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Sarver DC, Xu C, Velez LM, Aja S, Jaffe AE, Seldin MM, Reeves RH, Wong GW. Dysregulated systemic metabolism in a Down syndrome mouse model. Mol Metab 2023; 68:101666. [PMID: 36587842 PMCID: PMC9841171 DOI: 10.1016/j.molmet.2022.101666] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE Trisomy 21 is one of the most complex genetic perturbations compatible with postnatal survival. Dosage imbalance arising from the triplication of genes on human chromosome 21 (Hsa21) affects multiple organ systems. Much of Down syndrome (DS) research, however, has focused on addressing how aneuploidy dysregulates CNS function leading to cognitive deficit. Although obesity, diabetes, and associated sequelae such as fatty liver and dyslipidemia are well documented in the DS population, only limited studies have been conducted to determine how gene dosage imbalance affects whole-body metabolism. Here, we conduct a comprehensive and systematic analysis of key metabolic parameters across different physiological states in the Ts65Dn trisomic mouse model of DS. METHODS Ts65Dn mice and euploid littermates were subjected to comprehensive metabolic phenotyping under basal (chow-fed) state and the pathophysiological state of obesity induced by a high-fat diet (HFD). RNA sequencing of liver, skeletal muscle, and two major fat depots were conducted to determine the impact of aneuploidy on tissue transcriptome. Pathway enrichments, gene-centrality, and key driver estimates were performed to provide insights into tissue autonomous and non-autonomous mechanisms contributing to the dysregulation of systemic metabolism. RESULTS Under the basal state, chow-fed Ts65Dn mice of both sexes had elevated locomotor activity and energy expenditure, reduced fasting serum cholesterol levels, and mild glucose intolerance. Sexually dimorphic deterioration in metabolic homeostasis became apparent when mice were challenged with a high-fat diet. While obese Ts65Dn mice of both sexes exhibited dyslipidemia, male mice also showed impaired systemic insulin sensitivity, reduced mitochondrial activity, and elevated fibrotic and inflammatory gene signatures in the liver and adipose tissue. Systems-level analysis highlighted conserved pathways and potential endocrine drivers of adipose-liver crosstalk that contribute to dysregulated glucose and lipid metabolism. CONCLUSIONS A combined alteration in the expression of trisomic and disomic genes in peripheral tissues contribute to metabolic dysregulations in Ts65Dn mice. These data lay the groundwork for understanding the impact of aneuploidy on in vivo metabolism.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cheng Xu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leandro M Velez
- Department of Biological Chemistry, University of California, Irvine, Irvine, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, USA
| | - Susan Aja
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; The Lieber Institute for Brain Development, Baltimore, MD, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, Irvine, Irvine, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, USA
| | - Roger H Reeves
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Sarver DC, Xu C, Rodriguez S, Aja S, Jaffe AE, Gao FJ, Delannoy M, Periasamy M, Kazuki Y, Oshimura M, Reeves RH, Wong GW. Hypermetabolism in mice carrying a near complete human chromosome 21. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526183. [PMID: 36778465 PMCID: PMC9915508 DOI: 10.1101/2023.01.30.526183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The consequences of aneuploidy have traditionally been studied in cell and animal models in which the extrachromosomal DNA is from the same species. Here, we explore a fundamental question concerning the impact of aneuploidy on systemic metabolism using a non-mosaic transchromosomic mouse model (TcMAC21) carrying a near complete human chromosome 21. Independent of diets and housing temperatures, TcMAC21 mice consume more calories, are hyperactive and hypermetabolic, remain consistently lean and profoundly insulin sensitive, and have a higher body temperature. The hypermetabolism and elevated thermogenesis are due to sarcolipin overexpression in the skeletal muscle, resulting in futile sarco(endo)plasmic reticulum Ca 2+ ATPase (SERCA) activity and energy dissipation. Mitochondrial respiration is also markedly increased in skeletal muscle to meet the high ATP demand created by the futile cycle. This serendipitous discovery provides proof-of-concept that sarcolipin-mediated thermogenesis via uncoupling of the SERCA pump can be harnessed to promote energy expenditure and metabolic health.
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Affiliation(s)
- Dylan C. Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Cheng Xu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Susana Rodriguez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Susan Aja
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E. Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,The Lieber Institute for Brain Development, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Feng J. Gao
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Delannoy
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Muthu Periasamy
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Yasuhiro Kazuki
- Division of Genome and Cellular Functions, Department of Molecular and Cellular Biology, School of Life Science, Faculty of Medicine, Tottori University, Tottori, Japan,Chromosome Engineering Research Center, Tottori University, Tottori, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, Tottori, Japan
| | - Roger H. Reeves
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - G. William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Correspondence:
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3
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Roper RJ, Goodlett CR. A new Down syndrome rat model races forward. Trends Genet 2022; 38:1101-1102. [PMID: 35581033 PMCID: PMC9561036 DOI: 10.1016/j.tig.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 01/24/2023]
Abstract
Animal models of Down syndrome (DS) provide an essential resource for understanding genetic, cellular, and molecular contributions to traits associated with trisomy 21 (Ts21). Recent genetic enhancements in the development of DS models, including the new TcHSA21rat model (Kazuki et al.), have potential to transform our understanding of and potential therapies for Ts21.
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Affiliation(s)
- Randall J Roper
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Charles R Goodlett
- Department of Psychology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA; Graduate Program in Addiction Neuroscience, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
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4
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Banerjee R, Sotero-Caio CG, Fu B, Yang F. Chromosomal instability (CIN) in HAP1 cell lines revealed by multiplex fluorescence in situ hybridisation (M-FISH). Mol Cytogenet 2022; 15:46. [PMID: 36289492 PMCID: PMC9609465 DOI: 10.1186/s13039-022-00625-x] [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: 08/17/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HAP1, a near-haploid human leukemic cancer cell line is often used in combination with CRISPR-Cas9 gene editing technology for genetic screens. HAP1 carries the Philadelphia chromosome (Ph) and an additional ~ 30 Mb fragment of chromosome 15 inserted into chromosome 19. The potential use of an in vitro cell line as a model system in biomedical research studies depends on its ability to maintain genome stability. Being a cancer cell line with a near-haploid genome, HAP1 is prone to genetic instability, which is further compounded by its tendency to diploidise in culture spontaneously. Moreover, CRISPR-Cas9 gene editing coupled with prolonged in-vitro cell culturing has the potential to induce unintended 'off-target' cytogenetic mutations. To gain an insight into chromosomal instability (CIN) and karyotype heterogeneity, 19 HAP1 cell lines were cytogenetically characterised, 17 of which were near-haploids and two double-haploids, using multiplex fluorescence in situ hybridisation (M-FISH), at single cell resolution. We focused on novel numerical (N) and structural (S) CIN and discussed the potential causal factors for the observed instability. For each cell line we examined its ploidy, gene editing status and its length of in-vitro cell culturing. RESULTS Sixteen of the 19 cell lines had been gene edited with passage numbers ranging from 10 to 35. Diploidisation in 17 near-haploid cell lines ranged from 4 to 35% and percentage of N- and S-CIN in [1n] and [2n] metaphases ranged from 7 to 50% with two cell lines showing no CIN. Percentage of cells with CIN in the two double-haploid cell lines were 96% and 100% respectively. The most common S-CIN observed was deletion followed by translocation of both types, non-reciprocal and Robertsonian. Interestingly, we observed a prevalence of S-CIN associated with chromosome 13 in both near-and double-haploid cell lines, with a high incidence of Robertsonian translocation involving chromosome 13. Furthermore, locus-specific BAC (bacterial artificial chromosome) FISH enabled us to show for the first time that the additional chromosome 15 fragment is inserted into the p-arm rather than the q-arm of chromosome 19 of the HAP1 genome. CONCLUSION Our study revealed a high incidence of CIN leading to karyotype heterogeneity in majority of the HAP1 cell lines with the number of chromosomal aberrations varying between cell lines. A noteworthy observation was the high frequency of structural chromosomal aberrations associated with chromosome 13. We showed that CRISPR-Cas9 gene editing technology in combination with spontaneous diploidisation and prolonged in-vitro cell culturing is potentially instrumental in inducing further chromosomal rearrangements in the HAP1 cell lines with existing CIN. We highlight the importance of maintaining cell lines at low passage and the need for regular monitoring to prevent implications in downstream applications. Our study also established that the additional fragment of chromosome 15 in the HAP1 genome is inserted into chromosome 19p rather than 19q.
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Affiliation(s)
- Ruby Banerjee
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Cibele G. Sotero-Caio
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Beiyuan Fu
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Fengtang Yang
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK ,grid.412509.b0000 0004 1808 3414School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong People’s Republic of China
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5
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Mumford P, Tosh J, Anderle S, Gkanatsiou Wikberg E, Lau G, Noy S, Cleverley K, Saito T, Saido TC, Yu E, Brinkmalm G, Portelius E, Blennow K, Zetterberg H, Tybulewicz V, Fisher EMC, Wiseman FK. Genetic Mapping of APP and Amyloid-β Biology Modulation by Trisomy 21. J Neurosci 2022; 42:6453-6468. [PMID: 35835549 PMCID: PMC9398545 DOI: 10.1523/jneurosci.0521-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/03/2022] [Accepted: 06/18/2022] [Indexed: 12/04/2022] Open
Abstract
Individuals who have Down syndrome (DS) frequently develop early onset Alzheimer's disease (AD), a neurodegenerative condition caused by the buildup of aggregated amyloid-β (Aβ) and tau proteins in the brain. Aβ is produced by amyloid precursor protein (APP), a gene located on chromosome 21. People who have DS have three copies of chromosome 21 and thus also an additional copy of APP; this genetic change drives the early development of AD in these individuals. Here we use a combination of next-generation mouse models of DS (Tc1, Dp3Tyb, Dp(10)2Yey and Dp(17)3Yey) and a knockin mouse model of Aβ accumulation (AppNL-F ) to determine how chromosome 21 genes, other than APP, modulate APP/Aβ in the brain when in three copies. Using both male and female mice, we demonstrate that three copies of other chromosome 21 genes are sufficient to partially ameliorate Aβ accumulation in the brain. We go on to identify a subregion of chromosome 21 that contains the gene(s) causing this decrease in Aβ accumulation and investigate the role of two lead candidate genes, Dyrk1a and Bace2 Thus, an additional copy of chromosome 21 genes, other than APP, can modulate APP/Aβ in the brain under physiological conditions. This work provides critical mechanistic insight into the development of disease and an explanation for the typically later age of onset of dementia in people who have AD in DS, compared with those who have familial AD caused by triplication of APP SIGNIFICANCE STATEMENT Trisomy of chromosome 21 is a commonly occurring genetic risk factor for early-onset Alzheimer's disease (AD), which has been previously attributed to people with Down syndrome having three copies of the amyloid precursor protein (APP) gene, which is encoded on chromosome 21. However, we have shown that an extra copy of other chromosome 21 genes modifies AD-like phenotypes independently of APP copy number (Wiseman et al., 2018; Tosh et al., 2021). Here, we use a mapping approach to narrow down the genetic cause of the modulation of pathology, demonstrating that gene(s) on chromosome 21 decrease Aβ accumulation in the brain, independently of alterations to full-length APP or C-terminal fragment abundance and that just 38 genes are sufficient to cause this.
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Affiliation(s)
- Paige Mumford
- The UK Dementia Research Institute, University College London, London, WC1N 3BG, United Kingdom
| | - Justin Tosh
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, United Kingdom
| | - Silvia Anderle
- The UK Dementia Research Institute, University College London, London, WC1N 3BG, United Kingdom
| | - Eleni Gkanatsiou Wikberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg S-431 80, Sweden
| | - Gloria Lau
- The UK Dementia Research Institute, University College London, London, WC1N 3BG, United Kingdom
| | - Sue Noy
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, United Kingdom
| | - Karen Cleverley
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, United Kingdom
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, Saitama Japan, 351-0198
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, Saitama Japan, 351-0198
| | - Eugene Yu
- Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Children's Guild Foundation Down Syndrome Research Program, Buffalo, New York NY 14263
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg S-431 80, Sweden
| | - Erik Portelius
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg S-431 80, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg S-431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal S-43180, Sweden
| | - Henrik Zetterberg
- The UK Dementia Research Institute, University College London, London, WC1N 3BG, United Kingdom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg S-431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal S-43180, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Victor Tybulewicz
- The Francis Crick Institute, London, NW1 1AT, United Kingdom
- Department of Immunology and Inflammation, Imperial College, London, W12 0NN, United Kingdom
- LonDownS: London Down Syndrome Consortium
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, United Kingdom
- LonDownS: London Down Syndrome Consortium
| | - Frances K Wiseman
- The UK Dementia Research Institute, University College London, London, WC1N 3BG, United Kingdom
- LonDownS: London Down Syndrome Consortium
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Klein JA, Haydar TF. Neurodevelopment in Down syndrome: Concordance in humans and models. Front Cell Neurosci 2022; 16:941855. [PMID: 35910249 PMCID: PMC9334873 DOI: 10.3389/fncel.2022.941855] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Great strides have been made over the past 30 years in understanding the neurodevelopmental changes underlying the intellectual disability (ID) in Down syndrome (DS). Detailed studies of human tissue coupled with findings from rodent and induced pluripotent stem cells (iPSCs) model systems have uncovered the changes in neurogenesis, synaptic connectivity, and myelination that drive the anatomical and physiological changes resulting in the disability. However, there remain significant conflicting data between human studies and the models. To fully understand the development of ID in DS, these inconsistencies need to be reconciled. Here, we review the well documented neurodevelopmental phenotypes found in individuals with DS and examine the degree to which widely used models recapitulate these phenotypes. Resolving these areas of discord will further research on the molecular underpinnings and identify potential treatments to improve the independence and quality of life of people with DS.
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Affiliation(s)
- Jenny A. Klein
- Graduate Program for Neuroscience, Boston University, Boston, MA, United States
| | - Tarik F. Haydar
- Children’s National Hospital, Center for Neuroscience Research, Washington, DC, United States
- Departments of Pediatrics, Physiology and Pharmacology, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
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Farrell C, Mumford P, Wiseman FK. Rodent Modeling of Alzheimer's Disease in Down Syndrome: In vivo and ex vivo Approaches. Front Neurosci 2022; 16:909669. [PMID: 35747206 PMCID: PMC9209729 DOI: 10.3389/fnins.2022.909669] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 12/30/2022] Open
Abstract
There are an estimated 6 million people with Down syndrome (DS) worldwide. In developed countries, the vast majority of these individuals will develop Alzheimer's disease neuropathology characterized by the accumulation of amyloid-β (Aβ) plaques and tau neurofibrillary tangles within the brain, which leads to the early onset of dementia (AD-DS) and reduced life-expectancy. The mean age of onset of clinical dementia is ~55 years and by the age of 80, approaching 100% of individuals with DS will have a dementia diagnosis. DS is caused by trisomy of chromosome 21 (Hsa21) thus an additional copy of a gene(s) on the chromosome must cause the development of AD neuropathology and dementia. Indeed, triplication of the gene APP which encodes the amyloid precursor protein is sufficient and necessary for early onset AD (EOAD), both in people who have and do not have DS. However, triplication of other genes on Hsa21 leads to profound differences in neurodevelopment resulting in intellectual disability, elevated incidence of epilepsy and perturbations to the immune system. This different biology may impact on how AD neuropathology and dementia develops in people who have DS. Indeed, genes on Hsa21 other than APP when in three-copies can modulate AD-pathogenesis in mouse preclinical models. Understanding this biology better is critical to inform drug selection for AD prevention and therapy trials for people who have DS. Here we will review rodent preclinical models of AD-DS and how these can be used for both in vivo and ex vivo (cultured cells and organotypic slice cultures) studies to understand the mechanisms that contribute to the early development of AD in people who have DS and test the utility of treatments to prevent or delay the development of disease.
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8
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Cell models for Down syndrome-Alzheimer’s disease research. Neuronal Signal 2022; 6:NS20210054. [PMID: 35449591 PMCID: PMC8996251 DOI: 10.1042/ns20210054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Down syndrome (DS) is the most common chromosomal abnormality and leads to intellectual disability, increased risk of cardiac defects, and an altered immune response. Individuals with DS have an extra full or partial copy of chromosome 21 (trisomy 21) and are more likely to develop early-onset Alzheimer’s disease (AD) than the general population. Changes in expression of human chromosome 21 (Hsa21)-encoded genes, such as amyloid precursor protein (APP), play an important role in the pathogenesis of AD in DS (DS-AD). However, the mechanisms of DS-AD remain poorly understood. To date, several mouse models with an extra copy of genes syntenic to Hsa21 have been developed to characterise DS-AD-related phenotypes. Nonetheless, due to genetic and physiological differences between mouse and human, mouse models cannot faithfully recapitulate all features of DS-AD. Cells differentiated from human-induced pluripotent stem cells (iPSCs), isolated from individuals with genetic diseases, can be used to model disease-related cellular and molecular pathologies, including DS. In this review, we will discuss the limitations of mouse models of DS and how these can be addressed using recent advancements in modelling DS using human iPSCs and iPSC-mouse chimeras, and potential applications of iPSCs in preclinical studies for DS-AD.
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9
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Altered cell and RNA isoform diversity in aging Down syndrome brains. Proc Natl Acad Sci U S A 2021; 118:2114326118. [PMID: 34795060 PMCID: PMC8617492 DOI: 10.1073/pnas.2114326118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
Down syndrome (DS) neurocognitive disabilities associated with trisomy 21 are known; however, gene changes within individual brain cells occurring with age are unknown. Here, we interrogated >170,000 cells from 29 aging DS and control brains using single-nucleus RNA sequencing. We observed increases in inhibitory-over-excitatory neurons, microglial activation in the youngest DS brains coinciding with overexpression of genes associated with microglial-mediated synaptic pruning, and overexpression of the chromosome 21 gene RUNX1 that may be a potential driving factor in microglial activation. Single-nucleus long-read sequencing revealed hundreds of thousands of unannotated RNA transcripts. These included diverse species for the Alzheimer’s disease gene—amyloid precursor protein—that contained intra-exonic junctions previously associated with somatic gene recombination, which was also identified in ∼8,000 other genes. Down syndrome (DS), trisomy of human chromosome 21 (HSA21), is characterized by lifelong cognitive impairments and the development of the neuropathological hallmarks of Alzheimer’s disease (AD). The cellular and molecular modifications responsible for these effects are not understood. Here we performed single-nucleus RNA sequencing (snRNA-seq) employing both short- (Illumina) and long-read (Pacific Biosciences) sequencing technologies on a total of 29 DS and non-DS control prefrontal cortex samples. In DS, the ratio of inhibitory-to-excitatory neurons was significantly increased, which was not observed in previous reports examining sporadic AD. DS microglial transcriptomes displayed AD-related aging and activation signatures in advance of AD neuropathology, with increased microglial expression of C1q complement genes (associated with dendritic pruning) and the HSA21 transcription factor gene RUNX1. Long-read sequencing detected vast RNA isoform diversity within and among specific cell types, including numerous sequences that differed between DS and control brains. Notably, over 8,000 genes produced RNAs containing intra-exonic junctions, including amyloid precursor protein (APP) that had previously been associated with somatic gene recombination. These and related results illuminate large-scale cellular and transcriptomic alterations as features of the aging DS brain.
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10
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Mouse models of aneuploidy to understand chromosome disorders. Mamm Genome 2021; 33:157-168. [PMID: 34719726 PMCID: PMC8913467 DOI: 10.1007/s00335-021-09930-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/20/2021] [Indexed: 12/04/2022]
Abstract
An organism or cell carrying a number of chromosomes that is not a multiple of the haploid count is in a state of aneuploidy. This condition results in significant changes in the level of expression of genes that are gained or lost from the aneuploid chromosome(s) and most cases in humans are not compatible with life. However, a few aneuploidies can lead to live births, typically associated with deleterious phenotypes. We do not understand why phenotypes arise from aneuploid syndromes in humans. Animal models have the potential to provide great insight, but less than a handful of mouse models of aneuploidy have been made, and no ideal system exists in which to study the effects of aneuploidy per se versus those of raised gene dosage. Here, we give an overview of human aneuploid syndromes, the effects on physiology of having an altered number of chromosomes and we present the currently available mouse models of aneuploidy, focusing on models of trisomy 21 (which causes Down syndrome) because this is the most common, and therefore, the most studied autosomal aneuploidy. Finally, we discuss the potential role of carrying an extra chromosome on aneuploid phenotypes, independent of changes in gene dosage, and methods by which this could be investigated further.
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11
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Trisomy of Human Chromosome 21 Orthologs Mapping to Mouse Chromosome 10 Cause Age and Sex-Specific Learning Differences: Relevance to Down Syndrome. Genes (Basel) 2021; 12:genes12111697. [PMID: 34828303 PMCID: PMC8618694 DOI: 10.3390/genes12111697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023] Open
Abstract
Down syndrome (DS), trisomy of human chromosome 21 (Hsa21), is the most common genetic cause of intellectual disability. The Dp10(1)Yey (Dp10) is a mouse model of DS that is trisomic for orthologs of 25% of the Hsa21 protein-coding genes, the entirety of the Hsa21 syntenic region on mouse chromosome 10. Trisomic genes include several involved in brain development and function, two that modify and regulate the activities of sex hormones, and two that produce sex-specific phenotypes as null mutants. These last four are the only Hsa21 genes with known sexually dimorphic properties. Relatively little is known about the potential contributions to the DS phenotype of segmental trisomy of Mmu10 orthologs. Here, we have tested separate cohorts of female and male Dp10 mice, at 3 and 9 months of age, in an open field elevated zero maze, rotarod, and balance beam, plus the learning and memory tasks, spontaneous alternation, puzzle box, double-H maze, context fear conditioning, and acoustic startle/prepulse inhibition, that depend upon the function of the prefrontal cortex, striatum, hippocampus, and cerebellum. We show that there are age and sex-specific differences in strengths and weaknesses, suggesting that genes within the telomere proximal region of Hsa21 influence the DS phenotype.
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Li Y, Xing Z, Yu T, Pao A, Daadi M, Yu YE. Coat Color-Facilitated Efficient Generation and Analysis of a Mouse Model of Down Syndrome Triplicated for All Human Chromosome 21 Orthologous Regions. Genes (Basel) 2021; 12:genes12081215. [PMID: 34440389 PMCID: PMC8393392 DOI: 10.3390/genes12081215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/31/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Down syndrome (DS) is one of the most complex genetic disorders in humans and a leading genetic cause of developmental delays and intellectual disabilities. The mouse remains an essential model organism in DS research because human chromosome 21 (Hsa21) is orthologously conserved with three regions in the mouse genome. Recent studies have revealed complex interactions among different triplicated genomic regions and Hsa21 gene orthologs that underlie major DS phenotypes. Because we do not know conclusively which triplicated genes are indispensable in such interactions for a specific phenotype, it is desirable that all evolutionarily conserved Hsa21 gene orthologs are triplicated in a complete model. For this reason, the Dp(10)1Yey/+;Dp(16)1Yey/+;Dp(17)1Yey/+ mouse is the most complete model of DS to reflect gene dosage effects because it is the only mutant triplicated for all Hsa21 orthologous regions. Recently, several groups have expressed concerns that efforts needed to generate the triple compound model would be so overwhelming that it may be impractical to take advantage of its unique strength. To alleviate these concerns, we developed a strategy to drastically improve the efficiency of generating the triple compound model with the aid of a targeted coat color, and the results confirmed that the mutant mice generated via this approach exhibited cognitive deficits.
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Affiliation(s)
- Yichen Li
- 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 14263, USA; (Y.L.); (Z.X.); (T.Y.); (A.P.)
| | - 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 14263, USA; (Y.L.); (Z.X.); (T.Y.); (A.P.)
| | - Tao 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 14263, USA; (Y.L.); (Z.X.); (T.Y.); (A.P.)
| | - 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 14263, USA; (Y.L.); (Z.X.); (T.Y.); (A.P.)
| | - Marcel Daadi
- Regenerative Medicine and Aging Unit, Texas Biomedical Research Institute, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245, USA;
| | - 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 14263, USA; (Y.L.); (Z.X.); (T.Y.); (A.P.)
- Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Correspondence:
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Illouz T, Nicola R, Ben-Shushan L, Madar R, Biragyn A, Okun E. Maternal antibodies facilitate Amyloid-β clearance by activating Fc-receptor-Syk-mediated phagocytosis. Commun Biol 2021; 4:329. [PMID: 33712740 PMCID: PMC7955073 DOI: 10.1038/s42003-021-01851-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Maternal antibodies (MAbs) protect against infections in immunologically-immature neonates. Maternally transferred immunity may also be harnessed to target diseases associated with endogenous protein misfolding and aggregation, such as Alzheimer's disease (AD) and AD-pathology in Down syndrome (DS). While familial early-onset AD (fEOAD) is associated with autosomal dominant mutations in the APP, PSEN1,2 genes, promoting cerebral Amyloid-β (Aβ) deposition, DS features a life-long overexpression of the APP and DYRK1A genes, leading to a cognitive decline mediated by Aβ overproduction and tau hyperphosphorylation. Although no prenatal screening for fEOAD-related mutations is in clinical practice, DS can be diagnosed in utero. We hypothesized that anti-Aβ MAbs might promote the removal of early Aβ accumulation in the central nervous system of human APP-expressing mice. To this end, a DNA-vaccine expressing Aβ1-11 was delivered to wild-type female mice, followed by mating with 5xFAD males, which exhibit early Aβ plaque formation. MAbs reduce the offspring's cortical Aβ levels 4 months after antibodies were undetectable, along with alleviating short-term memory deficits. MAbs elicit a long-term shift in microglial phenotype in a mechanism involving activation of the FcγR1/Syk/Cofilin pathway. These data suggest that maternal immunization can alleviate cognitive decline mediated by early Aβ deposition, as occurs in EOAD and DS.
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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
| | - Raneen Nicola
- 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
| | - Linoy Ben-Shushan
- 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
| | - Ravit Madar
- 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
| | - Arya Biragyn
- Immunoregulation Section, Laboratory of Immunology and Molecular Biology, National Institute on Aging, Baltimore, MD, USA
| | - 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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Lanzillotta C, Di Domenico F. Stress Responses in Down Syndrome Neurodegeneration: State of the Art and Therapeutic Molecules. Biomolecules 2021; 11:biom11020266. [PMID: 33670211 PMCID: PMC7916967 DOI: 10.3390/biom11020266] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Down syndrome (DS) is the most common genomic disorder characterized by the increased incidence of developing early Alzheimer’s disease (AD). In DS, the triplication of genes on chromosome 21 is intimately associated with the increase of AD pathological hallmarks and with the development of brain redox imbalance and aberrant proteostasis. Increasing evidence has recently shown that oxidative stress (OS), associated with mitochondrial dysfunction and with the failure of antioxidant responses (e.g., SOD1 and Nrf2), is an early signature of DS, promoting protein oxidation and the formation of toxic protein aggregates. In turn, systems involved in the surveillance of protein synthesis/folding/degradation mechanisms, such as the integrated stress response (ISR), the unfolded stress response (UPR), and autophagy, are impaired in DS, thus exacerbating brain damage. A number of pre-clinical and clinical studies have been applied to the context of DS with the aim of rescuing redox balance and proteostasis by boosting the antioxidant response and/or inducing the mechanisms of protein re-folding and clearance, and at final of reducing cognitive decline. So far, such therapeutic approaches demonstrated their efficacy in reverting several aspects of DS phenotype in murine models, however, additional studies aimed to translate these approaches in clinical practice are still needed.
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Feng H, Hockin M, Capecchi M, Gale B, Sant H. Size and shape based chromosome separation in the inertial focusing device. BIOMICROFLUIDICS 2020; 14:064109. [PMID: 33312330 PMCID: PMC7714521 DOI: 10.1063/5.0026281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
In this paper, we use a spiral channel inertial focusing device for isolation and purification of chromosomes, which are highly asymmetric. The method developed is proposed as a sample preparation process for transchromosomic research. The proposed microfluidics-based chromosome separation approach enables rapid, label-free isolation of bioactive chromosomes and is compatible with chromosome buffer. As part of this work, particle force analysis during the separation process is performed utilizing mathematic models to estimate the expected behavior of chromosomes in the channel and the model validated with experiments employing fluorescent beads. The chromosome sample is further divided into subtypes utilizing fluorescent activated cell sorting , including small condensed chromosomes, single chromosomes, and groups of two chromosomes (four sister chromatids). The separation of chromosome subtypes is realized based on their shape differences in the spiral channel device under high flow rate conditions. When chromosomes become aligned in the shear flow, the balance between the inertial focusing force and the Dean flow drag force is determined by the chromosome projection area and aspect ratio, or shape difference, leading to different focusing locations in the channel. The achieved results indicate a new separation regime in inertial microfluidics that can be used for the separation of non-spherical particles based on particle aspect ratios, which could potentially be applied in fields such as bacteria subtype separation and chromosome karyotyping.
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Affiliation(s)
- Haidong Feng
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, USA
| | - Matthew Hockin
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mario Capecchi
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Bruce Gale
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, USA
| | - Himanshu Sant
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, USA
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Moyer AJ, Gardiner K, Reeves RH. All Creatures Great and Small: New Approaches for Understanding Down Syndrome Genetics. Trends Genet 2020; 37:444-459. [PMID: 33097276 DOI: 10.1016/j.tig.2020.09.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/26/2022]
Abstract
Human chromosome 21 (Hsa21) contains more than 500 genes, making trisomy 21 one of the most complex genetic perturbations compatible with life. The ultimate goal of Down syndrome (DS) research is to design therapies that improve quality of life for individuals with DS by understanding which subsets of Hsa21 genes contribute to DS-associated phenotypes throughout the lifetime. However, the complexity of DS pathogenesis has made developing appropriate animal models an ongoing challenge. Here, we examine lessons learned from a variety of model systems, including yeast, nematode, fruit fly, and zebrafish, and discuss emerging methods for creating murine models that better reflect the genetic basis of trisomy 21.
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Affiliation(s)
- Anna J Moyer
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Katheleen Gardiner
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA (retired)
| | - Roger H Reeves
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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17
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Ma D, Cardoso MJ, Zuluaga MA, Modat M, Powell NM, Wiseman FK, Cleary JO, Sinclair B, Harrison IF, Siow B, Popuri K, Lee S, Matsubara JA, Sarunic MV, Beg MF, Tybulewicz VLJ, Fisher EMC, Lythgoe MF, Ourselin S. Substantially thinner internal granular layer and reduced molecular layer surface in the cerebellar cortex of the Tc1 mouse model of down syndrome - a comprehensive morphometric analysis with active staining contrast-enhanced MRI. Neuroimage 2020; 223:117271. [PMID: 32835824 PMCID: PMC8417772 DOI: 10.1016/j.neuroimage.2020.117271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Down Syndrome is a chromosomal disorder that affects the development of cerebellar cortical lobules. Impaired neurogenesis in the cerebellum varies among different types of neuronal cells and neuronal layers. In this study, we developed an imaging analysis framework that utilizes gadolinium-enhanced ex vivo mouse brain MRI. We extracted the middle Purkinje layer of the mouse cerebellar cortex, enabling the estimation of the volume, thickness, and surface area of the entire cerebellar cortex, the internal granular layer, and the molecular layer in the Tc1 mouse model of Down Syndrome. The morphometric analysis of our method revealed that a larger proportion of the cerebellar thinning in this model of Down Syndrome resided in the inner granule cell layer, while a larger proportion of the surface area shrinkage was in the molecular layer.
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Affiliation(s)
- Da Ma
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; Centre for Advanced Biomedical Imaging, University College London, United Kingdom; School of Engineering Science, Simon Fraser University, Burnaby, Canada.
| | - Manuel J Cardoso
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; School of Biomedical Engineering & Imaging Sciences, King's College London, United Kingdom
| | - Maria A Zuluaga
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; Data Science Department, EURECOM, France
| | - Marc Modat
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; School of Biomedical Engineering & Imaging Sciences, King's College London, United Kingdom
| | - Nick M Powell
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Frances K Wiseman
- UK Dementia Research Institute at University College London, UK London; Down Syndrome Consortium (LonDownS), London, United Kingdom
| | - Jon O Cleary
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom; Department of Radiology, Guy´s and St Thomas' NHS Foundation Trust, United Kingdom; Melbourne Brain Centre Imaging Unit, Department of Medicine and Radiology, University of Melbourne, Melbourne, Australia
| | - Benjamin Sinclair
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Ian F Harrison
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Bernard Siow
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Karteek Popuri
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Sieun Lee
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Joanne A Matsubara
- Department of Ophthalmology & Visual Science, University of British Columbia, Vancouver, Canada
| | - Marinko V Sarunic
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Mirza Faisal Beg
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Victor L J Tybulewicz
- The Francis Crick Institute, London, United Kingdom; Department of Immunology and Inflammation, Imperial College, London, United Kingdom
| | | | - Mark F Lythgoe
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Sebastien Ourselin
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; School of Biomedical Engineering & Imaging Sciences, King's College London, United Kingdom
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18
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Roper RJ, Goodlett CR, Martínez de Lagrán M, Dierssen M. Behavioral Phenotyping for Down Syndrome in Mice. ACTA ACUST UNITED AC 2020; 10:e79. [PMID: 32780566 DOI: 10.1002/cpmo.79] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Down syndrome (DS) is the most frequent genetic cause of intellectual disability, characterized by alterations in different behavioral symptom domains: neurodevelopment, motor behavior, and cognition. As mouse models have the potential to generate data regarding the neurological basis for the specific behavioral profile of DS, and may indicate pharmacological treatments with the potential to affect their behavioral phenotype, it is important to be able to assess disease-relevant behavioral traits in animal models in order to provide biological plausibility to the potential findings. The field is at a juncture that requires assessments that may effectively translate the findings acquired in mouse models to humans with DS. In this article, behavioral tests are described that are relevant to the domains affected in DS. A neurodevelopmental behavioral screen, the balance beam test, and the Multivariate Concentric Square Field test to assess multiple behavioral phenotypes and locomotion are described, discussing the ways to merge these findings to more fully understand cognitive strengths and weaknesses in this population. New directions for approaches to cognitive assessment in mice and humans are discussed. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preweaning neurodevelopmental battery Basic Protocol 2: Balance beam Basic Protocol 3: Multivariate concentric square field test (MCSF).
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Affiliation(s)
| | | | - María Martínez de Lagrán
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain
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19
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Almarri MA, Bergström A, Prado-Martinez J, Yang F, Fu B, Dunham AS, Chen Y, Hurles ME, Tyler-Smith C, Xue Y. Population Structure, Stratification, and Introgression of Human Structural Variation. Cell 2020; 182:189-199.e15. [PMID: 32531199 PMCID: PMC7369638 DOI: 10.1016/j.cell.2020.05.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.
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Affiliation(s)
| | - Anders Bergström
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Beiyuan Fu
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Alistair S Dunham
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; EMBL-EBI, Hinxton CB10 1SD, UK
| | - Yuan Chen
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
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20
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Kazuki Y, Gao FJ, Li Y, Moyer AJ, Devenney B, Hiramatsu K, Miyagawa-Tomita S, Abe S, Kazuki K, Kajitani N, Uno N, Takehara S, Takiguchi M, Yamakawa M, Hasegawa A, Shimizu R, Matsukura S, Noda N, Ogonuki N, Inoue K, Matoba S, Ogura A, Florea LD, Savonenko A, Xiao M, Wu D, Batista DA, Yang J, Qiu Z, Singh N, Richtsmeier JT, Takeuchi T, Oshimura M, Reeves RH. A non-mosaic transchromosomic mouse model of down syndrome carrying the long arm of human chromosome 21. eLife 2020; 9:56223. [PMID: 32597754 PMCID: PMC7358007 DOI: 10.7554/elife.56223] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/28/2020] [Indexed: 01/01/2023] Open
Abstract
Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs, provide insights into better understanding and treatment options. The only existing transchromosomic (Tc) mouse DS model, Tc1, carries a HSA21 with over 50 protein coding genes (PCGs) disrupted. Tc1 is mosaic, compromising interpretation of results. Here, we “clone” the 34 MB long arm of HSA21 (HSA21q) as a mouse artificial chromosome (MAC). Through multiple steps of microcell-mediated chromosome transfer, we created a new Tc DS mouse model, Tc(HSA21q;MAC)1Yakaz (“TcMAC21”). TcMAC21 is not mosaic and contains 93% of HSA21q PCGs that are expressed and regulatable. TcMAC21 recapitulates many DS phenotypes including anomalies in heart, craniofacial skeleton and brain, molecular/cellular pathologies, and impairments in learning, memory and synaptic plasticity. TcMAC21 is the most complete genetic mouse model of DS extant and has potential for supporting a wide range of basic and preclinical research.
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Affiliation(s)
- Yasuhiro Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan.,Chromosome Engineering Research Center (CERC), Tottori University, Yonago, Japan
| | - Feng J Gao
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Yicong Li
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Anna J Moyer
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, United States
| | - Benjamin Devenney
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Kei Hiramatsu
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Sachiko Miyagawa-Tomita
- Department of Animal Nursing Science, Yamazaki University of Animal Health Technology, Hachioji, Tokyo, Japan.,Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Abe
- Chromosome Engineering Research Center (CERC), Tottori University, Yonago, Japan
| | - Kanako Kazuki
- Chromosome Engineering Research Center (CERC), Tottori University, Yonago, Japan
| | - Naoyo Kajitani
- Chromosome Engineering Research Center (CERC), Tottori University, Yonago, Japan
| | - Narumi Uno
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Shoko Takehara
- Chromosome Engineering Research Center (CERC), Tottori University, Yonago, Japan
| | - Masato Takiguchi
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Miho Yamakawa
- Chromosome Engineering Research Center (CERC), Tottori University, Yonago, Japan
| | - Atsushi Hasegawa
- Department of Molecular Hematology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ritsuko Shimizu
- Department of Molecular Hematology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Satoko Matsukura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Narumi Ogonuki
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Tsukuba, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Tsukuba, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Tsukuba, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Tsukuba, Japan
| | - Liliana D Florea
- Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, United States
| | - Alena Savonenko
- Departments of Pathology and Neurology, John Hopkins University School of Medicine, Baltimore, United States
| | - Meifang Xiao
- Department of Neuroscience, John Hopkins University School of Medicine, Baltimore, United States
| | - Dan Wu
- Department of Biomedical Engineering, Zhejiang University, Hangzhou, China
| | - Denise As Batista
- Department of Pathology, John Hopkins University School of Medicine, Baltimore, United States
| | - Junhua Yang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Zhaozhu Qiu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Nandini Singh
- Department of Anthropology, Penn State University, State College, United States
| | - Joan T Richtsmeier
- Division of Biosignaling, School of Life Sciences, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Takashi Takeuchi
- Department of Anthropology, California State University, Sacramento, United States
| | - Mitsuo Oshimura
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Roger H Reeves
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, United States
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21
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Enhanced chromosome extraction from cells using a pinched flow microfluidic device. Biomed Microdevices 2020; 22:25. [DOI: 10.1007/s10544-020-0477-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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22
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Moriwaki T, Abe S, Oshimura M, Kazuki Y. Transchromosomic technology for genomically humanized animals. Exp Cell Res 2020; 390:111914. [PMID: 32142854 DOI: 10.1016/j.yexcr.2020.111914] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
"Genomically" humanized animals are invaluable tools for generating human disease models and for biomedical research. Humanized animal models have generally been developed via conventional transgenic technologies; however, conventional gene delivery vectors such as viruses, plasmids, bacterial artificial chromosomes, P1 phase-derived artificial chromosomes, and yeast artificial chromosomes have limitations for transgenic animal creation as their loading gene capacity is restricted, and the expression of transgenes is unstable. Transchromosomic (Tc) techniques using mammalian artificial chromosomes, including human chromosome fragments, human artificial chromosomes, and mouse artificial chromosomes, have overcome these limitations. These tools can carry multiple genes or Mb-sized genomic loci and their associated regulatory elements, which has facilitated the creation of more useful and complex transgenic models for human disease, drug development, and humanized animal research. This review describes the history of Tc animal development, the applications of Tc animals, and future prospects.
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Affiliation(s)
- Takashi Moriwaki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Satoshi Abe
- Trans Chromosomics, Inc., 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Mitsuo Oshimura
- Trans Chromosomics, Inc., 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan; Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Yasuhiro Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan; Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
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23
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Antonarakis SE, Skotko BG, Rafii MS, Strydom A, Pape SE, Bianchi DW, Sherman SL, Reeves RH. Down syndrome. Nat Rev Dis Primers 2020; 6:9. [PMID: 32029743 PMCID: PMC8428796 DOI: 10.1038/s41572-019-0143-7] [Citation(s) in RCA: 325] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/17/2019] [Indexed: 12/11/2022]
Abstract
Trisomy 21, the presence of a supernumerary chromosome 21, results in a collection of clinical features commonly known as Down syndrome (DS). DS is among the most genetically complex of the conditions that are compatible with human survival post-term, and the most frequent survivable autosomal aneuploidy. Mouse models of DS, involving trisomy of all or part of human chromosome 21 or orthologous mouse genomic regions, are providing valuable insights into the contribution of triplicated genes or groups of genes to the many clinical manifestations in DS. This endeavour is challenging, as there are >200 protein-coding genes on chromosome 21 and they can have direct and indirect effects on homeostasis in cells, tissues, organs and systems. Although this complexity poses formidable challenges to understanding the underlying molecular basis for each of the many clinical features of DS, it also provides opportunities for improving understanding of genetic mechanisms underlying the development and function of many cell types, tissues, organs and systems. Since the first description of trisomy 21, we have learned much about intellectual disability and genetic risk factors for congenital heart disease. The lower occurrence of solid tumours in individuals with DS supports the identification of chromosome 21 genes that protect against cancer when overexpressed. The universal occurrence of the histopathology of Alzheimer disease and the high prevalence of dementia in DS are providing insights into the pathology and treatment of Alzheimer disease. Clinical trials to ameliorate intellectual disability in DS signal a new era in which therapeutic interventions based on knowledge of the molecular pathophysiology of DS can now be explored; these efforts provide reasonable hope for the future.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
| | - Brian G Skotko
- Down Syndrome Program, Division of Medical Genetics, Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael S Rafii
- Keck School of Medicine of University of Southern California, California, CA, USA
| | - Andre Strydom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Sarah E Pape
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie L Sherman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Roger H Reeves
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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24
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Martínez de Lagrán M. Mapping behavioral landscapes in Down syndrome animal models. PROGRESS IN BRAIN RESEARCH 2020; 251:145-179. [DOI: 10.1016/bs.pbr.2020.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Cannavo C, Tosh J, Fisher EMC, Wiseman FK. Using mouse models to understand Alzheimer's disease mechanisms in the context of trisomy of chromosome 21. PROGRESS IN BRAIN RESEARCH 2019; 251:181-208. [PMID: 32057307 DOI: 10.1016/bs.pbr.2019.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
People who have Down syndrome are at significantly elevated risk of developing early onset Alzheimer's disease that causes dementia (AD-DS). Here we review recent progress in modeling the development of AD-DS in mouse models. These studies provide insight into mechanisms underlying Alzheimer's disease and generate new clinical research questions. In addition, they suggest potential new targets for disease prevention therapies.
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Affiliation(s)
- Claudia Cannavo
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom; UK Dementia Research Institute at University College, London, United Kingdom
| | - Justin Tosh
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom; The London Down Syndrome Consortium (LonDownS), London, United Kingdom
| | - Frances K Wiseman
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom; The London Down Syndrome Consortium (LonDownS), London, United Kingdom; UK Dementia Research Institute at University College, London, United Kingdom.
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26
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Gough G, O'Brien NL, Alic I, Goh PA, Yeap YJ, Groet J, Nizetic D, Murray A. Modeling Down syndrome in cells: From stem cells to organoids. PROGRESS IN BRAIN RESEARCH 2019; 251:55-90. [PMID: 32057312 DOI: 10.1016/bs.pbr.2019.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Down Syndrome (DS) is a complex chromosomal disorder, with neurological issues, featuring among the symptoms. Primary neuronal cells and tissues are extremely useful, but limited both in supply and experimental manipulability. To better understand the cellular, molecular and pathological mechanisms involved in DS neurodevelopment and neurodegeneration, a range of different cellular models have been developed over the years including human: mouse hybrid cells, transchromosomic mouse embryonic stem cells (ESCs) and human ESC and induced pluripotent stem cells derived from different sources. All of these model systems have provided useful information in the study of DS. Furthermore, different technologies to genetically modify or correct trisomy of either single genes or the whole chromosome have been developed using these cellular models. New techniques and protocols to allow better modeling of cellular mechanisms and disease processes are being developed and the use of cerebral organoids offers great promise for future research into the neural phenotypes seen in DS.
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Affiliation(s)
- Gillian Gough
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Niamh L O'Brien
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom; LonDownS Consortium, London, United Kingdom
| | - Ivan Alic
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Pollyanna A Goh
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom; LonDownS Consortium, London, United Kingdom
| | - Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jurgen Groet
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom; LonDownS Consortium, London, United Kingdom
| | - Dean Nizetic
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom; LonDownS Consortium, London, United Kingdom.
| | - Aoife Murray
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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27
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Roper RJ, Hawley L, Goodlett CR. Influence of allelic differences in Down syndrome. PROGRESS IN BRAIN RESEARCH 2019; 251:29-54. [PMID: 32057311 PMCID: PMC7500172 DOI: 10.1016/bs.pbr.2019.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Both trisomic and non-trisomic genes may affect the incidence and severity of phenotypes associated with Down syndrome (DS). The importance of extra (trisomic) genetic material is emphasized in DS, with less emphasis to the allelic composition of candidate trisomic genes in defining the trisomic gene-phenotype relationship in DS. Allelic differences in non-trisomic genes have been shown to be important moderators of cardiac, leukemia, and developmental phenotypes associated with DS. Trisomic mouse models provide an in vivo genetic platform for examining the gene-phenotype relationship, including the influence of allelic variants, on DS-like phenotypes. DS mouse models have differing trisomic genetic makeup, and optimal development, viability and translational value of these mouse models may require a non-inbred genetic background with heterogeneity at many loci. Additionally, understanding the contribution of specific genes or regions to DS phenotypes often requires the utilization of genetically manipulated mice that may be established on a different inbred background than the trisomic mice. The impact of allelic differences of trisomic and background genes in human and model systems may offer insight into the variability in occurrence and severity of trisomic phenotypes.
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Affiliation(s)
- Randall J Roper
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States.
| | - Laura Hawley
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Charles R Goodlett
- Department of Psychology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
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28
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Muñiz Moreno MDM, Brault V, Birling MC, Pavlovic G, Herault Y. Modeling Down syndrome in animals from the early stage to the 4.0 models and next. PROGRESS IN BRAIN RESEARCH 2019; 251:91-143. [PMID: 32057313 DOI: 10.1016/bs.pbr.2019.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genotype-phenotype relationship and the physiopathology of Down Syndrome (DS) have been explored in the last 20 years with more and more relevant mouse models. From the early age of transgenesis to the new CRISPR/CAS9-derived chromosomal engineering and the transchromosomic technologies, mouse models have been key to identify homologous genes or entire regions homologous to the human chromosome 21 that are necessary or sufficient to induce DS features, to investigate the complexity of the genetic interactions that are involved in DS and to explore therapeutic strategies. In this review we report the new developments made, how genomic data and new genetic tools have deeply changed our way of making models, extended our panel of animal models, and increased our understanding of the neurobiology of the disease. But even if we have made an incredible progress which promises to make DS a curable condition, we are facing new research challenges to nurture our knowledge of DS pathophysiology as a neurodevelopmental disorder with many comorbidities during ageing.
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Affiliation(s)
- Maria Del Mar Muñiz Moreno
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Véronique Brault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France.
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29
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Picco G, Chen ED, Alonso LG, Behan FM, Gonçalves E, Bignell G, Matchan A, Fu B, Banerjee R, Anderson E, Butler A, Benes CH, McDermott U, Dow D, Iorio F, Stronach E, Yang F, Yusa K, Saez-Rodriguez J, Garnett MJ. Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening. Nat Commun 2019; 10:2198. [PMID: 31097696 PMCID: PMC6522557 DOI: 10.1038/s41467-019-09940-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Many gene fusions are reported in tumours and for most their role remains unknown. As fusions are used for diagnostic and prognostic purposes, and are targets for treatment, it is crucial to assess their function in cancer. To systematically investigate the role of fusions in tumour cell fitness, we utilized RNA-sequencing data from 1011 human cancer cell lines to functionally link 8354 fusion events with genomic data, sensitivity to >350 anti-cancer drugs and CRISPR-Cas9 loss-of-fitness effects. Established clinically-relevant fusions were identified. Overall, detection of functional fusions was rare, including those involving cancer driver genes, suggesting that many fusions are dispensable for tumour fitness. Therapeutically actionable fusions involving RAF1, BRD4 and ROS1 were verified in new histologies. In addition, recurrent YAP1-MAML2 fusions were identified as activators of Hippo-pathway signaling in multiple cancer types. Our approach discriminates functional fusions, identifying new drivers of carcinogenesis and fusions that could have clinical implications. Gene fusions are observed in many cancers but their link to tumour fitness is largely unknown. Here, transcriptomic analysis combined with pharmacological and CRISPR-Cas9 screening of cancer cell lines was used to evaluate the functional linkage between fusions and tumour fitness.
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Affiliation(s)
- Gabriele Picco
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elisabeth D Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Luz Garcia Alonso
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Fiona M Behan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emanuel Gonçalves
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Graham Bignell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Angela Matchan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ruby Banerjee
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elizabeth Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Adam Butler
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Cyril H Benes
- Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Ultan McDermott
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,AstraZeneca, CRUK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - David Dow
- Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Research and Development, GlaxoSmithKline, Stevenage, SG1 2NY, UK.,Research and Development, GlaxoSmithKline, Collegeville, PA, 19426-0989, USA
| | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Euan Stronach
- Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Research and Development, GlaxoSmithKline, Stevenage, SG1 2NY, UK.,Research and Development, GlaxoSmithKline, Collegeville, PA, 19426-0989, USA
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Institute for Computational Biomedicine, Faculty of Medicine, Bioquant, Heidelberg University, 69120, Heidelberg, Germany
| | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK. .,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
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30
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Granno S, Nixon-Abell J, Berwick DC, Tosh J, Heaton G, Almudimeegh S, Nagda Z, Rain JC, Zanda M, Plagnol V, Tybulewicz VLJ, Cleverley K, Wiseman FK, Fisher EMC, Harvey K. Downregulated Wnt/β-catenin signalling in the Down syndrome hippocampus. Sci Rep 2019; 9:7322. [PMID: 31086297 PMCID: PMC6513850 DOI: 10.1038/s41598-019-43820-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/29/2019] [Indexed: 12/14/2022] Open
Abstract
Pathological mechanisms underlying Down syndrome (DS)/Trisomy 21, including dysregulation of essential signalling processes remain poorly understood. Combining bioinformatics with RNA and protein analysis, we identified downregulation of the Wnt/β-catenin pathway in the hippocampus of adult DS individuals with Alzheimer's disease and the 'Tc1' DS mouse model. Providing a potential underlying molecular pathway, we demonstrate that the chromosome 21 kinase DYRK1A regulates Wnt signalling via a novel bimodal mechanism. Under basal conditions, DYRK1A is a negative regulator of Wnt/β-catenin. Following pathway activation, however, DYRK1A exerts the opposite effect, increasing signalling activity. In summary, we identified downregulation of hippocampal Wnt/β-catenin signalling in DS, possibly mediated by a dose dependent effect of the chromosome 21-encoded kinase DYRK1A. Overall, we propose that dosage imbalance of the Hsa21 gene DYRK1A affects downstream Wnt target genes. Therefore, modulation of Wnt signalling may open unexplored avenues for DS and Alzheimer's disease treatment.
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Affiliation(s)
- Simone Granno
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Jonathon Nixon-Abell
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Daniel C Berwick
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
- School of Health, Life and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK6 7AA, UK
| | - Justin Tosh
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - George Heaton
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Sultan Almudimeegh
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Zenisha Nagda
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Jean-Christophe Rain
- Hybrigenics Services - Fondation Jérôme Lejeune, 3-5 Impasse Reille, 75014, Paris, France
| | - Manuela Zanda
- UCL Genetics Institute, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Vincent Plagnol
- UCL Genetics Institute, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Victor L J Tybulewicz
- The Francis Crick Institute, 1 Midland Rd, Kings Cross, London, NW1 1AT, UK
- Department of Medicine, Imperial College, London, W12 0NN, UK
- London Down Syndrome Consortium (LonDownS), London, UK
| | - Karen Cleverley
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Frances K Wiseman
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- London Down Syndrome Consortium (LonDownS), London, UK
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- London Down Syndrome Consortium (LonDownS), London, UK
| | - Kirsten Harvey
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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31
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Schill EM, Wright CM, Jamil A, LaCombe JM, Roper RJ, Heuckeroth RO. Down syndrome mouse models have an abnormal enteric nervous system. JCI Insight 2019; 5:124510. [PMID: 30998504 PMCID: PMC6629165 DOI: 10.1172/jci.insight.124510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/17/2019] [Indexed: 12/16/2022] Open
Abstract
Children with trisomy 21 (Down syndrome [DS]) have a 130-fold increased incidence of Hirschsprung Disease (HSCR), a developmental defect where the enteric nervous system (ENS) is missing from distal bowel (i.e., distal bowel is aganglionic). Treatment for HSCR is surgical resection of aganglionic bowel, but many children have bowel problems after surgery. Post-surgical problems like enterocolitis and soiling are especially common in children with DS. To determine how trisomy 21 affects ENS development, we evaluated the ENS in two DS mouse models, Ts65Dn and Tc1. These mice are trisomic for many chromosome 21 homologous genes, including Dscam and Dyrk1a, which are hypothesized to contribute to HSCR risk. Ts65Dn and Tc1 mice have normal ENS precursor migration at E12.5 and almost normal myenteric plexus structure as adults. However, Ts65Dn and Tc1 mice have markedly reduced submucosal plexus neuron density throughout the bowel. Surprisingly, the submucosal neuron defect in Ts65Dn mice is not due to excess Dscam or Dyrk1a, since normalizing copy number for these genes does not rescue the defect. These findings suggest the possibility that the high frequency of bowel problems in children with DS and HSCR may occur because of additional unrecognized problems with ENS structure.
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Affiliation(s)
- Ellen M. Schill
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia Research Institute and Perelman School of Medicine at the University of Pennsylvania, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Christina M. Wright
- Department of Pediatrics, Children’s Hospital of Philadelphia Research Institute and Perelman School of Medicine at the University of Pennsylvania, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Alisha Jamil
- Department of Pediatrics, Children’s Hospital of Philadelphia Research Institute and Perelman School of Medicine at the University of Pennsylvania, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Jonathan M. LaCombe
- Department of Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Randall J. Roper
- Department of Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Robert O. Heuckeroth
- Department of Pediatrics, Children’s Hospital of Philadelphia Research Institute and Perelman School of Medicine at the University of Pennsylvania, Abramson Research Center, Philadelphia, Pennsylvania, USA
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32
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Algady W, Louzada S, Carpenter D, Brajer P, Färnert A, Rooth I, Ngasala B, Yang F, Shaw MA, Hollox EJ. The Malaria-Protective Human Glycophorin Structural Variant DUP4 Shows Somatic Mosaicism and Association with Hemoglobin Levels. Am J Hum Genet 2018; 103:769-776. [PMID: 30388403 PMCID: PMC6218809 DOI: 10.1016/j.ajhg.2018.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 01/23/2023] Open
Abstract
Glycophorin A and glycophorin B are red blood cell surface proteins and are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A-glycophorin B fusion gene and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant and reveal somatic variation in copy number of the glycophorin B-glycophorin A fusion gene. By developing a simple, specific, PCR-based assay for DUP4, we show that the DUP4 variant reaches a frequency of 13% in the population of a malaria-endemic village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation and show that DUP4 is associated with a malarial-related phenotype in a longitudinally followed population.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Danielle Carpenter
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Ingegerd Rooth
- Nyamisati Malaria Research, Rufiji, National Institute for Medical Research, Dar-es-Salaam, Tanzania
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania; Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala Universitet, 75185 Uppsala, Sweden
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds LS9 7TF, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
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33
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Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet 2018; 50:1388-1398. [PMID: 30202056 PMCID: PMC6301019 DOI: 10.1038/s41588-018-0195-8] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/16/2018] [Indexed: 01/19/2023]
Abstract
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms. Despite their importance, the identification of SVs in cancer genomes remains challenging. Here, we present a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole-genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines. We identify the unique strengths of each method and demonstrate that only integrative approaches can comprehensively identify SVs in the genome. By combining Hi-C and optical mapping, we resolve complex SVs and phase multiple SV events to a single haplotype. Furthermore, we observe widespread structural variation events affecting the functions of noncoding sequences, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel three-dimensional chromatin structural domains. Our results indicate that noncoding SVs may be underappreciated mutational drivers in cancer genomes.
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Affiliation(s)
- Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Victoria T Le
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Darrin V Bann
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Royden Clark
- Penn State College of Medicine, Informatics and Technology, Hershey, PA, USA
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Sriranga Iyyanki
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Lin An
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Christopher Pool
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | | | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rajinder Kaul
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | | | - Kristen Lee
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Morgan Diegel
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Dubravka Pezic
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, Heidelberg, Germany
| | | | - James R Broach
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | | | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA.
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34
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Wiseman FK, Pulford LJ, Barkus C, Liao F, Portelius E, Webb R, Chávez-Gutiérrez L, Cleverley K, Noy S, Sheppard O, Collins T, Powell C, Sarell CJ, Rickman M, Choong X, Tosh JL, Siganporia C, Whittaker HT, Stewart F, Szaruga M, Murphy MP, Blennow K, de Strooper B, Zetterberg H, Bannerman D, Holtzman DM, Tybulewicz VLJ, Fisher EMC. Trisomy of human chromosome 21 enhances amyloid-β deposition independently of an extra copy of APP. Brain 2018; 141:2457-2474. [PMID: 29945247 PMCID: PMC6061702 DOI: 10.1093/brain/awy159] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 01/11/2023] Open
Abstract
Down syndrome, caused by trisomy of chromosome 21, is the single most common risk factor for early-onset Alzheimer's disease. Worldwide approximately 6 million people have Down syndrome, and all these individuals will develop the hallmark amyloid plaques and neurofibrillary tangles of Alzheimer's disease by the age of 40 and the vast majority will go on to develop dementia. Triplication of APP, a gene on chromosome 21, is sufficient to cause early-onset Alzheimer's disease in the absence of Down syndrome. However, whether triplication of other chromosome 21 genes influences disease pathogenesis in the context of Down syndrome is unclear. Here we show, in a mouse model, that triplication of chromosome 21 genes other than APP increases amyloid-β aggregation, deposition of amyloid-β plaques and worsens associated cognitive deficits. This indicates that triplication of chromosome 21 genes other than APP is likely to have an important role to play in Alzheimer's disease pathogenesis in individuals who have Down syndrome. We go on to show that the effect of trisomy of chromosome 21 on amyloid-β aggregation correlates with an unexpected shift in soluble amyloid-β 40/42 ratio. This alteration in amyloid-β isoform ratio occurs independently of a change in the carboxypeptidase activity of the γ-secretase complex, which cleaves the peptide from APP, or the rate of extracellular clearance of amyloid-β. These new mechanistic insights into the role of triplication of genes on chromosome 21, other than APP, in the development of Alzheimer's disease in individuals who have Down syndrome may have implications for the treatment of this common cause of neurodegeneration.
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Affiliation(s)
- Frances K Wiseman
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
- The LonDownS Consortium, Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London, SE5 8AF, UK
| | - Laura J Pulford
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Chris Barkus
- Department of Experimental Psychology, University of Oxford, Oxford, OX1 3PH, UK
| | - Fan Liao
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, 63110, USA
| | - Erik Portelius
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, S-405 30, Sweden
| | - Robin Webb
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, 40507, USA
| | - Lucia Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain and Disease Research, VIB-Leuven 3000, Center for Human Genetics, Universitaire Ziekenhuizen and LIND, KU Leuven, Leuven, Belgium
| | - Karen Cleverley
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Sue Noy
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Olivia Sheppard
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Toby Collins
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Caroline Powell
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London W1W 7FF, UK
| | - Claire J Sarell
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London W1W 7FF, UK
| | - Matthew Rickman
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Xun Choong
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Justin L Tosh
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Carlos Siganporia
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Heather T Whittaker
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
| | - Floy Stewart
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, 63110, USA
| | - Maria Szaruga
- VIB-KU Leuven Center for Brain and Disease Research, VIB-Leuven 3000, Center for Human Genetics, Universitaire Ziekenhuizen and LIND, KU Leuven, Leuven, Belgium
| | - London Down syndrome consortium
- The LonDownS Consortium, Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London, SE5 8AF, UK
| | - Michael P Murphy
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, 40507, USA
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, S-405 30, Sweden
| | - Bart de Strooper
- VIB-KU Leuven Center for Brain and Disease Research, VIB-Leuven 3000, Center for Human Genetics, Universitaire Ziekenhuizen and LIND, KU Leuven, Leuven, Belgium
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 3BG, UK
- UK Dementia Research Institute, London, WC2B 4AN, UK
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, S-405 30, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 3BG, UK
- UK Dementia Research Institute, London, WC2B 4AN, UK
| | - David Bannerman
- Department of Experimental Psychology, University of Oxford, Oxford, OX1 3PH, UK
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, 63110, USA
| | - Victor L J Tybulewicz
- The LonDownS Consortium, Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London, SE5 8AF, UK
- Francis Crick Institute, London, NW1 1AT, UK
- Department of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Elizabeth M C Fisher
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG UK
- The LonDownS Consortium, Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London, SE5 8AF, UK
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35
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Herault Y, Delabar JM, Fisher EMC, Tybulewicz VLJ, Yu E, Brault V. Rodent models in Down syndrome research: impact and future opportunities. Dis Model Mech 2018; 10:1165-1186. [PMID: 28993310 PMCID: PMC5665454 DOI: 10.1242/dmm.029728] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Down syndrome is caused by trisomy of chromosome 21. To date, a multiplicity of mouse models with Down-syndrome-related features has been developed to understand this complex human chromosomal disorder. These mouse models have been important for determining genotype-phenotype relationships and identification of dosage-sensitive genes involved in the pathophysiology of the condition, and in exploring the impact of the additional chromosome on the whole genome. Mouse models of Down syndrome have also been used to test therapeutic strategies. Here, we provide an overview of research in the last 15 years dedicated to the development and application of rodent models for Down syndrome. We also speculate on possible and probable future directions of research in this fast-moving field. As our understanding of the syndrome improves and genome engineering technologies evolve, it is necessary to coordinate efforts to make all Down syndrome models available to the community, to test therapeutics in models that replicate the whole trisomy and design new animal models to promote further discovery of potential therapeutic targets. Summary: Mouse models have boosted therapeutic options for Down syndrome, and improved models are being developed to better understand the pathophysiology of this genetic condition.
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Affiliation(s)
- Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris
| | - Jean M Delabar
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, 75205 Paris, France.,INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et la Moelle épinière, ICM, 75013 Paris, France.,Brain and Spine Institute (ICM) CNRS UMR7225, INSERM UMRS 975, 75013 Paris, France
| | - Elizabeth M C Fisher
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, WC1N 3BG, UK.,LonDownS Consortium, London, W1T 7NF UK
| | - Victor L J Tybulewicz
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,LonDownS Consortium, London, W1T 7NF UK.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Eugene Yu
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.,Department of Cellular and Molecular Biology, Roswell Park Division of Graduate School, Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
| | - Veronique Brault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
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36
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Watson-Scales S, Kalmar B, Lana-Elola E, Gibbins D, La Russa F, Wiseman F, Williamson M, Saccon R, Slender A, Olerinyova A, Mahmood R, Nye E, Cater H, Wells S, Yu YE, Bennett DLH, Greensmith L, Fisher EMC, Tybulewicz VLJ. Analysis of motor dysfunction in Down Syndrome reveals motor neuron degeneration. PLoS Genet 2018; 14:e1007383. [PMID: 29746474 PMCID: PMC5963810 DOI: 10.1371/journal.pgen.1007383] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 05/22/2018] [Accepted: 04/27/2018] [Indexed: 11/23/2022] Open
Abstract
Down Syndrome (DS) is caused by trisomy of chromosome 21 (Hsa21) and results in a spectrum of phenotypes including learning and memory deficits, and motor dysfunction. It has been hypothesized that an additional copy of a few Hsa21 dosage-sensitive genes causes these phenotypes, but this has been challenged by observations that aneuploidy can cause phenotypes by the mass action of large numbers of genes, with undetectable contributions from individual sequences. The motor abnormalities in DS are relatively understudied-the identity of causative dosage-sensitive genes and the mechanism underpinning the phenotypes are unknown. Using a panel of mouse strains with duplications of regions of mouse chromosomes orthologous to Hsa21 we show that increased dosage of small numbers of genes causes locomotor dysfunction and, moreover, that the Dyrk1a gene is required in three copies to cause the phenotype. Furthermore, we show for the first time a new DS phenotype: loss of motor neurons both in mouse models and, importantly, in humans with DS, that may contribute to locomotor dysfunction.
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Affiliation(s)
| | | | | | | | - Federica La Russa
- Wolfson Centre for Age-Related Diseases, Kings College London, London, United Kingdom
| | | | | | | | - Amy Slender
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Emma Nye
- The Francis Crick Institute, London, United Kingdom
| | - Heather Cater
- MRC Harwell Institute, Harwell Campus, Oxfordshire, United Kingdom
| | - Sara Wells
- MRC Harwell Institute, Harwell Campus, Oxfordshire, United Kingdom
| | - 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, United States of America
| | - David L. H. Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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37
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Naert G, Ferré V, Keller E, Slender A, Gibbins D, Fisher EMC, Tybulewicz VLJ, Maurice T. In vivo and ex vivo analyses of amyloid toxicity in the Tc1 mouse model of Down syndrome. J Psychopharmacol 2018; 32:174-190. [PMID: 29215943 PMCID: PMC5815426 DOI: 10.1177/0269881117743484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RATIONALE The prevalence of Alzheimer's disease is increased in people with Down syndrome. The pathology appears much earlier than in the general population, suggesting a predisposition to develop Alzheimer's disease. Down syndrome results from trisomy of human chromosome 21, leading to overexpression of possible Alzheimer's disease candidate genes, such as amyloid precursor protein gene. To better understand how the Down syndrome context results in increased vulnerability to Alzheimer's disease, we analysed amyloid-β [25-35] peptide toxicity in the Tc1 mouse model of Down syndrome, in which ~75% of protein coding genes are functionally trisomic but, importantly, not amyloid precursor protein. RESULTS Intracerebroventricular injection of oligomeric amyloid-β [25-35] peptide in three-month-old wildtype mice induced learning deficits, oxidative stress, synaptic marker alterations, activation of glycogen synthase kinase-3β, inhibition of protein kinase B (AKT), and apoptotic pathways as compared to scrambled peptide-treated wildtype mice. Scrambled peptide-treated Tc1 mice presented high levels of toxicity markers as compared to wildtype mice. Amyloid-β [25-35] peptide injection in Tc1 mice induced significant learning deficits and enhanced glycogen synthase kinase-3β activity in the cortex and expression of apoptotic markers in the hippocampus and cortex. Interestingly, several markers, including oxidative stress, synaptic markers, glycogen synthase kinase-3β activity in the hippocampus and AKT activity in the hippocampus and cortex, were unaffected by amyloid-β [25-35] peptide injection in Tc1 mice. CONCLUSIONS Tc1 mice present several toxicity markers similar to those observed in amyloid-β [25-35] peptide-treated wildtype mice, suggesting that developmental modifications in these mice modify their response to amyloid peptide. However, amyloid toxicity led to severe memory deficits in this Down syndrome mouse model.
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Affiliation(s)
- Gaëlle Naert
- INSERM U1198, Montpellier, France
- EPHE, Paris, France
| | | | | | | | | | | | | | - Tangui Maurice
- INSERM U1198, Montpellier, France
- EPHE, Paris, France
- Tangui Maurice, INSERM U1198, University of Montpellier, CC105, Place Eugene Bataillon, Montpellier Cedex 5, 34095, France.
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38
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Garaycoechea JI, Crossan GP, Langevin F, Mulderrig L, Louzada S, Yang F, Guilbaud G, Park N, Roerink S, Nik-Zainal S, Stratton MR, Patel KJ. Alcohol and endogenous aldehydes damage chromosomes and mutate stem cells. Nature 2018; 553:171-177. [PMID: 29323295 PMCID: PMC6047743 DOI: 10.1038/nature25154] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022]
Abstract
Haematopoietic stem cells renew blood. Accumulation of DNA damage in these cells promotes their decline, while misrepair of this damage initiates malignancies. Here we describe the features and mutational landscape of DNA damage caused by acetaldehyde, an endogenous and alcohol-derived metabolite. This damage results in DNA double-stranded breaks that, despite stimulating recombination repair, also cause chromosome rearrangements. We combined transplantation of single haematopoietic stem cells with whole-genome sequencing to show that this damage occurs in stem cells, leading to deletions and rearrangements that are indicative of microhomology-mediated end-joining repair. Moreover, deletion of p53 completely rescues the survival of aldehyde-stressed and mutated haematopoietic stem cells, but does not change the pattern or the intensity of genome instability within individual stem cells. These findings characterize the mutation of the stem-cell genome by an alcohol-derived and endogenous source of DNA damage. Furthermore, we identify how the choice of DNA-repair pathway and a stringent p53 response limit the transmission of aldehyde-induced mutations in stem cells.
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Affiliation(s)
- Juan I Garaycoechea
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Gerry P Crossan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Frédéric Langevin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Lee Mulderrig
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sandra Louzada
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fentang Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Guillaume Guilbaud
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Naomi Park
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sophie Roerink
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | - Ketan J Patel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Rd, Cambridge CB2 0QQ, UK
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39
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Liu C, Yu T, Xing Z, Jiang X, Li Y, Pao A, Mu J, Wallace PK, Stoica G, Bakin AV, Yu YE. Triplications of human chromosome 21 orthologous regions in mice result in expansion of megakaryocyte-erythroid progenitors and reduction of granulocyte-macrophage progenitors. Oncotarget 2017; 9:4773-4786. [PMID: 29435140 PMCID: PMC5797011 DOI: 10.18632/oncotarget.23463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
Individuals with Down syndrome (DS) frequently have hematopoietic abnormalities, including transient myeloproliferative disorder and acute megakaryoblastic leukemia which are often accompanied by acquired GATA1 mutations that produce a truncated protein, GATA1s. The mouse has been used for modeling DS based on the syntenic conservation between human chromosome 21 (Hsa21) and three regions in the mouse genome located on mouse chromosome 10 (Mmu10), Mmu16 and Mmu17. To assess the impact of the dosage increase of Hsa21 gene orthologs on the hematopoietic system, we characterized the related phenotype in the Dp(10)1Yey/+;Dp(16)1Yey/+;Dp(17)1Yey/+ model which carries duplications spanning the entire Hsa21 orthologous regions on Mmu10, Mmu16 and Mmu17, and the Dp(10)1Yey/+;Dp(16)1Yey/+;Dp(17)1Yey/+;Gata1Yeym2 model which carries a Gata1s mutation we engineered. Both models exhibited anemia, macrocytosis, and myeloproliferative disorder. Similar to human DS, the megakaryocyte-erythrocyte progenitors (MEPs) and granulocyte-monocyte progenitors (GMPs) were significantly increased and reduced, respectively, in both models. The subsequent identification of all the aforementioned phenotypes in the Dp(16)1Yey/+ model suggests that the causative dosage sensitive gene(s) are in the Hsa21 orthologous region on Mmu16. Therefore, we reveal here for the first time that the human trisomy 21-associated major segmental chromosomal alterations in mice can lead to expanded MEP and reduced GMP populations, mimicking the dynamics of these myeloid progenitors in DS. These models will provide the critical systems for unraveling the molecular and cellular mechanism of DS-associated myeloproliferative disorder, and particularly for determining how human trisomy 21 leads to expansion of MEPs as well as how such an alteration leads to myeloproliferative disorder.
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Affiliation(s)
- Chunhong Liu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Tao Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.,Department of Medical Genetics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Xiaoling Jiang
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Yichen Li
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Justin Mu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Paul K Wallace
- Department of Flow and Image Cytometry, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - George Stoica
- Department of Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - Andrei V Bakin
- Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - 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 Cancer Institute, Buffalo, NY 14263, USA.,Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
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40
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Revealing hidden complexities of genomic rearrangements generated with Cas9. Sci Rep 2017; 7:12867. [PMID: 28993641 PMCID: PMC5634419 DOI: 10.1038/s41598-017-12740-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/18/2017] [Indexed: 12/26/2022] Open
Abstract
Modelling human diseases caused by large genomic rearrangements has become more accessible since the utilization of CRISPR/Cas9 in mammalian systems. In a previous study, we showed that genomic rearrangements of up to one million base pairs can be generated by direct injection of CRISPR/Cas9 reagents into mouse zygotes. Although these rearrangements are ascertained by junction PCR, we describe here a variety of unanticipated structural changes often involving reintegration of the region demarcated by the gRNAs in the vicinity of the edited locus. We illustrate here some of this diversity detected by high-resolution fibre-FISH and conclude that extensive molecular analysis is required to fully understand the structure of engineered chromosomes generated by Cas9.
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41
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Ahmed MM, Block A, Tong S, Davisson MT, Gardiner KJ. Age exacerbates abnormal protein expression in a mouse model of Down syndrome. Neurobiol Aging 2017. [PMID: 28641136 DOI: 10.1016/j.neurobiolaging.2017.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Ts65Dn is a popular mouse model of Down syndrome (DS). It displays DS-relevant features of learning/memory deficits and age-related loss of functional markers in basal forebrain cholinergic neurons. Here we describe protein expression abnormalities in brain regions of 12-month-old male Ts65Dn mice. We show that the magnitudes of abnormalities of human chromosome 21 and non-human chromosome 21 orthologous proteins are greater at 12 months than at ∼6 months. Age-related exacerbations involve the number of components affected in the mechanistic target of rapamycin pathway, the levels of components of the mitogen-activated protein kinase pathway, and proteins associated with Alzheimer's disease. Among brain regions, the number of abnormalities in cerebellum decreased while the number in cortex greatly increased with age. The Ts65Dn is being used in preclinical evaluations of drugs for cognition in DS. Most commonly, drug evaluations are tested in ∼4- to 6-month-old mice. Data on age-related changes in magnitude and specificity of protein perturbations can be used to understand the molecular basis of changes in cognitive ability and to predict potential age-related specificities in drug efficacies.
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Affiliation(s)
| | - Aaron Block
- Linda Crnic Institute for Down Syndrome, Aurora, CO, USA
| | - Suhong Tong
- School of Public Health, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | | | - Katheleen J Gardiner
- Linda Crnic Institute for Down Syndrome, Aurora, CO, USA; Department of Pediatrics, University of Colorado Denver School of Medicine, Aurora, CO, USA; Human Medical Genetics and Genomics, and Neuroscience Programs, University of Colorado Denver School of Medicine, Aurora, CO, USA.
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42
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Shwan NAA, Louzada S, Yang F, Armour JAL. Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series. Hum Mutat 2017; 38:532-539. [PMID: 28101908 DOI: 10.1002/humu.23182] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 01/17/2023]
Abstract
The human amylase gene cluster includes the human salivary (AMY1) and pancreatic amylase genes (AMY2A and AMY2B), and is a highly variable and dynamic region of the genome. Copy number variation (CNV) of AMY1 has been implicated in human dietary adaptation, and in population association with obesity, but neither of these findings has been independently replicated. Despite these functional implications, the structural genomic basis of CNV has only been defined in detail very recently. In this work, we use high-resolution analysis of copy number, and analysis of segregation in trios, to define new, independent allelic series of amylase CNVs in sub-Saharan Africans, including a series of higher-order expansions of a unit consisting of one copy each of AMY1, AMY2A, and AMY2B. We use fiber-FISH (fluorescence in situ hybridization) to define unexpected complexity in the accompanying rearrangements. These findings demonstrate recurrent involvement of the amylase gene region in genomic instability, involving at least five independent rearrangements of the pancreatic amylase genes (AMY2A and AMY2B). Structural features shared by fundamentally distinct lineages strongly suggest that the common ancestral state for the human amylase cluster contained more than one, and probably three, copies of AMY1.
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Affiliation(s)
- Nzar A A Shwan
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK.,Scientific Research Centre, University of Salahaddin, Erbil, Kurdistan, Iraq
| | - Sandra Louzada
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Fengtang Yang
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - John A L Armour
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
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43
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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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44
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Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, Ward MC, Connor F, Rayner TF, Lukk M, Klose RJ, Kutter C, Odom DT. Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis. eLife 2016; 5:e20235. [PMID: 27855777 PMCID: PMC5161449 DOI: 10.7554/elife.20235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Most human aneuploidies originate maternally, due in part to the presence of highly stringent checkpoints during male meiosis. Indeed, male sterility is common among aneuploid mice used to study chromosomal abnormalities, and male germline transmission of exogenous DNA has been rarely reported. Here we show that, despite aberrant testis architecture, males of the aneuploid Tc1 mouse strain produce viable sperm and transmit human chromosome 21 to create aneuploid offspring. In these offspring, we mapped transcription, transcriptional initiation, enhancer activity, non-methylated DNA, and transcription factor binding in adult tissues. Remarkably, when compared with mice derived from female passage of human chromosome 21, the chromatin condensation during spermatogenesis and the extensive epigenetic reprogramming specific to male germline transmission resulted in almost indistinguishable patterns of transcriptional deployment. Our results reveal an unexpected tolerance of aneuploidy during mammalian spermatogenesis, and the surprisingly robust ability of mouse developmental machinery to accurately deploy an exogenous chromosome, regardless of germline transmission.
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Affiliation(s)
- Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jeremy Pike
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Aitken
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Histopathology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Hannah K Long
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United states
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Nils Eling
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michelle C Ward
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Frances Connor
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Timothy F Rayner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Margus Lukk
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
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45
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Qiu J, McQueen J, Bilican B, Dando O, Magnani D, Punovuori K, Selvaraj BT, Livesey M, Haghi G, Heron S, Burr K, Patani R, Rajan R, Sheppard O, Kind PC, Simpson TI, Tybulewicz VLJ, Wyllie DJA, Fisher EMC, Lowell S, Chandran S, Hardingham GE. Evidence for evolutionary divergence of activity-dependent gene expression in developing neurons. eLife 2016; 5:e20337. [PMID: 27692071 PMCID: PMC5092045 DOI: 10.7554/elife.20337] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022] Open
Abstract
Evolutionary differences in gene regulation between humans and lower mammalian experimental systems are incompletely understood, a potential translational obstacle that is challenging to surmount in neurons, where primary tissue availability is poor. Rodent-based studies show that activity-dependent transcriptional programs mediate myriad functions in neuronal development, but the extent of their conservation in human neurons is unknown. We compared activity-dependent transcriptional responses in developing human stem cell-derived cortical neurons with those induced in developing primary- or stem cell-derived mouse cortical neurons. While activity-dependent gene-responsiveness showed little dependence on developmental stage or origin (primary tissue vs. stem cell), notable species-dependent differences were observed. Moreover, differential species-specific gene ortholog regulation was recapitulated in aneuploid mouse neurons carrying human chromosome-21, implicating promoter/enhancer sequence divergence as a factor, including human-specific activity-responsive AP-1 sites. These findings support the use of human neuronal systems for probing transcriptional responses to physiological stimuli or indeed pharmaceutical agents.
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Affiliation(s)
- Jing Qiu
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jamie McQueen
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Bilada Bilican
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Owen Dando
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Bangalore, India
| | - Dario Magnani
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Karolina Punovuori
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Bhuvaneish T Selvaraj
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthew Livesey
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ghazal Haghi
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel Heron
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Karen Burr
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rickie Patani
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rinku Rajan
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Olivia Sheppard
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - Peter C Kind
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Bangalore, India
| | - T Ian Simpson
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Victor LJ Tybulewicz
- The Francis Crick Institute, London, United Kingdom
- Imperial College, London, United Kingdom
| | - David JA Wyllie
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Elizabeth MC Fisher
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - Sally Lowell
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharthan Chandran
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Bangalore, India
| | - Giles E Hardingham
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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46
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Powell NM, Modat M, Cardoso MJ, Ma D, Holmes HE, Yu Y, O’Callaghan J, Cleary JO, Sinclair B, Wiseman FK, Tybulewicz VLJ, Fisher EMC, Lythgoe MF, Ourselin S. Fully-Automated μMRI Morphometric Phenotyping of the Tc1 Mouse Model of Down Syndrome. PLoS One 2016; 11:e0162974. [PMID: 27658297 PMCID: PMC5033246 DOI: 10.1371/journal.pone.0162974] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/31/2016] [Indexed: 01/07/2023] Open
Abstract
We describe a fully automated pipeline for the morphometric phenotyping of mouse brains from μMRI data, and show its application to the Tc1 mouse model of Down syndrome, to identify new morphological phenotypes in the brain of this first transchromosomic animal carrying human chromosome 21. We incorporate an accessible approach for simultaneously scanning multiple ex vivo brains, requiring only a 3D-printed brain holder, and novel image processing steps for their separation and orientation. We employ clinically established multi-atlas techniques–superior to single-atlas methods–together with publicly-available atlas databases for automatic skull-stripping and tissue segmentation, providing high-quality, subject-specific tissue maps. We follow these steps with group-wise registration, structural parcellation and both Voxel- and Tensor-Based Morphometry–advantageous for their ability to highlight morphological differences without the laborious delineation of regions of interest. We show the application of freely available open-source software developed for clinical MRI analysis to mouse brain data: NiftySeg for segmentation and NiftyReg for registration, and discuss atlases and parameters suitable for the preclinical paradigm. We used this pipeline to compare 29 Tc1 brains with 26 wild-type littermate controls, imaged ex vivo at 9.4T. We show an unexpected increase in Tc1 total intracranial volume and, controlling for this, local volume and grey matter density reductions in the Tc1 brain compared to the wild-types, most prominently in the cerebellum, in agreement with human DS and previous histological findings.
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Affiliation(s)
- Nick M. Powell
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
- * E-mail:
| | - Marc Modat
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
| | - M. Jorge Cardoso
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
| | - Da Ma
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Holly E. Holmes
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Yichao Yu
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - James O’Callaghan
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Jon O. Cleary
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
- Melbourne Brain Centre Imaging Unit, Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ben Sinclair
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Frances K. Wiseman
- Department of Neurodegenerative Disease, Institute of Neurology, University College, London WC1N 3BG, United Kingdom
| | - Victor L. J. Tybulewicz
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
- Imperial College, London W12 0NN, United Kingdom
| | - Elizabeth M. C. Fisher
- Department of Neurodegenerative Disease, Institute of Neurology, University College, London WC1N 3BG, United Kingdom
| | - Mark F. Lythgoe
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Sébastien Ourselin
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
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47
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Delabar JM, Allinquant B, Bianchi D, Blumenthal T, Dekker A, Edgin J, O'Bryan J, Dierssen M, Potier MC, Wiseman F, Guedj F, Créau N, Reeves R, Gardiner K, Busciglio J. Changing Paradigms in Down Syndrome: The First International Conference of the Trisomy 21 Research Society. Mol Syndromol 2016; 7:251-261. [PMID: 27867340 DOI: 10.1159/000449049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 01/26/2023] Open
Abstract
Down syndrome (DS) is the most common genetic cause of intellectual disability (ID) in humans with an incidence of ∼1:1,000 live births worldwide. It is caused by the presence of an extra copy of all or a segment of the long arm of human chromosome 21 (trisomy 21). People with DS present with a constellation of phenotypic alterations involving most organs and organ systems. ID is present in all people with DS, albeit with variable severity. DS is also the most frequent genetic cause of Alzheimer's disease (AD), and ∼50% of those with DS will develop AD-related dementia. In the last few years, significant progress has been made in understanding the crucial genotype-phenotype relationships in DS, in identifying the alterations in molecular pathways leading to the various clinical conditions present in DS, and in preclinical evaluations of potential therapies to improve the overall health and well-being of individuals with DS. In June 2015, 230 scientists, advocates, patients, and family members met in Paris for the 1st International Conference of the Trisomy 21 Research Society. Here, we report some of the most relevant presentations that took place during the meeting.
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Affiliation(s)
- Jean-Maurice Delabar
- Brain and Spine Institute, Hospital Pitié-Salpêtrière, Paris, France; University of Paris Diderot, Paris, France
| | | | | | - Tom Blumenthal
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colo., USA
| | - Alain Dekker
- Department of Neurology, University Medical Center, Groningen, The Netherlands
| | - Jamie Edgin
- Department of Psychology, University of Arizona, Tucson, Ariz., USA
| | - John O'Bryan
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Ill., USA
| | - Mara Dierssen
- Center for Genomic Regulation (CRG), Barcelona, Spain
| | | | | | | | - Nicole Créau
- Brain and Spine Institute, Hospital Pitié-Salpêtrière, Paris, France; University of Paris Diderot, Paris, France
| | - Roger Reeves
- John Hopkins University School of Medicine, Baltimore, Md., USA
| | | | - Jorge Busciglio
- Department of Neurobiology and Behavior, University of California-Irvine, Irvine, Calif., USA
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48
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Créau N, Cabet E, Daubigney F, Souchet B, Bennaï S, Delabar J. Specific age-related molecular alterations in the cerebellum of Down syndrome mouse models. Brain Res 2016; 1646:342-353. [PMID: 27297494 DOI: 10.1016/j.brainres.2016.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/07/2016] [Accepted: 06/02/2016] [Indexed: 12/27/2022]
Abstract
Down syndrome, or trisomy 21, has been modeled with various trisomic and transgenic mice to help understand the consequences of an altered gene dosage in brain development and function. Though Down syndrome has been associated with premature aging, little is known about the molecular and cellular alterations that target brain function. To help identify alterations at specific ages, we analyzed the cerebellum of Ts1Cje mice, trisomic for 77 HSA21 orthologs, at three ages-young (4 months), middle-age (12 months), and old (17 months)-compared to age-matched controls. Quantification of neuronal and glial markers (n=11) revealed increases in GFAP, with an age effect, and S100B, with age and genotype effects. The genotype effect on S100B with age was unexpected as Ts1Cje has only two copies of the S100b gene. Interestingly, the different increase in GFAP observed between Ts1Cje (trisomic segment includes Pcp4 gene) and controls was magnified in TgPCP4 mice (1 extra copy of the human PCP4 gene) at the same age. S100B increase was not found in the TgPCP4 confirming a difference of regulation with aging for GFAP and S100B and excluding the calcium signaling regulator, Pcp4, as a potential candidate for increase of S100B in the Ts1Cje. To understand these differences, comparison of GFAP and S100B immunostainings at young and middle-age were performed. Immunohistochemical detection of differences in GFAP and S100B localization with aging implicate S100B+ oligodendrocytes as a new phenotypic target in this specific aging process.
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Affiliation(s)
- Nicole Créau
- Univ Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, Paris, France.
| | - Eva Cabet
- Univ Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, Paris, France
| | - Fabrice Daubigney
- Univ Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, Paris, France
| | - Benoit Souchet
- Univ Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, Paris, France
| | - Soumia Bennaï
- Univ Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, Paris, France
| | - Jean Delabar
- Univ Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, Paris, France
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49
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Long HK, King HW, Patient RK, Odom DT, Klose RJ. Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic Acids Res 2016; 44:6693-706. [PMID: 27084945 PMCID: PMC5001583 DOI: 10.1093/nar/gkw258] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/09/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022] Open
Abstract
DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species.
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Affiliation(s)
- Hannah K Long
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Roger K Patient
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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Mouse models of Down syndrome: gene content and consequences. Mamm Genome 2016; 27:538-555. [PMID: 27538963 DOI: 10.1007/s00335-016-9661-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/27/2016] [Indexed: 12/25/2022]
Abstract
Down syndrome (DS), trisomy of human chromosome 21 (Hsa21), is challenging to model in mice. Not only is it a contiguous gene syndrome spanning 35 Mb of the long arm of Hsa21, but orthologs of Hsa21 genes map to segments of three mouse chromosomes, Mmu16, Mmu17, and Mmu10. The Ts65Dn was the first viable segmental trisomy mouse model for DS; it is a partial trisomy currently popular in preclinical evaluations of drugs for cognition in DS. Limitations of the Ts65Dn are as follows: (i) it is trisomic for 125 human protein-coding orthologs, but only 90 of these are Hsa21 orthologs and (ii) it lacks trisomy for ~75 Hsa21 orthologs. In recent years, several additional mouse models of DS have been generated, each trisomic for a different subset of Hsa21 genes or their orthologs. To best exploit these models and interpret the results obtained with them, prior to proposing clinical trials, an understanding of their trisomic gene content, relative to full trisomy 21, is necessary. Here we first review the functional information on Hsa21 protein-coding genes and the more recent annotation of a large number of functional RNA genes. We then discuss the conservation and genomic distribution of Hsa21 orthologs in the mouse genome and the distribution of mouse-specific genes. Lastly, we consider the strengths and weaknesses of mouse models of DS based on the number and nature of the Hsa21 orthologs that are, and are not, trisomic in each, and discuss their validity for use in preclinical evaluations of drug responses.
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