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| Status |
Public on Jun 13, 2014 |
| Title |
Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Background: Turner syndrome, a common sex chromosome aneuploidy, has characteristics and malformations associated with the phenotype. Fetal amniotic fluid is a complex biological material that could contribute to the understanding Turner syndrome pathogenesis. Global gene expression analysis of Turner syndrome fetal amniotic fluid supernatant was utilized to identify organ systems and specific genes that may play a role in the pathophysiologic changes that are seen in individuals with Turner syndrome.
Methods: Global gene expression analysis was performed utilizing cell-free RNA from five midtrimester fetuses with Turner syndrome matched with five euploid female fetuses. Total RNA was extracted, amplified, hybridized onto GeneChip® Human Genome U133 Plus 2.0 arrays. Network and pathway analysis of differentially expressed genes were completed. Chromosomal distribution of gene expression differences, differential expression by pathway and organ system (a “Turner syndrome core transcriptome”), and candidate genes that could play a pathological role were identified.
Results: There were 470 differentially expressed genes identified in the Turner syndrome transcriptome. The differentially expressed genes were distributed randomly across different chromosomes. Among genes on the X chromosome, XIST was down-regulated, and SHOX not differentially expressed. The most highly represented organ systems were hematologic/immune and neurologic. Increased representation of differentially expressed genes in the hematologic/immune system distinguishes the Turner syndrome transcriptome from the euploid, trisomy 18 and trisomy 21 transcriptomes previously studied in our laboratory. Manual curation of the differentially expressed gene list identified genes including NFATC3, IGFBP5, and LDLR that warrant further study.
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| Overall design |
2nd trimester amniotic fluid mRNA expression was compared between 5 Turners and 5 euploid fetuses.
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| Contributor(s) |
Massingham LJ, Johnson KL, Scholl T, Slonim DK, Wick HC, Bianchi DW |
| Citation(s) |
24850140 |
| Submission date |
Jun 12, 2014 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Heather C Wick |
| E-mail(s) |
heather.c.wick@gmail.com
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| Organization name |
Tufts University
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| Department |
Department of Computer Science
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| Street address |
161 College Ave
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| City |
Medford |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA252607 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE58435_RAW.tar |
38.3 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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