Genome-wide analyses of radioresistance-associated miRNA expression profile in nasopharyngeal carcinoma using next generation deep sequencing

Abstract

Background: Rapidly growing evidence suggests that microRNAs (miRNAs) are involved in a wide range of cancer malignant behaviours including radioresistance. Therefore, the present study was designed to investigate miRNA expression patterns associated with radioresistance in NPC.

Methods: The differential expression profiles of miRNAs and mRNAs associated with NPC radioresistance were constructed. The predicted target mRNAs of miRNAs and their enriched signaling pathways were analyzed via biological informatical algorithms. Finally, partial miRNAs and pathways-correlated target mRNAs were validated in two NPC radioreisitant cell models.

Results: 50 known and 9 novel miRNAs with significant difference were identified, and their target mRNAs were narrowed down to 53 nasopharyngeal-/NPC-specific mRNAs. Subsequent KEGG analyses demonstrated that the 53 mRNAs were enriched in 37 signaling pathways. Further qRT-PCR assays confirmed 3 down-regulated miRNAs (miR-324-3p, miR-93-3p and miR-4501), 3 up-regulated miRNAs (miR-371a-5p, miR-34c-5p and miR-1323) and 2 novel miRNAs. Additionally, corresponding alterations of pathways-correlated target mRNAs were observed including 5 up-regulated mRNAs (ICAM1, WNT2B, MYC, HLA-F and TGF-β1) and 3 down-regulated mRNAs (CDH1, PTENP1 and HSP90AA1).

Conclusions: Our study provides an overview of miRNA expression profile and the interactions between miRNA and their target mRNAs, which will deepen our understanding of the important roles of miRNAs in NPC radioresistance.

Figure 1. Work flow of the whole miRNA identifying procedure in details.

Figure 2. Results of the small RNA information analysis.

(A) The size distribution of the small RNAs in CNE-2 and CNE-2-Rs. The sRNAs with 22 nt had the highest abundance. (B) The miRNAs identified in CNE-2 and CNE-2-Rs. The dark park were the miRNAs found in both samples, the red part and blue part showed the number of miRNAs expressed in sample CNE-2 and CNE-2-Rs, respectively. (C) Scatter plot of miR expression profiles in radiosensitive CNE-2 (x-axis) and radio-resistant CNE-2R cells (y-axis).The up-reugulated miRNAs with statistical significance were marked in red and the down-regulated ones in green (p < 0.05).

Figure 3. Network of the miRNAs and their prediction target gene.

miRNA-gene interactions were built into a bipartite network. The red triangles indicate the up-regulated miRNAs, the blue triangles indicate the down-regulated miRNAs. The red circles indicate the up-regulated target genes, the blue circles indicate the down-regulated target genes (prediction value > 1).

Figure 4. Differential miR expression between radioreisistant cell and their parent cell.

Relative expression levels of several representative miRNAs with differential expression levels were presented, including 2 novel miRNAs and 10 known miRNAs.

Figure 5. Differential mRNA expression between radioreisistant cell and their parent cell.

(A) Target genes mRNAs of down-regulated miRNAs with differential expression levels were presented (p < 0.05). (B) Target genes mRNAs of up-regulated miRNAs with differential expression levels were presented (p < 0.05).