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Zhang S, Wang R, Zhang L, Birchler JA, Sun L. Inverse and Proportional Trans Modulation of Gene Expression in Human Aneuploidies. Genes (Basel) 2024; 15:637. [PMID: 38790266 PMCID: PMC11121296 DOI: 10.3390/genes15050637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Genomic imbalance in aneuploidy is often detrimental to organisms. To gain insight into the molecular basis of aneuploidies in humans, we analyzed transcriptome data from several autosomal and sex chromosome aneuploidies. The results showed that in human aneuploid cells, genes located on unvaried chromosomes are inversely or proportionally trans-modulated, while a subset of genes on the varied chromosomes are compensated. Less genome-wide modulation is found for sex chromosome aneuploidy compared with autosomal aneuploidy due to X inactivation and the retention of dosage sensitive regulators on both sex chromosomes to limit the effective dosage change. We also found that lncRNA and mRNA can have different responses to aneuploidy. Furthermore, we analyzed the relationship between dosage-sensitive transcription factors and their targets, which illustrated the modulations and indicates genomic imbalance is related to stoichiometric changes in components of gene regulatory complexes.In summary, this study demonstrates the existence of trans-acting effects and compensation mechanisms in human aneuploidies and contributes to our understanding of gene expression regulation in unbalanced genomes and disease states.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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2
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Chapman LR, Ramnarine IVP, Zemke D, Majid A, Bell SM. Gene Expression Studies in Down Syndrome: What Do They Tell Us about Disease Phenotypes? Int J Mol Sci 2024; 25:2968. [PMID: 38474215 DOI: 10.3390/ijms25052968] [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: 02/04/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Down syndrome is a well-studied aneuploidy condition in humans, which is associated with various disease phenotypes including cardiovascular, neurological, haematological and immunological disease processes. This review paper aims to discuss the research conducted on gene expression studies during fetal development. A descriptive review was conducted, encompassing all papers published on the PubMed database between September 1960 and September 2022. We found that in amniotic fluid, certain genes such as COL6A1 and DSCR1 were found to be affected, resulting in phenotypical craniofacial changes. Additionally, other genes such as GSTT1, CLIC6, ITGB2, C21orf67, C21orf86 and RUNX1 were also identified to be affected in the amniotic fluid. In the placenta, dysregulation of genes like MEST, SNF1LK and LOX was observed, which in turn affected nervous system development. In the brain, dysregulation of genes DYRK1A, DNMT3L, DNMT3B, TBX1, olig2 and AQP4 has been shown to contribute to intellectual disability. In the cardiac tissues, dysregulated expression of genes GART, ETS2 and ERG was found to cause abnormalities. Furthermore, dysregulation of XIST, RUNX1, SON, ERG and STAT1 was observed, contributing to myeloproliferative disorders. Understanding the differential expression of genes provides insights into the genetic consequences of DS. A better understanding of these processes could potentially pave the way for the development of genetic and pharmacological therapies.
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Affiliation(s)
- Laura R Chapman
- Sheffield Children's NHS Foundation Trust, Clarkson St, Sheffield S10 2TH, UK
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
| | - Isabela V P Ramnarine
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
| | - Dan Zemke
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
| | - Arshad Majid
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Glossop Road, Sheffield S10 2GJ, UK
| | - Simon M Bell
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Glossop Road, Sheffield S10 2GJ, UK
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3
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Stagni F, Bartesaghi R. The Challenging Pathway of Treatment for Neurogenesis Impairment in Down Syndrome: Achievements and Perspectives. Front Cell Neurosci 2022; 16:903729. [PMID: 35634470 PMCID: PMC9130961 DOI: 10.3389/fncel.2022.903729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 12/17/2022] Open
Abstract
Down syndrome (DS), also known as trisomy 21, is a genetic disorder caused by triplication of Chromosome 21. Gene triplication may compromise different body functions but invariably impairs intellectual abilities starting from infancy. Moreover, after the fourth decade of life people with DS are likely to develop Alzheimer’s disease. Neurogenesis impairment during fetal life stages and dendritic pathology emerging in early infancy are thought to be key determinants of alterations in brain functioning in DS. Although the progressive improvement in medical care has led to a notable increase in life expectancy for people with DS, there are currently no treatments for intellectual disability. Increasing evidence in mouse models of DS reveals that pharmacological interventions in the embryonic and neonatal periods may greatly benefit brain development and cognitive performance. The most striking results have been obtained with pharmacotherapies during embryonic life stages, indicating that it is possible to pharmacologically rescue the severe neurodevelopmental defects linked to the trisomic condition. These findings provide hope that similar benefits may be possible for people with DS. This review summarizes current knowledge regarding (i) the scope and timeline of neurogenesis (and dendritic) alterations in DS, in order to delineate suitable windows for treatment; (ii) the role of triplicated genes that are most likely to be the key determinants of these alterations, in order to highlight possible therapeutic targets; and (iii) prenatal and neonatal treatments that have proved to be effective in mouse models, in order to rationalize the choice of treatment for human application. Based on this body of evidence we will discuss prospects and challenges for fetal therapy in individuals with DS as a potential means of drastically counteracting the deleterious effects of gene triplication.
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Affiliation(s)
- Fiorenza Stagni
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
| | - Renata Bartesaghi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- *Correspondence: Renata Bartesaghi,
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Deng L, Lu Y, Yang D, Yang F, Ruan H, Wei C, Lai K, Pang L. Placental transcriptome sequencing combined with bioinformatics predicts potential genes and circular RNAs associated with hemoglobin Bart's hydrops fetalis syndrome. J Obstet Gynaecol Res 2021; 48:313-327. [PMID: 34935248 DOI: 10.1111/jog.15126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/17/2021] [Accepted: 11/28/2021] [Indexed: 02/06/2023]
Abstract
AIM Hemoglobin Bart's hydrops fetalis syndrome (BHFS) is the most severe form of α-thalassemia. Histological alternations can be observed in placenta, but placental transcriptome profile and circular RNAs have not been studied in this disease. The aim of this study was to define the placental transcriptional changes and find relevant circular RNAs in BHFS. METHODS We performed high-throughput RNA sequencing to detect placental samples from fetuses affected by BHFS (n = 5) and normal fetuses (NF, n = 5), quantitative reverse transcription polymerase chain reaction (RT-qPCR), and Sanger sequencing to validate the differentially expressed circRNAs and their potentially related miRNAs (BHFS, n = 22; NF, n = 11). Bioinformatics methods were performed for further analysis. RESULTS Our results showed 152 differentially expressed genes (DEGs), 112 circRNAs, and 45 microRNAs that were differentially expressed. DEGs were found to be involved in Gene Ontology terms related to gas transport, cell adhesion, oxidative stress, organ development, hemopoiesis, and others. RT-qPCR results showed that hsa_circ_0003961 and hsa_circ_0006687 were upregulated (p < 0.05). The competing endogenous RNA and co-expression networks showed that hsa_circ_0003961 and hsa_circ_0006687 were connected with 3 miRNAs and some DEGs, including cell adhesion genes (e.g., CLDN19), hemoglobin related genes (e.g., SOX6 and HBZ) and angiogenesis related genes (e.g., EPHB2). Downregulations of hsa-miR-1299 and hsa-miR-625-5p in ceRNA network were also validated by RT-qPCR. Gene set enrichment analysis results for the two circRNAs showed that some gene sets associated with cell adhesion, hematopoietic system and apoptosis were significantly enriched. CONCLUSIONS Our study characterized the placental transcriptome of BHFS. The circRNAs hsa_circ_0003961 and hsa_circ_0006687 in placenta may be relevant to BHFS.
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Affiliation(s)
- Lingjie Deng
- Department of Prenatal Diagnosis and Genetic Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yebin Lu
- Guangxi Medical University, Nanning, China.,Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Gaungxi Medical University), Ministry of Education, Nanning, China
| | - Dongmei Yang
- Department of Prenatal Diagnosis and Genetic Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Fang Yang
- Department of Prenatal Diagnosis and Genetic Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Heyun Ruan
- Guangxi Medical University, Nanning, China
| | | | - Ketong Lai
- Guangxi Medical University, Nanning, China
| | - Lihong Pang
- Department of Prenatal Diagnosis and Genetic Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Salemi M, Cannarella R, Marchese G, Salluzzo MG, Ravo M, Barone C, Giudice ML, Calogero AE, Romano C. Role of long non-coding RNAs in Down syndrome patients: a transcriptome analysis study. Hum Cell 2021; 34:1662-1670. [PMID: 34510387 DOI: 10.1007/s13577-021-00602-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022]
Abstract
Down syndrome (DS) is defined by the presence of a third copy of chromosome 21. Several comorbidities can be found in these patients, such as intellectual disability (ID), muscle weakness, hypotonia, congenital heart disease, and autoimmune diseases. The molecular mechanisms playing a role in the development of such comorbidities are still unclear. The regulation and expression of genes that map to chromosome 21 are dynamic and complex, so it is important to perform global gene expression studies with high statistical power to fully characterize the transcriptome in DS patients. This study was undertaken to evaluate mRNAs and lncRNA expression in patients with DS versus a matched cohort of healthy subjects. RNA sequencing was used to perform this transcriptome study. Differential expression analysis revealed 967 transcripts with padj ≤ 0.05. Among them, 447 transcripts were differentially expressed in patients with DS compared to controls. Particularly, 203 transcripts were down expressed (151 protein-coding mRNAs, 45 lncRNAs, 1 microRNA, 1 mitochondrial tRNA, 1 ribozyme, and 1 small nuclear RNA) and 244 were over expressed (210 protein-coding mRNAs and 34 lncRNAs). Interestingly, deregulated lncRNAs are involved in pathways that play a role in developmental disorders, neurological diseases, DNA replication and repair mechanisms, and cancer development in DS patients. In conclusion, these results suggest a role of lncRNAs in the phenotype of DS patients.
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Affiliation(s)
| | - Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | | | | | | | | | - Aldo E Calogero
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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Bayona-Bafaluy MP, Garrido-Pérez N, Meade P, Iglesias E, Jiménez-Salvador I, Montoya J, Martínez-Cué C, Ruiz-Pesini E. Down syndrome is an oxidative phosphorylation disorder. Redox Biol 2021; 41:101871. [PMID: 33540295 PMCID: PMC7859316 DOI: 10.1016/j.redox.2021.101871] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/29/2020] [Accepted: 01/13/2021] [Indexed: 02/07/2023] Open
Abstract
Down syndrome is the most common genomic disorder of intellectual disability and is caused by trisomy of chromosome 21. Several genes in this chromosome repress mitochondrial biogenesis. The goal of this study was to evaluate whether early overexpression of these genes may cause a prenatal impairment of oxidative phosphorylation negatively affecting neurogenesis. Reduction in the mitochondrial energy production and a lower mitochondrial function have been reported in diverse tissues or cell types, and also at any age, including early fetuses, suggesting that a defect in oxidative phosphorylation is an early and general event in Down syndrome individuals. Moreover, many of the medical conditions associated with Down syndrome are also frequently found in patients with oxidative phosphorylation disease. Several drugs that enhance mitochondrial biogenesis are nowadays available and some of them have been already tested in mouse models of Down syndrome restoring neurogenesis and cognitive defects. Because neurogenesis relies on a correct mitochondrial function and critical periods of brain development occur mainly in the prenatal and early neonatal stages, therapeutic approaches intended to improve oxidative phosphorylation should be provided in these periods.
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Affiliation(s)
- M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza. C/ Mariano Esquillor (Edificio I+D), 50018, Zaragoza, Spain.
| | - Nuria Garrido-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza. C/ Mariano Esquillor (Edificio I+D), 50018, Zaragoza, Spain.
| | - Patricia Meade
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza. C/ Mariano Esquillor (Edificio I+D), 50018, Zaragoza, Spain.
| | - Eldris Iglesias
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain.
| | - Irene Jiménez-Salvador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain.
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Carmen Martínez-Cué
- Departamento de Fisiología y Farmacología. Facultad de Medicina, Universidad de Cantabria. Av. Herrera Oría, 39011, Santander, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
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The Amniotic Fluid Cell-Free Transcriptome Provides Novel Information about Fetal Development and Placental Cellular Dynamics. Int J Mol Sci 2021; 22:ijms22052612. [PMID: 33807645 PMCID: PMC7961801 DOI: 10.3390/ijms22052612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022] Open
Abstract
The amniotic fluid (AF) is a complex biofluid that reflects fetal well-being during development. AF con be divided into two fractions, the supernatant and amniocytes. The supernatant contains cell-free components, including placenta-derived microparticles, protein, cell-free fetal DNA, and cell-free fetal RNA from the fetus. Cell-free mRNA (cfRNA) analysis holds a special position among high-throughput analyses, such as transcriptomics, proteomics, and metabolomics, owing to its ease of profiling. The AF cell-free transcriptome differs from the amniocyte transcriptome and alters with the progression of pregnancy and is often associated with the development of various organ systems including the fetal lung, skin, brain, pancreas, adrenal gland, gastrointestinal system, etc. The AF cell-free transcriptome is affected not only by normal physiologies, such as fetal sex, gestational age, and fetal maturity, but also by pathologic mechanisms such as maternal obesity, and genetic syndromes (Down, Edward, Turner, etc.), as well as pregnancy complications (preeclampsia, intrauterine growth restriction, preterm birth, etc.). cfRNA in the amniotic fluid originates from the placenta and fetal organs directly contacting the amniotic fluid as well as from the fetal plasma across the placenta. The AF transcriptome may reflect the fetal and placental development and therefore aid in the monitoring of normal and abnormal development.
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De Toma I, Dierssen M. Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19. Sci Rep 2021; 11:1930. [PMID: 33479353 PMCID: PMC7820501 DOI: 10.1038/s41598-021-81451-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 infection has spread uncontrollably worldwide while it remains unknown how vulnerable populations, such as Down syndrome (DS) individuals are affected by the COVID-19 pandemic. Individuals with DS have more risk of infections with respiratory complications and present signs of auto-inflammation. They also present with multiple comorbidities that are associated with poorer COVID-19 prognosis in the general population. All this might place DS individuals at higher risk of SARS-CoV-2 infection or poorer clinical outcomes. In order to get insight into the interplay between DS genes and SARS-cov2 infection and pathogenesis we identified the genes associated with the molecular pathways involved in COVID-19 and the host proteins interacting with viral proteins from SARS-CoV-2. We then analyzed the overlaps of these genes with HSA21 genes, HSA21 interactors and other genes consistently differentially expressed in DS (using public transcriptomic datasets) and created a DS-SARS-CoV-2 network. We detected COVID-19 protective and risk factors among HSA21 genes and interactors and/or DS deregulated genes that might affect the susceptibility of individuals with DS both at the infection stage and in the progression to acute respiratory distress syndrome. Our analysis suggests that at the infection stage DS individuals might be more susceptible to infection due to triplication of TMPRSS2, that primes the viral S protein for entry in the host cells. However, as the anti-viral interferon I signaling is also upregulated in DS, this might increase the initial anti-viral response, inhibiting viral genome release, viral replication and viral assembly. In the second pro-inflammatory immunopathogenic phase of the infection, the prognosis for DS patients might worsen due to upregulation of inflammatory genes that might favor the typical cytokine storm of COVID-19. We also detected strong downregulation of the NLRP3 gene, critical for maintenance of homeostasis against pathogenic infections, possibly leading to bacterial infection complications.
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Affiliation(s)
- Ilario De Toma
- 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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Pecze L, Szabo C. Meta-analysis of gene expression patterns in Down syndrome highlights significant alterations in mitochondrial and bioenergetic pathways. Mitochondrion 2021; 57:163-172. [PMID: 33412332 DOI: 10.1016/j.mito.2020.12.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022]
Abstract
Individuals with Down syndrome (DS) have an extra copy of chromosome 21. Clinical observations and preclinical studies both suggest that DS is associated with altered bioenergetic pathways. Several studies have reported that differentially expressed genes in DS are located not only on chromosome 21 but also on all other chromosomes. Numerous sets of microarray and RNA-seq data are publicly accessible through the Gene Expression Omnibus. We have conducted a meta-analysis on differentially expressed genes between DS and control subjects. Data deposited before July 1, 2020, were identified by using the search terms "Down syndrome" or "trisomy 21" and "human". Gene expression data were analyzed and normalized for each study. The mixed effect model was used to identify the differentially expressed genes. We conclude that in DS more than 60% of the genes located on chromosome 21 are significantly upregulated and none of them are downregulated. In addition, a significant dysregulation of genes occurs on all other chromosomes as well. Several of the upregulated genes in DS encode for important components of various bioenergetic pathways, for instance PFKL and ACLY. Genes involved in oxidative phosphorylation are mostly downregulated in DS. The gene expression alterations are consistent with the development of significant metabolic disturbances ("pseudohypoxia") in DS cells, which may explain some of the well-known functional defects (ranging from neuronal dysfunction to reduced exercise tolerance) associated with DS.
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Affiliation(s)
- Laszlo Pecze
- Chair of Pharmacology, Section of Medicine, University of Fribourg, Switzerland
| | - Csaba Szabo
- Chair of Pharmacology, Section of Medicine, University of Fribourg, Switzerland.
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Yim A, Koti P, Bonnard A, Marchiano F, Dürrbaum M, Garcia-Perez C, Villaveces J, Gamal S, Cardone G, Perocchi F, Storchova Z, Habermann BH. mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. Nucleic Acids Res 2020; 48:605-632. [PMID: 31799603 PMCID: PMC6954439 DOI: 10.1093/nar/gkz1128] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/30/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Mitochondria participate in metabolism and signaling. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochondrial function (mito-genes) in various cell types, conditions and organisms. Yet, we lack an easy way of extracting these data for mito-genes. Here, we introduce the visual data mining platform mitoXplorer, which integrates expression and mutation data of mito-genes with a manually curated mitochondrial interactome containing ∼1200 genes grouped in 38 mitochondrial processes. User-friendly analysis and visualization tools allow to mine mitochondrial expression dynamics and mutations across various datasets from four model species including human. To test the predictive power of mitoXplorer, we quantify mito-gene expression dynamics in trisomy 21 cells, as mitochondrial defects are frequent in trisomy 21. We uncover remarkable differences in the regulation of the mitochondrial transcriptome and proteome in one of the trisomy 21 cell lines, caused by dysregulation of the mitochondrial ribosome and resulting in severe defects in oxidative phosphorylation. With the newly developed Fiji plugin mitoMorph, we identify mild changes in mitochondrial morphology in trisomy 21. Taken together, mitoXplorer (http://mitoxplorer.ibdm.univ-mrs.fr) is a user-friendly, web-based and freely accessible software, aiding experimental scientists to quantify mitochondrial expression dynamics.
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Affiliation(s)
- Annie Yim
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Prasanna Koti
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adrien Bonnard
- Aix-Marseille University, INSERM, TAGC U1090, 13009 Marseille, France
| | - Fabio Marchiano
- Aix-Marseille University, CNRS, IBDM UMR 7288, 13009 Marseille, France
| | - Milena Dürrbaum
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Cecilia Garcia-Perez
- Functional Genomics of Mitochondrial Signaling, Gene Center, Ludwig Maximilian University (LMU), Munich, Germany
| | - Jose Villaveces
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Salma Gamal
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Giovanni Cardone
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Fabiana Perocchi
- Functional Genomics of Mitochondrial Signaling, Gene Center, Ludwig Maximilian University (LMU), Munich, Germany
| | - Zuzana Storchova
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.,Department of Molecular Genetics, TU Kaiserslautern, Paul Ehrlich Strasse 24, 67663 Kaiserslautern, Germany
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.,Aix-Marseille University, CNRS, IBDM UMR 7288, 13009 Marseille, France
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11
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Salemi M, Rappazzo G, Ridolfo F, Salluzzo MG, Cannarella R, Castiglione R, Caniglia S, Tirolo C, Calogero AE, Romano C. Cerebellar degeneration-related protein 1 expression in fibroblasts of patients affected by down syndrome. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1832922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
| | - Giancarlo Rappazzo
- Laboratory of Molecular Genetics, Department of Biological Geological Environmental Sciences, University of Catania, Catania, Italy
| | - Federico Ridolfo
- UOSD of Clinical Pathology, ASUR Marche – AV2, Hospital of Senigallia, Senigallia, Italy
| | | | - Rossella Cannarella
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
| | - Roberto Castiglione
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
| | | | | | - Aldo E. Calogero
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
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12
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Hou J, Shi X, Chen C, Islam MS, Johnson AF, Kanno T, Huettel B, Yen MR, Hsu FM, Ji T, Chen PY, Matzke M, Matzke AJM, Cheng J, Birchler JA. Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proc Natl Acad Sci U S A 2018; 115:E11321-E11330. [PMID: 30429332 PMCID: PMC6275517 DOI: 10.1073/pnas.1807796115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.
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Affiliation(s)
- Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Md Soliman Islam
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Adam F Johnson
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam 550000
| | - Tatsuo Kanno
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding, Cologne, Germany 50829
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Fei-Man Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO 65211
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Antonius J M Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211;
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13
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Volk M, Maver A, Hodžić A, Lovrečić L, Peterlin B. Transcriptome Profiling Uncovers Potential Common Mechanisms in Fetal Trisomies 18 and 21. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:565-570. [PMID: 29049012 PMCID: PMC5655413 DOI: 10.1089/omi.2017.0123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human trisomies have recently been investigated using transcriptomics approaches to identify the gene expression (GE) signatures characteristic of each of these specific aneuploidy conditions. We hypothesized that the viability of cells with gross genomic imbalances might be associated with the activation of resilience mechanisms that are common to different trisomies and that are reflected by specific shared GE patterns. We report in this article our microarray GE analyses of amniocytes from fetuses with viable trisomy conditions, trisomy 21 or trisomy 18, to detect such common expression signatures. Comparative analysis of significantly differentially expressed genes in trisomies 18 and 21 revealed six dysregulated genes common to both: OTUD5, ADAMTSL1, TADA2A, PPID, PIAS2, and MAPRE2. These genes are involved in ubiquitination, protein folding, cell proliferation, and apoptosis. Pathway-based enrichment analyses demonstrated that both trisomies showed dysregulation of the PI3K/AKT pathway, cell cycle G2/M DNA damage checkpoint regulation, and cell death and survival, as well as inhibition of the upstream regulator TP53. Our data collectively suggest that trisomies 18 and 21 share common functional GE signatures, implying that common mechanisms of resilience might be activated in aneuploid cells to resist large genomic imbalances. To the best of our knowledge, this is the first study to use global GE profiling data to identify potential common mechanisms in fetal trisomies. Studies of other trisomies using transcriptomics and multiomics approaches might further clarify mechanisms activated in trisomy syndromes.
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Affiliation(s)
- Marija Volk
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Alenka Hodžić
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
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14
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Stagni F, Giacomini A, Emili M, Guidi S, Bartesaghi R. Neurogenesis impairment: An early developmental defect in Down syndrome. Free Radic Biol Med 2018; 114:15-32. [PMID: 28756311 DOI: 10.1016/j.freeradbiomed.2017.07.026] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 02/06/2023]
Abstract
Down syndrome (DS) is characterized by brain hypotrophy and intellectual disability starting from early life stages. Accumulating evidence shows that the phenotypic features of the DS brain can be traced back to the fetal period since the DS brain exhibits proliferation potency reduction starting from the critical time window of fetal neurogenesis. This defect is worsened by the fact that neural progenitor cells exhibit reduced acquisition of a neuronal phenotype and an increase in the acquisition of an astrocytic phenotype. Consequently, the DS brain has fewer neurons in comparison with the typical brain. Although apoptotic cell death may be increased in DS, this does not seem to be the major cause of brain hypocellularity. Evidence obtained in brains of individuals with DS, DS-derived induced pluripotent stem cells (iPSCs), and DS mouse models has provided some insight into the mechanisms underlying the developmental defects due to the trisomic condition. Although many triplicated genes may be involved, in the light of the studies reviewed here, DYRK1A, APP, RCAN1 and OLIG1/2 appear to be particularly important determinants of many neurodevelopmental alterations that characterize DS because their triplication affects both the proliferation and fate of neural precursor cells as well as apoptotic cell death. Based on the evidence reviewed here, pathways downstream to these genes may represent strategic targets, for the design of possible interventions.
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Affiliation(s)
- Fiorenza Stagni
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Andrea Giacomini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Marco Emili
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Sandra Guidi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Renata Bartesaghi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
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15
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Spatial organization of chromosome territories in the interphase nucleus of trisomy 21 cells. Chromosoma 2017; 127:247-259. [PMID: 29238858 DOI: 10.1007/s00412-017-0653-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 12/16/2022]
Abstract
In the interphase cell nucleus, chromosomes adopt a conserved and non-random arrangement in subnuclear domains called chromosome territories (CTs). Whereas chromosome translocation can affect CT organization in tumor cell nuclei, little is known about how aneuploidies can impact CT organization. Here, we performed 3D-FISH on control and trisomic 21 nuclei to track the patterning of chromosome territories, focusing on the radial distribution of trisomic HSA21 as well as 11 disomic chromosomes. We have established an experimental design based on cultured chorionic villus cells which keep their original mesenchymal features including a characteristic ellipsoid nuclear morphology and a radial CT distribution that correlates with chromosome size. Our study suggests that in trisomy 21 nuclei, the extra HSA21 induces a shift of HSA1 and HSA3 CTs out toward a more peripheral position in nuclear space and a higher compaction of HSA1 and HSA17 CTs. We posit that the presence of a supernumerary chromosome 21 alters chromosome compaction and results in displacement of other chromosome territories from their usual nuclear position.
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16
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Zadesenets KS, Schärer L, Rubtsov NB. New insights into the karyotype evolution of the free-living flatworm Macrostomum lignano (Platyhelminthes, Turbellaria). Sci Rep 2017; 7:6066. [PMID: 28729552 PMCID: PMC5519732 DOI: 10.1038/s41598-017-06498-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/13/2017] [Indexed: 01/02/2023] Open
Abstract
The free-living flatworm Macrostomum lignano is a model organism for evolutionary and developmental biology studies. Recently, an unusual karyotypic diversity was revealed in this species. Specifically, worms are either ‘normal’ 2n = 8, or they are aneuploid with one or two additional large chromosome(s) (i.e. 2n = 9 or 2n = 10, respectively). Aneuploid worms did not show visible behavioral or morphological abnormalities and were successful in reproduction. In this study, we generated microdissected DNA probes from chromosome 1 (further called MLI1), chromosome 2 (MLI2), and a pair of similar-sized smaller chromosomes (MLI3, MLI4). FISH using these probes revealed that MLI1 consists of contiguous regions homologous to MLI2-MLI4, suggesting that MLI1 arose due to the whole genome duplication and subsequent fusion of one full chromosome set into one large metacentric chromosome. Therefore, one presumably full haploid genome was packed into MLI1, leading to hidden tetraploidy in the M. lignano genome. The study of Macrostomum sp. 8 — a sibling species of M. lignano — revealed that it usually has one additional pair of large chromosomes (2n = 10) showing a high homology to MLI1, thus suggesting hidden hexaploidy in its genome. Possible evolutionary scenarios for the emergence of the M. lignano and Macrostomum sp. 8 genomes are discussed.
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Affiliation(s)
- Kira S Zadesenets
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk, 630090, Russian Federation.
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, CH-4051, Switzerland
| | - Nikolay B Rubtsov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, Pirogova str., 2, Novosibirsk, 630090, Russian Federation
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17
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Abstract
Renal anomalies are common birth defects that may manifest as a wide spectrum of anomalies from hydronephrosis (dilation of the renal pelvis and calyces) to renal aplasia (complete absence of the kidney(s)). Aneuploidies and mosaicisms are the most common syndromes associated with CAKUT. Syndromes with single gene and renal developmental defects are less common but have facilitated insight into the mechanism of renal and other organ development. Analysis of underlying genetic mutations with transgenic and mutant mice has also led to advances in our understanding of mechanisms of renal development.
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18
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Ma K, Li F, Yu Y, Li H. Screening of potential biomarkers for prenatal diagnosis of trisomy 21. J OBSTET GYNAECOL 2016; 37:435-440. [PMID: 28019128 DOI: 10.1080/01443615.2016.1250730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We aimed to identify key genes located on chromosome 21 as potential biomarkers for prenatal diagnosis of trisomy 21 (Ts21). The microarray data of GSE48051, including 10 cultivated amniocyte samples with Ts21 and 9 controls with normal euploid constitution, was obtained from Gene Expression Omnibus database. The differentially expressed genes (DEGs) in cultivated amniocyte samples with Ts21 compared to normal controls were screened using limma package. Then, we performed GO enrichment analysis using DAVID and chromosomal location of DEGs based on the information of the University of California Santa Cruz (UCSC) Genome Browser Database. Finally, protein-protein interaction (PPI) network analysis was performed using STRING. Total 155 DEGs in cultivated amniocyte samples with Ts21 were identified, including 89 up- and 66 down-regulated DEGs. The over-represented GO terms of DEGs were mainly related with apoptosis, programmed cell death and cell death. In total, 13 DEGs were located on chromosome 21, thereinto, only 6 DEGs were included into the PPI network, including superoxide dismutase 1 (SOD1), phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase (GART), downstream neighbour of SON (DONSON), ATP synthase, H + transporting, mitochondrial F1 complex, O subunit (ATP5O), chromatin assembly factor 1, subunit B (p60) (CHAF1B) and proteasome (prosome, macropain) assembly chaperone 1 (PSMG1). Our results suggest that SOD1, GART, DONSON, ATP5O, CHAF1B and PSMG1 may play important roles in the pathogenesis of Down syndrome and may serve as potential biomarkers for prenatal diagnosis of Ts21.
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Affiliation(s)
- Ke Ma
- a Department of Pediatric Emergency , First Hospital of Jilin University , Changchun , Jilin , China
| | - Feng Li
- a Department of Pediatric Emergency , First Hospital of Jilin University , Changchun , Jilin , China
| | - Yang Yu
- b Department of Clinical Laboratory , Hospital of Stomatology, Jilin University , Changchun , Jilin , China
| | - Haibo Li
- a Department of Pediatric Emergency , First Hospital of Jilin University , Changchun , Jilin , China
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19
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Zadesenets KS, Vizoso DB, Schlatter A, Konopatskaia ID, Berezikov E, Schärer L, Rubtsov NB. Evidence for Karyotype Polymorphism in the Free-Living Flatworm, Macrostomum lignano, a Model Organism for Evolutionary and Developmental Biology. PLoS One 2016; 11:e0164915. [PMID: 27755577 PMCID: PMC5068713 DOI: 10.1371/journal.pone.0164915] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/03/2016] [Indexed: 11/19/2022] Open
Abstract
Over the past decade, the free-living flatworm Macrostomum lignano has been successfully used in many areas of biology, including embryology, stem cells, sexual selection, bioadhesion and aging. The increased use of this powerful laboratory model, including the establishment of genomic resources and tools, makes it essential to have a detailed description of the chromosome organization of this species, previously suggested to have a karyotype with 2n = 8 and one pair of large and three pairs of small metacentric chromosomes. We performed cytogenetic analyses for chromosomes of one commonly used inbred line of M. lignano (called DV1) and uncovered unexpected chromosome number variation in the form of aneuploidies of the largest chromosomes. These results prompted us to perform karyotypic studies in individual specimens of this and other lines of M. lignano reared under laboratory conditions, as well as in freshly field-collected specimens from different natural populations. Our analyses revealed a high frequency of aneuploids and in some cases other numerical and structural chromosome abnormalities in laboratory-reared lines of M. lignano, and some cases of aneuploidy were also found in freshly field-collected specimens. Moreover, karyological analyses were performed in specimens of three further species: Macrostomum sp. 8 (a close relative of M. lignano), M. spirale and M. hystrix. Macrostomum sp. 8 showed a karyotype that was similar to that of M. lignano, with tetrasomy for its largest chromosome being the most common karyotype, while the other two species showed a simpler karyotype that is more typical of the genus Macrostomum. These findings suggest that M. lignano and Macrostomum sp. 8 can be used as new models for studying processes of partial genome duplication in genome evolution.
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Affiliation(s)
- Kira S. Zadesenets
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- * E-mail:
| | - Dita B. Vizoso
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Aline Schlatter
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Eugene Berezikov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Nikolay B. Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
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20
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Svobodová I, Korabečná M, Calda P, Břešťák M, Pazourková E, Pospíšilová Š, Krkavcová M, Novotná M, Hořínek A. Differentially expressed miRNAs in trisomy 21 placentas. Prenat Diagn 2016; 36:775-84. [PMID: 27323694 DOI: 10.1002/pd.4861] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/30/2016] [Accepted: 06/16/2016] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Molecular pathogenesis of Down syndrome (DS) is still incompletely understood. Epigenetic mechanisms, including miRNAs gene expression regulation, belong to potential influencing factors. The aims of this study were to compare miRNAs expressions in placentas with normal and trisomic karyotype and to associate differentially expressed miRNAs with concrete biological pathways. METHODS A total of 80 CVS samples - 41 with trisomy 21 and 39 with normal karyotype - were included in our study. Results obtained in the pilot study using real-time PCR technology and TaqMan Human miRNA Array Cards were subsequently validated on different samples using individual TaqMan miRNA Assays. RESULTS Seven miRNAs were verified as upregulated in DS placentas (miR-99a, miR-542-5p, miR-10b, miR-125b, miR-615, let-7c and miR-654); three of these miRNAs are located on chromosome 21 (miR-99a, miR-125b and let-7c). Many essential biological processes, transcriptional regulation or apoptosis, were identified as being potentially influenced by altered miRNA levels. Moreover, miRNAs overexpressed in DS placenta apparently regulate genes involved in placenta development (GJA1, CDH11, EGF, ERVW-1, ERVFRD-1, LEP or INHA). CONCLUSION These findings suggest the possible participation of miRNAs in Down syndrome impaired placentation and connected pregnancy pathologies. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Iveta Svobodová
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Marie Korabečná
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Pavel Calda
- Department of Obstetrics and Gynecology of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Miroslav Břešťák
- Department of Obstetrics and Gynecology of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Screening Center ProfiG2, Prague, Czech Republic
| | - Eva Pazourková
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Šárka Pospíšilová
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | | | - Michaela Novotná
- Department of Obstetrics and Gynecology of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Aleš Hořínek
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,3rd Medical Department of Internal Medicine of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
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21
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Hervé B, Coussement A, Gilbert T, Dumont F, Jacques S, Cuisset L, Chicard M, Hizem S, Bourdoncle P, Letourneur F, Dupont C, Vialard F, Choiset A, Dupont JM. Aneuploidy: the impact of chromosome imbalance on nuclear organization and overall genome expression. Clin Genet 2016; 90:35-48. [PMID: 27283765 DOI: 10.1111/cge.12731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/05/2016] [Accepted: 01/05/2016] [Indexed: 12/19/2022]
Abstract
The organization and dynamics of chromatin within the interphase nucleus as chromosome territories (CTs) and the relationship with transcriptional regulation are not fully understood. We studied a natural example of chromosomal disorganization: aneuploidy due to trisomies 13, 18 and 21. We hypothesized that the presence of an extra copy of one chromosome alters the CT distribution, which perturbs transcriptional activity. We used 3D-FISH to study the position of the chromosomes of interest (18 and 21) in cultured amniocytes and chorionic villus cells from pregnancies with a normal or aneuploid karyotype. We studied the volumes of nuclei and CTs in both conditions and performed a compared transcriptome analysis. We did not observe any differences between euploid and aneuploid cells in terms of the radial and relative CT positions, suggesting that the same rules govern nuclear organization in cases of trisomy. We observed lower volumes for CTs 18 and 21. Overall genome expression profiles highlighted changes in the expression of a subset of genes in trisomic chromosomes, while the majority of transcriptional changes concerned genes located on euploid chromosomes. Our results suggest that a dosage imbalance of the genes on trisomic chromosomes is associated with a disturbance of overall genomic expression.
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Affiliation(s)
- B Hervé
- UFR des Sciences de la Santé Simone Veil, GIG, EA7404, Montigny le Bretonneux, France.,Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France.,Service de Cytogénétique, Centre Hospitalier Intercommunal de Poissy Saint-Germain-en-Laye, Poissy, France
| | - A Coussement
- Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
| | - T Gilbert
- Plate-Forme Cochin Imagerie, Université Paris Descartes, Institut Cochin, Paris, France
| | - F Dumont
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - S Jacques
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - L Cuisset
- Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Biochimie et Génétique Moléculaire, APHP - Hôpital Cochin, Paris, France
| | - M Chicard
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - S Hizem
- Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
| | - P Bourdoncle
- Plate-Forme Cochin Imagerie, Université Paris Descartes, Institut Cochin, Paris, France
| | - F Letourneur
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - C Dupont
- Unité fonctionnelle de Cytogénétique-Département de Génétique- APHP, Hôpital Robert Debré, Paris, France
| | - F Vialard
- UFR des Sciences de la Santé Simone Veil, GIG, EA7404, Montigny le Bretonneux, France.,Service de Cytogénétique, Centre Hospitalier Intercommunal de Poissy Saint-Germain-en-Laye, Poissy, France
| | - A Choiset
- Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
| | - J-M Dupont
- Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
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22
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Explore the dynamic alternation of gene PLAC4 mRNA expression levels in maternal plasma in second trimester for nonivasive detection of trisomy 21. Obstet Gynecol Sci 2015. [PMID: 26217595 PMCID: PMC4515474 DOI: 10.5468/ogs.2015.58.4.261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVE Noninvasive prenatal detection of trisomy 21 (T21) has been achieved by measuring the ratio of two alleles of a single nucleotide polymorphism in circulating placenta specific 4 (PLAC4) mRNA in maternal plasma with a few assays in recent years. Our research is to explore the variations of PLAC4 mRNA expression level in maternal plasma with normal pregnancies in second trimester, which can provide pregnant women deeper insights with suitable detection period for the non-invasive prenatal detection of T21. METHODS We measured a serial plasma PLAC4 mRNA concentrations weekly from the same 25 singleton normal pregnant women. We recruited maternal plasma samples from 45 singleton pregnant women, comprising of 25 euploid pregnancies (control group; range, 17 to 21 weeks) and 20 T21 pregnancies (T21 group; range, 19 to 24 weeks). With the application of reverse transcription polymerase chain reaction, we achieved an insight of PLAC4 mRNA expression levels in maternal plasma during second trimester with euploid pregnancies. RESULTS Among the control group, the levels of PLAC4 mRNA expression in the gestation of 17 to 18 weeks were significantly less than those in the gestation of 18 to 21 weeks (P<0.05). The average PLAC4 mRNA concentration of the normal pregnant women was not higher than that of the T21 group (P>0.05). CONCLUSION The PLAC4 mRNA showed a higher level of expression in the gestation of 18 to 21 weeks with an euploid pregnancy of pregnant women. We also found that there was no significant difference in plasma PLAC4 mRNA concentration between the normal and the T21 pregnancies in second trimester.
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Zwemer LM, Bianchi DW. The amniotic fluid transcriptome as a guide to understanding fetal disease. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a023101. [PMID: 25680981 DOI: 10.1101/cshperspect.a023101] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Numerous recent studies have shown the power of cell-free fetal RNA, obtained from amniotic fluid supernatant, to report on the development of the living fetus in real time. Examination of these transcripts on a genome-wide basis has led to new insights into the prenatal pathophysiology of multiple genetic, developmental, and environmental diseases. Each studied condition presents a unique, characteristic fetal transcriptome, which points to specific disrupted molecular pathways. These studies have also improved our knowledge of the normal development of the human fetus, revealing gestational age-related dynamic gene expression from a variety of organs. Analysis of the fetal transcriptome in normal and abnormal development has led to novel approaches for in utero prenatal treatment.
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Affiliation(s)
- Lillian M Zwemer
- Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts 02111
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts 02111
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Abstract
In many animals, males have one X and females have two X chromosomes. The difference in X chromosome dosage between the two sexes is compensated by mechanisms that regulate X chromosome transcription. Recent advances in genomic techniques have provided new insights into the molecular mechanisms of X chromosome dosage compensation. In this review, I summarize our current understanding of dosage imbalance in general, and then review the molecular mechanisms of X chromosome dosage compensation with an emphasis on the parallels and differences between the three well-studied model systems, M. musculus, D. melanogaster and C. elegans.
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Affiliation(s)
- Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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Liu B, Filippi S, Roy A, Roberts I. Stem and progenitor cell dysfunction in human trisomies. EMBO Rep 2014; 16:44-62. [PMID: 25520324 DOI: 10.15252/embr.201439583] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Trisomy 21, the commonest constitutional aneuploidy in humans, causes profound perturbation of stem and progenitor cell growth, which is both cell context dependent and developmental stage specific and mediated by complex genetic mechanisms beyond increased Hsa21 gene dosage. While proliferation of fetal hematopoietic and testicular stem/progenitors is increased and may underlie increased susceptibility to childhood leukemia and testicular cancer, fetal stem/progenitor proliferation in other tissues is markedly impaired leading to the characteristic craniofacial, neurocognitive and cardiac features in individuals with Down syndrome. After birth, trisomy 21-mediated premature aging of stem/progenitor cells may contribute to the progressive multi-system deterioration, including development of Alzheimer's disease.
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Affiliation(s)
- Binbin Liu
- Department of Paediatrics and Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Sarah Filippi
- Department of Statistics, University of Oxford, Oxford, UK
| | - Anindita Roy
- Centre for Haematology, Imperial College London, London, UK
| | - Irene Roberts
- Department of Paediatrics and Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
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Gene expression profiling and qRT-PCR expression of RRP1B, PCNT, KIF21A and ADRB2 in leucocytes of Down’s syndrome subjects. J Genet 2014. [DOI: 10.1007/s12041-012-0132-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Davidsson J. The epigenetic landscape of aneuploidy: constitutional mosaicism leading the way? Epigenomics 2014; 6:45-58. [PMID: 24579946 DOI: 10.2217/epi.13.78] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The role of structural genetic changes in human disease has received substantial attention in recent decades, but surprisingly little is known about numerical chromosomal abnormalities, even though they have been recognized since the days of Boveri as partaking in different cellular pathophysiological processes such as cancer and genomic disorders. The current knowledge of the genetic and epigenetic consequences of aneuploidy is reviewed herein, with a special focus on using mosaic genetic syndromes to study the DNA methylation footprints and expressional effects associated with whole-chromosomal gains. Recent progress in understanding the debated role of aneuploidy as a driver or passenger in malignant transformation, as well as how the cell responds to and regulates excess genetic material in experimental settings, is also discussed in detail.
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Affiliation(s)
- Josef Davidsson
- Division of Molecular Medicine & Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 84 Lund, Sweden
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Birchler JA. Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 2014; 123:459-69. [DOI: 10.1007/s00412-014-0478-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
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Volk M, Maver A, Lovrečić L, Juvan P, Peterlin B. Expression signature as a biomarker for prenatal diagnosis of trisomy 21. PLoS One 2013; 8:e74184. [PMID: 24066117 PMCID: PMC3774664 DOI: 10.1371/journal.pone.0074184] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/30/2013] [Indexed: 11/17/2022] Open
Abstract
A universal biomarker panel with the potential to predict high-risk pregnancies or adverse pregnancy outcome does not exist. Transcriptome analysis is a powerful tool to capture differentially expressed genes (DEG), which can be used as biomarker-diagnostic-predictive tool for various conditions in prenatal setting. In search of biomarker set for predicting high-risk pregnancies, we performed global expression profiling to find DEG in Ts21. Subsequently, we performed targeted validation and diagnostic performance evaluation on a larger group of case and control samples. Initially, transcriptomic profiles of 10 cultivated amniocyte samples with Ts21 and 9 with normal euploid constitution were determined using expression microarrays. Datasets from Ts21 transcriptomic studies from GEO repository were incorporated. DEG were discovered using linear regression modelling and validated using RT-PCR quantification on an independent sample of 16 cases with Ts21 and 32 controls. The classification performance of Ts21 status based on expression profiling was performed using supervised machine learning algorithm and evaluated using a leave-one-out cross validation approach. Global gene expression profiling has revealed significant expression changes between normal and Ts21 samples, which in combination with data from previously performed Ts21 transcriptomic studies, were used to generate a multi-gene biomarker for Ts21, comprising of 9 gene expression profiles. In addition to biomarker’s high performance in discriminating samples from global expression profiling, we were also able to show its discriminatory performance on a larger sample set 2, validated using RT-PCR experiment (AUC=0.97), while its performance on data from previously published studies reached discriminatory AUC values of 1.00. Our results show that transcriptomic changes might potentially be used to discriminate trisomy of chromosome 21 in the prenatal setting. As expressional alterations reflect both, causal and reactive cellular mechanisms, transcriptomic changes may thus have future potential in the diagnosis of a wide array of heterogeneous diseases that result from genetic disturbances.
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Affiliation(s)
- Marija Volk
- Clinical Institute of Medical Genetics, Department of Obstetrics and Gynecology, University Medical Center, Ljubljana, Ljubljana, Slovenia
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Olszewska M, Fraczek M, Huleyuk N, Czernikiewicz A, Wiland E, Boksa M, Zastavna D, Panasiuk B, Midro AT, Kurpisz M. Chromatin structure analysis of spermatozoa from reciprocal chromosome translocation (RCT) carriers with known meiotic segregation patterns. Reprod Biol 2013; 13:209-20. [DOI: 10.1016/j.repbio.2013.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 05/21/2013] [Accepted: 06/21/2013] [Indexed: 10/26/2022]
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Castiglione A, Guaran V, Astolfi L, Orioli E, Zeri G, Gemmati D, Bovo R, Montaldi A, Alghisi A, Martini A. Karyotype-phenotype correlation in partial trisomies of the short arm of chromosome 6: a family case report and review of the literature. Cytogenet Genome Res 2013; 141:243-59. [PMID: 23942271 DOI: 10.1159/000353846] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2013] [Indexed: 11/19/2022] Open
Abstract
The first child (proband) of nonconsanguineous Caucasian parents underwent genetic investigation because she was affected with congenital choanal atresia, heart defects and kidney hyposplasia with mild transient renal insufficiency. The direct DNA sequencing after PCR of the CHD7 gene, which is thought to be responsible for approximately 60-70% of the cases of CHARGE syndrome/association, found no mutations. The cytogenetic analysis (standard GTG banding karyotype) revealed the presence of extrachromosomal material on 10q. The chromosome analysis was completed with array CGH (30 kb resolution), MLPA and FISH, which allowed the identification of three 6p regions (6p.25.3p23 × 3): 2 of these regions are normally located on chromosome 6, and the third region is translocated to the long arm of chromosome 10. The same chromosomal rearrangement was subsequently found in the father, who was affected with congenital ptosis and progressive hearing loss, and in the proband's sister, the second child, who presented at birth with choanal atresia and congenital heart defects. The mutated karyotypes, which were directly inherited, are thought to be responsible for a variable phenotype, including craniofacial dysmorphisms, choanal atresia, congenital ptosis, sensorineural hearing loss, heart defects, developmental delay, and renal dysfunction. Nevertheless, to achieve a complete audiological assessment of the father, he underwent further investigation that revealed an increased level of the coagulation factor XIII (300% increased activity), fluctuating levels of fibrin D-dimer degradation products (from 296 to 1,587 ng/ml) and a homoplasmic mitochondrial DNA mutation: T961G in the MTRNR1 (12S rRNA) gene. He was made a candidate for cochlear implantation. Preoperative high-resolution computed tomography and magnetic resonance imaging of the temporal bone revealed the presence of an Arnold-Chiari malformation type I. To the best of our knowledge, this study is the second report on partial 6p trisomy that involves the 10q terminal region. Furthermore, we report the first case of documented Arnold-Chiari malformation type I and increased factor XIII activity associated with 6p trisomy. We present a comprehensive report of the familial cases and an exhaustive literature review.
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Affiliation(s)
- A Castiglione
- Department of Neurosciences, Complex Operative Unit of Otorhinolaryngology and Otosurgery, Padua University Hospital, Padua, Italy
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Granese B, Scala I, Spatuzza C, Valentino A, Coletta M, Vacca RA, De Luca P, Andria G. Validation of microarray data in human lymphoblasts shows a role of the ubiquitin-proteasome system and NF-kB in the pathogenesis of Down syndrome. BMC Med Genomics 2013; 6:24. [PMID: 23830204 PMCID: PMC3717290 DOI: 10.1186/1755-8794-6-24] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/29/2013] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Down syndrome (DS) is a complex disorder caused by the trisomy of either the entire, or a critical region of chromosome 21 (21q22.1-22.3). Despite representing the most common cause of mental retardation, the molecular bases of the syndrome are still largely unknown. METHODS To better understand the pathogenesis of DS, we analyzed the genome-wide transcription profiles of lymphoblastoid cell lines (LCLs) from six DS and six euploid individuals and investigated differential gene expression and pathway deregulation associated with trisomy 21. Connectivity map and PASS-assisted exploration were used to identify compounds whose molecular signatures counteracted those of DS lymphoblasts and to predict their therapeutic potential. An experimental validation in DS LCLs and fetal fibroblasts was performed for the most deregulated GO categories, i.e. the ubiquitin mediated proteolysis and the NF-kB cascade. RESULTS We show, for the first time, that the level of protein ubiquitination is reduced in human DS cell lines and that proteasome activity is increased in both basal conditions and oxidative microenvironment. We also provide the first evidence that NF-kB transcription levels, a paradigm of gene expression control by ubiquitin-mediated degradation, is impaired in DS due to reduced IkB-alfa ubiquitination, increased NF-kB inhibitor (IkB-alfa) and reduced p65 nuclear fraction. Finally, the DSCR1/DYRK1A/NFAT genes were analysed. In human DS LCLs, we confirmed the presence of increased protein levels of DSCR1 and DYRK1A, and showed that the levels of the transcription factor NFATc2 were decreased in DS along with a reduction of its nuclear translocation upon induction of calcium fluxes. CONCLUSIONS The present work offers new perspectives to better understand the pathogenesis of DS and suggests a rationale for innovative approaches to treat some pathological conditions associated to DS.
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Affiliation(s)
- Barbara Granese
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Iris Scala
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Carmen Spatuzza
- Department of Biotechnological Sciences, Federico II University, Naples 80131, Italy
| | - Anna Valentino
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Marcella Coletta
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Rosa Anna Vacca
- Institute of Biomembranes and Bioenergetics, National Council of Research, Bari 70126, Italy
| | - Pasquale De Luca
- Stazione Zoologica “A. Dohrn”, c/o BioGeM, Via Camporeale, Ariano Irpino 83031, Italy
| | - Generoso Andria
- Department of Pediatrics, Federico II University, Naples 80131, Italy
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Davidsson J, Veerla S, Johansson B. Constitutional trisomy 8 mosaicism as a model for epigenetic studies of aneuploidy. Epigenetics Chromatin 2013; 6:18. [PMID: 23816241 PMCID: PMC3704342 DOI: 10.1186/1756-8935-6-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 05/30/2013] [Indexed: 12/21/2022] Open
Abstract
Background To investigate epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism (CT8M) as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient; this circumvents any bias introduced by using cells from unrelated, healthy individuals as controls. We profiled gene and miRNA expression as well as genome-wide and promoter specific DNA methylation and hydroxymethylation patterns in trisomic and disomic fibroblasts, using microarrays and methylated DNA immunoprecipitation. Results Trisomy 8-positive fibroblasts displayed a characteristic expression and methylation phenotype distinct from disomic fibroblasts, with the majority (65%) of chromosome 8 genes in the trisomic cells being overexpressed. However, 69% of all deregulated genes and non-coding RNAs were not located on this chromosome. Pathway analysis of the deregulated genes revealed that cancer, genetic disorder, and hematopoiesis were top ranked. The trisomy 8-positive cells displayed depletion of 5-hydroxymethylcytosine and global hypomethylation of gene-poor regions on chromosome 8, thus partly mimicking the inactivated X chromosome in females. Conclusions Trisomy 8 affects genes situated also on other chromosomes which, in cooperation with the observed chromosome 8 gene dosage effect, has an impact on the clinical features of CT8M, as demonstrated by the pathway analysis revealing key features that might explain the increased incidence of hematologic malignancies in CT8M patients. Furthermore, we hypothesize that the general depletion of hydroxymethylation and global hypomethylation of chromosome 8 may be unrelated to gene expression regulation, instead being associated with a general mechanism of chromatin processing and compartmentalization of additional chromosomes.
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Affiliation(s)
- Josef Davidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE 221 85, Lund, Sweden.
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Dosage compensation and inverse effects in triple X metafemales of Drosophila. Proc Natl Acad Sci U S A 2013; 110:7383-8. [PMID: 23589863 DOI: 10.1073/pnas.1305638110] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dosage compensation, the equalized X chromosome gene expression between males and females in Drosophila, has also been found in triple X metafemales. Inverse dosage effects, produced by genomic imbalance, are believed to account for this modulated expression, but they have not been studied on a global level. Here, we show a global expression comparison of metafemales (XXX; AA) with normal females (XX; AA) with high-throughput RNA-sequencing. We found that the majority of the X-linked genes in metafemales exhibit dosage compensation with an expression level similar to that of normal diploid females. In parallel, most of the autosomal genes were expressed at about two-thirds the level of normal females, the ratio of inverse dosage effects produced by the extra X chromosome. Both compensation and inverse effects were further confirmed by combination of X-linked and autosomally located miniwhite reporter genes in metafemales and relative quantitative PCR of selected genes. These data provide evidence for an inverse dosage component to X chromosome compensation.
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Chatterjee A, Dutta S, Mukherjee S, Mukherjee N, Dutta A, Mukherjee A, Sinha S, Panda CK, Chaudhuri K, Roy AL, Mukhopadhyay K. Potential contribution of SIM2 and ETS2 functional polymorphisms in Down syndrome associated malignancies. BMC MEDICAL GENETICS 2013; 14:12. [PMID: 23343470 PMCID: PMC3563522 DOI: 10.1186/1471-2350-14-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 01/18/2013] [Indexed: 01/04/2023]
Abstract
Background Proper expression and functioning of transcription factors (TFs) are essential for regulation of different traits and thus could be crucial for the development of complex diseases. Subjects with Down syndrome (DS) have a higher incidence of acute lymphoblastic leukemia (ALL) while solid tumors, like breast cancer (BC) and oral cancer (OC), show rare incidences. Triplication of the human chromosome 21 in DS is associated with altered genetic dosage of different TFs. V-ets erythroblastosis virus E26 oncogene homolog 2 (ETS2) and Single Minded 2 (SIM2) are two such TFs that regulate several downstream genes involved in developmental and neurological pathways. Here we studied functional genetic polymorphisms (fSNP) in ETS2 and SIM2 encoding genes in a group of patients and control subjects to better understand association of these variants with DS phenotypes. Methods We employed an in silico approach to identify potential target pathways of ETS2 and SIM2. fSNPs in genes encoding for these two TFs were identified using available databases. Selected sites were genotyped in individuals with DS, their parents, ALL, BC, OC as well as ethnically matched control individuals. We further analyzed these data by population-based statistical methods. Results Allelic/genotypic association analysis showed significant (P < 0.03) differences of rs2070530, rs1051476, rs11254, rs711 for DS subjects compared to control. rs711 also exhibited significantly different genotypic distribution pattern in parents of DS probands (P < 0.02) and BC patients (P < 0.02). Interaction analysis revealed independent main effect of rs711 in all the groups, while rs11254 exhibited independent main effect in DS subjects only. High entropy values were noticed for rs461155 in the solid tumor groups. Significant interactive effects of rs2070531 with rs1051475, rs1051476, rs11254 were observed in all the groups except DS. Conclusions We infer from the present investigation that the difference in frequencies of fSNPs and their independent as well as interactive effects may be the cause for altered expression of SIM2 and ETS2 in DS and malignant groups, which affects different downstream biological pathways. Thus, altered expression of SIM2 and ETS2 could be one of the reasons for variable occurrence of different malignant conditions in DS.
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Affiliation(s)
- Arpita Chatterjee
- Manovikas Biomedical Research and Diagnostic Centre, MRIH, Kolkata, India
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Ayed W, Gouas L, Penault-Llorca F, Amouri A, Tchirkov A, Vago P. [Trisomy 21 and cancers]. Morphologie 2012; 96:57-66. [PMID: 23141635 DOI: 10.1016/j.morpho.2012.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/02/2012] [Indexed: 11/29/2022]
Abstract
Patients with trisomy 21, still called Down's syndrome (DS), present a particular tumoral profile compared to the general population with an increased incidence of leukaemia in the childhood and a low risk of solid cancer in the adulthood. DS children indeed present a 50-fold risk of developing a leukaemia compared to age-matched non-trisomic children and most of them develop a specific myelodysplasic disorder called transient myelodysplasic disorder. In spite of the low incidence of solid tumors, some are very rare as breast cancer, nephroblastoma, neuroblastoma and medulloblastoma, whereas the others remain more frequent as retinoblastoma, lymphoma and gonadal and extragonadal germ cell tumours. In this review, we present possible mechanisms which can favour, or on the contrary repress the formation and progression of tumours in DS patients, which are related to gene effect dosage of oncogenes or tumour repressors on chromosome 21, tumour angiogenesis, apoptosis and epithelial cell-stroma interactions.
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Affiliation(s)
- W Ayed
- Université Clermont 1, UFR médecine, cytologie histologie embryologie cytogénétique, 63001 Clermont-Ferrand, France
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Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A 2012; 109:14746-53. [PMID: 22908297 DOI: 10.1073/pnas.1207726109] [Citation(s) in RCA: 377] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We summarize, in this review, the evidence that genomic balance influences gene expression, quantitative traits, dosage compensation, aneuploid syndromes, population dynamics of copy number variants and differential evolutionary fate of genes after partial or whole-genome duplication. Gene balance effects are hypothesized to result from stoichiometric differences among members of macromolecular complexes, the interactome, and signaling pathways. The implications of gene balance are discussed.
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Abstract
Aneuploidy, or an aberrant karyotype, results in developmental disabilities and has been implicated in tumorigenesis. However, the causes of aneuploidy-induced phenotypes and the consequences of aneuploidy on cell physiology remain poorly understood. We have performed a metaanalysis on gene expression data from aneuploid cells in diverse organisms, including yeast, plants, mice, and humans. We found highly related gene expression patterns that are conserved between species: genes that were involved in the response to stress were consistently upregulated, and genes associated with the cell cycle and cell proliferation were downregulated in aneuploid cells. Within species, different aneuploidies induced similar changes in gene expression, independent of the specific chromosomal aberrations. Taken together, our results demonstrate that aneuploidies of different chromosomes and in different organisms impact similar cellular pathways and cause a stereotypical antiproliferative response that must be overcome before transformation.
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Hui L, Slonim DK, Wick HC, Johnson KL, Koide K, Bianchi DW. Novel neurodevelopmental information revealed in amniotic fluid supernatant transcripts from fetuses with trisomies 18 and 21. Hum Genet 2012; 131:1751-9. [PMID: 22752091 DOI: 10.1007/s00439-012-1195-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/19/2012] [Indexed: 01/15/2023]
Abstract
Trisomies 18 and 21 are the two most common live born autosomal aneuploidies in humans. While the anatomic abnormalities in affected fetuses are well documented, the dysregulated biological pathways associated with the development of the aneuploid phenotype are less clear. Amniotic fluid (AF) cell-free RNA is a valuable source of biological information obtainable from live fetuses. In this study, we mined gene expression data previously produced by our group from mid-trimester AF supernatant samples. We identified the euploid, trisomy 18 and trisomy 21 AF transcriptomes, and analyzed them with a particular focus on the nervous system. We used multiple bioinformatics resources, including DAVID, Ingenuity Pathway Analysis, and the BioGPS Gene Expression Atlas. Our analyses confirmed that AF supernatant from aneuploid fetuses is enriched for nervous system gene expression and neurological disease pathways. Tissue analysis showed that fetal brain cortex and Cajal-Retzius cells were significantly enriched for genes contained in the AF transcriptomes. We also examined AF transcripts known to be dysregulated in aneuploid fetuses compared with euploid controls and identified several brain-specific transcripts among them. Many of these genes play critical roles in nervous system development. NEUROD2, which was downregulated in trisomy 18, induces neurogenic differentiation. SOX11, downregulated in trisomy 21, is a transcription factor that is essential for pan-neuronal protein expression and axonal growth of sensory neurons. Our results show that whole transcriptome analysis of cell-free RNA in AF from live pregnancies permits discovery of biomarkers of abnormal human neurodevelopment and advances our understanding of the pathophysiology of aneuploidy.
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Affiliation(s)
- Lisa Hui
- Mother Infant Research Institute and the Division of Genetics, Department of Pediatrics, The Floating Hospital for Children at Tufts Medical Center, 800 Washington St, Boston, MA 02111, USA.
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Identification of Inverse Regulator-a (Inr-a) as Synonymous with Pre-mRNA Cleavage Complex II Protein (Pcf11) in Drosophila. G3-GENES GENOMES GENETICS 2012; 2:701-6. [PMID: 22690379 PMCID: PMC3362299 DOI: 10.1534/g3.112.002071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 04/11/2012] [Indexed: 11/18/2022]
Abstract
A common modulation of gene expression in aneuploids is an inverse correlation of the monitored gene with the dosage of another segment of the genome. Such effects can be reduced to the action of single genes. One gene previously found to modulate leaky alleles of the white eye color gene in Drosophila is Inverse regulator-a (Inr-a). Heterozygotes of mutations increase the expression of white about 2-fold, and trisomic regions surrounding the gene reduce the expression to about two-thirds of the normal diploid level. Further cytological definition of the location of this gene on the second chromosome led to a candidate pre-mRNA cleavege complex II protein (Pcf11) as the only gene in the remaining region whose mutations exhibit recessive lethality as do alleles of Inr-a. The product of Pcf11 has been implicated in transcriptional initiation, elongation, and termination reactions. Four mutant alleles showed molecular lesions predicted to lead to nonfunctional products of Pcf11. The identification of the molecular lesion of Inr-a provides insight into the basis of this common aneuploidy effect.
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Abstract
Chromosome aberration assays are employed to detect the induction of chromosome breakage (clastogenesis) in somatic and germ cells by direct observation of the chromosomal damage during metaphase analysis, or by indirect observation of chromosomal fragments. Thus, various types of cytogenetic change can be detected such as structural chromosome aberrations (CA), sister chromatid exchanges (SCE), ploidy changes, and micronuclei. Following the induction of the chromosomal damage, most of the aberrations and abnormalities detected by these assays can be detrimental or even lethal to the cell. Their presence, however, indicates a potential to also induce more subtle and therefore transmissible chromosomal damage which survives cell division to produce heritable cytogenetic changes. Usually, induced cytogenetic damage is accompanied by other genotoxic damage such as gene mutations.
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43
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Genomic determinants in the phenotypic variability of Down syndrome. PROGRESS IN BRAIN RESEARCH 2012; 197:15-28. [PMID: 22541286 DOI: 10.1016/b978-0-444-54299-1.00002-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Down syndrome caused by trisomy 21 is a collection of phenotypes with variable expressivity and penetrance. The significant advances in exploring the human genome now provide the tools to better understand the contribution of trisomy 21 in the different manifestations of Down syndrome, and the functional links between the genome variability and the phenotypic variability.
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Vorsanova SG, Yurov YB, Soloviev IV, Iourov IY. Molecular cytogenetic diagnosis and somatic genome variations. Curr Genomics 2011; 11:440-6. [PMID: 21358989 PMCID: PMC3018725 DOI: 10.2174/138920210793176010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 12/22/2022] Open
Abstract
Human molecular cytogenetics integrates the knowledge on chromosome and genome organization at the molecular and cellular levels in health and disease. Molecular cytogenetic diagnosis is an integral part of current genomic medicine and is the standard of care in medical genetics and cytogenetics, reproductive medicine, pediatrics, neuropsychiatry and oncology. Regardless numerous advances in this field made throughout the last two decades, researchers and practitioners who apply molecular cytogenetic techniques may encounter several problems that are extremely difficult to solve. One of them is undoubtedly the occurrence of somatic genome and chromosome variations, leading to genomic and chromosomal mosaicism, which are related but not limited to technological and evaluative limitations as well as multiplicity of interpretations. More dramatically, current biomedical literature almost lacks descriptions, guidelines or solutions of these problems. The present article overviews all these problems and gathers those exclusive data acquired from studies of genome and chromosome instability that is relevant to identification and interpretations of this fairly common cause of somatic genomic variations and chromosomal mosaicism. Although the way to define pathogenic value of all the intercellular variations of the human genome is far from being completely understood, it is possible to propose recommendations on molecular cytogenetic diagnosis and management of somatic genome variations in clinical population.
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Affiliation(s)
- S G Vorsanova
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii
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Sukenik-Halevy R, Biron-Shental T, Sharony R, Fejgin MD, Amiel A. Telomeres in trisomy 21 amniocytes. Cytogenet Genome Res 2011; 135:12-8. [PMID: 21734364 DOI: 10.1159/000329714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2011] [Indexed: 12/23/2022] Open
Abstract
Individuals with trisomy 21 have an increased risk of developing leukemia and premature dementia. They also have a higher rate of telomere loss. The aim of the study was to compare telomere length and the hTERC gene copy number, which encodes the telomerase RNA subunit, in amniocytes of trisomy 21 conceptions and normal pregnancies. A quantitative fluorescence-in-situ protocol (Q-FISH) was used to compare telomere length in amniocytes cultured from 11 trisomy 21 conceptions and from 14 normal pregnancies. Quantification was conducted using novel computer software. Fluorescence in situ hybridization (FISH) was used to assess the percentage of cells with additional copies of hTERC. We found that the immunofluorescence intensity, which represents telomere length, was significantly lower in amniocytes from trisomy 21 conceptions compared to the control group. The trisomy 21 group had a higher number of cells with additional copies of hTERC. This observation could be one of the cytogenetic parameters that represent a state of genetic instability and might play a role in the pathomechanism of typical features of Down syndrome, such as dementia and malignancy.
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Affiliation(s)
- R Sukenik-Halevy
- Genetics Institute, Meir Medical Center, Kfar Saba, Israel. riki.sukenik @ gmail.com
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46
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Koide K, Slonim DK, Johnson KL, Tantravahi U, Cowan JM, Bianchi DW. Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18. Hum Genet 2011; 129:295-305. [PMID: 21152935 PMCID: PMC3206603 DOI: 10.1007/s00439-010-0923-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 11/17/2010] [Indexed: 11/30/2022]
Abstract
Trisomy 18 is a common human aneuploidy that is associated with significant perinatal mortality. Unlike the well-characterized "critical region" in trisomy 21 (21q22), there is no corresponding region on chromosome 18 associated with its pathogenesis. The high morbidity and mortality of affected individuals has limited extensive investigations. In order to better understand the molecular mechanisms underlying the congenital anomalies observed in this condition, we investigated the in utero gene expression profile of second trimester fetuses affected with trisomy 18. Total RNA was extracted from cell-free amniotic fluid supernatant from aneuploid fetuses and euploid controls matched for gestational age and hybridized to Affymetrix U133 Plus 2.0 arrays. Individual differentially expressed transcripts were obtained by two-tailed t tests. Over-represented functional pathways among these genes were identified with DAVID and Ingenuity(®) Pathways Analysis. Results show that three hundred and fifty-two probe sets representing 251 annotated genes were statistically significantly differentially expressed between trisomy 18 and controls. Only 7 genes (2.8% of the annotated total) were located on chromosome 18, including ROCK1, an up-regulated gene involved in valvuloseptal and endocardial cushion formation. Pathway analysis indicated disrupted function in ion transport, MHCII/T cell mediated immunity, DNA repair, G-protein mediated signaling, kinases, and glycosylation. Significant down-regulation of genes involved in adrenal development was identified, which may explain both the abnormal maternal serum estriols and the pre and postnatal growth restriction in trisomy 18. Comparison of this gene set to one previously generated for trisomy 21 fetuses revealed only six overlapping differentially regulated genes. This study contributes novel information regarding functional developmental gene expression differences in fetuses with trisomy 18.
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Affiliation(s)
- Keiko Koide
- Division of Genetics, Department of Pediatrics, Floating Hospital for Children at Tufts Medical Center, Boston, MA02111, USA
| | - Donna K. Slonim
- Department of Computer Science, Tufts University School of Engineering, Medford, MA02155, USA
| | - Kirby L. Johnson
- Division of Genetics, Department of Pediatrics, Floating Hospital for Children at Tufts Medical Center, Boston, MA02111, USA
| | - Umadevi Tantravahi
- Department of Pathology, Women and Infants’ Hospital, Providence, RI 02905, USA
| | - Janet M. Cowan
- Division of Genetics, Department of Pediatrics, Floating Hospital for Children at Tufts Medical Center, Boston, MA02111, USA
| | - Diana W. Bianchi
- Division of Genetics, Department of Pediatrics, Floating Hospital for Children at Tufts Medical Center, Boston, MA02111, USA
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47
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Wolf JB, Bryk J. General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq. BMC Genomics 2011; 12:91. [PMID: 21284834 PMCID: PMC3040151 DOI: 10.1186/1471-2164-12-91] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 02/01/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology. RESULTS We here exemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution. CONCLUSIONS This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system.
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Affiliation(s)
- Jochen Bw Wolf
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemannstr, 2, 24306 Plön, Germany.
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Lintas C, Sacco R, Persico AM. Genome-wide expression studies in autism spectrum disorder, Rett syndrome, and Down syndrome. Neurobiol Dis 2010; 45:57-68. [PMID: 21130877 DOI: 10.1016/j.nbd.2010.11.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 11/11/2010] [Accepted: 11/16/2010] [Indexed: 12/19/2022] Open
Abstract
Though different in their aetiology, autism spectrum disorder (ASD), Rett syndrome (RTT) and Down syndrome (DS) are three neurodevelopmental disorders sharing significant clinical and neuropathological overlaps. Genome-wide expression studies are reviewed and available datasets from post-mortem brains reanalyzed to identify genes and gene pathways dysregulated in all three disorders. Our results surprisingly converge upon immune, and not neurodevelopmental genes, as the most consistently shared abnormality in genome-wide expression patterns. A dysregulated immune response, accompanied by enhanced oxidative stress and abnormal mitochondrial metabolism seemingly represents the common molecular underpinning of these neurodevelopmental disorders. This conclusion may be important for the definition of pharmacological therapies able to ameliorate clinical symptoms across these disorders.
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Affiliation(s)
- Carla Lintas
- Laboratory of Molecular Psychiatry and Neurogenetics, University Campus Bio-Medico, Rome, Italy
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49
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Rearick D, Prakash A, McSweeny A, Shepard SS, Fedorova L, Fedorov A. Critical association of ncRNA with introns. Nucleic Acids Res 2010; 39:2357-66. [PMID: 21071396 PMCID: PMC3064772 DOI: 10.1093/nar/gkq1080] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
It has been widely acknowledged that non-coding RNAs are master-regulators of genomic functions. However, the significance of the presence of ncRNA within introns has not received proper attention. ncRNA within introns are commonly produced through the post-splicing process and are specific signals of gene transcription events, impacting many other genes and modulating their expression. This study, along with the following discussion, details the association of thousands of ncRNAs—snoRNA, miRNA, siRNA, piRNA and long ncRNA—within human introns. We propose that such an association between human introns and ncRNAs has a pronounced synergistic effect with important implications for fine-tuning gene expression patterns across the entire genome.
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Affiliation(s)
- David Rearick
- University of Toledo Health Science Campus, University of Toledo Health Science Campus, University of Toledo Health Science Campus, Toledo, OH 43614, USA
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50
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Abstract
BACKGROUND Research into cell-free fetal (cff) nucleic acids has primarily focused on maternal plasma; however, cff DNA and RNA are also detectable in other body fluids such as amniotic fluid (AF). In AF, cff DNA is present in much greater concentrations than in maternal plasma and represents a pure fetal sample uncontaminated by maternal- and trophoblast-derived nucleic acids. The aim of this review was to summarize the current knowledge on cff nucleic acids in AF and to outline future research directions. METHODS MEDLINE and PREMEDLINE were searched up to August 2010 for original investigations of cell-free RNA or DNA in AF. Sixteen studies were included in the review. RESULTS AF cff DNA represents a physiologically separate pool from cff DNA in maternal plasma. The placenta is not a major source of nucleic acids in AF. It is feasible to isolate cff nucleic acids from small volumes of discarded AF supernatant in sufficient quality and quantity to perform microarray studies and downstream applications such as pathway analysis. This 'discovery-driven approach' has resulted in new information on the pathogenesis of Down syndrome and polyhydramnios. There is otherwise a paucity of information relating to the basic biology and clinical applications of cff nucleic acids in AF. CONCLUSIONS AF supernatant is a valuable and widely available but under-utilized biological resource. Further studies of cff nucleic acids in AF may lead to new insights into human fetal development and ultimately new approaches to antenatal treatment of human disease.
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Affiliation(s)
- L Hui
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA 02111, USA.
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