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Hu H, Ho D, Tan DS, MacCarthy C, Yu CH, Weng M, Schöler H, Jauch R. Evaluation of the determinants for improved pluripotency induction and maintenance by engineered SOX17. Nucleic Acids Res 2023; 51:8934-8956. [PMID: 37607832 PMCID: PMC10516664 DOI: 10.1093/nar/gkad597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/24/2023] Open
Abstract
An engineered SOX17 variant with point mutations within its DNA binding domain termed SOX17FNV is a more potent pluripotency inducer than SOX2, yet the underlying mechanism remains unclear. Although wild-type SOX17 was incapable of inducing pluripotency, SOX17FNV outperformed SOX2 in mouse and human pluripotency reprogramming. In embryonic stem cells, SOX17FNV could replace SOX2 to maintain pluripotency despite considerable sequence differences and upregulated genes expressed in cleavage-stage embryos. Mechanistically, SOX17FNV co-bound OCT4 more cooperatively than SOX2 in the context of the canonical SoxOct DNA element. SOX2, SOX17, and SOX17FNV were all able to bind nucleosome core particles in vitro, which is a prerequisite for pioneer transcription factors. Experiments using purified proteins and in cellular contexts showed that SOX17 variants phase-separated more efficiently than SOX2, suggesting an enhanced ability to self-organise. Systematic deletion analyses showed that the N-terminus of SOX17FNV was dispensable for its reprogramming activity. However, the C-terminus encodes essential domains indicating multivalent interactions that drive transactivation and reprogramming. We defined a minimal SOX17FNV (miniSOX) that can support reprogramming with high activity, reducing the payload of reprogramming cassettes. This study uncovers the mechanisms behind SOX17FNV-induced pluripotency and establishes engineered SOX factors as powerful cell engineering tools.
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Affiliation(s)
- Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Derek Hoi Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Cheng-han Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | | | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
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Dave A, Nekritz E, Charytonowicz D, Beaumont M, Smith M, Beaumont K, Silva J, Sebra R. Integration of Single-Cell Transcriptomics With a High Throughput Functional Screening Assay to Resolve Cell Type, Growth Kinetics, and Stemness Heterogeneity Within the Comma-1D Cell Line. Front Genet 2022; 13:894597. [PMID: 36630696 PMCID: PMC9237515 DOI: 10.3389/fgene.2022.894597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/20/2022] [Indexed: 01/14/2023] Open
Abstract
Cell lines are one of the most frequently implemented model systems in life sciences research as they provide reproducible high throughput testing. Differentiation of cell cultures varies by line and, in some cases, can result in functional modifications within a population. Although research is increasingly dependent on these in vitro model systems, the heterogeneity within cell lines has not been thoroughly investigated. Here, we have leveraged high throughput single-cell assays to investigate the Comma-1D mouse cell line that is known to differentiate in culture. Using scRNASeq and custom single-cell phenotype assays, we resolve the clonal heterogeneity within the referenced cell line on the genomic and functional level. We performed a cohesive analysis of the transcriptome of 5,195 sequenced cells, of which 85.3% of the total reads successfully mapped to the mm10-3.0.0 reference genome. Across multiple gene expression analysis pipelines, both luminal and myoepithelial lineages were observed. Deep differential gene expression analysis revealed eight subclusters identified as luminal progenitor, luminal differentiated, myoepithelial differentiated, and fibroblast subpopulations-suggesting functional clustering within each lineage. Gene expression of published mammary stem cell (MaSC) markers Epcam, Cd49f, and Sca-1 was detected across the population, with 116 (2.23%) sequenced cells expressing all three markers. To gain insight into functional heterogeneity, cells with patterned MaSC marker expression were isolated and phenotypically investigated through a custom single-cell high throughput assay. The comparison of growth kinetics demonstrates functional heterogeneity within each cell cluster while also illustrating significant limitations in current cell isolation methods. We outlined the upstream use of our novel automated cell identification platform-to be used prior to single-cell culture-for reduced cell stress and improved rare cell identification and capture. Through compounding single-cell pipelines, we better reveal the heterogeneity within Comma-1D to identify subpopulations with specific functional characteristics.
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Affiliation(s)
- Arpit Dave
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Erin Nekritz
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Michael Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Melissa Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Kristin Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jose Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Sema4, A Mount Sinai Venture, Stamford, CT, United States
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Kang Y, Nack LM, Liu Y, Qi B, Huang Y, Liu Z, Chakraborty I, Schulz F, Ahmed AAA, Clavo Poveda M, Hafizi F, Roy S, Mutas M, Holzapfel M, Sanchez-Cano C, Wegner KD, Feliu N, Parak WJ. Quantitative considerations about the size dependence of cellular entry and excretion of colloidal nanoparticles for different cell types. CHEMTEXTS 2022; 8:9. [PMID: 35223376 PMCID: PMC8827143 DOI: 10.1007/s40828-021-00159-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/28/2021] [Indexed: 12/17/2022]
Abstract
Most studies about the interaction of nanoparticles (NPs) with cells have focused on how the physicochemical properties of NPs will influence their uptake by cells. However, much less is known about their potential excretion from cells. However, to control and manipulate the number of NPs in a cell, both cellular uptake and excretion must be studied quantitatively. Monitoring the intracellular and extracellular amount of NPs over time (after residual noninternalized NPs have been removed) enables one to disentangle the influences of cell proliferation and exocytosis, the major pathways for the reduction of NPs per cell. Proliferation depends on the type of cells, while exocytosis depends in addition on properties of the NPs, such as their size. Examples are given herein on the role of these two different processes for different cells and NPs.
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Affiliation(s)
- Yanan Kang
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | - Leroy Marwin Nack
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | - Yang Liu
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | - Bing Qi
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | - Yalan Huang
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | - Ziyao Liu
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
- Present Address: Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Indranath Chakraborty
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | - Florian Schulz
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | - Abdullah A. A. Ahmed
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
| | | | - Fereshta Hafizi
- Fraunhofer Center for Applied Nanotechnology (CAN), Hamburg, Germany
| | - Sathi Roy
- Fraunhofer Center for Applied Nanotechnology (CAN), Hamburg, Germany
| | - Marina Mutas
- Fraunhofer Center for Applied Nanotechnology (CAN), Hamburg, Germany
- Mildred Scheel Cancer Career Centre Hamburg, Universitätklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Holzapfel
- Fraunhofer Center for Applied Nanotechnology (CAN), Hamburg, Germany
| | - Carlos Sanchez-Cano
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), San Sebastián, Spain
| | - K. David Wegner
- Division Biophotonics, Federal Institute of Materials Research and Testing (BAM), Berlin, Germany
| | - Neus Feliu
- Fraunhofer Center for Applied Nanotechnology (CAN), Hamburg, Germany
| | - Wolfgang J. Parak
- Center for Hybrid Nanostructures (CHyN) and Fachbereich Physik and Chemie, Universität Hamburg, Hamburg, Germany
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