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Trisomy 21 fibroblasts (pevsn-affy-human-512801)

ABSTRACT: Down syndrome (DS) is caused by an extra copy of chromosome 21. We are characterizing protein changes in human skin fibroblasts. We propose to study corresponding changes at the DNA level (by SNP analysis) and the RNA level (using Affymetrix chips). These studies will detail transcriptional and translational regulation in trisomy. The Specific Aim is to obtain data on RNA transcript levels using Affymetrix expression arrays in a group of trisomy 21 and euploid fibroblast cell lines. In parallel, we will acquire SNP data to determine both genotype (call) and copy number changes for trisomic samples. The results will allow us to identify the patterns of change in a trisomic chromosome (relative to control). [1] We hypothesize that in genomic DNA samples derived from trisomy 21 (TS21) fibroblasts there will be an increased copy number on chr21 with additional microdeletions and microdeletions. [2] We hypothesize that the RNA transcripts derived from chr21 will be elevated relative to euploid controls. [3] We hypothesize that altered RNA transcript levels will be significantly correlated with altered protein levels from these same fibroblast cell lines. The experimental design is as follows. All samples are from deidentified individuals and were obtained from the Brain and Tissue Bank for Developmental Disorders at the University of Maryland, with Johns Hopkins IRB approval.[1] There are five trisomy 21 samples and five euploid samples (total n=10). Fibroblasts were grown in culture to comparable confluency and passage number. Cells were harvested. Total RNA was isolated with a Qiagen kit. The quantity and purity of the RNA was confirmed by spectrophotometry and by electrophoresing an aliquot on a 1% agarose gel. Approximately 10 micrograms of total RNA will be sent to TGen on dry ice for analysis on Affymetrix U133 PlusTwo arrays. Data analysis will be with Affymetrix and Partek software. Keywords: other

ORGANISM(S): Homo sapiens

PROVIDER: GSE9762 | GEO | 2007/12/04

SECONDARY ACCESSION(S): PRJNA103691

REPOSITORIES: GEO

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Project description:Background: Among full autosomal trisomies, only trisomies of chromosome 21 (Down syndrome, DS), 18 (Edward syndrome, ES) and 13 (Patau syndrome, PS) are compatible with postnatal survival. But the mechanisms, how a supernumerary chromosome disrupts the normal development and causes specific phenotypes, are still not fully explained. As an alternative to gene dosage effects due to the trisomic chromosome, a genome-wide transcriptional dysregulation has been postulated. The aim of this study was to define the transcriptional changes in trisomy 13, 18, and 21 during early fetal development in order to define whether (1) overexpression of genes of the trisomic chromosome contributes solely to the phenotype, if (2) all genes of the trisomic chromosome are upregulated similarly and whether the ratio of gene expression is in agreement with the gene dosis, (3) whether the different trisomies behave similarly in the characteristics of transcriptional dysregulation, and (4) whether transcriptional pattern can be potentially used in prenatal diagnosis. Methods: Using oligonucleotide microarrays (Affymetrix, U133 Plus 2.0), we analyzed whole genome expression profiles representing 54.000 probe sets in cultured amniocytes (AC) and chorion villus cells (CV) from pregnancies with a normal karyotype and with trisomies of human chromosomes 21, 18 and 13. Findings: We observed a low to moderate up-regulation for a subset of genes of the trisomic chromosomes. Transcriptional level of approximately 12-13 % of the supernumerary chromosome appeared similar to the respective chromosome pair in normal karyotypes. Expression values as well as the expression patterns of genes from the trisomic chromosome can distinguish the respective trisomic samples from euploid controls. A subset of chromosome 21-genes including the DSCR1-gene involved in fetal heart development was consistently up-regulated in different tissues (AC, CV) of trisomy 21 fetuses whereas only minor changes were found for genes of all other chromosomes. In contrast, in trisomy 13 and trisomy 18 vigorous downstream transcriptional changes were found. Interpretation: Global transcriptome analysis for autosomal trisomies 13, 18, and 21 supported a combination of the two major hypotheses. As several transcriptional pathways are altered, complex regulatory mechanisms are involved in the pathogenesis of autosomal trisomies. A genome-wide transcriptional dysregulation was predominantly observed in trisomies 13 and 18, whereas a more to chromosome 21 restricted expression alteration was found in trisomy 21. Experiment Overall Design: The study included the following samples: Three samples with normal chromosomes in Amniocytes (AC) and chorion villus cells (CV) each, three samples with trisomy 13 in AC, three samples with trisomy 18 in CV, and three samples with trisomy 21 in AC and CV each.

Project description:Background: Among full autosomal trisomies, only trisomies of chromosome 21 (Down syndrome, DS), 18 (Edward syndrome, ES) and 13 (Patau syndrome, PS) are compatible with postnatal survival. But the mechanisms, how a supernumerary chromosome disrupts the normal development and causes specific phenotypes, are still not fully explained. As an alternative to gene dosage effects due to the trisomic chromosome, a genome-wide transcriptional dysregulation has been postulated. The aim of this study was to define the transcriptional changes in trisomy 13, 18, and 21 during early fetal development in order to define whether (1) overexpression of genes of the trisomic chromosome contributes solely to the phenotype, if (2) all genes of the trisomic chromosome are upregulated similarly and whether the ratio of gene expression is in agreement with the gene dosis, (3) whether the different trisomies behave similarly in the characteristics of transcriptional dysregulation, and (4) whether transcriptional pattern can be potentially used in prenatal diagnosis. Methods: Using oligonucleotide microarrays (Affymetrix, U133 Plus 2.0), we analyzed whole genome expression profiles representing 54.000 probe sets in cultured amniocytes (AC) and chorion villus cells (CV) from pregnancies with a normal karyotype and with trisomies of human chromosomes 21, 18 and 13. Findings: We observed a low to moderate up-regulation for a subset of genes of the trisomic chromosomes. Transcriptional level of approximately 12-13 % of the supernumerary chromosome appeared similar to the respective chromosome pair in normal karyotypes. Expression values as well as the expression patterns of genes from the trisomic chromosome can distinguish the respective trisomic samples from euploid controls. A subset of chromosome 21-genes including the DSCR1-gene involved in fetal heart development was consistently up-regulated in different tissues (AC, CV) of trisomy 21 fetuses whereas only minor changes were found for genes of all other chromosomes. In contrast, in trisomy 13 and trisomy 18 vigorous downstream transcriptional changes were found. Interpretation: Global transcriptome analysis for autosomal trisomies 13, 18, and 21 supported a combination of the two major hypotheses. As several transcriptional pathways are altered, complex regulatory mechanisms are involved in the pathogenesis of autosomal trisomies. A genome-wide transcriptional dysregulation was predominantly observed in trisomies 13 and 18, whereas a more to chromosome 21 restricted expression alteration was found in trisomy 21. Keywords: Trisomy, Down syndrome, Patau syndrome, Edward syndrome, microarray, gene expression, amniocytes, chorion villus cells, gene dosage effect, DSCR1

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Trisomy 21 fibroblasts (pevsn-affy-human-512801)

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