Research on the expression pattern and coding potential of circRNAs in hepatocellular carcinoma
Objective:As a special class of non-coding RNAs,circular RNAs(circRNAs)have been frequently reported to participate in the evolution and progress of malignant tumors by encoding polypeptides.However,its functions in hepatocellular carcinoma(HCC)are rarely addressed in previous research.Based on the RNA-seq and online data,our study investigated the ex-pression pattern and coding potential of circRNAs in HCC.Methods:The circRNA sequencing procedure was performed on three pairs of HCC and adjacent tissues using a Novaseq 6 000 PE150 high-throughput sequencer.Bioinformatics analysis was conducted to identify circRNAs that expressed differentially and reveal the sequence characteristics of these circRNAs.GO,KEGG,and Re-actome studies were performed to analyze the functions and pathway enrichment of the identified circRNAs.Translatable cir-cRNAs were screened through online databases such as Transcirc and Ribocirc.The IRES finder,ORF finder,and m6A SRAMP were used to predict IRES elements,ORF sequences,and m6A sites,respectively.The coding potential was evaluated following the CPAT method.The expression of differentially expressed circRNA was detected by qPCR.Results:A total of 416 circRNAs were found to be relatively abundant,of which 35 were up-regulated and 31 were down-regulated circRNAs(P<0.05 for all the circRNAs).Sequence analysis suggested that the majority of these circRNAs are of a small molecular weight(length<1 000 nt)and the exon-exon type that contains 2-5 exons.GO analysis showed that differentially expressed circRNAs were enriched in the regulation of GTPase activity(P<0.001),the regulation of small GTPase mediated signal transduction(P<0.001),and the pos-itive regulation of GTPase activity(P<0.001)in the biological process;the nuclear speck(P=0.016)in the cellular component;the GTPase regulator activity(P<0.001),and the GTPase activator activity(P<0.001)in the molecular function,respectively.KEGG analysis indicated that the circRNAs were mainly enriched in the complement and coagulation cascades(P=0.002),the mRNA surveillance pathway(P=0.003),and the platelet activation(P=0.005),while Reactome analysis revealed that the RHO GTPase cycle(P=0.008),the RAC1 GTPase cycle(P<0.001),and the CDC42 GTPase cycle(P=0.001)were the main pathway columns where enrichment of the studied circRNAs appeared.Furthermore,a total of 17 circRNAs were obtained from the intersection of Transcirc and Ribocirc databases,of which 11 genes(hsa_circ_0000231,hsa_circ_0000417,hsa_circ_0000745,hsa_circ_0005455,hsa_circ_0000847,hsa_circ_0005552,hsa_circ_0060849,hsa_circ_0008234,hsa_circ_0075796,hsa_circ_0001742,and hsa_circ_0001686)had the most significant coding potential scores greater than 0.9.At the same time,we used qPCR to verify 10 cases of liver cancer and adjacent tissues,suggesting:hsa_circ_0000231,hsa_circ_0000745,hsa_circ_0005552,and hsa_circ_0000847 are highly expressed in liver cancer tissue,while hsa_circ_0060849 and hsa_circ_0008234 are low expressed,the difference was significant(P<0.05).Conclusion:We comprehensively analyzed the expression patterns of cicRNA in liver cancer,and found that 6 Circrnas with differential expression and high translation potential score were worthy of further study.
万方数据
维普
