Identification and validation of a novel pyroptosis-related lncRNAs signature associated with prognosis and immune regulation of hepatocellular carcinoma

Abstract

Pyroptosis is an inflammatory form of cell death triggered by certain inflammasomes. However, research concerning pyroptosis-related lncRNAs in hepatocellular carcinoma (HCC) remains scarce. This study aims to explore the prognostic pyroptosis-related long non-coding RNAs (lncRNAs) of HCC patients. Data of 373 HCC patients were obtained from the TCGA database. The entire cohort was randomly divided into a training cohort and a validation cohort in a 2:1 ratio. Pyroptosis-related lncRNAs were identified by the Pearson correlation analysis with reported pyroptosis-related genes. LASSO Cox regression was used to construct the signature. A prognostic signature consisting of nine pyroptosis-related lncRNAs was identified, and patients with lower risk scores had a better prognosis than those with higher risk scores. Multivariate Cox regression analysis showed that the signature was an independent risk factor for prognosis in both the training and validation cohorts. In the training cohort, the area under the signature curve reached 0.8043 at 1-year, 0.7878 at 2-year, and 0.8118 at 3-year; in the validation cohort, it reached 0.7315 at 1-year, 0.7372 at 2-year, and 0.7222 at 3-year. Gene set enrichment analysis (GSEA) suggested associations between the signature and several immune-related pathways. The expression of multiple immune checkpoints was also increased in the high-risk group, including PD-1, PD-L1, CTLA4, B7-H3, VSIR, LAG3, and TIGIT. A novel pyroptosis-related lncRNA signature, which may be associated with tumor immunity and potentially serve as an indicator for immunotherapy, has been identified to precisely predict the prognosis of HCC patients.

Figure 1

Identification of the pyroptosis-associated lncRNAs in HCC patients. (a) The flow chart of constructing the pyroptosis-related lncRNAs signature. (b) The heatmap of 9 prognostic pyroptosis-related lncRNAs in HCC tissues and adjacent normal tissues. (c) The barplots comparing the 9 prognostic pyroptosis-related lncRNAs between HCC tissues and adjacent normal tissues. HCC, hepatocellular carcinoma. *P < 0.05; **P < 0.01; ***P < 0.001.

Figure 2

The prognostic value of pyroptosis-associated lncRNAs in HCC patients. (a–i) Kaplan-Meire curve of AC019080.5 (a), AP003392.4 (b), MKLN1-AS (c), AL031985.3 (d), PCCA-DT (e), AC007128.1 (f), LNCSRLR (g), AL445228.3 (h), AC023157.2 (i) on overall survival of HCC patients. (j) Univariate Cox regression of 9 prognostic pyroptosis-related lncRNAs in the training cohort.

Figure 3

The mRNA-lncRNA co-expression network. (a) mRNA-lncRNA co-expression network of the pyroptosis-related genes and the selected pyroptosis-related lncRNAs. (b) The Sankey diagram showing the connection degree between the pyroptosis-related lncRNAs and the pyroptosis-related genes.

Figure 4

Prognostic analysis of pyroptosis-related lncRNA signature in the training cohort and validation cohort. (a) The distribution of the risk scores in the training cohort. (b) The distribution of the risk scores in the validation cohort. (c) The distributions of overall survival status, overall survival, and risk score in the training cohort. (d) The distributions of overall survival status, overall survival, and risk score in the validation cohort. (e) Kaplan–Meier curves for the overall survival of patients in the high- and low-risk groups in the training cohort. (f) Kaplan–Meier curves for the overall survival of patients in the high- and low-risk groups in the validation cohort. (g) AUC of time-dependent ROC curves verified the prognostic accuracy of the risk score in the training cohort. (h) AUC of time-dependent ROC curves verified the prognostic accuracy of the risk score in the validation cohort.

Figure 5

The prognostic values of pyroptosis-related lncRNA signature. (a) Multivariate Cox regression of patient characters and the signature in the whole cohort. (b) The nomogram constructed using patient characters and the signature.

Figure 6

Gene set enrichment analysis (GSEA) about the pyroptosis-related lncRNA prognostic signature. (a) CTLA4 pathway. (b) antigen presentation folding assembly and peptide loading of class I MHC. (c) autoimmune thyroid disease. (d) inflam pathway. (e) antigen processing and presentation. (f) IL5 pathway. (g) cytokines and inflammatory response. (h) TCR signaling. (i) TH1TH2 pathway.

Figure 7

The interactions between pyroptosis-related lncRNA signature and immune regulation in HCC patients. (a) The barplot of the tumor-infiltrating cell proportions. (b) The heatmap of the tumor-infiltrating cell proportions. (c) Correlation matrix of immune cell proportions in the low-risk group. (d) Correlation matrix of immune cell proportions in the high-risk group. (e) Comparisons of immune cell proportions between the low-risk group and the high-risk group. (f) Comparisons of multiple immune checkpoints between the low-risk group and the high-risk group, including PD-1, PD-L1, CTLA4, B7-H3, VSIR, LAG3, TIGIT.