A Potential Nine-lncRNAs Signature Identification and Nomogram Diagnostic Model Establishment for Papillary Thyroid Cancer

Abstract

The purpose of our current study was to establish a long non-coding RNA(lncRNA) signature and assess its prognostic and diagnostic power in papillary thyroid cancer (PTC). LncRNA expression profiles were obtained from the Cancer Genome Atlas (TCGA). The key module and hub lncRNAs related to PTC were determined by weighted gene co-expression network analysis (WGCNA) and LASSO Cox regression analyses, respectively. Functional enrichment analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis were implemented to analyze the possible biological processes and signaling pathways of hub lncRNAs. Associations between key lncRNA expressions and tumor-infiltrating immune cells were identified using the TIMER website, and proportions of immune cells in high/low risk score groups were compared. Kaplan-Meier Plotter was used to evaluate the prognostic significance of hub genes in PTC. A diagnostic model was conducted with logistic regression analysis, and its diagnostic performance was assessed by calibration/receiver operating characteristic curves and principal component analysis. A nine-lncRNAs signature (SLC12A5-AS1, LINC02028, KIZ-AS1, LINC02019, LINC01877, LINC01444, LINC01176, LINC01290, and LINC00581) was established in PTC, which has significant diagnostic and prognostic power. Functional enrichment analyses elucidated the regulatory mechanism of the nine-lncRNAs signature in the development of PTC. This signature and expressions of nine hub lncRNAs were correlated with the distributions of tumor infiltrating immune cells. A diagnostic nomogram was also established for PTC. By comparing with the published models with less than or equal to nine lncRNAs, our signature showed a preferable performace for prognosis prediction. In conclusion, our present research established an innovative nine-lncRNAs signature and a six-lncRNAs nomogram that might act as a potential indicator for PTC prognosis and diagnosis, which could be conducive to the PTC treatment.

Differential expression profiles and functional analysis of long non-coding RNAs in calcific aortic valve disease

“…By FEELnc, we predicted the key cis- mRNAs MMP9 , CCL3 , and TGFB3 which are both classic ossification genes. The research of key cis- lncRNA SLC12A5-AS1 , AC243829.4 and TGFB3 mainly concentrated in cancer [ 35 , 36 ] and immune respone [ 37 ]. It is interesting to note that the lncRNA AC243829.4 is the ferroptosis-related lncRNA.…”

Analysis of Long Noncoding RNAs-Related Regulatory Mechanisms in Duchenne Muscular Dystrophy Using a Disease-Related lncRNA-mRNA Pathway Network

“…GAS5 reportedly promotes wound healing by activating the HIF1A/ VEGF pathway [43]. Dysregulation of the lncRNAs MBNL1-AS1, CCDC18-AS1, LINC01290, MIR29B2CHG, and PSMB8-AS1 has been observed in many cancers [44][45][46][47][48]. NF-κB signaling is activated during DMD pathogenesis and leads to infammation and muscle degeneration [49].…”