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Autio MI, Motakis E, Perrin A, Bin Amin T, Tiang Z, Do DV, Wang J, Tan J, Ding SSL, Tan WX, Lee CJM, Teo AKK, Foo RSY. Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells. eLife 2024; 13:e79592. [PMID: 38164941 PMCID: PMC10836832 DOI: 10.7554/elife.79592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites in vitro using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easy targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.
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Affiliation(s)
- Matias I Autio
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Singapore, Singapore
| | - Efthymios Motakis
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Arnaud Perrin
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Talal Bin Amin
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Singapore, Singapore
| | - Zenia Tiang
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Dang Vinh Do
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Jiaxu Wang
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, Singapore, Singapore
| | - Joanna Tan
- Center for Genome Diagnostics, Genome Institute of Singapore, Singapore, Singapore
| | - Shirley Suet Lee Ding
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Wei Xuan Tan
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chang Jie Mick Lee
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Precision Medicine Translational Research Programme, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Roger S Y Foo
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
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