An RNA-seq-Based Expression Profiling of Radiation-Induced Esophageal Injury in a Rat Model

Abstract

Radiation-induced acute injury is the main reason for the suspension of radiotherapy and unsuccessful treatment of cancer. It is of great importance to understand the molecular mechanism of radiation-induced esophageal injury. We used RNA-seq data from normal esophageal tissue and irradiated esophageal tissues and applied computational approaches to identify and characterize differentially expressed genes and detected 40 059 messenger RNAs (mRNAs) previously annotated and 717 novel long noncoding RNAs (lncRNAs). There were 14 upregulated and 32 downregulated lncRNAs among the differentially expressed lncRNA group. Their target genes were involved in the mRNA surveillance pathway, pathological immune responses, and cellular homeostasis. Additionally, we found 853 differentially expressed mRNAs, and there were 384 upregulated and 469 downregulated mRNAs. Notably, we found that the differentially expressed mRNAs were enriched for steroid biosynthesis, the tumor necrosis factor signaling pathway, focal adhesion, pathways in cancer, extracellular matrix-receptor interaction, and so on. The response of normal esophageal tissues to ionizing radiation is multifarious. The radiation-induced cell damage response by multiple pathways followed by pathological immune responses activated. Studies on the dynamic network of molecules involved in radiation-induced esophageal injury are under way to clarify the regulatory mechanisms and identify the candidate targets.

Keywords: RNA-sequence; esophageal injury; ionizing radiation; lncRNAs; mRNA.

Figure 1.

Overview of the RNA-seq data analysis. A, Box plot of log2 (FPKM) values across control and IR expressed transcripts. Control represents normal esophageal tissue sample, and IR represents ionizing radiation-treated sample. B, Volcano plot of 2 samples (control and IR) of different genes. C, Venn diagram of the significantly differentially expressed genes (lncRNAs and mRNAs) in the 2 samples (control and IR). FPKM indicates fragments per kilobase of transcript per million fragments mapped; lncRNAs, long non-coding RNAs; mRNA, messenger RNA.

Figure 2.

Identification of lncRNAs and the distribution of differentially expressed transcripts. A, Venn diagram of the predicted lncRNAs using HMMer+Pfam, CPC, CPAT, and CNCI. B Violin plot of log2 (FPKM) values across lncRNA and mRNA expressed transcripts. C, Venn diagram of the mRNAs in 2 samples (control and IR). D, Venn diagram of lncRNAs in 2 samples (control and IR). LncRNA indicates long non-coding RNA, and mRNA, messenger RNA.

Figure 3.

A heat map of transcriptomic expression patterns. A, A heat map of the significant mRNA expression patterns in control and IR group populations. B, A heat map of the significant lncRNA expression patterns in control and IR group populations. LncRNA indicates long non-coding RNA, and mRNA, messenger RNA.

Figure 4.

The network between lncRNAs and their target genes. A, The coexpression network between cis-lncRNAs (TCONS_00062404 and TCONS_00012350) and their target genes. B, The coexpression network between trans-lncRNAs (TCONS_00076064, TCONS_00008311, and TCONS_00012350) and their target genes. The big box indicates novel lncRNAs, and the small box indicates the target genes. The red box indicates upregulated novel genes, and the green box indicates upregulated genes. LncRNA indicates long non-coding RNA, and mRNA, messenger RNA.

Figure 5.

DEG distribution in rat chromosomes. Black bars above the horizontal line represent all DEGLs; red and blue bars represent upregulated and downregulated DEGs, respectively. DEG indicates differentially expressed gene.