1
|
Mueller LM, Isaacson A, Wilson H, Salowka A, Tay I, Gong M, Elbarbary NS, Raile K, Spagnoli FM. Heterozygous missense variant in GLI2 impairs human endocrine pancreas development. Nat Commun 2024; 15:2483. [PMID: 38509065 PMCID: PMC10954617 DOI: 10.1038/s41467-024-46740-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Missense variants are the most common type of coding genetic variants. Their functional assessment is fundamental for defining any implication in human diseases and may also uncover genes that are essential for human organ development. Here, we apply CRISPR-Cas9 gene editing on human iPSCs to study a heterozygous missense variant in GLI2 identified in two siblings with early-onset and insulin-dependent diabetes of unknown cause. GLI2 is a primary mediator of the Hedgehog pathway, which regulates pancreatic β-cell development in mice. However, neither mutations in GLI2 nor Hedgehog dysregulation have been reported as cause or predisposition to diabetes. We establish and study a set of isogenic iPSC lines harbouring the missense variant for their ability to differentiate into pancreatic β-like cells. Interestingly, iPSCs carrying the missense variant show altered GLI2 transcriptional activity and impaired differentiation of pancreatic progenitors into endocrine cells. RNASeq and network analyses unveil a crosstalk between Hedgehog and WNT pathways, with the dysregulation of non-canonical WNT signaling in pancreatic progenitors carrying the GLI2 missense variant. Collectively, our findings underscore an essential role for GLI2 in human endocrine development and identify a gene variant that may lead to diabetes.
Collapse
Affiliation(s)
- Laura M Mueller
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Abigail Isaacson
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Heather Wilson
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Anna Salowka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Isabel Tay
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Maolian Gong
- Department of Pediatric Endocrinology and Diabetology, Charité, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Charité Medical Faculty, Max-Delbrueck-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Nancy Samir Elbarbary
- Department of Pediatrics, Diabetes and Endocrine Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Klemens Raile
- Department of Pediatric Endocrinology and Diabetology, Charité, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Charité Medical Faculty, Max-Delbrueck-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Francesca M Spagnoli
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London, SE1 9RT, United Kingdom.
| |
Collapse
|
2
|
Miyamoto H, Kobayashi H, Kishima N, Yamazaki K, Hamamichi S, Uno N, Abe S, Hiramuki Y, Kazuki K, Tomizuka K, Kazuki Y. Rapid human genomic DNA cloning into mouse artificial chromosome via direct chromosome transfer from human iPSC and CRISPR/Cas9-mediated translocation. Nucleic Acids Res 2024; 52:1498-1511. [PMID: 38180813 PMCID: PMC10853801 DOI: 10.1093/nar/gkad1218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/26/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
A 'genomically' humanized animal stably maintains and functionally expresses the genes on human chromosome fragment (hCF; <24 Mb) loaded onto mouse artificial chromosome (MAC); however, cloning of hCF onto the MAC (hCF-MAC) requires a complex process that involves multiple steps of chromosome engineering through various cells via chromosome transfer and Cre-loxP chromosome translocation. Here, we aimed to develop a strategy to rapidly construct the hCF-MAC by employing three alternative techniques: (i) application of human induced pluripotent stem cells (hiPSCs) as chromosome donors for microcell-mediated chromosome transfer (MMCT), (ii) combination of paclitaxel (PTX) and reversine (Rev) as micronucleation inducers and (iii) CRISPR/Cas9 genome editing for site-specific translocations. We achieved a direct transfer of human chromosome 6 or 21 as a model from hiPSCs as alternative human chromosome donors into CHO cells containing MAC. MMCT was performed with less toxicity through induction of micronucleation by PTX and Rev. Furthermore, chromosome translocation was induced by simultaneous cleavage between human chromosome and MAC by using CRISPR/Cas9, resulting in the generation of hCF-MAC containing CHO clones without Cre-loxP recombination and drug selection. Our strategy facilitates rapid chromosome cloning and also contributes to the functional genomic analyses of human chromosomes.
Collapse
Affiliation(s)
- Hitomaru Miyamoto
- Department of Chromosome Biomedical Engineering, Integrated Medical Sciences, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Hiroaki Kobayashi
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Nanami Kishima
- Department of Chromosome Biomedical Engineering, Integrated Medical Sciences, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kyotaro Yamazaki
- Chromosome Engineering Research Group, The Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Shusei Hamamichi
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Narumi Uno
- Laboratory of Bioengineering, Faculty of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Satoshi Abe
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Yosuke Hiramuki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kanako Kazuki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kazuma Tomizuka
- Laboratory of Bioengineering, Faculty of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yasuhiro Kazuki
- Department of Chromosome Biomedical Engineering, Integrated Medical Sciences, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Chromosome Engineering Research Group, The Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| |
Collapse
|
3
|
Namipashaki A, Pugsley K, Liu X, Abrehart K, Lim SM, Sun G, Herold MJ, Polo JM, Bellgrove MA, Hawi Z. Integration of xeno-free single-cell cloning in CRISPR-mediated DNA editing of human iPSCs improves homogeneity and methodological efficiency of cellular disease modeling. Stem Cell Reports 2023; 18:2515-2527. [PMID: 37977144 PMCID: PMC10724053 DOI: 10.1016/j.stemcr.2023.10.013] [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: 12/13/2022] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
The capability to generate induced pluripotent stem cell (iPSC) lines, in tandem with CRISPR-Cas9 DNA editing, offers great promise to understand the underlying genetic mechanisms of human disease. The low efficiency of available methods for homogeneous expansion of singularized CRISPR-transfected iPSCs necessitates the coculture of transfected cells in mixed populations and/or on feeder layers. Consequently, edited cells must be purified using labor-intensive screening and selection, culminating in inefficient editing. Here, we provide a xeno-free method for single-cell cloning of CRISPRed iPSCs achieving a clonal survival of up to 70% within 7-10 days. This is accomplished through improved viability of the transfected cells, paralleled with provision of an enriched environment for the robust establishment and proliferation of singularized iPSC clones. Enhanced cell survival was accompanied by a high transfection efficiency exceeding 97%, and editing efficiencies of 50%-65% for NHEJ and 10% for HDR, indicative of the method's utility in stem cell disease modeling.
Collapse
Affiliation(s)
- Atefeh Namipashaki
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Kealan Pugsley
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Xiaodong Liu
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Kirra Abrehart
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Sue Mei Lim
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Guizhi Sun
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Marco J Herold
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jose M Polo
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia; Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia.
| |
Collapse
|
4
|
Mehra V, Chhetri JB, Ali S, Roddie C. The Emerging Role of Induced Pluripotent Stem Cells as Adoptive Cellular Immunotherapeutics. BIOLOGY 2023; 12:1419. [PMID: 37998018 PMCID: PMC10669440 DOI: 10.3390/biology12111419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023]
Abstract
Adoptive cell therapy (ACT) has transformed the treatment landscape for cancer and infectious disease through the investigational use of chimeric antigen receptor T-cells (CAR-Ts), tumour-infiltrating lymphocytes (TILs) and viral-specific T-cells (VSTs). Whilst these represent breakthrough treatments, there are subsets of patients who fail to respond to autologous ACT products. This is frequently due to impaired patient T-cell function or "fitness" as a consequence of prior treatments and age, and can be exacerbated by complex manufacturing protocols. Further, the manufacture of autologous, patient-specific products is time-consuming, expensive and non-standardised. Induced pluripotent stem cells (iPSCs) as an allogeneic alternative to patient-specific products can potentially overcome the issues outlined above. iPSC technology provides an unlimited source of rejuvenated iPSC-derived T-cells (T-iPSCs) or natural killer (NK) cells (NK-iPSCs), and in the context of the growing field of allogeneic ACT, iPSCs have enormous potential as a platform for generating off-the-shelf, standardised, "fit" therapeutics for patients. In this review, we evaluate current and future applications of iPSC technology in the CAR-T/NK, TIL and VST space. We discuss current and next-generation iPSC manufacturing protocols, and report on current iPSC-based adoptive therapy clinical trials to elucidate the potential of this technology as the future of ACT.
Collapse
Affiliation(s)
| | | | | | - Claire Roddie
- Research Department of Haematology, Cancer Institute, University College London, Paul O’Gorman Building, London WCIE 6DD, UK
| |
Collapse
|
5
|
Cota P, Saber L, Taskin D, Jing C, Bastidas-Ponce A, Vanheusden M, Shahryari A, Sterr M, Burtscher I, Bakhti M, Lickert H. NEUROD2 function is dispensable for human pancreatic β cell specification. Front Endocrinol (Lausanne) 2023; 14:1286590. [PMID: 37955006 PMCID: PMC10634430 DOI: 10.3389/fendo.2023.1286590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction The molecular programs regulating human pancreatic endocrine cell induction and fate allocation are not well deciphered. Here, we investigated the spatiotemporal expression pattern and the function of the neurogenic differentiation factor 2 (NEUROD2) during human endocrinogenesis. Methods Using Crispr-Cas9 gene editing, we generated a reporter knock-in transcription factor (TF) knock-out human inducible pluripotent stem cell (iPSC) line in which the open reading frame of both NEUROD2 alleles are replaced by a nuclear histone 2B-Venus reporter (NEUROD2nVenus/nVenus). Results We identified a transient expression of NEUROD2 mRNA and its nuclear Venus reporter activity at the stage of human endocrine progenitor formation in an iPSC differentiation model. This expression profile is similar to what was previously reported in mice, uncovering an evolutionarily conserved gene expression pattern of NEUROD2 during endocrinogenesis. In vitro differentiation of the generated homozygous NEUROD2nVenus/nVenus iPSC line towards human endocrine lineages uncovered no significant impact upon the loss of NEUROD2 on endocrine cell induction. Moreover, analysis of endocrine cell specification revealed no striking changes in the generation of insulin-producing b cells and glucagon-secreting a cells upon lack of NEUROD2. Discussion Overall, our results suggest that NEUROD2 is expendable for human b cell formation in vitro.
Collapse
Affiliation(s)
- Perla Cota
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Lama Saber
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Damla Taskin
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Changying Jing
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Munich Medical Research School (MMRS), Ludwig Maximilian University (LMU), Munich, Germany
| | - Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthew Vanheusden
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Alireza Shahryari
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
| |
Collapse
|
6
|
Ludwik KA, Telugu N, Schommer S, Stachelscheid H, Diecke S. ASSURED-optimized CRISPR protocol for knockout/SNP knockin in hiPSCs. STAR Protoc 2023; 4:102406. [PMID: 37481731 PMCID: PMC10382939 DOI: 10.1016/j.xpro.2023.102406] [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: 02/08/2023] [Revised: 04/21/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
CRISPR-Cas9 technology coupled with human induced pluripotent stem cells allows precise disease modeling in pluripotent cells and subsequently derived specialized cell types. Here, we present an optimized CRISPR-Cas9 pipeline, ASSURED (affordable, successful, specific, user-friendly, rapid, efficient, and deliverable), to produce gene-modified single-cell-derived knockout or single-nucleotide-polymorphism-modified knockin hiPSCs clones. We describe steps for analyzing targeted genomic sequence and designing guide RNAs and homology repair template. We then detail the CRISPR-Cas9 delivery workflow, evaluation of editing efficiency, and automated cell isolation followed by clone screening.
Collapse
Affiliation(s)
- Katarzyna A Ludwik
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Pluripotent Stem Cells & Organoids, 13353 Berlin, Germany
| | - Narasimha Telugu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Sandra Schommer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Harald Stachelscheid
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Pluripotent Stem Cells & Organoids, 13353 Berlin, Germany.
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research) (partner site), Berlin, Germany.
| |
Collapse
|
7
|
Tristan CA, Hong H, Jethmalani Y, Chen Y, Weber C, Chu PH, Ryu S, Jovanovic VM, Hur I, Voss TC, Simeonov A, Singeç I. Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail. Nat Protoc 2023; 18:58-80. [PMID: 36261632 PMCID: PMC11009857 DOI: 10.1038/s41596-022-00753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/05/2022] [Indexed: 01/14/2023]
Abstract
Human pluripotent stem cells (hPSCs) are inherently sensitive cells. Single-cell dissociation and the establishment of clonal cell lines have been long-standing challenges. This inefficiency of cell cloning represents a major obstacle for the standardization and streamlining of gene editing in induced pluripotent stem cells for basic and translational research. Here we describe a chemically defined protocol for robust single-cell cloning using microfluidics-based cell sorting in combination with the CEPT small-molecule cocktail. This advanced strategy promotes the viability and cell fitness of self-renewing stem cells. The use of low-pressure microfluidic cell dispensing ensures gentle and rapid dispensing of single cells into 96- and 384-well plates, while the fast-acting CEPT cocktail minimizes cellular stress and maintains cell structure and function immediately after cell dissociation. The protocol also facilitates clone picking and produces genetically stable clonal cell lines from hPSCs in a safe and cost-efficient fashion. Depending on the proliferation rate of the clone derived from a single cell, this protocol can be completed in 7-14 d and requires experience with aseptic cell culture techniques. Altogether, the relative ease, scalability and robustness of this workflow should boost gene editing in hPSCs and leverage a wide range of applications, including cell line development (e.g., reporter and isogenic cell lines), disease modeling and applications in regenerative medicine.
Collapse
Affiliation(s)
- Carlos A Tristan
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA.
| | - Hyenjong Hong
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Yogita Jethmalani
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Yu Chen
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Claire Weber
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Pei-Hsuan Chu
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Seungmi Ryu
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Vukasin M Jovanovic
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Inae Hur
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Ty C Voss
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Anton Simeonov
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Ilyas Singeç
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA.
| |
Collapse
|
8
|
Dicks AR, Steward N, Guilak F, Wu CL. Chondrogenic Differentiation of Human-Induced Pluripotent Stem Cells. Methods Mol Biol 2023; 2598:87-114. [PMID: 36355287 PMCID: PMC9830630 DOI: 10.1007/978-1-0716-2839-3_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The generation of large quantities of genetically defined human chondrocytes remains a critical step for the development of tissue engineering strategies for cartilage regeneration and high-throughput drug screening. This protocol describes chondrogenic differentiation of human-induced pluripotent stem cells (hiPSCs), which can undergo genetic modification and the capacity for extensive cell expansion. The hiPSCs are differentiated in a stepwise manner in monolayer through the mesodermal lineage for 12 days using defined growth factors and small molecules. This is followed by 28 days of chondrogenic differentiation in a 3D pellet culture system using transforming growth factor beta 3 and specific compounds to inhibit off-target differentiation. The 6-week protocol results in hiPSC-derived cartilaginous tissue that can be characterized by histology, immunohistochemistry, and gene expression or enzymatically digested to isolate chondrocyte-like cells. Investigators can use this protocol for experiments including genetic engineering, in vitro disease modeling, or tissue engineering.
Collapse
Affiliation(s)
- Amanda R Dicks
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, USA
- Shriners Hospitals for Children - St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University, St. Louis, MO, USA
| | - Nancy Steward
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, USA
- Shriners Hospitals for Children - St. Louis, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University, St. Louis, MO, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, USA.
- Shriners Hospitals for Children - St. Louis, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University, St. Louis, MO, USA.
| | - Chia-Lung Wu
- Department of Orthopaedic Surgery and Rehabilitation, Center for Musculoskeletal Research, University of Rochester, Rochester, NY, USA.
| |
Collapse
|
9
|
Bernhard P, Feilen T, Rogg M, Fröhlich K, Cosenza-Contreras M, Hause F, Schell C, Schilling O. Proteome alterations during clonal isolation of established human pancreatic cancer cell lines. Cell Mol Life Sci 2022; 79:561. [PMID: 36271971 PMCID: PMC9587952 DOI: 10.1007/s00018-022-04584-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022]
Abstract
Clonal isolation is an integral step of numerous workflows in genome editing and cell engineering. It comprises the isolation of a single progenitor cell from a defined cell line population with subsequent expansion to obtain a monoclonal cell population. This process is associated with transient loss of cell–cell contacts and absence of a multicellular microenvironment. Previous studies have revealed transcriptomic changes upon clonal isolation with cell line specific extent. Since transcriptome alterations are only partially reflected on the proteome level, we sought to investigate the impact of clonal isolation on the cellular proteome to a depth of > 6000 proteins in three established pancreatic cancer cell lines. We show that clonal isolation does have an impact on the cellular proteome, however, with cell line specific extent, affecting different biological processes, and also depending on the isolation method. We demonstrate a different impact of clonal isolation on mesenchymal- and epithelial-derived cell lines mainly affecting cell proliferation, metabolism, cell adhesion and cellular stress. The results bear relevance to the field of genomic editing and cell engineering and highlight the need to consider the impact of clonal isolation when interpreting data stemming from experiments that include this step.
Collapse
Affiliation(s)
- P Bernhard
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - T Feilen
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - M Rogg
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany
| | - K Fröhlich
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - M Cosenza-Contreras
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - F Hause
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany
| | - C Schell
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - O Schilling
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany. .,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
10
|
Caillaud A, Lévêque A, Thédrez A, Girardeau A, Canac R, Bray L, Baudic M, Barc J, Gaborit N, Lamirault G, Gardie B, Idriss S, Rimbert A, Le May C, Cariou B, Si-Tayeb K. FACS-assisted CRISPR-Cas9 genome editing of human induced pluripotent stem cells. STAR Protoc 2022; 3:101680. [PMID: 36115027 PMCID: PMC9490201 DOI: 10.1016/j.xpro.2022.101680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/30/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023] Open
Abstract
This manuscript proposes an efficient and reproducible protocol for the generation of genetically modified human induced pluripotent stem cells (hiPSCs) by genome editing using CRISPR-Cas9 technology. Here, we describe the experimental strategy for generating knockout (KO) and knockin (KI) clonal populations of hiPSCs using single-cell sorting by flow cytometry. We efficiently achieved up to 15 kb deletions, molecular tag insertions, and single-nucleotide editing in hiPSCs. We emphasize the efficacy of this approach in terms of cell culture time. For complete details on the use and execution of this protocol, please refer to Canac et al. (2022) and Bray et al. (2022).
Collapse
Affiliation(s)
- Amandine Caillaud
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France,Corresponding author
| | - Antoine Lévêque
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Aurélie Thédrez
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Aurore Girardeau
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Robin Canac
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Lise Bray
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Manon Baudic
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Julien Barc
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Nathalie Gaborit
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Guillaume Lamirault
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Betty Gardie
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France,Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
| | - Salam Idriss
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Antoine Rimbert
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Cédric Le May
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Bertrand Cariou
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France,Corresponding author
| | - Karim Si-Tayeb
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| |
Collapse
|
11
|
Jamehdor S, Pajouhanfar S, Saba S, Uzan G, Teimoori A, Naserian S. Principles and Applications of CRISPR Toolkit in Virus Manipulation, Diagnosis, and Virus-Host Interactions. Cells 2022; 11:999. [PMID: 35326449 PMCID: PMC8946942 DOI: 10.3390/cells11060999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Viruses are one of the most important concerns for human health, and overcoming viral infections is a worldwide challenge. However, researchers have been trying to manipulate viral genomes to overcome various disorders, including cancer, for vaccine development purposes. CRISPR (clustered regularly interspaced short palindromic repeats) is becoming one of the most functional and widely used tools for RNA and DNA manipulation in multiple organisms. This approach has provided an unprecedented opportunity for creating simple, inexpensive, specific, targeted, accurate, and practical manipulations of viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus-1 (HIV-1), and vaccinia virus. Furthermore, this method can be used to make an effective and precise diagnosis of viral infections. Nevertheless, a valid and scientifically designed CRISPR system is critical to make more effective and accurate changes in viruses. In this review, we have focused on the best and the most effective ways to design sgRNA, gene knock-in(s), and gene knock-out(s) for virus-targeted manipulation. Furthermore, we have emphasized the application of CRISPR technology in virus diagnosis and in finding significant genes involved in virus-host interactions.
Collapse
Affiliation(s)
- Saleh Jamehdor
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan 989155432609, Iran;
| | - Sara Pajouhanfar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Sadaf Saba
- Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
| | - Georges Uzan
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, 94800 Villejuif, France;
- Paris-Saclay University, 94800 Villejuif, France
| | - Ali Teimoori
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 6517838738, Iran
| | - Sina Naserian
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, 94800 Villejuif, France;
- Paris-Saclay University, 94800 Villejuif, France
- CellMedEx, 94100 Saint Maur Des Fossés, France
| |
Collapse
|
12
|
Flores‐Romero H, Hohorst L, John M, Albert M, King LE, Beckmann L, Szabo T, Hertlein V, Luo X, Villunger A, Frenzel LP, Kashkar H, Garcia‐Saez AJ. BCL‐2‐family protein tBID can act as a BAX‐like effector of apoptosis. EMBO J 2021; 41:e108690. [PMID: 34931711 PMCID: PMC8762556 DOI: 10.15252/embj.2021108690] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/14/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
During apoptosis, the BCL‐2‐family protein tBID promotes mitochondrial permeabilization by activating BAX and BAK and by blocking anti‐apoptotic BCL‐2 members. Here, we report that tBID can also mediate mitochondrial permeabilization by itself, resulting in release of cytochrome c and mitochondrial DNA, caspase activation and apoptosis even in absence of BAX and BAK. This previously unrecognized activity of tBID depends on helix 6, homologous to the pore‐forming regions of BAX and BAK, and can be blocked by pro‐survival BCL‐2 proteins. Importantly, tBID‐mediated mitochondrial permeabilization independent of BAX and BAK is physiologically relevant for SMAC release in the immune response against Shigella infection. Furthermore, it can be exploited to kill leukaemia cells with acquired venetoclax resistance due to lack of active BAX and BAK. Our findings define tBID as an effector of mitochondrial permeabilization in apoptosis and provide a new paradigm for BCL‐2 proteins, with implications for anti‐bacterial immunity and cancer therapy.
Collapse
Affiliation(s)
- Hector Flores‐Romero
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
| | - Lisa Hohorst
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Malina John
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
| | - Marie‐Christine Albert
- Institute for Molecular Immunology, and Center for Molecular Medicine Cologne (CMMC) Faculty of Medicine University Hospital of Cologne University of Cologne Cologne Germany
| | - Louise E King
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Laura Beckmann
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Department I of Internal Medicine University Hospital of Cologne Cologne Germany
- Center of Integrated Oncology ABCD University Hospital of Cologne Cologne Germany
| | - Tamas Szabo
- Division of Developmental Immunology Biocenter Medical University of Innsbruck Innsbruck Austria
| | - Vanessa Hertlein
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
| | - Xu Luo
- Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center University of Nebraska Medical Center Omaha ME USA
- Department of Pathology and Microbiology University of Nebraska Medical Center Omaha NE USA
| | - Andreas Villunger
- Division of Developmental Immunology Biocenter Medical University of Innsbruck Innsbruck Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases Vienna Austria
| | - Lukas P Frenzel
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Department I of Internal Medicine University Hospital of Cologne Cologne Germany
- Center of Integrated Oncology ABCD University Hospital of Cologne Cologne Germany
| | - Hamid Kashkar
- Institute for Molecular Immunology, and Center for Molecular Medicine Cologne (CMMC) Faculty of Medicine University Hospital of Cologne University of Cologne Cologne Germany
| | - Ana J Garcia‐Saez
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
| |
Collapse
|
13
|
Shahryari A, Moya N, Siehler J, Wang X, Burtscher I, Lickert H. Increasing Gene Editing Efficiency for CRISPR-Cas9 by Small RNAs in Pluripotent Stem Cells. CRISPR J 2021; 4:491-501. [PMID: 34406042 DOI: 10.1089/crispr.2021.0014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gene manipulations of human induced pluripotent stem cells (iPSCs) by CRISPR-Cas9 genome engineering are widely used for disease modeling and regenerative medicine applications. There are two competing pathways, non-homologous end joining (NHEJ) and homology directed repair (HDR) that correct the double-strand break generated by CRISPR-Cas9. Here, we improved gene editing efficiency of gene knock-in (KI) in iPSCs with minimum components by manipulating the Cas9 expression vector. Either we inserted short hairpin RNA expression cassettes to downregulate DNAPK and XRCC4, two main players of the NHEJ pathway, or we increased cell survival by inserting an anti-apoptotic expression cassette of miRNA-21 into the Cas9 vector. For an easy readout, the pluripotency gene SOX2 was targeted with a T2A-tdTomato reporter construct. In vitro downregulating DNAPK and XRCC4 increased the targeting efficiency of SOX2 KI by around twofold. Furthermore, co-expression of miRNA-21 and Cas9 improved the efficiency of SOX2 KI by around threefold. Altogether, our strategies provide a simple and valuable approach for efficient CRISPR-Cas9 gene editing in iPSCs.
Collapse
Affiliation(s)
- Alireza Shahryari
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Technical University of Munich, School of Medicine, Klinikum Rechts der Isar, Munich, Germany; and Golestan University of Medical Sciences, Gorgan, Iran
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Noel Moya
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
| | - Johanna Siehler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Technical University of Munich, School of Medicine, Klinikum Rechts der Isar, Munich, Germany; and Golestan University of Medical Sciences, Gorgan, Iran
| | - Xianming Wang
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany; Golestan University of Medical Sciences, Gorgan, Iran
- Technical University of Munich, School of Medicine, Klinikum Rechts der Isar, Munich, Germany; and Golestan University of Medical Sciences, Gorgan, Iran
| |
Collapse
|
14
|
Vitelli M, Budman H, Pritzker M, Tamer M. Applications of flow cytometry sorting in the pharmaceutical industry: A review. Biotechnol Prog 2021; 37:e3146. [PMID: 33749147 DOI: 10.1002/btpr.3146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
The article reviews applications of flow cytometry sorting in manufacturing of pharmaceuticals. Flow cytometry sorting is an extremely powerful tool for monitoring, screening and separating single cells based on any property that can be measured by flow cytometry. Different applications of flow cytometry sorting are classified into groups and discussed in separate sections as follows: (a) isolation of cell types, (b) high throughput screening, (c) cell surface display, (d) droplet fluorescent-activated cell sorting (FACS). Future opportunities are identified including: (a) sorting of particular fractions of the cell population based on a property of interest for generating inoculum that will result in improved outcomes of cell cultures and (b) the use of population balance models in combination with FACS to design and optimize cell cultures.
Collapse
Affiliation(s)
- Michael Vitelli
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Hector Budman
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Mark Pritzker
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Melih Tamer
- Department of Manufacturing Technology, Sanofi Pasteur, Toronto, Canada
| |
Collapse
|
15
|
Inak G, Rybak-Wolf A, Lisowski P, Pentimalli TM, Jüttner R, Glažar P, Uppal K, Bottani E, Brunetti D, Secker C, Zink A, Meierhofer D, Henke MT, Dey M, Ciptasari U, Mlody B, Hahn T, Berruezo-Llacuna M, Karaiskos N, Di Virgilio M, Mayr JA, Wortmann SB, Priller J, Gotthardt M, Jones DP, Mayatepek E, Stenzel W, Diecke S, Kühn R, Wanker EE, Rajewsky N, Schuelke M, Prigione A. Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome. Nat Commun 2021; 12:1929. [PMID: 33771987 PMCID: PMC7997884 DOI: 10.1038/s41467-021-22117-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Leigh syndrome (LS) is a severe manifestation of mitochondrial disease in children and is currently incurable. The lack of effective models hampers our understanding of the mechanisms underlying the neuronal pathology of LS. Using patient-derived induced pluripotent stem cells and CRISPR/Cas9 engineering, we developed a human model of LS caused by mutations in the complex IV assembly gene SURF1. Single-cell RNA-sequencing and multi-omics analysis revealed compromised neuronal morphogenesis in mutant neural cultures and brain organoids. The defects emerged at the level of neural progenitor cells (NPCs), which retained a glycolytic proliferative state that failed to instruct neuronal morphogenesis. LS NPCs carrying mutations in the complex I gene NDUFS4 recapitulated morphogenesis defects. SURF1 gene augmentation and PGC1A induction via bezafibrate treatment supported the metabolic programming of LS NPCs, leading to restored neuronal morphogenesis. Our findings provide mechanistic insights and suggest potential interventional strategies for a rare mitochondrial disease.
Collapse
Affiliation(s)
- Gizem Inak
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Duesseldorf University Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC), Hannoversche Str 28, 10115, Berlin, Germany
| | - Pawel Lisowski
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Duesseldorf University Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
- Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec, n/Warsaw, Magdalenka, Poland
| | - Tancredi M Pentimalli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC), Hannoversche Str 28, 10115, Berlin, Germany
| | - René Jüttner
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Petar Glažar
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC), Hannoversche Str 28, 10115, Berlin, Germany
| | | | - Emanuela Bottani
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Dario Brunetti
- Mitochondrial Medicine Laboratory, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
- Unit of Medical Genetics and Neurogenetics Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
| | - Christopher Secker
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Department of Neurology, Berlin, Germany
| | - Annika Zink
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Duesseldorf University Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
- Charité - Universitätsmedizin Berlin, Department of Neuropsychiatry, Berlin, Germany
| | | | - Marie-Thérèse Henke
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Department of Neuropediatrics, Berlin, Germany
| | - Monishita Dey
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Ummi Ciptasari
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Barbara Mlody
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Tobias Hahn
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | | | - Nikos Karaiskos
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC), Hannoversche Str 28, 10115, Berlin, Germany
| | | | - Johannes A Mayr
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Josef Priller
- Charité - Universitätsmedizin Berlin, Department of Neuropsychiatry, Berlin, Germany
- University of Edinburgh and UK DRI, Edinburgh, UK
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | | | | | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Duesseldorf University Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Werner Stenzel
- Charité - Universitätsmedizin, Department of Neuropathology, Berlin, Germany
| | - Sebastian Diecke
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC), Hannoversche Str 28, 10115, Berlin, Germany.
| | - Markus Schuelke
- Charité - Universitätsmedizin Berlin, Department of Neuropediatrics, Berlin, Germany.
- NeuroCure Clinical Research Center, Berlin, Germany.
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Duesseldorf University Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany.
| |
Collapse
|
16
|
Siehler J, Blöchinger AK, Akgün M, Wang X, Shahryari A, Geerlof A, Lickert H, Burtscher I. Generation of a heterozygous C-peptide-mCherry reporter human iPSC line (HMGUi001-A-8). Stem Cell Res 2020; 50:102126. [PMID: 33373890 DOI: 10.1016/j.scr.2020.102126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/21/2020] [Accepted: 12/13/2020] [Indexed: 01/20/2023] Open
Abstract
The peptide hormone insulin produced by pancreatic β-cells undergoes post-transcriptional processing before secretion. In particular, C-peptide is cleaved from pro-insulin to generate mature insulin. Here, we introduce a C-peptide-mCherry human iPSC line (HMGUi001-A-8). The line was generated by CRISPR/Cas9 mediated heterozygous insertion of the mCherry sequence into exon 3 of the insulin locus. We demonstrate that the line is pluripotent and efficiently differentiates towards pancreatic β-like cells, which localize a red fluorescent C-peptide-mCherry fusion protein in insulin containing granules. Hence, the HMGUi001-A-8 line is a valuable resource to purify derived β-like cells and follow insulin-containing granules in real time.
Collapse
Affiliation(s)
- Johanna Siehler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Anna Karolina Blöchinger
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Melis Akgün
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Xianming Wang
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Alireza Shahryari
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany; Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| |
Collapse
|
17
|
"Betwixt Mine Eye and Heart a League Is Took": The Progress of Induced Pluripotent Stem-Cell-Based Models of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2020; 21:ijms21196997. [PMID: 32977524 PMCID: PMC7582534 DOI: 10.3390/ijms21196997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
The ultimate goal of precision disease modeling is to artificially recreate the disease of affected people in a highly controllable and adaptable external environment. This field has rapidly advanced which is evident from the application of patient-specific pluripotent stem-cell-derived precision therapies in numerous clinical trials aimed at a diverse set of diseases such as macular degeneration, heart disease, spinal cord injury, graft-versus-host disease, and muscular dystrophy. Despite the existence of semi-adequate treatments for tempering skeletal muscle degeneration in dystrophic patients, nonischemic cardiomyopathy remains one of the primary causes of death. Therefore, cardiovascular cells derived from muscular dystrophy patients' induced pluripotent stem cells are well suited to mimic dystrophin-associated cardiomyopathy and hold great promise for the development of future fully effective therapies. The purpose of this article is to convey the realities of employing precision disease models of dystrophin-associated cardiomyopathy. This is achieved by discussing, as suggested in the title echoing William Shakespeare's words, the settlements (or "leagues") made by researchers to manage the constraints ("betwixt mine eye and heart") distancing them from achieving a perfect precision disease model.
Collapse
|
18
|
Blöchinger AK, Siehler J, Wißmiller K, Shahryari A, Burtscher I, Lickert H. Generation of an INSULIN-H2B-Cherry reporter human iPSC line. Stem Cell Res 2020; 45:101797. [PMID: 32361463 DOI: 10.1016/j.scr.2020.101797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/14/2020] [Indexed: 11/26/2022] Open
Abstract
Differentiating human induced pluripotent stem cells (hiPSCs) into insulin (INS)-producing β-like cells has potential for diabetes research and therapy. Here, we generated a heterozygous fluorescent hiPSC reporter, labeling INS-producing β-like cells. We used CRISPR/Cas9 technology to knock-in a T2A-H2B-Cherry cassette to replace the translational INS stop codon, enabling co-transcription and T2A-peptide mediated co-translational cleavage of INS-T2A and H2B-Cherry. The hiPSC-INS-T2A-H2B-Cherry reporter cells were pluripotent and showed multi-lineage differentiation potential. Cells expressing the β-cell specific hormone INS are identified by nuclear localized H2B-Cherry reporter upon pancreatic endocrine differentiation. Thus, the generated reporter hiPSCs enable live identification of INS hormone-producing β-like cells.
Collapse
Affiliation(s)
- Anna Karolina Blöchinger
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Johanna Siehler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Katharina Wißmiller
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Alireza Shahryari
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaninger Straße 22, 81675 München, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| |
Collapse
|
19
|
Abstract
PURPOSE OF REVIEW We review the ways in which stem cells are used in psychiatric disease research, including the related advances in gene editing and directed cell differentiation. RECENT FINDINGS The recent development of induced pluripotent stem cell (iPSC) technologies has created new possibilities for the study of psychiatric disease. iPSCs can be derived from patients or controls and differentiated to an array of neuronal and non-neuronal cell types. Their genomes can be edited as desired, and they can be assessed for a variety of phenotypes. This makes them especially interesting for studying genetic variation, which is particularly useful today now that our knowledge on the genetics of psychiatric disease is quickly expanding. The recent advances in cell engineering have led to powerful new methods for studying psychiatric illness including schizophrenia, bipolar disorder, and autism. There is a wide array of possible applications as illustrated by the many examples from the literature, most of which are cited here.
Collapse
Affiliation(s)
- Debamitra Das
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyra Feuer
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marah Wahbeh
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
20
|
Dicks A, Wu CL, Steward N, Adkar SS, Gersbach CA, Guilak F. Prospective isolation of chondroprogenitors from human iPSCs based on cell surface markers identified using a CRISPR-Cas9-generated reporter. Stem Cell Res Ther 2020; 11:66. [PMID: 32070421 PMCID: PMC7026983 DOI: 10.1186/s13287-020-01597-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 12/29/2022] Open
Abstract
Background Articular cartilage shows little or no capacity for intrinsic repair, generating a critical need of regenerative therapies for joint injuries and diseases such as osteoarthritis. Human-induced pluripotent stem cells (hiPSCs) offer a promising cell source for cartilage tissue engineering and in vitro human disease modeling; however, off-target differentiation remains a challenge during hiPSC chondrogenesis. Therefore, the objective of this study was to identify cell surface markers that define the true chondroprogenitor population and use these markers to purify iPSCs as a means of improving the homogeneity and efficiency of hiPSC chondrogenic differentiation. Methods We used a CRISPR-Cas9-edited COL2A1-GFP knock-in reporter hiPSC line, coupled with a surface marker screen, to identify a novel chondroprogenitor population. Single-cell RNA sequencing was then used to analyze the distinct clusters within the population. An unpaired t test with Welch’s correction or an unpaired Kolmogorov-Smirnov test was performed with significance reported at a 95% confidence interval. Results Chondroprogenitors expressing CD146, CD166, and PDGFRβ, but not CD45, made up an average of 16.8% of the total population. Under chondrogenic culture conditions, these triple-positive chondroprogenitor cells demonstrated decreased heterogeneity as measured by single-cell RNA sequencing with fewer clusters (9 clusters in unsorted vs. 6 in sorted populations) closer together. Additionally, there was more robust and homogenous matrix production (unsorted: 1.5 ng/ng vs. sorted: 19.9 ng/ng sGAG/DNA; p < 0.001) with significantly higher chondrogenic gene expression (i.e., SOX9, COL2A1, ACAN; p < 0.05). Conclusions Overall, this study has identified a unique hiPSC-derived subpopulation of chondroprogenitors that are CD146+/CD166+/PDGFRβ+/CD45− and exhibit high chondrogenic potential, providing a purified cell source for cartilage tissue engineering or disease modeling studies.
Collapse
Affiliation(s)
- Amanda Dicks
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, 63110, USA.,Shriners Hospitals for Children - St. Louis, St. Louis, MO, 63110, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, 63110, USA.,Center of Regenerative Medicine, Washington University, St. Louis, MO, 63110, USA
| | - Chia-Lung Wu
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, 63110, USA.,Shriners Hospitals for Children - St. Louis, St. Louis, MO, 63110, USA.,Center of Regenerative Medicine, Washington University, St. Louis, MO, 63110, USA
| | - Nancy Steward
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, 63110, USA.,Shriners Hospitals for Children - St. Louis, St. Louis, MO, 63110, USA.,Center of Regenerative Medicine, Washington University, St. Louis, MO, 63110, USA
| | - Shaunak S Adkar
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, 27710, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, 63110, USA. .,Shriners Hospitals for Children - St. Louis, St. Louis, MO, 63110, USA. .,Department of Biomedical Engineering, Washington University, St. Louis, MO, 63110, USA. .,Center of Regenerative Medicine, Washington University, St. Louis, MO, 63110, USA.
| |
Collapse
|
21
|
Volpato V, Webber C. Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility. Dis Model Mech 2020; 13:dmm042317. [PMID: 31953356 PMCID: PMC6994963 DOI: 10.1242/dmm.042317] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem cell (iPSC) technologies have provided in vitro models of inaccessible human cell types, yielding new insights into disease mechanisms especially for neurological disorders. However, without due consideration, the thousands of new human iPSC lines generated in the past decade will inevitably affect the reproducibility of iPSC-based experiments. Differences between donor individuals, genetic stability and experimental variability contribute to iPSC model variation by impacting differentiation potency, cellular heterogeneity, morphology, and transcript and protein abundance. Such effects will confound reproducible disease modelling in the absence of appropriate strategies. In this Review, we explore the causes and effects of iPSC heterogeneity, and propose approaches to detect and account for experimental variation between studies, or even exploit it for deeper biological insight.
Collapse
Affiliation(s)
- Viola Volpato
- UK Dementia Research Institute at Cardiff University, Division of Psychological Medicine and Clinical Neuroscience, Haydn Ellis Building, Maindy Rd, Cardiff CF24 4HQ, UK
| | - Caleb Webber
- UK Dementia Research Institute at Cardiff University, Division of Psychological Medicine and Clinical Neuroscience, Haydn Ellis Building, Maindy Rd, Cardiff CF24 4HQ, UK
| |
Collapse
|
22
|
Abstract
Huntington's disease (HD) is a hereditary neurological disorder caused by expansion of the CAG repeat tract in the huntingtin gene (HTT). The mutant protein with a long polyglutamine tract is toxic to cells, especially neurons, leading to their progressive degeneration. Similar to many other monogenic diseases, HD is a good target for gene therapy approaches, including the use of programmable endonucleases. Here, we describe a protocol for HTT gene knock out using a modified Cas9 protein (nickase, Cas9n) and a pair of sgRNAs flanking the repeats. Recently, we showed that excision of the CAG repeat tract resulted in a frameshift mutation and premature translation termination. As a model, we used HD patient-derived fibroblasts electroporated with a pair of plasmid vectors expressing CRISPR-Cas9n tools. Efficient HTT inactivation independent of the CAG tract length was confirmed by Western blotting. A modified version of this protocol involving precise excision of the CAG repeats and insertion of a new DNA sequence by homology directed repair may also be used for the generation of new isogenic cellular models of HD.
Collapse
Affiliation(s)
- Magdalena Dabrowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| |
Collapse
|
23
|
Hyttel P, de Figueiredo Pessôa LV, Secher JBM, Dittlau KS, Freude K, Hall VJ, Fair T, Assey RJ, Laurincik J, Callesen H, Greve T, Stroebech LB. Oocytes, embryos and pluripotent stem cells from a biomedical perspective. Anim Reprod 2019; 16:508-523. [PMID: 32435294 PMCID: PMC7234146 DOI: 10.21451/1984-3143-ar2019-0054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The veterinary and animal science professions are rapidly developing and their inherent and historical connection to agriculture is challenged by more biomedical and medical directions of research. While some consider this development as a risk of losing identity, it may also be seen as an opportunity for developing further and more sophisticated competences that may ultimately feed back to veterinary and animal science in a synergistic way. The present review describes how agriculture-related studies on bovine in vitro embryo production through studies of putative bovine and porcine embryonic stem cells led the way to more sophisticated studies of human induced pluripotent stem cells (iPSCs) using e.g. gene editing for modeling of neurodegeneration in man. However, instead of being a blind diversion from veterinary and animal science into medicine, these advanced studies of human iPSC-derived neurons build a set of competences that allowed us, in a more competent way, to focus on novel aspects of more veterinary and agricultural relevance in the form of porcine and canine iPSCs. These types of animal stem cells are of biomedical importance for modeling of iPSC-based therapy in man, but in particular the canine iPSCs are also important for understanding and modeling canine diseases, as e.g. canine cognitive dysfunction, for the benefit and therapy of dogs.
Collapse
Affiliation(s)
- Poul Hyttel
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | | | | | - Katarina Stoklund Dittlau
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Kristine Freude
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Vanessa J Hall
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Trudee Fair
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Remmy John Assey
- Department of Anatomy and Pathology, Sokoine University of Agriculture, Tanzania
| | - Jozef Laurincik
- Constantine the Philosopher University in Nitra, Nitra, Slovakia.,The Czech Academy of Sciences, Institute of Animal Physiology and Genetics, Liběchov, Czech Republic
| | - Henrik Callesen
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | | | | |
Collapse
|
24
|
Rozov SM, Permyakova NV, Deineko EV. The Problem of the Low Rates of CRISPR/Cas9-Mediated Knock-ins in Plants: Approaches and Solutions. Int J Mol Sci 2019; 20:E3371. [PMID: 31323994 PMCID: PMC6651222 DOI: 10.3390/ijms20133371] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
The main number of genome editing events in plant objects obtained during the last decade with the help of specific nucleases zinc finger (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas are the microindels causing frameshift and subsequent gene knock-out. The knock-ins of genes or their parts, i.e., the insertion of them into a target genome region, are between one and two orders of magnitude less frequent. First and foremost, this is associated with the specific features of the repair systems of higher eukaryotes and the availability of the donor template in accessible proximity during double-strand break (DSB) repair. This review briefs the main repair pathways in plants according to the aspect of their involvement in genome editing. The main methods for increasing the frequency of knock-ins are summarized both along the homologous recombination pathway and non-homologous end joining, which can be used for plant objects.
Collapse
Affiliation(s)
- Serge M Rozov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Natalya V Permyakova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Deineko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Plant Physiology and Biotechnology, Tomsk State University, Tomsk 634050, Russia
| |
Collapse
|
25
|
Wang X, Sterr M, Ansarullah, Burtscher I, Böttcher A, Beckenbauer J, Siehler J, Meitinger T, Häring HU, Staiger H, Cernilogar FM, Schotta G, Irmler M, Beckers J, Wright CVE, Bakhti M, Lickert H. Point mutations in the PDX1 transactivation domain impair human β-cell development and function. Mol Metab 2019; 24:80-97. [PMID: 30930126 PMCID: PMC6531841 DOI: 10.1016/j.molmet.2019.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE Hundreds of missense mutations in the coding region of PDX1 exist; however, if these mutations predispose to diabetes mellitus is unknown. METHODS In this study, we screened a large cohort of subjects with increased risk for diabetes and identified two subjects with impaired glucose tolerance carrying common, heterozygous, missense mutations in the PDX1 coding region leading to single amino acid exchanges (P33T, C18R) in its transactivation domain. We generated iPSCs from patients with heterozygous PDX1P33T/+, PDX1C18R/+ mutations and engineered isogenic cell lines carrying homozygous PDX1P33T/P33T, PDX1C18R/C18R mutations and a heterozygous PDX1 loss-of-function mutation (PDX1+/-). RESULTS Using an in vitro β-cell differentiation protocol, we demonstrated that both, heterozygous PDX1P33T/+, PDX1C18R/+ and homozygous PDX1P33T/P33T, PDX1C18R/C18R mutations impair β-cell differentiation and function. Furthermore, PDX1+/- and PDX1P33T/P33T mutations reduced differentiation efficiency of pancreatic progenitors (PPs), due to downregulation of PDX1-bound genes, including transcription factors MNX1 and PDX1 as well as insulin resistance gene CES1. Additionally, both PDX1P33T/+ and PDX1P33T/P33T mutations in PPs reduced the expression of PDX1-bound genes including the long-noncoding RNA, MEG3 and the imprinted gene NNAT, both involved in insulin synthesis and secretion. CONCLUSIONS Our results reveal mechanistic details of how common coding mutations in PDX1 impair human pancreatic endocrine lineage formation and β-cell function and contribute to the predisposition for diabetes.
Collapse
Affiliation(s)
- Xianming Wang
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Ansarullah
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Julia Beckenbauer
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johanna Siehler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hans-Ulrich Häring
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Harald Staiger
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Filippo M Cernilogar
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Gunnar Schotta
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Beckers
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Christopher V E Wright
- Vanderbilt University Program in Developmental Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| |
Collapse
|
26
|
Gridina ММ. Improvement of the knock-in effciency in the genome of human induced pluripotent stem cells using the CRISPR/Cas9 system. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj18.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human induced pluripotent stem (hiPS) cells are a powerful tool for biomedical research. The ability to create patient-specifc pluripotent cells and their subsequent differentiation into any somatic cell type makes hiPS cells a valuable object for creating in vitro models of human diseases, screening drugs and a future source of cells for regenerative medicine. To realize entirely a potential of hiPScells, effective and precise methods for their genome editing are needed. The CRISPR/Cas9 system is the most widely used method for introducing site-specifc double-stranded breaks into DNA. It allows genes of interest to be knocked out with high efciency. However, knock-in into the target site of the genome is a much more difcult task. Moreover, many researchers have noted a low efciency of introducing target constructs into the hiPS cells’ genome. In this review, I attempt to describe the currently known information regarding the matter of increasing efciency of targeted insertions into hiPS cells’ genome. Here I will describe the most effective strategies for designing the donor template for homology-directed repair, methods to manipulate the double-strand break repair pathways introduced by a nuclease, including control of CRISPR/Cas9 delivery time. A low survival rate of hiPS cells following genome editing experiments is another difculty on the way towards successful knock-in, and here several highly effective approaches addressing it are proposed. Finally, I describe the most promising strategies, one-step reprogramming and genome editing, which allows gene-modifed integration-free hiPS cells to be efciently generated directly from somatic cells.
Collapse
|
27
|
Yumlu S, Bashir S, Stumm J, Kühn R. Efficient Gene Editing of Human Induced Pluripotent Stem Cells Using CRISPR/Cas9. Methods Mol Biol 2019; 1961:137-151. [PMID: 30912045 DOI: 10.1007/978-1-4939-9170-9_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The generation of targeted mutants is a crucial step toward studying the biomedical effect of genes of interest. The generation of such mutants in human induced pluripotent stem cells (iPSCs) is of an utmost importance as these cells carry the potential to be differentiated into any cell lineage. Using the CRISPR/Cas9 nuclease system for induction of targeted double-strand breaks, gene editing of target loci in iPSCs can be achieved with high efficiency. This chapter covers protocols for the preparation of reagents to target loci of interest, the transfection, and for the genotyping of single cell-derived iPSC clones. Furthermore, we provide a protocol for the convenient generation of plasmids enabling multiplex gene targeting.
Collapse
Affiliation(s)
- Saniye Yumlu
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Sanum Bashir
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Jürgen Stumm
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany.
| |
Collapse
|
28
|
Smirnikhina SA, Anuchina AA, Lavrov AV. Ways of improving precise knock-in by genome-editing technologies. Hum Genet 2018; 138:1-19. [DOI: 10.1007/s00439-018-1953-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023]
|
29
|
Engle SJ, Blaha L, Kleiman RJ. Best Practices for Translational Disease Modeling Using Human iPSC-Derived Neurons. Neuron 2018; 100:783-797. [DOI: 10.1016/j.neuron.2018.10.033] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/07/2018] [Accepted: 10/19/2018] [Indexed: 01/26/2023]
|
30
|
Chen YH, Pruett-Miller SM. Improving single-cell cloning workflow for gene editing in human pluripotent stem cells. Stem Cell Res 2018; 31:186-192. [PMID: 30099335 DOI: 10.1016/j.scr.2018.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/27/2018] [Accepted: 08/02/2018] [Indexed: 01/01/2023] Open
Abstract
The availability of human pluripotent stem cells (hPSCs) and progress in genome engineering technology have altered the way we approach scientific research and drug development screens. Unfortunately, the procedures for genome editing of hPSCs often subject cells to harsh conditions that compromise viability: a major problem that is compounded by the innate challenge of single-cell culture. Here we describe a generally applicable workflow that supports single-cell cloning and expansion of hPSCs after genome editing and single-cell sorting. Stem-Flex and RevitaCell supplement, in combination with Geltrex or Vitronectin (VN), promote reliable single-cell growth in a feeder-free and defined environment. Characterization of final genome-edited clones reveals that pluripotency and normal karyotype are retained following this single-cell culture protocol. This time-efficient and simplified culture method paves the way for high-throughput hPSC culture and will be valuable for both basic research and clinical applications.
Collapse
Affiliation(s)
- Yi-Hsien Chen
- Washington University School of Medicine, Department of Genetics, St. Louis 63110, USA; Genome Engineering and iPSC Center, USA.
| | - Shondra M Pruett-Miller
- St. Jude Children's Research Hospital, Department of Cell & Molecular Biology, Memphis 38105, USA; Center for Advanced Genome Engineering, USA.
| |
Collapse
|
31
|
Burnight ER, Giacalone JC, Cooke JA, Thompson JR, Bohrer LR, Chirco KR, Drack AV, Fingert JH, Worthington KS, Wiley LA, Mullins RF, Stone EM, Tucker BA. CRISPR-Cas9 genome engineering: Treating inherited retinal degeneration. Prog Retin Eye Res 2018; 65:28-49. [PMID: 29578069 PMCID: PMC8210531 DOI: 10.1016/j.preteyeres.2018.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 12/18/2022]
Abstract
Gene correction is a valuable strategy for treating inherited retinal degenerative diseases, a major cause of irreversible blindness worldwide. Single gene defects cause the majority of these retinal dystrophies. Gene augmentation holds great promise if delivered early in the course of the disease, however, many patients carry mutations in genes too large to be packaged into adeno-associated viral vectors and some, when overexpressed via heterologous promoters, induce retinal toxicity. In addition to the aforementioned challenges, some patients have sustained significant photoreceptor cell loss at the time of diagnosis, rendering gene replacement therapy insufficient to treat the disease. These patients will require cell replacement to restore useful vision. Fortunately, the advent of induced pluripotent stem cell and CRISPR-Cas9 gene editing technologies affords researchers and clinicians a powerful means by which to develop strategies to treat patients with inherited retinal dystrophies. In this review we will discuss the current developments in CRISPR-Cas9 gene editing in vivo in animal models and in vitro in patient-derived cells to study and treat inherited retinal degenerative diseases.
Collapse
Affiliation(s)
- Erin R Burnight
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Joseph C Giacalone
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Jessica A Cooke
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Jessica R Thompson
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Laura R Bohrer
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Kathleen R Chirco
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Arlene V Drack
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - John H Fingert
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Kristan S Worthington
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States; Department of Biochemical Engineering, University of Iowa, Iowa City, IA, United States
| | - Luke A Wiley
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Robert F Mullins
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Edwin M Stone
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Budd A Tucker
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States.
| |
Collapse
|
32
|
Grzybek M, Golonko A, Górska A, Szczepaniak K, Strachecka A, Lass A, Lisowski P. The CRISPR/Cas9 system sheds new lights on the biology of protozoan parasites. Appl Microbiol Biotechnol 2018; 102:4629-4640. [PMID: 29626235 PMCID: PMC5954013 DOI: 10.1007/s00253-018-8927-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 01/04/2023]
Abstract
The CRISPR/Cas9 system, a natural defence system of bacterial organisms, has recently been used to modify genomes of the most important protozoa parasites. Successful genome manipulations with the CRISPR/Cas9 system are changing the present view of genetics in parasitology. The application of this system offers a major chance to overcome the current restriction in culturing, maintaining and analysing protozoan parasites, and allows dynamic analysis of parasite genes functions, leading to a better understanding of pathogenesis. CRISPR/Cas9 system will have a significant influence on the process of developing novel drugs and treatment strategies against protozoa parasites.
Collapse
Affiliation(s)
- Maciej Grzybek
- Department of Tropical Parasitology, Medical University of Gdansk, Powstania Styczniowego 9b, 81-519 Gdynia, Poland
| | - Aleksandra Golonko
- Department of Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351, Bialystok, Poland
| | - Aleksandra Górska
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Klaudiusz Szczepaniak
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Aneta Strachecka
- Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Anna Lass
- Department of Tropical Parasitology, Medical University of Gdansk, Powstania Styczniowego 9b, 81-519 Gdynia, Poland
| | - Paweł Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding PAS, Postepu 36A, 05-552 Jastrzebiec, Poland
- iPS Cell-Based Disease Modeling Group, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| |
Collapse
|
33
|
Wang X, Sterr M, Burtscher I, Chen S, Hieronimus A, Machicao F, Staiger H, Häring HU, Lederer G, Meitinger T, Cernilogar FM, Schotta G, Irmler M, Beckers J, Hrabě de Angelis M, Ray M, Wright CVE, Bakhti M, Lickert H. Genome-wide analysis of PDX1 target genes in human pancreatic progenitors. Mol Metab 2018; 9:57-68. [PMID: 29396371 PMCID: PMC5870105 DOI: 10.1016/j.molmet.2018.01.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/05/2018] [Accepted: 01/16/2018] [Indexed: 12/14/2022] Open
Abstract
Objective Homozygous loss-of-function mutations in the gene coding for the homeobox transcription factor (TF) PDX1 leads to pancreatic agenesis, whereas heterozygous mutations can cause Maturity-Onset Diabetes of the Young 4 (MODY4). Although the function of Pdx1 is well studied in pre-clinical models during insulin-producing β-cell development and homeostasis, it remains elusive how this TF controls human pancreas development by regulating a downstream transcriptional program. Also, comparative studies of PDX1 binding patterns in pancreatic progenitors and adult β-cells have not been conducted so far. Furthermore, many studies reported the association between single nucleotide polymorphisms (SNPs) and T2DM, and it has been shown that islet enhancers are enriched in T2DM-associated SNPs. Whether regions, harboring T2DM-associated SNPs are PDX1 bound and active at the pancreatic progenitor stage has not been reported so far. Methods In this study, we have generated a novel induced pluripotent stem cell (iPSC) line that efficiently differentiates into human pancreatic progenitors (PPs). Furthermore, PDX1 and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify PDX1 transcriptional targets and active enhancer and promoter regions. To address potential differences in the function of PDX1 during development and adulthood, we compared PDX1 binding profiles from PPs and adult islets. Moreover, combining ChIP-seq and GWAS meta-analysis data we identified T2DM-associated SNPs in PDX1 binding sites and active chromatin regions. Results ChIP-seq for PDX1 revealed a total of 8088 PDX1-bound regions that map to 5664 genes in iPSC-derived PPs. The PDX1 target regions include important pancreatic TFs, such as PDX1 itself, RFX6, HNF1B, and MEIS1, which were activated during the differentiation process as revealed by the active chromatin mark H3K27ac and mRNA expression profiling, suggesting that auto-regulatory feedback regulation maintains PDX1 expression and initiates a pancreatic TF program. Remarkably, we identified several PDX1 target genes that have not been reported in the literature in human so far, including RFX3, required for ciliogenesis and endocrine differentiation in mouse, and the ligand of the Notch receptor DLL1, which is important for endocrine induction and tip-trunk patterning. The comparison of PDX1 profiles from PPs and adult human islets identified sets of stage-specific target genes, associated with early pancreas development and adult β-cell function, respectively. Furthermore, we found an enrichment of T2DM-associated SNPs in active chromatin regions from iPSC-derived PPs. Two of these SNPs fall into PDX1 occupied sites that are located in the intronic regions of TCF7L2 and HNF1B. Both of these genes are key transcriptional regulators of endocrine induction and mutations in cis-regulatory regions predispose to diabetes. Conclusions Our data provide stage-specific target genes of PDX1 during in vitro differentiation of stem cells into pancreatic progenitors that could be useful to identify pathways and molecular targets that predispose for diabetes. In addition, we show that T2DM-associated SNPs are enriched in active chromatin regions at the pancreatic progenitor stage, suggesting that the susceptibility to T2DM might originate from imperfect execution of a β-cell developmental program. PDX1 ChIP-seq analysis revealed 5664 target genes in human pancreatic progenitors, including unreported target genes. Comparison of PDX1 profiles from PPs and adult human islets identified stage-specific PDX1 target gene sets. T2DM-associated SNPs are enriched in active chromatin regions from iPSC-derived PPs. Three SNPs fall into PDX1 occupied sites, located in intronic regions of the developmental regulatory TFs TCF7L2 and HNF1B.
Collapse
Affiliation(s)
- Xianming Wang
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Parkring 11, 85748, Garching, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Chair of ß-Cell Biology, Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Parkring 11, 85748, Garching, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Chair of ß-Cell Biology, Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Parkring 11, 85748, Garching, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Shen Chen
- iPS and Cancer Research Unit, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Anja Hieronimus
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Disease, Nephrology and Clinical Chemistry, University of Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Fausto Machicao
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Harald Staiger
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Hans-Ulrich Häring
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Disease, Nephrology and Clinical Chemistry, University of Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Gabriele Lederer
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Filippo M Cernilogar
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Gunnar Schotta
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Michael Ray
- Vanderbilt University Program in Developmental Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher V E Wright
- Vanderbilt University Program in Developmental Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Parkring 11, 85748, Garching, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Parkring 11, 85748, Garching, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Chair of ß-Cell Biology, Technische Universität München, Ismaningerstraße 22, 81675 München, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| |
Collapse
|
34
|
Kyrychenko V, Kyrychenko S, Tiburcy M, Shelton JM, Long C, Schneider JW, Zimmermann WH, Bassel-Duby R, Olson EN. Functional correction of dystrophin actin binding domain mutations by genome editing. JCI Insight 2017; 2:95918. [PMID: 28931764 DOI: 10.1172/jci.insight.95918] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/15/2017] [Indexed: 12/26/2022] Open
Abstract
Dystrophin maintains the integrity of striated muscles by linking the actin cytoskeleton with the cell membrane. Duchenne muscular dystrophy (DMD) is caused by mutations in the dystrophin gene (DMD) that result in progressive, debilitating muscle weakness, cardiomyopathy, and a shortened lifespan. Mutations of dystrophin that disrupt the amino-terminal actin-binding domain 1 (ABD-1), encoded by exons 2-8, represent the second-most common cause of DMD. In the present study, we compared three different strategies for CRISPR/Cas9 genome editing to correct mutations in the ABD-1 region of the DMD gene by deleting exons 3-9, 6-9, or 7-11 in human induced pluripotent stem cells (iPSCs) and by assessing the function of iPSC-derived cardiomyocytes. All three exon deletion strategies enabled the expression of truncated dystrophin protein and restoration of cardiomyocyte contractility and calcium transients to varying degrees. We show that deletion of exons 3-9 by genomic editing provides an especially effective means of correcting disease-causing ABD-1 mutations. These findings represent an important step toward eventual correction of common DMD mutations and provide a means of rapidly assessing the expression and function of internally truncated forms of dystrophin-lacking portions of ABD-1.
Collapse
Affiliation(s)
- Viktoriia Kyrychenko
- Department of Molecular Biology.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, and.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sergii Kyrychenko
- Department of Molecular Biology.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, and.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Malte Tiburcy
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| | - John M Shelton
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chengzu Long
- Department of Molecular Biology.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, and.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jay W Schneider
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, and.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Wolfram-Hubertus Zimmermann
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| | - Rhonda Bassel-Duby
- Department of Molecular Biology.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, and.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Eric N Olson
- Department of Molecular Biology.,Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, and.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
35
|
Concordet JP, Giovannangeli C. CRISPR-Cas systems for genome engineering and investigation. Methods 2017. [DOI: 10.1016/j.ymeth.2017.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
36
|
Guichard SM. CRISPR–Cas9 for Drug Discovery in Oncology. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1016/bs.armc.2017.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|