Identification and bioinformatic analysis of target genes of lncRNA LOC102606465 induced by ionizing radiation

Abstract

Objective To screen the target genes of long non-coding RNA LOC102606465, which was previously identified to be induced by ionizing radiation, in order to examine its potential biological role. Methods The downstream differentially expressed genes (DEGs) of LOC102606465 were detected by microarray and partially verified by qRT-PCR. GO and KEGG enrichment analysis was performed, and PPI protein interaction network was constructed to screen significant modules and hub genes. Results The expression of LOC102606465 targeted by siRNA-447 and siRNA-541 was significantly lower than that of siRNA-NC (t=29.095, 13.751, P<0.01). A total of 374 common DEGs were identified(112 up-regulated/262 down-regulated) in both siRNA-447 and siRNA-541. The qRT-PCR was used to validate the expression of DEGs, which was consistent with the microarray result. In GO enrichment analysis, down-regulated DEGs were significantly enriched in " oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor" (molecular function), " basal lamina" (cellular component), " ammonium ion metabolic process" (biological process). Up-regulated DEGs were mainly enriched in " protein phosphatase inhibitor activity" (molecular function), " SNARE complex" (cellular component), " negative regulation of fibrinolysis" (biological process). In addition, the KEGG enrichment analysis revealed that DEGs were significantly enriched in " metabolism of xenobiotics by cytochrome P450" , " dorso-ventral axis formation" , " lysosome glycerophospholipid metabolism" and " p53 signaling pathway" . Based on the STRING database, the PPI network was constructed (including 194 nodes and 268 edges), and one significant module and five key hub genes ACTRT3, CDKN1A, DPYD, TMP4, and PRKACB were identified. Conclusions LOC102606465 could be a potential biomarker for the regulation of ionizing radiation sensitivity, and the down-regulation of LOC102606465 plays an important role in the response to radiation, which would be an important target for regulating radiation sensitivity. Key words: Bioinformatic analysis; Microarray; LOC102606465; Ionizing radiation