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E-GEOD-70102 - Placental Transcriptomes in the Common Aneuploidies Reveal Critical Regions on the Trisomic Chromosomes and Genome-Wide Effects

Status
Released on 23 June 2015, last updated on 27 June 2015
Organism
Homo sapiens
Samples (20)
Array (1)
Protocols (5)
Description
We profiled gene expression at the maternal-fetal interface during the second trimester of pregnancy (13-22 wks) in trisomy 13 (T13; Patau syndrome, n = 4), trisomy 18 (T18; Edwards syndrome, n = 4), trisomy 21 (T21; Down syndrome, n = 8), and in euploid pregnancies (n = 4). FISH confirmed the ploidy of the samples. Global transcriptional profiling identified differentially expressed transcripts (≥ 2-fold) in T21 (n = 160), T18 (n = 80), and T13 (n = 125). The majority were upregulated. Unexpectedly, most of the misexpressed genes were not located on the relevant trisomic chromosome, suggesting genome-wide dysregulation. A much smaller proportion of the differentially expressed transcripts were encoded on the aneuploid chromosome, also implicating gene dosage (1-5). In T21, <10% of the genes were transcribed from that chromosome, all but one from the Down syndrome critical region (21q21-22), which is postulated to play an important role in the clinical phenotype. For T13 and T18, a higher proportion of the overexpressed genes were located on the trisomic chromosome. In T13, 15% of the upregulated genes were on the affected chromosome; 15 resided on the long arm, 13q11-14. In T18, the percentage increased to 24, 15 of which were also located on the long arm (18q11-22). Our data suggested that the placental (and possibly fetal) phenotypes that are associated with T13, T18 and T21 are driven by the combined effects of genome-wide phenomena and increased gene dosage from critical regions of the triploid chromosome. We profiled gene expression at the maternal-fetal interface during the second trimester of pregnancy (13-22 wks) in trisomy 13 (T13; Patau syndrome, n = 4), trisomy 18 (T18; Edwards syndrome, n = 4), trisomy 21 (T21; Down syndrome, n = 8), and in euploid pregnancies (n = 4). FISH confirmed the ploidy of the samples.
Experiment type
transcription profiling by array 
Contacts
Susan Fisher <geo@ncbi.nlm.nih.gov>, Hannah Tilden, Jason Farrell, Katherine Bianco, Matthew Gormley, Michael McMaster, Oliver Oliverio, Susan J FIsher, Yan Zhou
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-70102.idf.txt
Sample and data relationshipE-GEOD-70102.sdrf.txt
Raw data (1)E-GEOD-70102.raw.1.zip
Processed data (1)E-GEOD-70102.processed.1.zip
Additional data (1)E-GEOD-70102.additional.1.zip
Array designA-AFFY-44.adf.txt
Links