Study on the function and prognosis of circular RNA in colorectal cancer tissues based on high-throughput sequencing

doi:10.3969/j.issn.1674-8115.2021.02.010

Abstract

Abstract: Objective

·To reveal the mechanism of colorectal cancer and the association between differential expression of circular RNAs (circRNAs) and patients' prognosis.

Methods

·Colorectal cancer tissues and normal tumor-adjacent tissues were harvested from 12 patients undergoing radical resection of colorectal cancer in the Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, and the expressions of circRNAs were detected by high-throughput sequencing. Function predictions of differentially expressed circRNAs were carried out by gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Two circRNAs were selected from the significantly up-regulated and down-regulated circRNAs respectively, and the accuracy of sequencing results was verified in 44 sets of colorectal cancer tissues by real-time fluorescent quantitative PCR (RT-qPCR). The circRNA-miRNA targeting binding network map was constructed by searching the public database for the four circRNAs. Finally, the relationships between differential expression of circRNAs and prognosis were determined based on the patients' clinical data.

Results

·A total of 20 924 differentially expressed circRNAs were detected after high-throughput sequencing. Compared with normal colorectal tissues, there were 373 circRNAs (︱log₂FC︱>1, P<0.05) abnormally and significantly expressed in colorectal cancer tissues, of which 243 were significantly up-regulated and 130 were significantly down-regulated. In 44 pairs of colorectal cancer samples, the results verified by RT-qPCR were basically consistent with the sequencing data. After the circRNA-miRNA-mRNA interactions being plotted, it was found that miRNA and target genes associated with circRNA may play an important role in the pathogenesis of colorectal cancer. Combined with the prognosis information, the patients with high expression of hsa_circ_0023984 or hsa_circ_0008192 had poorer prognosis while patients with high expression of hsa_circ_0020093 or hsa_circ_0069922 had better prognosis.

Conclusion

·Abnormally expressed circRNAs in colorectal cancer tissues lay a foundation for further studies on the occurrence and development of colorectal cancer, and provide valuable information for the development of new clinical diagnostic markers and treatments in the future.

Key words: colorectal cancer, circular RNA (circRNA), prognosis, regulatory network

CLC Number:

R735.3

Zhong-mao FU, Zai LUO, Ze-yin RONG, Jian-ming ZHANG, Teng-fei LI, Zhi-long YU, Chen HUANG. Study on the function and prognosis of circular RNA in colorectal cancer tissues based on high-throughput sequencing[J]. JOURNAL OF SHANGHAI JIAOTONG UNIVERSITY (MEDICAL SCIENCE), 2021, 41(2): 187-195.

Figures/Tables 6

TrendMD

References 29

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Gene	Primer sequence （5'→3'）
hsa_circ_0023984
Forward	5'-GTCAGTATATTACTCTACATTGTCCCAG-3'
Reverse	5'-TCTAAATTAGTTTGATACTTCAGCAGC-3'
hsa_circ_0008192
Forward	5'-TGTCAGTGCCGTCCAATC-3'
Reverse	5'-GCGAACAGGGAGGTCTAT-3'
hsa_circ_0020093
Forward	5'-CGGTTACTGTGACCTGACTGGAG -3'
Reverse	5'-TGGGCCATCTGTTAAATATCCAG-3'
hsa_circ_0069922
Forward	5'-GCTGATGAATCCAGCAGCAGC-3'
Reverse	5'-TCCAGGACAGCTTCATCCTCC-3'
GAPDH
Forward	5'-GTCTCCTCTGACTTCAACAGCG-3'
Reverse	5'-ACCACCCTGTTGCTGTAGCCAA-3'

Gene	Primer sequence （5'→3'）
hsa_circ_0023984
Forward	5'-GTCAGTATATTACTCTACATTGTCCCAG-3'
Reverse	5'-TCTAAATTAGTTTGATACTTCAGCAGC-3'
hsa_circ_0008192
Forward	5'-TGTCAGTGCCGTCCAATC-3'
Reverse	5'-GCGAACAGGGAGGTCTAT-3'
hsa_circ_0020093
Forward	5'-CGGTTACTGTGACCTGACTGGAG -3'
Reverse	5'-TGGGCCATCTGTTAAATATCCAG-3'
hsa_circ_0069922
Forward	5'-GCTGATGAATCCAGCAGCAGC-3'
Reverse	5'-TCCAGGACAGCTTCATCCTCC-3'
GAPDH
Forward	5'-GTCTCCTCTGACTTCAACAGCG-3'
Reverse	5'-ACCACCCTGTTGCTGTAGCCAA-3'

circRNA ID	FC	P value	Regulation	circRNA chromosome	Gene
hsa_circ_0079534	14.24	<0.001	Up	NC_000007.14:20154193_20161870_-	MACC1
hsa_circ_0023984	10.43	<0.001	Up	NC_000011.10:89400017_89402542_-	NOX4
hsa_circ_0008192	10.27	<0.001	Up	NC_000009.12:112262435_112297916_-	PTBP3
hsa_circ_0008694	8.55	<0.001	Up	NC_000020.11:51712966_51729978_-	ATP9A
hsa_circ_0004705	7.40	<0.001	Up	NC_000003.12:14443624_14447816_+	SLC6A6
hsa_circ_0020093	-8.27	<0.001	Down	NC_000010.11:115120185_115129535_+	ATRNL1
hsa_circ_0069922	-7.22	<0.001	Down	NC_000004.12:71236576_71255399_+	SLC4A4
hsa_circ_0073244	-6.54	<0.001	Down	NC_000005.10:84060300_84066606_-	EDIL3
hsa_circ_0005720	-5.31	0.001	Down	NC_000001.11:95143891_95173889_+	TMEM56
hsa_circ_0008676	-5.26	0.002	Down	NC_000004.12:71339370_71357187_+	SLC4A4

circRNA ID	FC	P value	Regulation	circRNA chromosome	Gene
hsa_circ_0079534	14.24	<0.001	Up	NC_000007.14:20154193_20161870_-	MACC1
hsa_circ_0023984	10.43	<0.001	Up	NC_000011.10:89400017_89402542_-	NOX4
hsa_circ_0008192	10.27	<0.001	Up	NC_000009.12:112262435_112297916_-	PTBP3
hsa_circ_0008694	8.55	<0.001	Up	NC_000020.11:51712966_51729978_-	ATP9A
hsa_circ_0004705	7.40	<0.001	Up	NC_000003.12:14443624_14447816_+	SLC6A6
hsa_circ_0020093	-8.27	<0.001	Down	NC_000010.11:115120185_115129535_+	ATRNL1
hsa_circ_0069922	-7.22	<0.001	Down	NC_000004.12:71236576_71255399_+	SLC4A4
hsa_circ_0073244	-6.54	<0.001	Down	NC_000005.10:84060300_84066606_-	EDIL3
hsa_circ_0005720	-5.31	0.001	Down	NC_000001.11:95143891_95173889_+	TMEM56
hsa_circ_0008676	-5.26	0.002	Down	NC_000004.12:71339370_71357187_+	SLC4A4

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