Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids

Jong-Hwan Kim; Seon Ju Mun; Jeong-Hwan Kim; Myung Jin Son; Seon-Young Kim

doi:10.1016/j.isci.2023.107675

Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids

iScience. 2023 Aug 18;26(9):107675. doi: 10.1016/j.isci.2023.107675. eCollection 2023 Sep 15.

Authors

Jong-Hwan Kim¹, Seon Ju Mun^{2

3}, Jeong-Hwan Kim⁴, Myung Jin Son^{2

3

5}, Seon-Young Kim^{1

4

3}

Affiliations

¹ Korean Bioinformation Center, Daejeon, Korea.
² Stem Cell Convergence Research Center, Daejeon, Korea.
³ Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea.
⁴ Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
⁵ School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.

Abstract

To gain deeper insights into transcriptomes and epigenomes of organoids, liver organoids from two states (expandable and more differentiated) were subjected to single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) analyses. Mitochondrial gene expression was higher in differentiated than in non-differentiated hepatocytes, with ATAC-seq peaks increasing near the mitochondrial control region. Differentiation of liver organoids resulted in the expression of transcription factors that act as enhancers and repressors. In addition, epigenetic mechanisms regulating the expression of alpha-fetoprotein (AFP) and albumin (ALB) differed in liver organoids and adult liver. Knockdown of PDX1, an essential transcription factor for pancreas development, led to the hepatic maturation of liver organoids through regulation of AFP and ALB expression. This integrative analysis of the transcriptomes and epigenomes of liver organoids at the single-cell level may contribute to a better understanding of the regulatory networks during liver development and the further development of mature in vitro human liver models.

Keywords: Experimental models in systems biology; Integrative aspects of cell biology; Molecular mechanism of gene regulation; Transcriptomics.