Co-expression networks in generation of induced pluripotent stem cells
We developed an adenoviral vector, in which Yamanaka's four reprogramming factors (RFs) were controlled by individual CMV promoters in a single cassette (Ad-SOcMK). This permitted coordinated expression of RFs (SOX2, OCT3/4, c-MYC and KLF4) in a cell for a transient period of time, synchronizin...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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The Company of Biologists
2016-03-01
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| Series: | Biology Open |
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| Online Access: | http://bio.biologists.org/content/5/3/300 |
| _version_ | 1818440100230463488 |
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| author | Sharan Paul Lance Pflieger Warunee Dansithong Karla P. Figueroa Fuying Gao Giovanni Coppola Stefan M. Pulst |
| author_facet | Sharan Paul Lance Pflieger Warunee Dansithong Karla P. Figueroa Fuying Gao Giovanni Coppola Stefan M. Pulst |
| author_sort | Sharan Paul |
| collection | DOAJ |
| description | We developed an adenoviral vector, in which Yamanaka's four reprogramming factors (RFs) were controlled by individual CMV promoters in a single cassette (Ad-SOcMK). This permitted coordinated expression of RFs (SOX2, OCT3/4, c-MYC and KLF4) in a cell for a transient period of time, synchronizing the reprogramming process with the majority of transduced cells assuming induced pluripotent stem cell (iPSC)-like characteristics as early as three days post-transduction. These reprogrammed cells resembled human embryonic stem cells (ESCs) with regard to morphology, biomarker expression, and could be differentiated into cells of the germ layers in vitro and in vivo. These iPSC-like cells, however, failed to expand into larger iPSC colonies. The short and synchronized reprogramming process allowed us to study global transcription changes within short time intervals. Weighted gene co-expression network analysis (WGCNA) identified sixteen large gene co-expression modules, each including members of gene ontology categories involved in cell differentiation and development. In particular, the brown module contained a significant number of ESC marker genes, whereas the turquoise module contained cell-cycle-related genes that were downregulated in contrast to upregulation in human ESCs. Strong coordinated expression of all four RFs via adenoviral transduction may constrain stochastic processes and lead to silencing of genes important for cellular proliferation. |
| first_indexed | 2024-12-14T18:06:59Z |
| format | Article |
| id | doaj.art-c65c1114de0c4010a5dfdc8c2dae2b27 |
| institution | Directory Open Access Journal |
| issn | 2046-6390 |
| language | English |
| last_indexed | 2024-12-14T18:06:59Z |
| publishDate | 2016-03-01 |
| publisher | The Company of Biologists |
| record_format | Article |
| series | Biology Open |
| spelling | doaj.art-c65c1114de0c4010a5dfdc8c2dae2b272022-12-21T22:52:22ZengThe Company of BiologistsBiology Open2046-63902016-03-015330031010.1242/bio.016402016402Co-expression networks in generation of induced pluripotent stem cellsSharan Paul0Lance Pflieger1Warunee Dansithong2Karla P. Figueroa3Fuying Gao4Giovanni Coppola5Stefan M. Pulst6 Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA We developed an adenoviral vector, in which Yamanaka's four reprogramming factors (RFs) were controlled by individual CMV promoters in a single cassette (Ad-SOcMK). This permitted coordinated expression of RFs (SOX2, OCT3/4, c-MYC and KLF4) in a cell for a transient period of time, synchronizing the reprogramming process with the majority of transduced cells assuming induced pluripotent stem cell (iPSC)-like characteristics as early as three days post-transduction. These reprogrammed cells resembled human embryonic stem cells (ESCs) with regard to morphology, biomarker expression, and could be differentiated into cells of the germ layers in vitro and in vivo. These iPSC-like cells, however, failed to expand into larger iPSC colonies. The short and synchronized reprogramming process allowed us to study global transcription changes within short time intervals. Weighted gene co-expression network analysis (WGCNA) identified sixteen large gene co-expression modules, each including members of gene ontology categories involved in cell differentiation and development. In particular, the brown module contained a significant number of ESC marker genes, whereas the turquoise module contained cell-cycle-related genes that were downregulated in contrast to upregulation in human ESCs. Strong coordinated expression of all four RFs via adenoviral transduction may constrain stochastic processes and lead to silencing of genes important for cellular proliferation.http://bio.biologists.org/content/5/3/300Adenoviral deliveryGene expressionReprogrammingiPSC |
| spellingShingle | Sharan Paul Lance Pflieger Warunee Dansithong Karla P. Figueroa Fuying Gao Giovanni Coppola Stefan M. Pulst Co-expression networks in generation of induced pluripotent stem cells Biology Open Adenoviral delivery Gene expression Reprogramming iPSC |
| title | Co-expression networks in generation of induced pluripotent stem cells |
| title_full | Co-expression networks in generation of induced pluripotent stem cells |
| title_fullStr | Co-expression networks in generation of induced pluripotent stem cells |
| title_full_unstemmed | Co-expression networks in generation of induced pluripotent stem cells |
| title_short | Co-expression networks in generation of induced pluripotent stem cells |
| title_sort | co expression networks in generation of induced pluripotent stem cells |
| topic | Adenoviral delivery Gene expression Reprogramming iPSC |
| url | http://bio.biologists.org/content/5/3/300 |
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