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Rastogi M, Bartolucci M, Nanni M, Aloisio M, Vozzi D, Petretto A, Contestabile A, Cancedda L. Integrative multi-omic analysis reveals conserved cell-projection deficits in human Down syndrome brains. Neuron 2024:S0896-6273(24)00329-5. [PMID: 38810652 DOI: 10.1016/j.neuron.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/17/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Down syndrome (DS) is the most common genetic cause of cognitive disability. However, it is largely unclear how triplication of a small gene subset may impinge on diverse aspects of DS brain physiopathology. Here, we took a multi-omic approach and simultaneously analyzed by RNA-seq and proteomics the expression signatures of two diverse regions of human postmortem DS brains. We found that the overexpression of triplicated genes triggered global expression dysregulation, differentially affecting transcripts, miRNAs, and proteins involved in both known and novel biological candidate pathways. Among the latter, we observed an alteration in RNA splicing, specifically modulating the expression of genes involved in cytoskeleton and axonal dynamics in DS brains. Accordingly, we found an alteration in axonal polarization in neurons from DS human iPSCs and mice. Thus, our study provides an integrated multilayer expression database capable of identifying new potential targets to aid in designing future clinical interventions for DS.
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Affiliation(s)
- Mohit Rastogi
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Martina Bartolucci
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genova 16147, Italy
| | - Marina Nanni
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | | | - Diego Vozzi
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Andrea Petretto
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genova 16147, Italy
| | - Andrea Contestabile
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy.
| | - Laura Cancedda
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy; Dulbecco Telethon Institute, Rome 00185, Italy.
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Xiao B, Dai W, Zhan Y, Qiu W, Zhang H, Liu D, Xu N, Yu Y. Genome-wide epigenetic signatures facilitated the variant classification of the PURA gene and uncovered the pathomechanism of PURA-related neurodevelopmental disorders. Genet Med 2024; 26:101167. [PMID: 38770750 DOI: 10.1016/j.gim.2024.101167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
PURPOSE Rare genetic variants in the PURA gene cause the PURA-related neurodevelopmental disorder (PURA-NDD), characterized by neonatal abnormalities and developmental delay. Using genome-wide DNA methylation analysis on patients with PURA variants, we aim to establish a PURA-NDD-specific methylation profile and provide further insights on the molecular basis of the PURA-NDD. METHODS Twenty three individuals (including 12 unpublished) carrying PURA variants were enrolled. We conducted the Illumina Infinium EPIC microarray analysis in 17 PURA-NDD individuals. In vitro experiments were performed to examine how PURA variants affect Pur-a expression. RESULTS Additional phenotypes in 12 newly identified patients were described in this study. Genome-wide DNA methylation analysis unveiled distinctive methylation profiles to PURA-NDD, and the established classifier can reclassify PURA variants of uncertain significance. Patients bearing PURA hapoloinsufficient and missense variants have comparable DNA methylation profiles, and cells expressing these PURA variants showed consistent Pur-a downregulation, suggesting a haploinsufficiency mechanism. CONCLUSION Patients with PURA-NDD exhibit a specific episignature, which has potential to aid identification and diagnosis of PURA-NDD patients and offer implications for further functional investigations.
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Affiliation(s)
- Bing Xiao
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Weiqian Dai
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yongkun Zhan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | | | - Na Xu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China.
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3
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Hao W, Yang W, Yang Y, Cheng T, Wei T, Tang L, Qian N, Yang Y, Li X, Jiang H, Wang M. Identification of lncRNA-miRNA-mRNA Networks in the Lenticular Nucleus Region of the Brain Contributes to Hepatolenticular Degeneration Pathogenesis and Therapy. Mol Neurobiol 2024; 61:1673-1686. [PMID: 37759104 PMCID: PMC10896925 DOI: 10.1007/s12035-023-03631-1] [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: 04/12/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a recently discovered group of non-coding RNAs that play a crucial role in the regulation of various human diseases, especially in the study of nervous system diseases which has garnered significant attention. However, there is limited knowledge on the identification and function of lncRNAs in hepatolenticular degeneration (HLD). The objective of this study was to identify novel lncRNAs and determine their involvement in the networks associated with HLD. We conducted a comprehensive analysis of RNA sequencing (RNA-seq) data, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and computational biology to identify novel lncRNAs and explore their potential mechanisms in HLD. We identified 212 differently expressed lncRNAs, with 98 upregulated and 114 downregulated. Additionally, 32 differently expressed mRNAs were found, with 15 upregulated and 17 downregulated. We obtained a total of 1131 pairs of co-expressed lncRNAs and mRNAs by Pearson correlation test and prediction and annotation of the lncRNA-targeted miRNA-mRNA network. The differential lncRNAs identified in this study were found to be involved in various biological functions and signaling pathways. These include translational initiation, motor learning, locomotors behavior, dioxygenase activity, integral component of postsynaptic membrane, neuroactive ligand-receptor interaction, nuclear factor-kappa B (NF-κB) signaling pathway, cholinergic synapse, sphingolipid signaling pathway, and Parkinson's disease signaling pathway, as revealed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Six lncRNAs, including XR_001782921.1 (P < 0.01), XR_ 001780581.1 (P < 0.01), ENSMUST_00000207119 (P < 0.01), XR_865512.2 (P < 0.01), TCONS_00005916 (P < 0.01), and TCONS_00020683 (P < 0.01), showed significant differences in expression levels between the model group and normal group by RT-qPCR. Among these, four lncRNAs (TCONS_00020683, XR_865512.2, XR_001780581.1, and ENSMUST00000207119) displayed a high degree of conservation. This study provides a unique perspective for the pathogenesis and therapy of HLD by constructing the lncRNA-miRNA-mRNA network. This insight provides a foundation for future exploration in this field.
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Affiliation(s)
- Wenjie Hao
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Wenming Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China.
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China.
| | - Yue Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Ting Cheng
- Department of Graduate, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Taohua Wei
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Lulu Tang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Nannan Qian
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Yulong Yang
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Xiang Li
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hailin Jiang
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Meixia Wang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
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Biswas S, Hilser JR, Woodward NC, Wang Z, Gukasyan J, Nemet I, Schwartzman WS, Huang P, Han Y, Fouladian Z, Charugundla S, Spencer NJ, Pan C, Tang WW, Lusis AJ, Hazen SL, Hartiala JA, Allayee H. Effect of Genetic and Dietary Perturbation of Glycine Metabolism on Atherosclerosis in Humans and Mice. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.08.23299748. [PMID: 38168321 PMCID: PMC10760269 DOI: 10.1101/2023.12.08.23299748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Objective Epidemiological and genetic studies have reported inverse associations between circulating glycine levels and risk of coronary artery disease (CAD). However, these findings have not been consistently observed in all studies. We sought to evaluate the causal relationship between circulating glycine levels and atherosclerosis using large-scale genetic analyses in humans and dietary supplementation experiments in mice. Methods Serum glycine levels were evaluated for association with prevalent and incident CAD in the UK Biobank. A multi-ancestry genome-wide association study (GWAS) meta-analysis was carried out to identify genetic determinants for circulating glycine levels, which were then used to evaluate the causal relationship between glycine and risk of CAD by Mendelian randomization (MR). A glycine feeding study was carried out with atherosclerosis-prone apolipoprotein E deficient (ApoE-/-) mice to determine the effects of increased circulating glycine levels on amino acid metabolism, metabolic traits, and aortic lesion formation. Results Among 105,718 subjects from the UK Biobank, elevated serum glycine levels were associated with significantly reduced risk of prevalent CAD (Quintile 5 vs. Quintile 1 OR=0.76, 95% CI 0.67-0.87; P<0.0001) and incident CAD (Quintile 5 vs. Quintile 1 HR=0.70, 95% CI 0.65-0.77; P<0.0001) in models adjusted for age, sex, ethnicity, anti-hypertensive and lipid-lowering medications, blood pressure, kidney function, and diabetes. A meta-analysis of 13 GWAS datasets (total n=230,947) identified 61 loci for circulating glycine levels, of which 26 were novel. MR analyses provided modest evidence that genetically elevated glycine levels were causally associated with reduced systolic blood pressure and risk of type 2 diabetes, but did provide evidence for an association with risk of CAD. Furthermore, glycine-supplementation in ApoE-/- mice did not alter cardiometabolic traits, inflammatory biomarkers, or development of atherosclerotic lesions. Conclusions Circulating glycine levels were inversely associated with risk of prevalent and incident CAD in a large population-based cohort. While substantially expanding the genetic architecture of circulating glycine levels, MR analyses and in vivo feeding studies in humans and mice, respectively, did not provide evidence that the clinical association of this amino acid with CAD represents a causal relationship, despite being associated with two correlated risk factors.
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Affiliation(s)
- Subarna Biswas
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - James R. Hilser
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Nicholas C. Woodward
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Janet Gukasyan
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Ina Nemet
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
| | - William S. Schwartzman
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Pin Huang
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Yi Han
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Zachary Fouladian
- Department of Medicine, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - Sarada Charugundla
- Department of Medicine, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - Neal J. Spencer
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Calvin Pan
- Department of Human Genetics, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - W.H. Wilson Tang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Aldons J. Lusis
- Department of Medicine, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
- Department of Human Genetics, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
- Department of Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - Stanley L. Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Jaana A. Hartiala
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Hooman Allayee
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
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Zhegalova IV, Vasiluev PA, Flyamer IM, Shtompel AS, Glazyrina E, Shilova N, Minzhenkova M, Markova Z, Petrova NV, Dashinimaev EB, Razin SV, Ulianov SV. Trisomies Reorganize Human 3D Genome. Int J Mol Sci 2023; 24:16044. [PMID: 38003233 PMCID: PMC10671006 DOI: 10.3390/ijms242216044] [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: 09/06/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
Trisomy is the presence of one extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies are associated with severe developmental abnormalities leading to embryonic lethality, miscarriage or pronounced deviations of various organs and systems at birth. Trisomies are characterized by alterations in gene expression level, not exclusively on the trisomic chromosome, but throughout the genome. Here, we applied the high-throughput chromosome conformation capture technique (Hi-C) to study chromatin 3D structure in human chorion cells carrying either additional chromosome 13 (Patau syndrome) or chromosome 16 and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome). The presence of extra chromosomes results in systematic changes of contact frequencies between small and large chromosomes. Analyzing the behavior of individual chromosomes, we found that a limited number of chromosomes change their contact patterns stochastically in trisomic cells and that it could be associated with lamina-associated domains (LAD) and gene content. For trisomy 13 and 18, but not for trisomy 16, the proportion of compacted loci on a chromosome is correlated with LAD content. We also found that regions of the genome that become more compact in trisomic cells are enriched in housekeeping genes, indicating a possible decrease in chromatin accessibility and transcription level of these genes. These results provide a framework for understanding the mechanisms of pan-genome transcription dysregulation in trisomies in the context of chromatin spatial organization.
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Affiliation(s)
- Irina V. Zhegalova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | | | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anastasia S. Shtompel
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | | | | | | | - Zhanna Markova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Natalia V. Petrova
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Erdem B. Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Sergey V. Razin
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Sergey V. Ulianov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
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Transition from Animal-Based to Human Induced Pluripotent Stem Cells (iPSCs)-Based Models of Neurodevelopmental Disorders: Opportunities and Challenges. Cells 2023; 12:cells12040538. [PMID: 36831205 PMCID: PMC9954744 DOI: 10.3390/cells12040538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) arise from the disruption of highly coordinated mechanisms underlying brain development, which results in impaired sensory, motor and/or cognitive functions. Although rodent models have offered very relevant insights to the field, the translation of findings to clinics, particularly regarding therapeutic approaches for these diseases, remains challenging. Part of the explanation for this failure may be the genetic differences-some targets not being conserved between species-and, most importantly, the differences in regulation of gene expression. This prompts the use of human-derived models to study NDDS. The generation of human induced pluripotent stem cells (hIPSCs) added a new suitable alternative to overcome species limitations, allowing for the study of human neuronal development while maintaining the genetic background of the donor patient. Several hIPSC models of NDDs already proved their worth by mimicking several pathological phenotypes found in humans. In this review, we highlight the utility of hIPSCs to pave new paths for NDD research and development of new therapeutic tools, summarize the challenges and advances of hIPSC-culture and neuronal differentiation protocols and discuss the best way to take advantage of these models, illustrating this with examples of success for some NDDs.
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Huang K, Fan X, Jiang Y, Jin S, Huang J, Pang L, Wang Y, Wu Y, Sun X. Integrative identification of hub genes in development of atrial fibrillation related stroke. PLoS One 2023; 18:e0283617. [PMID: 36952494 PMCID: PMC10035830 DOI: 10.1371/journal.pone.0283617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND As the most common arrhythmia, atrial fibrillation (AF) is associated with a significantly increased risk of stroke, which causes high disability and mortality. To date, the underlying mechanism of stroke occurring after AF remains unclear. Herein, we studied hub genes and regulatory pathways involved in AF and secondary stroke and aimed to reveal biomarkers and therapeutic targets of AF-related stroke. METHODS The GSE79768 and GSE58294 datasets were used to analyze AF- and stroke-related differentially expressed genes (DEGs) to obtain a DEG1 dataset. Weighted correlation network analysis (WGCNA) was used to identify modules associated with AF-related stroke in GSE66724 (DEG2). DEG1 and DEG2 were merged, and hub genes were identified based on protein-protein interaction networks. Gene Ontology terms were used to analyze the enriched pathways. The GSE129409 and GSE70887 were applied to construct a circRNA-miRNA-mRNA network in AF-related stroke. Hub genes were verified in patients using quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS We identified 3,132 DEGs in blood samples and 253 DEGs in left atrial specimens. Co-expressed hub genes of EIF4E3, ZNF595, ZNF700, MATR3, ACKR4, ANXA3, SEPSECS-AS1, and RNF166 were significantly associated with AF-related stroke. The hsa_circ_0018657/hsa-miR-198/EIF4E3 pathway was explored as the regulating axis in AF-related stroke. The qRT-PCR results were consistent with the bioinformatic analysis. CONCLUSIONS Hub genes EIF4E3, ZNF595, ZNF700, MATR3, ACKR4, ANXA3, SEPSECS-AS1, and RNF166 have potential as novel biomarkers and therapeutic targets in AF-related stroke. The hsa_circ_0018657/hsa-miR-198/EIF4E3 axis could play an important role regulating the development of AF-related stroke.
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Affiliation(s)
- Kai Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Xi Fan
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yuwen Jiang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Sheng Jin
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Jiechun Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Liewen Pang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yiqing Wang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yuming Wu
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Xiaotian Sun
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
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Buczyńska A, Sidorkiewicz I, Hameed A, Krętowski AJ, Zbucka-Krętowska M. Future Perspectives in Oxidative Stress in Trisomy 13 and 18 Evaluation. J Clin Med 2022; 11:jcm11071787. [PMID: 35407395 PMCID: PMC8999694 DOI: 10.3390/jcm11071787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/22/2022] [Indexed: 02/05/2023] Open
Abstract
Autosomal aneuploidies are the most frequently occurring congenital abnormalities and are related to many metabolic disorders, hormonal dysfunctions, neurotransmitter abnormalities, and intellectual disabilities. Trisomies are generated by an error of chromosomal segregation during cell division. Accumulating evidence has shown that deregulated gene expression resulting from the triplication of chromosomes 13 and 18 is associated with many disturbed cellular processes. Moreover, a disturbed oxidative stress status may be implicated in the occurrence of fetal malformations. Therefore, a literature review was undertaken to provide novel insights into the evaluation of trisomy 13 (T13) and 18 (T18) pathogeneses, with a particular concern on the oxidative stress. Corresponding to the limited literature data focused on factors leading to T13 and T18 phenotype occurrence, the importance of oxidative stress evaluation in T13 and T18 could enable the determination of subsequent disturbed metabolic pathways, highlighting the related role of mitochondrial dysfunction or epigenetics. This review illustrates up-to-date T13 and T18 research and discusses the strengths, limitations, and possible directions for future studies. The progressive unification of trisomy-related research protocols might provide potential medical targets in the future along with the implementation of the foundation of modern prenatal medicine.
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Affiliation(s)
- Angelika Buczyńska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
- Correspondence: (A.B.); (M.Z.-K.); Tel.: +48-85-746-85-13 (A.B.); +48-85-746-83-36 (M.Z.-K.)
| | - Iwona Sidorkiewicz
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
| | - Ahsan Hameed
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
| | - Adam Jacek Krętowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Monika Zbucka-Krętowska
- Department of Gynecological Endocrinology and Adolescent Gynecology, Medical University of Bialystok, 15-276 Bialystok, Poland
- Correspondence: (A.B.); (M.Z.-K.); Tel.: +48-85-746-85-13 (A.B.); +48-85-746-83-36 (M.Z.-K.)
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9
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Cell models for Down syndrome-Alzheimer’s disease research. Neuronal Signal 2022; 6:NS20210054. [PMID: 35449591 PMCID: PMC8996251 DOI: 10.1042/ns20210054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Down syndrome (DS) is the most common chromosomal abnormality and leads to intellectual disability, increased risk of cardiac defects, and an altered immune response. Individuals with DS have an extra full or partial copy of chromosome 21 (trisomy 21) and are more likely to develop early-onset Alzheimer’s disease (AD) than the general population. Changes in expression of human chromosome 21 (Hsa21)-encoded genes, such as amyloid precursor protein (APP), play an important role in the pathogenesis of AD in DS (DS-AD). However, the mechanisms of DS-AD remain poorly understood. To date, several mouse models with an extra copy of genes syntenic to Hsa21 have been developed to characterise DS-AD-related phenotypes. Nonetheless, due to genetic and physiological differences between mouse and human, mouse models cannot faithfully recapitulate all features of DS-AD. Cells differentiated from human-induced pluripotent stem cells (iPSCs), isolated from individuals with genetic diseases, can be used to model disease-related cellular and molecular pathologies, including DS. In this review, we will discuss the limitations of mouse models of DS and how these can be addressed using recent advancements in modelling DS using human iPSCs and iPSC-mouse chimeras, and potential applications of iPSCs in preclinical studies for DS-AD.
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10
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Zeinalzadeh E, Valerievich Yumashev A, Rahman HS, Marofi F, Shomali N, Kafil HS, Solali S, Sajjadi-Dokht M, Vakili-Samiani S, Jarahian M, Hagh MF. The Role of Janus Kinase/STAT3 Pathway in Hematologic Malignancies With an Emphasis on Epigenetics. Front Genet 2021; 12:703883. [PMID: 34992627 PMCID: PMC8725977 DOI: 10.3389/fgene.2021.703883] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway has been known to be involved in cell growth, cellular differentiation processes development, immune cell survival, and hematopoietic system development. As an important member of the STAT family, STAT3 participates as a major regulator of cellular development and differentiation-associated genes. Prolonged and persistent STAT3 activation has been reported to be associated with tumor cell survival, proliferation, and invasion. Therefore, the JAK-STAT pathway can be a potential target for drug development to treat human cancers, e.g., hematological malignancies. Although STAT3 upregulation has been reported in hematopoietic cancers, protein-level STAT3 mutations have also been reported in invasive leukemias/lymphomas. The principal role of STAT3 in tumor cell growth clarifies the importance of approaches that downregulate this molecule. Epigenetic modifications are a major regulatory mechanism controlling the activity and function of STAT3. So far, several compounds have been developed to target epigenetic regulatory enzymes in blood malignancies. Here, we discuss the current knowledge about STAT3 abnormalities and carcinogenic functions in hematopoietic cancers, novel STAT3 inhibitors, the role of epigenetic mechanisms in STAT3 regulation, and targeted therapies, by focusing on STAT3-related epigenetic modifications.
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Affiliation(s)
- Elham Zeinalzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Heshu Sulaiman Rahman
- College of Medicine, University of Sulaimani, Sulaimaniyah, Iraq
- Department of Medical Laboratory Sciences, Komar University of Science and Technology, Sulaimaniyah, Iraq
| | - Faroogh Marofi
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Navid Shomali
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- German Cancer Research Center, Toxicology and Chemotherapy Unit (G401), Heidelberg, Germany
| | - Saeed Solali
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Sajjadi-Dokht
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sajjad Vakili-Samiani
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mostafa Jarahian
- German Cancer Research Center, Toxicology and Chemotherapy Unit (G401), Heidelberg, Germany
| | - Majid Farshdousti Hagh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Dong D, Zhang R, Shao J, Zhang A, Wang Y, Zhou Y, Li Y. Promoter methylation-mediated repression of UNC5 receptors and the associated clinical significance in human colorectal cancer. Clin Epigenetics 2021; 13:225. [PMID: 34922605 PMCID: PMC8684698 DOI: 10.1186/s13148-021-01211-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background Deregulated methylation of tumor suppressor genes is a hallmark event in colorectal cancer (CRC) carcinogenesis. UNC5 receptors, down-regulated in various human malignancies due to epigenetic alterations, have been proposed as putative tumor suppressor genes. In this study, we focused on the methylation-mediated inhibition of UNC5 receptors and the associated clinical significance in CRC. Methods Methylation and expression analysis was performed in TCGA datasets. And the results were confirmed in vitro in CRC cell lines treated with 5-aza-deoxycytidine. Then, the expression and epigenetic alterations of UNC5 receptors were evaluated in clinical specimens. Moreover, the diagnostic and prognostic values of the methylation alterations were also analyzed. Results Methylation-mediated repression was observed in UNC5C and UNC5D, but not in UNC5A and UNC5B, which was confirmed in CRC cell lines. Except for UNC5B, significantly elevated methylation was observed in UNC5A, UNC5C, and UNC5D in CRC. The discrimination efficiency of the three receptors was comparable with that of SEPT9. Kaplan–Meier curve survival analysis showed that hypermethylation of UNC5A, UNC5C and UNC5D was associated with poor progression-free and overall survival. Moreover, methylation levels of UNC5C and UNC5D were independent predictors of CRC progression-free (P = 0.001, P = 0.003, respectively) and overall survival (P = 0.008, P = 0.004, respectively). Conclusions Hypermethylation of UNC5C and UNC5D mediates the repression and has promising diagnostic and prognostic values in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01211-5.
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Affiliation(s)
- Dong Dong
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, People's Republic of China
| | - Runshi Zhang
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, People's Republic of China.,Department of Clinical Laboratory, Xi'an No. 1 Hospital, Xi'an, 710002, Shaanxi, People's Republic of China
| | - Jie Shao
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, People's Republic of China
| | - Aimin Zhang
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, People's Republic of China
| | - Yichao Wang
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), No.999 Donghai Road, Jiaojiang District, Taizhou, 318000, Zhejiang Province, People's Republic of China.
| | - Yunli Zhou
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, People's Republic of China.
| | - Yueguo Li
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, People's Republic of China.
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12
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Naumova OY, Lipschutz R, Rychkov SY, Zhukova OV, Grigorenko EL. DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome. Genes (Basel) 2021; 12:genes12081115. [PMID: 34440289 PMCID: PMC8391316 DOI: 10.3390/genes12081115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
Recent research has provided evidence on genome-wide alterations in DNA methylation patterns due to trisomy 21, which have been detected in various tissues of individuals with Down syndrome (DS) across different developmental stages. Here, we report new data on the systematic genome-wide DNA methylation perturbations in blood cells of individuals with DS from a previously understudied age group—young children. We show that the study findings are highly consistent with those from the prior literature. In addition, utilizing relevant published data from two other developmental stages, neonatal and adult, we track a quasi-longitudinal trend in the DS-associated DNA methylation patterns as a systematic epigenomic destabilization with age.
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Affiliation(s)
- Oxana Yu. Naumova
- Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia; (S.Y.R.); (O.V.Z.)
- Department of Psychology, University of Houston, Houston, TX 77204, USA;
- Correspondence: or (O.Y.N.); (E.L.G.)
| | - Rebecca Lipschutz
- Department of Psychology, University of Houston, Houston, TX 77204, USA;
| | - Sergey Yu. Rychkov
- Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia; (S.Y.R.); (O.V.Z.)
| | - Olga V. Zhukova
- Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia; (S.Y.R.); (O.V.Z.)
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, TX 77204, USA;
- Department of Psychology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: or (O.Y.N.); (E.L.G.)
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13
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Szu J, Wojcinski A, Jiang P, Kesari S. Impact of the Olig Family on Neurodevelopmental Disorders. Front Neurosci 2021; 15:659601. [PMID: 33859549 PMCID: PMC8042229 DOI: 10.3389/fnins.2021.659601] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
The Olig genes encode members of the basic helix-loop-helix (bHLH) family of transcription factors. Olig1, Olig2, and Olig3 are expressed in both the developing and mature central nervous system (CNS) and strictly regulate cellular specification and differentiation. Extensive studies have established functional roles of Olig1 and Olig2 in directing neuronal and glial formation during different stages in development. Recently, Olig2 overexpression was implicated in neurodevelopmental disorders down syndrome (DS) and autism spectrum disorder (ASD) but its influence on cognitive and intellectual defects remains unknown. In this review, we summarize the biological functions of the Olig family and how it uniquely promotes cellular diversity in the CNS. This is followed up with a discussion on how abnormal Olig2 expression impacts brain development and function in DS and ASD. Collectively, the studies described here emphasize vital features of the Olig members and their distinctive potential roles in neurodevelopmental disease states.
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Affiliation(s)
- Jenny Szu
- Department of Translational Neurosciences and Neurotherapeutics, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, United States
| | - Alexandre Wojcinski
- Department of Translational Neurosciences and Neurotherapeutics, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, United States
| | - Peng Jiang
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
| | - Santosh Kesari
- Department of Translational Neurosciences and Neurotherapeutics, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, United States.,Pacific Neuroscience Institute, Providence Saint John's Health Center, Santa Monica, CA, United States
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14
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Laufer BI, Gomez JA, Jianu JM, LaSalle JM. Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature. Epigenetics Chromatin 2021; 14:13. [PMID: 33750431 PMCID: PMC7942011 DOI: 10.1186/s13072-021-00387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00387-7.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA. .,Genome Center, University of California, Davis, CA, 95616, USA. .,MIND Institute, University of California, Davis, CA, 95616, USA.
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15
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Qin L, Qiao C, Sheen V, Wang Y, Lu J. DNMT3L promotes neural differentiation by enhancing STAT1 and STAT3 phosphorylation independent of DNA methylation. Prog Neurobiol 2021; 201:102028. [PMID: 33636226 DOI: 10.1016/j.pneurobio.2021.102028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/10/2021] [Accepted: 02/21/2021] [Indexed: 01/13/2023]
Abstract
Previously, we reported global hypermethylation in DS might be attributed to the overexpression of HSA21 gene DNMT3L, which can enhance DNMT3A and DNMT3B activities in DNA methylation. To test this hypothesis, we compared the DNA methylation and RNA expression profiles of early-differentiated human neuroprogenitors with and without DNMT3L overexpression. We found DNMT3L overexpression only moderately increased the DNA methylation of limited genes, yet significantly altered global RNA expression of genes involved in neural differentiation. We further found that DNMT3L bound STAT1 or STAT3, and increased its phosphorylation and nuclear translocation, which in turn activated the expression of transcription factors including HES3, ASCL1, NEUROD2 and NEUROG2 and CDK inhibitor CDKN1A, which promoted cell cycle exit and neural differentiation. This phenomenon was also confirmed in Dnmt3l conditional knockin mice, which could be rescued by STAT1 and STAT3 phosphorylation inhibitors (Fludarabine and SH-4-54) but not DNA methylation inhibitor (Decitabine). These results suggest that DNMT3L play an important role during neurodevelopment independent of DNA methylation, which may contribute to the abnormal phenotypes observed in Down syndrome cortex.
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Affiliation(s)
- Lin Qin
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, 110122, China; Department of Obstetrics & Gynecology, Shenyang Women & Children's Hospital, Shenyang, Liaoning Province, 110121, China.
| | - Chong Qiao
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China.
| | - Volney Sheen
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
| | - Yu Wang
- Department of Obstetrics & Gynecology, Shenyang Women & Children's Hospital, Shenyang, Liaoning Province, 110121, China.
| | - Jie Lu
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, 110122, China.
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16
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Schuster J, Hoeber J, Sobol M, Fatima A, Annerén G, Dahl N. Generation of two human iPSC lines (UUIGPi013-A and UUIPGi014-A) from cases with Down syndrome and full trisomy for chromosome 21 (T21). Stem Cell Res 2020; 49:102081. [PMID: 33220594 DOI: 10.1016/j.scr.2020.102081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022] Open
Abstract
Down syndrome (DS) is caused by trisomy for chromosome 21 (T21). We generated two induced pluripotent stem cell (iPSC) lines from skin fibroblasts of two males with DS using Sendai virus delivery of OCT4, SOX2, KLF4, and c-MYC. Characterization of the two iPSC lines, UUIGPi013-A and UUIPGi014-A, showed that they are genetically stable with a 47,XY,+21 karyotype. Both lines displayed expression of pluripotency markers and trilineage differentiation capacity. These two iPSC lines provide a useful resource for DS modeling and pharmacological interventions.
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Affiliation(s)
- Jens Schuster
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden.
| | - Jan Hoeber
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Maria Sobol
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Ambrin Fatima
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Göran Annerén
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Niklas Dahl
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden.
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17
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Laufer BI, Hwang H, Jianu JM, Mordaunt CE, Korf IF, Hertz-Picciotto I, LaSalle JM. Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles. Hum Mol Genet 2020; 29:3465-3476. [PMID: 33001180 PMCID: PMC7788293 DOI: 10.1093/hmg/ddaa218] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Neonatal dried blood spots (NDBS) are a widely banked sample source that enables retrospective investigation into early life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q < 0.05) differentially methylated regions (DMRs) that distinguished DS from typical development and idiopathic developmental delay were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons with previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q < 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q < 0.05) enriched for blood-specific chromatin states. A ~28 kb block of hypermethylation was observed on chromosome 21 in the RUNX1 locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q < 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early life mechanisms of epigenomic dysregulation resulting from trisomy 21.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Ian F Korf
- Genome Center, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Irva Hertz-Picciotto
- MIND Institute, University of California, Davis, CA 95616, USA.,Department of Public Health Sciences, School of Medicine, University of California, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
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