DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion.

ABSTRACT:

Motivation

Direct reprogramming (DR) is a process that directly converts somatic cells to target cells. Although DR via small molecules is safer than using transcription factors (TFs) in terms of avoidance of tumorigenic risk, the determination of DR-inducing small molecules is challenging.

Results

Here we present a novel in silico method, DIRECTEUR, to predict small molecules that replace TFs for DR. We extracted DR-characteristic genes using transcriptome profiles of cells in which DR was induced by TFs, and performed a variant of simulated annealing to explore small molecule combinations with similar gene expression patterns with DR-inducing TFs. We applied DIRECTEUR to predicting combinations of small molecules that convert fibroblasts into neurons or cardiomyocytes, and

SUBMITTER: Hamano M 

PROVIDER: S-EPMC10868337 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature