Prioritization and functional validation of target genes from single-cell transcriptomics studies
Liliana Sokol, Anne Cuypers, Anh-Co Khanh Truong, Ann Bouché, Katleen Brepoels, Joris Souffreau, Kateřina Rohlenová, Stefan Vinckier, Luc Schoonjans, Guy Eelen, Mieke Dewerchin, Laura de Rooij, Peter Carmeliet
Abstract
Translation of academic results into clinical practice is a formidable unmet medical need. Single-cell RNA-sequencing (scRNA-seq) studies generate long descriptive ranks of markers with predicted biological function, but without functional validation, it remains challenging to know which markers truly exert the putative function. Given the lengthy/costly nature of validation studies, gene prioritization is required to select candidates. We address these issues by studying tip endothelial cell (EC) marker genes because of their importance for angiogenesis. Here, by tailoring Guidelines On Target Assessment for Innovative Therapeutics, we in silico prioritize previously unreported/poorly described, high-ranking tip EC markers. Notably, functional validation reveals that four of six candidates behave as tip EC genes. We even discover a tip EC function for a gene lacking in-depth functional annotation. Thus, validating prioritized genes from scRNA-seq studies offers opportunities for identifying targets to be considered for possible translation, but not all top-ranked scRNA-seq markers exert the predicted function.