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Prioritization and functional validation of target genes from single-cell transcriptomics studies.

Liliana Sokol1, Anne Cuypers1, Anh-Co K Truong1

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Summary

Prioritizing candidate genes from single-cell RNA sequencing (scRNA-seq) studies is crucial for translating research into clinical practice. Functional validation confirmed four of six prioritized tip endothelial cell markers, highlighting a pathway for therapeutic target discovery.

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Area of Science:

  • Biomedical research
  • Molecular biology
  • Translational medicine

Background:

  • Translating academic findings into clinical practice remains a significant challenge in medicine.
  • Single-cell RNA sequencing (scRNA-seq) generates extensive lists of potential functional markers, but functional validation is often lacking.
  • Prioritizing candidate genes is essential due to the time and cost associated with validation studies.

Purpose of the Study:

  • To develop a method for in silico prioritization of novel or poorly characterized tip endothelial cell (EC) marker genes.
  • To identify high-ranking tip EC markers from scRNA-seq data for functional validation.
  • To assess the potential of prioritized genes for therapeutic target discovery in angiogenesis.

Main Methods:

  • Tailoring the Guidelines On Target Assessment for Innovative Therapeutics (GOFAI) framework for gene prioritization.
  • In silico prioritization of tip EC marker genes identified through scRNA-seq.
  • Functional validation of selected candidate genes in endothelial cells.

Main Results:

  • Six high-ranking, previously unreported or poorly described tip EC marker candidates were prioritized.
  • Functional validation confirmed that four of the six prioritized candidates indeed function as tip EC genes.
  • A novel tip EC function was identified for a gene with limited prior annotation.

Conclusions:

  • In silico prioritization of scRNA-seq data, guided by established assessment frameworks, can effectively identify functionally relevant genes.
  • Validated tip EC markers derived from scRNA-seq offer promising avenues for therapeutic target identification.
  • Not all top-ranked markers from scRNA-seq studies necessarily perform their predicted functions, underscoring the need for rigorous validation.