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Molugu K, Khajanchi N, Lazzarotto CR, Tsai SQ, Saha K. Trichostatin A for Efficient CRISPR-Cas9 Gene Editing of Human Pluripotent Stem Cells. CRISPR J 2023; 6:473-485. [PMID: 37676985 PMCID: PMC10611976 DOI: 10.1089/crispr.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Genome-edited human-induced pluripotent stem cells (iPSCs) have broad applications in disease modeling, drug discovery, and regenerative medicine. Despite the development of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system, the gene editing process is inefficient and can take several weeks to months to generate edited iPSC clones. We developed a strategy to improve the efficiency of the iPSC gene editing process via application of a small-molecule, trichostatin A (TSA), a Class I and II histone deacetylase inhibitor. We observed that TSA decreased global chromatin condensation and further resulted in increased gene-editing efficiency of iPSCs by twofold to fourfold while concurrently ensuring no increased off-target effects. The edited iPSCs could be clonally expanded while maintaining genomic integrity and pluripotency. The rapid generation of therapeutically relevant gene-edited iPSCs could be enabled by these findings.
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Affiliation(s)
- Kaivalya Molugu
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Namita Khajanchi
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Biomedical and Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Biomedical and Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and St Jude Children's Research Hospital, Memphis, Tennessee, USA
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Srivastava P, Romanazzo S, Kopecky C, Nemec S, Ireland J, Molley TG, Lin K, Jayathilaka PB, Pandzic E, Yeola A, Chandrakanthan V, Pimanda J, Kilian K. Defined Microenvironments Trigger In Vitro Gastrulation in Human Pluripotent Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203614. [PMID: 36519269 PMCID: PMC9929265 DOI: 10.1002/advs.202203614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/19/2022] [Indexed: 06/17/2023]
Abstract
Gastrulation is a stage in embryo development where three germ layers arise to dictate the human body plan. In vitro models of gastrulation have been demonstrated by treating pluripotent stem cells with soluble morphogens to trigger differentiation. However, in vivo gastrulation is a multistage process coordinated through feedback between soluble gradients and biophysical forces, with the multipotent epiblast transforming to the primitive streak followed by germ layer segregation. Here, the authors show how constraining pluripotent stem cells to hydrogel islands triggers morphogenesis that mirrors the stages preceding in vivo gastrulation, without the need for exogenous supplements. Within hours of initial seeding, cells display a contractile phenotype at the boundary, which leads to enhanced proliferation, yes-associated protein (YAP) translocation, epithelial to mesenchymal transition, and emergence of SRY-box transcription factor 17 (SOX17)+ T/BRACHYURY+ cells. Molecular profiling and pathway analysis reveals a role for mechanotransduction-coupled wingless-type (WNT) signaling in orchestrating differentiation, which bears similarities to processes observed in whole organism models of development. After two days, the colonies form multilayered aggregates, which can be removed for further growth and differentiation. This approach demonstrates how materials alone can initiate gastrulation, thereby providing in vitro models of development and a tool to support organoid bioengineering efforts.
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Affiliation(s)
- Pallavi Srivastava
- School of ChemistryAustralian Centre for NanoMedicineUniversity of New South WalesSydneyNSW2052Australia
- School of Biomedical SciencesUniversity of New South WalesSydneyNSW2052Australia
- Adult Cancer ProgramSchool of Clinical Medicine, Lowy Cancer Research CentreUNSW SydneySydneyNSW2052Australia
| | - Sara Romanazzo
- School of ChemistryAustralian Centre for NanoMedicineUniversity of New South WalesSydneyNSW2052Australia
| | - Chantal Kopecky
- School of ChemistryAustralian Centre for NanoMedicineUniversity of New South WalesSydneyNSW2052Australia
- Adult Cancer ProgramSchool of Clinical Medicine, Lowy Cancer Research CentreUNSW SydneySydneyNSW2052Australia
| | - Stephanie Nemec
- School of Materials Science and EngineeringUniversity of New South WalesSydneyNSW2052Australia
| | - Jake Ireland
- School of ChemistryAustralian Centre for NanoMedicineUniversity of New South WalesSydneyNSW2052Australia
| | - Thomas G. Molley
- School of Materials Science and EngineeringUniversity of New South WalesSydneyNSW2052Australia
| | - Kang Lin
- School of Materials Science and EngineeringUniversity of New South WalesSydneyNSW2052Australia
| | - Pavithra B. Jayathilaka
- School of ChemistryAustralian Centre for NanoMedicineUniversity of New South WalesSydneyNSW2052Australia
| | - Elvis Pandzic
- Katharina Gaus Light Microscopy FacilityMark Wainwright Analytical CentreUniversity of New South WalesSydneyNSW2052Australia
| | - Avani Yeola
- Adult Cancer ProgramSchool of Clinical Medicine, Lowy Cancer Research CentreUNSW SydneySydneyNSW2052Australia
| | - Vashe Chandrakanthan
- School of Biomedical SciencesUniversity of New South WalesSydneyNSW2052Australia
- Adult Cancer ProgramSchool of Clinical Medicine, Lowy Cancer Research CentreUNSW SydneySydneyNSW2052Australia
| | - John Pimanda
- School of Biomedical SciencesUniversity of New South WalesSydneyNSW2052Australia
- Adult Cancer ProgramSchool of Clinical Medicine, Lowy Cancer Research CentreUNSW SydneySydneyNSW2052Australia
- Department of HaematologyPrince of Wales HospitalRandwickNSW2031Australia
| | - Kristopher Kilian
- School of ChemistryAustralian Centre for NanoMedicineUniversity of New South WalesSydneyNSW2052Australia
- Adult Cancer ProgramSchool of Clinical Medicine, Lowy Cancer Research CentreUNSW SydneySydneyNSW2052Australia
- School of Materials Science and EngineeringUniversity of New South WalesSydneyNSW2052Australia
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Molugu K, Battistini GA, Heaster TM, Rouw J, Guzman EC, Skala MC, Saha K. Label-Free Imaging to Track Reprogramming of Human Somatic Cells. GEN BIOTECHNOLOGY 2022; 1:176-191. [PMID: 35586336 PMCID: PMC9092522 DOI: 10.1089/genbio.2022.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
The process of reprogramming patient samples to human-induced pluripotent stem cells (iPSCs) is stochastic, asynchronous, and inefficient, leading to a heterogeneous population of cells. In this study, we track the reprogramming status of patient-derived erythroid progenitor cells (EPCs) at the single-cell level during reprogramming with label-free live-cell imaging of cellular metabolism and nuclear morphometry to identify high-quality iPSCs. EPCs isolated from human peripheral blood of three donors were used for our proof-of-principle study. We found distinct patterns of autofluorescence lifetime for the reduced form of nicotinamide adenine dinucleotide (phosphate) and flavin adenine dinucleotide during reprogramming. Random forest models classified iPSCs with ∼95% accuracy, which enabled the successful isolation of iPSC lines from reprogramming cultures. Reprogramming trajectories resolved at the single-cell level indicated significant reprogramming heterogeneity along different branches of cell states. This combination of micropatterning, autofluorescence imaging, and machine learning provides a unique, real-time, and nondestructive method to assess the quality of iPSCs in a biomanufacturing process, which could have downstream impacts in regenerative medicine, cell/gene therapy, and disease modeling.
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Affiliation(s)
- Kaivalya Molugu
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
| | - Giovanni A. Battistini
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
| | - Tiffany M. Heaster
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Jacob Rouw
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
| | | | - Melissa C. Skala
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
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Schlick T. Multiscale Genome Organization: Dazzling Subject and Inventive Methods. Biophys J 2020; 118:E1-E3. [PMID: 32305070 PMCID: PMC7161524 DOI: 10.1016/j.bpj.2020.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 01/20/2023] Open
Affiliation(s)
- Tamar Schlick
- Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, New York, New York.
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