1
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Prondzynski M, Berkson P, Trembley MA, Tharani Y, Shani K, Bortolin RH, Sweat ME, Mayourian J, Yucel D, Cordoves AM, Gabbin B, Hou C, Anyanwu NJ, Nawar F, Cotton J, Milosh J, Walker D, Zhang Y, Lu F, Liu X, Parker KK, Bezzerides VJ, Pu WT. Efficient and reproducible generation of human iPSC-derived cardiomyocytes and cardiac organoids in stirred suspension systems. Nat Commun 2024; 15:5929. [PMID: 39009604 PMCID: PMC11251028 DOI: 10.1038/s41467-024-50224-0] [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: 02/13/2023] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
Human iPSC-derived cardiomyocytes (hiPSC-CMs) have proven invaluable for cardiac disease modeling and regeneration. Challenges with quality, inter-batch consistency, cryopreservation and scale remain, reducing experimental reproducibility and clinical translation. Here, we report a robust stirred suspension cardiac differentiation protocol, and we perform extensive morphological and functional characterization of the resulting bioreactor-differentiated iPSC-CMs (bCMs). Across multiple different iPSC lines, the protocol produces 1.2E6/mL bCMs with ~94% purity. bCMs have high viability after cryo-recovery (>90%) and predominantly ventricular identity. Compared to standard monolayer-differentiated CMs, bCMs are more reproducible across batches and have more mature functional properties. The protocol also works with magnetically stirred spinner flasks, which are more economical and scalable than bioreactors. Minor protocol modifications generate cardiac organoids fully in suspension culture. These reproducible, scalable, and resource-efficient approaches to generate iPSC-CMs and organoids will expand their applications, and our benchmark data will enable comparison to cells produced by other cardiac differentiation protocols.
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Affiliation(s)
| | - Paul Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Michael A Trembley
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Yashasvi Tharani
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Kevin Shani
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
| | - Raul H Bortolin
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Joshua Mayourian
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Dogacan Yucel
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Albert M Cordoves
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
| | - Beatrice Gabbin
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Cuilan Hou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Cardiology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Nnaemeka J Anyanwu
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
| | - Farina Nawar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Justin Cotton
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Joseph Milosh
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - David Walker
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Yan Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Fujian Lu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Fuwai Hospital, Chinese Academy of Medical Science, Shenzhen, Shenzhen, Guangdong Province, 518057, China
| | - Kevin Kit Parker
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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2
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Aguilar G, Bauer M, Vigano MA, Schnider ST, Brügger L, Jiménez-Jiménez C, Guerrero I, Affolter M. Seamless knockins in Drosophila via CRISPR-triggered single-strand annealing. Dev Cell 2024:S1534-5807(24)00383-6. [PMID: 38971155 DOI: 10.1016/j.devcel.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/06/2023] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
CRISPR-Cas greatly facilitated the integration of exogenous sequences into specific loci. However, knockin generation in multicellular animals remains challenging, partially due to the complexity of insertion screening. Here, we describe SEED/Harvest, a method to generate knockins in Drosophila, based on CRISPR-Cas and the single-strand annealing (SSA) repair pathway. In SEED (from "scarless editing by element deletion"), a switchable cassette is first integrated into the target locus. In a subsequent CRISPR-triggered repair event, resolved by SSA, the cassette is seamlessly removed. Germline excision of SEED cassettes allows for fast and robust knockin generation of both fluorescent proteins and short protein tags in tandem. Tissue-specific expression of Cas9 results in somatic cassette excision, conferring spatiotemporal control of protein labeling and the conditional rescue of mutants. Finally, to achieve conditional protein labeling and manipulation of short tag knockins, we developed a genetic toolbox by functionalizing the ALFA nanobody.
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Affiliation(s)
- Gustavo Aguilar
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Milena Bauer
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - M Alessandra Vigano
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Sophie T Schnider
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Lukas Brügger
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Carlos Jiménez-Jiménez
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Isabel Guerrero
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Markus Affolter
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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3
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Lee S, Vander Roest AS, Blair CA, Kao K, Bremner SB, Childers MC, Pathak D, Heinrich P, Lee D, Chirikian O, Mohran SE, Roberts B, Smith JE, Jahng JW, Paik DT, Wu JC, Gunawardane RN, Ruppel KM, Mack DL, Pruitt BL, Regnier M, Wu SM, Spudich JA, Bernstein D. Incomplete-penetrant hypertrophic cardiomyopathy MYH7 G256E mutation causes hypercontractility and elevated mitochondrial respiration. Proc Natl Acad Sci U S A 2024; 121:e2318413121. [PMID: 38683993 PMCID: PMC11087781 DOI: 10.1073/pnas.2318413121] [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: 10/22/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024] Open
Abstract
Determining the pathogenicity of hypertrophic cardiomyopathy-associated mutations in the β-myosin heavy chain (MYH7) can be challenging due to its variable penetrance and clinical severity. This study investigates the early pathogenic effects of the incomplete-penetrant MYH7 G256E mutation on myosin function that may trigger pathogenic adaptations and hypertrophy. We hypothesized that the G256E mutation would alter myosin biomechanical function, leading to changes in cellular functions. We developed a collaborative pipeline to characterize myosin function across protein, myofibril, cell, and tissue levels to determine the multiscale effects on structure-function of the contractile apparatus and its implications for gene regulation and metabolic state. The G256E mutation disrupts the transducer region of the S1 head and reduces the fraction of myosin in the folded-back state by 33%, resulting in more myosin heads available for contraction. Myofibrils from gene-edited MYH7WT/G256E human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) exhibited greater and faster tension development. This hypercontractile phenotype persisted in single-cell hiPSC-CMs and engineered heart tissues. We demonstrated consistent hypercontractile myosin function as a primary consequence of the MYH7 G256E mutation across scales, highlighting the pathogenicity of this gene variant. Single-cell transcriptomic and metabolic profiling demonstrated upregulated mitochondrial genes and increased mitochondrial respiration, indicating early bioenergetic alterations. This work highlights the benefit of our multiscale platform to systematically evaluate the pathogenicity of gene variants at the protein and contractile organelle level and their early consequences on cellular and tissue function. We believe this platform can help elucidate the genotype-phenotype relationships underlying other genetic cardiovascular diseases.
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Affiliation(s)
- Soah Lee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Biopharmaceutical Convergence, Sungkyunkwan University School of Pharmacy, Suwon, Gyeonggi-do16419South Korea
- School of Pharmacy, Sungkyunkwan University School of Pharmacy, Suwon, Gyeonggi-do16419, South Korea
| | - Alison S. Vander Roest
- Department of Pediatrics (Cardiology), Stanford University School of Medicine, Stanford, CA94305
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI48109
| | - Cheavar A. Blair
- Biological Engineering, University of California, Santa Barbara, CA93106
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY40536
| | - Kerry Kao
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Samantha B. Bremner
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Matthew C. Childers
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Divya Pathak
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Paul Heinrich
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Daniel Lee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Orlando Chirikian
- Biological Engineering, University of California, Santa Barbara, CA93106
| | - Saffie E. Mohran
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | | | | | - James W. Jahng
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - David T. Paik
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | | | - Kathleen M. Ruppel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - David L. Mack
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Beth L. Pruitt
- Biological Engineering, University of California, Santa Barbara, CA93106
| | - Michael Regnier
- Department of Bioengineering, University of Washington School of Medicine and College of Engineering, Seattle, WA98195
| | - Sean M. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - James A. Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Daniel Bernstein
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Pediatrics (Cardiology), Stanford University School of Medicine, Stanford, CA94305
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4
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Husser MC, Pham NP, Law C, Araujo FRB, Martin VJJ, Piekny A. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies. eLife 2024; 12:RP92819. [PMID: 38652106 PMCID: PMC11037917 DOI: 10.7554/elife.92819] [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] [Indexed: 04/25/2024] Open
Abstract
Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.
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Affiliation(s)
| | - Nhat P Pham
- Biology Department, Concordia University, Montreal, Canada
| | - Chris Law
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
| | - Flavia R B Araujo
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Biology Department, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Alisa Piekny
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
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5
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Novoa J, Westra I, Steeneveld E, Neves NF, Daleman L, Asensio AB, Davis RP, Carlotti F, Freund C, Rabelink T, Meij P, Wieles B. Validating human induced pluripotent stem cell-specific quality control tests for the release of an intermediate drug product in a Good Manufacturing Practice quality system. Cytotherapy 2024:S1465-3249(24)00610-8. [PMID: 38703154 DOI: 10.1016/j.jcyt.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
One of the challenges in Good Manufacturing Practice (GMP)-compliant human induced pluripotent stem cell (hiPSC) production is the validation of quality control (QC) tests specific for hiPSCs, which are required for GMP batch release. This study presents a comprehensive description of the validation process for hiPSC-specific GMP-compliant QC assays; more specifically, the validation of assays to assess the potential presence of residual episomal vectors (REVs), the expression of markers of the undifferentiated state and the directed differentiation potential of hiPSCs. Critical aspects and specific acceptance criteria were formulated in a validation plan prior to assay validation. Assay specificity, sensitivity and reproducibility were tested, and the equipment used for each assay was subjected to performance qualification. A minimum input of 20 000 cells (120 ng of genomic DNA) was defined for accurate determination of the presence of REVs. Furthermore, since vector loss in hiPSC lines is a passage-dependent process, we advocate screening for REVs between passages eight and 10, as testing at earlier passages might lead to unnecessary rejection of hiPSC lines. The cutoff value for assessment of markers of the undifferentiated state was set to the expression of at least three individual markers on at least 75% of the cells. When multi-color flow cytometry panels are used, a fluorescence minus one control is advised to ensure the control for fluorescent spread. For the assay to assess the directed differentiation potential, the detection limit was set to two of three positive lineage-specific markers for each of the three individual germ layers. All of our assays proved to be reproducible and specific. Our data demonstrate that our implemented analytical procedures are suitable as QC assays for the batch release of GMP-compliant hiPSCs.
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Affiliation(s)
- Juan Novoa
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Inge Westra
- Center for Cell and Gene Therapy, Leiden University Medical Center, Leiden, the Netherlands
| | - Esther Steeneveld
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Natascha Fonseca Neves
- Center for Cell and Gene Therapy, Leiden University Medical Center, Leiden, the Netherlands
| | - Lizanne Daleman
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Albert Blanch Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; Novo Nordisk Foundation Center for Stem Cell Medicine, Leiden University Medical Center, the Netherlands
| | - Richard P Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; Novo Nordisk Foundation Center for Stem Cell Medicine, Leiden University Medical Center, the Netherlands
| | - Françoise Carlotti
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Christian Freund
- Leiden University Medical Center hiPSC Hotel, Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ton Rabelink
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands; Novo Nordisk Foundation Center for Stem Cell Medicine, Leiden University Medical Center, the Netherlands.
| | - Pauline Meij
- Center for Cell and Gene Therapy, Leiden University Medical Center, Leiden, the Netherlands
| | - Brigitte Wieles
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
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6
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Xiong J, He Z, Wang L, Fan C, Chao J. DNA Origami-Enabled Gene Localization of Repetitive Sequences. J Am Chem Soc 2024; 146:6317-6325. [PMID: 38391280 DOI: 10.1021/jacs.4c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Repetitive sequences, which make up over 50% of human DNA, have diverse applications in disease diagnosis, forensic identification, paternity testing, and population genetic analysis due to their crucial functions for gene regulation. However, representative detection technologies such as sequencing and fluorescence imaging suffer from time-consuming protocols, high cost, and inaccuracy of the position and order of repetitive sequences. Here, we develop a precise and cost-effective strategy that combines the high resolution of atomic force microscopy with the shape customizability of DNA origami for repetitive sequence-specific gene localization. "Tri-block" DNA structures were specifically designed to connect repetitive sequences to DNA origami tags, thereby revealing precise genetic information in terms of position and sequence for high-resolution and high-precision visualization of repetitive sequences. More importantly, we achieved the results of simultaneous detection of different DNA repetitive sequences on the gene template with a resolution of ∼6.5 nm (19 nt). This strategy is characterized by high efficiency, high precision, low operational complexity, and low labor/time costs, providing a powerful complement to sequencing technologies for gene localization of repetitive sequences.
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Affiliation(s)
- Jinxin Xiong
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Zhimei He
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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7
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Prondzynski M, Bortolin RH, Berkson P, Trembley MA, Shani K, Sweat ME, Mayourian J, Cordoves AM, Anyanwu NJ, Tharani Y, Cotton J, Milosh JB, Walker D, Zhang Y, Liu F, Liu X, Parker KK, Bezzerides VJ, Pu WT. Efficient and reproducible generation of human iPSC-derived cardiomyocytes using a stirred bioreactor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581789. [PMID: 38464269 PMCID: PMC10925150 DOI: 10.1101/2024.02.24.581789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
In the last decade human iPSC-derived cardiomyocytes (hiPSC-CMs) proved to be valuable for cardiac disease modeling and cardiac regeneration, yet challenges with scale, quality, inter-batch consistency, and cryopreservation remain, reducing experimental reproducibility and limiting clinical translation. Here, we report a robust cardiac differentiation protocol that uses Wnt modulation and a stirred suspension bioreactor to produce on average 124 million hiPSC-CMs with >90% purity using a variety of hiPSC lines (19 differentiations; 10 iPSC lines). After controlled freeze and thaw, bioreactor-derived CMs (bCMs) showed high viability (>90%), interbatch reproducibility in cellular morphology, function, drug response and ventricular identity, which was further supported by single cell transcriptomes. bCMs on microcontact printed substrates revealed a higher degree of sarcomere maturation and viability during long-term culture compared to monolayer-derived CMs (mCMs). Moreover, functional investigation of bCMs in 3D engineered heart tissues showed earlier and stronger force production during long-term culture, and robust pacing capture up to 4 Hz when compared to mCMs. bCMs derived from this differentiation protocol will expand the applications of hiPSC-CMs by providing a reproducible, scalable, and resource efficient method to generate cardiac cells with well-characterized structural and functional properties superior to standard mCMs.
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Affiliation(s)
| | - Raul H Bortolin
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Paul Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael A Trembley
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kevin Shani
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joshua Mayourian
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Albert M Cordoves
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
| | - Nnaemeka J Anyanwu
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
| | - Yashasvi Tharani
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Justin Cotton
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joseph B Milosh
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - David Walker
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yan Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fujian Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Fuwai Hospital, Chinese Academy of Medical Science, Shenzhen. Shenzhen, Guangdong Province, 518057, China
| | - Kevin K Parker
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
- Harvard Stem Cell Institute, Cambridge, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, USA
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8
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Santhosh Kumar S, Naseri NN, Pather SR, Hallacli E, Ndayisaba A, Buenaventura C, Acosta K, Roof J, Fazelinia H, Spruce LA, Luk K, Khurana V, Rhoades E, Shalem O. Sequential CRISPR screening reveals partial NatB inhibition as a strategy to mitigate alpha-synuclein levels in human neurons. SCIENCE ADVANCES 2024; 10:eadj4767. [PMID: 38335281 PMCID: PMC10857481 DOI: 10.1126/sciadv.adj4767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Alpha-synuclein (αSyn) protein levels correlate with the risk and severity of Parkinson's disease and related neurodegenerative diseases. Lowering αSyn is being actively investigated as a therapeutic modality. Here, we systematically map the regulatory network that controls endogenous αSyn using sequential CRISPR-knockout and -interference screens in an αSyn gene (SNCA)-tagged cell line and induced pluripotent stem cell-derived neurons (iNeurons). We uncover αSyn modifiers at multiple regulatory layers, with amino-terminal acetyltransferase B (NatB) enzymes being the most potent endogenous αSyn modifiers in both cell lines. Amino-terminal acetylation protects the cytosolic αSyn from rapid degradation by the proteasome in a Ube2w-dependent manner. Moreover, we show that pharmacological inhibition of methionyl-aminopeptidase 2, a regulator of NatB complex formation, attenuates endogenous αSyn in iNeurons carrying SNCA triplication. Together, our study reveals several gene networks that control endogenous αSyn, identifies mechanisms mediating the degradation of nonacetylated αSyn, and illustrates potential therapeutic pathways for decreasing αSyn levels in synucleinopathies.
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Affiliation(s)
- Saranya Santhosh Kumar
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nima N. Naseri
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarshan R. Pather
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erinc Hallacli
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Alain Ndayisaba
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Chris Buenaventura
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karen Acosta
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Roof
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A. Spruce
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelvin Luk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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9
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Yun WS, Cho H, Jeon SI, Lim DK, Kim K. Fluorescence-Based Mono- and Multimodal Imaging for In Vivo Tracking of Mesenchymal Stem Cells. Biomolecules 2023; 13:1787. [PMID: 38136656 PMCID: PMC10742164 DOI: 10.3390/biom13121787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The advancement of stem cell therapy has offered transformative therapeutic outcomes for a wide array of diseases over the past decades. Consequently, stem cell tracking has become significant in revealing the mechanisms of action and ensuring safe and effective treatments. Fluorescence stands out as a promising choice for stem cell tracking due to its myriad advantages, including high resolution, real-time monitoring, and multi-fluorescence detection. Furthermore, combining fluorescence with other tracking modalities-such as bioluminescence imaging (BLI), positron emission tomography (PET), photoacoustic (PA), computed tomography (CT), and magnetic resonance (MR)-can address the limitations of single fluorescence detection. This review initially introduces stem cell tracking using fluorescence imaging, detailing various labeling strategies such as green fluorescence protein (GFP) tagging, fluorescence dye labeling, and nanoparticle uptake. Subsequently, we present several combinations of strategies for efficient and precise detection.
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Affiliation(s)
- Wan Su Yun
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea; (W.S.Y.); (D.-K.L.)
| | - Hanhee Cho
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Woman’s University, Seoul 03760, Republic of Korea; (H.C.); (S.I.J.)
| | - Seong Ik Jeon
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Woman’s University, Seoul 03760, Republic of Korea; (H.C.); (S.I.J.)
| | - Dong-Kwon Lim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea; (W.S.Y.); (D.-K.L.)
| | - Kwangmeyung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Woman’s University, Seoul 03760, Republic of Korea; (H.C.); (S.I.J.)
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10
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Woldeyes RA, Nishiga M, Vander Roest AS, Engel L, Giri P, Montenegro GC, Wu AC, Dunn AR, Spudich JA, Bernstein D, Schmid MF, Wu JC, Chiu W. Cryo-electron tomography reveals the structural diversity of cardiac proteins in their cellular context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564098. [PMID: 37961228 PMCID: PMC10634850 DOI: 10.1101/2023.10.26.564098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cardiovascular diseases are a leading cause of death worldwide, but our understanding of the underlying mechanisms is limited, in part because of the complexity of the cellular machinery that controls the heart muscle contraction cycle. Cryogenic electron tomography (cryo-ET) provides a way to visualize diverse cellular machinery while preserving contextual information like subcellular localization and transient complex formation, but this approach has not been widely applied to the study of heart muscle cells (cardiomyocytes). Here, we deploy a platform for studying cardiovascular disease by combining cryo-ET with human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). After developing a cryo-ET workflow for visualizing macromolecules in hiPSC-CMs, we reconstructed sub-nanometer resolution structures of the human thin filament, a central component of the contractile machinery. We also visualized a previously unobserved organization of a regulatory complex that connects muscle contraction to calcium signaling (the troponin complex), highlighting the value of our approach for interrogating the structures of cardiac proteins in their cellular context.
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Affiliation(s)
- Rahel A. Woldeyes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alison S. Vander Roest
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - Leeya Engel
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Prerna Giri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Andrew C. Wu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Alexander R. Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - James A. Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Bernstein
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael F. Schmid
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
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11
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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12
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Dash S, Lamb MC, Lange JJ, McKinney MC, Tsuchiya D, Guo F, Zhao X, Corbin TJ, Kirkman M, Delventhal K, Moore EL, McKinney S, Shiang R, Trainor PA. rRNA transcription is integral to phase separation and maintenance of nucleolar structure. PLoS Genet 2023; 19:e1010854. [PMID: 37639467 PMCID: PMC10513380 DOI: 10.1371/journal.pgen.1010854] [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: 04/03/2023] [Revised: 09/21/2023] [Accepted: 07/03/2023] [Indexed: 08/31/2023] Open
Abstract
Transcription of ribosomal RNA (rRNA) by RNA Polymerase (Pol) I in the nucleolus is necessary for ribosome biogenesis, which is intimately tied to cell growth and proliferation. Perturbation of ribosome biogenesis results in tissue specific disorders termed ribosomopathies in association with alterations in nucleolar structure. However, how rRNA transcription and ribosome biogenesis regulate nucleolar structure during normal development and in the pathogenesis of disease remains poorly understood. Here we show that homozygous null mutations in Pol I subunits required for rRNA transcription and ribosome biogenesis lead to preimplantation lethality. Moreover, we discovered that Polr1a-/-, Polr1b-/-, Polr1c-/- and Polr1d-/- mutants exhibit defects in the structure of their nucleoli, as evidenced by a decrease in number of nucleolar precursor bodies and a concomitant increase in nucleolar volume, which results in a single condensed nucleolus. Pharmacological inhibition of Pol I in preimplantation and midgestation embryos, as well as in hiPSCs, similarly results in a single condensed nucleolus or fragmented nucleoli. We find that when Pol I function and rRNA transcription is inhibited, the viscosity of the granular compartment of the nucleolus increases, which disrupts its phase separation properties, leading to a single condensed nucleolus. However, if a cell progresses through mitosis, the absence of rRNA transcription prevents reassembly of the nucleolus and manifests as fragmented nucleoli. Taken together, our data suggests that Pol I function and rRNA transcription are required for maintaining nucleolar structure and integrity during development and in the pathogenesis of disease.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Maureen C. Lamb
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Mary C. McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Xia Zhao
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Timothy J. Corbin
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - MaryEllen Kirkman
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kym Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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13
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Lee S, Roest ASV, Blair CA, Kao K, Bremner SB, Childers MC, Pathak D, Heinrich P, Lee D, Chirikian O, Mohran S, Roberts B, Smith JE, Jahng JW, Paik DT, Wu JC, Gunawardane RN, Spudich JA, Ruppel K, Mack D, Pruitt BL, Regnier M, Wu SM, Bernstein D. Multi-scale models reveal hypertrophic cardiomyopathy MYH7 G256E mutation drives hypercontractility and elevated mitochondrial respiration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544276. [PMID: 37333118 PMCID: PMC10274883 DOI: 10.1101/2023.06.08.544276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Rationale Over 200 mutations in the sarcomeric protein β-myosin heavy chain (MYH7) have been linked to hypertrophic cardiomyopathy (HCM). However, different mutations in MYH7 lead to variable penetrance and clinical severity, and alter myosin function to varying degrees, making it difficult to determine genotype-phenotype relationships, especially when caused by rare gene variants such as the G256E mutation. Objective This study aims to determine the effects of low penetrant MYH7 G256E mutation on myosin function. We hypothesize that the G256E mutation would alter myosin function, precipitating compensatory responses in cellular functions. Methods We developed a collaborative pipeline to characterize myosin function at multiple scales (protein to myofibril to cell to tissue). We also used our previously published data on other mutations to compare the degree to which myosin function was altered. Results At the protein level, the G256E mutation disrupts the transducer region of the S1 head and reduces the fraction of myosin in the folded-back state by 50.9%, suggesting more myosins available for contraction. Myofibrils isolated from hiPSC-CMs CRISPR-edited with G256E (MYH7 WT/G256E ) generated greater tension, had faster tension development and slower early phase relaxation, suggesting altered myosin-actin crossbridge cycling kinetics. This hypercontractile phenotype persisted in single-cell hiPSC-CMs and engineered heart tissues. Single-cell transcriptomic and metabolic profiling demonstrated upregulation of mitochondrial genes and increased mitochondrial respiration, suggesting altered bioenergetics as an early feature of HCM. Conclusions MYH7 G256E mutation causes structural instability in the transducer region, leading to hypercontractility across scales, perhaps from increased myosin recruitment and altered crossbridge cycling. Hypercontractile function of the mutant myosin was accompanied by increased mitochondrial respiration, while cellular hypertrophy was modest in the physiological stiffness environment. We believe that this multi-scale platform will be useful to elucidate genotype-phenotype relationships underlying other genetic cardiovascular diseases.
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14
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Friedman CE, Fayer S, Pendyala S, Chien WM, Loiben A, Tran L, Chao LS, Mckinstry A, Ahmed D, Karbassi E, Fenix AM, Murry CE, Starita LM, Fowler DM, Yang KC. CRaTER enrichment for on-target gene editing enables generation of variant libraries in hiPSCs. J Mol Cell Cardiol 2023; 179:60-71. [PMID: 37019277 PMCID: PMC10208587 DOI: 10.1016/j.yjmcc.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
Standard transgenic cell line generation requires screening 100-1000s of colonies to isolate correctly edited cells. We describe CRISPRa On-Target Editing Retrieval (CRaTER) which enriches for cells with on-target knock-in of a cDNA-fluorescent reporter transgene by transient activation of the targeted locus followed by flow sorting to recover edited cells. We show CRaTER recovers rare cells with heterozygous, biallelic-editing of the transcriptionally-inactive MYH7 locus in human induced pluripotent stem cells (hiPSCs), enriching on average 25-fold compared to standard antibiotic selection. We leveraged CRaTER to enrich for heterozygous knock-in of a library of variants in MYH7, a gene in which missense mutations cause cardiomyopathies, and recovered hiPSCs with 113 different variants. We differentiated these hiPSCs to cardiomyocytes and show MHC-β fusion proteins can localize as expected. Additionally, single-cell contractility analyses revealed cardiomyocytes with a pathogenic, hypertrophic cardiomyopathy-associated MYH7 variant exhibit salient HCM physiology relative to isogenic controls. Thus, CRaTER substantially reduces screening required for isolation of gene-edited cells, enabling generation of functional transgenic cell lines at unprecedented scale.
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Affiliation(s)
- Clayton E Friedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Shawn Fayer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sriram Pendyala
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Wei-Ming Chien
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS, Seattle, WA 98108, USA
| | - Alexander Loiben
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Linda Tran
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Leslie S Chao
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Ashley Mckinstry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Dania Ahmed
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Elaheh Karbassi
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA
| | - Aidan M Fenix
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Kai-Chun Yang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS, Seattle, WA 98108, USA.
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15
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Qiao H, Chiu Y, Liang X, Xia S, Ayrapetyan M, Liu S, He C, Song R, Zeng J, Deng X, Yuan W, Zhao Z. Microglia innate immune response contributes to the antiviral defense and blood-CSF barrier function in human choroid plexus organoids during HSV-1 infection. J Med Virol 2023; 95:e28472. [PMID: 36606611 PMCID: PMC10107173 DOI: 10.1002/jmv.28472] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/07/2023]
Abstract
The choroid plexus (ChP) is the source of cerebrospinal fluid (CSF). The ChP-CSF system not only provides the necessary cushion for the brain but also works as a sink for waste clearance. During sepsis, pathogens and host immune cells can weaken the ChP barrier and enter the brain, causing cerebral dysfunctions known as sepsis-associated encephalophagy. Here, we used human ChP organoid (ChPO) to model herpes simplex virus type 1 (HSV-1) infection and found ChP epithelial cells were highly susceptible to HSV-1. Since the current ChPO model lacks a functional innate immune component, particularly microglia, we next developed a new microglia-containing ChPO model, and found microglia could effectively limit HSV-1 infection and protect epithelial barrier in ChPOs. Furthermore, we found the innate immune cyclic GMP-AMP synthase (cGAS)-STING pathway and its downstream interferon response were essential, as cGAS inhibitor RU.512 or STING inhibitor H-151 abolished microglia antiviral function and worsened ChP barrier in organoids. These results together indicated that cGAS-STING pathway coordinates antiviral response in ChP and contributes to treating sepsis or related neurological conditions.
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Affiliation(s)
- Haowen Qiao
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Yuanpu Chiu
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Xinyan Liang
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Neuroscience Graduate ProgramUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Shangzhou Xia
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Neuroscience Graduate ProgramUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Mariam Ayrapetyan
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Siqi Liu
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Cuiling He
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Ruocen Song
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jianxiong Zeng
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnanChina
- KIZ‐CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnanChina
| | - Xiangxue Deng
- Department of Molecular Microbiology and Immunology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Weiming Yuan
- Department of Molecular Microbiology and Immunology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Zhen Zhao
- Department of Physiology and Biophysics, Keck School of Medicine, Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Neuroscience Graduate ProgramUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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16
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Friedman CE, Fayer S, Pendyala S, Chien WM, Tran L, Chao L, Mckinstry A, Karbassi E, Fenix AM, Loiben A, Murry CE, Starita LM, Fowler DM, Yang KC. CRaTER enrichment for on-target gene-editing enables generation of variant libraries in hiPSCs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525582. [PMID: 36747685 PMCID: PMC9900876 DOI: 10.1101/2023.01.25.525582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Standard transgenic cell line generation requires screening 100-1000s of colonies to isolate correctly edited cells. We describe CR ISPR a On- T arget E diting R etrieval (CRaTER) which enriches for cells with on-target knock-in of a cDNA-fluorescent reporter transgene by transient activation of the targeted locus followed by flow sorting to recover edited cells. We show CRaTER recovers rare cells with heterozygous, biallelic-editing of the transcriptionally-inactive MYH7 locus in human induced pluripotent stem cells (hiPSCs), enriching on average 25-fold compared to standard antibiotic selection. We leveraged CRaTER to enrich for heterozygous knock-in of a library of single nucleotide variants (SNVs) in MYH7 , a gene in which missense mutations cause cardiomyopathies, and recovered hiPSCs with 113 different MYH7 SNVs. We differentiated these hiPSCs to cardiomyocytes and show MYH7 fusion proteins can localize as expected. Thus, CRaTER substantially reduces screening required for isolation of gene-edited cells, enabling generation of transgenic cell lines at unprecedented scale.
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17
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Pantazis CB, Yang A, Lara E, McDonough JA, Blauwendraat C, Peng L, Oguro H, Kanaujiya J, Zou J, Sebesta D, Pratt G, Cross E, Blockwick J, Buxton P, Kinner-Bibeau L, Medura C, Tompkins C, Hughes S, Santiana M, Faghri F, Nalls MA, Vitale D, Ballard S, Qi YA, Ramos DM, Anderson KM, Stadler J, Narayan P, Papademetriou J, Reilly L, Nelson MP, Aggarwal S, Rosen LU, Kirwan P, Pisupati V, Coon SL, Scholz SW, Priebe T, Öttl M, Dong J, Meijer M, Janssen LJM, Lourenco VS, van der Kant R, Crusius D, Paquet D, Raulin AC, Bu G, Held A, Wainger BJ, Gabriele RMC, Casey JM, Wray S, Abu-Bonsrah D, Parish CL, Beccari MS, Cleveland DW, Li E, Rose IVL, Kampmann M, Calatayud Aristoy C, Verstreken P, Heinrich L, Chen MY, Schüle B, Dou D, Holzbaur ELF, Zanellati MC, Basundra R, Deshmukh M, Cohen S, Khanna R, Raman M, Nevin ZS, Matia M, Van Lent J, Timmerman V, Conklin BR, Johnson Chase K, Zhang K, Funes S, Bosco DA, Erlebach L, Welzer M, Kronenberg-Versteeg D, Lyu G, Arenas E, Coccia E, Sarrafha L, Ahfeldt T, Marioni JC, Skarnes WC, Cookson MR, Ward ME, Merkle FT. A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell Stem Cell 2022; 29:1685-1702.e22. [PMID: 36459969 PMCID: PMC9782786 DOI: 10.1016/j.stem.2022.11.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.
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Affiliation(s)
- Caroline B Pantazis
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Andrian Yang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Erika Lara
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lirong Peng
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA; Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Hideyuki Oguro
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jitendra Kanaujiya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | | | - Marianita Santiana
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Daniel Vitale
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Shannon Ballard
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kailyn M Anderson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julia Stadler
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Priyanka Narayan
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Genetics and Biochemistry Branch, NIDDK, NINDS, National Institutes of Health, Bethesda, MD 20814, USA
| | - Jason Papademetriou
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Luke Reilly
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sanya Aggarwal
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Leah U Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Kirwan
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Venkat Pisupati
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Steven L Coon
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Theresa Priebe
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Miriam Öttl
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Jian Dong
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Marieke Meijer
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Lara J M Janssen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Vanessa S Lourenco
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Rik van der Kant
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, the Netherlands
| | - Dennis Crusius
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | | | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian J Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rebecca M C Gabriele
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jackie M Casey
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Dad Abu-Bonsrah
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Emmy Li
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Carles Calatayud Aristoy
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Laurin Heinrich
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Max Y Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dan Dou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria Clara Zanellati
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Basundra
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mohanish Deshmukh
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Khanna
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | | | | | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | | | | | - Ke Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Salome Funes
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Daryl A Bosco
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Lena Erlebach
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Marc Welzer
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Deborah Kronenberg-Versteeg
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Guochang Lyu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ernest Arenas
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elena Coccia
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Mark R Cookson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Michael E Ward
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Florian T Merkle
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
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18
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Blanch-Asensio A, Grandela C, Brandão KO, de Korte T, Mei H, Ariyurek Y, Yiangou L, Mol MP, van Meer BJ, Kloet SL, Mummery CL, Davis RP. STRAIGHT-IN enables high-throughput targeting of large DNA payloads in human pluripotent stem cells. CELL REPORTS METHODS 2022; 2:100300. [PMID: 36313798 PMCID: PMC9606106 DOI: 10.1016/j.crmeth.2022.100300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/12/2022] [Accepted: 08/31/2022] [Indexed: 04/20/2023]
Abstract
Inserting large DNA payloads (>10 kb) into specific genomic sites of mammalian cells remains challenging. Applications ranging from synthetic biology to evaluating the pathogenicity of disease-associated variants for precision medicine initiatives would greatly benefit from tools that facilitate this process. Here, we merge the strengths of different classes of site-specific recombinases and combine these with CRISPR-Cas9-mediated homologous recombination to develop a strategy for stringent site-specific replacement of genomic fragments at least 50 kb in size in human induced pluripotent stem cells (hiPSCs). We demonstrate the versatility of STRAIGHT-IN (serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation) by (1) inserting various combinations of fluorescent reporters into hiPSCs to assess the excitation-contraction coupling cascade in derivative cardiomyocytes and (2) simultaneously targeting multiple variants associated with inherited cardiac arrhythmic disorders into a pool of hiPSCs. STRAIGHT-IN offers a precise approach to generate genetically matched panels of hiPSC lines efficiently and cost effectively.
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Affiliation(s)
- Albert Blanch-Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Catarina Grandela
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Karina O. Brandão
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Tessa de Korte
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Loukia Yiangou
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Mervyn P.H. Mol
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Berend J. van Meer
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Susan L. Kloet
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Christine L. Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, 7500AE Enschede, the Netherlands
| | - Richard P. Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
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19
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Romero-Morales AI, Robertson GL, Rastogi A, Rasmussen ML, Temuri H, McElroy GS, Chakrabarty RP, Hsu L, Almonacid PM, Millis BA, Chandel NS, Cartailler JP, Gama V. Human iPSC-derived cerebral organoids model features of Leigh syndrome and reveal abnormal corticogenesis. Development 2022; 149:275911. [PMID: 35792828 PMCID: PMC9357378 DOI: 10.1242/dev.199914] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 05/18/2022] [Indexed: 01/12/2023]
Abstract
Leigh syndrome (LS) is a rare, inherited neurometabolic disorder that presents with bilateral brain lesions caused by defects in the mitochondrial respiratory chain and associated nuclear-encoded proteins. We generated human induced pluripotent stem cells (iPSCs) from three LS patient-derived fibroblast lines. Using whole-exome and mitochondrial sequencing, we identified unreported mutations in pyruvate dehydrogenase (GM0372, PDH; GM13411, MT-ATP6/PDH) and dihydrolipoyl dehydrogenase (GM01503, DLD). These LS patient-derived iPSC lines were viable and capable of differentiating into progenitor populations, but we identified several abnormalities in three-dimensional differentiation models of brain development. LS patient-derived cerebral organoids showed defects in neural epithelial bud generation, size and cortical architecture at 100 days. The double mutant MT-ATP6/PDH line produced organoid neural precursor cells with abnormal mitochondrial morphology, characterized by fragmentation and disorganization, and showed an increased generation of astrocytes. These studies aim to provide a comprehensive phenotypic characterization of available patient-derived cell lines that can be used to study Leigh syndrome.
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Affiliation(s)
| | - Gabriella L. Robertson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Anuj Rastogi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Megan L. Rasmussen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Hoor Temuri
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Gregory Scott McElroy
- Feinberg School of Medicine, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ram Prosad Chakrabarty
- Feinberg School of Medicine, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lawrence Hsu
- Creative Data Solutions, Vanderbilt Center for Stem Cell Biology,Vanderbilt University,Nashville, TN 37232, USA
| | | | - Bryan A. Millis
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA,Vanderbilt Biophotonics Center,Vanderbilt University, Nashville, TN 37232, USA
| | - Navdeep S. Chandel
- Feinberg School of Medicine, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL 60611, USA,Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-Philippe Cartailler
- Creative Data Solutions, Vanderbilt Center for Stem Cell Biology,Vanderbilt University,Nashville, TN 37232, USA
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA,Creative Data Solutions, Vanderbilt Center for Stem Cell Biology,Vanderbilt University,Nashville, TN 37232, USA,Vanderbilt Brain Institute,Vanderbilt University,Nashville, TN 37232, USA,Author for correspondence ()
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20
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Stein JM, Arslan U, Franken M, de Greef JC, E Harding S, Mohammadi N, Orlova VV, Bellin M, Mummery CL, van Meer BJ. Software Tool for Automatic Quantification of Sarcomere Length and Organization in Fixed and Live 2D and 3D Muscle Cell Cultures In Vitro. Curr Protoc 2022; 2:e462. [PMID: 35789134 DOI: 10.1002/cpz1.462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sarcomeres are the structural units of the contractile apparatus in cardiac and skeletal muscle cells. Changes in sarcomere characteristics are indicative of changes in the sarcomeric proteins and function during development and disease. Assessment of sarcomere length, alignment, and organization provides insight into disease and drug responses in striated muscle cells and models, ranging from cardiomyocytes and skeletal muscle cells derived from human pluripotent stem cells to adult muscle cells isolated from animals or humans. However, quantification of sarcomere length is typically time consuming and prone to user-specific selection bias. Automated analysis pipelines exist but these often require either specialized software or programming experience. In addition, these pipelines are often designed for only one type of cell model in vitro. Here, we present an easy-to-implement protocol and software tool for automated sarcomere length and organization quantification in a variety of striated muscle in vitro models: Two dimensional (2D) cardiomyocytes, three dimensional (3D) cardiac microtissues, isolated adult cardiomyocytes, and 3D tissue engineered skeletal muscles. Based on an existing mathematical algorithm, this image analysis software (SotaTool) automatically detects the direction in which the sarcomere organization is highest over the entire image and outputs the length and organization of sarcomeres. We also analyzed videos of live cells during contraction, thereby allowing measurement of contraction parameters like fractional shortening, contraction time, relaxation time, and beating frequency. In this protocol, we give a step-by-step guide on how to prepare, image, and automatically quantify sarcomere and contraction characteristics in different types of in vitro models and we provide basic validation and discussion of the limitations of the software tool. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Staining and analyzing static hiPSC-CMs with SotaTool Alternate Protocol: Sample preparation, acquisition, and quantification of fractional shortening in live reporter hiPSC lines Support Protocol 1: Finding the image resolution Support Protocol 2: Advanced analysis settings Support Protocol 3: Finding sarcomere length in non-aligned cells.
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Affiliation(s)
- Jeroen M Stein
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ulgu Arslan
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marnix Franken
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sian E Harding
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Neda Mohammadi
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Valeria V Orlova
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Milena Bellin
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Biology, University of Padua, Padua, Italy
- Veneto Institute of Molecular Medicine, Padua, Italy
| | - Christine L Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, Enschede, The Netherlands
| | - Berend J van Meer
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
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21
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Li J, Feng X, Wei X. Modeling hypertrophic cardiomyopathy with human cardiomyocytes derived from induced pluripotent stem cells. Stem Cell Res Ther 2022; 13:232. [PMID: 35659761 PMCID: PMC9166443 DOI: 10.1186/s13287-022-02905-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/16/2022] Open
Abstract
One of the obstacles in studying the pathogenesis of hypertrophic cardiomyopathy (HCM) is the poor availability of myocardial tissue samples at the early stages of disease development. This has been addressed by the advent of induced pluripotent stem cells (iPSCs), which allow us to differentiate patient-derived iPSCs into cardiomyocytes (iPSC-CMs) in vitro. In this review, we summarize different approaches to establishing iPSC models and the application of genome editing techniques in iPSC. Because iPSC-CMs cultured at the present stage are immature in structure and function, researchers have attempted several methods to mature iPSC-CMs, such as prolonged culture duration, and mechanical and electrical stimulation. Currently, many researchers have established iPSC-CM models of HCM and employed diverse methods for performing measurements of cellular morphology, contractility, electrophysiological property, calcium handling, mitochondrial function, and metabolism. Here, we review published results in humans to date within the growing field of iPSC-CM models of HCM. Although there is no unified consensus, preliminary results suggest that this approach to modeling disease would provide important insights into our understanding of HCM pathogenesis and facilitate drug development and safety testing.
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Affiliation(s)
- Jiangtao Li
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xin Feng
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xiang Wei
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
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22
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Yücel D, Garay BI, Perlingeiro RCR, van Berlo JH. Stimulation of Cardiomyocyte Proliferation Is Dependent on Species and Level of Maturation. Front Cell Dev Biol 2022; 10:806564. [PMID: 35663393 PMCID: PMC9160302 DOI: 10.3389/fcell.2022.806564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/28/2022] [Indexed: 11/24/2022] Open
Abstract
The heart is one of the least regenerative organs. This is in large part due to the inability of adult mammalian cardiomyocytes to proliferate and divide. In recent years, a number of small molecules and molecular targets have been identified to stimulate cardiomyocyte proliferation, including p38 inhibition, YAP-Tead activation, fibroblast growth factor 1 and Neuregulin 1. Despite these exciting initial findings, a therapeutic approach to enhance cardiomyocyte proliferation in vivo is still lacking. We hypothesized that a more comprehensive in vitro validation using live-cell imaging and assessment of the proliferative effects on various cardiomyocyte sources might identify the most potent proliferative stimuli. Here, we used previously published stimuli to determine their proliferative effect on cardiomyocytes from different species and isolated from different developmental timepoints. Although all stimuli enhanced DNA synthesis and Histone H3 phosphorylation in neonatal rat ventricular cardiomyocytes to similar degrees, these effects varied substantially in mouse cardiomyocytes and human iPSC-derived cardiomyocytes. Our results highlight p21 inhibition and Yap-Tead activation as potent proliferative strategies to induce cultured cardiomyocyte cell cycle activity across mouse, rat and human cardiomyocytes.
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Affiliation(s)
- Dogacan Yücel
- Department of Medicine, Lillehei Heart Institute, Cardiovascular Division, University of Minnesota, Minneapolis, MN, United States
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, United States
| | - Bayardo I. Garay
- Department of Medicine, Lillehei Heart Institute, Cardiovascular Division, University of Minnesota, Minneapolis, MN, United States
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, United States
- Medical Scientist Training Program, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Rita C. R. Perlingeiro
- Department of Medicine, Lillehei Heart Institute, Cardiovascular Division, University of Minnesota, Minneapolis, MN, United States
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, United States
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
| | - Jop H. van Berlo
- Department of Medicine, Lillehei Heart Institute, Cardiovascular Division, University of Minnesota, Minneapolis, MN, United States
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Jop H. van Berlo,
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23
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Acharya A, Nemade H, Rajendra Prasad K, Khan K, Hescheler J, Blackburn N, Hemmersbach R, Papadopoulos S, Sachinidis A. Live-Cell Imaging of the Contractile Velocity and Transient Intracellular Ca2+ Fluctuations in Human Stem Cell-Derived Cardiomyocytes. Cells 2022; 11:cells11081280. [PMID: 35455960 PMCID: PMC9031802 DOI: 10.3390/cells11081280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
Live-cell imaging techniques are essential for acquiring vital physiological and pathophysiological knowledge to understand and treat heart disease. For live-cell imaging of transient alterations of [Ca2+]i in human cardiomyocytes, we engineered human-induced pluripotent stem cells carrying a genetically-encoded Ca2+-indicator (GECI). To monitor sarcomere shortening and relaxation in cardiomyocytes in real-time, we generated a α-cardiac actinin (ACTN2)-copepod (cop) green fluorescent protein (GFP+)-human-induced pluripotent stem cell line by using the CRISPR-Cas9 and a homology directed recombination approach. The engineered human-induced pluripotent stem cells were differentiated in transgenic GECI-enhanced GFP+-cardiomyocytes and ACTN2-copGFP+-cardiomyocytes, allowing real-time imaging of [Ca2+]i transients and live recordings of the sarcomere shortening velocity of ACTN2-copGFP+-cardiomyocytes. We developed a video analysis software tool to quantify various parameters of sarcoplasmic Ca2+ fluctuations recorded during contraction of cardiomyocytes and to calculate the contraction velocity of cardiomyocytes in the presence and absence of different drugs affecting cardiac function. Our cellular and software tool not only proved the positive and negative inotropic and lusitropic effects of the tested cardioactive drugs but also quantified the expected effects precisely. Our platform will offer a human-relevant in vitro alternative for high-throughput drug screenings, as well as a model to explore the underlying mechanisms of cardiac diseases.
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Affiliation(s)
- Aviseka Acharya
- Working Group Sachinidis, Center for Physiology, Faculty of Medicine and University Hospital Cologne, The University of Cologne, 50931 Cologne, Germany; (A.A.); (H.N.); (K.R.P.); (K.K.); (J.H.); (S.P.)
| | - Harshal Nemade
- Working Group Sachinidis, Center for Physiology, Faculty of Medicine and University Hospital Cologne, The University of Cologne, 50931 Cologne, Germany; (A.A.); (H.N.); (K.R.P.); (K.K.); (J.H.); (S.P.)
| | - Krishna Rajendra Prasad
- Working Group Sachinidis, Center for Physiology, Faculty of Medicine and University Hospital Cologne, The University of Cologne, 50931 Cologne, Germany; (A.A.); (H.N.); (K.R.P.); (K.K.); (J.H.); (S.P.)
| | - Khadija Khan
- Working Group Sachinidis, Center for Physiology, Faculty of Medicine and University Hospital Cologne, The University of Cologne, 50931 Cologne, Germany; (A.A.); (H.N.); (K.R.P.); (K.K.); (J.H.); (S.P.)
| | - Jürgen Hescheler
- Working Group Sachinidis, Center for Physiology, Faculty of Medicine and University Hospital Cologne, The University of Cologne, 50931 Cologne, Germany; (A.A.); (H.N.); (K.R.P.); (K.K.); (J.H.); (S.P.)
| | - Nick Blackburn
- Bioras Company, Kaarsbergsvej 2, 8400 Ebeltoft, Denmark;
| | - Ruth Hemmersbach
- German Aerospace Center, Institute of Aerospace Medicine, Gravitational Biology, Linder Hoehe, 51147 Cologne, Germany;
| | - Symeon Papadopoulos
- Working Group Sachinidis, Center for Physiology, Faculty of Medicine and University Hospital Cologne, The University of Cologne, 50931 Cologne, Germany; (A.A.); (H.N.); (K.R.P.); (K.K.); (J.H.); (S.P.)
| | - Agapios Sachinidis
- Working Group Sachinidis, Center for Physiology, Faculty of Medicine and University Hospital Cologne, The University of Cologne, 50931 Cologne, Germany; (A.A.); (H.N.); (K.R.P.); (K.K.); (J.H.); (S.P.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence: ; Tel.: +49-2214787373
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24
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Mianné J, Nasri A, Van CN, Bourguignon C, Fieldès M, Ahmed E, Duthoit C, Martin N, Parrinello H, Louis A, Iché A, Gayon R, Samain F, Lamouroux L, Bouillé P, Bourdin A, Assou S, De Vos J. CRISPR/Cas9-mediated gene knockout and interallelic gene conversion in human induced pluripotent stem cells using non-integrative bacteriophage-chimeric retrovirus-like particles. BMC Biol 2022; 20:8. [PMID: 34996449 PMCID: PMC8742436 DOI: 10.1186/s12915-021-01214-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The application of CRISPR/Cas9 technology in human induced pluripotent stem cells (hiPSC) holds tremendous potential for basic research and cell-based gene therapy. However, the fulfillment of these promises relies on the capacity to efficiently deliver exogenous nucleic acids and harness the repair mechanisms induced by the nuclease activity in order to knock-out or repair targeted genes. Moreover, transient delivery should be preferred to avoid persistent nuclease activity and to decrease the risk of off-target events. We recently developed bacteriophage-chimeric retrovirus-like particles that exploit the properties of bacteriophage coat proteins to package exogenous RNA, and the benefits of lentiviral transduction to achieve highly efficient, non-integrative RNA delivery in human cells. Here, we investigated the potential of bacteriophage-chimeric retrovirus-like particles for the non-integrative delivery of RNA molecules in hiPSC for CRISPR/Cas9 applications. RESULTS We found that these particles efficiently convey RNA molecules for transient expression in hiPSC, with minimal toxicity and without affecting the cell pluripotency and subsequent differentiation. We then used this system to transiently deliver in a single step the CRISPR-Cas9 components (Cas9 mRNA and sgRNA) to generate gene knockout with high indel rate (up to 85%) at multiple loci. Strikingly, when using an allele-specific sgRNA at a locus harboring compound heterozygous mutations, the targeted allele was not altered by NHEJ/MMEJ, but was repaired at high frequency using the homologous wild type allele, i.e., by interallelic gene conversion. CONCLUSIONS Our results highlight the potential of bacteriophage-chimeric retrovirus-like particles to efficiently and safely deliver RNA molecules in hiPSC, and describe for the first time genome engineering by gene conversion in hiPSC. Harnessing this DNA repair mechanism could facilitate the therapeutic correction of human genetic disorders in hiPSC.
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Affiliation(s)
- Joffrey Mianné
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Amel Nasri
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Chloé Nguyen Van
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Chloé Bourguignon
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Mathieu Fieldès
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Engi Ahmed
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | | | | | - Hugues Parrinello
- Univ. Montpellier, CNRS, INSERM, Montpellier, France
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Anaïs Louis
- Univ. Montpellier, CNRS, INSERM, Montpellier, France
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | | | | | | | | | | | - Arnaud Bourdin
- PhyMedExp, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Said Assou
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - John De Vos
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France.
- Department of Cell and Tissue Engineering, Univ Montpellier, CHU Montpellier, Montpellier, France.
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25
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Sun D, Evans L, Perrone F, Sokleva V, Lim K, Rezakhani S, Lutolf M, Zilbauer M, Rawlins EL. A functional genetic toolbox for human tissue-derived organoids. eLife 2021; 10:67886. [PMID: 34612202 PMCID: PMC8553336 DOI: 10.7554/elife.67886] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Human organoid systems recapitulate key features of organs offering platforms for modelling developmental biology and disease. Tissue-derived organoids have been widely used to study the impact of extrinsic niche factors on stem cells. However, they are rarely used to study endogenous gene function due to the lack of efficient gene manipulation tools. Previously, we established a human foetal lung organoid system (Nikolić et al., 2017). Here, using this organoid system as an example, we have systematically developed and optimised a complete genetic toolbox for use in tissue-derived organoids. This includes ‘Organoid Easytag’, our efficient workflow for targeting all types of gene loci through CRISPR-mediated homologous recombination followed by flow cytometry for enriching correctly targeted cells. Our toolbox also incorporates conditional gene knockdown or overexpression using tightly inducible CRISPR interference and CRISPR activation which is the first efficient application of these techniques to tissue-derived organoids. These tools will facilitate gene perturbation studies in tissue-derived organoids facilitating human disease modelling and providing a functional counterpart to many ongoing descriptive studies, such as the Human Cell Atlas Project.
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Affiliation(s)
- Dawei Sun
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Lewis Evans
- Developmental Biology and Cancer Development, University College London, London, United Kingdom
| | | | | | - Kyungtae Lim
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Saba Rezakhani
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matthias Lutolf
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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26
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Grancharova T, Gerbin KA, Rosenberg AB, Roco CM, Arakaki JE, DeLizo CM, Dinh SQ, Donovan-Maiye RM, Hirano M, Nelson AM, Tang J, Theriot JA, Yan C, Menon V, Palecek SP, Seelig G, Gunawardane RN. A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes. Sci Rep 2021; 11:15845. [PMID: 34349150 PMCID: PMC8338992 DOI: 10.1038/s41598-021-94732-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
We performed a comprehensive analysis of the transcriptional changes occurring during human induced pluripotent stem cell (hiPSC) differentiation to cardiomyocytes. Using single cell RNA-seq, we sequenced > 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. Differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables.
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Affiliation(s)
| | | | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,, Parse Biosciences, Seattle, WA, USA
| | - Charles M Roco
- , Parse Biosciences, Seattle, WA, USA.,Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Matthew Hirano
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA
| | | | - Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Julie A Theriot
- Allen Institute for Cell Science, Seattle, WA, USA.,Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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27
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Gerbin KA, Grancharova T, Donovan-Maiye RM, Hendershott MC, Anderson HG, Brown JM, Chen J, Dinh SQ, Gehring JL, Johnson GR, Lee H, Nath A, Nelson AM, Sluzewski MF, Viana MP, Yan C, Zaunbrecher RJ, Cordes Metzler KR, Gaudreault N, Knijnenburg TA, Rafelski SM, Theriot JA, Gunawardane RN. Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes. Cell Syst 2021; 12:670-687.e10. [PMID: 34043964 DOI: 10.1016/j.cels.2021.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/07/2020] [Accepted: 04/30/2021] [Indexed: 12/11/2022]
Abstract
Although some cell types may be defined anatomically or by physiological function, a rigorous definition of cell state remains elusive. Here, we develop a quantitative, imaging-based platform for the systematic and automated classification of subcellular organization in single cells. We use this platform to quantify subcellular organization and gene expression in >30,000 individual human induced pluripotent stem cell-derived cardiomyocytes, producing a publicly available dataset that describes the population distributions of local and global sarcomere organization, mRNA abundance, and correlations between these traits. While the mRNA abundance of some phenotypically important genes correlates with subcellular organization (e.g., the beta-myosin heavy chain, MYH7), these two cellular metrics are heterogeneous and often uncorrelated, which suggests that gene expression alone is not sufficient to classify cell states. Instead, we posit that cell state should be defined by observing full distributions of quantitative, multidimensional traits in single cells that also account for space, time, and function.
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Affiliation(s)
- Kaytlyn A Gerbin
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Tanya Grancharova
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | | | - Helen G Anderson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jackson M Brown
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jianxu Chen
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Stephanie Q Dinh
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jamie L Gehring
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Gregory R Johnson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - HyeonWoo Lee
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Aditya Nath
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | - M Filip Sluzewski
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Matheus P Viana
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | | | | | | | | | - Julie A Theriot
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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28
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Hofbauer P, Jahnel SM, Papai N, Giesshammer M, Deyett A, Schmidt C, Penc M, Tavernini K, Grdseloff N, Meledeth C, Ginistrelli LC, Ctortecka C, Šalic Š, Novatchkova M, Mendjan S. Cardioids reveal self-organizing principles of human cardiogenesis. Cell 2021; 184:3299-3317.e22. [PMID: 34019794 DOI: 10.1016/j.cell.2021.04.034] [Citation(s) in RCA: 214] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 02/12/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022]
Abstract
Organoids capable of forming tissue-like structures have transformed our ability to model human development and disease. With the notable exception of the human heart, lineage-specific self-organizing organoids have been reported for all major organs. Here, we established self-organizing cardioids from human pluripotent stem cells that intrinsically specify, pattern, and morph into chamber-like structures containing a cavity. Cardioid complexity can be controlled by signaling that instructs the separation of cardiomyocyte and endothelial layers and by directing epicardial spreading, inward migration, and differentiation. We find that cavity morphogenesis is governed by a mesodermal WNT-BMP signaling axis and requires its target HAND1, a transcription factor linked to developmental heart chamber defects. Upon cryoinjury, cardioids initiated a cell-type-dependent accumulation of extracellular matrix, an early hallmark of both regeneration and heart disease. Thus, human cardioids represent a powerful platform to mechanistically dissect self-organization, congenital heart defects and serve as a foundation for future translational research.
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Affiliation(s)
- Pablo Hofbauer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Stefan M Jahnel
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Nora Papai
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Magdalena Giesshammer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Alison Deyett
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Clara Schmidt
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Mirjam Penc
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Katherina Tavernini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Nastasja Grdseloff
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Christy Meledeth
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Lavinia Ceci Ginistrelli
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Claudia Ctortecka
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Šejla Šalic
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Pathology (IMP), Vienna Biocenter 1, 1030 Vienna, Austria
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria.
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29
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Hendriks D, Clevers H, Artegiani B. CRISPR-Cas Tools and Their Application in Genetic Engineering of Human Stem Cells and Organoids. Cell Stem Cell 2021; 27:705-731. [PMID: 33157047 DOI: 10.1016/j.stem.2020.10.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas technology has revolutionized biological research and holds great therapeutic potential. Here, we review CRISPR-Cas systems and their latest developments with an emphasis on application to human cells. We also discuss how different CRISPR-based strategies can be used to accomplish a particular genome engineering goal. We then review how different CRISPR tools have been used in genome engineering of human stem cells in vitro, covering both the pluripotent (iPSC/ESC) and somatic adult stem cell fields and, in particular, 3D organoid cultures. Finally, we discuss the progress and challenges associated with CRISPR-based genome editing of human stem cells for therapeutic use.
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Affiliation(s)
- Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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30
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Anzai T, Hara H, Chanthra N, Sadahiro T, Ieda M, Hanazono Y, Uosaki H. Generation of Efficient Knock-in Mouse and Human Pluripotent Stem Cells Using CRISPR-Cas9. Methods Mol Biol 2021; 2320:247-259. [PMID: 34302663 DOI: 10.1007/978-1-0716-1484-6_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A knock-in can generate fluorescent or Cre-reporter under the control of an endogenous promoter. It also generates knock-out or tagged-protein with fluorescent protein and short tags for tracking and purification. Recent advances in genome editing with clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein 9 (Cas9) significantly increased the efficiencies of making knock-in cells. Here we describe the detailed protocols of generating knock-in mouse and human pluripotent stem cells (PSCs) by electroporation and lipofection, respectively.
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Affiliation(s)
- Tatsuya Anzai
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Department of Pediatrics, Jichi Medical University, Tochigi, Japan
| | - Hiromasa Hara
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Animal Resource Laboratory, Center for Development of Advanced Medical Technology, Jichi Medical University, Tochigi, Japan
| | - Nawin Chanthra
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Taketaro Sadahiro
- Department of Cardiology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masaki Ieda
- Department of Cardiology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yutaka Hanazono
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Translational Research Laboratory, Center for Development of Advanced Medical Technology, Jichi Medical University, Tochigi, Japan
| | - Hideki Uosaki
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan.
- Translational Research Laboratory, Center for Development of Advanced Medical Technology, Jichi Medical University, Tochigi, Japan.
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Plant AL, Halter M, Stinson J. Probing pluripotency gene regulatory networks with quantitative live cell imaging. Comput Struct Biotechnol J 2020; 18:2733-2743. [PMID: 33101611 PMCID: PMC7560648 DOI: 10.1016/j.csbj.2020.09.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/12/2022] Open
Abstract
Live cell imaging uniquely enables the measurement of dynamic events in single cells, but it has not been used often in the study of gene regulatory networks. Network components can be examined in relation to one another by quantitative live cell imaging of fluorescent protein reporter cell lines that simultaneously report on more than one network component. A series of dual-reporter cell lines would allow different combinations of network components to be examined in individual cells. Dynamical information about interacting network components in individual cells is critical to predictive modeling of gene regulatory networks, and such information is not accessible through omics and other end point techniques. Achieving this requires that gene-edited cell lines are appropriately designed and adequately characterized to assure the validity of the biological conclusions derived from the expression of the reporters. In this brief review we discuss what is known about the importance of dynamics to network modeling and review some recent advances in optical microscopy methods and image analysis approaches that are making the use of quantitative live cell imaging for network analysis possible. We also discuss how strategies for genetic engineering of reporter cell lines can influence the biological relevance of the data.
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Affiliation(s)
- Anne L Plant
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, United States
| | - Michael Halter
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, United States
| | - Jeffrey Stinson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, United States
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32
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Kohama Y, Higo S, Masumura Y, Shiba M, Kondo T, Ishizu T, Higo T, Nakamura S, Kameda S, Tabata T, Inoue H, Motooka D, Okuzaki D, Takashima S, Miyagawa S, Sawa Y, Hikoso S, Sakata Y. Adeno-associated virus-mediated gene delivery promotes S-phase entry-independent precise targeted integration in cardiomyocytes. Sci Rep 2020; 10:15348. [PMID: 32948788 PMCID: PMC7501291 DOI: 10.1038/s41598-020-72216-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Post-mitotic cardiomyocytes have been considered to be non-permissive to precise targeted integration including homology-directed repair (HDR) after CRISPR/Cas9 genome editing. Here, we demonstrate that direct delivery of large amounts of transgene encoding guide RNA (gRNA) and repair template DNA via intra-ventricular injection of adeno-associated virus (AAV) promotes precise targeted genome replacement in adult murine cardiomyocytes expressing Cas9. Neither systemic injection of AAV nor direct injection of adenovirus promotes targeted integration, suggesting that high copy numbers of single-stranded transgenes are required in cardiomyocytes. Notably, AAV-mediated targeted integration in cardiomyocytes both in vitro and in vivo depends on the Fanconi anemia pathway, a key component of the single-strand template repair mechanism. In human cardiomyocytes differentiated from induced pluripotent stem cells, AAV-mediated targeted integration fluorescently labeled Mlc2v protein after differentiation, independently of DNA synthesis, and enabled real-time detection of sarcomere contraction in monolayered beating cardiomyocytes. Our findings provide a wide range of applications for targeted genome replacement in non-dividing cardiomyocytes.
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Affiliation(s)
- Yasuaki Kohama
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shuichiro Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Medical Therapeutics for Heart Failure, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
| | - Yuki Masumura
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mikio Shiba
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takumi Kondo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takamaru Ishizu
- Higashiosaka City Medical Center, Higashiosaka, Osaka, 578-8588, Japan
| | - Tomoaki Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Satoki Nakamura
- Department of Medical Therapeutics for Heart Failure, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
- Department of Medical Biochemistry, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Satoshi Kameda
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoka Tabata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroyuki Inoue
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
| | - Seiji Takashima
- Department of Medical Biochemistry, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yoshiki Sawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shungo Hikoso
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Mianné J, Bourguignon C, Nguyen Van C, Fieldès M, Nasri A, Assou S, De Vos J. Pipeline for the Generation and Characterization of Transgenic Human Pluripotent Stem Cells Using the CRISPR/Cas9 Technology. Cells 2020; 9:cells9051312. [PMID: 32466123 PMCID: PMC7290981 DOI: 10.3390/cells9051312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
Recent advances in genome engineering based on the CRISPR/Cas9 technology have revolutionized our ability to manipulate genomic DNA. Its use in human pluripotent stem cells (hPSCs) has allowed a wide range of mutant cell lines to be obtained at an unprecedented rate. The combination of these two groundbreaking technologies has tremendous potential, from disease modeling to stem cell-based therapies. However, the generation, screening and molecular characterization of these cell lines remain a cumbersome and multi-step endeavor. Here, we propose a pipeline of strategies to efficiently generate, sub-clone, and characterize CRISPR/Cas9-edited hPSC lines in the function of the introduced mutation (indels, point mutations, insertion of large constructs, deletions).
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Affiliation(s)
- Joffrey Mianné
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Chloé Bourguignon
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Chloé Nguyen Van
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Mathieu Fieldès
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Amel Nasri
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Said Assou
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
- Correspondence: (S.A.); (J.D.V.)
| | - John De Vos
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
- Department of Cell and Tissue Engineering, Univ Montpellier, CHU Montpellier, 34000 Montpellier, France
- Correspondence: (S.A.); (J.D.V.)
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Camp JG, Platt R, Treutlein B. Mapping human cell phenotypes to genotypes with single-cell genomics. Science 2020; 365:1401-1405. [PMID: 31604266 DOI: 10.1126/science.aax6648] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cumulative activity of all of the body's cells, with their myriad interactions, life histories, and environmental experiences, gives rise to a condition that is distinctly human and specific to each individual. It is an enduring goal to catalog our human cell types, to understand how they develop, how they vary between individuals, and how they fail in disease. Single-cell genomics has revolutionized this endeavor because sequencing-based methods provide a means to quantitatively annotate cell states on the basis of high-information content and high-throughput measurements. Together with advances in stem cell biology and gene editing, we are in the midst of a fascinating journey to understand the cellular phenotypes that compose human bodies and how the human genome is used to build and maintain each cell. Here, we will review recent advances into how single-cell genomics is being used to develop personalized phenotyping strategies that cross subcellular, cellular, and tissue scales to link our genome to our cumulative cellular phenotypes.
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Affiliation(s)
- J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Randall Platt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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35
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Filice F, Schwaller B, Michel TM, Grünblatt E. Profiling parvalbumin interneurons using iPSC: challenges and perspectives for Autism Spectrum Disorder (ASD). Mol Autism 2020; 11:10. [PMID: 32000856 PMCID: PMC6990584 DOI: 10.1186/s13229-020-0314-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Autism spectrum disorders (ASD) are persistent conditions resulting from disrupted/altered neurodevelopment. ASD multifactorial etiology-and its numerous comorbid conditions-heightens the difficulty in identifying its underlying causes, thus obstructing the development of effective therapies. Increasing evidence from both animal and human studies suggests an altered functioning of the parvalbumin (PV)-expressing inhibitory interneurons as a common and possibly unifying pathway for some forms of ASD. PV-expressing interneurons (short: PVALB neurons) are critically implicated in the regulation of cortical networks' activity. Their particular connectivity patterns, i.e., their preferential targeting of perisomatic regions and axon initial segments of pyramidal cells, as well as their reciprocal connections, enable PVALB neurons to exert a fine-tuned control of, e.g., spike timing, resulting in the generation and modulation of rhythms in the gamma range, which are important for sensory perception and attention.New methodologies such as induced pluripotent stem cells (iPSC) and genome-editing techniques (CRISPR/Cas9) have proven to be valuable tools to get mechanistic insight in neurodevelopmental and/or neurodegenerative and neuropsychiatric diseases. Such technological advances have enabled the generation of PVALB neurons from iPSC. Tagging of these neurons would allow following their fate during the development, from precursor cells to differentiated (and functional) PVALB neurons. Also, it would enable a better understanding of PVALB neuron function, using either iPSC from healthy donors or ASD patients with known mutations in ASD risk genes. In this concept paper, the strategies hopefully leading to a better understanding of PVALB neuron function(s) are briefly discussed. We envision that such an iPSC-based approach combined with emerging (genetic) technologies may offer the opportunity to investigate in detail the role of PVALB neurons and PV during "neurodevelopment ex vivo."
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Affiliation(s)
- Federica Filice
- Department of Neuroscience & Movements Science, Section of Medicine, University of Fribourg, Fribourg, Switzerland.
| | - Beat Schwaller
- Department of Neuroscience & Movements Science, Section of Medicine, University of Fribourg, Fribourg, Switzerland
| | - Tanja M Michel
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Psychiatry in the Region of Southern Denmark, Department of Psychiatry, Odense University Hospital Southern Denmark, Odense, Denmark
- Research Unit for Psychiatry Odense, Institute for Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Neumuensterallee 3, 8032, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
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Cota-Coronado A, Thompson LH, Diaz-Martinez NE. Novel pluripotent stem cell lines for enriched grafting in Parkinson's disease. Neural Regen Res 2020; 15:255-256. [PMID: 31552892 PMCID: PMC6905335 DOI: 10.4103/1673-5374.265548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Agustin Cota-Coronado
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Australia
| | - Lachlan H Thompson
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Australia
| | - N Emmanuel Diaz-Martinez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
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Brodehl A, Ebbinghaus H, Deutsch MA, Gummert J, Gärtner A, Ratnavadivel S, Milting H. Human Induced Pluripotent Stem-Cell-Derived Cardiomyocytes as Models for Genetic Cardiomyopathies. Int J Mol Sci 2019; 20:ijms20184381. [PMID: 31489928 PMCID: PMC6770343 DOI: 10.3390/ijms20184381] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
In the last few decades, many pathogenic or likely pathogenic genetic mutations in over hundred different genes have been described for non-ischemic, genetic cardiomyopathies. However, the functional knowledge about most of these mutations is still limited because the generation of adequate animal models is time-consuming and challenging. Therefore, human induced pluripotent stem cells (iPSCs) carrying specific cardiomyopathy-associated mutations are a promising alternative. Since the original discovery that pluripotency can be artificially induced by the expression of different transcription factors, various patient-specific-induced pluripotent stem cell lines have been generated to model non-ischemic, genetic cardiomyopathies in vitro. In this review, we describe the genetic landscape of non-ischemic, genetic cardiomyopathies and give an overview about different human iPSC lines, which have been developed for the disease modeling of inherited cardiomyopathies. We summarize different methods and protocols for the general differentiation of human iPSCs into cardiomyocytes. In addition, we describe methods and technologies to investigate functionally human iPSC-derived cardiomyocytes. Furthermore, we summarize novel genome editing approaches for the genetic manipulation of human iPSCs. This review provides an overview about the genetic landscape of inherited cardiomyopathies with a focus on iPSC technology, which might be of interest for clinicians and basic scientists interested in genetic cardiomyopathies.
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Affiliation(s)
- Andreas Brodehl
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Hans Ebbinghaus
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Marcus-André Deutsch
- Department of Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Jan Gummert
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
- Department of Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Sandra Ratnavadivel
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
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