Identification of m7G-Related LncRNA Signature for Predicting Prognosis and Evaluating Tumor Immune Infiltration in Pancreatic Adenocarcinoma

Abstract

N7-Methylguanosine (m7G) modification holds significant importance in regulating posttranscriptional gene expression in epigenetics. Long non-coding RNAs (lncRNAs) have been demonstrated to play a crucial role in cancer progression. m7G-related lncRNA may be involved in the progression of pancreatic cancer (PC), although the underlying mechanism of regulation remains obscure. We obtained RNA sequence transcriptome data and relevant clinical information from the TCGA and GTEx databases. Univariate and multivariate Cox proportional risk analyses were performed to build a twelve-m7G-associated lncRNA risk model with prognostic value. The model was verified using receiver operating characteristic curve analysis and Kaplan-Meier analysis. The expression level of m7G-related lncRNAs in vitro was validated. Knockdown of SNHG8 increased the proliferation and migration of PC cells. Differentially expressed genes between high- and low-risk groups were identified for gene set enrichment analysis, immune infiltration, and potential drug exploration. We conducted an m7G-related lncRNA predictive risk model for PC patients. The model had independent prognostic significance and offered an exact survival prediction. The research provided us with better knowledge of the regulation of tumor-infiltrating lymphocytes in PC. The m7G-related lncRNA risk model may serve as a precise prognostic tool and indicate prospective therapeutic targets for PC patients.

Keywords: immune infiltration; lncRNA; m7G; overall survival; pancreatic adenocarcinoma; prognostic signature.

Figure 1

The flowchart of this study.

Figure 2

Correlations between m7G-related genes. (a) Heatmap depicting the differences in m7G-related genes expression between T and N groups. N, normal samples; T, tumor samples. (b,c) Network of protein–protein interactions illustrating the relationships between differentially expressed m7G-related genes. (d) Pearson correlation analysis of the m7G-related genes.

Figure 3

Construction of the m7G-related lncRNAs risk model. (a,b) Coexpression network of m7G-related lncRNAs−mRNAs. (c) Heatmap indicated the different expression of m7G-related lncRNAs in low- and high-risk groups. (d) Kaplan−Meier survival subgroup analysis for overall survival in high- and low-risk scores group (p < 0.001). (e,f) Risk score distribution based on the prognostic signature of m7G-related lncRNAs and survival status in patients with PC.

Figure 4

The association between the expression of m7G−LPS and clinicopathological factors. (a) Overall survival analysis of the 12 m7G-related lncRNAs between high- and low-risk groups. (b) Heatmap displaying the relationship between clinicopathological characteristics and different expressed m7G-related lncRNAs. (c) Box plot showing the different expression of 12 m7G-related lncRNAs in T, N, S, and G stage groups. * p < 0.5, ** p < 0.01, and *** p < 0.001. ns, no significant.

Figure 5

Verification of the model and establishment of a nomogram. (a–d) Principal component analysis was performed for the low- and high-risk groups based on the entire genes, m7G-related genes, m7G-related lncRNAs, and risk model lncRNAs. (e) ROC curves of the clinical characteristics and risk score. (f) The nomogram predicts the probability of overall survival at 1, 3, and 5 years.

Figure 6

Functional enrichment analysis based on the m7G−LPS. (a) Gene set enrichment analysis shows seven significant enrichments of GO in the high-risk group. (b–e) The barplot and bubble chart illustrate the GO enrichment analysis among the differentially expressed genes.

Figure 7

Immune landscape associated with the m7G-related lncRNA signature. (a) Heatmap of tumor−infiltrating immune cells in high- and low-risk groups. (b) Bubble graphic illustrating the correlation between risk score and immune cells. (c) Spearman correlation analysis of 21 tumor−infiltrating immune cells. (d) Violin plot showing the distribution of immune cells in high- and low-groups.

Figure 8

Half maximal inhibitory concentration (IC50) of drugs (docetaxel, paclitaxel, erlotinib, AKT inhibitor VIII, camptothecin, and etoposide) in low- and high-risk groups. * p < 0.5 and *** p < 0.001.

Figure 9

In vitro functional verification in PC cells. (a) Expression level of m7G-related lncRNAs in HPDE6-c7 cells and PC cells. (b,c) The proliferation ability of PC cell lines was detected by CCK-8 and EdU assays after SNHG8 knockdown. (d,e) Wound healing and Transwell assays were used to determine the migration capacities of PC cell lines after SNHG8 knockdown. * p < 0.5, ** p < 0.01, *** p < 0.001, and **** p < 0.0001.