Identification of novel high-risk genes in gastric cancer through single-cell RNA sequencing, eQTL Mendelian randomization, and in vitro validation

Abstract

Background Current targeted therapies for gastric cancer have limited efficacy, and recently discovered markers have not significantly improved survival rates in patients with gastric cancer. Therefore, it is imperative to identify more specific genes associated with the occurrence and progression of gastric cancer to achieve prevention and treatment. The aim of this study is to discover high-risk genes for gastric cancer by integrating single-cell transcriptomics and Mendelian randomization (MR) analysis.

Methods This study integrates gastric cancer genome-wide association study (GWAS) data, single-cell transcriptomics (sc-RNA-seq), and expression quantitative trait loci (eQTL) data for analysis, and employs two-sample MR to elucidate the causal relationships between genes and gastric cancer, thereby identifying high-risk genes for gastric cancer. Subsequently, in vitro cellular experiments are conducted to validate the transcriptional expression levels of these genes.

Results After quality control of the sc-RNA-seq data, we identified 2463 markers for gastric cancer cell subtypes. Subsequently, we utilized eQTL data and GWAS data for gastric cancer to perform MR analysis, yielding 149 genes with a causal relationship with gastric cancer. By applying log2FC filtering, we ultimately identified 5 high-risk gastric cancer genes: SORBS3, RMND5A, FBXO6, LPGAT1, and EPHB4. Finally, in vitro validation confirmed the differential expression of these 5 high-risk genes between normal gastric epithelial cell lines and gastric cancer cell lines.

Conclusions Our study reveals previously unattended high-risk gastric cancer genes, potentially offering new directions and evidence for the molecular diagnosis and treatment of gastric cancer.

Keywords

Mendelian randomization / Gastric cancer / Sc-RNA-seq

Consent to Publish Declaration

Not applicable.

Ethics approval and consent to participate

Not applicable.

Funding

This work was supported by the National Natural Science Foundation of China (No. 82405293), the Natural Science Foundation of Beijing (No.7232281), the Hebei Province Traditional Chinese Medicine Administration Scientific Research Program (No. 2024012), the Beijing University of Chinese Medicine Basic Scientific Research Business Fund Jie-Bang-Gua-Shuai Project (No. 2025-JYB-JBGS-001) and Hebei Province Graduate Student Innovative Capacity Building Grant Program (No. CXZZBS2025171).

Data Availability

The genome-wide association study (GWAS) data for gastric cancer utilized in this study were sourced from BioBank Japan. The whole-blood eQTL data were obtained from the eQTLGen Consortium (www.eQTLgen.org). The eQTL data are publicly available through the eQTLGen Consortium website, and interested researchers can access the data by following the consortium's data usage guidelines. The single-cell RNA sequencing (sc-RNA-seq) data were derived from the GSE183904 dataset in the Gene Expression Omnibus (GEO) public database. In summary, the data used in this study are available through the respective sources mentioned above, subject to the data access and usage policies of each repository. The data supporting the findings of this study are available from the corresponding author.

Conflict of Interest

The authors declare that they have no competing interests.

Acknowledgments

We would like to acknowledge the essential contributions of all staff and students who participated in this work.

Appendix A. Supplementary material

Supplementary data associated with this article can be found in the online version at doi:10.1016/j.gmg.2025.100077.

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