Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNAseq from disomic and trisomic fibroblasts and lymphoblastoids

ABSTRACT: RNA was sequenced from individuals Disomic and Trisomic for chromosome 21 to identify consistent changes in gene expression across individuals Cells were cultured at subconfluency and RNA harvested for sequencing

ORGANISM(S): Homo sapiens

SUBMITTER: Ahwan Pandey

PROVIDER: E-GEOD-79842 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Trisomy 21 consistently activates the interferon response.

Sullivan Kelly D KD Lewis Hannah C HC Hill Amanda A AA Pandey Ahwan A Jackson Leisa P LP Cabral Joseph M JM Smith Keith P KP Liggett L Alexander LA Gomez Eliana B EB Galbraith Matthew D MD DeGregori James J Espinosa Joaquín M JM

eLife 20160729

Although it is clear that trisomy 21 causes Down syndrome, the molecular events acting downstream of the trisomy remain ill defined. Using complementary genomics analyses, we identified the interferon pathway as the major signaling cascade consistently activated by trisomy 21 in human cells. Transcriptome analysis revealed that trisomy 21 activates the interferon transcriptional response in fibroblast and lymphoblastoid cell lines, as well as circulating monocytes and T cells. Trisomy 21 cells s ...[more]

PMID: 27472900

Similar Datasets

Project description:Down syndrome, which results from a trisomic imbalance for chromosome 21, has been associated with 80+ phenotypic traits. However, the cellular changes that arise in somatic cells due to this aneuploid condition are not fully understood. The primary aim of this study was to determine if germline trisomy 21 is associated with an increase in spontaneous somatic cell chromosomal instability frequencies (SCINF). To achieve this aim, we quantified SCINF in people with mosaic Down syndrome using a cytokinesis-blocked micronucleus assay. By comparing values in their isogenic trisomic/disomic cells, we obtained a measure of differences in SCINF that are directly attributable to a trisomy 21 imbalance, since differential effects attributable to "background" genetic factors and environmental exposures could be eliminated. A cross-sectional assessment of 69 people with mosaic Down syndrome (ages 1 to 44; mean age of 12.84 years) showed a significantly higher frequency of micronuclei in their trisomic (0.37 ± 0.35 [mean ± standard deviation]) compared to disomic cells (0.18 ± 0.11)(P <0.0001). The daughter binucleates also showed significantly higher levels of abnormal patterns in the trisomic (1.68 ± 1.21) compared to disomic (0.35 ± 0.45) cells (P <0.0001). Moreover, a significant Age x Cell Type interaction was noted (P = 0.0113), indicating the relationship between age and SCINF differed between the trisomic and disomic cells. Similarly, a longitudinal assessment (mean time interval of 3.9 years; range of 2 to 6 years) of 18 participants showed a mean 1.63-fold increase in SCINF within individuals over time for their trisomic cells (P = 0.0186), compared to a 1.13-fold change in their disomic cells (P = 0.0464). In summary, these results showed a trisomy 21-associated, age-related increase in SCINF. They also underscore the strength of the isogenic mosaic Down syndrome model system for "unmasking" cellular changes arising from a trisomy 21 imbalance.

Dataset Information

RNAseq from disomic and trisomic fibroblasts and lymphoblastoids

Publications

Trisomy 21 consistently activates the interferon response.

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