E-GEOD-44590 - VGLL4 is a novel regulator of survival in human embryonic stem cells

Status
Released on 1 December 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (8)
Array (1)
Protocols (7)
Description
Human embryonic stem cells (hESCs) are maintained in a self-renewing state by an interconnected network of mechanisms that sustain pluripotency, promote proliferation and survival, and prevent differentiation. We sought to find novel genes that could contribute to one or more of these processes by using a gain-of-function screen of a large collection of human open reading frames. We identified Vestigial-like 4 (VGLL4), a co-transcriptional regulator with no previously described function in hESCs, as a positive regulator of survival in hESCs. Specifically, VGLL4 overexpression in hESCs significantly decreases cell death in response to dissociation stress. Additionally, VGLL4 overexpression enhances hESC colony formation from single cells. These effects may be attributable, in part, to a decreased activity of initiator and effector caspases observed in the context of VGLL4 overexpression. Additionally, we show an interaction between VGLL4 and the Rho/Rock pathway, previously implicated in hESC survival. This study introduces a novel gain-of-function approach for studying hESC maintenance and presents VGLL4 as a previously undescribed regulator of this process. The goal of this experiment was to compare the global transcriptional profile of hESCs overexpressing VGLL4 to wild-type hESCs in order to understand the transcriptional differences behind the phenotype exhibited by VGLL4-overexpressing cells. This list was then used for subsequent analysis where genes were filtered individually, but also per sample, such that only genes with a pvalue of detection of less than 0.05 on at least 5 of the samples were kept. Next, the SAM statistical suite was used to generate a list of genes that are expressed at a significantly higher level in the 4 Vgll4 samples compared to the 4 WT samples using an FDR of 7% for discovery purposes. RNA was purified from total cultures of HUES6 human embryonic stem cells (wildtype vs cells overexpressing VGLL4 from a lentiviral vector). Samples were collected in quadruplicates (biological replicates) using a Qiagen RNeasy kit and 200 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit. Human ES cells were grown in the presence of mouse embryonic fibroblasts.
Experiment type
transcription profiling by array 
Contacts
Adriana Tajonar, Dena E Cohen, Douglas A Melton, Guang Hu, Jose Rivera-Feliciano, Julie B Sneddon, Rene Maehr, Stephen J Elledge
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-44590.idf.txt
Sample and data relationshipE-GEOD-44590.sdrf.txt
Processed data (1)E-GEOD-44590.processed.1.zip
Array designA-GEOD-10558.adf.txt
Links