Integrative eQTL and Mendelian randomization analysis reveals key genetic markers in mesothelioma

Abstract

Background: Mesothelioma is a rare cancer that originates from the pleura and peritoneum, with its incidence increasing due to asbestos exposure. Patients are frequently diagnosed at advanced stages, resulting in poor survival rates. Therefore, the identification of molecular markers for early detection and diagnosis is essential.

Methods: Three mesothelioma datasets were downloaded from the GEO database for differential gene expression analysis. Instrumental variables (IVs) were identified based on expression quantitative trait locus (eQTL) data for Mendelian randomization (MR) analysis using mesothelioma Genome-Wide Association Study (GWAS) data from the FINNGEN database. The intersecting genes from MR-identified risk genes and differentially expressed genes were identified as key co-expressed genes for mesothelioma. Functional enrichment analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA), as well as immune cell correlation analysis, were performed to elucidate the roles of key genes in mesothelioma. Additionally, the differential expression of key genes in mesothelioma was validated in independent GEO datasets and TCGA datasets. This integrative research combining multiple databases and analytical methods established a robust model for identifying mesothelioma risk genes.

Results: The research conducted in our study identified 1608 genes that were expressed differentially in mesothelioma GEO datasets. By combining these genes with 192 genes from MR analysis, we identified 14 key genes. Notably, MPZL1, SOAT1, TACC3, and CYBRD1 are linked to a high risk of mesothelioma, while TGFBR3, NDRG2, EPAS1, CPA3, MNDA, PRKCD, MTUS1, ALOX15, LRRN3, and ITGAM are associated with a lower risk. These genes were found to be enriched in pathways associated with superoxide metabolism, cell cycle regulation, and proteasome function, all of which are linked to the development of mesothelioma. Noteworthy observations included a significant infiltration of M1 macrophages and CD4 + T cells in mesothelioma, with genes SOAT1, MNDA, and ITGAM showing a positive correlation with the level of M1 macrophage infiltration. Furthermore, the differential expression analyses conducted on the GEO validation set and TCGA data confirmed the significance of the identified key genes.

Conclusion: This integrative eQTL and Mendelian randomization analysis provides evidence of a positive causal association between 14 key co-expressed genes and mesothelioma genetically. These disease critical genes are implicated in correlations with biological processes and infiltrated immune cells related to mesothelioma. Moreover, our study lays a theoretical foundation for further research into the mechanisms of mesothelioma and potential clinical applications.

Keywords: Biomarkers; Mendelian randomization; Mesothelioma; Tumor immunity; eQTL localization.

Fig. 1

Workflow diagram of this study

Fig. 2

Batch correction and variance analysis. (A) Before the batch correction. (B) After the batch correction. (C) Volcano plot of differential expression genes. (D) Heatmap of differential expression genes

Fig. 3

Screening and localization of critical genes. (A) Disease upregulated DEGs are intersected with genes with OR values greater than one in the MR results. (B) Disease downregulated DEGs are intersected with genes with OR values less than one in the MR results. (C) Position of disease-critical genes on human chromosomes

Fig. 4

Disease critical genes causally associated with mesothelioma

Fig. 5

Scatterplot of MR analysis of the association between mesothelioma critical genes and mesothelioma. (A) Scatterplot of MR analysis of ALOX15. (B) Scatterplot of MR analysis of CPA3. (C) Scatterplot of MR analysis of CYBRD1. (D) Scatterplot of MR analysis of EPAS1. (E) Scatterplot of MR analysis of ITGAM. (F) Scatterplot of MR analysis of LRRN3. (G) Scatterplot of MR analysis of MNDA. (H) Scatterplot of MR analysis of MPZL1. (I) Scatterplot of MR analysis of MTUS1. (J) Scatterplot of MR analysis of NDRG2. (K) Scatterplot of MR analysis of PRKCD. (L) Scatterplot of MR analysis of SOAT1. (M) Scatterplot of MR analysis of TACC3. (N) Scatterplot of MR analysis of TGFBR3

Fig. 6

Expression validation of disease critical genes in GEO testing group and TCGA database. (A) GEO testing group, (B) TCGA database. *P < 0.05, **P < 0.01, ***P < 0.001. TCGA: The Cancer Genome Atlas. GEO: Gene Expression Omnibus.

Fig. 7

Functional enrichment analysis of critical genes. (A) GO enrichment analysis of mesothelioma critical genes. (B) KEGG enrichment analysis of mesothelioma critical genes

Fig. 8

GSEA enrichment analysis of disease critical genes in mesothelioma. (A) GSEA enrichment results of ALOX15 high expression group. (B) GSEA enrichment results of CPA3 high expression group. (C) GSEA enrichment results of CYBRD1 high expression group. (D) GSEA enrichment results of EPAS1 high expression group. (E) GSEA enrichment results of ITGAM high expression group. (F) GSEA enrichment results of LRRN3 high expression group. (G) GSEA enrichment results of MNDA high expression group. (H) GSEA enrichment results of MPZL1 high expression group. (I) GSEA enrichment results of MTUS1 high expression group. (J) GSEA enrichment results of NDRG2 high expression group. (K) GSEA enrichment results of PRKCD high expression group. (L) GSEA enrichment results of SOAT1 high expression group. (M) GSEA enrichment results of TACC3 high expression group. (N) GSEA enrichment results of TGFBR3 high expression group

Fig. 9

GSEA enrichment analysis of disease critical genes in mesothelioma. (A) GSEA enrichment results of ALOX15 low expression group. (B) GSEA enrichment results of CPA3 low expression group. (C) GSEA enrichment results of CYBRD1 low expression group. (D) GSEA enrichment results of EPAS1 low expression group. (E) GSEA enrichment results of ITGAM low expression group. (F) GSEA enrichment results of LRRN3 low expression group. (G) GSEA enrichment results of MNDA low expression group. (H) GSEA enrichment results of MPZL1 low expression group. (I) GSEA enrichment results of MTUS1 low expression group. (J) GSEA enrichment results of NDRG2 low expression group. (K) GSEA enrichment results of PRKCD low expression group. (L) GSEA enrichment results of SOAT1 low expression group. (M) GSEA enrichment results of TACC3 low expression group. (N) GSEA enrichment results of TGFBR3 low expression group

Fig. 10

Immune infiltration analyses, correlations between disease critical genes and infiltrating immune cell types. (A) Stacked histogram of the proportions of immune infiltration cells between control and mesothelioma groups. (B) Box plot of the infiltration level of immune cells between control and mesothelioma groups. (C) Correlation analysis between disease critical genes and infiltrated immune cells. *P < 0.05, **P < 0.01