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Tsubouchi A, An Y, Kawamura Y, Yanagihashi Y, Nakayama H, Murata Y, Teranishi K, Ishiguro S, Aburatani H, Yachie N, Ota S. Pooled CRISPR screening of high-content cellular phenotypes using ghost cytometry. Cell Rep Methods 2024; 4:100737. [PMID: 38531306 PMCID: PMC10985231 DOI: 10.1016/j.crmeth.2024.100737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/30/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024]
Abstract
Recent advancements in image-based pooled CRISPR screening have facilitated the mapping of diverse genotype-phenotype associations within mammalian cells. However, the rapid enrichment of cells based on morphological information continues to pose a challenge, constraining the capacity for large-scale gene perturbation screening across diverse high-content cellular phenotypes. In this study, we demonstrate the applicability of multimodal ghost cytometry-based cell sorting, including both fluorescent and label-free high-content phenotypes, for rapid pooled CRISPR screening within vast cell populations. Using the high-content cell sorter operating in fluorescence mode, we successfully executed kinase-specific CRISPR screening targeting genes influencing the nuclear translocation of RelA. Furthermore, using the multiparametric, label-free mode, we performed large-scale screening to identify genes involved in macrophage polarization. Notably, the label-free platform can enrich target phenotypes without requiring invasive staining, preserving untouched cells for downstream assays and expanding the potential for screening cellular phenotypes even when suitable markers are absent.
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Affiliation(s)
| | - Yuri An
- ThinkCyte Inc., Tokyo 113-8654, Japan
| | | | | | | | | | | | - Soh Ishiguro
- School of Biomedical Engineering, Faculty of Medicine and Faculty of Applied Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hiroyuki Aburatani
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Nozomu Yachie
- School of Biomedical Engineering, Faculty of Medicine and Faculty of Applied Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Sadao Ota
- ThinkCyte Inc., Tokyo 113-8654, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.
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2
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Atasoy-Zeybek A, Hawse GP, Nagelli CV, Lopez De Padilla C, Abdel MP, Evans CH. Transcriptomic changes during the replicative senescence of human articular chondrocytes. bioRxiv 2023:2023.11.07.565835. [PMID: 37986862 PMCID: PMC10659330 DOI: 10.1101/2023.11.07.565835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Osteoarthritis (OA) is a degenerative joint disease and a leading cause of disability worldwide. Aging is a major risk factor for OA, but the specific mechanisms underlying this connection remain unclear. Although chondrocytes rarely divide in adult articular cartilage, they undergo replicative senescence in vitro which provides an opportunity to study changes related to aging under controlled laboratory conditions. In this pilot study, we performed bulk RNA sequencing on early- and late-passage human articular chondrocytes to identify transcriptomic changes associated with cellular aging. Chondrocytes were isolated from the articular cartilage of three donors, two with OA (age 70-80 years) and one with healthy cartilage (age 26 years). Chondrocytes were serially passaged until replicative senescence and RNA extracted from early- and late-passage cells. Principal component analysis of all genes showed clear separation between early- and late-passage chondrocytes, indicating substantial age-related differences in gene expression. Differentially expressed genes (DEGs) analysis confirmed distinct transcriptomic profiles between early- and late-passage chondrocytes. Hierarchical clustering revealed contrasting expression patterns between the two isolates from osteoarthritic samples and the healthy sample. Focused analysis of DEGs on transcripts associated with turnover of the extra-cellular matrix and the senescence-associated secretory phenotype (SASP) showed consistent downregulation of Col2A1 and ACAN, and upregulation of MMP19, ADAMTS4, and ADAMTS8 in late passage chondrocytes across all samples. SASP components including IL-1α, IL-1β, IL-6, IL-7, p16INK4A (CDKN2A) and CCL2 demonstrated significant upregulation in late passage chondrocytes originally isolated from OA samples. Pathway analysis between sexes with OA revealed shared pathways such as extracellular matrix (ECM) organization, collagen formation, skeletal and muscle development, and nervous system development. Sex-specific differences were observed, with males showing distinctions in ECM organization, regulation of the cell cycle process as well as neuron differentiation. In contrast, females exhibited unique variations in the regulation of the cell cycle process, DNA metabolic process, and the PID-PLK1 pathway.
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Affiliation(s)
- Aysegul Atasoy-Zeybek
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Gresin P. Hawse
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Christopher V. Nagelli
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Consuelo Lopez De Padilla
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Christopher H. Evans
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
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3
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Hildebrandt MR, Reuter MS, Wei W, Tayebi N, Liu J, Sharmin S, Mulder J, Lesperance LS, Brauer PM, Mok RSF, Kinnear C, Piekna A, Romm A, Howe J, Pasceri P, Meng G, Rozycki M, Rodrigues DC, Martinez EC, Szego MJ, Zúñiga-Pflücker JC, Anderson MK, Prescott SA, Rosenblum ND, Kamath BM, Mital S, Scherer SW, Ellis J. Precision Health Resource of Control iPSC Lines for Versatile Multilineage Differentiation. Stem Cell Reports 2020; 13:1126-1141. [PMID: 31813827 PMCID: PMC6915802 DOI: 10.1016/j.stemcr.2019.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 06/11/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 01/15/2023] Open
Abstract
Induced pluripotent stem cells (iPSC) derived from healthy individuals are important controls for disease-modeling studies. Here we apply precision health to create a high-quality resource of control iPSCs. Footprint-free lines were reprogrammed from four volunteers of the Personal Genome Project Canada (PGPC). Multilineage-directed differentiation efficiently produced functional cortical neurons, cardiomyocytes and hepatocytes. Pilot users demonstrated versatility by generating kidney organoids, T lymphocytes, and sensory neurons. A frameshift knockout was introduced into MYBPC3 and these cardiomyocytes exhibited the expected hypertrophic phenotype. Whole-genome sequencing-based annotation of PGPC lines revealed on average 20 coding variants. Importantly, nearly all annotated PGPC and HipSci lines harbored at least one pre-existing or acquired variant with cardiac, neurological, or other disease associations. Overall, PGPC lines were efficiently differentiated by multiple users into cells from six tissues for disease modeling, and variant-preferred healthy control lines were identified for specific disease settings.
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Affiliation(s)
- Matthew R Hildebrandt
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S Reuter
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wei Wei
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Naeimeh Tayebi
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jiajie Liu
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sazia Sharmin
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jaap Mulder
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - L Stephen Lesperance
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Patrick M Brauer
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - Rebecca S F Mok
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Caroline Kinnear
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Alina Piekna
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Asli Romm
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer Howe
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Peter Pasceri
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Guoliang Meng
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Matthew Rozycki
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Deivid C Rodrigues
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Elisa C Martinez
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - Michael J Szego
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, ON M5C 2T2, Canada; The Joint Centre for Bioethics, University of Toronto, Toronto, ON, Canada; Unity Health Toronto, Toronto, ON M5T 3M6, Canada
| | - Juan C Zúñiga-Pflücker
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - Michele K Anderson
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - Steven A Prescott
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Norman D Rosenblum
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Binita M Kamath
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Seema Mital
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5G 0A4, Canada.
| | - James Ellis
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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van den Hurk M, Erwin JA, Yeo GW, Gage FH, Bardy C. Corrigendum: Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. Front Mol Neurosci 2019; 12:150. [PMID: 31244603 PMCID: PMC6580186 DOI: 10.3389/fnmol.2019.00150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/24/2019] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fnmol.2018.00261.].
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Affiliation(s)
- Mark van den Hurk
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia
| | - Jennifer A Erwin
- The Lieber Institute for Brain Development, Baltimore, MD, United States.,Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
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5
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van den Hurk M, Erwin JA, Yeo GW, Gage FH, Bardy C. Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. Front Mol Neurosci 2018; 11:261. [PMID: 30147644 PMCID: PMC6096303 DOI: 10.3389/fnmol.2018.00261] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 04/23/2018] [Accepted: 07/12/2018] [Indexed: 11/13/2022] Open
Abstract
The human brain is composed of a complex assembly of about 171 billion heterogeneous cellular units (86 billion neurons and 85 billion non-neuronal glia cells). A comprehensive description of brain cells is necessary to understand the nervous system in health and disease. Recently, advances in genomics have permitted the accurate analysis of the full transcriptome of single cells (scRNA-seq). We have built upon such technical progress to combine scRNA-seq with patch-clamping electrophysiological recording and morphological analysis of single human neurons in vitro. This new powerful method, referred to as Patch-seq, enables a thorough, multimodal profiling of neurons and permits us to expose the links between functional properties, morphology, and gene expression. Here, we present a detailed Patch-seq protocol for isolating single neurons from in vitro neuronal cultures. We have validated the Patch-seq whole-transcriptome profiling method with human neurons generated from embryonic and induced pluripotent stem cells (ESCs/iPSCs) derived from healthy subjects, but the procedure may be applied to any kind of cell type in vitro. Patch-seq may be used on neurons in vitro to profile cell types and states in depth to unravel the human molecular basis of neuronal diversity and investigate the cellular mechanisms underlying brain disorders.
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Affiliation(s)
- Mark van den Hurk
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia
| | - Jennifer A Erwin
- The Lieber Institute for Brain Development, Baltimore, MD, United States.,Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
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