Transcriptomic Profile of Directed Differentiation of iPSCs into Hepatocyte-like Cells

The aim of this study was to comprehensively characterize gene expression changes at each differentiation stage and compare them with reference human liver total RNA gene expression data at final differentiation stages. To thoroughly evaluate protocol efficiency, we performed whole-genome transcriptomic analysis (RNA-seq) at all differentiation stages in both 2D and 3D cultures, including comparative analysis of gene expression profiles between distinct differentiation stages and with reference human liver RNA sequencing data at final stages. The study utilized iPSC lines generated at the Research Centre for Medical Genetics (Russia, Moscow) from two healthy donors and three patients with rare genetic disorders: glycogen storage disease type 1a (OMIM #232200), mucopolysaccharidosis type IVB (OMIM #253010), and type VI (OMIM #253200). Transcriptomic analysis at each differentiation stage enabled the identification of key differentiation points, determination of marker genes for quality control, and monitoring of dynamic gene expression changes in gene expression profiles. The resulting model demonstrated high reproducibility across different cell lines and matched the expected transcriptomic expression patterns at all differentiation stages.