NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module

BMC Systems Biology
Claudia C PrestonRandolph S Faustino

Abstract

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. Embryonic stem (ES) cell lines (n = 5) with truncated 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. 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. 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 crit...Continue Reading

References

Oct 13, 1950·Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character·H G CALLAN, S G TOMLIN
Feb 14, 2004·The EMBO Journal·Jian-Hua DingXiang-Dong Fu
Oct 6, 2006·The New England Journal of Medicine·W Bruce Fye
Jan 19, 2007·Nature Clinical Practice. Cardiovascular Medicine·Carmen Perez-TerzicAndre Terzic
Nov 30, 2007·Nature·Frank AlberMichael P Rout
Jan 11, 2008·Genome Biology·Randolph S FaustinoAndre Terzic
Jun 7, 2008·Circulation Research·Elisabetta Cerbai, Laura Sartiani
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Jun 23, 2009·EMBO Reports·Maya Capelson, Martin W Hetzer
Oct 13, 2009·Cardiovascular Research·Raquel CortésManuel Portolés
Feb 9, 2010·Journal of Molecular and Cellular Cardiology·Erol SaygiliObaida R Rana
Mar 2, 2010·American Journal of Physiology. Heart and Circulatory Physiology·Christina U LorentzBeth A Habecker
Mar 23, 2010·Developmental Biology·Nicolas Di-PoïDenis Duboule
Apr 3, 2010·Circulation Research·Marco MeloniCostanza Emanueli
Apr 6, 2011·The Journal of Cell Biology·Izhak KehatJeffery D Molkentin
Oct 30, 2012·Clinics in Geriatric Medicine·Mahek MirzaArshad Jahangir
Mar 5, 2013·Cell·David W Van de VosseRichard W Wozniak
Apr 2, 2013·Biochemical and Biophysical Research Communications·Tatsuyoshi FunasakaRichard W Wong
Jul 11, 2013·European Journal of Human Genetics : EJHG·Morten S OlesenJesper H Svendsen
Aug 31, 2013·PLoS Genetics·Slavé PetrovskiDavid B Goldstein
Sep 26, 2013·Proceedings of the National Academy of Sciences of the United States of America·Hyuk-Soo SeoGünter Blobel
Dec 24, 2013·Journal of Cell Science·Nathalie EisenhardtWolfram Antonin
Apr 26, 2014·Circulation Research·Nathan R Tucker, Patrick T Ellinor
Sep 13, 2014·Cardiology in the Young·Won Kyoung JhangHan-Wook Yoo
Nov 27, 2014·Current Opinion in Cardiology·Alban-Elouen BaruteauHugues Abriel
Mar 6, 2015·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Dong SuoChristopher D Deppmann
Mar 18, 2015·The Journal of Cell Biology·J Sebastian Gomez-Cavazos, Martin W Hetzer
Jul 17, 2015·BMC Systems Biology·Randolph S FaustinoCarmen Perez-Terzic
Aug 12, 2015·Journal of Molecular Cell Biology·Liang XuYi-Han Chen
Sep 6, 2015·Genes & Development·Manuel Breuer, Hiroyuki Ohkura
Oct 29, 2015·BioMed Research International·Limin WangZhonglin Liu
Nov 29, 2015·International Review of Cell and Molecular Biology·Achim DickmannsBirthe Fahrenkrog
Jan 23, 2016·Journal of Molecular Biology·Alexander von Appen, Martin Beck
Aug 19, 2016·Nature·Monkol LekUNKNOWN Exome Aggregation Consortium
Nov 26, 2016·Scientific Reports·Teruyoshi Kobayashi, Naoki Masuda
Dec 17, 2016·Epigenetics & Chromatin·Ajay S LabadeKundan Sengupta

❮ Previous
Next ❯

Citations

Nov 6, 2018·Canadian Journal of Physiology and Pharmacology·Claudia C PrestonRandolph S Faustino
Sep 27, 2019·PLoS Computational Biology·G Elisabeta MaraiJohn H Morris
Mar 3, 2020·Frontiers in Cardiovascular Medicine·Riley J LeonardRandolph S Faustino
Sep 1, 2018·Epigenomes·Claudia C Preston, Randolph S Faustino
Dec 17, 2020·Development·Valeria GuglielmiMaximiliano A D'Angelo

❮ Previous
Next ❯

Datasets Mentioned

BETA
GDS3729
GSE111596

Methods Mentioned

BETA
histone acetylation
RNAseq
PCR
acetylation

Software Mentioned

Strand NGS
Cytoscape
Ingenuity Pathways Analysis
RefSeq
IPA
DAVID
DESeq
Genespring GX
ZEN
Excel

Related Concepts

Related Feeds

Atrial Filbrillation

Atrial fibrillation refers to the abnormal heart rhythm characterized by rapid and irregular beating of the atria. Here is the latest research.

Adult Stem Cells

Adult stem cells reside in unique niches that provide vital cues for their survival, self-renewal, and differentiation. They hold great promise for use in tissue repair and regeneration as a novel therapeutic strategies. Here is the latest research.

Atrial Fibrillation

Atrial fibrillation is a common arrhythmia that is associated with substantial morbidity and mortality, particularly due to stroke and thromboembolism. Here is the latest research.

Arrhythmia

Arrhythmias are abnormalities in heart rhythms, which can be either too fast or too slow. They can result from abnormalities of the initiation of an impulse or impulse conduction or a combination of both. Here is the latest research on arrhythmias.

Cardiogenic Shock

Cardiogenic shock is a devastating consequence of acute myocardial infarction and is associated with an extremely high mortality. Here is the latest research.