target as it is essential for the fungus viability and virulence. Although the relevance of such epigenetic regulator is documented for the development of new antifungal therapies, the molecular mechanism behind Hst3p-mediated epigenetic regulation remains unrevealed. Here, we provide the first genome-wide profiling of H3K56ac in C. albicans resulting in H3K56ac enriched regions associated with Candida sp. pathogenicity. Upon Hst3p inhibition, 447 regions gain H3K56ac. Importantly, these genomic areas contain genes encoding for adhesin proteins, degradative enzymes, and white-opaque switching. Moreover, our RNA-seq analysis revealed 1330 upregulated and 1081 downregulated transcripts upon Hst3p inhibition, and among them, we identified 87 genes whose transcriptional increase well correlates with the enrichment of H3K56 acetylation on their promoters, including some well-known regulators of phenotypic switching and virulence. Based on our evidence, Hst3p is an appealing target for the development of new potential antifungal drugs.
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Affiliation(s)
- Marisa Conte
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Daniela Eletto
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Martina Pannetta
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Anna M. Petrone
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Maria C. Monti
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Department of Pharmacy, University of Naples ‘Federico II’, Naples, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salerno, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salerno, Italy
| | - Peter Tessarz
- Max Planck Research Group “Chromatin and Ageing”, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- *Correspondence: Amalia Porta, ; Alessandra Tosco,
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- *Correspondence: Amalia Porta, ; Alessandra Tosco,
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14
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Sidorova-Darmos E, Fallah MS, Logan R, Lin CY, Eubanks JH. Mitochondrial brain proteome acetylation levels and behavioural responsiveness to amphetamine are altered in mice lacking Sirt3. Front Physiol 2022; 13:948387. [PMID: 36148309 PMCID: PMC9489219 DOI: 10.3389/fphys.2022.948387] [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: 05/19/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Post-translational modification of mitochondrial proteins represents one mechanism by which the functional activity of mitochondria can be regulated. In the brain, these modifications can influence the functional properties of different neural circuitries. Given that the sirtuin family member Sirt3 represents the primary protein deacetylase enzyme in mitochondria, we tested whether brain mitochondrial proteome acetylation would increase in male or female mice lacking Sirt3. Our results confirm that whole brain mitochondrial proteome acetylation levels are indeed elevated in both sexes of Sirt3-KO mice relative to controls. Consistently, we found the mitochondria of mouse embryonic fibroblast (MEF) cells derived from Sirt3-KO mice were smaller in size, and fewer in number than in wild-type MEFs, and that mitochondrial free calcium levels were elevated within the mitochondria of these cells. As protein acetylation can influence mitochondrial function, and changes in mitochondrial function have been linked to alterations in neural circuit function regulating motor activity and anxiety-like behavior, we tested whether Sirt3-deficient mice would display sensitized responsiveness to the stimulant amphetamine. Both male and female Sirt3-KO mice displayed hyper-locomotion and attenuated anxiety-like behavior in response to a dose of amphetamine that was insufficient to promote any behavioural responses in wild-type mice. Collectively, these results confirm that Sirt3 regulates mitochondrial proteome acetylation levels in brain tissue, and that the absence of Sirt3 increases the sensitivity of neural systems to amphetamine-induced behavioural responses.
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Affiliation(s)
- Elena Sidorova-Darmos
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
| | - Merrick S. Fallah
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Richard Logan
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
| | - Cheng Yu Lin
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
| | - James H. Eubanks
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
- Department of Surgery (Neurosurgery), University of Toronto, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- *Correspondence: James H. Eubanks,
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15
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Abu-Hanna J, Patel JA, Anastasakis E, Cohen R, Clapp LH, Loizidou M, Eddama MMR. Therapeutic potential of inhibiting histone 3 lysine 27 demethylases: a review of the literature. Clin Epigenetics 2022; 14:98. [PMID: 35915507 PMCID: PMC9344682 DOI: 10.1186/s13148-022-01305-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022] Open
Abstract
Histone 3 lysine 27 (H3K27) demethylation constitutes an important epigenetic mechanism of gene activation. It is mediated by the Jumonji C domain-containing lysine demethylases KDM6A and KDM6B, both of which have been implicated in a wide myriad of diseases, including blood and solid tumours, autoimmune and inflammatory disorders, and infectious diseases. Here, we review and summarise the pre-clinical evidence, both in vitro and in vivo, in support of the therapeutic potential of inhibiting H3K27-targeting demethylases, with a focus on the small-molecule inhibitor GSK-J4. In malignancies, KDM6A/B inhibition possesses the ability to inhibit proliferation, induce apoptosis, promote differentiation, and heighten sensitivity to currently employed chemotherapeutics. KDM6A/B inhibition also comprises a potent anti-inflammatory approach in inflammatory and autoimmune disorders associated with inappropriately exuberant inflammatory and autoimmune responses, restoring immunological homeostasis to inflamed tissues. With respect to infectious diseases, KDM6A/B inhibition can suppress the growth of infectious pathogens and attenuate the immunopathology precipitated by these pathogens. The pre-clinical in vitro and in vivo data, summarised in this review, suggest that inhibiting H3K27 demethylases holds immense therapeutic potential in many diseases.
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Affiliation(s)
- Jeries Abu-Hanna
- Division of Surgery and Interventional Science, Research Department of Surgical Biotechnology, University College London, GI Services, Ground Floor, 250 Euston Road, London, NW1 2PG, UK
| | - Jigisha A Patel
- Division of Surgery and Interventional Science, Research Department of Surgical Biotechnology, University College London, GI Services, Ground Floor, 250 Euston Road, London, NW1 2PG, UK
| | | | - Richard Cohen
- Division of Surgery and Interventional Science, Research Department of Surgical Biotechnology, University College London, GI Services, Ground Floor, 250 Euston Road, London, NW1 2PG, UK.,Department of Gastroenterology, University College London Hospital, London, UK
| | - Lucie H Clapp
- Institute of Cardiovascular Science, University College London, London, UK
| | - Marilena Loizidou
- Division of Surgery and Interventional Science, Research Department of Surgical Biotechnology, University College London, GI Services, Ground Floor, 250 Euston Road, London, NW1 2PG, UK
| | - Mohammad M R Eddama
- Division of Surgery and Interventional Science, Research Department of Surgical Biotechnology, University College London, GI Services, Ground Floor, 250 Euston Road, London, NW1 2PG, UK. .,Department of Gastroenterology, University College London Hospital, London, UK.
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16
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Martinez-Delgado B, Barrero MJ. Epigenomic Approaches for the Diagnosis of Rare Diseases. EPIGENOMES 2022; 6:epigenomes6030021. [PMID: 35997367 PMCID: PMC9397041 DOI: 10.3390/epigenomes6030021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
Rare diseases affect more than 300 million people worldwide. Diagnosing rare diseases is a major challenge as they have different causes and etiologies. Careful assessment of clinical symptoms often leads to the testing of the most common genetic alterations that could explain the disease. Patients with negative results for these tests frequently undergo whole exome or genome sequencing, leading to the identification of the molecular cause of the disease in 50% of patients at best. Therefore, a significant proportion of patients remain undiagnosed after sequencing their genome. Recently, approaches based on functional aspects of the genome, including transcriptomics and epigenomics, are beginning to emerge. Here, we will review these approaches, including studies that have successfully provided diagnoses for complex undiagnosed cases.
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Affiliation(s)
- Beatriz Martinez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER U758, 28029 Madrid, Spain
| | - Maria J. Barrero
- Models and Mechanisms Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain
- Correspondence:
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17
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Ojaimi MA, Banimortada BJ, Othman A, Riedhammer KM, Almannai M, El-Hattab AW. Disorders of histone methylation: molecular basis and clinical syndromes. Clin Genet 2022; 102:169-181. [PMID: 35713103 DOI: 10.1111/cge.14181] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
Epigenetic modifications of DNA and histone tails are essential for gene expression regulation. They play an essential role in neurodevelopment as nervous system development is a complex process requiring a dynamic pattern of gene expression. Histone methylation is one of the vital epigenetic regulators and mostly occurs on lysine residues of histones H3 and H4. Histone methylation is catalyzed by two sets of enzymes: histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). KMT2 enzymes form a distinct multi-subunit complex known as COMPASS to enhance their catalytic activity and diversify their biologic functions. Several neurodevelopmental syndromes result from defects of histone methylation which can be caused by deficiencies in histone methyltransferases and demethylases, loss of the histone methyltransferase activator TASP1, or derangements in COMPASS formation. In this review article, the molecular mechanism of histone methylation is discussed followed by summarizing clinical syndromes caused by monogenic defects in histone methylation.
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Affiliation(s)
- Mode Al Ojaimi
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Amna Othman
- Genetics and Genomic Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Mohammed Almannai
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital, Riyadh, Saudi Arabia
| | - Ayman W El-Hattab
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Pediatrics Department, University Hospital Sharjah, Sharjah, United Arab Emirates.,Genetics and Metabolic Department, KidsHeart Medical Center, Abu Dhabi, United Arab Emirates
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18
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Nothof SA, Magdinier F, Van-Gils J. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication. Genes (Basel) 2022; 13:genes13040639. [PMID: 35456445 PMCID: PMC9029427 DOI: 10.3390/genes13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Chromatin structure is an essential regulator of gene expression. Its state of compaction contributes to the regulation of genetic programs, in particular during differentiation. Epigenetic processes, which include post-translational modifications of histones, DNA methylation and implication of non-coding RNA, are powerful regulators of gene expression. Neurogenesis and neuronal differentiation are spatio-temporally regulated events that allow the formation of the central nervous system components. Here, we review the chromatin structure and post-translational histone modifications associated with neuronal differentiation. Studying the impact of histone modifications on neuronal differentiation improves our understanding of the pathophysiological mechanisms of chromatinopathies and opens up new therapeutic avenues. In addition, we will discuss techniques for the analysis of histone modifications on a genome-wide scale and the pathologies associated with the dysregulation of the epigenetic machinery.
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Affiliation(s)
- Sophie A. Nothof
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Frédérique Magdinier
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Julien Van-Gils
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
- Reference Center AD SOOR, AnDDI-RARE, Inserm U 1211, Medical Genetics Department, Bordeaux University, Center Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France
- Correspondence:
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19
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Harnessing the Power of Stem Cell Models to Study Shared Genetic Variants in Congenital Heart Diseases and Neurodevelopmental Disorders. Cells 2022; 11:cells11030460. [PMID: 35159270 PMCID: PMC8833927 DOI: 10.3390/cells11030460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/03/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Advances in human pluripotent stem cell (hPSC) technology allow one to deconstruct the human body into specific disease-relevant cell types or create functional units representing various organs. hPSC-based models present a unique opportunity for the study of co-occurring disorders where “cause and effect” can be addressed. Poor neurodevelopmental outcomes have been reported in children with congenital heart diseases (CHD). Intuitively, abnormal cardiac function or surgical intervention may stunt the developing brain, leading to neurodevelopmental disorders (NDD). However, recent work has uncovered several genetic variants within genes associated with the development of both the heart and brain that could also explain this co-occurrence. Given the scalability of hPSCs, straightforward genetic modification, and established differentiation strategies, it is now possible to investigate both CHD and NDD as independent events. We will first overview the potential for shared genetics in both heart and brain development. We will then summarize methods to differentiate both cardiac & neural cells and organoids from hPSCs that represent the developmental process of the heart and forebrain. Finally, we will highlight strategies to rapidly screen several genetic variants together to uncover potential phenotypes and how therapeutic advances could be achieved by hPSC-based models.
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20
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Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 253] [Impact Index Per Article: 126.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
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Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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21
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Dai R, Xu W, Chen W, Cui L, Li L, Zhou J, Jin X, Wang Y, Wang L, Sun Y. Epigenetic modification of <i>Kiss1</i> gene expression in the AVPV is essential for female reproductive aging. Biosci Trends 2022; 16:346-358. [DOI: 10.5582/bst.2022.01358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ruoxi Dai
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Wen Xu
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Wei Chen
- Department of Urology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Liyuan Cui
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Lisha Li
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Jing Zhou
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Xueling Jin
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Yan Wang
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Ling Wang
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Yan Sun
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
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22
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Rautenberg EK, Hamzaoui Y, Coletta DK. Mini-review: Mitochondrial DNA methylation in type 2 diabetes and obesity. Front Endocrinol (Lausanne) 2022; 13:968268. [PMID: 36093112 PMCID: PMC9453027 DOI: 10.3389/fendo.2022.968268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Type 2 diabetes (T2D) and obesity are two of the most challenging public health problems of our time. Therefore, understanding the molecular mechanisms that contribute to these complex metabolic disorders is essential. An underlying pathophysiological condition of T2D and obesity is insulin resistance (IR), a reduced biological response to insulin in peripheral tissues such as the liver, adipose tissue, and skeletal muscle. Many factors contribute to IR, including lifestyle variables such as a high-fat diet and physical inactivity, genetics, and impaired mitochondrial function. It is well established that impaired mitochondria structure and function occur in insulin-resistant skeletal muscle volunteers with T2D or obesity. Therefore, it could be hypothesized that the mitochondrial abnormalities are due to epigenetic regulation of mitochondrial and nuclear-encoded genes that code for mitochondrial structure and function. In this review, we describe the normal function and structure of mitochondria and highlight some of the key studies that demonstrate mitochondrial abnormalities in skeletal muscle of volunteers with T2D and obesity. Additionally, we describe epigenetic modifications in the context of IR and mitochondrial abnormalities, emphasizing mitochondria DNA (mtDNA) methylation, an emerging area of research.
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Affiliation(s)
- Emma K. Rautenberg
- Department of Physiology, The University of Arizona College of Medicine, Tucson, AZ, United States
| | - Yassin Hamzaoui
- Department of Physiology, The University of Arizona College of Medicine, Tucson, AZ, United States
| | - Dawn K. Coletta
- Department of Physiology, The University of Arizona College of Medicine, Tucson, AZ, United States
- Department of Medicine, Division of Endocrinology, The University of Arizona College of Medicine, Tucson, AZ, United States
- Center for Disparities in Diabetes, Obesity and Metabolism, The University of Arizona, Tucson, AZ, United States
- *Correspondence: Dawn K. Coletta,
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23
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Oluwole OG, James K, Yalcouye A, Wonkam A. Hearing loss and brain disorders: A review of multiple pathologies. Open Med (Wars) 2021; 17:61-69. [PMID: 34993346 PMCID: PMC8678477 DOI: 10.1515/med-2021-0402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/22/2021] [Accepted: 11/05/2021] [Indexed: 11/29/2022] Open
Abstract
Several causative factors are associated with hearing loss (HL) and brain disorders. However, there are many unidentified disease modifiers in these conditions. Our study summarised the most common brain disorders associated with HL and highlighted mechanisms of pathologies. We searched the literature for published articles on HL and brain disorders. Alzheimer's disease/dementia, Parkinson's disease, cognitive impairment, autism spectrum disorder, ataxia, epilepsy, stroke, and hypoxic-ischaemic encephalopathy majorly co-interact with HL. The estimated incidence rate was 113 per 10,000 person-years. Genetic, epigenetic, early life/neonatal stress, hypoxia, inflammation, nitric oxide infiltration, endoplasmic reticulum stress, and excess glutamate were the distinguished modifiers identified. Various mechanisms like adhesion molecules, transport proteins, hair cell apoptosis, and neurodegeneration have been implicated in these conditions and are serving as potential targets for therapies. To improve the quality of life of patients, these understandings will improve clinical diagnoses and management of HL and brain disorders.
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Affiliation(s)
- Oluwafemi Gabriel Oluwole
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, 3.14 Wernher & Beit North Building, P.O Box 7925, Cape Town, South Africa
| | - Kili James
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, 3.14 Wernher & Beit North Building, P.O Box 7925, Cape Town, South Africa
| | - Abdoulaye Yalcouye
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, 3.14 Wernher & Beit North Building, P.O Box 7925, Cape Town, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, 3.14 Wernher & Beit North Building, P.O Box 7925, Cape Town, South Africa
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Jennings EQ, Fritz KS, Galligan JJ. Biochemical genesis of enzymatic and non-enzymatic post-translational modifications. Mol Aspects Med 2021; 86:101053. [PMID: 34838336 PMCID: PMC9126990 DOI: 10.1016/j.mam.2021.101053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 12/20/2022]
Abstract
Post-translational modifications (PTMs) alter protein structure, function, and localization and play a pivotal role in physiological and pathophysiological conditions. Many PTMs arise from endogenous metabolic intermediates and serve as sensors for metabolic feedback to maintain cell growth and homeostasis. A key feature to PTMs is their biochemical genesis, which can result from either non-enzymatic adduction (nPTMs) or through enzyme-catalyzed reactions (ePTMs). The abundance and site-specificity of PTMs are determined by dedicated classes of enzymes that add (writers) or remove (erasers) the chemical addition. In this review we will highlight the biochemical genesis and regulation of a few of the 700+ PTMs that have been identified.
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Affiliation(s)
- Erin Q Jennings
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Kristofer S Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - James J Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
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Yang Y, Luan Y, Yuan RX, Luan Y. Histone Methylation Related Therapeutic Challenge in Cardiovascular Diseases. Front Cardiovasc Med 2021; 8:710053. [PMID: 34568453 PMCID: PMC8458636 DOI: 10.3389/fcvm.2021.710053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
The epidemic of cardiovascular diseases (CVDs) is predicted to spread rapidly in advanced countries accompanied by the high prevalence of risk factors. In terms of pathogenesis, the pathophysiology of CVDs is featured by multiple disorders, including vascular inflammation accompanied by simultaneously perturbed pathways, such as cell death and acute/chronic inflammatory reactions. Epigenetic alteration is involved in the regulation of genome stabilization and cellular homeostasis. The association between CVD progression and histone modifications is widely known. Among the histone modifications, histone methylation is a reversible process involved in the development and homeostasis of the cardiovascular system. Abnormal methylation can promote CVD progression. This review discusses histone methylation and the enzymes involved in the cardiovascular system and determine the effects of histone methyltransferases and demethylases on the pathogenesis of CVDs. We will further demonstrate key proteins mediated by histone methylation in blood vessels and review histone methylation-mediated cardiomyocytes and cellular functions and pathways in CVDs. Finally, we will summarize the role of inhibitors of histone methylation and demethylation in CVDs and analyze their therapeutic potential, based on previous studies.
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Affiliation(s)
- Yang Yang
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Luan
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Rui-Xia Yuan
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Luan
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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