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. 2020 Mar 23;20(1):242.
doi: 10.1186/s12885-020-06717-4.

Identification of microRNAs and their Endonucleolytic Cleavaged target mRNAs in colorectal cancer

Fangbin Zhou  1   2 , Donge Tang  1 , Yong Xu  1 , Huiyan He  1 , Yan Wu  1 , Liewen Lin  1 , Jun Dong  3 , Wenyong Tan  4   5 , Yong Dai  6
Affiliations

Identification of microRNAs and their Endonucleolytic Cleavaged target mRNAs in colorectal cancer

Fangbin Zhou et al. BMC Cancer. .

Abstract

Background: Colorectal cancer (CRC) ranks the third among the most common malignancies globally. It is well known that microRNAs (miRNAs) play vital roles in destabilizing mRNAs and repressing their translations in this disease. However, the mechanism of miRNA-induced mRNA cleavage remains to be investigated.

Method: In this study, high-throughput small RNA (sRNA) sequencing was utilized to identify and profile miRNAs from six pairs of colorectal cancer tissues (CTs) and adjacent tissues (CNs). Degradome sequencing (DS) was employed to detect the cleaved target genes. The Database for Annotation, Visualization and Integrated Discovery (DAVID) software was used for GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis.

Results: In total, 1278 known miRNAs (clustered into 337 families) and 131 novel miRNAs were characterized in the CT and CN libraries, respectively. Of those, 420 known and eight novel miRNAs were defined as differentially expressed miRNAs (DEmiRNAs) by comparing the expression levels observed in the CT and CN libraries. Furthermore, through DS, 9685 and 202 potential target transcripts were characterized as target genes for 268 known and 33 novel miRNAs, respectively. It was further predicted that a total of 264 targeted genes for the 85 DEmiRNAs are involved in proteoglycans in cancer and the AMP-activated protein kinase signaling pathway. After systemic analysis of prognosis-related miRNA targets in those cancer-related signal pathways, we found that two targets ezrin (EZR) and hematopoietic cell-specific Lyn substrate 1 (HCLS1) had the potential prognostic characteristics with CRC regarding over survival (OS) or recurrence.

Conclusion: In total, we found that endonucleolytic miRNA-directed mRNA cleavage occurs in CRC. A number of potential genes targeted by CRC-related miRNAs were identified and some may have the potential as prognosis markers of CRC. The present findings may lead to an improved better appreciation of the novel interaction mode between miRNAs and target genes in CRC.

Keywords: Colorectal Cancer; Degradome sequencing; Endonucleolytic cleavage; High-throughput small RNA sequencing; microRNA.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The flowchart of the study. High-throughput sRNA sequencing was employed to identify and profile miRNAs and DS was used to identify the cleaved target genes. After a series of data processing and bioinformatic analysis, targets cleaved by DEmiRNAs were found to be enriched in the cancer-related signaling pathways
Fig. 2
Fig. 2
Volcanic diagrams showing the number of DEmiRNAs between CTs and CNs. The red dots indicate miRNAs with significant differences, and the blue dots indicate that miRNAs without significant differences
Fig. 3
Fig. 3
Comparisons of the expression levels of seven miRNAs between RNA-seq and qPCR. Fold change (log2) in CN libraries relative to CT libraries were detected by RNA-seq. The relative expression levels of miRNAs were normalized to the expression of U6 in qPCR
Fig. 4
Fig. 4
Examples of T-plots of miRNA targets identified by DS. The red lines indicate miRNA-mediated cleavage. a hsa-let-7b-5p slicing ENST00000217254 at 704; b miR-196a-5p slicing ENST00000239144 at 1390; c hsa-miR-196b-5p_R + 1 slicing ENST00000239144 at 1390; d ppy-mir-1268-p3_1ss13TC slicing ENST000002575724 at 3990
Fig. 5
Fig. 5
Comparisons of the expression levels of 12 miRNAs between RNA-seq and qPCR. Fold change (log2) in CN libraries relative to CT libraries were detected by RNA-seq. The relative expression levels of miRNAs were normalized to the expression of U6 in qPCR
Fig. 6
Fig. 6
KEGG pathway analysis of targeted genes involved into proteoglycans in cancer pathway. mmu-mir-6236-p3_2 targeted the FN1 gene; hsa-miR-665_R-2, was involved in proliferation and survival, and controlled the accumulation level of the PIK3R5 protein in the PI3K-Akt signaling pathway; hsa-miR-1296-5p targeted the HCLS1 gene, to respond to the MAPK signaling pathway. Red rectangle represents up-regulated targets and blue rectangle represents down-regulated targets
Fig. 7
Fig. 7
Analysis of the correlation between CRC prognosis (OS) and the expression of miRNA targeted genes in cancer-related pathways. a targets regulating proteoglycans; b targets regulating the AMP-activated protein kinase signaling pathway
Fig. 8
Fig. 8
Analysis of the correlation between CRC prognosis (PFS) and the expression of miRNA targeted genes in cancer-related pathways. a targets regulating proteoglycans; b targets regulating the AMP-activated protein kinase signaling pathway
Fig. 9
Fig. 9
Analysis of the correlation between CRC diagnosis age and the expression of miRNA targeted genes in cancer-related pathways. a targets regulating proteoglycans; b targets regulating the AMP-activated protein kinase signaling pathway
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References

    1. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75(5):843–854. doi: 10.1016/0092-8674(93)90529-Y. - DOI - PubMed
    1. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol. 2006;57:19–53. doi: 10.1146/annurev.arplant.57.032905.105218. - DOI - PubMed
    1. Wang Y, Li L, Tang S, Liu J, Zhang H, Zhi H, Jia G, Diao X. Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet. BMC Genet. 2016;17:57. doi: 10.1186/s12863-016-0364-7. - DOI - PMC - PubMed
    1. Candar-Cakir B, Arican E, Zhang B. Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes. Plant Biotechnol J. 2016;14(8):1727–1746. doi: 10.1111/pbi.12533. - DOI - PMC - PubMed
    1. Ma X, Zhang X, Zhao K, Li F, Li K, Ning L, He J, Xin Z, Yin D. Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Seed Expansion in Peanut (Arachis hypogaea L.) Front Plant Sci. 2018;9:349. doi: 10.3389/fpls.2018.00349. - DOI - PMC - PubMed