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De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, Kohler TN, Amadei G, Handford CE, Findlay GM, Zernicka-Goetz M, Teichmann SA, Hollfelder F. spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content. Nat Commun 2023; 14:4788. [PMID: 37553326 PMCID: PMC10409775 DOI: 10.1038/s41467-023-40322-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
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Affiliation(s)
- Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - David B Morse
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Gianluca Amadei
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte E Handford
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | | | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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Kohler TN, De Jonghe J, Ellermann AL, Yanagida A, Herger M, Slatery EM, Weberling A, Munger C, Fischer K, Mulas C, Winkel A, Ross C, Bergmann S, Franze K, Chalut K, Nichols J, Boroviak TE, Hollfelder F. Plakoglobin is a mechanoresponsive regulator of naive pluripotency. Nat Commun 2023; 14:4022. [PMID: 37419903 PMCID: PMC10329048 DOI: 10.1038/s41467-023-39515-0] [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: 03/14/2022] [Accepted: 06/09/2023] [Indexed: 07/09/2023] Open
Abstract
Biomechanical cues are instrumental in guiding embryonic development and cell differentiation. Understanding how these physical stimuli translate into transcriptional programs will provide insight into mechanisms underlying mammalian pre-implantation development. Here, we explore this type of regulation by exerting microenvironmental control over mouse embryonic stem cells. Microfluidic encapsulation of mouse embryonic stem cells in agarose microgels stabilizes the naive pluripotency network and specifically induces expression of Plakoglobin (Jup), a vertebrate homolog of β-catenin. Overexpression of Plakoglobin is sufficient to fully re-establish the naive pluripotency gene regulatory network under metastable pluripotency conditions, as confirmed by single-cell transcriptome profiling. Finally, we find that, in the epiblast, Plakoglobin was exclusively expressed at the blastocyst stage in human and mouse embryos - further strengthening the link between Plakoglobin and naive pluripotency in vivo. Our work reveals Plakoglobin as a mechanosensitive regulator of naive pluripotency and provides a paradigm to interrogate the effects of volumetric confinement on cell-fate transitions.
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Affiliation(s)
- Timo N Kohler
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Ayaka Yanagida
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Veterinary Anatomy, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Stem Cell Therapy Laboratory, Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Michael Herger
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Erin M Slatery
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Antonia Weberling
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Clara Munger
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Katrin Fischer
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Carla Mulas
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Alex Winkel
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Connor Ross
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Sophie Bergmann
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Institute of Medical Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 91, 91052, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91054, Erlangen, Germany
| | - Kevin Chalut
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Thorsten E Boroviak
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK.
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