Qualification of Necroptosis-Related lncRNA to Forecast the Treatment Outcome, Immune Response, and Therapeutic Effect of Kidney Renal Clear Cell Carcinoma

Abstract

Background. Kidney renal clear cell carcinoma (KIRC) is considered as a highly immune infiltrative tumor. Necroptosis is an inflammatory programmed cell death associated with a wide range of diseases. Long noncoding RNAs (lncRNAs) play important roles in gene regulation and immune function. lncRNA associated with necroptosis could systematically explore the prognostic value, regulate tumor microenvironment (TME), etc. Method. The patients’ data was collected from TCGA datasets. We used the univariate Cox regression (UCR) to select prediction lncRNAs that are related to necroptosis. Meanwhile, risk models were constructed using LASSO Cox regression (LCR). Kaplan–Meier (KM) analysis, accompanied with receiver operating characteristic (ROC) curves, was performed to assess the independent risk factors of different clinical characteristics. The evaluated factors are age, gender, disease staging, grade, and their related risk score. Databases such as Gene Ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and Gene set enrichment analysis (GSEA) were used to search the probable biological characteristics that could influence the risk groups, containing signaling pathway and immue-related pathways. The single-sample gene set enrichment analysis (ssGSEA) was chosen to perform gene set variation analysis (GSVA), and the GSEABase package was selected to detect the immune and inflammatory infiltration profiles. The TIDE and I C 50 evaluation were used to estimate the effectiveness of clinical treatment on KIRC. Results. Based on the above analysis, we have got a conclusion that patients who show high risk had higher immune infiltration, immune checkpoint expression, and poorer prognosis. We identified 19 novel prognostic necroptosis-related lncRNAs, which could offer opinions for a deeper study of KIRC. Conclusion. The risk model we constructed makes it possible to predict the prognosis of KIRC patients and offers directions for further research on the prognostication and treatment strategies for KIRC.

ANXA5: A Key Regulator of Immune Cell Infiltration in Hepatocellular Carcinoma

“…We used the GSVA (version 1.50.0), limma (version 3.58.1), and GSEABase (version 1.64.0) packages in R to compute the enrichment scores for ARG score, immune cells, and immune function in the HCC transcriptome data. GSVA and GSEABase offer greater capability to detect subtle pathway activity changes within sample populations [ 29 , 30 ]. The limma package is an R/Bioconductor software package that provides an integrated solution for analyzing data from gene expression experiments [ 31 ].…”