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Nikolouli E, Reichstein J, Hansen G, Lachmann N. In vitro systems to study inborn errors of immunity using human induced pluripotent stem cells. Front Immunol 2022; 13:1024935. [DOI: 10.3389/fimmu.2022.1024935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
In the last two decades, the exponential progress in the field of genetics could reveal the genetic impact on the onset and progression of several diseases affecting the immune system. This knowledge has led to the discovery of more than 400 monogenic germline mutations, also known as “inborn errors of immunity (IEI)”. Given the rarity of various IEI and the clinical diversity as well as the limited available patients’ material, the continuous development of novel cell-based in vitro models to elucidate the cellular and molecular mechanisms involved in the pathogenesis of these diseases is imperative. Focusing on stem cell technologies, this review aims to provide an overview of the current available in vitro models used to study IEI and which could lay the foundation for new therapeutic approaches. We elaborate in particular on the use of induced pluripotent stem cell-based systems and their broad application in studying IEI by establishing also novel infection culture models. The review will critically discuss the current limitations or gaps in the field of stem cell technology as well as the future perspectives from the use of these cell culture systems.
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Rao I, Crisafulli L, Paulis M, Ficara F. Hematopoietic Cells from Pluripotent Stem Cells: Hope and Promise for the Treatment of Inherited Blood Disorders. Cells 2022; 11:cells11030557. [PMID: 35159366 PMCID: PMC8834203 DOI: 10.3390/cells11030557] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 01/26/2023] Open
Abstract
Inherited blood disorders comprise a large spectrum of diseases due to germline mutations in genes with key function in the hematopoietic system; they include immunodeficiencies, anemia or metabolic diseases. For most of them the only curative treatment is bone marrow transplantation, a procedure associated to severe complications; other therapies include red blood cell and platelet transfusions, which are dependent on donor availability. An alternative option is gene therapy, in which the wild-type form of the mutated gene is delivered into autologous hematopoietic stem cells using viral vectors. A more recent therapeutic perspective is gene correction through CRISPR/Cas9-mediated gene editing, that overcomes safety concerns due to insertional mutagenesis and allows correction of base substitutions in large size genes difficult to incorporate into vectors. However, applying this technique to genomic disorders caused by large gene deletions is challenging. Chromosomal transplantation has been proposed as a solution, using a universal source of wild-type chromosomes as donor, and induced pluripotent stem cells (iPSCs) as acceptor. One of the obstacles to be addressed for translating PSC research into clinical practice is the still unsatisfactory differentiation into transplantable hematopoietic stem or mature cells. We provide an overview of the recent progresses in this field and discuss challenges and potential of iPSC-based therapies for the treatment of inherited blood disorders.
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Affiliation(s)
- Ilaria Rao
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Italy
| | - Laura Crisafulli
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, 20138 Milan, Italy
| | - Marianna Paulis
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, 20138 Milan, Italy
| | - Francesca Ficara
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, 20138 Milan, Italy
- Correspondence:
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Zbinden A, Canté-Barrett K, Pike-Overzet K, Staal FJT. Stem Cell-Based Disease Models for Inborn Errors of Immunity. Cells 2021; 11:cells11010108. [PMID: 35011669 PMCID: PMC8750661 DOI: 10.3390/cells11010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022] Open
Abstract
The intrinsic capacity of human hematopoietic stem cells (hHSCs) to reconstitute myeloid and lymphoid lineages combined with their self-renewal capacity hold enormous promises for gene therapy as a viable treatment option for a number of immune-mediated diseases, most prominently for inborn errors of immunity (IEI). The current development of such therapies relies on disease models, both in vitro and in vivo, which allow the study of human pathophysiology in great detail. Here, we discuss the current challenges with regards to developmental origin, heterogeneity and the subsequent implications for disease modeling. We review models based on induced pluripotent stem cell technology and those relaying on use of adult hHSCs. We critically review the advantages and limitations of current models for IEI both in vitro and in vivo. We conclude that existing and future stem cell-based models are necessary tools for developing next generation therapies for IEI.
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4
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Induced Pluripotent Stem Cells as a Tool for Modeling Hematologic Disorders and as a Potential Source for Cell-Based Therapies. Cells 2021; 10:cells10113250. [PMID: 34831472 PMCID: PMC8623953 DOI: 10.3390/cells10113250] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022] Open
Abstract
The breakthrough in human induced pluripotent stem cells (hiPSCs) has revolutionized the field of biomedical and pharmaceutical research and opened up vast opportunities for drug discovery and regenerative medicine, especially when combined with gene-editing technology. Numerous healthy and patient-derived hiPSCs for human disease modeling have been established, enabling mechanistic studies of pathogenesis, platforms for preclinical drug screening, and the development of novel therapeutic targets/approaches. Additionally, hiPSCs hold great promise for cell-based therapy, serving as an attractive cell source for generating stem/progenitor cells or functional differentiated cells for degenerative diseases, due to their unlimited proliferative capacity, pluripotency, and ethical acceptability. In this review, we provide an overview of hiPSCs and their utility in the study of hematologic disorders through hematopoietic differentiation. We highlight recent hereditary and acquired genetic hematologic disease modeling with patient-specific iPSCs, and discuss their applications as instrumental drug screening tools. The clinical applications of hiPSCs in cell-based therapy, including the next-generation cancer immunotherapy, are provided. Lastly, we discuss the current challenges that need to be addressed to fulfill the validity of hiPSC-based disease modeling and future perspectives of hiPSCs in the field of hematology.
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Kouchaki R, Abd-Nikfarjam B, Maali AH, Abroun S, Foroughi F, Ghaffari S, Azad M. Induced Pluripotent Stem Cell Meets Severe Combined Immunodeficiency. CELL JOURNAL 2020; 22:1-10. [PMID: 32779449 PMCID: PMC7481889 DOI: 10.22074/cellj.2020.6849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022]
Abstract
Severe combined immunodeficiency (SCID) is classified as a primary immunodeficiency, which is characterized by impaired
T-lymphocytes differentiation. IL2RG, IL7Ralpha, JAK3, ADA, RAG1/RAG2, and DCLE1C (Artemis) are the most defective
genes in SCID. The most recent SCID therapies are based on gene therapy (GT) of hematopoietic stem cells (HSC), which
are faced with many challenges. The new studies in the field of stem cells have made great progress in overcoming the
challenges ahead. In 2006, Yamanaka et al. achieved "reprogramming" technology by introducing four transcription factors
known as Yamanaka factors, which generate induced pluripotent stem cells (iPSC) from somatic cells. It is possible to apply
iPSC-derived HSC for transplantation in patients with abnormality or loss of function in specific cells or damaged tissue, such
as T-cells and NK-cells in the context of SCID. The iPSC-based HSC transplantation in SCID and other hereditary disorders
needs gene correction before transplantation. Furthermore, iPSC technology has been introduced as a promising tool in
cellular-molecular disease modeling and drug discovery. In this article, we review iPSC-based GT and modeling for SCID
disease and novel approaches of iPSC application in SCID.
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Affiliation(s)
- Reza Kouchaki
- Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Bahareh Abd-Nikfarjam
- Department of Immunology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Saeid Abroun
- Department of Hematology and Blood Banking, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farshad Foroughi
- Department of Immunology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sasan Ghaffari
- Hematology Department, School of Allied Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Azad
- Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran. Electronic Address:
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Efficient Generation and Correction of Mutations in Human iPS Cells Utilizing mRNAs of CRISPR Base Editors and Prime Editors. Genes (Basel) 2020. [PMID: 32384610 DOI: 10.3390/genes11050511.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In contrast to CRISPR/Cas9 nucleases, CRISPR base editors (BE) and prime editors (PE) enable predefined nucleotide exchanges in genomic sequences without generating DNA double strand breaks. Here, we employed BE and PE mRNAs in conjunction with chemically synthesized sgRNAs and pegRNAs for efficient editing of human induced pluripotent stem cells (iPSC). Whereas we were unable to correct a disease-causing mutation in patient derived iPSCs using a CRISPR/Cas9 nuclease approach, we corrected the mutation back to wild type with high efficiency utilizing an adenine BE. We also used adenine and cytosine BEs to introduce nine different cancer associated TP53 mutations into human iPSCs with up to 90% efficiency, generating a panel of cell lines to investigate the biology of these mutations in an isogenic background. Finally, we pioneered the use of prime editing in human iPSCs, opening this important cell type for the precise modification of nucleotides not addressable by BEs and to multiple nucleotide exchanges. These approaches eliminate the necessity of deriving disease specific iPSCs from human donors and allows the comparison of different disease-causing mutations in isogenic genetic backgrounds.
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Sürün D, Schneider A, Mircetic J, Neumann K, Lansing F, Paszkowski-Rogacz M, Hänchen V, Lee-Kirsch MA, Buchholz F. Efficient Generation and Correction of Mutations in Human iPS Cells Utilizing mRNAs of CRISPR Base Editors and Prime Editors. Genes (Basel) 2020; 11:E511. [PMID: 32384610 PMCID: PMC7288465 DOI: 10.3390/genes11050511] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 01/01/2023] Open
Abstract
In contrast to CRISPR/Cas9 nucleases, CRISPR base editors (BE) and prime editors (PE) enable predefined nucleotide exchanges in genomic sequences without generating DNA double strand breaks. Here, we employed BE and PE mRNAs in conjunction with chemically synthesized sgRNAs and pegRNAs for efficient editing of human induced pluripotent stem cells (iPSC). Whereas we were unable to correct a disease-causing mutation in patient derived iPSCs using a CRISPR/Cas9 nuclease approach, we corrected the mutation back to wild type with high efficiency utilizing an adenine BE. We also used adenine and cytosine BEs to introduce nine different cancer associated TP53 mutations into human iPSCs with up to 90% efficiency, generating a panel of cell lines to investigate the biology of these mutations in an isogenic background. Finally, we pioneered the use of prime editing in human iPSCs, opening this important cell type for the precise modification of nucleotides not addressable by BEs and to multiple nucleotide exchanges. These approaches eliminate the necessity of deriving disease specific iPSCs from human donors and allows the comparison of different disease-causing mutations in isogenic genetic backgrounds.
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Affiliation(s)
- Duran Sürün
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Aksana Schneider
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Jovan Mircetic
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
- Mildred Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC), Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Katrin Neumann
- Stem Cell Engineering Facility, Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden, 01307 Dresden, Germany;
| | - Felix Lansing
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Vanessa Hänchen
- Department of Pediatrics, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (V.H.); (M.A.L.-K.)
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (V.H.); (M.A.L.-K.)
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
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Brault J, Vigne B, Stasia MJ. Ex Vivo Models of Chronic Granulomatous Disease. Methods Mol Biol 2020; 1982:587-622. [PMID: 31172497 DOI: 10.1007/978-1-4939-9424-3_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Induced pluripotent stem cells (iPSCs) are pluripotent stem cells that can be established from dedifferentiation of all somatic cell types by epigenetic phenomena. iPSCs can be differentiated into any mature cells like neurons, hepatocytes, or pancreatic cells that have not been easily available to date. Thus, iPSCs are widely used for disease modeling, drug discovery, and cell therapy development. Here, we describe a protocol to obtain human mature and functional neutrophils and macrophages as ex vivo models of X-linked chronic granulomatous disease (X-CGD). This method can be applied to model the other genetic forms of CGD. We also describe methods for testing the characteristics and functions of neutrophils and macrophages by morphology, phagocytosis assay, release of granule markers or cytokines, cell surface markers, and NADPH oxidase activity.
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Affiliation(s)
- Julie Brault
- Centre Diagnostic et Recherche CGD (CDiReC), Pôle Biologie, CHU Grenoble Alpes, Grenoble, France
| | - Bénédicte Vigne
- Centre Diagnostic et Recherche CGD (CDiReC), Pôle Biologie, CHU Grenoble Alpes, Grenoble, France
| | - Marie José Stasia
- Centre Diagnostic et Recherche CGD (CDiReC), Pôle Biologie, CHU Grenoble Alpes, Grenoble, France. .,Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France.
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9
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Brault J, Vigne B, Meunier M, Beaumel S, Mollin M, Park S, Stasia MJ. NOX4 is the main NADPH oxidase involved in the early stages of hematopoietic differentiation from human induced pluripotent stem cells. Free Radic Biol Med 2020; 146:107-118. [PMID: 31626946 DOI: 10.1016/j.freeradbiomed.2019.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023]
Abstract
Reactive oxygen species (ROS) produced in hematopoietic stem cells (HSCs) are involved in the balance between quiescence, self-renewal, proliferation and differentiation processes. However the role of NOX enzymes on the early stages of hematopoietic differentiation is poorly investigated. For that, we used induced pluripotent stem cells (iPSCs) derived from X-linked Chronic Granulomatous Disease (X0CGD) patients with deficiency in NOX2, and AR220CGD patients with deficiency in p22phox subunit which decreases NOX1, NOX2, NOX3 and NOX4 activities. CD34+ hematopoietic progenitors were obtained after 7, 10 and 13 days of iPS/OP9 co-culture differentiation system. Neither NOX expression nor activity was found in Wild-type (WT), X0CGD and AR220CGD iPSCs. Although NOX2 and NOX4 mRNA were found in WT, X0CGD and AR220CGD iPSC-derived CD34+ cells at day 10 and 13 of differentiation, NOX4 protein was the only NOX enzyme expressed in these cells. A NADPH oxidase activity was measured in WT and X0CGD iPSC-derived CD34+ cells but not in AR220CGD iPSC-derived CD34+ cells because of the absence of p22phox, which is essential for the NOX4 activity. The absence of NOX4 activity and the poor NOX-independent ROS production in AR220CGD iPSC-derived CD34+ cells favored the CD34+ cells production but lowered their hematopoietic potential compared to WT and X0CGD iPSC-derived CD34+ cells. In addition we found a large production of primitive AR220CGD iPSC-derived progenitors at day 7 compared to the WT and X0CGD cell types. In conclusion NOX4 is the major NOX enzyme involved in the early stages of hematopoietic differentiation from iPSCs and its activity can modulate the production, the hematopoietic potential and the phenotype of iPSC-derived CD34+.
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Affiliation(s)
- Julie Brault
- Centre Hospitalier Universitaire Grenoble Alpes, CGD Diagnosis and Research Centre (CDiReC), Grenoble, France.
| | - Bénédicte Vigne
- Centre Hospitalier Universitaire Grenoble Alpes, CGD Diagnosis and Research Centre (CDiReC), Grenoble, France.
| | - Mathieu Meunier
- Centre Hospitalier Universitaire Grenoble Alpes, University Clinic of Hematology, Grenoble, France; CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France.
| | - Sylvain Beaumel
- Centre Hospitalier Universitaire Grenoble Alpes, CGD Diagnosis and Research Centre (CDiReC), Grenoble, France.
| | - Michelle Mollin
- Centre Hospitalier Universitaire Grenoble Alpes, CGD Diagnosis and Research Centre (CDiReC), Grenoble, France.
| | - Sophie Park
- Centre Hospitalier Universitaire Grenoble Alpes, University Clinic of Hematology, Grenoble, France; CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France.
| | - Marie José Stasia
- Centre Hospitalier Universitaire Grenoble Alpes, CGD Diagnosis and Research Centre (CDiReC), Grenoble, France; Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38044, Grenoble, France, Grenoble, France.
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Georgomanoli M, Papapetrou EP. Modeling blood diseases with human induced pluripotent stem cells. Dis Model Mech 2019; 12:12/6/dmm039321. [PMID: 31171568 PMCID: PMC6602313 DOI: 10.1242/dmm.039321] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are derived from somatic cells through a reprogramming process, which converts them to a pluripotent state, akin to that of embryonic stem cells. Over the past decade, iPSC models have found increasing applications in the study of human diseases, with blood disorders featuring prominently. Here, we discuss methodological aspects pertaining to iPSC generation, hematopoietic differentiation and gene editing, and provide an overview of uses of iPSCs in modeling the cell and gene therapy of inherited genetic blood disorders, as well as their more recent use as models of myeloid malignancies. We also discuss the strengths and limitations of iPSCs compared to model organisms and other cellular systems commonly used in hematology research.
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Affiliation(s)
- Maria Georgomanoli
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eirini P Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šarić T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. Cell Stem Cell 2019; 24:736-752.e12. [PMID: 30982769 DOI: 10.1016/j.stem.2019.03.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 01/03/2019] [Accepted: 03/06/2019] [Indexed: 11/18/2022]
Abstract
The pathological consequences of structural variants disrupting 3D genome organization can be difficult to elucidate in vivo due to differences in gene dosage sensitivity between mice and humans. This is illustrated by branchiooculofacial syndrome (BOFS), a rare congenital disorder caused by heterozygous mutations within TFAP2A, a neural crest regulator for which humans, but not mice, are haploinsufficient. Here, we present a BOFS patient carrying a heterozygous inversion with one breakpoint located within a topologically associating domain (TAD) containing enhancers essential for TFAP2A expression in human neural crest cells (hNCCs). Using patient-specific hiPSCs, we show that, although the inversion shuffles the TFAP2A hNCC enhancers with novel genes within the same TAD, this does not result in enhancer adoption. Instead, the inversion disconnects one TFAP2A allele from its cognate enhancers, leading to monoallelic and haploinsufficient TFAP2A expression in patient hNCCs. Our work illustrates the power of hiPSC differentiation to unveil long-range pathomechanisms.
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Affiliation(s)
- Magdalena Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Institute of Human Genetics, CMMC, University Hospital Cologne, Cologne, Germany
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hafiza Alirzayeva
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Agathi Karaolidou
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Giuliano Crispatzu
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Peter Zentis
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Milos Nikolic
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Petros Kolovos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Tomo Šarić
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Katrin Koehler
- Department of Pediatrics, University Clinic Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Peter Frommolt
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Katherine Lachlan
- Human Genetics & Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK; Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton, UK
| | - Julia Baptista
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK; Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain.
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12
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Castelli A, Susani L, Menale C, Muggeo S, Caldana E, Strina D, Cassani B, Recordati C, Scanziani E, Ficara F, Villa A, Vezzoni P, Paulis M. Chromosome Transplantation: Correction of the Chronic Granulomatous Disease Defect in Mouse Induced Pluripotent Stem Cells. Stem Cells 2019; 37:876-887. [PMID: 30895693 DOI: 10.1002/stem.3006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/12/2019] [Accepted: 03/12/2019] [Indexed: 12/21/2022]
Abstract
In spite of the progress in gene editing achieved in recent years, a subset of genetic diseases involving structural chromosome abnormalities, including aneuploidies, large deletions and complex rearrangements, cannot be treated with conventional gene therapy approaches. We have previously devised a strategy, dubbed chromosome transplantation (CT), to replace an endogenous mutated chromosome with an exogenous normal one. To establish a proof of principle for our approach, we chose as disease model the chronic granulomatous disease (CGD), an X-linked severe immunodeficiency due to abnormalities in CYBB (GP91) gene, including large genomic deletions. We corrected the gene defect by CT in induced pluripotent stem cells (iPSCs) from a CGD male mouse model. The Hprt gene of the endogenous X chromosome was inactivated by CRISPR/Cas9 technology thus allowing the exploitation of the hypoxanthine-aminopterin-thymidine selection system to introduce a normal donor X chromosome by microcell-mediated chromosome transfer. X-transplanted clones were obtained, and diploid XY clones which spontaneously lost the endogenous X chromosome were isolated. These cells were differentiated toward the myeloid lineage, and functional granulocytes producing GP91 protein were obtained. We propose the CT approach to correct iPSCs from patients affected by other X-linked diseases with large deletions, whose treatment is still unsatisfactory. Stem Cells 2019;37:876-887.
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Affiliation(s)
- Alessandra Castelli
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Lucia Susani
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Ciro Menale
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Sharon Muggeo
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Elena Caldana
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Dario Strina
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Barbara Cassani
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Camilla Recordati
- Department of Veterinary Sciences and Public Health, University of Milan, Milan, Italy
| | - Eugenio Scanziani
- Department of Veterinary Sciences and Public Health, University of Milan, Milan, Italy
| | - Francesca Ficara
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Anna Villa
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Vezzoni
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Marianna Paulis
- National Research Council (CNR)-IRGB/UOS of Milan, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
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13
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Brault J, Vaganay G, Le Roy A, Lenormand JL, Cortes S, Stasia MJ. Therapeutic effects of proteoliposomes on X-linked chronic granulomatous disease: proof of concept using macrophages differentiated from patient-specific induced pluripotent stem cells. Int J Nanomedicine 2017; 12:2161-2177. [PMID: 28356734 PMCID: PMC5367562 DOI: 10.2147/ijn.s128611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chronic granulomatous disease (CGD) is a rare inherited immunodeficiency due to dysfunction of the phagocytic nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex leading to severe and recurrent infections in early childhood. The main genetic form is the X-linked CGD leading to the absence of cytochrome b558 composed of NOX2 and p22phox, the membrane partners of the NADPH oxidase complex. The first cause of death of CGD patients is pulmonary infections. Recombinant proteoliposome-based therapy is an emerging and innovative approach for membrane protein delivery, which could be an alternative local, targeted treatment to fight lung infections in CGD patients. We developed an enzyme therapy using recombinant NOX2/p22phox liposomes to supply the NADPH oxidase activity in X0-linked CGD (X0-CGD) macrophages. Using an optimized prokaryotic cell-free protein synthesis system, a recombinant cytochrome b558 containing functional hemes was produced and directly inserted into the lipid bilayer of specific liposomes. The size of the NOX2/p22phox liposomes was estimated to be around 700 nm. These proteoliposomes were able to generate reactive oxygen species (ROS) in an activated reconstituted cell-free NADPH oxidase activation assay in the presence of recombinant p47phox, p67phox and Rac, the cytosolic components of the NADPH oxidase complex. Furthermore, using flow cytometry and fluorescence microscopy, we demonstrated that cytochrome b558 was successfully delivered to the plasma membrane of X0-CGD-induced pluripotent stem cell (iPSC)-derived macrophages. In addition, NADPH oxidase activity was restored in X0-CGD iPSC-derived macrophages treated with NOX2/p22phox liposomes for 8 h without any toxicity. In conclusion, we confirmed that proteoliposomes provide a new promising technology for the delivery of functional proteins to the membrane of targeted cells. This efficient liposomal enzyme replacement therapy will be useful for future treatment of pulmonary infections in CGD patients refractory to conventional anti-infectious treatments.
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Affiliation(s)
- Julie Brault
- UMR CNRS 5525, University of Grenoble Alpes, Grenoble, France; CGD Diagnosis and Research Centre, University Hospital Centre of Grenoble Alpes, Grenoble, France
| | | | - Aline Le Roy
- IBS, University of Grenoble Alpes, Grenoble, France; CNRS, IBS, University Grenoble Alpes, Grenoble, France; CEA, IBS, University of Grenoble Alpes, Grenoble, France
| | | | | | - Marie José Stasia
- UMR CNRS 5525, University of Grenoble Alpes, Grenoble, France; CGD Diagnosis and Research Centre, University Hospital Centre of Grenoble Alpes, Grenoble, France
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14
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Sweeney CL, Zou J, Choi U, Merling RK, Liu A, Bodansky A, Burkett S, Kim JW, De Ravin SS, Malech HL. Targeted Repair of CYBB in X-CGD iPSCs Requires Retention of Intronic Sequences for Expression and Functional Correction. Mol Ther 2017; 25:321-330. [PMID: 28153086 PMCID: PMC5368476 DOI: 10.1016/j.ymthe.2016.11.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 01/03/2023] Open
Abstract
X-linked chronic granulomatous disease (X-CGD) is an immune deficiency resulting from defective production of microbicidal reactive oxygen species (ROS) by phagocytes. Causative mutations occur throughout the CYBB gene, resulting in absent or defective gp91phox protein expression. To correct CYBB exon 5 mutations while retaining normal gene regulation, we utilized TALEN or Cas9 for exon 5 replacement in induced pluripotent stem cells (iPSCs) from patients, which restored gp91phox expression and ROS production in iPSC-derived granulocytes. Alternate approaches for correcting the majority of X-CGD mutations were assessed, involving TALEN- or Cas9-mediated insertion of CYBB minigenes at exon 1 or 2 of the CYBB locus. Targeted insertion of an exon 1-13 minigene into CYBB exon 1 resulted in no detectable gp91phox expression or ROS activity in iPSC-derived granulocytes. In contrast, targeted insertion of an exon 2-13 minigene into exon 2 restored both gp91phox and ROS activity. This demonstrates the efficacy of two correction strategies: seamless repair of specific CYBB mutations by exon replacement or targeted insertion of an exon 2-13 minigene to CYBB exon 2 while retaining exon/intron 1. Furthermore, it highlights a key issue for targeted insertion strategies for expression from an endogenous promoter: retention of intronic elements can be necessary for expression.
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Affiliation(s)
- Colin L Sweeney
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Jizhong Zou
- Center for Molecular Medicine, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Uimook Choi
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Randall K Merling
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexander Liu
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Aaron Bodansky
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sandra Burkett
- Molecular Cytogenetics Section, MCGP, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Jung-Woong Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Suk See De Ravin
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Harry L Malech
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
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15
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Santilli G, Thrasher AJ. A New Chapter on Targeted Gene Insertion for X-CGD: Do Not Skip the Intro(n). Mol Ther 2017; 25:307-309. [PMID: 28109956 DOI: 10.1016/j.ymthe.2017.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Giorgia Santilli
- Molecular Immunology Unit, Centre for Immunodeficiency, Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Adrian J Thrasher
- Molecular Immunology Unit, Centre for Immunodeficiency, Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK.
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16
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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17
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Abstract
Chronic granulomatous disease (CGD) is the most common symptomatic phagocytic defect. It is caused by mutations in genes encoding protein subunits of the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex. CGD is characterized by a defective intracellular killing of phagocytosed organisms due to a defective oxidative burst in the neutrophils and macrophages. It is inherited in either X-linked recessive or autosomal recessive pattern. Staphylococcus aureus and Aspergillus species are the most common organisms reported. Infections with Burkholderia, Serratia, and Nocardia warrant a screen for CGD. Suppurative lymphadenitis, cutaneous abscesses, pneumonia and diarrhea constitute the most common problems in children with CGD. A small percentage of children develop autoimmune manifestations (e.g., rheumatoid arthritis, systemic lupus erythematosus, colitis, autoimmune hepatitis) and warrant immunosuppression. X-linked carriers of CGD are at an increased risk of developing autoimmune diseases. Nitroblue-tetrazolium dye reduction test and dihydro-rhodamine assay by flow cytometry are the screening tests for this disorder. While most children do well on long term antibiotic and antifungal prophylaxis, those with severe forms warrant hematopoietic stem cell transplant. The role of regular interferon-γ injections is debatable. Evidence for white cell transfusions is sparse, and gene therapy is under trial.This current review highlights various aspects and studies in CGD. X-linked form of CGD has been noted to carry a poorer prognosis compared to autosomal recessive variants. However, recent evidence suggests that outcome in CGD is determined by the amount of residual NADPH oxidase activity irrespective of mode of inheritance.
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