GSE117095
RNA-seq analysis of RNA-binding protein HuR knockout mice oral epithelial tissues
Purpose:  The goals of this study is to compare NGS-derived oral epithelial transcriptome profiling (RNA-seq) of WT and HuR KO tongue tissues exposed with carcinogen 4-nitroquinoline 1-oxide (4-NQO) induced oral tumorigenesis. Methods: Oral tongue tissues mRNA profiles of six-weeks old wild-type (WT) and epithelial HuR knockout (HuR-/-) mice exposed with 4NQO were generated by deep sequencing, in triplicate, using Illumina hiseq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks - fill in William Results: There were no over-represented sequences, derived from primers and adapters from the library, and no bad quality nucleotides, the pre-process step was not necessary. On average, there were 64,096,543 reads per sample of 50 pair bases each. The alignment to the genome average rate of total mapped reads was 98.28%, which is a really good result considering we are working with Mouse data. There is a clear separation of the sample by the groups in the PCA plot and the samples cluster according by the groups in the identity plot. Nonetheless, Group B seems to be more heterogeneous, with sample Group_B-4_S4 showing signs of a hybrid expression profile that encompasses groups A and B.  The system level analysis was made using iPathway Guide from Advaitabio. For system level analysis we used adjusted p value threshold of 0.1. A total of 32 pathways were considered statistically significant in an adjp threshold of 0.05. Interesting to note the presence of terms related to an altered function of the mitochondria. “ECM-receptor interaction” is changed with adj.p of 1.6 x 10-4. GO Biological term “epidermal cell differentiation” ” is changed with adj.p of 7.4  1.6 x 10-8.  The gene Elavl1, although what seems to be a great expression in both group (baseMean = 2431.1 counts) have a log2 fold change of -0.2 and an adjp = 0.2.  Number of DE genes  Group-B_vs_Group-A   adjp = 0.1 =  5,849 DE genes  adjp = 0.01 = 2,258 DE genes Conclusions: Our study represents the first detailed analysis of HuR WT and HuR-/- oral epithelial tissue transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that HuR controls subset of genes responsible for epithelial differentiation and energy metabolism. We conclude that HuR is critical factor in epithelial homeostasis. Overall design: Three replicates of HuR WT and HuR KO tongue tissues exposed with 4-nitroquinoline 1-oxide (4NQO) carcinogen.