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| Status |
Public on May 21, 2019 |
| Title |
NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module of a pluripotent network |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background: Atrial fibrillation is a cardiac disease driven by numerous idiopathic etiologies. NUP155 is a nuclear pore complex protein that has been identified as a clinical driver of atrial fibrillation, yet the precise mechanism is unknown. The present study employs a systems biology algorithm to identify effects of NUP155 disruption on cardiogenicity in a model of stem cell-derived differentiation.
Methods: Embryonic stem (ES) cell lines (n=5) with truncated NUP155 (Nup155+/-) were cultured in parallel with wild type (WT) ES cells (n=5), and then harvested for RNAseq. Samples were run on an Illumina HiSeq 2000. Reads were analyzed using Strand NGS, Cytoscape, DAVID and Ingenuity Pathways Analysis to deconvolute the NUP155-disrupted transcriptome. Network topological analysis identified key features that controlled framework architecture and functional enrichment.
Results: In NUP155 truncated ES cells, significant expression changes were detected in 326 genes compared to WT. These genes segregated into clusters that enriched for specific gene ontologies. Major network drivers included TP53, a regulator of genome integrity. Deconvolution of the collective framework into discrete sub-networks identified a module with the highest score that enriched for Cardiovascular System Development, and revealed NTRK1/TRKA and SRSF2/SC35 as critical hubs within this cardiogenic module.
Conclusions: The strategy of pluripotent transcriptome deconvolution used here identified a novel association of NUP155 with potential drivers of arrhythmogenic AF. Here, NUP155 regulates cardioplasticity of a sub-network embedded within a larger framework of genome integrity, and exemplifies how transcriptome cardiogenicity in an embryonic stem cell genome is recalibrated by nucleoporin dysfunction.
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| Overall design |
Embryonic stem (ES) cell lines (n=5) with truncated NUP155 were cultured in parallel with wild type (WT) ES cells (n=5), harvested for RNAseq and run on an Illumina HiSeq 2000.
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| Contributor(s) |
Preston CC, Faustino RS |
| Citation(s) |
29848314 |
| |
| Submission date |
Mar 08, 2018 |
| Last update date |
May 21, 2019 |
| Contact name |
Randolph S Faustino |
| E-mail(s) |
randolph.faustino@sanfordhealth.org
|
| Phone |
605-312-6443
|
| Organization name |
Sanford Research
|
| Department |
Genetics and Genomics
|
| Lab |
Faustino laboratory
|
| Street address |
2301 East 60th Street North
|
| City |
Sioux Falls |
| State/province |
SD |
| ZIP/Postal code |
57104 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA437489 |
| SRA |
SRP134207 |
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