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Analysis of differentially expressed genes among human hair follicle-derived iPSCs, induced hepatocyte-like cells, and primary hepatocytes.

ABSTRACT: BACKGROUND:Differentiation of human induced pluripotent stem cells (hiPSCs) into hepatocytes has important clinical significance in providing a new stem cell source for cell therapy of terminal liver disease. The differential gene expression analysis of hiPSCs, induced hepatocyte-like cells (HLCs), and primary human hepatocytes (PHHs) provides valuable information for optimization of an induction scheme and exploration of differentiation mechanisms. METHODS:Human hair follicle-derived iPSCs (hHF-iPSCs) were induced in vitro by mimicking the environment of a developing liver for 19 days. Expression of specific proteins was determined by immunofluorescence staining; the function of HLCs in storage and metabolism was identified by detecting periodic acid-Schiff, indocyanine green, and low-density lipoprotein. Based on the transcriptomics data, the differential gene expression profiles of hHF-iPSCs, HLCs, and PHHs were analyzed by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, FunRich, and network analysis methods. RESULTS:HLCs were able to express albumin (ALB), alpha-fetoprotein, CYP3A4, and CYP7A1, and exhibited matured liver cell functions such as glycogen synthesis and storage. Complement and coagulation cascades and metabolic pathways ranked top in the downregulated list of HLCs/PHHs, while the cell cycle ranked top in the upregulated list of HLCs/PHHs. In the protein-protein interaction network, according to the degree rankings, TOP2A, CDK1, etc. were the important upregulated differentially expressed genes (DEGs), while ALB, ACACB, etc. were the major downregulated DEGs in HLCs/PHHs; the module analysis indicated that CDCA8, AURKB, and AURKA were the top upregulated DEGs in HLCs/PHHs. CONCLUSIONS:We presented the differences in gene expression among hHF-iPSCs, HLCs, and PHHs through transcriptome array data and provided new ideas for the optimization of induction.

SUBMITTER: Xu Z

PROVIDER: S-EPMC6085644 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Analysis of differentially expressed genes among human hair follicle-derived iPSCs, induced hepatocyte-like cells, and primary hepatocytes.

Xu Ziran Z He Xia X Shi Xu X Xia Yuhan Y Liu Xiaomei X Wu Haitao H Li Pengdong P Zhang Hongyu H Yin Weisi W Du Xiubo X Li Lisha L Li Yulin Y

Stem cell research & therapy 20180809 1

<h4>Background</h4>Differentiation of human induced pluripotent stem cells (hiPSCs) into hepatocytes has important clinical significance in providing a new stem cell source for cell therapy of terminal liver disease. The differential gene expression analysis of hiPSCs, induced hepatocyte-like cells (HLCs), and primary human hepatocytes (PHHs) provides valuable information for optimization of an induction scheme and exploration of differentiation mechanisms.<h4>Methods</h4>Human hair follicle-der ...[more]

PMID: 30092828

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Project description:Simple Summary Wool fiber diameter (WFD) is one of the most important economic traits of wool, especially in Angora rabbits. Emerging studies have been conducted on sheep and goats. However, few studies of WFD have been reported in rabbits. In our study, the diameter of coarse and fine wool and their respective hair follicles in Wan strain Angora rabbits were analyzed, and it was found that the diameter of coarse wool and hair follicles was larger than that of fine wool and hair follicles. High-throughput sequencing analysis was performed using hair follicles from coarse and fine wool. Differentially expressed genes (DEGs), including transcription factors, keratin-associated protein (KAP) and keratin (KRT) families, and extracellular matrix (ECM)-related genes, were screened. Enrichment analysis showed that skin development, epidermal cell and keratinocyte differentiation, epithelium development, and Notch and ribosome signaling pathways were important in regulating hair structure. Gene set enrichment analysis (GSEA) and protein–protein interaction (PPI) analysis further identified six important signaling pathways and functional DEGs, including LEF1, FZD3, SMAD3, ITGB6, and BMP4. The results provide valuable data for screening molecular markers involved in hair structure and facilitating enhanced selection of super-fine wool rabbits through gene-assisted selection. Abstract Wool fiber diameter (WFD) is an important index of wool traits and the main determinant of wool quality and value. However, the genetic determinants of fiber diameter have not yet been fully elucidated. Here, coarse and fine wool of Wan strain Angora rabbits and their hair follicle traits were characterized. The results indicated significant differences in the diameters of wool fibers and their hair follicles. The RNA sequencing (RNA-Seq) technique was used to identify differences in gene expression in hair follicles between coarse and fine wool. In total, 2574 differentially expressed genes (DEGs) were found between the two hair follicle groups. Transcription factors, keratin-associated protein (KAP) and keratin (KRT) families, and ECM-related genes may control the structure of fine fibers in rabbits. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that skin development, epidermal cell and keratinocyte differentiation, epithelium development, and Notch and ribosome signaling pathways were significantly enriched, respectively. GSEA further filtered six important pathways and related core genes. PPI analysis also mined functional DEGs associated with hair structure, including LEF1, FZD3, SMAD3, ITGB6, and BMP4. Our findings provide valuable information for researching the molecular mechanisms regulating wool fiber and could facilitate enhanced selection of super-fine wool rabbits through gene-assisted selection in the future.

Dataset Information

Analysis of differentially expressed genes among human hair follicle-derived iPSCs, induced hepatocyte-like cells, and primary hepatocytes.

Publications

Analysis of differentially expressed genes among human hair follicle-derived iPSCs, induced hepatocyte-like cells, and primary hepatocytes.

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