A workflow integrating R/Bioconductor, GSEA, and TIMER 2.0 to explore the role of the Vav protein family in cutaneous melanoma

ÁVILA, AYLEN; ANSELMINO, LUICANO; CESATTI LALUCE, NAHUEL; MAMBERTO, MACARENA; ZANOTTI, LUCIA; MALIZIA, FLORENCIA; MENACHO MÁRQUEZ, MAURICIO

Congreso; XIII CAB2C, XIII SoIBio, III RiaBio - 2023; 2023

Background:Vav proteins are RHO guanine nucleotide exchange factors (GEFs), comprising three members known for their functional redundancy and proactive roles in cancer. However, their involvement in melanoma remains largely unexplored.Objective:Our aim was to establish a systematic approach, leveraging bioinformatic techniques, to probe the role of each Vav family member in melanoma.Methodology:Gene expression data from cutaneous melanoma patients were sourced from the 'Cancer Genome Atlas' database. Raw counts were normalized to counts per million (CPM) using the 'edgeR' package. The patient cohort (n=460) was stratified based on high or low expression levels of VAV1, VAV2, and VAV3. Survival analysis was performed using the Kaplan-Meier estimator and the 'survminer' package. The log-rank test uncovered an association between high VAV2 expression and poorer prognosis, while elevated VAV1 and VAV3 expressions correlated with increased patient survival probability (p<0.05 in each case).Results:Gene set enrichment analysis was conducted for each comparison group using GSEA software. Immune Score and Microenvironment Score, reflecting immune and stromal cell infiltration in tumor tissues, were calculated based on gene expression profiles employing the ESTIMATE and xCell algorithms. Both Scores exhibited a strong and positive association with VAV1 and VAV3 expressions (p<0.001). Using eight different algorithms and the 'estimate' package along with the TIMER2.0 application, correlation with various cell types was evaluated. A robust positive correlation was identified between VAV1 expression and certain immune cell signatures (p<0.001), whereas no significant correlation was observed between VAV2 or VAV3 expression and cell types.Conclusion:Our findings suggest that a favorable prognosis in melanoma is linked to elevated expressions of VAV1 and VAV3, coupled with reduced VAV2 expression. This favorable prognosis may arise from Vav1's impact on intercellular communication within the tumor microenvironment, while heightened VAV3 expression could regulate the activation of tumor cell signaling pathways, thereby promoting greater immunogenicity.Significance:This study presents a comprehensive pipeline that could serve to explore the implications of other proteins in diverse diseases.