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Series GSE67848 Query DataSets for GSE67848
Status Public on Sep 22, 2016
Title Characterization of Type I Interferon pathway during Hepatic Differentiation of Human Pluripotent Stem Cells and hepatitis C virus infection
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. For long term survival of engrafting cells in the body, not only do the cells have to execute liverspecific function but also withstand the physical strains and invading pathogens. The cellular innate immune system orchestrated by the interferon (IFN) pathway provides the first line of defense against pathogens. The objective of this study is to assess the innate immune function as well as to systematically profile the IFN-induced genes during hepatic differentiation of pluripotent stem cells. To address this objective, we derived endodermal cells (day 5 postdifferentiation), hepatoblast (day 15) and immature hepatocytes (day 21) from human embryonic stem cells (hESC). Day 5, 15 and 21 cells were stimulated with IFN-α and subjected to IFN pathway analysis. Transcriptome analysis was carried out by RNA sequencing. The results showed that the IFN-α treatment activated STAT-JAK pathway in differentiating cells. Transcriptome analysis indicated stage specific expression of classical and non-classical IFNstimulated genes (ISGs). Subsequent validation confirmed the expression of novel ISGs including RASGRP3, CLMP and TRANK1 by differentiated hepatocytes upon IFN treatment. Hepatitis C virus replication in hESC-derived hepatic cells induced the expression of ISGs – LAMP3, ETV7, RASGRP3, and TRANK1. The hESC-derived hepatic cells contain intact innate system and can recognize invading pathogens. Besides assessing the tissue-specific functions for cell therapy applications, it may also be important to test the innate immune function of engrafting cells to ensure adequate defense against infections and improve graft survival.
Overall design 12 samples total, 4 samples in each time point (day 5, day 15, day 21). Each group of 4 within each time point has 2 control and 2 treatment samples in which the cells were stimulated with human interferon-alpha A (R and D Systems) at a concentration of 5000 IU for 6 hours.
Contributor(s) Irudayam JI, Contreras D, Spurka L, Subramanian A, Allen J, Ren S, Kanagavel V, Nguyen Q, Ramaiah A, Ramamoorthy K, French SW, Klein AS, Funari V, Arumugaswami V
Citation(s) 26702414, 26313525
Submission date Apr 14, 2015
Last update date Jul 31, 2019
Contact name Wolf Wiedemeyer
Organization name Cedars-Sinai
Department BMS
Street address 8700 Beverly Blvd.
City Los Angeles
State/province California
ZIP/Postal code 90048
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1657139 day 5 control sample - biological replicate #1
GSM1657140 day 5 control sample - biological replicate #2
GSM1657141 day 5 sample stimulated with human interferon-alpha A - biological replicate #1
BioProject PRJNA281064
SRA SRP057149

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Supplementary file Size Download File type/resource
GSE67848_FPKM_data.txt.gz 1.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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