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Volume 48 Number 5
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Volume 48 Number 3 Volume 48 Number 4 Volume 48 Number 5

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Research articles

ScienceAsia 48 (2022): 379-386 |doi: 10.2306/scienceasia1513-1874.2022.049


Bioinformatics and qPCR analyses of laminins' cognate receptors in cholangiocarcinoma tissues reveal the integrin ITGB4 as a potential biomarker


Kittiya Islama, Brinda Balasubramanianb, Simran Venkatramanb, Janpen Puetkasichonpasuthaa, Rutaiwan Tohtonga, Nisana Namwatc,d, Prakasit Sa-Ngiamwiboold,e, Attapol Titapund,f, Tuangporn Suthiphongchaia,*

 
ABSTRACT:     Cholangiocarcinoma (CCA), a devastating epithelial tumor arising in bile ducts with dismal prognosis and high mortality rate, has the highest worldwide incidence in Northeastern Thailand, raising a serious health public concern to the country. Due to a desmoplastic nature of CCA, understanding CCA cell-matrix interaction is necessitated. Here, an in silico analysis using two RNA-sequencing (Pan-Cancer Analysis of Whole Genomes and The Cancer Genome Atlas) databases and ten microarray datasets from the Gene Expression Omnibus database, was utilized to compare the mRNA expression of 19 genes of laminins? cognate receptors between CCA and adjacent noncancerous tissues. The results were further validated in tissues of Thai patients using qPCR analysis. Bioinformatics analyses revealed that there were five common dysregulated genes in the three transcriptomic databases, in which four were upregulated genes (ITGAV, ITGA2, ITGB1, and ITGB4), and one was downregulated gene (SDC2). Of these differentially expressed genes, qPCR analysis confirmed the elevated mRNA expression of ITGB4 encoding integrin ?4 in 97% of the CCA cases and pinpointing the ITGB4 as a potential diagnostic biomarker for CCA.

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a Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400 Thailand
b Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400 Thailand
c Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002 Thailand
d Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002 Thailand
e Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002 Thailand
f Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002 Thailand

* Corresponding author, E-mail: tuangporn.sut@mahidol.ac.th

Received 15 Dec 2021, Accepted 9 Jan 2022