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Series GSE9707 Query DataSets for GSE9707
Status Public on Dec 31, 2018
Title Affymetrix microarray analysis of the effects of isonicotinamide on HEK293 cells
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Sirtuin deacetylases and forkhead box class O (FOXO) transcription factors are central regulators of cell survival, cell cycle and cellular resistance to stress in response to signals from hormones, growth factors and oxidative stress. FOXO activity is modulated by the sirtuins, which function in a NAD+-dependent manner. Sirtuin activity, on the other hand is subject to inhibition by a natural compound nicotinamide (NAM). This study aims to investigate the effects of NAM on the
sirtuin pathway and cellular homeostasis. It was hypothesized that NAM inhibits the sirtuin deacetylase activity, which then shifts FOXO-dependent responses away from stress resistance and towards apoptosis. Expression analysis using Affymetrix microarray was employed to determine differential gene expression in HEK293 cells in response to NAM treatment. Data analyses were performed using multiple algorithms, computational methods and interaction analyses. Significant changes in gene expression were detected with the generation of an expansive list of genes and interaction amongst gene groups were identified from the NAM treatment at different concentration. Substantial changes in expression profiles were detected for genes involved in a number of unique cellular pathways and functions, including cell cycle arrest, cellular proliferation and differentiation, metabolism, apoptotic signaling, inflammatory regulation and various disease conditions such as
cancer. In addition, this study observed that sirtuin activities exhibit complex cell- and contextdependent behavior in modulating FOXO signaling. Contrasting roles of FOXOs and sirtuins appear to have opposite effects on cellular homeostasis. In addition, the coexistence of reciprocal regulations in this cell system suggested several levels of feedback control and illustrated the complexity of an existing fine-tuned regulatory network system between these two proteins. Future
work aims to characterize putative regulators and effectors of sirtuin- and FOXO-related pathways using molecular approaches such and RNA interference knockdown of individual FOXO-isoforms.
Inter-connectivity of the pathways will provide invaluable insight into current understanding of cell degeneration diseases such as diabetes, cancers and neurological disorders.
Keywords: Serial concentration experiment
 
Overall design Expression variation at the transcriptional level was studied with RNA samples(Batch 1) obtained from cells treated with isonicotinamide (INAM) at five different concentrations i.e., 0, 5, and 10 mM. The cytotoxicity of these concentrations was previously determined by Mark Pinese (Honours thesis 2005). This first experiment was to determine which concentration caused the most gene expression changes. Once this was determined, 2 replicate RNA samples (Batch 2 and 3) were subsequently assayed. In this case, 3 replicates of HEK293 cells treated at 0, 5 and 10 mM NAM were used.
 
Contributor(s) Lo Z, Lin R, Speirs HJ
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 27, 2007
Last update date Mar 25, 2019
Contact name Ruby CY Lin
E-mail(s) rubyl@unsw.edu.au, ruby.lin@sydney.edu.au
Organization name The Westmead Institute for Medical Research
Street address 176 Hawkesbury Road, Westmead
City Sydney
State/province NSW
ZIP/Postal code 2145
Country Australia
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (9)
GSM245300 HEK293 5 mM INAM treated - Batch 1
GSM245307 HEK293 5 mM INAM treated - Batch 2
GSM245311 HEK293 5 mM INAM treated - Batch 3
Relations
BioProject PRJNA103611

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Supplementary file Size Download File type/resource
GSE9707_RAW.tar 39.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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