Long Non-coding RNA Expression Patterns in Stomach Adenocarcinoma Serve as an Indicator of Tumor Mutation Burden and Are Associated With Tumor-Infiltrating Lymphocytes and Microsatellite Instability

Abstract

Long non-coding RNAs (lncRNAs) are crucial in controlling important aspects of tumor immunity. However, whether the expression pattern of lncRNAs in stomach adenocarcinoma (STAD) reflects tumor immunity is not fully understood. We screened differentially expressed lncRNAs (DElncRNAs) between high and low tumor mutation burden (TMB) STAD samples. Using the least absolute shrinkage and selection operator method, 33 DElncRNAs were chosen to establish a lncRNA-based signature classifier for predicting TMB levels. The accuracy of the 33-lncRNA-based signature classifier was 0.970 in the training set and 0.950 in the test set, suggesting the expression patterns of the 33 lncRNAs may be an indicator of TMB in STAD. Survival analysis showed that a lower classifier index reflected better prognosis for STAD patients, and the index showed correlation with expression of immune checkpoint molecules (PD1, PDL1, and CTLA4), tumor-infiltrating lymphocytes, and microsatellite instability. In conclusion, STAD samples with different tumor mutation burdens have different lncRNA expression patterns. The 33-lncRNA-based signature classifier index may be an indicator of TMB and is associated expression of immune checkpoints, tumor-infiltrating lymphocytes, and microsatellite instability.

Keywords: immune checkpoint molecules; lncRNAs; stomach adenocarcinoma; the Cancer Genome Atlas; tumor immunity.

FIGURE 1

The workflow of this study. TMB, tumor mutational burden; TCGA, the cancer genome atlas; STAD, stomach adenocarcinoma; lncRNA, long non-coding RNA; LASSO, least absolute shrinkage and selection operator; ICI, immune checkpoint inhibitor; TILs, tumor-infiltrating lymphocytes.

FIGURE 2

Differentially expressed long non-coding RNAs (DElncRNAs) between stomach adenocarcinoma (STAD) samples with high and low tumor mutation burden (TMB). (A) Volcano plot showing DElncRNAs. Red points represent up-regulated; blue points represent down-regulated RNAs; and black points represent no significant difference. (B) The expression pattern of DElncRNAs can basically distinguish the level of TMB in STAD.

FIGURE 3

Least absolute shrinkage and selection operator (LASSO) and receiver operating characteristic curve analysis. (A) 10-fold cross-validation for tuning parameter selection in the LASSO model. (B) Scatter plot of the first and second principal components. (C) Receiver operating characteristic curve analysis in the training set. (D) Receiver operating characteristic curve analysis in the test set. AUC, area under the curve.

FIGURE 4

Kaplan–Meier curves and gene set enrichment analysis. (A) Kaplan–Meier curves of overall survival in the high- and low-index groups. (B) Kaplan–Meier curves of relapse-free survival in the high- and low-index groups. (C) Top 5 significant biological processes enriched in samples with a high value of the 33-lncRNAs-based classifier index. (D) Top 5 significant biological processes enriched in samples with a low value of the 33-lncRNAs-based classifier index. (E) Top 5 significant KEGG pathways enriched in samples with a high value of the 33-lncRNAs-based classifier index. (F) Top 5 significant KEGG pathways enriched in samples with a low value of the 33-lncRNAs-based classifier index.

FIGURE 5

Correlation of the 33-lncRNA-based signature index with expression of ICIs index (CD274, CTLA4 and PDCD1) and TMB. (A) Correlation of the 33-lncRNA-based signature index with expression of CD274. (B) Correlation of the 33-lncRNA-based signature index with expression of CTLA4. (C) Correlation of the 33-lncRNA-based signature index with expression of PDCD1. (D) Correlation of the 33-lncRNA-based signature index with expression of TMB.

FIGURE 6

The associations between the 33-lncRNA-based classifier index and tumor infiltrating lymphocytes, and microsatellite status. (A) The correlations between the 33-lncRNA-based classifier index and tumor-infiltrating lymphocytes. (B) The 33-lncRNA-based classifier index in patients with different microsatellite status.