A Novel Prognostic Prediction Model for Colorectal Cancer Based on Nine Autophagy-Related Long Noncoding RNAs

Abstract

IntroductionColorectal cancer (CRC) is the most common gastrointestinal cancer and has a low overall survival rate. Tumor–node–metastasis staging alone is insufficient to predict patient prognosis. Autophagy and long noncoding RNAs play important roles in regulating the biological behavior of CRC. Therefore, establishing an autophagy-related lncRNA (ARlncRNA)-based bioinformatics model is important for predicting survival and facilitating clinical treatment.MethodsCRC data were retrieved from The Cancer Genome Atlas. The database was randomly divided into train set and validation set; then, univariate and multivariate Cox regression analyses were performed to screen prognosis-related ARlncRNAs for prediction model construction. Interactive network and Sankey diagrams of ARlncRNAs and messenger RNAs were plotted. We analyzed the survival rate of high- and low-risk patients and plotted survival curves and determined whether the risk score was an independent predictor of CRC. Receiver operating characteristic curves were used to evaluate model sensitivity and specificity. Then, the expression level of lncRNA was detected by quantitative real-time polymerase chain reaction, and the location of lncRNA was observed by fluorescence in situ hybridization. Additionally, the protein expression was detected by Western blot.ResultsA prognostic prediction model of CRC was built based on nine ARlncRNAs (NKILA, LINC00174, AC008760.1, LINC02041, PCAT6, AC156455.1, LINC01503, LINC00957, and CD27-AS1). The 5-year overall survival rate was significantly lower in the high-risk group than in the low-risk group among train set, validation set, and all patients (all p < 0.001). The model had high sensitivity and accuracy in predicting the 1-year overall survival rate (area under the curve = 0.717). The prediction model risk score was an independent predictor of CRC. LINC00174 and NKILA were expressed in the nucleus and cytoplasm of normal colonic epithelial cell line NCM460 and colorectal cancer cell lines HT29. Additionally, LINC00174 and NKILA were overexpressed in HT29 compared with NCM460. After autophagy activation, LINCC00174 expression was significantly downregulated both in NCM460 and HT29, while NKILA expression was significantly increased.ConclusionThe new ARlncRNA-based model predicts CRC patient prognosis and provides new research ideas regarding potential mechanisms regulating the biological behavior of CRC. ARlncRNAs may play important roles in personalized cancer treatment.

Identification of an m6A-Related Long Noncoding RNA Risk Model for Predicting Prognosis and Directing Treatments in Patients With Colon Adenocarcinoma

“…Our study identified 29 prognosis-associated, m6A-related lncRNAs based on data from 379 COAD patients, and 12 of them were used to construct the m6A-LPS. NKILA and BOLA3-AS1 have been identified as unfavorable factors for colon cancer (Xu et al, 2021a;Guo et al, 2021;Chen et al, 2022;Qiu et al, 2022), which is consistent with the findings of this study. PCED1B-AS1 was reported to promote the proliferation of COAD by regulating the miR-633/HOXA9 axis, which was proven by in vitro and in vivo experiments (Liu et al, 2022).…”

Prognostic Analysis of a Hypoxia-Associated lncRNA Signature in Glioblastoma and its Pan-Cancer Landscape

“…According to previous literature, [23][24] combined with the relationship between six HALs and GBM prognosis, as well as the results of GSEA analysis, we speculate that LINC00957 is a lncRNA with research potential, and may have a close relationship with the tumor immune microenvironment…”

“…S1A-K), and LINC00957 was also confirmed by bioinformatics analysis to be associated with the prognosis of colon cancer. 23 Next for LINC00957, we further explored its role in pancancer. Considering the small number of normal samples for TCGA, we integrated the data from normal tissues in the GTEx database and the data from TCGA tumor tissues and analyzed 34 cancer species and found that significant upregulation was observed in PAAD (p ¼ 1.2e-11), LAML (p ¼ 6.2e-3), PCPG (p ¼ 5.2e-3), KICH (p ¼ 1.9e-25), and CHOL (p ¼ 1.7e-5), and significant downregulation was observed in GBM (p ¼ The tumor mutation landscape was demonstrated to be associated with antitumor immunity.…”

Cuprotosis Programmed-Cell-Death-Related lncRNA Signature Predicts Prognosis and Immune Landscape in PAAD Patients

“…We used Lasso regression analysis and Cox risk regression analysis to identify five CRLs (AC005332.6, AC090114.2, LINC00857, LINC02041, and AL117382.1) that were shown to be independent prognostic variables for PAAD and correctly classified PAAD patients into two separate prognosis categories. Evidence suggests that AC005332.6, AC090114.2, and LINC02041 may serve as prognostic markers for many cancers, including pancreatic cancer [ 42 , 53 , 54 , 55 , 56 ]. Through a ceRNA-mediated mechanism, LINC00857 promotes the growth and invasion of pancreatic cancer cells [ 51 ].…”