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Bisogno LS, Yang J, Bennett BD, Ward JM, Mackey LC, Annab LA, Bushel PR, Singhal S, Schurman SH, Byun JS, Nápoles AM, Pérez-Stable EJ, Fargo DC, Gardner K, Archer TK. Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes. SCIENCE ADVANCES 2020; 6:6/47/eabc3851. [PMID: 33219026 PMCID: PMC7679169 DOI: 10.1126/sciadv.abc3851] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/02/2020] [Indexed: 05/10/2023]
Abstract
Induced pluripotent stem cells (iPSCs) can be derived from differentiated cells, enabling the generation of personalized disease models by differentiating patient-derived iPSCs into disease-relevant cell lines. While genetic variability between different iPSC lines affects differentiation potential, how this variability in somatic cells affects pluripotent potential is less understood. We generated and compared transcriptomic data from 72 dermal fibroblast-iPSC pairs with consistent variation in reprogramming efficiency. By considering equal numbers of samples from self-reported African Americans and White Americans, we identified both ancestry-dependent and ancestry-independent transcripts associated with reprogramming efficiency, suggesting that transcriptomic heterogeneity can substantially affect reprogramming. Moreover, reprogramming efficiency-associated genes are involved in diverse dynamic biological processes, including cancer and wound healing, and are predictive of 5-year breast cancer survival in an independent cohort. Candidate genes may provide insight into mechanisms of ancestry-dependent regulation of cell fate transitions and motivate additional studies for improvement of reprogramming.
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Affiliation(s)
- Laura S Bisogno
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jun Yang
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Brian D Bennett
- Integrative Bioinformatics, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - James M Ward
- Integrative Bioinformatics, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Lantz C Mackey
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Lois A Annab
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sandeep Singhal
- Department of Pathology, Department of Computer Science, University of North Dakota, Grand Forks, ND, USA
| | - Shepherd H Schurman
- Clinical Research Unit, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jung S Byun
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Anna María Nápoles
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Eliseo J Pérez-Stable
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - David C Fargo
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Kevin Gardner
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, Columbia University, New York, NY, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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