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Kozlov G, Franceschi C, Vedunova M. Intricacies of aging and Down syndrome. Neurosci Biobehav Rev 2024; 164:105794. [PMID: 38971514 DOI: 10.1016/j.neubiorev.2024.105794] [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: 04/11/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Down syndrome is the most frequently occurring genetic condition, with a substantial escalation in risk associated with advanced maternal age. The syndrome is characterized by a diverse range of phenotypes, affecting to some extent all levels of organization, and its progeroid nature - early manifestation of aspects of the senile phenotype. Despite extensive investigations, many aspects and mechanisms of the disease remain unexplored. The current review aims to provide an overview of the main causes and manifestations of Down syndrome, while also examining the phenomenon of accelerated aging and exploring potential therapeutic strategies.
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Affiliation(s)
- G Kozlov
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Gagarin ave., 23, 603022, Russia
| | - C Franceschi
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Gagarin ave., 23, 603022, Russia
| | - M Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Gagarin ave., 23, 603022, Russia; Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov str., 119991 Moscow, Russia.
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2
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Maslen CL. Human Genetics of Atrioventricular Septal Defect. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:559-571. [PMID: 38884732 DOI: 10.1007/978-3-031-44087-8_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Atrioventricular septal defects (AVSD), also known as a common atrioventricular canal (CAVC), are clinically severe heart malformations that affect about 1 out of every 2100 live births. AVSD makes up about 5% of all congenital heart defects. AVSD is associated with cytogenetic disorders such as Down syndrome and numerous other rare genetic syndromes, but also occurs as a simplex trait. Studies in mouse models have identified over 100 genetic mutations that have the potential to cause an AVSD. However, studies in humans indicate that AVSD is genetically heterogeneous, and that the cause in humans is very rarely a single-gene defect. Familial cases do occur albeit rarely, usually with autosomal dominant inheritance and variable expression. In addition, the frequent occurrence of AVSD in some syndromes with known genetic causes such as heterotaxy syndrome points to additional genes/pathways that increase AVSD risk. Accordingly, while the genetic underpinnings for most AVSD remain unknown, there have been advances in identifying genetic risk factors for AVSD in both syndromic and nonsyndromic cases. This chapter summarizes the current knowledge of the genetic basis for AVSD.
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Affiliation(s)
- Cheryl L Maslen
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA.
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3
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Sun S, Liu K, Xue C, Hu Y, Yu H, Qi G, Chen J, Li X, Zhao X, Gong Z. Genome-Wide Effects on Gene Expression Between Parental and Filial Generations of Trisomy 11 and 12 of Rice. RICE (NEW YORK, N.Y.) 2023; 16:17. [PMID: 36964817 PMCID: PMC10039966 DOI: 10.1186/s12284-023-00632-5] [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: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Aneuploid refers to the gene dosage imbalance due to copy number alterations. Aneuploidy is generally harmful to the growth, development and reproduction of organisms according to the numerous research. However, it has rarely been reported on whether aneuploid have a relevant pattern of genome expression between the parental and its offspring generations. In this study, mRNA sequencing analysis was performed on rice (Oryza sativa L.) primary trisomes 11 and 12, same primary trisomes and normal individuals in their filial generation. We systematically summarized the changes in gene expression patterns that occur on cis genes and on trans genes between parental and filial generations. In T11 and T12, the ratio of cis-gene expression showed intermediate type in parents and dosage compensation in filial generations, which maybe due to more genes being downregulated. The trans genes were also affected by aneuploidy and manifested as cis-related. The strains with normal chromosomes in filial generations, there are still aneuploid-sensitive genes differentially expressed in their genomes, indicating that the effect of aneuploidy is far-reaching and could not be easily eliminated. Meanwhile, among these differentially expressed genes, genes with low-expression level were more likely to be upregulated, while genes with medium- and high-expression level were easy to be downregulated. For the different types of rice aneuploid, upregulated genes were mainly associated with genomic imbalance while downregulated genes were mainly influenced by the specific added chromosome. In conclusion, our results provide new insights into the genetic characterization and evolution of biological aneuploidy genomes.
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Affiliation(s)
- Shang Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Kai Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Chao Xue
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yingying Hu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Hengxiu Yu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Guoxiao Qi
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jijin Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiya Li
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Xinru Zhao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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4
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Zhao HH, Haddad GG. Alzheimer's disease like neuropathology in Down syndrome cortical organoids. Front Cell Neurosci 2022; 16:1050432. [PMID: 36568886 PMCID: PMC9773144 DOI: 10.3389/fncel.2022.1050432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction: Down syndrome (DS) is a genetic disorder with an extra copy of chromosome 21 and DS remains one of the most common causes of intellectual disabilities in humans. All DS patients have Alzheimer's disease (AD)-like neuropathological changes including accumulation of plaques and tangles by their 40s, much earlier than the onset of such neuropathological changes in AD patients. Due to the lack of human samples and appropriate techniques, our understanding of DS neuropathology during brain development or before the clinical onset of the disease remains largely unexplored at the cellular and molecular levels. Methods: We used induced pluripotent stem cell (iPSC) and iPSC-derived 3D cortical organoids to model Alzheimer's disease in Down syndrome and explore the earliest cellular and molecular changes during DS fetal brain development. Results: We report that DS iPSCs have a decreased growth rate than control iPSCs due to a decreased cell proliferation. DS iPSC-derived cortical organoids have a much higher immunoreactivity of amyloid beta (Aß) antibodies and a significantly higher amount of amyloid plaques than control organoids. Although Elisa results did not detect a difference of Aß40 and Aß42 level between the two groups, the ratio of Aß42/Aß40 in the detergent-insoluble fraction of DS organoids was significantly higher than control organoids. Furthermore, an increased Tau phosphorylation (pTau S396) in DS organoids was confirmed by immunostaining and Western blot. Elisa data demonstrated that the ratio of insoluble Tau/total Tau in DS organoids was significantly higher than control organoids. Conclusion: DS iPSC-derived cortical organoids mimic AD-like pathophysiologyical phenotype in vitro, including abnormal Aß and insoluble Tau accumulation. The molecular neuropathologic signature of AD is present in DS much earlier than predicted, even in early fetal brain development, illustrating the notion that brain organoids maybe a good model to study early neurodegenerative conditions.
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Affiliation(s)
- Helen H. Zhao
- Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Gabriel G. Haddad
- Department of Pediatrics, University of California San Diego, La Jolla, CA, United States,Department of Neurosciences, University of California San Diego, La Jolla, CA, United States,The Rady Children’s Hospital, San Diego, CA, United States,*Correspondence: Gabriel G. Haddad
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5
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Henneman P, Mul AN, Li Yim AY, Krzyzewska IM, Alders M, Adelia A, Mizee MR, Mannens MM. Prenatal NeuN+ neurons of Down syndrome display aberrant integrative DNA methylation and gene expression profiles. Epigenomics 2022; 14:375-390. [PMID: 35232286 DOI: 10.2217/epi-2021-0523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To detect expression quantitative trait methylation (eQTM) loci within the cerebrum of prenatal Down syndrome (DS) and controls. Material & methods: DNA methylation gene expression profiles were acquired from NeuN+ nuclei, obtained from cerebrum sections of DS and controls. Linear regression models were applied to both datasets and were subsequently applied in an integrative analysis model to detect DS-associated eQTM loci. Results & conclusion: Widespread aberrant DNA methylation and gene expression were observed in DS. A substantial number of differentially methylated loci were replicated according to a previously reported study. Subsequent integrative analyses (eQTM) yielded numerous associated DS loci. the authors associated DNA methylation, gene expression and eQTM loci with DS that may underlie particular DS phenotypical characteristics.
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Affiliation(s)
- Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Adri N Mul
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Andrew Yf Li Yim
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Izabela M Krzyzewska
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Adelia Adelia
- Neuroimmunology Research Group & Netherlands Brain Bank, Netherlands Institute for Neuroscience, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Mark R Mizee
- Neuroimmunology Research Group & Netherlands Brain Bank, Netherlands Institute for Neuroscience, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Marcel M Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
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6
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Peng P, Zhang Y, Ju Y, Wang K, Li G, Calhoun VD, Wang YP. Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:479-490. [PMID: 32750856 PMCID: PMC7758677 DOI: 10.1109/tcbb.2020.2999397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
With the development of multi-model neuroimaging technology and gene detection technology, the efforts of integrating multi-model imaging genetics data to explore the virulence factors of schizophrenia (SZ) are still limited. To address this issue, we propose a novel algorithm called group sparse of joint non-negative matrix factorization on orthogonal subspace (GJNMFO). Our algorithm fuses single nucleotide polymorphism (SNP) data, function magnetic resonance imaging (fMRI) data and epigenetic factors (DNA methylation) by projecting three-model data into a common basis matrix and three different coefficient matrices to identify risk genes, epigenetic factors and abnormal brain regions associated with SZ. Specifically, we introduce orthogonal constraints on the basis matrix to discard unimportant features in the row of coefficient matrices. Since imaging genetics data have rich group information, we draw into group sparse on three coefficient matrices to make the extracted features more accurate. Both the simulated and real Mind Clinical Imaging Consortium (MCIC) datasets are performed to validate our approach. Simulation results show that our algorithm works better than other competing methods. Through the experiments of MCIC datasets, GJNMFO reveals a set of risk genes, epigenetic factors and abnormal brain functional regions, which have been verified to be both statistically and biologically significant.
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7
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Osuna-Marco MP, López-Barahona M, López-Ibor B, Tejera ÁM. Ten Reasons Why People With Down Syndrome are Protected From the Development of Most Solid Tumors -A Review. Front Genet 2021; 12:749480. [PMID: 34804119 PMCID: PMC8602698 DOI: 10.3389/fgene.2021.749480] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/21/2021] [Indexed: 12/27/2022] Open
Abstract
People with Down syndrome have unique characteristics as a result of the presence of an extra chromosome 21. Regarding cancer, they present a unique pattern of tumors, which has not been fully explained to date. Globally, people with Down syndrome have a similar lifetime risk of developing cancer compared to the general population. However, they have a very increased risk of developing certain tumors (e.g., acute leukemia, germ cell tumors, testicular tumors and retinoblastoma) and, on the contrary, there are some other tumors which appear only exceptionally in this syndrome (e.g., breast cancer, prostate cancer, medulloblastoma, neuroblastoma and Wilms tumor). Various hypotheses have been developed to explain this situation. The genetic imbalance secondary to the presence of an extra chromosome 21 has molecular consequences at several levels, not only in chromosome 21 but also throughout the genome. In this review, we discuss the different proposed mechanisms that protect individuals with trisomy 21 from developing solid tumors: genetic dosage effect, tumor suppressor genes overexpression, disturbed metabolism, impaired neurogenesis and angiogenesis, increased apoptosis, immune system dysregulation, epigenetic aberrations and the effect of different microRNAs, among others. More research into the molecular pathways involved in this unique pattern of malignancies is still needed.
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Affiliation(s)
- Marta Pilar Osuna-Marco
- Biology of Ageing Group, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain.,Pediatric Oncology and Hematology Unit, HM Hospitals, Madrid, Spain
| | | | | | - Águeda Mercedes Tejera
- Biology of Ageing Group, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
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8
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Interaction of Male Specific Lethal complex and genomic imbalance on global gene expression in Drosophila. Sci Rep 2021; 11:19679. [PMID: 34608252 PMCID: PMC8490464 DOI: 10.1038/s41598-021-99268-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/20/2021] [Indexed: 02/04/2023] Open
Abstract
The inverse dosage effect caused by chromosome number variations shows global consequences in genomic imbalance including sexual dimorphism and an X chromosome-specific response. To investigate the relationship of the MSL complex to genomic imbalance, we over-expressed MSL2 in autosomal and sex chromosomal aneuploids, and analyzed the different transcriptomes. Some candidate genes involved in regulatory mechanisms have also been tested during embryogenesis using TSA-FISH. Here we show that the de novo MSL complex assembled on the X chromosomes in females further reduced the global expression level on the basis of 2/3 down-regulation caused by the inverse dosage effect in trisomy through epigenetic modulations rather than induced dosage compensation. Plus, the sexual dimorphism effect in unbalanced genomes was further examined due to the pre-existing of the MSL complex in males. All these results demonstrate the dynamic functions of the MSL complex on global gene expression in different aneuploid genomes.
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9
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Rujeedawa T, Carrillo Félez E, Clare ICH, Fortea J, Strydom A, Rebillat AS, Coppus A, Levin J, Zaman SH. The Clinical and Neuropathological Features of Sporadic (Late-Onset) and Genetic Forms of Alzheimer's Disease. J Clin Med 2021; 10:4582. [PMID: 34640600 PMCID: PMC8509365 DOI: 10.3390/jcm10194582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
The purpose of this review is to compare and highlight the clinical and pathological aspects of genetic versus acquired Alzheimer's disease: Down syndrome-associated Alzheimer's disease in (DSAD) and Autosomal Dominant Alzheimer's disease (ADAD) are compared with the late-onset form of the disease (LOAD). DSAD and ADAD present in a younger population and are more likely to manifest with non-amnestic (such as dysexecutive function features) in the prodromal phase or neurological features (such as seizures and paralysis) especially in ADAD. The very large variety of mutations associated with ADAD explains the wider range of phenotypes. In the LOAD, age-associated comorbidities explain many of the phenotypic differences.
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Affiliation(s)
- Tanzil Rujeedawa
- Cambridge Intellectual & Developmental Disabilities Research Group, Department of Psychiatry, University of Cambridge, Cambridge CB2 8PQ, UK; (T.R.); (E.C.F.); (I.C.H.C.)
| | - Eva Carrillo Félez
- Cambridge Intellectual & Developmental Disabilities Research Group, Department of Psychiatry, University of Cambridge, Cambridge CB2 8PQ, UK; (T.R.); (E.C.F.); (I.C.H.C.)
| | - Isabel C. H. Clare
- Cambridge Intellectual & Developmental Disabilities Research Group, Department of Psychiatry, University of Cambridge, Cambridge CB2 8PQ, UK; (T.R.); (E.C.F.); (I.C.H.C.)
- Cambridgeshire and Peterborough Foundation NHS Trust, Fulbourn CB21 5EF, UK
| | - Juan Fortea
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain;
- Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
- Barcelona Down Medical Center, Fundació Catalana Síndrome de Down, 08029 Barcelona, Spain
| | - Andre Strydom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK;
- South London and the Maudsley NHS Foundation Trust, The LonDowns Consortium, London SE5 8AZ, UK
| | | | - Antonia Coppus
- Department for Primary and Community Care, Department of Primary and Community Care (149 ELG), Radboud University Nijmegen Medical Center, P.O. Box 9101, 6525 GA Nijmegen, The Netherlands;
| | - Johannes Levin
- Department of Neurology, Ludwig-Maximilians-Universität München, 80539 Munich, Germany;
- German Center for Neurodegenerative Diseases, Feodor-Lynen-Strasse 17, 81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
| | - Shahid H. Zaman
- Cambridge Intellectual & Developmental Disabilities Research Group, Department of Psychiatry, University of Cambridge, Cambridge CB2 8PQ, UK; (T.R.); (E.C.F.); (I.C.H.C.)
- Cambridgeshire and Peterborough Foundation NHS Trust, Fulbourn CB21 5EF, UK
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10
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Sadikovic B, Levy MA, Aref-Eshghi E. Functional annotation of genomic variation: DNA methylation episignatures in neurodevelopmental Mendelian disorders. Hum Mol Genet 2021; 29:R27-R32. [PMID: 32644126 DOI: 10.1093/hmg/ddaa144] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/19/2020] [Accepted: 07/06/2020] [Indexed: 11/13/2022] Open
Abstract
The breadth and complexity of genetic testing in patients with suspected Mendelian neurodevelopmental disorders has rapidly expanded in the past two decades. However, in spite of advances in genomic technologies, genetic diagnosis remains elusive in more than half of these patients. Epigenomics, and in particular genomic DNA methylation profiles, are now known to be associated with the underpinning genetic defects in a growing number of Mendelian disorders. These often highly specific and sensitive molecular biomarkers have been used to screen these patient populations, resolve ambiguous clinical cases and interpret genetic variants of unknown clinical significance. Increasing the diagnostic yield beyond genomic sequencing technologies has rapidly propelled epigenomics to clinical utilization, with recent introduction of DNA methylation 'EpiSign' analysis in clinical diagnostic laboratories. This review provides an overview of the principles, applications and limitations of DNA methylation episignature analysis in patients with neurodevelopmental Mendelian disorders, and discusses clinical implications of this emerging diagnostic technology.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario N6A5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario N6A3K7, Canada.,Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6A5C1, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario N6A5W9, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario N6A5W9, Canada
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11
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Yarema NM, Boyarchuk OR, Chornomydz IB, Panasiuk YV. Numerical and Structural Chromosomal Abnormalities Associated with Immunodeficiency. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721040137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Reza Karimzadeh M, Ehtesham N, Mortazavi D, Azhdari S, Mosallaei M, Nezamnia M. Alterations of epigenetic landscape in Down syndrome carrying pregnancies: A systematic review of case-control studies. Eur J Obstet Gynecol Reprod Biol 2021; 264:189-199. [PMID: 34325214 DOI: 10.1016/j.ejogrb.2021.06.027] [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: 01/07/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Great attention is currently paid to both the pathogenetic mechanisms and non-invasive prenatal diagnosis (NIPD) of Down syndrome (DS). It has been posited that dysregulation of epigenetic signatures including DNA methylation and microRNAs (miRNAs) crucially contribute to the pathomechanism of DS. Therefore, we aimed to perform a systematic review of case-control publications that have examined the differences in epigenetic landscape between pregnancies bearing euploid fetuses and those affected with DS to provide a focused insight into the pathophysiology of DS and also novel biomarkers for NIPD of DS. STUDY DESIGN Pertinent keywords were utilized to search into PubMed, Scopus, and Google Scholar. We enrolled studies that have compared the pattern of miRNAs expression profile or DNA methylation between pregnant women who carries DS fetuses and those with euploid fetuses. RESULTS An assessment of 599 articles resulted in, finally, 18 eligible studies (12 miRNAs and 6 DNA methylation). The most investigated miRNAs were those that are encoded by genes on chromosome 21 and more hypermethylation regions in DS fetuses than euploids with nearly evenly distribution on all chromosomes were found. Distinct mechanisms with potential therapeutic purposes have been put forward for the involvement of epigenetic perturbations in the etiopathogenesis of DS. CONCLUSION There is a disagreement in the recruiting of epigenetic biomarkers for NIPD of DS. This heterogeneity in results of the qualified publications emanates from confounding factors such as differences in demographic data of participants, analytical platforms, and study design. Hence, before harnessing epigenetic signatures for NIPD of DS, more experiments are required.
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Affiliation(s)
- Mohammad Reza Karimzadeh
- Department of Medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Naeim Ehtesham
- Student Research Committee, University of Social Welfare and Rehabilitation Sciences , Tehran, Iran; Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Deniz Mortazavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sara Azhdari
- Department of Anatomy and Embryology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Meysam Mosallaei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maria Nezamnia
- Department of Obstetrics and Gynecology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
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13
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Illouz T, Biragyn A, Iulita MF, Flores-Aguilar L, Dierssen M, De Toma I, Antonarakis SE, Yu E, Herault Y, Potier MC, Botté A, Roper R, Sredni B, London J, Mobley W, Strydom A, Okun E. Immune Dysregulation and the Increased Risk of Complications and Mortality Following Respiratory Tract Infections in Adults With Down Syndrome. Front Immunol 2021; 12:621440. [PMID: 34248930 PMCID: PMC8267813 DOI: 10.3389/fimmu.2021.621440] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The risk of severe outcomes following respiratory tract infections is significantly increased in individuals over 60 years, especially in those with chronic medical conditions, i.e., hypertension, diabetes, cardiovascular disease, dementia, chronic respiratory disease, and cancer. Down Syndrome (DS), the most prevalent intellectual disability, is caused by trisomy-21 in ~1:750 live births worldwide. Over the past few decades, a substantial body of evidence has accumulated, pointing at the occurrence of alterations, impairments, and subsequently dysfunction of the various components of the immune system in individuals with DS. This associates with increased vulnerability to respiratory tract infections in this population, such as the influenza virus, respiratory syncytial virus, SARS-CoV-2 (COVID-19), and bacterial pneumonias. To emphasize this link, here we comprehensively review the immunobiology of DS and its contribution to higher susceptibility to severe illness and mortality from respiratory tract infections.
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Affiliation(s)
- Tomer Illouz
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
- The Paul Feder Laboratory on Alzheimer’s Disease Research, Bar-Ilan University, Ramat Gan, Israel
| | - Arya Biragyn
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institute of Health, Baltimore, MD, United States
| | - Maria Florencia Iulita
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Biomedical Research Institute Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Lisi Flores-Aguilar
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Mara Dierssen
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
- Biomedical Research Networking Center for Rare Diseases (CIBERER), Barcelona, Spain
| | - Ilario De Toma
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
- Biomedical Research Networking Center for Rare Diseases (CIBERER), Barcelona, Spain
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Eugene Yu
- The Children’s Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
- Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire, IGBMC - UMR 7104 - Inserm U1258, Illkirch, France
| | - Marie-Claude Potier
- Paris Brain Institute (ICM), CNRS UMR7225, INSERM U1127, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Alexandra Botté
- Paris Brain Institute (ICM), CNRS UMR7225, INSERM U1127, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Randall Roper
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Benjamin Sredni
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - William Mobley
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Andre Strydom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry Psychology and Neuroscience, King’s College London, London, United Kingdom
- South London and Maudsley NHS Foundation Trust, London, United Kingdom
| | - Eitan Okun
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
- The Paul Feder Laboratory on Alzheimer’s Disease Research, Bar-Ilan University, Ramat Gan, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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14
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Abstract
OBJECTIVES Recent evidence from the fields of microbiology and immunology, as well as a small number of human sepsis studies, suggest that epigenetic regulation may play a central role in the pathogenesis of sepsis. The term "epigenetics" refers to regulatory mechanisms that control gene expression but are not related to changes in DNA sequence. These include DNA methylation, histone modifications, and regulation of transcription via non-coding RNAs. Epigenetic modifications, occurring in response to external stressors, lead to changes in gene expression, and thus lie at the intersection between genetics and the environment. In this review, we examine data from in vitro studies, animal studies, and the existing human sepsis studies in epigenetics to demonstrate that epigenetic mechanisms are likely central to the pathogenesis of sepsis and that epigenetic therapies may have potential in the treatment of sepsis and its associated organ failures. DATA SOURCES Online search of published scientific literature via Pubmed using the term "epigenetics" in combination with the terms "sepsis", "infection", "bacterial infection", "viral infection", "critical illness", "acute respiratory distress syndrome", and "acute lung injury". STUDY SELECTION Articles were chosen for inclusion based on their relevance to sepsis, acute inflammation, sepsis-related immune suppression, and sepsis-related organ failure. Reference lists were reviewed to identify additional relevant articles. DATA EXTRACTION Relevant data was extracted and synthesized for narrative review. DATA SYNTHESIS Epigenetic regulation is a key determinant of gene expression in sepsis. At the onset of infection, host-pathogen interactions often result in epigenetic alterations to host cells that favor pathogen survival. In parallel, the host inflammatory response is characterized by epigenetic modifications in key regulatory genes, including tumor necrosis factor and interleukin-1β. In human sepsis patients, multiple epigenetic modifying enzymes show differential expression in early sepsis, suggesting a role for epigenetics in coordinating the response to infection. In the later stages of sepsis, epigenetic modifications accompany endotoxin tolerance and the immune-suppressed state. In animal models, treatment with epigenetic modifiers can mitigate the effects of sepsis and improve survival as well as reverse sepsis-associated organ injury. CONCLUSIONS Epigenetic modifications are associated with key phases of sepsis, from the host-pathogen interaction, to acute inflammation, to immune suppression. Epigenetic markers show promise in the diagnosis and prognosis of sepsis and epigenetic modifying agents show promise as therapeutic tools in animal models of sepsis. Human studies in the area of epigenetics are sorely lacking and should be a priority for sepsis researchers.
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Abstract
Children show a higher incidence of leukaemia compared with young adolescents, yet their cells are less damaged because of their young age. Children with Down syndrome (DS) have an even higher risk of developing leukaemia during the first years of life. The presence of a constitutive trisomy of chromosome 21 (T21) in DS acts as a genetic driver for leukaemia development, however, additional oncogenic mutations are required. Therefore, T21 provides the opportunity to better understand leukaemogenesis in children. Here, we describe the increased risk of leukaemia in DS during childhood from a somatic evolutionary view. According to this idea, cancer is caused by a variation in inheritable phenotypes within cell populations that are subjected to selective forces within the tissue context. We propose a model in which the increased risk of leukaemia in DS children derives from higher rates of mutation accumulation, already present during fetal development, which is further enhanced by changes in selection dynamics within the fetal liver niche. This model could possibly be used to understand the rate-limiting steps of leukaemogenesis early in life.
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16
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Muskens IS, Li S, Jackson T, Elliot N, Hansen HM, Myint SS, Pandey P, Schraw JM, Roy R, Anguiano J, Goudevenou K, Siegmund KD, Lupo PJ, de Bruijn MFTR, Walsh KM, Vyas P, Ma X, Roy A, Roberts I, Wiemels JL, de Smith AJ. The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis. Nat Commun 2021; 12:821. [PMID: 33547282 PMCID: PMC7865055 DOI: 10.1038/s41467-021-21064-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Down syndrome is associated with genome-wide perturbation of gene expression, which may be mediated by epigenetic changes. We perform an epigenome-wide association study on neonatal bloodspots comparing 196 newborns with Down syndrome and 439 newborns without Down syndrome, adjusting for cell-type heterogeneity, which identifies 652 epigenome-wide significant CpGs (P < 7.67 × 10-8) and 1,052 differentially methylated regions. Differential methylation at promoter/enhancer regions correlates with gene expression changes in Down syndrome versus non-Down syndrome fetal liver hematopoietic stem/progenitor cells (P < 0.0001). The top two differentially methylated regions overlap RUNX1 and FLI1, both important regulators of megakaryopoiesis and hematopoietic development, with significant hypermethylation at promoter regions of these two genes. Excluding Down syndrome newborns harboring preleukemic GATA1 mutations (N = 30), identified by targeted sequencing, has minimal impact on the epigenome-wide association study results. Down syndrome has profound, genome-wide effects on DNA methylation in hematopoietic cells in early life, which may contribute to the high frequency of hematological problems, including leukemia, in children with Down syndrome.
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Affiliation(s)
- Ivo S Muskens
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Thomas Jackson
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Natalina Elliot
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Priyatama Pandey
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Jeremy M Schraw
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Ritu Roy
- Computational Biology and Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Joaquin Anguiano
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Katerina Goudevenou
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Kimberly D Siegmund
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Anindita Roy
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Irene Roberts
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA.
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Haghshenas S, Bhai P, Aref-Eshghi E, Sadikovic B. Diagnostic Utility of Genome-Wide DNA Methylation Analysis in Mendelian Neurodevelopmental Disorders. Int J Mol Sci 2020; 21:ijms21239303. [PMID: 33291301 PMCID: PMC7730976 DOI: 10.3390/ijms21239303] [Citation(s) in RCA: 14] [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: 11/22/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mendelian neurodevelopmental disorders customarily present with complex and overlapping symptoms, complicating the clinical diagnosis. Individuals with a growing number of the so-called rare disorders exhibit unique, disorder-specific DNA methylation patterns, consequent to the underlying gene defects. Besides providing insights to the pathophysiology and molecular biology of these disorders, we can use these epigenetic patterns as functional biomarkers for the screening and diagnosis of these conditions. This review summarizes our current understanding of DNA methylation episignatures in rare disorders and describes the underlying technology and analytical approaches. We discuss the computational parameters, including statistical and machine learning methods, used for the screening and classification of genetic variants of uncertain clinical significance. Describing the rationale and principles applied to the specific computational models that are used to develop and adapt the DNA methylation episignatures for the diagnosis of rare disorders, we highlight the opportunities and challenges in this emerging branch of diagnostic medicine.
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Affiliation(s)
- Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Correspondence:
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18
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Roubroeks JAY, Smith AR, Smith RG, Pishva E, Ibrahim Z, Sattlecker M, Hannon EJ, Kłoszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Wahlund LO, Aarsland D, Proitsi P, Hodges A, Lovestone S, Newhouse SJ, Dobson RJB, Mill J, van den Hove DLA, Lunnon K. An epigenome-wide association study of Alzheimer's disease blood highlights robust DNA hypermethylation in the HOXB6 gene. Neurobiol Aging 2020; 95:26-45. [PMID: 32745807 PMCID: PMC7649340 DOI: 10.1016/j.neurobiolaging.2020.06.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/27/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022]
Abstract
A growing number of epigenome-wide association studies have demonstrated a role for DNA methylation in the brain in Alzheimer's disease. With the aim of exploring peripheral biomarker potential, we have examined DNA methylation patterns in whole blood collected from 284 individuals in the AddNeuroMed study, which included 89 nondemented controls, 86 patients with Alzheimer's disease, and 109 individuals with mild cognitive impairment, including 38 individuals who progressed to Alzheimer's disease within 1 year. We identified significant differentially methylated regions, including 12 adjacent hypermethylated probes in the HOXB6 gene in Alzheimer's disease, which we validated using pyrosequencing. Using weighted gene correlation network analysis, we identified comethylated modules of genes that were associated with key variables such as APOE genotype and diagnosis. In summary, this study represents the first large-scale epigenome-wide association study of Alzheimer's disease and mild cognitive impairment using blood. We highlight the differences in various loci and pathways in early disease, suggesting that these patterns relate to cognitive decline at an early stage.
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Affiliation(s)
| | - Adam R Smith
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Rebecca G Smith
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- College of Medicine and Health, University of Exeter, Exeter, UK; School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Zina Ibrahim
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IOPPN), King's College London, London, UK; Farr Institute of Health Informatics Research, University College London, London, UK
| | - Martina Sattlecker
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IOPPN), King's College London, London, UK
| | - Eilis J Hannon
- College of Medicine and Health, University of Exeter, Exeter, UK
| | | | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland; Neurocenter, Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Magda Tsolaki
- 1st Department of Neurology, Memory and Dementia Unit, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Lars-Olof Wahlund
- NVS Department, Section for Clinical Geriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Dag Aarsland
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Centre for Age-Related Diseases, Stavanger University Hospital, Stavanger, Norway
| | - Petroula Proitsi
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, UK
| | - Angela Hodges
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simon Lovestone
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK; Current Affiliation at Janssen-Cilag UK
| | - Stephen J Newhouse
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, UK
| | - Richard J B Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IOPPN), King's College London, London, UK; Farr Institute of Health Informatics Research, University College London, London, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Daniël L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter, Exeter, UK.
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20
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Letko A, Minor KM, Jagannathan V, Seefried FR, Mickelson JR, Oliehoek P, Drögemüller C. Genomic diversity and population structure of the Leonberger dog breed. Genet Sel Evol 2020; 52:61. [PMID: 33054768 PMCID: PMC7557023 DOI: 10.1186/s12711-020-00581-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Leonberger is a giant dog breed formed in the 1850s in Germany. Its post-World War II popularity has resulted in a current global population of ~ 30,000 dogs. The breed has predispositions to neurodegenerative disorders and cancer, which is likely due in large part to limited genetic diversity. However, to date there is no scientific literature on the overall demography and genomic architecture of this breed. RESULTS We assessed extensive pedigree records, SNP array genotype data, and whole-genome sequences (WGS) on 142,072, 1203 and 39 Leonberger dogs, respectively. Pedigree analyses identified 22 founder animals and revealed an apparent popular sire effect. The average pedigree-based inbreeding coefficient of 0.29 and average kinship of 0.31 show a dramatic loss of genetic diversity. The observed average life span decreased over time from 9.4 years in 1989 to 7.7 years in 2004. A global health survey confirmed a high prevalence of cancer and neurological disorders. Analysis of SNP-based runs of homozygosity (ROH) identified 125,653 ROH with an average length of 5.88 Mb, and confirmed an average inbreeding coefficient of 0.28. Genome-wide filtering of the WGS data revealed 28 non-protein-changing variants that were present in all Leonberger individuals and a list of 22 potentially pathogenic variants for neurological disorders of which 50% occurred only in Leonbergers and 50% occurred rarely in other breeds. Furthermore, one of the two mtDNA haplogroups detected was present in one dog only. CONCLUSIONS The increasing size of the Leonberger population has been accompanied by a considerable loss of genetic diversity after the bottleneck that occurred in the 1940s due to the intensive use of popular sires resulting in high levels of inbreeding. This might explain the high prevalence of certain disorders; however, genomic data provide no evidence for fixed coding variants that explain these predispositions. The list of candidate causative variants for polyneuropathy needs to be further evaluated. Preserving the current genetic diversity is possible by increasing the number of individuals for breeding while restricting the number of litters per sire/dam. In addition, outcrossing would help optimize long-term genetic diversity and contribute to the sustainability and health of the population.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Katie M. Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | - James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108 USA
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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21
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Tolmacheva EN, Vasilyev SA, Lebedev IN. Aneuploidy and DNA Methylation as Mirrored Features of Early Human Embryo Development. Genes (Basel) 2020; 11:E1084. [PMID: 32957536 PMCID: PMC7564410 DOI: 10.3390/genes11091084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
Genome stability is an integral feature of all living organisms. Aneuploidy is the most common cause of fetal death in humans. The timing of bursts in increased aneuploidy frequency coincides with the waves of global epigenetic reprogramming in mammals. During gametogenesis and early embryogenesis, parental genomes undergo two waves of DNA methylation reprogramming. Failure of these processes can critically affect genome stability, including chromosome segregation during cell division. Abnormal methylation due to errors in the reprogramming process can potentially lead to aneuploidy. On the other hand, the presence of an entire additional chromosome, or chromosome loss, can affect the global genome methylation level. The associations of these two phenomena are well studied in the context of carcinogenesis, but here, we consider the relationship of DNA methylation and aneuploidy in early human and mammalian ontogenesis. In this review, we link these two phenomena and highlight the critical ontogenesis periods and genome regions that play a significant role in human reproduction and in the formation of pathological phenotypes in newborns with chromosomal aneuploidy.
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Affiliation(s)
- Ekaterina N. Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, 634050 Tomsk, Russia; (S.A.V.); (I.N.L.)
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22
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Down syndrome, accelerated aging and immunosenescence. Semin Immunopathol 2020; 42:635-645. [PMID: 32705346 PMCID: PMC7666319 DOI: 10.1007/s00281-020-00804-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Down syndrome is the most common chromosomal disorder, associated with moderate to severe intellectual disability. While life expectancy of Down syndrome population has greatly increased over the last decades, mortality rates are still high and subjects are facing prematurely a phenomenon of atypical and accelerated aging. The presence of an immune impairment in Down syndrome subjects is suggested for a long time by the existence of an increased incidence of infections, the incomplete efficacy of vaccinations, and a high prevalence of autoimmunity. Immunologic abnormalities have been described since many years in this population, both from a numerical and a functional points of view, and these abnormalities can mirror the ones observed during normal aging. In this review, we summarize our knowledge on immunologic disturbances commonly observed in subjects with Down syndrome, and in innate and adaptive immunity, as well as regarding chronic inflammation. We then discuss the role of accelerated aging in these observed abnormalities and finally review the potential age-associated molecular and cellular mechanisms involved.
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23
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Ponroy Bally B, Farmer WT, Jones EV, Jessa S, Kacerovsky JB, Mayran A, Peng H, Lefebvre JL, Drouin J, Hayer A, Ernst C, Murai KK. Human iPSC-derived Down syndrome astrocytes display genome-wide perturbations in gene expression, an altered adhesion profile, and increased cellular dynamics. Hum Mol Genet 2020; 29:785-802. [PMID: 31943018 PMCID: PMC7104679 DOI: 10.1093/hmg/ddaa003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/31/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Down syndrome (DS), caused by the triplication of human chromosome 21, leads to significant alterations in brain development and is a major genetic cause of intellectual disability. While much is known about changes to neurons in DS, the effects of trisomy 21 on non-neuronal cells such as astrocytes are poorly understood. Astrocytes are critical for brain development and function, and their alteration may contribute to DS pathophysiology. To better understand the impact of trisomy 21 on astrocytes, we performed RNA-sequencing on astrocytes from newly produced DS human induced pluripotent stem cells (hiPSCs). While chromosome 21 genes were upregulated in DS astrocytes, we found consistent up- and down-regulation of genes across the genome with a strong dysregulation of neurodevelopmental, cell adhesion and extracellular matrix molecules. ATAC (assay for transposase-accessible chromatin)-seq also revealed a global alteration in chromatin state in DS astrocytes, showing modified chromatin accessibility at promoters of cell adhesion and extracellular matrix genes. Along with these transcriptomic and epigenomic changes, DS astrocytes displayed perturbations in cell size and cell spreading as well as modifications to cell-cell and cell-substrate recognition/adhesion, and increases in cellular motility and dynamics. Thus, triplication of chromosome 21 is associated with genome-wide transcriptional, epigenomic and functional alterations in astrocytes that may contribute to altered brain development and function in DS.
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Affiliation(s)
- Blandine Ponroy Bally
- Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
| | - W Todd Farmer
- Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
| | - Emma V Jones
- Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
| | - Selin Jessa
- Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 2A7, Canada
| | - J Benjamin Kacerovsky
- Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
| | - Alexandre Mayran
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Huashan Peng
- Department of Psychiatry, McGill University, Montreal, QC H4H 1R3, Canada
- Department of Human Genetics, McGill University, Montreal, QC H4H 1R3, Canada
- Douglas Hospital Research Institute, Verdun, QC H4H 1R3, Canada
| | - Julie L Lefebvre
- Department of Molecular Genetics, Program for Neuroscience and Mental Health, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Jacques Drouin
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Arnold Hayer
- Department of Biology, McGill University, Bellini Life Sciences Complex, Montreal, QC H3G 0B1, Canada
| | - Carl Ernst
- Department of Psychiatry, McGill University, Montreal, QC H4H 1R3, Canada
- Department of Human Genetics, McGill University, Montreal, QC H4H 1R3, Canada
- Douglas Hospital Research Institute, Verdun, QC H4H 1R3, Canada
| | - Keith K Murai
- Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 2A7, Canada
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Gomez W, Morales R, Maracaja-Coutinho V, Parra V, Nassif M. Down syndrome and Alzheimer's disease: common molecular traits beyond the amyloid precursor protein. Aging (Albany NY) 2020; 12:1011-1033. [PMID: 31918411 PMCID: PMC6977673 DOI: 10.18632/aging.102677] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/25/2019] [Indexed: 02/07/2023]
Abstract
Alzheimer’s disease (AD) is the most prevalent type of dementia. Down syndrome (DS) is the leading genetic risk factor for Early-Onset AD, prematurely presenting the classic pathological features of the brain with AD. Augmented gene dosage, including the APP gene, could partially cause this predisposition. Recent works have revealed that alterations in chromosome location due to the extra Chromosome 21, as well as epigenetic modifications, could promote changes in gene expression other than those from Chromosome 21. As a result, similar pathological features and cellular dysfunctions in DS and AD, including impaired autophagy, lysosomal activity, and mitochondrial dysfunction, could be controlled beyond APP overexpression. In this review, we highlight some recent data regarding the origin of the shared features between DS and AD and explore the mechanisms concerning cognitive deficiencies in DS associated with dementia, which could shed some light into the search for new therapeutic targets for AD treatment.
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Affiliation(s)
- Wileidy Gomez
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile.,Departamento de Bioquímica y Biología Molecular and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Rodrigo Morales
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,CIBQA, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Vinicius Maracaja-Coutinho
- Departamento de Bioquímica y Biología Molecular and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.,Centro de Modelamiento Molecular, Biofísica y Bioinformática (CM2B2), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Valentina Parra
- Departamento de Bioquímica y Biología Molecular and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.,Center for Exercise, Metabolism, and Cancer Studies (CEMC), Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Autophagy Research Center, Universidad de Chile, Santiago, Chile
| | - Melissa Nassif
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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25
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Laan L, Klar J, Sobol M, Hoeber J, Shahsavani M, Kele M, Fatima A, Zakaria M, Annerén G, Falk A, Schuster J, Dahl N. DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors. Clin Epigenetics 2020; 12:9. [PMID: 31915063 PMCID: PMC6950999 DOI: 10.1186/s13148-019-0803-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Background Down syndrome (DS) is characterized by neurodevelopmental abnormalities caused by partial or complete trisomy of human chromosome 21 (T21). Analysis of Down syndrome brain specimens has shown global epigenetic and transcriptional changes but their interplay during early neurogenesis remains largely unknown. We differentiated induced pluripotent stem cells (iPSCs) established from two DS patients with complete T21 and matched euploid donors into two distinct neural stages corresponding to early- and mid-gestational ages. Results Using the Illumina Infinium 450K array, we assessed the DNA methylation pattern of known CpG regions and promoters across the genome in trisomic neural iPSC derivatives, and we identified a total of 500 stably and differentially methylated CpGs that were annotated to CpG islands of 151 genes. The genes were enriched within the DNA binding category, uncovering 37 factors of importance for transcriptional regulation and chromatin structure. In particular, we observed regional epigenetic changes of the transcription factor genes ZNF69, ZNF700 and ZNF763 as well as the HOXA3, HOXB3 and HOXD3 genes. A similar clustering of differential methylation was found in the CpG islands of the HIST1 genes suggesting effects on chromatin remodeling. Conclusions The study shows that early established differential methylation in neural iPSC derivatives with T21 are associated with a set of genes relevant for DS brain development, providing a novel framework for further studies on epigenetic changes and transcriptional dysregulation during T21 neurogenesis.
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Affiliation(s)
- Loora Laan
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Maria Sobol
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | | | - Malin Kele
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Muhammad Zakaria
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jens Schuster
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden.
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26
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Haertle L, Müller T, Lardenoije R, Maierhofer A, Dittrich M, Riemens RJM, Stora S, Roche M, Leber M, Riedel-Heller S, Wagner M, Scherer M, Ravel A, Mircher C, Cieuta-Walti C, Durand S, van de Hove DLA, Hoffmann P, Ramirez A, Haaf T, El Hajj N, Mégarbané A. Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer's disease-related dysregulation. Clin Epigenetics 2019; 11:195. [PMID: 31843015 PMCID: PMC6916110 DOI: 10.1186/s13148-019-0787-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/25/2019] [Indexed: 11/28/2022] Open
Abstract
Abstract Background Trisomy 21 (T21) is associated with intellectual disability that ranges from mild to profound with an average intellectual quotient of around 50. Furthermore, T21 patients have a high risk of developing Alzheimer’s disease (AD) early in life, characterized by the presence of senile plaques of amyloid protein and neurofibrillary tangles, leading to neuronal loss and cognitive decline. We postulate that epigenetic factors contribute to the observed variability in intellectual disability, as well as at the level of neurodegeneration seen in T21 individuals. Materials and Methods A genome-wide DNA methylation study was performed using Illumina Infinium® MethylationEPIC BeadChips on whole blood DNA of 3 male T21 patients with low IQ, 8 T21 patients with high IQ (4 males and 4 females), and 21 age- and sex-matched control samples (12 males and 9 females) in order to determine whether DNA methylation alterations could help explain variation in cognitive impairment between individuals with T21. In view of the increased risk of developing AD in T21 individuals, we additionally investigated the T21-associated sites in published blood DNA methylation data from the AgeCoDe cohort (German study on Ageing, Cognition, and Dementia). AgeCoDe represents a prospective longitudinal study including non-demented individuals at baseline of which a part develops AD dementia at follow-up. Results Two thousand seven hundred sixteen differentially methylated sites and regions discriminating T21 and healthy individuals were identified. In the T21 high and low IQ comparison, a single CpG located in the promoter of PELI1 was differentially methylated after multiple testing adjustment. For the same contrast, 69 differentially methylated regions were identified. Performing a targeted association analysis for the significant T21-associated CpG sites in the AgeCoDe cohort, we found that 9 showed significant methylation differences related to AD dementia, including one in the ADAM10 gene. This gene has previously been shown to play a role in the prevention of amyloid plaque formation in the brain. Conclusion The differentially methylated regions may help understand the interaction between methylation alterations and cognitive function. In addition, ADAM10 might be a valuable blood-based biomarker for at least the early detection of AD.
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Affiliation(s)
- Larissa Haertle
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Division of Hematology and Oncology, Department of Internal Medicine II, University Hospital, Wuerzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilian University, Wuerzburg, Germany
| | - Roy Lardenoije
- Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Department of Bioinformatics, Julius Maximilian University, Wuerzburg, Germany
| | - Renzo J M Riemens
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands
| | - Samantha Stora
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Mathilde Roche
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Markus Leber
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937, Cologne, Germany.,Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103, Leipzig, Germany
| | - Michael Wagner
- Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Centre Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Aimé Ravel
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Clotilde Mircher
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | | | - Sophie Durand
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Daniel L A van de Hove
- Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 53127, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, 53127, Bonn, Germany.,Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, CH-4058, Basel, Switzerland
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937, Cologne, Germany.,Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - André Mégarbané
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France.
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27
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Lim JH, Kang YJ, Lee BY, Han YJ, Chung JH, Kim MY, Kim MH, Kim JW, Cho YH, Ryu HM. Epigenome-wide base-resolution profiling of DNA methylation in chorionic villi of fetuses with Down syndrome by methyl-capture sequencing. Clin Epigenetics 2019; 11:180. [PMID: 31801612 PMCID: PMC6894197 DOI: 10.1186/s13148-019-0756-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenetic mechanisms provide an interface between environmental factors and the genome and are influential in various diseases. These mechanisms, including DNA methylation, influence the regulation of development, differentiation, and establishment of cellular identity. Here, we performed high-throughput methylome profiling to determine whether differential patterns of DNA methylation correlate with Down syndrome (DS). MATERIALS AND METHODS We extracted DNA from the chorionic villi cells of five normal and five DS fetuses at the early developmental stage (12-13 weeks of gestation). Methyl-capture sequencing (MC-Seq) was used to investigate the methylation levels of CpG sites distributed across the whole genome to identify differentially methylated CpG sites (DMCs) and regions (DMRs) in DS. New functional annotations of DMR genes using bioinformatics tools were predicted. RESULTS DNA hypermethylation was observed in DS fetal chorionic villi cells. Significant differences were evident for 4,439 DMCs, including hypermethylation (n = 4,261) and hypomethylation (n = 178). Among them, 140 hypermethylated DMRs and only 1 hypomethylated DMR were located on 121 genes and 1 gene, respectively. One hundred twenty-two genes, including 141 DMRs, were associated with heart morphogenesis and development of the ear, thyroid gland, and nervous systems. The genes were significantly associated with DS and various diseases, including hepatopulmonary syndrome, conductive hearing loss, holoprosencephaly, heart diseases, glaucoma, and musculoskeletal abnormalities. CONCLUSIONS This is the first study to compare the whole-epigenome DNA methylation pattern of the chorionic villi cells from normal and DS fetuses at the early developmental-stage using MC-seq. Overall, our results indicate that the chorionic villi cells of DS fetuses are hypermethylated in all autosomes and suggested that altered DNA methylation may be a recurrent and functionally relevant downstream response to DS in human cells. This study provides basic information for future research focused on the pathophysiology of the DS and its potential effects, as well as the role DNA methylation plays in the early developmental stage of DS fetuses.
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Affiliation(s)
- Ji Hyae Lim
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea.,Department of Medical Genetics, College of Medicine, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Yu-Jung Kang
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea
| | - Bom Yi Lee
- SD Genomics Co., Ltd., Seoul, Republic of Korea
| | - You Jung Han
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Jin Hoon Chung
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Moon Young Kim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Min Hyoung Kim
- Department of Obstetrics Gynecology, Mizmedi Hospital, Seoul, Republic of Korea
| | - Jin Woo Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Republic of Korea
| | - Youl-Hee Cho
- Department of Medical Genetics, College of Medicine, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Hyun Mee Ryu
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea. .,Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, 59, Yatap-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13496, Republic of Korea.
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28
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Abstract
Aneuploidy (i.e., abnormal chromosome number) is the leading cause of miscarriage and congenital defects in humans. Moreover, aneuploidy is ubiquitous in cancer. The deleterious phenotypes associated with aneuploidy are likely a result of the imbalance in the levels of gene products derived from the additional chromosome(s). Here, we summarize the current knowledge on how the presence of extra chromosomes impacts gene expression. We describe studies that have found a strict correlation between gene dosage and transcript levels as wells as studies that have found a less stringent correlation, hinting at the possible existence of dosage compensation mechanisms. We conclude by peering into the epigenetic changes found in aneuploid cells and outlining current knowledge gaps and potential areas of future investigation.
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Affiliation(s)
- Shihoko Kojima
- Department of Biological Sciences & Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Daniela Cimini
- Department of Biological Sciences & Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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29
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Yu YE, Xing Z, Do C, Pao A, Lee EJ, Krinsky-McHale S, Silverman W, Schupf N, Tycko B. Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019; 251:1-28. [PMID: 32057305 PMCID: PMC7286740 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of an extra copy of human chromosome 21 (Hsa21) leads to a constellation of phenotypic manifestations in Down syndrome (DS), including prominent effects on the brain and immune system. Intensive efforts to unravel the molecular mechanisms underlying these phenotypes may help developing effective therapies, both in DS and in the general population. Here we review recent progress in genetic and epigenetic analysis of trisomy 21 (Ts21). New mouse models of DS based on syntenic conservation of segments of the mouse and human chromosomes are starting to clarify the contributions of chromosomal subregions and orthologous genes to specific phenotypes in DS. The expression of genes on Hsa21 is regulated by epigenetic mechanisms, and with recent findings of highly recurrent gene-specific changes in DNA methylation patterns in brain and immune system cells with Ts21, the epigenomics of DS has become an active research area. Here we highlight the value of combining human studies with mouse models for defining DS critical genes and understanding the trans-acting effects of a simple chromosomal aneuploidy on genome-wide epigenetic patterning. These genetic and epigenetic studies are starting to uncover fundamental biological mechanisms, leading to insights that may soon become therapeutically relevant.
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Affiliation(s)
- Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States; Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States.
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Catherine Do
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Eun Joon Lee
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Sharon Krinsky-McHale
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pediatrics, University of California at Irvine, Irvine, CA, United States
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Benjamin Tycko
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States.
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30
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Laufer BI, Hwang H, Vogel Ciernia A, Mordaunt CE, LaSalle JM. Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights. Epigenetics 2019; 14:672-684. [PMID: 31010359 PMCID: PMC6557615 DOI: 10.1080/15592294.2019.1609867] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/08/2019] [Accepted: 04/15/2019] [Indexed: 01/07/2023] Open
Abstract
Down Syndrome (DS) is the most common genetic cause of intellectual disability, in which an extra copy of human chromosome 21 (HSA21) affects regional DNA methylation profiles across the genome. Although DNA methylation has been previously examined at select regulatory regions across the genome in a variety of DS tissues and cells, differentially methylated regions (DMRs) have yet to be examined in an unbiased sequencing-based approach. Here, we present the first analysis of DMRs from whole genome bisulfite sequencing (WGBS) data of human DS and matched control brain, specifically frontal cortex. While no global differences in DNA methylation were observed, we identified 3,152 DS-DMRs across the entire genome, the majority of which were hypermethylated in DS. DS-DMRs were significantly enriched at CpG islands and de-enriched at specific gene body and regulatory regions. Functionally, the hypermethylated DS-DMRs were enriched for one-carbon metabolism, membrane transport, and glutamatergic synaptic signalling, while the hypomethylated DMRs were enriched for proline isomerization, glial immune response, and apoptosis. Furthermore, in a cross-tissue comparison to previous studies of DNA methylation from diverse DS tissues and reference epigenomes, hypermethylated DS-DMRs showed a strong cross-tissue concordance, while a more tissue-specific pattern was observed for the hypomethylated DS-DMRs. Overall, this approach highlights that low-coverage WGBS of clinical samples can identify epigenetic alterations to known biological pathways, which are potentially relevant to therapeutic treatments and include metabolic pathways. These results also provide new insights into the genome-wide effects of genetic alterations on DNA methylation profiles indicative of altered neurodevelopment and brain function.
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Affiliation(s)
- Benjamin I. Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Annie Vogel Ciernia
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Charles E. Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
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31
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Abstract
During the past decades, life expectancy of subjects with Down syndrome (DS) has greatly improved, but age-specific mortality rates are still important and DS subjects are characterized by an acceleration of the ageing process, which affects particularly the immune and central nervous systems. In this chapter, we will first review the characteristics of the ageing phenomenon in brain and in immune system in DS and we will then discuss the biological hallmarks of ageing in this specific population. Finally, we will also consider in detail the knowledge on epigenetics in DS, particularly DNA methylation.
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32
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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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33
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Down syndrome: Neurobiological alterations and therapeutic targets. Neurosci Biobehav Rev 2019; 98:234-255. [DOI: 10.1016/j.neubiorev.2019.01.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 12/12/2022]
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34
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Hou J, Shi X, Chen C, Islam MS, Johnson AF, Kanno T, Huettel B, Yen MR, Hsu FM, Ji T, Chen PY, Matzke M, Matzke AJM, Cheng J, Birchler JA. Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proc Natl Acad Sci U S A 2018; 115:E11321-E11330. [PMID: 30429332 PMCID: PMC6275517 DOI: 10.1073/pnas.1807796115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.
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Affiliation(s)
- Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Md Soliman Islam
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Adam F Johnson
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam 550000
| | - Tatsuo Kanno
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding, Cologne, Germany 50829
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Fei-Man Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO 65211
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Antonius J M Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211;
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DNA methylation dynamics in aging: how far are we from understanding the mechanisms? Mech Ageing Dev 2018; 174:3-17. [DOI: 10.1016/j.mad.2017.12.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
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Ciccarone F, Valentini E, Malavolta M, Zampieri M, Bacalini MG, Calabrese R, Guastafierro T, Reale A, Franceschi C, Capri M, Breusing N, Grune T, Moreno‐Villanueva M, Bürkle A, Caiafa P. DNA Hydroxymethylation Levels Are Altered in Blood Cells From Down Syndrome Persons Enrolled in the MARK-AGE Project. J Gerontol A Biol Sci Med Sci 2018; 73:737-744. [PMID: 29069286 PMCID: PMC5946825 DOI: 10.1093/gerona/glx198] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Down syndrome (DS) is caused by the presence of part or an entire extra copy of chromosome 21, a phenomenon that can cause a wide spectrum of clinically defined phenotypes of the disease. Most of the clinical signs of DS are typical of the aging process including dysregulation of immune system. Beyond the causative genetic defect, DS persons display epigenetic alterations, particularly aberrant DNA methylation patterns that can contribute to the heterogeneity of the disease. In the present work, we investigated the levels of 5-hydroxymethylcytosine and of the Ten-eleven translocation dioxygenase enzymes, which are involved in DNA demethylation processes and are often deregulated in pathological conditions as well as in aging. Analyses were carried out on peripheral blood mononuclear cells of DS volunteers enrolled in the context of the MARK-AGE study, a large-scale cross-sectional population study with subjects representing the general population in eight European countries. We observed a decrease in 5-hydroxymethylcytosine, TET1, and other components of the DNA methylation/demethylation machinery in DS subjects, indicating that aberrant DNA methylation patterns in DS, which may have consequences on the transcriptional status of immune cells, may be due to a global disturbance of methylation control in DS.
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Affiliation(s)
- Fabio Ciccarone
- Department of Biology, University of Rome “Tor Vergata,” Rome
| | - Elisabetta Valentini
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | - Marco Malavolta
- National Institute of Health and Science on Aging (INRCA), Nutrition and Ageing Centre, Scientific and Technological Research Area, Ancona
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | | | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | - Tiziana Guastafierro
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | - Anna Reale
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna, Italy
- CIG-Interdepartmental Center “L. Galvani,” Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna, Italy
- CIG-Interdepartmental Center “L. Galvani,” Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Nicolle Breusing
- Institute of Nutritional Medicine (180c), University of Hohenheim, Stuttgart
| | - Tilman Grune
- German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal
| | - María Moreno‐Villanueva
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Alexander Bürkle
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
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Henneman P, Bouman A, Mul A, Knegt L, van der Kevie-Kersemaekers AM, Zwaveling-Soonawala N, Meijers-Heijboer HEJ, van Trotsenburg ASP, Mannens MM. Widespread domain-like perturbations of DNA methylation in whole blood of Down syndrome neonates. PLoS One 2018; 13:e0194938. [PMID: 29601581 PMCID: PMC5877863 DOI: 10.1371/journal.pone.0194938] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Down syndrome (DS) is the most frequent genetic cause of intellectual disability. Despite the fact that more than 50 years have passed since the discovery of its genetic aberrations, the exact pathogenesis of the DS phenotype has remained largely unexplained. It was recently hypothesized that the DS pathogenesis involves complex (epi)genetic, molecular and cellular determinants. To date, many reports have addressed epigenetic aberrations associated with DS at different developmental stages/ages and tissue types, but to our best knowledge not in DS newborns. This study aimed to investigate genome-wide methylation patterns in DS newborns compared to non-trisomic newborns. METHOD We analyzed blood samples obtained from ten newborns with DS and five age-matched non-trisomic newborns. Epigenetic profiles were obtained from extracted DNA using the Illumina Infinium 450K array. Since aberrant blood cell distribution is known to be present in DS, we applied two distinct models: with and without correction for estimated blood cell distribution. RESULTS Differentially methylated position (DMP) analysis of the uncorrected model detected 19525 significant hits (51,2% hypomethylated). In the corrected model, we found 121953 significant DMPs (49,8% hypomethylated). Independent of the used model we observed a chromosome 21 dosage effect. Moreover, we detected 46 and 145 differentially methylated regions in the uncorrected and corrected model respectively, both showing hypomethylation overrepresentation. Replication analyses of DMPs and DMRs found by Bacalini et al. (2015) showed a large overlap. CONCLUSION In this study, we found methylation profile differences between DS newborns and controls reflecting a systematically affected epigenetic profile. The observed chromosome 21 dosage effect suggests the involvement of affected essential regulatory factors/regions or altered expression of chromatin modeling enzymes located on chromosome 21. Additional research is necessary to substantiate these hypotheses.
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Affiliation(s)
- Peter Henneman
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Adri Mul
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Lia Knegt
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Nitash Zwaveling-Soonawala
- Department of Pediatric Endocrinology, Emma Children’s Hospital, Academic Medical Center, Amsterdam, The Netherlands
| | | | - A. S. Paul van Trotsenburg
- Department of Pediatrics and Translational Genetics, Emma Children’s Hospital, Academic Medical Center, Amsterdam, The Netherlands
| | - Marcel M. Mannens
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
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García-Giménez JL, Romá-Mateo C, Pérez-Machado G, Peiró-Chova L, Pallardó FV. Role of glutathione in the regulation of epigenetic mechanisms in disease. Free Radic Biol Med 2017; 112:36-48. [PMID: 28705657 DOI: 10.1016/j.freeradbiomed.2017.07.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/29/2017] [Accepted: 07/06/2017] [Indexed: 12/14/2022]
Abstract
Epigenetics is a rapidly growing field that studies gene expression modifications not involving changes in the DNA sequence. Histone H3, one of the basic proteins in the nucleosomes that make up chromatin, is S-glutathionylated in mammalian cells and tissues, making Gamma-L-glutamyl-L-cysteinylglycine, glutathione (GSH), a physiological antioxidant and second messenger in cells, a new post-translational modifier of the histone code that alters the structure of the nucleosome. However, the role of GSH in the epigenetic mechanisms likely goes beyond a mere structural function. Evidence supports the hypothesis that there is a link between GSH metabolism and the control of epigenetic mechanisms at different levels (i.e., substrate availability, enzymatic activity for DNA methylation, changes in the expression of microRNAs, and participation in the histone code). However, little is known about the molecular pathways by which GSH can control epigenetic events. Studying mutations in enzymes involved in GSH metabolism and the alterations of the levels of cofactors affecting epigenetic mechanisms appears challenging. However, the number of diseases induced by aberrant epigenetic regulation is growing, so elucidating the intricate network between GSH metabolism, oxidative stress and epigenetics could shed light on how their deregulation contributes to the development of neurodegeneration, cancer, metabolic pathologies and many other types of diseases.
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Affiliation(s)
- José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER) Institute of Health Carlos III, Valencia, Spain; Mixed Unit INCLIVA-CIPF Research Institutes, Valencia, Spain; Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain.
| | - Carlos Romá-Mateo
- Center for Biomedical Network Research on Rare Diseases (CIBERER) Institute of Health Carlos III, Valencia, Spain; Mixed Unit INCLIVA-CIPF Research Institutes, Valencia, Spain; Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain; Faculty of Biomedicine and Health Sciences, Universidad Europea de Valencia, Valencia, Spain
| | - Gisselle Pérez-Machado
- Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain
| | | | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER) Institute of Health Carlos III, Valencia, Spain; Mixed Unit INCLIVA-CIPF Research Institutes, Valencia, Spain; Dept. Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain; Epigenetics Research Platform (CIBERER/UV), Valencia, Spain.
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Colvin KL, Yeager ME. What people with Down Syndrome can teach us about cardiopulmonary disease. Eur Respir Rev 2017; 26:26/143/160098. [DOI: 10.1183/16000617.0098-2016] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/13/2016] [Indexed: 12/19/2022] Open
Abstract
Down syndrome is the most common chromosomal abnormality among live-born infants. Through full or partial trisomy of chromosome 21, Down syndrome is associated with cognitive impairment, congenital malformations (particularly cardiovascular) and dysmorphic features. Immune disturbances in Down syndrome account for an enormous disease burden ranging from quality-of-life issues (autoimmune alopecia) to more serious health issues (autoimmune thyroiditis) and life-threatening issues (leukaemia, respiratory tract infections and pulmonary hypertension). Cardiovascular and pulmonary diseases account for ∼75% of the mortality seen in persons with Down syndrome. This review summarises the cardiovascular, respiratory and immune challenges faced by individuals with Down syndrome, and the genetic underpinnings of their pathobiology. We strongly advocate increased comparative studies of cardiopulmonary disease in persons with and without Down syndrome, as we believe these will lead to new strategies to prevent and treat diseases affecting millions of people worldwide.
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Do C, Xing Z, Yu YE, Tycko B. Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models. Epigenomics 2016; 9:189-207. [PMID: 27911079 PMCID: PMC5549717 DOI: 10.2217/epi-2016-0138] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An important line of postgenomic research seeks to understand how genetic factors can influence epigenetic patterning. Here we review epigenetic effects of chromosomal aneuploidies, focusing on findings in Down syndrome (DS, trisomy 21). Recent work in human DS and mouse models has shown that the extra chromosome 21 acts in trans to produce epigenetic changes, including differential CpG methylation (DS-DM), in specific sets of downstream target genes, mostly on other chromosomes. Mechanistic hypotheses emerging from these data include roles of chromosome 21-linked methylation pathway genes (DNMT3L and others) and transcription factor genes (RUNX1, OLIG2, GABPA, ERG and ETS2) in shaping the patterns of DS-DM. The findings may have broader implications for trans-acting epigenetic effects of chromosomal and subchromosomal aneuploidies in other human developmental and neuropsychiatric disorders, and in cancers.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Taub Institute for Research on Alzheimer's disease & the Aging Brain, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
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Xing Z, Li Y, Pao A, Bennett AS, Tycko B, Mobley WC, Yu YE. Mouse-based genetic modeling and analysis of Down syndrome. Br Med Bull 2016; 120:111-122. [PMID: 27789459 PMCID: PMC5146682 DOI: 10.1093/bmb/ldw040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/07/2016] [Accepted: 10/03/2016] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Down syndrome (DS), caused by human trisomy 21 (Ts21), can be considered as a prototypical model for understanding the effects of chromosomal aneuploidies in other diseases. Human chromosome 21 (Hsa21) is syntenically conserved with three regions in the mouse genome. SOURCES OF DATA A review of recent advances in genetic modeling and analysis of DS. Using Cre/loxP-mediated chromosome engineering, a substantial number of new mouse models of DS have recently been generated, which facilitates better understanding of disease mechanisms in DS. AREAS OF AGREEMENT Based on evolutionary conservation, Ts21 can be modeled by engineered triplication of Hsa21 syntenic regions in mice. The validity of the models is supported by the exhibition of DS-related phenotypes. AREAS OF CONTROVERSY Although substantial progress has been made, it remains a challenge to unravel the relative importance of specific candidate genes and molecular mechanisms underlying the various clinical phenotypes. GROWING POINTS Further understanding of mechanisms based on data from mouse models, in parallel with human studies, may lead to novel therapies for clinical manifestations of Ts21 and insights to the roles of aneuploidies in other developmental disorders and cancers.
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Affiliation(s)
- Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Yichen Li
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Abigail S Bennett
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - William C Mobley
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA .,Cellular and Molecular Biology Program, Roswell Park Division of Graduate School, Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
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Epigenomic engineering for Down syndrome. Neurosci Biobehav Rev 2016; 71:323-327. [DOI: 10.1016/j.neubiorev.2016.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/11/2016] [Accepted: 09/15/2016] [Indexed: 12/27/2022]
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Microarray-Based Analysis of Methylation of 1st Trimester Trisomic Placentas from Down Syndrome, Edwards Syndrome and Patau Syndrome. PLoS One 2016; 11:e0160319. [PMID: 27490343 PMCID: PMC4973974 DOI: 10.1371/journal.pone.0160319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022] Open
Abstract
Methylation-based non-invasive prenatal testing of fetal aneuploidies is an alternative method that could possibly improve fetal aneuploidy diagnosis, especially for trisomy 13(T13) and trisomy 18(T18). Our aim was to study the methylation landscape in placenta DNA from trisomy 13, 18 and 21 pregnancies in an attempt to find trisomy-specific methylation differences better suited for non-invasive prenatal diagnosis. We have conducted high-resolution methylation specific bead chip microarray analyses assessing more than 450,000 CpGs analyzing placentas from 12 T21 pregnancies, 12 T18 pregnancies and 6 T13 pregnancies. We have compared the methylation landscape of the trisomic placentas to the methylation landscape from normal placental DNA and to maternal blood cell DNA. Comparing trisomic placentas to normal placentas we identified 217 and 219 differentially methylated CpGs for CVS T18 and CVS T13, respectively (delta β>0.2, FDR<0.05), but only three differentially methylated CpGs for T21. However, the methylation differences was only modest (delta β<0.4), making them less suitable as diagnostic markers. Gene ontology enrichment analysis revealed that the gene set connected to theT18 differentially methylated CpGs was highly enriched for GO terms related to"DNA binding" and "transcription factor binding" coupled to the RNA polymerase II transcription. In the gene set connected to the T13 differentially methylated CpGs we found no significant enrichments.
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El Hajj N, Dittrich M, Böck J, Kraus TFJ, Nanda I, Müller T, Seidmann L, Tralau T, Galetzka D, Schneider E, Haaf T. Epigenetic dysregulation in the developing Down syndrome cortex. Epigenetics 2016; 11:563-78. [PMID: 27245352 PMCID: PMC4990229 DOI: 10.1080/15592294.2016.1192736] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 12/18/2022] Open
Abstract
Using Illumina 450K arrays, 1.85% of all analyzed CpG sites were significantly hypermethylated and 0.31% hypomethylated in fetal Down syndrome (DS) cortex throughout the genome. The methylation changes on chromosome 21 appeared to be balanced between hypo- and hyper-methylation, whereas, consistent with prior reports, all other chromosomes showed 3-11 times more hyper- than hypo-methylated sites. Reduced NRSF/REST expression due to upregulation of DYRK1A (on chromosome 21q22.13) and methylation of REST binding sites during early developmental stages may contribute to this genome-wide excess of hypermethylated sites. Upregulation of DNMT3L (on chromosome 21q22.4) could lead to de novo methylation in neuroprogenitors, which then persists in the fetal DS brain where DNMT3A and DNMT3B become downregulated. The vast majority of differentially methylated promoters and genes was hypermethylated in DS and located outside chromosome 21, including the protocadherin gamma (PCDHG) cluster on chromosome 5q31, which is crucial for neural circuit formation in the developing brain. Bisulfite pyrosequencing and targeted RNA sequencing showed that several genes of PCDHG subfamilies A and B are hypermethylated and transcriptionally downregulated in fetal DS cortex. Decreased PCDHG expression is expected to reduce dendrite arborization and growth in cortical neurons. Since constitutive hypermethylation of PCDHG and other genes affects multiple tissues, including blood, it may provide useful biomarkers for DS brain development and pharmacologic targets for therapeutic interventions.
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Affiliation(s)
- Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Theo F. J. Kraus
- Center for Neuropathology and Prion Research, Ludwig Maximilians University, Munich, Germany
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Larissa Seidmann
- Department of Pathology, University Medical Center, Mainz, Germany
| | - Tim Tralau
- Rehabilitation Clinic for Children and Adolescents, Westerland/Sylt, Germany
| | - Danuta Galetzka
- Department of Radiation Oncology and Radiotherapy, University Medical Center, Mainz, Germany
| | - Eberhard Schneider
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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Lu Z, Liu Y, Ren Z, Yan J. PRDM8 internal promoter hyperhydroxymethylation correlates with increased expression of the corresponding transcript in Down syndrome. Mol Med Rep 2016; 14:1227-34. [DOI: 10.3892/mmr.2016.5375] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 02/24/2016] [Indexed: 11/05/2022] Open
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Lu J, Mccarter M, Lian G, Esposito G, Capoccia E, Delli-Bovi LC, Hecht J, Sheen V. Global hypermethylation in fetal cortex of Down syndrome due to DNMT3L overexpression. Hum Mol Genet 2016; 25:1714-27. [PMID: 26911678 PMCID: PMC4986328 DOI: 10.1093/hmg/ddw043] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/12/2016] [Indexed: 01/02/2023] Open
Abstract
Down syndrome (DS) is caused by a triplication of chromosome 21 (HSA21). Increased oxidative stress, decreased neurogenesis and synaptic dysfunction from HSA21 gene overexpression are thought to cause mental retardation, dementia and seizure in this disorder. Recent epigenetic studies have raised the possibility that DNA methylation has significant effects on DS neurodevelopment. Here, we performed methylome profiling in normal and DS fetal cortices and observed a significant hypermethylation in ∼4% of probes in the DS samples compared with age-matched normals. The probes with differential methylation were distributed across all chromosomes, with no enrichment on HSA21. Functional annotation and pathway analyses showed that genes in the ubiquitination pathway were significantly altered, including: BRCA1, TSPYL5 and PEX10 HSA21 located DNMT3L was overexpressed in DS neuroprogenitors, and this overexpression increased the promoter methylation of TSPYL5 potentially through DNMT3B, and decreased its mRNA expression. DNMT3L overexpression also increased mRNA levels for TP53 and APP, effectors of TSPYL5 Furthermore, DNMT3L overexpression increased APP and PSD95 expression in differentiating neurons, whereas DNMT3LshRNA could partially rescue the APP and PSD95 up-regulation in DS cells. These results provide some of the first mechanistic insights into causes for epigenetic changes in DS, leading to modification of genes relevant for the DS neural endophenotype.
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Affiliation(s)
- Jie Lu
- Department of Neurology and
| | | | | | - Giuseppe Esposito
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy and
| | - Elena Capoccia
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy and
| | - Laurent C Delli-Bovi
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jonathan Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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Alves da Silva AF, Machado FB, Pavarino ÉC, Biselli-Périco JM, Zampieri BL, da Silva Francisco Junior R, Mozer Rodrigues PT, Terra Machado D, Santos-Rebouças CB, Gomes Fernandes M, Chuva de Sousa Lopes SM, Lopes Rios ÁF, Medina-Acosta E. Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. PLoS One 2016; 11:e0154108. [PMID: 27100087 PMCID: PMC4839675 DOI: 10.1371/journal.pone.0154108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 04/09/2016] [Indexed: 12/31/2022] Open
Abstract
The supernumerary chromosome 21 in Down syndrome differentially affects the methylation statuses at CpG dinucleotide sites and creates genome-wide transcriptional dysregulation of parental alleles, ultimately causing diverse pathologies. At present, it is unknown whether those effects are dependent or independent of the parental origin of the nondisjoined chromosome 21. Linkage analysis is a standard method for the determination of the parental origin of this aneuploidy, although it is inadequate in cases with deficiency of samples from the progenitors. Here, we assessed the reliability of the epigenetic 5mCpG imprints resulting in the maternally (oocyte)-derived allele methylation at a differentially methylated region (DMR) of the candidate imprinted WRB gene for asserting the parental origin of chromosome 21. We developed a methylation-sensitive restriction enzyme-specific PCR assay, based on the WRB DMR, across single nucleotide polymorphisms (SNPs) to examine the methylation statuses in the parental alleles. In genomic DNA from blood cells of either disomic or trisomic subjects, the maternal alleles were consistently methylated, while the paternal alleles were unmethylated. However, the supernumerary chromosome 21 did alter the methylation patterns at the RUNX1 (chromosome 21) and TMEM131 (chromosome 2) CpG sites in a parent-of-origin-independent manner. To evaluate the 5mCpG imprints, we conducted a computational comparative epigenomic analysis of transcriptome RNA sequencing (RNA-Seq) and histone modification expression patterns. We found allele fractions consistent with the transcriptional biallelic expression of WRB and ten neighboring genes, despite the similarities in the confluence of both a 17-histone modification activation backbone module and a 5-histone modification repressive module between the WRB DMR and the DMRs of six imprinted genes. We concluded that the maternally inherited 5mCpG imprints at the WRB DMR are uncoupled from the parental allele expression of WRB and ten neighboring genes in several tissues and that trisomy 21 alters DNA methylation in parent-of-origin-dependent and -independent manners.
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Affiliation(s)
- Antônio Francisco Alves da Silva
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Graduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- * E-mail: (AFAS); (FBM); (EM-A)
| | - Filipe Brum Machado
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Postgraduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- * E-mail: (AFAS); (FBM); (EM-A)
| | | | | | | | - Ronaldo da Silva Francisco Junior
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Pedro Thyago Mozer Rodrigues
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Douglas Terra Machado
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | | | - Maria Gomes Fernandes
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | | | - Álvaro Fabricio Lopes Rios
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
| | - Enrique Medina-Acosta
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Graduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- * E-mail: (AFAS); (FBM); (EM-A)
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Davidsson J, Johansson B. Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p. Epigenetics 2016; 11:194-204. [PMID: 26890086 DOI: 10.1080/15592294.2016.1146854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
To ascertain the epigenomic features, i.e., the methylation, non-coding RNA, and gene expression patterns, associated with gain of i(12p) in Pallister-Killian syndrome (PKS), we investigated single cell clones, harboring either disomy 12 or tetrasomy 12p, from a patient with PKS. The i(12p)-positive cells displayed a characteristic expression and methylation signature. Of all the genes on 12p, 13% were overexpressed, including the ATN1, COPS7A, and NECAP1 genes in 12p13.31, a region previously implicated in PKS. However, the median expression fold change (1.3) on 12p was lower than expected by tetrasomy 12p. Thus, partial dosage compensation occurs in cells with i(12p). The majority (89%) of the significantly deregulated genes were not situated on 12p, indicating that global perturbation of gene expression is a key pathogenetic event in PKS. Three genes-ATP6V1G1 in 9q32, GMPS in 3q25.31, and TBX5 in 12q24.21-exhibited concomitant hypermethylation and decreased expression. The i(12p)-positive cells displayed global hypomethylation of gene-poor regions on 12p, a footprint previously associated with constitutional and acquired gains of whole chromosomes as well as with X-chromosome inactivation in females. We hypothesize that this non-genic hypomethylation is associated with chromatin processing that facilitates cellular adaptation to excess genetic material.
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Affiliation(s)
- Josef Davidsson
- a Division of Molecular Hematology, Department of Laboratory Medicine , Lund University , Lund , Sweden.,b Division of Clinical Genetics, Department of Laboratory Medicine , Lund University , Lund , Sweden
| | - Bertil Johansson
- b Division of Clinical Genetics, Department of Laboratory Medicine , Lund University , Lund , Sweden.,c Department of Clinical Genetics, Office for Medical Services , Division of Laboratory Medicine , Lund , Sweden
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Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. Genome Biol 2015; 16:263. [PMID: 26607552 PMCID: PMC4659173 DOI: 10.1186/s13059-015-0827-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0827-6) contains supplementary material, which is available to authorized users.
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