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Zebrauskiene D, Sadauskiene E, Dapkunas J, Kairys V, Balciunas J, Konovalovas A, Masiuliene R, Petraityte G, Valeviciene N, Mataciunas M, Barysiene J, Mikstiene V, Tomkuviene M, Preiksaitiene E. Aortic disease and cardiomyopathy in patients with a novel DNMT3A gene variant causing Tatton-Brown-Rahman syndrome. Clin Epigenetics 2024; 16:76. [PMID: 38845031 PMCID: PMC11157947 DOI: 10.1186/s13148-024-01686-y] [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: 04/05/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
Tatton-Brown-Rahman syndrome (TBRS) is a rare congenital genetic disorder caused by autosomal dominant pathogenic variants in the DNA methyltransferase DNMT3A gene. Typical TBRS clinical features are overgrowth, intellectual disability, and minor facial anomalies. However, since the syndrome was first described in 2014, a widening spectrum of abnormalities is being described. Cardiovascular abnormalities are less commonly reported but can be a major complication of the syndrome. This article describes a family of three individuals diagnosed with TBRS in adulthood and highlights the variable expression of cardiovascular features. A 34-year-old proband presented with progressive aortic dilatation, mitral valve (MV) regurgitation, left ventricular (LV) dilatation, and ventricular arrhythmias. The affected family members (mother and brother) were diagnosed with MV regurgitation, LV dilatation, and arrhythmias. Exome sequencing and computational protein analysis suggested that the novel familial DNMT3A mutation Ser775Tyr is located in the methyltransferase domain, however, distant from the active site or DNA-binding loops. Nevertheless, this bulky substitution may have a significant effect on DNMT3A protein structure, dynamics, and function. Analysis of peripheral blood cfDNA and transcriptome showed shortened mononucleosome fragments and altered gene expression in a number of genes related to cardiovascular health and of yet undescribed function, including several lncRNAs. This highlights the importance of epigenetic regulation by DNMT3A on cardiovascular system development and function. From the clinical perspective, we suggest that new patients diagnosed with congenital DNMT3A variants and TBRS require close examination and follow-up for aortic dilatation and valvular disease because these conditions can progress rapidly. Moreover, personalized treatments, based on the specific DNMT3A variants and the different pathways of their function loss, can be envisioned in the future.
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Affiliation(s)
- Dovile Zebrauskiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania.
| | - Egle Sadauskiene
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Justas Dapkunas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Joris Balciunas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | | | | | - Gunda Petraityte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
| | - Nomeda Valeviciene
- Department of Radiology, Nuclear Medicine and Medical Physics, Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, Vilnius, Lithuania
| | - Mindaugas Mataciunas
- Department of Radiology, Nuclear Medicine and Medical Physics, Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, Vilnius, Lithuania
| | - Jurate Barysiene
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Violeta Mikstiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
| | - Migle Tomkuviene
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania.
| | - Egle Preiksaitiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
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Wu Y, Li B, Yu X, Liu Y, Chui R, Sun K, Geng D, Ma L. Histone deacetylase 6 as a novel promising target to treat cardiovascular disease. CANCER INNOVATION 2024; 3:e114. [PMID: 38947757 PMCID: PMC11212282 DOI: 10.1002/cai2.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 07/02/2024]
Abstract
Histone deacetylase 6 (HDAC6) belongs to a class of epigenetic targets that have been found to be a key protein in the association between tumors and cardiovascular disease. Recent studies have focused on the crucial role of HDAC6 in regulating cardiovascular diseases such as atherosclerosis, myocardial infarction, myocardial hypertrophy, myocardial fibrosis, hypertension, pulmonary hypertension, and arrhythmia. Here, we review the association between HDAC6 and cardiovascular disease, the research progress of HDAC6 inhibitors in the treatment of cardiovascular disease, and discuss the feasibility of combining HDAC6 inhibitors with other therapeutic agents to treat cardiovascular disease.
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Affiliation(s)
- Ya‐Xi Wu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Bing‐Qian Li
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Xiao‐Qian Yu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Yu‐Lin Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Rui‐Hao Chui
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Kai Sun
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Dian‐Guang Geng
- Key Laboratory of Cardio‐Cerebrovascular Drugs'China Meheco Topfond Pharmaceutical Co.ZhumadianHenanChina
| | - Li‐Ying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
- Key Laboratory of Cardio‐Cerebrovascular Drugs'China Meheco Topfond Pharmaceutical Co.ZhumadianHenanChina
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Abdulwahab HG, Mansour RES, Farghaly TA, El-Sehrawi HM. Discovery of novel benzimidazole derivatives as potent HDACs inhibitors against leukemia with (Thio)Hydantoin as zinc-binding moiety: Design, synthesis, enzyme inhibition, and cellular mechanistic study. Bioorg Chem 2024; 146:107284. [PMID: 38493640 DOI: 10.1016/j.bioorg.2024.107284] [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: 01/30/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
Based on the well-established pharmacophoric features required for histone deacetylase (HDAC) inhibition, a novel series of easy-to-synthesize benzimidazole-linked (thio)hydantoin derivatives was designed and synthesized as HDAC6 inhibitors. All target compounds potently inhibited HDAC6 at nanomolar levels with compounds 2c, 2d, 4b and 4c (IC50s = 51.84-74.36 nM) being more potent than SAHA reference drug (IC50 = 91.73 nM). Additionally, the most potent derivatives were further assessed for their in vitro cytotoxic activity against two human leukemia cells. Hydantoin derivative 4c was equipotent/superior to SAHA against MOLT-4/CCRF-CEM leukemia cells, respectively and demonstrated safety profile better than that of SAHA against non-cancerous human cells. 4c was also screened against different HDAC isoforms. 4c was superior to SAHA against HDAC1. Cell-based assessment of 4c revealed a significant cell cycle arrest and apoptosis induction. Moreover, western blotting analysis showed increased levels of acetylated histone H3, histone H4 and α-tubulin in CCRF-CEM cells. Furthermore, docking study exposed the ability of title compounds to chelate Zn2+ located within HDAC6 active site. As well, in-silico evaluation of physicochemical properties showed that target compounds are promising candidates in terms of pharmacokinetic aspects.
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Affiliation(s)
- Hanan Gaber Abdulwahab
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
| | - Reda El-Sayed Mansour
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Thoraya A Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hend M El-Sehrawi
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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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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Lourdes VH, Mario SC, Didac CA, Mercè B, Loreto M, Leticia P, Lucia FA, Martínez-Monseny AF, Mercedes S. Beyond the known phenotype of sotos syndrome: a 31-individuals cohort study. Front Pediatr 2023; 11:1184529. [PMID: 37384309 PMCID: PMC10298147 DOI: 10.3389/fped.2023.1184529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Sotos Syndrome (SS, OMIM#117550) is a heterogeneous genetic condition, recognized by three main clinical features present in most cases: overgrowth with macrocephaly, typical facial appearance and different degrees of intellectual disability. Three different types are described caused by variants or deletions/duplications in NSD1, NFIX and APC2 genes. We aimed to describe a cohort of pediatric patients reporting the typical and unexpected findings in order to expand the phenotype of this syndrome and trying to find genotype-phenotype correlations. Methods In our referral center, we collected and analyzed clinical and genetic data of 31-patients cohort diagnosed with SS. Results All of them presented with overgrowth, typical dysmorphic features and different degree of developmental delay. Although structural cardiac defects have been reported in SS, non-structural diseases such as pericarditis were outstanding in our cohort. Moreover, we described here novel oncological malignancies not previously linked to SS such as splenic hamartoma, retinal melanocytoma and acute lymphocytic leukemia. Finally, five patients suffered from recurrent onychocryptosis that required surgical procedures, as an unreported prevalent medical condition. Discussion This is the first study focusing on multiple atypical symptoms in SS at the time that revisits the spectrum of clinical and molecular basis of this heterogeneous entity trying to unravel a genotype-phenotype correlation.
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Affiliation(s)
- Vega-Hanna Lourdes
- Department of Pediatrics, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Sanz-Cuesta Mario
- Department of Pediatrics, Hospital de Sant Boi, Parc Sanitari Sant Joan de Déu, Barcelona, Spain
| | - Casas-Alba Didac
- Department of Genetic and Molecular Medicine/IPER, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Bolasell Mercè
- Department of Genetic and Molecular Medicine/IPER, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Martorell Loreto
- Department of Genetic and Molecular Medicine/IPER, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Pías Leticia
- Department of Genetic and Molecular Medicine/IPER, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Feller Ana Lucia
- Departamen of Pediatrics, Hospital J P Garrahan, Buenos Aires, Argentine
| | | | - Serrano Mercedes
- Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
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Di Bello E, Sian V, Bontempi G, Zwergel C, Fioravanti R, Noce B, Castiello C, Tomassi S, Corinti D, Passeri D, Pellicciari R, Mercurio C, Varasi M, Altucci L, Tripodi M, Strippoli R, Nebbioso A, Valente S, Mai A. Novel pyridine-containing histone deacetylase inhibitors strongly arrest proliferation, induce apoptosis and modulate miRNAs in cancer cells. Eur J Med Chem 2023; 247:115022. [PMID: 36549114 DOI: 10.1016/j.ejmech.2022.115022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/16/2022]
Abstract
After over 30 years of research, the development of HDAC inhibitors led to five FDA/Chinese FDA-approved drugs and many others under clinical or preclinical investigation to treat cancer and non-cancer diseases. Herein, based on our recent development of pyridine-based isomers as HDAC inhibitors, we report a series of novel 5-acylamino-2-pyridylacrylic- and -picolinic hydroxamates and 2'-aminoanilides 5-8 as anticancer agents. The hydroxamate 5d proved to be quite HDAC3/6-selective exhibiting IC50 values of 80 and 11 nM, respectively, whereas the congener 5e behaved as inhibitor of HDAC1-3, -6, -8, and -10 (class I/IIb-selective inhibitor) at nanomolar level. Compound 5e provided a huge antiproliferative activity (nanomolar IC50 values) against both haematological and solid cancer cell lines. In leukaemia U937 cells, the hydroxamate 5d and the 2'-aminoanilide 8f induced remarkable cell death after 48 h, with 76% and 100% pre-G1 phase arrest, respectively, showing a stronger effect with respect to SAHA and MS-275 used as reference compounds. In U937 cells, the highest dose- and time-dependent cytodifferentiation was obtained by the 2'-aminoanilide 8d (up to 35% of CD11c positive/propidium iodide negative cells at 5 μM for 48 h). The same 8d and the hydroxamates 5d and 5e were the most effective in inducing p21 protein expression in the same cell line. Mechanistically, 5d, 5e, 8d and 8f increased mRNA expression of p21, BAX and BAK, downregulated cyclin D1 and BCL-2 and modulated pro- and anti-apoptotic microRNAs towards apoptosis induction. Finally, 5e strongly arrested proliferation in nine different haematological cancer cell lines, with dual-digit nanomolar potency towards MV4-11, Kasumi-1, and NB4, being more potent than mocetinostat, used as reference drug.
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Affiliation(s)
- Elisabetta Di Bello
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Veronica Sian
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania, Via L. De Crecchio 7, 80138, Naples, Italy
| | - Giulio Bontempi
- Department of Molecular Medicine, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy; Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Via Portuense, 292, 00149, Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Beatrice Noce
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carola Castiello
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Davide Corinti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Daniela Passeri
- TES Pharma S.r.l., Via P. Togliatti 20, Corciano, 06073, Perugia, Italy
| | | | - Ciro Mercurio
- IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mario Varasi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Lucia Altucci
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania, Via L. De Crecchio 7, 80138, Naples, Italy
| | - Marco Tripodi
- Department of Molecular Medicine, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy; Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Via Portuense, 292, 00149, Rome, Italy
| | - Raffaele Strippoli
- Department of Molecular Medicine, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy; Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Via Portuense, 292, 00149, Rome, Italy.
| | - Angela Nebbioso
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania, Via L. De Crecchio 7, 80138, Naples, Italy.
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
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7
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Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
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Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
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8
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The Role of Epigenetics in Brain and Spinal Cord Tumors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1394:119-136. [PMID: 36587385 DOI: 10.1007/978-3-031-14732-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Identification of distinct genetic and epigenetic profiles in various neuroepithelial tumors has improved the classification and uncovered novel diagnostic, prognostic, and predictive molecular biomarkers for improved prediction of treatment response and outcome. Especially, in pediatric high-grade brain tumors, such as diffuse midline glioma, H3K27M-altered and posterior fossa group A-ependymoma, epigenetic changes predominate, along with changes in expression of known oncogenes and tumor suppressor genes induced by histone modifications and DNA methylation. The precise role of epigenetic abnormalities is important for understanding tumorigenesis and the establishment of brain tumor treatment strategies. Using powerful epigenetic-based therapies for cancer cells, the aberrantly regulated epigenome can be restored to a more normal state through epigenetic reprogramming. Combinations of agents targeting DNA methylation and/or other epigenetic modifications may be a promising cancer treatment. Therefore, the integration of multi-omics data including epigenomics is now important for classifying primary brain tumors and predicting their biological behavior. Recent advances in molecular genetics and epigenetic integrated diagnostics of brain tumors influence new strategies for targeted therapy.
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9
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Zhang L, Liu Y, Lu Y, Wang G. Targeting epigenetics as a promising therapeutic strategy for treatment of neurodegenerative diseases. Biochem Pharmacol 2022; 206:115295. [DOI: 10.1016/j.bcp.2022.115295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
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10
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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11
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Sakamuru S, Huang R, Xia M. Use of Tox21 Screening Data to Evaluate the COVID-19 Drug Candidates for Their Potential Toxic Effects and Related Pathways. Front Pharmacol 2022; 13:935399. [PMID: 35910344 PMCID: PMC9333127 DOI: 10.3389/fphar.2022.935399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
Currently, various potential therapeutic agents for coronavirus disease-2019 (COVID-19), a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are being investigated worldwide mainly through the drug repurposing approach. Several anti-viral, anti-bacterial, anti-malarial, and anti-inflammatory drugs were employed in randomized trials and observational studies for developing new therapeutics for COVID-19. Although an increasing number of repurposed drugs have shown anti-SARS-CoV-2 activities in vitro, so far only remdesivir has been approved by the US FDA to treat COVID-19, and several other drugs approved for Emergency Use Authorization, including sotrovimab, tocilizumab, baricitinib, paxlovid, molnupiravir, and other potential strategies to develop safe and effective therapeutics for SARS-CoV-2 infection are still underway. Many drugs employed as anti-viral may exert unwanted side effects (i.e., toxicity) via unknown mechanisms. To quickly assess these drugs for their potential toxicological effects and mechanisms, we used the Tox21 in vitro assay datasets generated from screening ∼10,000 compounds consisting of approved drugs and environmental chemicals against multiple cellular targets and pathways. Here we summarize the toxicological profiles of small molecule drugs that are currently under clinical trials for the treatment of COVID-19 based on their in vitro activities against various targets and cellular signaling pathways.
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12
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Brennan K, Zheng H, Fahrner JA, Shin JH, Gentles AJ, Schaefer B, Sunwoo JB, Bernstein JA, Gevaert O. NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Hum Mol Genet 2022; 31:2164-2184. [PMID: 35094088 PMCID: PMC9262396 DOI: 10.1093/hmg/ddac026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/04/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sotos syndrome (SS), the most common overgrowth with intellectual disability (OGID) disorder, is caused by inactivating germline mutations of NSD1, which encodes a histone H3 lysine 36 methyltransferase. To understand how NSD1 inactivation deregulates transcription and DNA methylation (DNAm), and to explore how these abnormalities affect human development, we profiled transcription and DNAm in SS patients and healthy control individuals. We identified a transcriptional signature that distinguishes individuals with SS from controls and was also deregulated in NSD1-mutated cancers. Most abnormally expressed genes displayed reduced expression in SS; these downregulated genes consisted mostly of bivalent genes and were enriched for regulators of development and neural synapse function. DNA hypomethylation was strongly enriched within promoters of transcriptionally deregulated genes: overexpressed genes displayed hypomethylation at their transcription start sites while underexpressed genes featured hypomethylation at polycomb binding sites within their promoter CpG island shores. SS patients featured accelerated molecular aging at the levels of both transcription and DNAm. Overall, these findings indicate that NSD1-deposited H3K36 methylation regulates transcription by directing promoter DNA methylation, partially by repressing polycomb repressive complex 2 (PRC2) activity. These findings could explain the phenotypic similarity of SS to OGID disorders that are caused by mutations in PRC2 complex-encoding genes.
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Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - June Ho Shin
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - John B Sunwoo
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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13
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Malekian N, Agrawal AA, Berendonk TU, Al-Fatlawi A, Schroeder M. A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance. Sci Rep 2022; 12:8037. [PMID: 35577863 PMCID: PMC9110714 DOI: 10.1038/s41598-022-11432-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/07/2022] [Indexed: 11/30/2022] Open
Abstract
Antibiotic resistance is a global health threat and consequently, there is a need to understand the mechanisms driving its emergence. Here, we hypothesize that genes and mutations under positive selection may contribute to antibiotic resistance. We explored wastewater E. coli, whose genomes are highly diverse. We subjected 92 genomes to a statistical analysis for positively selected genes. We obtained 75 genes under positive selection and explored their potential for antibiotic resistance. We found that eight genes have functions relating to antibiotic resistance, such as biofilm formation, membrane permeability, and bacterial persistence. Finally, we correlated the presence/absence of non-synonymous mutations in positively selected sites of the genes with a function in resistance against 20 most prescribed antibiotics. We identified mutations associated with antibiotic resistance in two genes: the porin ompC and the bacterial persistence gene hipA. These mutations are located at the surface of the proteins and may hence have a direct effect on structure and function. For hipA, we hypothesize that the mutations influence its interaction with hipB and that they enhance the capacity for dormancy as a strategy to evade antibiotics. Overall, genomic data and positive selection analyses uncover novel insights into mechanisms driving antibiotic resistance.
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14
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Genetically modified mice for research on human diseases: A triumph for Biotechnology or a work in progress? THE EUROBIOTECH JOURNAL 2022. [DOI: 10.2478/ebtj-2022-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022] Open
Abstract
Abstract
Genetically modified mice are engineered as models for human diseases. These mouse models include inbred strains, mutants, gene knockouts, gene knockins, and ‘humanized’ mice. Each mouse model is engineered to mimic a specific disease based on a theory of the genetic basis of that disease. For example, to test the amyloid theory of Alzheimer’s disease, mice with amyloid precursor protein genes are engineered, and to test the tau theory, mice with tau genes are engineered. This paper discusses the importance of mouse models in basic research, drug discovery, and translational research, and examines the question of how to define the “best” mouse model of a disease. The critiques of animal models and the caveats in translating the results from animal models to the treatment of human disease are discussed. Since many diseases are heritable, multigenic, age-related and experience-dependent, resulting from multiple gene-gene and gene-environment interactions, it will be essential to develop mouse models that reflect these genetic, epigenetic and environmental factors from a developmental perspective. Such models would provide further insight into disease emergence, progression and the ability to model two-hit and multi-hit theories of disease. The summary examines the biotechnology for creating genetically modified mice which reflect these factors and how they might be used to discover new treatments for complex human diseases such as cancers, neurodevelopmental and neurodegenerative diseases.
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15
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Kano S, Higashihori N, Thiha P, Takechi M, Iseki S, Moriyama K. The role of the histone methyltransferase SET domain bifurcated 1 during palatal development. Biochem Biophys Res Commun 2022; 598:74-80. [PMID: 35151207 DOI: 10.1016/j.bbrc.2022.01.127] [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: 12/01/2021] [Revised: 01/26/2022] [Accepted: 01/30/2022] [Indexed: 11/26/2022]
Abstract
The histone methyltransferase SET domain bifurcated 1 (SETDB1) catalyzes the trimethylation of lysine 9 of histone H3, thereby regulating gene expression. In this study, we used conditional knockout mice, where Setdb1 was deleted only in neural crest cells (Setdb1fl/fl,Wnt1-Cre + mice), to clarify the role of SETDB1 in palatal development. Setdb1fl/fl,Wnt1-Cre + mice died shortly after birth due to a cleft palate with full penetration. Reduced palatal mesenchyme proliferation was seen in Setdb1fl/fl,Wnt1-Cre + mice, which might be a possible mechanism of cleft palate development. Quantitative RT-PCR and in situ hybridization showed that expression of the Pax9, Bmp4, Bmpr1a, Wnt5a, and Fgf10 genes, known to be important for palatal development, were markedly decreased in the palatal mesenchyme of Setdb1fl/fl,Wnt1-Cre + mice. Along with these phenomena, SMAD1/5/9 phosphorylation was decreased by the loss of Setdb1. Our results demonstrated that SETDB1 is indispensable for palatal development partially through its proliferative effect. Taken together with previous reports that PAX9 regulates BMP signaling during palatal development which implies that loss of Setdb1 may be involved in the cleft palate development by decreasing SMAD-dependent BMP signaling through Pax9.
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Affiliation(s)
- Sakurako Kano
- Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Norihisa Higashihori
- Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Phyo Thiha
- Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Masaki Takechi
- Maxillofacial Anatomy, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Sachiko Iseki
- Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Keiji Moriyama
- Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
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16
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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17
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Varghese R, Majumdar A. A New Prospect for the Treatment of Nephrotic Syndrome Based on Network Pharmacology Analysis. Curr Res Physiol 2022; 5:36-47. [PMID: 35098155 PMCID: PMC8783131 DOI: 10.1016/j.crphys.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/10/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
Abstract
Network pharmacology is an emerging field which is currently capturing interest in drug discovery and development. Chronic kidney conditions have become a threat globally due to its associated lifelong therapies. Nephrotic syndrome (NS) is a common glomerular disease that is seen in paediatric and adult population with characteristic manifestation of proteinuria, oedema, hypoalbuminemia, and hyperlipidemia. It involves podocyte damage with tubulointerstitial fibrosis and glomerulosclerosis. Till date there has been no specific treatment available for this condition that provides complete remission. Repurposing of drugs can thus be a potential strategy for the treatment of NS. Recently, epigenetic mechanisms were identified that promote progression of many renal diseases. Therefore, in the present study, we investigated two epigenetic drugs valproic acid (VPA) and all-trans retinoic acid (ATRA). Epigenetic drugs act by binging about changes in gene expression without altering the DNA sequence. The changes include DNA methylation or histone modifications. The targets for the two drugs ATRA and VPA were collated from ChEMBL and Binding DB. All the genes associated with NS were collected from DisGeNET and KEGG database. Interacting proteins for the target genes were acquired from STRING database. The genes were then subjected to gene ontology and pathway enrichment analysis using a functional enrichment software tool. A drug-target and drug-potential target-protein interaction network was constructed using the Cytoscape software. Our results revealed that the two drugs VPA and ATRA had 65 common targets that contributed to kidney diseases. Out of which, 25 targets were specifically NS associated. Further, our work exhibited that ATRA and VPA were synergistically involved in pathways of inflammation, renal fibrosis, glomerulosclerosis and possibly mitochondrial biogenesis and endoplasmic reticulum stress. We thus propose a synergistic potential of the two drugs for treating chronic kidney diseases, specifically NS. The outcomes will undoubtedly invigorate further preclinical and clinical explorative studies. We identify network pharmacology as an initial inherent approach in identifying drug candidates for repurposing and synergism.
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Affiliation(s)
- Rini Varghese
- Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai, Maharashtra, 400098, India
| | - Anuradha Majumdar
- Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai, Maharashtra, 400098, India
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18
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Rabaneda-Bueno R, Mena-Montes B, Torres-Castro S, Torres-Carrillo N, Torres-Carrillo NM. Advances in Genetics and Epigenetic Alterations in Alzheimer's Disease: A Notion for Therapeutic Treatment. Genes (Basel) 2021; 12:1959. [PMID: 34946908 PMCID: PMC8700838 DOI: 10.3390/genes12121959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease (AD) is a disabling neurodegenerative disorder that leads to long-term functional and cognitive impairment and greatly reduces life expectancy. Early genetic studies focused on tracking variations in genome-wide DNA sequences discovered several polymorphisms and novel susceptibility genes associated with AD. However, despite the numerous risk factors already identified, there is still no fully satisfactory explanation for the mechanisms underlying the onset of the disease. Also, as with other complex human diseases, the causes of low heritability are unclear. Epigenetic mechanisms, in which changes in gene expression do not depend on changes in genotype, have attracted considerable attention in recent years and are key to understanding the processes that influence age-related changes and various neurological diseases. With the recent use of massive sequencing techniques, methods for studying epigenome variations in AD have also evolved tremendously, allowing the discovery of differentially expressed disease traits under different conditions and experimental settings. This is important for understanding disease development and for unlocking new potential AD therapies. In this work, we outline the genomic and epigenomic components involved in the initiation and development of AD and identify potentially effective therapeutic targets for disease control.
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Affiliation(s)
- Rubén Rabaneda-Bueno
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic
- School of Biological Sciences, James Clerk Maxwell Building, The King’s Buildings Campus, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Beatriz Mena-Montes
- Laboratorio de Biología del Envejecimiento, Departamento de Investigación Básica, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Sara Torres-Castro
- Departamento de Epidemiología Demográfica y Determinantes Sociales, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
| | - Nora Magdalena Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
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19
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HDAC6 Negatively Regulates miR-155-5p Expression to Elicit Proliferation by Targeting RHEB in Microvascular Endothelial Cells under Mechanical Unloading. Int J Mol Sci 2021; 22:ijms221910527. [PMID: 34638868 PMCID: PMC8508889 DOI: 10.3390/ijms221910527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 12/20/2022] Open
Abstract
Mechanical unloading contributes to significant cardiovascular deconditioning. Endothelial dysfunction in the sites of microcirculation may be one of the causes of the cardiovascular degeneration induced by unloading, but the detailed mechanism is still unclear. Here, we first demonstrated that mechanical unloading inhibited brain microvascular endothelial cell proliferation and downregulated histone deacetylase 6 (HDAC6) expression. Furthermore, HDAC6 promoted microvascular endothelial cell proliferation and attenuated the inhibition of proliferation caused by clinorotation unloading. To comprehensively identify microRNAs (miRNAs) that are regulated by HDAC6, we analyzed differential miRNA expression in microvascular endothelial cells after transfection with HDAC6 siRNA and selected miR-155-5p, which was the miRNA with the most significantly increased expression. The ectopic expression of miR-155-5p inhibited microvascular endothelial cell proliferation and directly downregulated Ras homolog enriched in brain (RHEB) expression. Moreover, RHEB expression was downregulated under mechanical unloading and was essential for the miR-155-5p-mediated promotion of microvascular endothelial cell proliferation. Taken together, these results are the first to elucidate the role of HDAC6 in unloading-induced cell growth inhibition through the miR-155-5p/RHEB axis, suggesting that the HDAC6/miR-155-5p/RHEB pathway is a specific target for the preventative treatment of cardiovascular deconditioning.
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20
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Velasco G, Ulveling D, Rondeau S, Marzin P, Unoki M, Cormier-Daire V, Francastel C. Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders. Int J Mol Sci 2021; 22:3735. [PMID: 33916664 PMCID: PMC8038329 DOI: 10.3390/ijms22073735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation (DNAme) profiling is used to establish specific biomarkers to improve the diagnosis of patients with inherited neurodevelopmental disorders and to guide mutation screening. In the specific case of mendelian disorders of the epigenetic machinery, it also provides the basis to infer mechanistic aspects with regard to DNAme determinants and interplay between histone and DNAme that apply to humans. Here, we present comparative methylomes from patients with mutations in the de novo DNA methyltransferases DNMT3A and DNMT3B, in their catalytic domain or their N-terminal parts involved in reading histone methylation, or in histone H3 lysine (K) methylases NSD1 or SETD2 (H3 K36) or KMT2D/MLL2 (H3 K4). We provide disease-specific DNAme signatures and document the distinct consequences of mutations in enzymes with very similar or intertwined functions, including at repeated sequences and imprinted loci. We found that KMT2D and SETD2 germline mutations have little impact on DNAme profiles. In contrast, the overlapping DNAme alterations downstream of NSD1 or DNMT3 mutations underlines functional links, more specifically between NSD1 and DNMT3B at heterochromatin regions or DNMT3A at regulatory elements. Together, these data indicate certain discrepancy with the mechanisms described in animal models or the existence of redundant or complementary functions unforeseen in humans.
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Affiliation(s)
- Guillaume Velasco
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
| | - Damien Ulveling
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
| | - Sophie Rondeau
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Pauline Marzin
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
| | - Valérie Cormier-Daire
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Claire Francastel
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
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21
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Current Therapies in Nephrotic Syndrome: HDAC inhibitors, an Emerging Therapy for Kidney Diseases. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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22
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Zwergel C, Di Bello E, Fioravanti R, Conte M, Nebbioso A, Mazzone R, Brosch G, Mercurio C, Varasi M, Altucci L, Valente S, Mai A. Novel Pyridine-Based Hydroxamates and 2'-Aminoanilides as Histone Deacetylase Inhibitors: Biochemical Profile and Anticancer Activity. ChemMedChem 2020; 16:989-999. [PMID: 33220015 DOI: 10.1002/cmdc.202000854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 12/31/2022]
Abstract
Starting from the N-hydroxy-3-(4-(2-phenylbutanoyl)amino)phenyl)acrylamide (5 b) previously described by us as a HDAC inhibitor, we prepared four aza-analogues, 6-8, 9 b, as regioisomers containing the pyridine nucleus. Preliminary screening against mHDAC1 highlighted the N-hydroxy-5-(2-(2-phenylbutanoyl)amino)pyridyl)acrylamide (9 b) as the most potent inhibitor. Thus, we further developed both pyridylacrylic- and nicotinic-based hydroxamates (9 a, 9 c-f, and 11 a-f) and 2'-aminoanilides (10 a-f and 12 a-f), related to 9 b, to be tested against HDACs. Among them, the nicotinic hydroxamate 11 d displayed sub-nanomolar potency (IC50 : 0.5 nM) and selectivity up to 34 000 times that of HDAC4 and from 100 to 1300 times that of all the other tested HDAC isoforms. The 2'-aminoanilides were class I-selective HDAC inhibitors, generally more potent against HDAC3, with the nicotinic anilide 12 d being the most effective (IC50 HDAC3 =0.113 μM). When tested in U937 leukemia cells, the hydroxamates 9 e, 11 c, and 11 d blocked over 80 % of cells in G2/M phase, whereas the anilides did not alter cell-cycle progress. In the same cell line, the hydroxamate 11 c and the anilide 10 b induced about 30 % apoptosis, and the anilide 12 c displayed about 40 % cytodifferentiation. Finally, the most potent compounds in leukemia cells 9 b, 11 c, 10 b, 10 e, and 12 c were also tested in K562, HCT116, and A549 cancer cells, displaying antiproliferative IC50 values at single-digit to sub-micromolar level.
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Affiliation(s)
- Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro, 500185, Rome, Italy
| | - Elisabetta Di Bello
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro, 500185, Rome, Italy
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro, 500185, Rome, Italy
| | - Mariarosaria Conte
- Department of Precision Medicine Università degli Studi della Campania Luigi Vanvitelli, Vico L. De Crecchio 7, 80138, Naples, Italy
| | - Angela Nebbioso
- Department of Precision Medicine Università degli Studi della Campania Luigi Vanvitelli, Vico L. De Crecchio 7, 80138, Naples, Italy
| | - Roberta Mazzone
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro, 500185, Rome, Italy
| | - Gerald Brosch
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ciro Mercurio
- Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Mario Varasi
- Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Lucia Altucci
- Department of Precision Medicine Università degli Studi della Campania Luigi Vanvitelli, Vico L. De Crecchio 7, 80138, Naples, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro, 500185, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro, 500185, Rome, Italy
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23
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Pulya S, Amin SA, Adhikari N, Biswas S, Jha T, Ghosh B. HDAC6 as privileged target in drug discovery: A perspective. Pharmacol Res 2020; 163:105274. [PMID: 33171304 DOI: 10.1016/j.phrs.2020.105274] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/15/2020] [Accepted: 10/25/2020] [Indexed: 12/25/2022]
Abstract
HDAC6, a class IIB HDAC isoenzyme, stands unique in its structural and physiological functions. Besides histone modification, largely due to its cytoplasmic localization, HDAC6 also targets several non-histone proteins including Hsp90, α-tubulin, cortactin, HSF1, etc. Thus, it is one of the key regulators of different physiological and pathological disease conditions. HDAC6 is involved in different signaling pathways associated with several neurological disorders, various cancers at early and advanced stage, rare diseases and immunological conditions. Therefore, targeting HDAC6 has been found to be effective for various therapeutic purposes in recent years. Though several HDAC6 inhibitors (HDAC6is) have been developed till date, only two ACY-1215 (ricolinostat) and ACY-241 (citarinostat) are in the clinical trials. A lot of work is still needed to pinpoint strictly selective as well as potent HDAC6i. Considering the recent crystal structure of HDAC6, novel HDAC6is of significant therapeutic value can be designed. Notably, the canonical pharmacophore features of HDAC6is consist of a zinc binding group (ZBG), a linker function and a cap group. Significant modifications of cap function may lead to achieve better selectivity of the inhibitors. This review details the study about the structural biology of HDAC6, the physiological and pathological role of HDAC6 in several disease states and the detailed structure-activity relationships (SARs) of the known HDAC6is. This detailed review will provide key insights to design novel and highly effective HDAC6i in the future.
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Affiliation(s)
- Sravani Pulya
- Epigenetic Research Laboratory, Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata 700032, India
| | - Swati Biswas
- Epigenetic Research Laboratory, Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata 700032, India.
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
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24
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Elmezayen AD, Yelekçi K. Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes. J Biomol Struct Dyn 2020; 39:6396-6414. [PMID: 32715940 DOI: 10.1080/07391102.2020.1798812] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have no crystal structures, such as HDAC5 and HDAC9. Lacking proper and suitable crystal structure is obstructing the designing of appropriate isoform selective inhibitors. Here in this study, we constructed human HDAC5 and HDAC9 protein models using human HDAC4 (PDB:2VQM_A) as a template by the means of homology modeling approach. Based on the Z-score of the built models, model M0014 of HDAC5 and model M0020 of HDAC9 were selected. The models were verified by MODELLER and validated using the Web-based PROCHECK server. All selected known inhibitors displayed reasonable binding modes and equivalent predicted Ki values in comparison to the experimental binding affinities (Ki/IC50). The known inhibitor Rac26 showed the best binding affinity for HDAC5, while TMP269 showed the best binding affinity for HDAC9. The best two compounds, CHEMBL2114980 and CHEMBL217223, had relatively similar inhibition constants against HDAC5 and HDAC9. The built models and their complexes were subjected to molecular dynamic simulations (MD) for 100 ns. Examining the MD simulation results of all studied structures, including the RMSD, RMSF, radius of gyration and potential energy suggested the stability and reliability of the built models. Accordingly, the results obtained in this study could be used for designing de novo inhibitors against HDAC5 and HDAC9. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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25
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Shpargel KB, Mangini CL, Xie G, Ge K, Magnuson T. The KMT2D Kabuki syndrome histone methylase controls neural crest cell differentiation and facial morphology. Development 2020; 147:dev.187997. [PMID: 32541010 DOI: 10.1242/dev.187997] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Kabuki syndrome (KS) is a congenital craniofacial disorder resulting from mutations in the KMT2D histone methylase (KS1) or the UTX histone demethylase (KS2). With small cohorts of KS2 patients, it is not clear whether differences exist in clinical manifestations relative to KS1. We mutated KMT2D in neural crest cells (NCCs) to study cellular and molecular functions in craniofacial development with respect to UTX. Similar to UTX, KMT2D NCC knockout mice demonstrate hypoplasia with reductions in frontonasal bone lengths. We have traced the onset of KMT2D and UTX mutant NCC frontal dysfunction to a stage of altered osteochondral progenitor differentiation. KMT2D NCC loss-of-function does exhibit unique phenotypes distinct from UTX mutation, including fully penetrant cleft palate, mandible hypoplasia and deficits in cranial base ossification. KMT2D mutant NCCs lead to defective secondary palatal shelf elevation with reduced expression of extracellular matrix components. KMT2D mutant chondrocytes in the cranial base fail to properly differentiate, leading to defective endochondral ossification. We conclude that KMT2D is required for appropriate cranial NCC differentiation and KMT2D-specific phenotypes may underlie differences between Kabuki syndrome subtypes.
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Affiliation(s)
- Karl B Shpargel
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Cassidy L Mangini
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Guojia Xie
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Terry Magnuson
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
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26
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Squeo GM, Augello B, Massa V, Milani D, Colombo EA, Mazza T, Castellana S, Piccione M, Maitz S, Petracca A, Prontera P, Accadia M, Della Monica M, Di Giacomo MC, Melis D, Selicorni A, Giglio S, Fischetto R, Di Fede E, Malerba N, Russo M, Castori M, Gervasini C, Merla G. Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder. J Med Genet 2020; 57:760-768. [PMID: 32170002 DOI: 10.1136/jmedgenet-2019-106724] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods for testing multiple genes simultaneously is a logical step for the implementation of diagnostics of these disorders. METHODS We screened a heterogeneous cohort of 263 index patients by an NGS-targeted panel, containing 68 genes associated with more than 40 OMIM entries affecting chromatin function. RESULTS This strategy allowed us to identify clinically relevant variants in 87 patients (32%), including 30 for which an alternative clinical diagnosis was proposed after sequencing analysis and clinical re-evaluation. CONCLUSION Our findings indicate that this approach is effective not only in disorders with locus heterogeneity, but also in order to anticipate unexpected misdiagnoses due to clinical overlap among cognate disorders. Finally, this work highlights the utility of a prompt diagnosis in such a clinically and genetically heterogeneous group of disorders that we propose to group under the umbrella term of chromatinopathies.
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Affiliation(s)
- Gabriella Maria Squeo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Donatella Milani
- UOSD Pediatria ad alta intensità di cura, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Adele Colombo
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Antonio Petracca
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Italy
| | - Matteo Della Monica
- Medical Genetics Unit, Cardarelli Hospital, Largo A Cardarelli, Napoli, Italy
| | | | - Daniela Melis
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna General Hospital, Como, Italy
| | - Sabrina Giglio
- Department of Biomedical, Experimental and Clinical Sciences 'Mario Serio', Medical Genetics Unit, University Hospital Meyer, Firenze, Italy
| | - Rita Fischetto
- Metabolic Diseases, Clinical Genetics and Diabetology Unit, Paediatric Hospital Giovanni XXIII, Bari, Italy
| | - Elisabetta Di Fede
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Matteo Russo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Cristina Gervasini
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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27
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Kiany S, Harrison D, Gordon N. The Histone Deacetylase Inhibitor Entinostat/Syndax 275 in Osteosarcoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1257:75-83. [PMID: 32483732 DOI: 10.1007/978-3-030-43032-0_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The prognosis for metastatic osteosarcoma (OS) is poor and has not changed in several decades. Therapeutic paradigms that target and exploit novel molecular pathways are desperately needed. Recent preclinical data suggests that modulation of the Fas/FasL pathway may offer benefit in the treatment of refractory osteosarcoma. Fas and FasL are complimentary receptor-ligand proteins. Fas is expressed in multiple tissues, whereas FasL is restricted to privilege organs, such as the lung. Fas expression has been shown to inversely correlate with the metastatic potential of OS cells; tumor cells which express high levels of Fas have decreased metastatic potential and the ones that reach the lung undergo cell death upon interaction with constitutive FasL in the lung. Agents such as gemcitabine and the HDAC inhibitor, entinostat/Syndax 275, have been shown to upregulate Fas expression on OS cells, potentially leading to decreased OS pulmonary metastasis and improved outcome. Clinical trials are in development to evaluate this combination as a potential treatment option for patients with refractory OS.
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Affiliation(s)
- Simin Kiany
- Department of Pediatrics Research, MD Anderson Cancer Center, Houston, TX, USA
| | - Douglas Harrison
- Department of Pediatrics - Patient Care, MD Anderson Cancer Center, Houston, TX, USA
| | - Nancy Gordon
- Department of Pediatrics Research, MD Anderson Cancer Center, Houston, TX, USA.
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28
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Cytrynbaum C, Choufani S, Weksberg R. Epigenetic signatures in overgrowth syndromes: Translational opportunities. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:491-501. [PMID: 31828978 DOI: 10.1002/ajmg.c.31745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/04/2019] [Accepted: 09/12/2019] [Indexed: 12/21/2022]
Abstract
In recent years, numerous overgrowth syndromes have been found to be caused by pathogenic DNA sequence variants in "epigenes," genes that encode proteins that function in epigenetic regulation. Epigenetic marks, including DNA methylation (DNAm), histone modifications and chromatin conformation, have emerged as a vital genome-wide regulatory mechanism that modulate the transcriptome temporally and spatially to drive normal developmental and cellular processes. Evidence suggests that epigenetic marks are layered and engage in crosstalk, in that disruptions of any one component of the epigenetic machinery impact the others. This interdependence of epigenetic marks underpins the recent identification of gene-specific DNAm signatures for a variety of disorders caused by pathogenic variants in epigenes. Here, we discuss the power of DNAm signatures with respect to furthering our understanding of disease pathophysiology, enhancing the efficacy of molecular diagnostics and identifying new targets for therapeutics of overgrowth syndromes. These findings highlight the promise of the field of epigenomics to provide unprecedented insights into disease mechanisms generating a host of opportunities to advance precision medicine.
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Affiliation(s)
- Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario.,Department of Pediatrics, University of Toronto, Toronto, Ontario.,Institute of Medical Science, University of Toronto, Toronto, Ontario
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29
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
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MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
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Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
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30
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Brindisi M, Saraswati AP, Brogi S, Gemma S, Butini S, Campiani G. Old but Gold: Tracking the New Guise of Histone Deacetylase 6 (HDAC6) Enzyme as a Biomarker and Therapeutic Target in Rare Diseases. J Med Chem 2019; 63:23-39. [PMID: 31415174 DOI: 10.1021/acs.jmedchem.9b00924] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic regulation orchestrates many cellular processes and greatly influences key disease mechanisms. Histone deacetylase (HDAC) enzymes play a crucial role either as biomarkers or therapeutic targets owing to their involvement in specific pathophysiological pathways. Beyond their well-characterized role as histone modifiers, HDACs also interact with several nonhistone substrates and their increased expression has been highlighted in specific diseases. The HDAC6 isoform, due to its unique cytoplasmic localization, modulates the acetylation status of tubulin, HSP90, TGF-β, and peroxiredoxins. HDAC6 also exerts noncatalytic activities through its interaction with ubiquitin. Both catalytic and noncatalytic functions of HDACs are being actively studied in the field of specific rare disorders beyond the well-established role in carcinogenesis. This Perspective outlines the application of HDAC(6) inhibitors in rare diseases, such as Rett syndrome, inherited retinal disorders, idiopathic pulmonary fibrosis, and Charcot-Marie-Tooth disease, highlighting their therapeutic potential as innovative and targeted disease-modifying agents.
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Affiliation(s)
- Margherita Brindisi
- Department of Pharmacy, Department of Excellence 2018-2022 , University of Naples Federico II , Via D. Montesano 49 , I-80131 Naples , Italy
| | - A Prasanth Saraswati
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
| | - Simone Brogi
- Department of Pharmacy , University of Pisa , via Bonanno 6 , 56126 , Pisa , Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 , Siena , Italy
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31
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Abstract
Biomarker discovery and validation are necessary for improving the prediction of clinical outcomes and patient monitoring. Despite considerable interest in biomarker discovery and development, improvements in the range and quality of biomarkers are still needed. The main challenge is how to integrate preclinical data to obtain a reliable biomarker that can be measured with acceptable costs in routine clinical practice. Epigenetic alterations are already being incorporated as valuable candidates in the biomarker field. Furthermore, their reversible nature offers a promising opportunity to ameliorate disease symptoms by using epigenetic-based therapy. Thus, beyond helping to understand disease biology, clinical epigenetics is being incorporated into patient management in oncology, as well as being explored for clinical applicability for other human pathologies such as neurological and infectious diseases and immune system disorders.
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32
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Martínez-Cano J, Campos-Sánchez E, Cobaleda C. Epigenetic Priming in Immunodeficiencies. Front Cell Dev Biol 2019; 7:125. [PMID: 31355198 PMCID: PMC6635466 DOI: 10.3389/fcell.2019.00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Immunodeficiencies (IDs) are disorders of the immune system that increase susceptibility to infections and cancer, and are therefore associated with elevated morbidity and mortality. IDs can be primary (not caused by other condition or exposure) or secondary due to the exposure to different agents (infections, chemicals, aging, etc.). Most primary immunodeficiencies (PIDs) are of genetic origin, caused by mutations affecting genes with key roles in the development or function of the cells of the immune system. A large percentage of PIDs are associated with a defective development and/or function of lymphocytes and, especially, B cells, the ones in charge of generating the different types of antibodies. B-cell development is a tightly regulated process in which many different factors participate. Among the regulators of B-cell differentiation, a correct epigenetic control of cellular identity is essential for normal cell function. With the advent of next-generation sequencing (NGS) techniques, more and more alterations in different types of epigenetic regulators are being described at the root of PIDs, both in humans and in animal models. At the same time, it is becoming increasingly clear that epigenetic alterations triggered by the exposure to environmental agents have a key role in the development of secondary immunodeficiencies (SIDs). Due to their largely reversible nature, epigenetic modifications are quickly becoming key therapeutic targets in other diseases where their contribution has been known for more time, like cancer. Here, we establish a parallelism between IDs and the nowadays accepted role of epigenetics in cancer initiation and progression, and propose that epigenetics forms a "third axis" (together with genetics and external agents) to be considered in the etiology of IDs, and linking PIDs and SIDs at the molecular level. We therefore postulate that IDs arise due to a variable contribution of (i) genetic, (ii) environmental, and (iii) epigenetic causes, which in fact form a continuum landscape of all possible combinations of these factors. Additionally, this implies the possibility of a fully epigenetically triggered mechanism for some IDs. This concept would have important prophylactic and translational implications, and would also imply a more blurred frontier between primary and secondary immunodeficiencies.
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Affiliation(s)
| | | | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas –Universidad Autónoma de Madrid), Madrid, Spain
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33
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Nguyen KV. Potential epigenomic co-management in rare diseases and epigenetic therapy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:752-780. [PMID: 31079569 DOI: 10.1080/15257770.2019.1594893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The purpose of this review is to highlight the impact of the alternative splicing process on human disease. Epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced. The recent progress in the field of epigenetics has important implications for the study of rare diseases. The role of epigenetics in rare diseases is a key issue in molecular physiology and medicine because not only rare diseases can benefit from epigenetic research, but can also provide useful principles for other common and complex disorders such as cancer, cardiovascular, type 2 diabetes, obesity, and neurological diseases. Predominantly, epigenetic modifications include DNA methylation, histone modification, and RNA-associated silencing. These modifications in the genome regulate numerous cellular activities. Disruption of epigenetic regulation process can contribute to the etiology of numerous diseases during both prenatal and postnatal life. Here, I discuss current knowledge about this matter including some current epigenetic therapies and future directions in the field by emphasizing on the RNA-based therapy via antisense oligonucleotides to correct splicing defects.
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Affiliation(s)
- Khue Vu Nguyen
- a Department of Medicine, Biochemical Genetics and Metabolism, The Mitochondrial and Metabolic Disease Center, School of Medicine, University of California, San Diego , San Diego , CA , USA.,b Department of Pediatrics, UC San Diego School of Medicine , La Jolla , CA , USA
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34
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Suh JL, Barnash KD, Abramyan TM, Li F, The J, Engelberg IA, Vedadi M, Brown PJ, Kireev DB, Arrowsmith CH, James LI, Frye SV. Discovery of selective activators of PRC2 mutant EED-I363M. Sci Rep 2019; 9:6524. [PMID: 31024026 PMCID: PMC6484020 DOI: 10.1038/s41598-019-43005-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/12/2019] [Indexed: 01/08/2023] Open
Abstract
Many common disease-causing mutations result in loss-of-function (LOF) of the proteins in which they occur. LOF mutations have proven recalcitrant to pharmacologic intervention, presenting a challenge for the development of targeted therapeutics. Polycomb repressive complex 2 (PRC2), which contains core subunits (EZH2, EED, and SUZ12), regulates gene activity by trimethylation of histone 3 lysine 27. The dysregulation of PRC2 catalytic activity by mutations has been implicated in cancer and other diseases. Among the mutations that cause PRC2 malfunction, an I363M LOF mutation of EED has been identified in myeloid disorders, where it prevents allosteric activation of EZH2 catalysis. We describe structure-based design and computational simulations of ligands created to ameliorate this LOF. Notably, these compounds selectively stimulate the catalytic activity of PRC2-EED-I363M over wildtype-PRC2. Overall, this work demonstrates the feasibility of developing targeted therapeutics for PRC2-EED-I363M that act as allosteric agonists, potentially correcting this LOF mutant phenotype.
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Affiliation(s)
- Junghyun L Suh
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Kimberly D Barnash
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Foghorn Therapeutics, Cambridge, MA, 02142, USA
| | - Tigran M Abramyan
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Juliana The
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Isabelle A Engelberg
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Dmitri B Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada. .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 2M9, Canada.
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.
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35
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Sadikovic B, Aref-Eshghi E, Levy MA, Rodenhiser D. DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype. Epigenomics 2019; 11:563-575. [PMID: 30875234 DOI: 10.2217/epi-2018-0192] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS). We propose that these episignatures be considered as echoes and/or legacies of the initiating mutational events within proteins of the so-called epigenetic machinery. As well, we discuss approaches to directly confirm the functional consequences and the implications of these episignatures to patient management and treatment.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - David Rodenhiser
- Departments of Pediatrics, Biochemistry & Oncology, Western University, London, ON, N6A 3K7, Canada.,Children's Health Research Institute & Lawson Health Research Institute, London, ON, N6C 2V5, Canada.,London Regional Cancer Program, Lawson Health Research Institute, London, ON, N6A 5W9, Canada
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Abstract
PURPOSE OF REVIEW Sotos syndrome is among a growing list of disorders resulting from mutations in epigenetic machinery genes. These Mendelian disorders of the epigenetic machinery (MDEMs) exhibit phenotypic overlap broadly characterized by intellectual disability and atypical growth and behaviors. Manifestations of Sotos syndrome include a distinct facial appearance, overgrowth, intellectual disability, and behavioral issues. Herein we review key aspects of Sotos syndrome, focusing on the neurobehavioral phenotype. Additionally, we highlight recent advances in our understanding of molecular pathogenesis implicating epigenetic mechanisms. RECENT FINDINGS Increasing evidence suggests MDEMs account for ∼19% of intellectual disability and ∼45% of overgrowth combined with intellectual disability, with Sotos syndrome constituting most of the latter. Although the genetic cause of Sotos syndrome, disruption of the histone methyltransferase writer NSD1, is well established, recent studies have further delineated the neurobehavioral phenotype and provided insight into disease pathogenesis. Explicitly, NSD1 target genes accounting for a subset of Sotos syndrome features and a specific DNA methylation signature have been identified. SUMMARY Sotos syndrome is, therefore, a genetic disorder with epigenetic consequences. Its characteristic neurobehavioral phenotype and those of related MDEMs illustrate the essential role epigenetic mechanisms play in neurologic development. Improvement in our understanding of molecular pathogenesis has important implications for development of diagnostic tests and therapeutic interventions.
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Campos-Sanchez E, Martínez-Cano J, Del Pino Molina L, López-Granados E, Cobaleda C. Epigenetic Deregulation in Human Primary Immunodeficiencies. Trends Immunol 2018; 40:49-65. [PMID: 30509895 DOI: 10.1016/j.it.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are immune disorders resulting from defects in genes involved in immune regulation, and manifesting as an increased susceptibility to infections, autoimmunity, and cancer. However, the molecular basis of some prevalent entities remains poorly understood. Epigenetic control is essential for immune functions, and epigenetic alterations have been identified in different PIDs, including syndromes such as immunodeficiency-centromeric-instability-facial-anomalies, Kabuki, or Wolf-Hirschhorn, among others. Although the epigenetic changes may differ among these PIDs, the reversibility of epigenetic modifications suggests that they might become potential therapeutic targets. Here, we review recent mechanistic advances in our understanding of epigenetic alterations associated with certain PIDs, propose that a fully epigenetically driven mechanism might underlie some PIDs, and discuss the possible prophylactic and therapeutic implications.
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Affiliation(s)
- Elena Campos-Sanchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Lucía Del Pino Molina
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain.
| | - Cesar Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain.
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38
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Bessa DS, Maschietto M, Aylwin CF, Canton APM, Brito VN, Macedo DB, Cunha-Silva M, Palhares HMC, de Resende EAMR, Borges MDF, Mendonca BB, Netchine I, Krepischi ACV, Lomniczi A, Ojeda SR, Latronico AC. Methylome profiling of healthy and central precocious puberty girls. Clin Epigenetics 2018; 10:146. [PMID: 30466473 PMCID: PMC6251202 DOI: 10.1186/s13148-018-0581-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022] Open
Abstract
Background Recent studies demonstrated that changes in DNA methylation (DNAm) and inactivation of two imprinted genes (MKRN3 and DLK1) alter the onset of female puberty. We aimed to investigate the association of DNAm profiling with the timing of human puberty analyzing the genome-wide DNAm patterns of peripheral blood leukocytes from ten female patients with central precocious puberty (CPP) and 33 healthy girls (15 pre- and 18 post-pubertal). For this purpose, we performed comparisons between the groups: pre- versus post-pubertal, CPP versus pre-pubertal, and CPP versus post-pubertal. Results Analyzing the methylome changes associated with normal puberty, we identified 120 differentially methylated regions (DMRs) when comparing pre- and post-pubertal healthy girls. Most of these DMRs were hypermethylated in the pubertal group (99%) and located on the X chromosome (74%). Only one genomic region, containing the promoter of ZFP57, was hypomethylated in the pubertal group. ZFP57 is a transcriptional repressor required for both methylation and imprinting of multiple genomic loci. ZFP57 expression in the hypothalamus of female rhesus monkeys increased during peripubertal development, suggesting enhanced repression of downstream ZFP57 target genes. Fourteen other zinc finger (ZNF) genes were related to the hypermethylated DMRs at normal puberty. Analyzing the methylome changes associated with CPP, we demonstrated that the patients with CPP exhibited more hypermethylated CpG sites compared to both pre-pubertal (81%) and pubertal (89%) controls. Forty-eight ZNF genes were identified as having hypermethylated CpG sites in CPP. Conclusion Methylome profiling of girls at normal and precocious puberty revealed a widespread pattern of DNA hypermethylation, indicating that the pubertal process in humans is associated with specific changes in epigenetically driven regulatory control. Moreover, changes in methylation of several ZNF genes appear to be a distinct epigenetic modification underlying the initiation of human puberty. Electronic supplementary material The online version of this article (10.1186/s13148-018-0581-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Danielle S Bessa
- Division of Endocrinology & Metabolism, Development Endocrinology Unit, Laboratory of Hormones and Molecular Genetics/LIM42, Clinical Hospital, Sao Paulo Medical School, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | | | - Ana P M Canton
- Division of Endocrinology & Metabolism, Development Endocrinology Unit, Laboratory of Hormones and Molecular Genetics/LIM42, Clinical Hospital, Sao Paulo Medical School, University of Sao Paulo, Sao Paulo, SP, Brazil.,Sorbonne Université, INSERM, UMR_S 938 Centre de Recherche Saint Antoine, APHP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes, Paris, France
| | - Vinicius N Brito
- Division of Endocrinology & Metabolism, Development Endocrinology Unit, Laboratory of Hormones and Molecular Genetics/LIM42, Clinical Hospital, Sao Paulo Medical School, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Delanie B Macedo
- Division of Endocrinology & Metabolism, Development Endocrinology Unit, Laboratory of Hormones and Molecular Genetics/LIM42, Clinical Hospital, Sao Paulo Medical School, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Marina Cunha-Silva
- Division of Endocrinology & Metabolism, Development Endocrinology Unit, Laboratory of Hormones and Molecular Genetics/LIM42, Clinical Hospital, Sao Paulo Medical School, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Heloísa M C Palhares
- Division of Endocrinology, Triangulo Mineiro Federal University, Uberaba, MG, Brazil
| | | | | | - Berenice B Mendonca
- Division of Endocrinology & Metabolism, Development Endocrinology Unit, Laboratory of Hormones and Molecular Genetics/LIM42, Clinical Hospital, Sao Paulo Medical School, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Irene Netchine
- Sorbonne Université, INSERM, UMR_S 938 Centre de Recherche Saint Antoine, APHP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes, Paris, France
| | - Ana C V Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Alejandro Lomniczi
- Division of Genetics, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA.,Division of Neuroscience, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA
| | - Sergio R Ojeda
- Division of Neuroscience, Oregon National Primate Research Center/OHSU, Beaverton, OR, USA
| | - Ana Claudia Latronico
- Division of Endocrinology & Metabolism, Development Endocrinology Unit, Laboratory of Hormones and Molecular Genetics/LIM42, Clinical Hospital, Sao Paulo Medical School, University of Sao Paulo, Sao Paulo, SP, Brazil. .,Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, Departamento de Clínica Médica, Disciplina de Endocrinologia e Metabologia, Av. Dr. Enéas de Carvalho Aguiar, 255, 7° andar, sala 7037, São Paulo, CEP: 05403-900, Brazil.
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Dual Requirement of CHD8 for Chromatin Landscape Establishment and Histone Methyltransferase Recruitment to Promote CNS Myelination and Repair. Dev Cell 2018; 45:753-768.e8. [PMID: 29920279 DOI: 10.1016/j.devcel.2018.05.022] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/16/2018] [Accepted: 05/19/2018] [Indexed: 01/02/2023]
Abstract
Disruptive mutations in chromatin remodeler CHD8 cause autism spectrum disorders, exhibiting widespread white matter abnormalities; however, the underlying mechanisms remain elusive. We show that cell-type specific Chd8 deletion in oligodendrocyte progenitors, but not in neurons, results in myelination defects, revealing a cell-intrinsic dependence on CHD8 for oligodendrocyte lineage development, myelination and post-injury remyelination. CHD8 activates expression of BRG1-associated SWI/SNF complexes that in turn activate CHD7, thus initiating a successive chromatin remodeling cascade that orchestrates oligodendrocyte lineage progression. Genomic occupancy analyses reveal that CHD8 establishes an accessible chromatin landscape, and recruits MLL/KMT2 histone methyltransferase complexes distinctively around proximal promoters to promote oligodendrocyte differentiation. Inhibition of histone demethylase activity partially rescues myelination defects of CHD8-deficient mutants. Our data indicate that CHD8 exhibits a dual function through inducing a cascade of chromatin reprogramming and recruiting H3K4 histone methyltransferases to establish oligodendrocyte identity, suggesting potential strategies of therapeutic intervention for CHD8-associated white matter defects.
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40
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Sekiguchi K, Itonaga T, Maeda T, Fukami M, Yorifuji T, Ihara K. A case of CHARGE syndrome associated with hyperinsulinemic hypoglycemia in infancy. Eur J Med Genet 2018; 61:312-314. [DOI: 10.1016/j.ejmg.2018.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/30/2017] [Accepted: 01/13/2018] [Indexed: 10/18/2022]
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41
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de Valles-Ibáñez G, Esteve-Solé A, Piquer M, González-Navarro EA, Hernandez-Rodriguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez Á, Martín-Nalda A, Martínez-Gallo M, García-Prat M, Del Pino-Molina L, Cuscó I, Codina-Solà M, Batlle-Masó L, Solís-Moruno M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobran R, Yagüe J, Alsina L, Juan M, Casals F. Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond. Front Immunol 2018; 9:636. [PMID: 29867916 PMCID: PMC5960686 DOI: 10.3389/fimmu.2018.00636] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2018] [Indexed: 12/16/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency characterized by recurrent infections, hypogammaglobulinemia and poor response to vaccines. Its diagnosis is made based on clinical and immunological criteria, after exclusion of other diseases that can cause similar phenotypes. Currently, less than 20% of cases of CVID have a known underlying genetic cause. We have analyzed whole-exome sequencing and copy number variants data of 36 children and adolescents diagnosed with CVID and healthy relatives to estimate the proportion of monogenic cases. We have replicated an association of CVID to p.C104R in TNFRSF13B and reported the second case of homozygous patient to date. Our results also identify five causative genetic variants in LRBA, CTLA4, NFKB1, and PIK3R1, as well as other very likely causative variants in PRKCD, MAPK8, or DOCK8 among others. We experimentally validate the effect of the LRBA stop-gain mutation which abolishes protein production and downregulates the expression of CTLA4, and of the frameshift indel in CTLA4 producing expression downregulation of the protein. Our results indicate a monogenic origin of at least 15–24% of the CVID cases included in the study. The proportion of monogenic patients seems to be lower in CVID than in other PID that have also been analyzed by whole exome or targeted gene panels sequencing. Regardless of the exact proportion of CVID monogenic cases, other genetic models have to be considered for CVID. We propose that because of its prevalence and other features as intermediate penetrancies and phenotypic variation within families, CVID could fit with other more complex genetic scenarios. In particular, in this work, we explore the possibility of CVID being originated by an oligogenic model with the presence of heterozygous mutations in interacting proteins or by the accumulation of detrimental variants in particular immunological pathways, as well as perform association tests to detect association with rare genetic functional variation in the CVID cohort compared to healthy controls.
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Affiliation(s)
- Guillem de Valles-Ibáñez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ana Esteve-Solé
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Mònica Piquer
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - E Azucena González-Navarro
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Bioinformatics Studies, ESCI-UPF, Barcelona, Spain
| | - Eva González-Roca
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ana María Plaza-Martin
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Ángela Deyà-Martínez
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina García-Prat
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Lucía Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Ivón Cuscó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Marta Codina-Solà
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Laura Batlle-Masó
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Manuel Solís-Moruno
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Juan Ignacio Aróstegui
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Manel Juan
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
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42
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Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data. Oncotarget 2018; 7:61215-61228. [PMID: 27542205 PMCID: PMC5308646 DOI: 10.18632/oncotarget.11304] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/08/2016] [Indexed: 11/25/2022] Open
Abstract
Epigenetics regulations have an important role in fertilization and proper embryonic development, and several human diseases are associated with epigenetic modification disorders, such as Rett syndrome, Beckwith-Wiedemann syndrome and Angelman syndrome. However, the dynamics and functions of long non-coding RNAs (lncRNAs), one type of epigenetic regulators, in human pre-implantation development have not yet been demonstrated. In this study, a comprehensive analysis of human and mouse early-stage embryonic lncRNAs was performed based on public single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs are expressed in a developmental stage-specific manner during human early-stage embryonic development, whereas a more temporal-specific expression pattern was identified in mouse embryos. Weighted gene co-expression network analysis suggested that lncRNAs involved in human early-stage embryonic development are associated with several important functions and processes, such as oocyte maturation, zygotic genome activation and mitochondrial functions. We also found that the network of lncRNAs involved in zygotic genome activation was highly preservative between human and mouse embryos, whereas in other stages no strong correlation between human and mouse embryo was observed. This study provides insight into the molecular mechanism underlying lncRNA involvement in human pre-implantation embryonic development.
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43
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Porntaveetus T, Abid MF, Theerapanon T, Srichomthong C, Ohazama A, Kawasaki K, Kawasaki M, Suphapeetiporn K, Sharpe PT, Shotelersuk V. Expanding the Oro-Dental and Mutational Spectra of Kabuki Syndrome and Expression of KMT2D and KDM6A in Human Tooth Germs. Int J Biol Sci 2018; 14:381-389. [PMID: 29725259 PMCID: PMC5930470 DOI: 10.7150/ijbs.23517] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/26/2018] [Indexed: 12/12/2022] Open
Abstract
Kabuki syndrome is a rare genetic disorder characterized by distinct dysmorphic facial features, intellectual disability, and multiple developmental abnormalities. Despite more than 350 documented cases, the oro-dental spectrum associated with kabuki syndrome and expression of KMT2D (histone-lysine N-methyltransferase 2D) or KDM6A (lysine-specific demethylase 6A) genes in tooth development have not been well defined. Here, we report seven unrelated Thai patients with Kabuki syndrome having congenital absence of teeth, malocclusion, high-arched palate, micrognathia, and deviated tooth shape and size. Exome sequencing successfully identified that six patients were heterozygous for mutations in KMT2D, and one in KDM6A. Six were novel mutations, of which five were in KMT2D and one in KDM6A. They were truncating mutations including four frameshift deletions and two nonsense mutations. The predicted non-functional KMT2D and KDM6A proteins are expected to cause disease by haploinsufficiency. Our study expands oro-dental, medical, and mutational spectra associated with Kabuki syndrome. We also demonstrate for the first time that KMT2D and KDM6A are expressed in the dental epithelium of human tooth germs.
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Affiliation(s)
- Thantrira Porntaveetus
- Craniofacial Genetics and Stem Cells Research Group, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mushriq F Abid
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Thanakorn Theerapanon
- Excellence Center in Regenerative Dentistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Atsushi Ohazama
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | | | - Maiko Kawasaki
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
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44
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Myers TR, Amendola PG, Lussi YC, Salcini AE. JMJD-1.2 controls multiple histone post-translational modifications in germ cells and protects the genome from replication stress. Sci Rep 2018; 8:3765. [PMID: 29491442 PMCID: PMC5830613 DOI: 10.1038/s41598-018-21914-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 02/13/2018] [Indexed: 01/29/2023] Open
Abstract
Post-translational modifications of histones, constitutive components of chromatin, regulate chromatin compaction and control all DNA-based cellular processes. C. elegans JMJD-1.2, a member of the KDM7 family, is a demethylase active towards several lysine residues on Histone 3 (H3), but its contribution in regulating histone methylation in germ cells has not been fully investigated. Here, we show that jmjd-1.2 is expressed abundantly in the germline where it controls the level of histone 3 lysine 9, lysine 23 and lysine 27 di-methylation (H3K9/K23/K27me2) both in mitotic and meiotic cells. Loss of jmjd-1.2 is not associated with major defects in the germ cells in animals grown under normal conditions or after DNA damage induced by UV or ionizing irradiation. However, jmjd-1.2 mutants are more sensitive to replication stress and the progeny of mutant animals exposed to hydroxyurea show increased embryonic lethality and mutational rate, compared to wild-type. Thus, our results suggest a role for jmjd-1.2 in the maintenance of genome integrity after replication stress and emphasize the relevance of the regulation of histone methylation in genomic stability.
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Affiliation(s)
- Toshia R Myers
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Pier Giorgio Amendola
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Yvonne C Lussi
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
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45
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Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders. Nature 2018; 554:112-117. [PMID: 29364875 DOI: 10.1038/nature25449] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/11/2017] [Indexed: 02/06/2023]
Abstract
Many craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as transcription or ribosome biogenesis. Although it is understood that many of these malformations are a consequence of defects in cranial neural crest cells, a cell type that gives rise to most of the facial structures during embryogenesis, the mechanism underlying cell-type selectivity of these defects remains largely unknown. By exploring molecular functions of DDX21, a DEAD-box RNA helicase involved in control of both RNA polymerase (Pol) I- and II-dependent transcriptional arms of ribosome biogenesis, we uncovered a previously unappreciated mechanism linking nucleolar dysfunction, ribosomal DNA (rDNA) damage, and craniofacial malformations. Here we demonstrate that genetic perturbations associated with Treacher Collins syndrome, a craniofacial disorder caused by heterozygous mutations in components of the Pol I transcriptional machinery or its cofactor TCOF1 (ref. 1), lead to relocalization of DDX21 from the nucleolus to the nucleoplasm, its loss from the chromatin targets, as well as inhibition of rRNA processing and downregulation of ribosomal protein gene transcription. These effects are cell-type-selective, cell-autonomous, and involve activation of p53 tumour-suppressor protein. We further show that cranial neural crest cells are sensitized to p53-mediated apoptosis, but blocking DDX21 loss from the nucleolus and chromatin rescues both the susceptibility to apoptosis and the craniofacial phenotypes associated with Treacher Collins syndrome. This mechanism is not restricted to cranial neural crest cells, as blood formation is also hypersensitive to loss of DDX21 functions. Accordingly, ribosomal gene perturbations associated with Diamond-Blackfan anaemia disrupt DDX21 localization. At the molecular level, we demonstrate that impaired rRNA synthesis elicits a DNA damage response, and that rDNA damage results in tissue-selective and dosage-dependent effects on craniofacial development. Taken together, our findings illustrate how disruption in general regulators that compromise nucleolar homeostasis can result in tissue-selective malformations.
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46
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Powis Z, Farwell Hagman K, Mroske C, McWalter K, Cohen J, Colombo R, Serretti A, Fatemi A, David K, Reynolds J, Immken L, Nagakura H, Cunniff C, Payne K, Barbaro-Dieber T, Gripp K, Baker L, Stamper T, Aleck K, Jordan E, Hersh J, Burton J, Wentzensen I, Guillen Sacoto M, Willaert R, Cho M, Petrik I, Huether R, Tang S. Expansion and further delineation of the SETD5
phenotype leading to global developmental delay, variable dysmorphic features, and reduced penetrance. Clin Genet 2018; 93:752-761. [DOI: 10.1111/cge.13132] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Z. Powis
- Division of Emerging Genetics Medicine; Ambry Genetics; Aliso Viejo California
| | | | - C. Mroske
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | | | - J.S. Cohen
- Division of Neurogenetics, Hugo W. Moser Research Institute; Kennedy Krieger Institute; Baltimore Maryland
| | - R. Colombo
- Faculty of Medicine, Institute of Clinical Biochemistry; Catholic University and Policlinico Agostino Gemelli; Rome Italy
- Center for the Study of Rare Hereditary Disease; Niguarda Ca’ Granda Metropolitan Hospital; Milan Italy
| | - A. Serretti
- Department of Biomedical and NeuroMotor Sciences; University of Bologna; Bologna Italy
| | - A. Fatemi
- Division of Neurogenetics, Hugo W. Moser Research Institute; Kennedy Krieger Institute; Baltimore Maryland
- Department of Neurology and Pediatrics; The Johns Hopkins Hospital; Baltimore Maryland
| | - K.L. David
- Department of Medicine, Division of Genetics, New York Methodist Hospital; Brooklyn New York
| | - J. Reynolds
- Department of Medical Genetics, Shodair Children's Hospital; Helena Montana
| | - L. Immken
- Department of Genetics Specially for Children Genetics; Austin Texas
| | - H. Nagakura
- Department of Genetics Specially for Children Genetics; Austin Texas
| | - C.M. Cunniff
- Department of Pediatrics, Weill Cornell Medicine; New York New York
| | - K. Payne
- Child Neurology; Riley Hospital for Children; Indianapolis Indiana
| | - T. Barbaro-Dieber
- Department of Genetics, Cook Children's Medical Center; Fort Worth Texas
| | - K.W. Gripp
- Department of Genetics, Cook Children's Medical Center; Fort Worth Texas
| | - L. Baker
- Division of Medical Genetics; A.I. duPont Hospital for Children; Wilmington Delaware
| | - T. Stamper
- Department of Pediatrics, Section on Medical Genetics; Wake Forest Baptist Medical Center; Winston-Salem North Carolina
| | - K.A. Aleck
- Department of Genetics and Metabolism, Phoenix Children's Hospital; Phoenix Arizona
| | - E.S. Jordan
- Weisskopf Center, University of Louisville Clinical Genetics Unit; Louisville Kentucky
| | - J.H. Hersh
- Weisskopf Center, University of Louisville Clinical Genetics Unit; Louisville Kentucky
| | - J. Burton
- Department of Genetics, University of Illinois College of Medicine at Peoria; Peoria Illinois
| | | | | | | | | | - I. Petrik
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | - R. Huether
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | - S. Tang
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
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47
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Aref-Eshghi E, Rodenhiser DI, Schenkel LC, Lin H, Skinner C, Ainsworth P, Paré G, Hood RL, Bulman DE, Kernohan KD, Boycott KM, Campeau PM, Schwartz C, Sadikovic B, Sadikovic B. Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes. Am J Hum Genet 2018; 102:156-174. [PMID: 29304373 DOI: 10.1016/j.ajhg.2017.12.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/10/2017] [Indexed: 01/23/2023] Open
Abstract
Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A5C1, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada.
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48
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Štiavnická M, Abril-Parreño L, Nevoral J, Králíčková M, García-Álvarez O. Non-Invasive Approaches to Epigenetic-Based Sperm Selection. Med Sci Monit 2017; 23:4677-4683. [PMID: 28961228 PMCID: PMC5633068 DOI: 10.12659/msm.904098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Since sperm size and form do not necessarily provide information on internal sperm structures, novel sperm markers need to be found in order to conduct assisted reproductive therapies (ART) successfully. Currently, the priority of andrologists is not only to select those sperm able to fertilize the oocyte, but also a high quality of sperm that will guarantee a healthy embryo. Evidence of this shows us the importance of studying sperm intensively on genetic and epigenetic levels, because these could probably be the cause of a percentage of infertility diagnosed as idiopathic. Thus, more attention is being paid to posttranslational modifications as the key for better understanding of the fertilization process and its impact on embryo and offspring. Advances in the discovery of new sperm markers should go hand in hand with finding appropriate techniques for selecting the healthiest sperm, guaranteeing its non-invasiveness. To date, most sperm selection techniques can be harmful to sperm due to centrifugation or staining procedures. Some methods, such as microfluidic techniques, sperm nanopurifications, and Raman spectroscopy, have the potential to make selection gentle to sperm, tracking small abnormalities undetected by methods currently used. The fact that live cells could be analyzed without harmful effects creates the expectation of using them routinely in ART. In this review, we focus on the combination of sperm epigenetic status (modifications) as quality markers, with non-invasive sperm selection methods as novel approaches to improve ART outcomes.
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Affiliation(s)
- Miriama Štiavnická
- Laboratory of Reproductive Medicine of Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Laura Abril-Parreño
- Laboratory of Reproductive Medicine of Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jan Nevoral
- Laboratory of Reproductive Medicine of Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milena Králíčková
- Laboratory of Reproductive Medicine of Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Olga García-Álvarez
- Laboratory of Reproductive Medicine of Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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49
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Green C, Willoughby J, Balasubramanian M. De novo SETD5
loss-of-function variant as a cause for intellectual disability in a 10-year old boy with an aberrant blind ending bronchus. Am J Med Genet A 2017; 173:3165-3171. [DOI: 10.1002/ajmg.a.38461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/11/2017] [Accepted: 08/04/2017] [Indexed: 02/03/2023]
Affiliation(s)
- Claire Green
- Sheffield Clinical Genetics Service; Sheffield Children's NHS Foundation Trust; Sheffield UK
| | - Joshua Willoughby
- Sheffield Diagnostic Genetics Service; Sheffield Children's NHS Foundation Trust; Sheffield UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service; Sheffield Children's NHS Foundation Trust; Sheffield UK
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50
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Chuang YF, Huang SW, Hsu YF, Yu MC, Ou G, Huang WJ, Hsu MJ. WMJ-8-B, a novel hydroxamate derivative, induces MDA-MB-231 breast cancer cell death via the SHP-1-STAT3-survivin cascade. Br J Pharmacol 2017. [PMID: 28646512 DOI: 10.1111/bph.13929] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND AND PURPOSE Histone deacetylase (HDAC) inhibitors have been demonstrate to have broad-spectrum anti-tumour properties and have attracted lots of attention in the field of drug discovery. However, the underlying anti-tumour mechanisms of HDAC inhibitors remain incompletely understood. In this study, we aimed to characterize the underlying mechanisms through which the novel hydroxamate-based HDAC inhibitor, WMJ-8-B, induces the death of MDA-MB-231 breast cancer cells. EXPERIMENTAL APPROACH Effects of WMJ-8-B on cell viability, cell cycle distribution, apoptosis and signalling molecules were analysed by the MTT assay, flowcytometric analysis, immunoblotting, reporter assay, chromatin immunoprecipitation analysis and use of siRNAs. A xenograft model was used to determine anti-tumour effects of WMJ-8-B in vivo. KEY RESULTS WMJ-8-B induced survivin reduction, G2/M cell cycle arrest and apoptosis in MDA-MB-231 cells. STAT3 phosphorylation, transactivity and its binding to the survivin promoter region were reduced in WMJ-8-B-treated cells. WMJ-8-B activated the protein phosphatase SHP-1 and when SHP-1 signalling was blocked, the effects of WMJ-8-B on STAT3 phosphorylation and survivin levels were abolished. However, WMJ-8-B increased the transcription factor Sp1 binding to the p21 promoter region and enhanced p21 levels. Moreover, WMJ-8-B induced α-tubulin acetylation and disrupted microtubule assembly. Inhibition of HDACs was shown to contribute to WMJ-8-B's actions. Furthermore, WMJ-8-B suppressed the growth of MDA-MB-231 xenografts in mammary fat pads in vivo. CONCLUSIONS AND IMPLICATIONS The SHP-1-STAT3-survivin and Sp1-p21 cascades are involved in WMJ-8-B-induced MDA-MB-231 breast cancer cell death. These results also indicate the potential of WMJ-8-B as a lead compound for treatment of breast cancer and warrant its clinical development.
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Affiliation(s)
- Yu-Fan Chuang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shiu-Wen Huang
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Fen Hsu
- Division of General Surgery, Department of Surgery, Landseed Hospital, Taoyuan, Taiwan
| | - Meng-Chieh Yu
- Division of General Surgery, Department of Surgery, Landseed Hospital, Taoyuan, Taiwan.,Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - George Ou
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Wei-Jan Huang
- Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan
| | - Ming-Jen Hsu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
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