Profiling gene expression and network analysis in human U937
cells in response to Solenopsin, a constituent of fire ant venom
Priya
a,
Das *,
Pawan K
b,
c
Dhar
Achuthsankar S.
a
Nair ,
Oommen V.
a,
d
Oommen
a
Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, 695581, Kerala, India
b Centre for Systems & Synthetic Biology, University of Kerala, Thiruvananthapuram, 695581, Kerala, India
c Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201314, Uttar Pradesh, India
dKerala State Biodiversity Board, Thiruvananthapuram, 695011, Kerala, India
BACKGROUND
The toxic effects of insect venom ranges from slight allergy to anaphylactic reactions and may even
lead to death in humans. Despite its toxic nature, studies have shown that venom components of
insects are of great therapeutic value (Ratclifee et al., 2011). Solenopsin, the alkaloidal content of the
fire ant (Solenopsis invicta) venom inhibits PI3K signaling pathway and nitric oxide synthases (Arbiser
et al., 2007, Yi et al., 2003). This implies the toxic effects of solenopsin is exhibited by altering cell
signaling pathways and thus resulting in changes at gene expression level. A high-throughput
analysis at this conjecture will help to analyze the changes at genes expression levels. With this aim,
this study analyzes gene regulation by solenopsin in a cDNA microarray data
OBJECTIVES
(a)
• Statistical analysis of gene expression data generated by an cDNA microarray[solenopsin induced
gene expression alteration in human U 937 cell line].
•Functional annotation of differentially expressed genes (DEGs).
•Network analysis and finding hub nodes in this protein-protein interaction network.
MATERIALS & METHODS
BACKGROUND EXPERIMENT
Publicly available GEO
data is retrieved. [Gene
Expression Omnibus
(GEO) accession id:
GSE13102]
Human U937 cell lines were
treated with Solenopsin B (13
ul-test)
and
cyclodextrin
(reference).
Triplicate
cultures were prepared at
two separate time points, 1
and
6
hours.
Intensity
measures were normalized
and the processed data was
used for further analysis.
Statistical analysis done
using Microsoft excel
2007 to infer the fold
change of 19200 probes.
(p- value of t- statistic
<0.05)
Genes satisfying the
statistical criteria; i.e.
genes with fold change
> 1.41 as upregulated
and < 1.41 as
downregulated were
screened
Pathway enrichment analysis and
hub nodes were also analyzed for in
the differentially expressed gene set.
RESULTS
• Out of 19,200 probes, a total of 433 genes were differentially regulated, of which 240 and 193
were upregulated and downregulated respectively
• 115 of upregulated genes were associated with GO term: phosphoproteins; most of which are
involved in metabolism
• Pathway analysis of downregulated genes revealed crosstalks between AKT/PIP3K, TGF-β and
Wnt signaling pathways. TGF-β signaling is downregulated.
•Significant genes which are upregulated are DCN, PAK4, BCL2, RHOA, ACTN1, VTN, RAD50,
RAD52, CAMK2B, IL6ST and genes downregulated are SMAD4, APC2, CHP, CUL1, FGFR4,
PIK3R1, PDPK1, ACVR2A and Cdc25B.
www.PosterPresentations.com
(d)
(b)
Upregulated and downregulated
genes
were
subjected
to
functional annotation tools :
DAVID & WebGestalt.
RESEARCH POSTER PRESENTATION DESIGN © 2012
(c)
Fig. (a) Volcano plot showing upregulated and downregulated genes; (b) Protein- protein
interaction network of differentially expressed genes; (c) Heatmap of some significant
upregulated and downregulated genes; (d) Gene annotation of genes (DAVID results)
CONCLUSIONS
Integrating the results of the present study with previous related studies allowed a more
comprehensive interpretation of the molecular mechanism underlying the gene expression
regulations induced by solenopsin in human U937 cell lines. TGF-β signaling as lies central to many
cellular pathways and goes awry in many disease conditions , the results may be routed for further
investigations.
REFERENCES
1) Ratcliffe, N. A., Mello, C. B., Garcia, E. S., Butt, T. M., & Azambuja, P. 2011. Insect natural products and
processes: new treatments for human disease. Insect Biochem Mol Biol., 41(10), 747-769.
2) Arbiser, J. L., Kau, T., Konar, M., Narra, K., Ramchandran, R., Summers, S. A et al., 2007. Solenopsin, the
alkaloidal component of the fire ant (Solenopsis invicta), is a naturally occurring inhibitor of
phosphatidylinositol-3-kinase signaling and angiogenesis. Blood, 109(2), 560-565.
3) Yi, G. B., Mc Clendon, D., Desaiah, D., Goddard, J., Lister, A., Moffitt, J., Vander Meer, R. K.,de Shazo, R.,
Lee, K.S., & Rockhold, R. W. 2003. Fire ant venom alkaloid, isosolenopsin A, a potent and selective inhibitor
of neuronal nitric oxide synthase. Int J Toxicol., 22(2), 81-86.
ACKNOWLEDGEMENTS
Financial support from DST-INSPIRE is greatly acknowledged. I sincerely thank my mentors at the
department for their active guidance. Special mention to Dr. P. R. Sudhakran, Senior Scientist,
Department of Computational Biology & Bioinformatics, University of Kerala for his keen advices.