Transcriptional change in intestinal crypts by TLR4 activation upon radiation exposure

Purpose: The activation of TLR4 was reported to effectively alleviate intestinal injury induced by irradiation (IR). The goals of this study are to investigate the transcriptome profiling (RNA-seq) of intestinal crypts thereby clarifying the underlying mechanism mediating the radio-protective activity of TLR4 on intestinal stem cells. Methods: Intestinal crypts mRNA profiles of mice treated or untreated with TLR4 low-toxic agonist monophosphyal lipid A (MPLA) upon abdominal body irradiation (AIR) exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 sequencer. To pre-treated the data, adaptor and low-grade reads removal, low-quality bases elimination from 3' or 5' ends, original and effective sequencing quantity analysis, as well as guanine and cytosine statistics were subjected, in turns. Differential expression genes were selected via correlation test, principal component analysis and cluster analysis, in which the fold change (FC) was greater than 2 and p value was less than 0.05 could be regarded significance. Different expressed genes (DEGs) were clustered into pathways of intestinal crypts through KEGG. Results: As compared to the nonirradiated group, 2733 DEGs were identified in intestinal crypts after AIR damage, while there were 2168 DEGs between irradiated group and irradiated plus MPLA treatment group. Among the DEGs, a series of genes involving intestinal stem cells regeneration, which mainly falls into three stem cell related pathway according to Gene ontology analysis and KEGG enrichment: Hippo, Wnt and Notch signaling pathway. Based on these DEGs, we focused on a group of genes which was suppressed by IR, while could be restored by TLR4 activation. Based on the criteria, 8 DEGs (SOX9, cMyc, MSI1, Lgr5, Notch1, Wnt5b, Axin2, DLL4) involving intestinal stem cell regulation were further selected for validation, from which the mRNA levels of 4 genes (SOX9, YAP1, cMyc) were confirmed to be up-regulated by MPLA treatment. Conclusions: Our study represents the first detailed analysis of intestinal crypts transcriptomes by TLR4 activation upon IR damage, with biologic replicates, generated by RNA-seq technology. And the confirmation of DEGs will facilitate the development of novel targets and techniques to efficiently stimulate the regeneration of intestinal stem cells to reconstruct the intestine after radiation injury.