<p>Competing Endogenous RNA (ceRNA) Network Analysis of Autophagy-Related Genes in Hepatocellular Carcinoma</p>

Abstract

Autophagy plays an important role in the occurrence and development of hepatocellular carcinoma (HCC). We aimed to develop an autophagy-related genes signature predicting the prognosis of HCC and to depict a competing endogenous RNA (ceRNA) network. Methods: Differentially expressed autophagy-related genes (DE-ATGs), miRNAs and lncRNAs and clinical data of HCC patients were extracted from TCGA. The GO and KEGG analysis were performed to investigate the gene function. Univariate and multivariate Cox regression analysis were used to identify a prognostic signature with the DE-ATGs. And a nomogram, adapted to the clinical characteristics, was established. Then, we established a ceRNA network related to autophagy genes. Results: We screened out 27 differentially expressed genes which were enriched in GO and KEGG pathways related to autophagy and cancers. In univariate and multivariate Cox regression analysis, BIRC5, HSPB8, and SQSTM1 were screened out to establish a prognostic risk score model (AUC=0.749, p<0.01). Kaplan-Meier survival analysis showed that the overall survival of high-risk patients was significantly worse. Furthermore, the signature was validated in the other two independent databases. The nomogram, including the autophagy-related risk signature, gender, stage and TNM, was constructed and validated (C-index=0.736). Finally, the ceRNA network was established based on DE-ATGs, differentially expressed miRNAs and lncRNAs. Conclusion: We constructed a reliable prognostic model of HCC with autophagy-related genes and depicted a ceRNA network of DE-ATGs in HCC which provides a basis for the study of post-transcriptional modification and regulation of autophagy-related genes in HCC.

A Novel Autophagy-Related lncRNA Gene Signature to Improve the Prognosis of Patients with Melanoma

“…In colorectal cancer cells, lncRNA SNHG6 targets miR-26a-5p to promote chemotherapy through autophagy induced by ULK1 [50]. At the same time, the ceRNA network analysis related to autophagy in hepatocellular carcinoma was also verified by Yang et al [51]. In this study, we found that autophagy-related lncRNA may affect the development of melanoma through ARGs.…”

Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

“…Given that genetic changes in genes can alter phenotypes and even result in diseases, the synonymous codon usage bias has a strong correlation with protein biological functions (Chakraborty et al, 2017;Chakraborty et al, 2019;De Mandal et al, 2020;Malakar et al, 2020). With the ongoing analyses for the genetic signatures of atg genes, some members have been regarded as markers for predicting some diseases (such as cancers) (Baradaran Ghavami et al, 2019;Chen et al, 2020;Yang et al, 2020;Lai et al, 2020;Wang et al, 2020). Despite a weak pressure caused by translation selection, the selective force from natural selection plays an obvious role in GC-conservative codons in different organisms, leading to alterations of the gene structures (Carlini et al, 2001;Carlini and Stephan, 2003;Galtier et al, 2018).…”

Long non‑coding RNA ZSCAN16‑AS1 promotes the malignant properties of hepatocellular carcinoma by decoying microRNA‑451a and consequently increasing ATF2 expression

“…miRNAs can bind directly to the 3'-untranslated region (UTR) of downstream target genes and consequently inhibit translation or mRNA degradation, thereby controlling gene expression at the posttranslational level (17). Notably, lncRNAs are capable of interacting with miRNAs and thus implementing their functions (18). As gene regulators, lncRNAs can work as competing endogenous RNAs (ceRNAs) by decoying or competing with shared miRNAs, thereby lowering the miRNA-induced inhibition of gene expression (19).…”