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| 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
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| 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.
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| 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.
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| 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
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| Department |
BMS
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| Street address |
8700 Beverly Blvd.
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90048 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| 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 |
| GSM1657142 |
day 5 sample stimulated with human interferon-alpha A - biological replicate #2 |
| GSM1657143 |
day 15 control sample - biological replicate #1 |
| GSM1657144 |
day 15 control sample - biological replicate #2 |
| GSM1657145 |
day 15 sample stimulated with human interferon-alpha A - biological replicate #1 |
| GSM1657146 |
day 15 sample stimulated with human interferon-alpha A - biological replicate #2 |
| GSM1657147 |
day 21 control sample - biological replicate #1 |
| GSM1657148 |
day 21 control sample - biological replicate #2 |
| GSM1657149 |
day 21 sample stimulated with human interferon-alpha A - biological replicate #1 |
| GSM1657150 |
day 21 sample stimulated with human interferon-alpha A - biological replicate #2 |
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| Relations |
| BioProject |
PRJNA281064 |
| SRA |
SRP057149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67848_FPKM_data.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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