Integrating single-cell analysis and machine learning to create glycosylation-based gene signature for prognostic prediction of uveal melanoma

BackgroundIncreasing evidence suggests a correlation between glycosylation and the onset of cancer. However, the clinical relevance of glycosylation-related genes (GRGs) in uveal melanoma (UM) is yet to be fully understood. This study aimed to shed light on the impact of GRGs on UM prognosis. MethodsTo identify the most influential genes in UM, we employed the AUCell and WGCNA algorithms. The GRGs signature was established by integrating bulk RNA-seq and scRNA-seq data. UM patients were separated into two groups based on their risk scores, the GCNS_low and GCNS_high groups, and the differences in clinicopathological correlation, functional enrichment, immune response, mutational burden, and immunotherapy between the two groups were examined. The role of the critical gene AUP1 in UM was validated through in vitro and in vivo experiments. ResultsThe GRGs signature was comprised of AUP1, HNMT, PARP8, ARC, ALG5, AKAP13, and ISG20. The GCNS was a significant prognostic factor for UM, and high GCNS correlated with poorer outcomes. Patients with high GCNS displayed heightened immune-related characteristics, such as immune cell infiltration and immune scores. In vitro experiments showed that the knockdown of AUP1 led to a drastic reduction in the viability, proliferation, and invasion capability of UM cells. ConclusionOur gene signature provides an independent predictor of UM patient survival and represents a starting point for further investigation of GRGs in UM. It offers a novel perspective on the clinical diagnosis and treatment of UM.

Automated summary

This study aimed to investigate the impact of glycosylation-related genes (GRGs) on the prognosis of uveal melanoma (UM). By integrating multiple omics data, a gene signature comprising seven key genes was established as a predictor for UM patient survival. The high gene signature score was associated with poorer prognosis and enhanced immune-related characteristics. In vitro experiments validated the role of one critical gene, AUP1, in UM. The study highlights the importance of exploring GRGs in UM for clinical diagnosis and treatment.