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Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Friedrich Ben-Nun I, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. eLife 2015; 4:e07103. [PMID: 26102527 PMCID: PMC4502404 DOI: 10.7554/elife.07103] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/22/2015] [Indexed: 12/20/2022] Open
Abstract
Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude. DOI:http://dx.doi.org/10.7554/eLife.07103.001 Comparing the genomes of different species can reveal how they are related to one another. Such comparative studies can also reveal how genomes are modified in species-specific ways to regulate gene activity. The genomes of humans and chimpanzees are very similar in sequence. It is therefore likely that differing patterns of gene regulation underlie many of the differences observed between the two species. However, only a few kinds of chimpanzee cell that can be grown in the laboratory are available for research; this lack of samples has limited the ability of researchers to perform such comparative studies. One way around this problem is to use induced pluripotent stem cells (or iPSCs). IPSCs are created by exposing mature cells—for example, skin cells—to conditions and molecules that convert them into an embryonic-like state. This state—called ‘induced pluripotency’—allows the cells to be coaxed into becoming many different cell types that can be grown in the laboratory. But it is more difficult to establish high quality iPSCs from chimpanzees than it is from humans or mice. Gallego Romero, Pavlovic et al. have now addressed this problem by creating iPSCs from skin cells taken from seven healthy chimpanzees. These cell lines were then analysed and compared to each other and to seven iPSC lines created from human cells. The chimpanzee iPSC lines were found to be much more similar to each other than the mature cells that were used to make them. Similar results were also observed for the human iSPCs, which likely reflects the conserved changes that take place when the genomes of mature cells are reprogrammed to pluripotency. This high level of similarity between iPSCs from different individuals of the same species allowed Gallego Romero, Pavlovic et al. to discover many subtle differences in gene regulation between chimpanzees and humans. For example, over 4500 genes were found to be expressed differently in human and chimpanzee iPSCs, and over 3500 genomic regions had different patterns of certain DNA modifications that can help to regulate gene expression. These newly created chimpanzee iPSC lines represent a valuable resource for comparative studies of gene regulation. In the future, this resource could help researchers to identify further differences in gene regulation between closely related primate species. DOI:http://dx.doi.org/10.7554/eLife.07103.002
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Affiliation(s)
| | - Bryan J Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, United States
| | | | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, United States
| | - Michelle C Ward
- Department of Human Genetics, University of Chicago, Chicago, United States
| | | | - Courtney L Kagan
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Jonathan E Burnett
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Constance H Huang
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Amy Mitrano
- Department of Human Genetics, University of Chicago, Chicago, United States
| | | | - Inbar Friedrich Ben-Nun
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Yingchun Li
- Department of Pathology, University of California San Diego, San Diego, United States
| | - Karen Sabatini
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Trevor R Leonardo
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Mana Parast
- Department of Pathology, University of California San Diego, San Diego, United States
| | | | - Louise C Laurent
- Sanford Consortium for Regenerative Medicine, La Jolla, United States
| | - Jeanne F Loring
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, United States
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Bullaughey K, Chavarria CI, Coop G, Gilad Y. Expression quantitative trait loci detected in cell lines are often present in primary tissues. Hum Mol Genet 2009; 18:4296-303. [PMID: 19671653 DOI: 10.1093/hmg/ddp382] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Expression quantitative trait loci (eQTL) mapping is a powerful tool for identifying genetic regulatory variation. However, at present, most eQTLs in humans were identified using gene expression data from cell lines, and it remains unknown whether these eQTLs also have a regulatory function in other expression contexts, such as human primary tissues. Here we investigate this question using a targeted strategy. Specifically, we selected a subset of large-effect eQTLs identified in the HapMap lymphoblastoid cell lines, and examined the association of these eQTLs with gene expression levels across individuals in five human primary tissues (heart, kidney, liver, lung and testes). We show that genotypes at the eQTLs we selected are often predictive of variation in gene expression levels in one or more of the five primary tissues. The genotype effects in the primary tissues are consistently in the same direction as the effects inferred in the cell lines. Additionally, a number of the eQTLs we tested are found in more than one of the tissues. Our results indicate that functional studies in cell lines may uncover a substantial amount of genetic variation that affects gene expression levels in human primary tissues.
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Affiliation(s)
- Kevin Bullaughey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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