overexpression of SOX11 and its possible ceRNA network in patients with small cell lung cancer tissue
overexpression of SOX11 and its possible ceRNA network in patients with small cell lung cancer tissue
Negar Safavi,1,*Mohammad Rezaei,2Mansoureh Azadeh,3
1. Zist Fanavari Novin Biotechnology Institute, Isfahan, Iran 3. Zist Fanavari Novin Biotechnology Institute, Isfahan, Iran
Introduction: Mortality from small cell lung cancer worldwide has made this
disease a significant health care problem.[1] The microarray technique is used for
environmental and/or clinical studies. Although microarray is an accurate and
sharp diagnostic tool, the expertized bioinformaticians were able to minimize the
outcome biases and maximize the flexibility and accuracy of the technique.[2]
Methods: First of all, Microarray expression data of 18 pairs
of small cell lung cancer (sclc) and tumor and adjacent lung tissues(GSE149507)
was collected from NCBI Gene Expression Omnibus (GEO)[3] and then GEO2R
analysis was used to find differentially expressed genes in small cell lung cancer
tumor and adjacent normal lung tissues.GEPIA2[4] was used to confirm the
accuracy of gene expression and the correlation between the target gene and
lung cancer. In addition, from the ENCORI[5]database obtained survival analysis
which handles time-to-event outcomes.[6] Gene ontology and biological pathway
plus molecular function were obtained by Enrichr[7] and KEGG[8] .furthermore,
String[9] database was searched to find significant interactions between proteins.
additionally, miRwalk[10] was operated to find miRNA-mRNA interaction based
on the 3'UTR region. then, target miRNA was investigated in lncbased.3 [11] to
find miRNA-lncRNA Significant interaction and create a predictive ceRNA network.
Results: Based on the GEO analysis, a gene named SOX11 was found to be an
upregulated gene (logFC= 3.92831595, adj. P value= 3.17E-06) In tissue lungs with
small cells of lung cancer.then,GEPIA2 provided Boxplot which was match with
first obtained datas.Survival analysis from ENCORI confirms the data obtained
from GEO again(log-Rank p=0.0055 in 235 low number and 234 high
number,Hazar ratio:0.76). The transcription factor SOX11 (SRY-related highmobility-group (HMG) box 11), a member of the SOXC group, is expressed during
embryogenesis but largely absent in most adult differentiated tissues. SOX11
regulates progenitor and stem cell behavior and often acts together with the
other two SOXC group members, SOX4 and SOX12, in regulating developmental
processes, including neurogenesis and skeletogenesis. [12] searches on KEGG
revealed SOX11 is participating in signaling pathways regulating pluripotency of
stem cells which is related to lung cancer.in addition,Investigated of possible
miRNA-mRNA interactions showed hsa-miR-6727-3p as a significant interactor to
SOX11 mRNA. Lncbase v3 searches indicated that selected miRNA had significant
interaction with TCL6 and HNF1A-AS1.
Conclusion: By way of conclusion ,SOX11 is overexpressed in small cells lung
cancer and constructs a Predictive ceRNA network among hsa-miR-6727-3p ,TCL6
and HNF1A-AS1. All in all, it can be said that SOX 11 is a possible biomarker for
lung cancer and it would be suggested to conduct more research on this gene.