1
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Chowdhury MM, Zimmerman S, Leeson H, Nefzger CM, Mar JC, Laslett A, Polo JM, Wolvetang E, Cooper-White JJ. Superior Induced Pluripotent Stem Cell Generation through Phactr3-Driven Mechanomodulation of Both Early and Late Phases of Cell Reprogramming. Biomater Res 2024; 28:0025. [PMID: 38774128 PMCID: PMC11106629 DOI: 10.34133/bmr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 05/24/2024] Open
Abstract
Human cell reprogramming traditionally involves time-intensive, multistage, costly tissue culture polystyrene-based cell culture practices that ultimately produce low numbers of reprogrammed cells of variable quality. Previous studies have shown that very soft 2- and 3-dimensional hydrogel substrates/matrices (of stiffnesses ≤ 1 kPa) can drive ~2× improvements in human cell reprogramming outcomes. Unfortunately, these similarly complex multistage protocols lack intrinsic scalability, and, furthermore, the associated underlying molecular mechanisms remain to be fully elucidated, limiting the potential to further maximize reprogramming outcomes. In screening the largest range of polyacrylamide (pAAm) hydrogels of varying stiffness to date (1 kPa to 1.3 MPa), we have found that a medium stiffness gel (~100 kPa) increased the overall number of reprogrammed cells by up to 10-fold (10×), accelerated reprogramming kinetics, improved both early and late phases of reprogramming, and produced induced pluripotent stem cells (iPSCs) having more naïve characteristics and lower remnant transgene expression, compared to the gold standard tissue culture polystyrene practice. Functionalization of these pAAm hydrogels with poly-l-dopamine enabled, for the first-time, continuous, single-step reprogramming of fibroblasts to iPSCs on hydrogel substrates (noting that even the tissue culture polystyrene practice is a 2-stage process). Comparative RNA sequencing analyses coupled with experimental validation revealed that a novel reprogramming regulator, protein phosphatase and actin regulator 3, up-regulated under the gel condition at a very early time point, was responsible for the observed enhanced reprogramming outcomes. This study provides a novel culture protocol and substrate for continuous hydrogel-based cell reprogramming and previously unattained clarity of the underlying mechanisms via which substrate stiffness modulates reprogramming kinetics and iPSC quality outcomes.
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Affiliation(s)
- Mohammad Mahfuz Chowdhury
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Hannah Leeson
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Jessica Cara Mar
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrew Laslett
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jose Maria Polo
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute and the Australian Regenerative Medicine Institute,
Monash University, Clayton, VIC 3800, Australia
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences,
The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ernst Wolvetang
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Justin John Cooper-White
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- School of Chemical Engineering, Andrew N. Liveris Building,
The University of Queensland, St. Lucia, QLD 4072, Australia
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2
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Beltran AS. Novel Approaches to Studying SLC13A5 Disease. Metabolites 2024; 14:84. [PMID: 38392976 PMCID: PMC10890222 DOI: 10.3390/metabo14020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
The role of the sodium citrate transporter (NaCT) SLC13A5 is multifaceted and context-dependent. While aberrant dysfunction leads to neonatal epilepsy, its therapeutic inhibition protects against metabolic disease. Notably, insights regarding the cellular and molecular mechanisms underlying these phenomena are limited due to the intricacy and complexity of the latent human physiology, which is poorly captured by existing animal models. This review explores innovative technologies aimed at bridging such a knowledge gap. First, I provide an overview of SLC13A5 variants in the context of human disease and the specific cell types where the expression of the transporter has been observed. Next, I discuss current technologies for generating patient-specific induced pluripotent stem cells (iPSCs) and their inherent advantages and limitations, followed by a summary of the methods for differentiating iPSCs into neurons, hepatocytes, and organoids. Finally, I explore the relevance of these cellular models as platforms for delving into the intricate molecular and cellular mechanisms underlying SLC13A5-related disorders.
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Affiliation(s)
- Adriana S Beltran
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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3
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Fares MB, Alijevic O, Johne S, Overk C, Hashimoto M, Kondylis A, Adame A, Dulize R, Peric D, Nury C, Battey J, Guedj E, Sierro N, Mc Hugh D, Rockenstein E, Kim C, Rissman RA, Hoeng J, Peitsch MC, Masliah E, Mathis C. Nicotine-mediated effects in neuronal and mouse models of synucleinopathy. Front Neurosci 2023; 17:1239009. [PMID: 37719154 PMCID: PMC10501483 DOI: 10.3389/fnins.2023.1239009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Alpha-synuclein (α-Syn) aggregation, transmission, and contribution to neurotoxicity represent central mechanisms underlying Parkinson's disease. The plant alkaloid "nicotine" was reported to attenuate α-Syn aggregation in different models, but its precise mode of action remains unclear. Methods In this study, we investigated the effect of 2-week chronic nicotine treatment on α-Syn aggregation, neuroinflammation, neurodegeneration, and motor deficits in D-line α-Syn transgenic mice. We also established a novel humanized neuronal model of α-Syn aggregation and toxicity based on treatment of dopaminergic neurons derived from human induced pluripotent stem cells (iPSC) with α-Syn preformed fibrils (PFF) and applied this model to investigate the effects of nicotine and other compounds and their modes of action. Results and discussion Overall, our results showed that nicotine attenuated α-Syn-provoked neuropathology in both models. Moreover, when investigating the role of nicotinic acetylcholine receptor (nAChR) signaling in nicotine's neuroprotective effects in iPSC-derived dopaminergic neurons, we observed that while α4-specific antagonists reduced the nicotine-induced calcium response, α4 agonists (e.g., AZD1446 and anatabine) mediated similar neuroprotective responses against α-Syn PFF-provoked neurodegeneration. Our results show that nicotine attenuates α-Syn-provoked neuropathology in vivo and in a humanized neuronal model of synucleinopathy and that activation of α4β2 nicotinic receptors might mediate these neuroprotective effects.
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Affiliation(s)
| | - Omar Alijevic
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Stephanie Johne
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Cassia Overk
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Makoto Hashimoto
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | | | - Anthony Adame
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Remi Dulize
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Dariusz Peric
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - James Battey
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Damian Mc Hugh
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Edward Rockenstein
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Changyoun Kim
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Robert A. Rissman
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Carole Mathis
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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4
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Fus-Kujawa A, Mendrek B, Bajdak-Rusinek K, Diak N, Strzelec K, Gutmajster E, Janelt K, Kowalczuk A, Trybus A, Rozwadowska P, Wojakowski W, Gawron K, Sieroń AL. Gene-repaired iPS cells as novel approach for patient with osteogenesis imperfecta. Front Bioeng Biotechnol 2023; 11:1205122. [PMID: 37456734 PMCID: PMC10348904 DOI: 10.3389/fbioe.2023.1205122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction: The benefits of patient's specific cell/gene therapy have been reported in relation to numerous genetic related disorders including osteogenesis imperfecta (OI). In osteogenesis imperfecta particularly also a drug therapy based on the administration of bisphosphonates partially helped to ease the symptoms. Methods: In this controlled trial, fibroblasts derived from patient diagnosed with OI type II have been successfully reprogrammed into induced Pluripotent Stem cells (iPSCs) using Yamanaka factors. Those cells were subjected to repair mutations found in the COL1A1 gene using homologous recombination (HR) approach facilitated with star polymer (STAR) as a carrier of the genetic material. Results: Delivery of the correct linear DNA fragment to the osteogenesis imperfecta patient's cells resulted in the repair of the DNA mutation with an 84% success rate. IPSCs showed 87% viability after STAR treatment and 82% with its polyplex. Discussion: The use of novel polymer Poly[N,N-Dimethylaminoethyl Methacrylate-co-Hydroxyl-Bearing Oligo(Ethylene Glycol) Methacrylate] Arms (P(DMAEMA-co-OEGMA-OH) with star-like structure has been shown as an efficient tool for nucleic acids delivery into cells (Funded by National Science Centre, Contract No. UMO-2020/37/N/NZ2/01125).
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Affiliation(s)
- Agnieszka Fus-Kujawa
- Department of Medical Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Barbara Mendrek
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, Zabrze, Poland
| | - Karolina Bajdak-Rusinek
- Department of Medical Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Natalia Diak
- Department of Medical Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Karolina Strzelec
- Department of Molecular Biology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Ewa Gutmajster
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Kamil Janelt
- Department of Medical Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Agnieszka Kowalczuk
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, Zabrze, Poland
| | - Anna Trybus
- Department of Medical Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
- Students Scientific Society, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Patrycja Rozwadowska
- Department of Medical Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
- Students Scientific Society, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Wojciech Wojakowski
- Division of Cardiology and Structural Heart Diseases, Medical University of Silesia, Katowice, Poland
| | - Katarzyna Gawron
- Department of Molecular Biology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Aleksander L. Sieroń
- Formerly Department of Molecular Biology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
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5
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Choi Y, Li R, Quon G. siVAE: interpretable deep generative models for single-cell transcriptomes. Genome Biol 2023; 24:29. [PMID: 36803416 PMCID: PMC9940350 DOI: 10.1186/s13059-023-02850-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/06/2023] [Indexed: 02/22/2023] Open
Abstract
Neural networks such as variational autoencoders (VAE) perform dimensionality reduction for the visualization and analysis of genomic data, but are limited in their interpretability: it is unknown which data features are represented by each embedding dimension. We present siVAE, a VAE that is interpretable by design, thereby enhancing downstream analysis tasks. Through interpretation, siVAE also identifies gene modules and hubs without explicit gene network inference. We use siVAE to identify gene modules whose connectivity is associated with diverse phenotypes such as iPSC neuronal differentiation efficiency and dementia, showcasing the wide applicability of interpretable generative models for genomic data analysis.
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Affiliation(s)
- Yongin Choi
- Graduate Group in Biomedical Engineering, University of California, Davis, Davis, CA, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Ruoxin Li
- Genome Center, University of California, Davis, Davis, CA, USA
- Graduate Group in Biostatistics, University of California, Davis, Davis, CA, USA
| | - Gerald Quon
- Graduate Group in Biomedical Engineering, University of California, Davis, Davis, CA, USA.
- Genome Center, University of California, Davis, Davis, CA, USA.
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA.
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6
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Mathews M, Wißfeld J, Flitsch LJ, Shahraz A, Semkova V, Breitkreuz Y, Neumann H, Brüstle O. Reenacting Neuroectodermal Exposure of Hematopoietic Progenitors Enables Scalable Production of Cryopreservable iPSC-Derived Human Microglia. Stem Cell Rev Rep 2023; 19:455-474. [PMID: 35971018 PMCID: PMC9902330 DOI: 10.1007/s12015-022-10433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 02/07/2023]
Abstract
Human microglia, as innate immune cells of the central nervous system (CNS), play a central role in the pathogenesis of a large number of neurological and psychiatric disorders. However, experimental access to primary human microglia for biomedical applications such as disease modeling is extremely limited. While induced pluripotent stem cells (iPSCs) could provide an alternative source of microglia, the reenactment of their complex ontogenesis with a yolk sac origin and subsequent priming upon CNS invasion has remained a challenge. Here, we report a developmentally informed in vitro differentiation method for large-scale production and cryopreservation of iPSC-derived microglia (iPSdMiG). Specifically, iPSCs were propagated in conditions yielding both yolk sac hematopoietic derivatives and early neuroepithelial cells. To enable large-scale production, we implemented 3D bioreactor-based dynamic culture conditions and the use of novel mesh macrocarriers. Under these conditions, microglia could be harvested across a time period of at least 6 weeks, with 1 × 106 iPSCs giving rise to up to 45 × 106 iPSdMiG. The transcriptomic profile of iPSdMiG showed high similarity to adult human microglia, and harvested cells were immunopositive for typical microglial markers. In addition, iPSdMiG were able to secrete pro-inflammatory cytokines, engaged in phagocytotic activity, produced reactive oxygen species and lent themselves to co-culture studies in neural 2D and 3D systems. Importantly, iPSdMiG were efficiently cryopreserved, enabling the establishment of donor-specific microglia cell banks for disease modeling, drug discovery and eventually cell therapy. Main points. Scalable generation of iPSC-derived multi-lineage embryoid bodies on macrocarriers, reproducibly releasing microglia exhibiting characteristic markers and function. Cells are transcriptomically similar to primary human microglia and cryopreservable.
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Affiliation(s)
- Mona Mathews
- LIFE & BRAIN GmbH, Venusberg-Campus 1, 53127, Bonn, Germany.,Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jannis Wißfeld
- Institute of Reconstructive Neurobiology, Neural Regeneration Group, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Lea Jessica Flitsch
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Anahita Shahraz
- Institute of Reconstructive Neurobiology, Neural Regeneration Group, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Vesselina Semkova
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Yannik Breitkreuz
- LIFE & BRAIN GmbH, Venusberg-Campus 1, 53127, Bonn, Germany.,Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Harald Neumann
- Institute of Reconstructive Neurobiology, Neural Regeneration Group, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Oliver Brüstle
- LIFE & BRAIN GmbH, Venusberg-Campus 1, 53127, Bonn, Germany. .,Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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7
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Karami Z, Moradi S, Eidi A, Soleimani M, Jafarian A. Induced pluripotent stem cells: Generation methods and a new perspective in COVID-19 research. Front Cell Dev Biol 2023; 10:1050856. [PMID: 36733338 PMCID: PMC9887183 DOI: 10.3389/fcell.2022.1050856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 01/18/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) exhibit an unlimited ability to self-renew and produce various differentiated cell types, thereby creating high hopes for both scientists and patients as a great tool for basic research as well as for regenerative medicine purposes. The availability and safety of iPSCs for therapeutic purposes require safe and highly efficient methods for production of these cells. Different methods have been used to produce iPSCs, each of which has advantages and disadvantages. Studying these methods would be very helpful in developing an easy, safe, and efficient method for the generation of iPSCs. Since iPSCs can be generated from somatic cells, they can be considered as valuable cellular resources available for important research needs and various therapeutic purposes. Coronavirus disease 2019 (COVID-19) is a disease that has endangered numerous human lives worldwide and currently has no definitive cure. Therefore, researchers have been rigorously studying and examining all aspects of COVID-19 and potential treatment modalities and various drugs in order to enable the treatment, control, and prevention of COVID-19. iPSCs have become one of the most attractive and promising tools in this field by providing the ability to study COVID-19 and the effectiveness of drugs on this disease outside the human body. In this study, we discuss the different methods of generation of iPSCs as well as their respective advantages and disadvantages. We also present recent applications of iPSCs in the study and treatment of COVID-19.
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Affiliation(s)
- Zahra Karami
- 1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Sharif Moradi
- 2Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Akram Eidi
- 1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Soleimani
- 3Hematology and Cell Therapy Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran,4Department of Tissue Engineering and Applied Cell Science, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arefeh Jafarian
- 5Iranian Tissue Bank and Research Center, Tehran University of Medical Sciences, Tehran, Iran,*Correspondence: Arefeh Jafarian,
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8
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Carberry CK, Ferguson SS, Beltran AS, Fry RC, Rager JE. Using liver models generated from human-induced pluripotent stem cells (iPSCs) for evaluating chemical-induced modifications and disease across liver developmental stages. Toxicol In Vitro 2022; 83:105412. [PMID: 35688329 PMCID: PMC9296547 DOI: 10.1016/j.tiv.2022.105412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/20/2022] [Accepted: 06/03/2022] [Indexed: 01/09/2023]
Abstract
The liver is a pivotal organ regulating critical developmental stages of fetal metabolism and detoxification. Though numerous studies have evaluated links between prenatal/perinatal exposures and adverse health outcomes in the developing fetus, the central role of liver to health disruptions resulting from these exposures remains understudied, especially concerning early development and later-in-life health outcomes. While numerous in vitro methods for evaluating liver toxicity have been established, the use of iPSC-derived hepatocytes appears to be particularly well suited to contribute to this critical research gap due to their potential to model a diverse range of disease phenotypes and different stages of liver development. The following key aspects are reviewed: (1) an introduction to developmental liver toxicity; (2) an introduction to embryonic and induced pluripotent stem cell models; (3) methods and challenges for deriving liver cells from stem cells; and (4) applications for iPSC-derived hepatocytes to evaluate liver developmental stages and their associated responses to insults. We conclude that iPSC-derived hepatocytes have great potential for informing liver toxicity and underlying disease mechanisms via the generation of patient-specific iPSCs; implementing large-scale drug and chemical screening; evaluating general biological responses as a potential surrogate target cell; and evaluating inter-individual disease susceptibility and response variability.
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Affiliation(s)
- Celeste K Carberry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephen S Ferguson
- Biomolecular Screening Branch, National Toxicology Program, Research Triangle Park, NC, USA
| | - Adriana S Beltran
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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9
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Mashinchian O, De Franceschi F, Nassiri S, Michaud J, Migliavacca E, Aouad P, Metairon S, Pruvost S, Karaz S, Fabre P, Molina T, Stuelsatz P, Hegde N, Le Moal E, Dammone G, Dumont NA, Lutolf MP, Feige JN, Bentzinger CF. An engineered multicellular stem cell niche for the 3D derivation of human myogenic progenitors from iPSCs. EMBO J 2022; 41:e110655. [PMID: 35703167 DOI: 10.15252/embj.2022110655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
Fate decisions in the embryo are controlled by a plethora of microenvironmental interactions in a three-dimensional niche. To investigate whether aspects of this microenvironmental complexity can be engineered to direct myogenic human-induced pluripotent stem cell (hiPSC) differentiation, we here screened murine cell types present in the developmental or adult stem cell niche in heterotypic suspension embryoids. We identified embryonic endothelial cells and fibroblasts as highly permissive for myogenic specification of hiPSCs. After two weeks of sequential Wnt and FGF pathway induction, these three-component embryoids are enriched in Pax7-positive embryonic-like myogenic progenitors that can be isolated by flow cytometry. Myogenic differentiation of hiPSCs in heterotypic embryoids relies on a specialized structural microenvironment and depends on MAPK, PI3K/AKT, and Notch signaling. After transplantation in a mouse model of Duchenne muscular dystrophy, embryonic-like myogenic progenitors repopulate the stem cell niche, reactivate after repeated injury, and, compared to adult human myoblasts, display enhanced fusion and lead to increased muscle function. Altogether, we provide a two-week protocol for efficient and scalable suspension-based 3D derivation of Pax7-positive myogenic progenitors from hiPSCs.
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Affiliation(s)
- Omid Mashinchian
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Sina Nassiri
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joris Michaud
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Patrick Aouad
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylviane Metairon
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Sonia Karaz
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Paul Fabre
- Faculty of Medicine, CHU Sainte-Justine Research Center, School of Rehabilitation, Université de Montréal, Montreal, QC, Canada
| | - Thomas Molina
- Faculty of Medicine, CHU Sainte-Justine Research Center, School of Rehabilitation, Université de Montréal, Montreal, QC, Canada
| | - Pascal Stuelsatz
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Nagabhooshan Hegde
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Emmeran Le Moal
- Département de pharmacologie-physiologie, Faculté de médecine et des sciences de la santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Gabriele Dammone
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Nicolas A Dumont
- Faculty of Medicine, CHU Sainte-Justine Research Center, School of Rehabilitation, Université de Montréal, Montreal, QC, Canada
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Institute of Chemical Sciences and Engineering, School of Basic Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jerome N Feige
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - C Florian Bentzinger
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,Département de pharmacologie-physiologie, Faculté de médecine et des sciences de la santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
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10
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Johansson M, Tangruksa B, Heydarkhan-Hagvall S, Jeppsson A, Sartipy P, Synnergren J. Data Mining Identifies CCN2 and THBS1 as Biomarker Candidates for Cardiac Hypertrophy. Life (Basel) 2022; 12:life12050726. [PMID: 35629393 PMCID: PMC9147176 DOI: 10.3390/life12050726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Cardiac hypertrophy is a condition that may contribute to the development of heart failure. In this study, we compare the gene-expression patterns of our in vitro stem-cell-based cardiac hypertrophy model with the gene expression of biopsies collected from hypertrophic human hearts. Twenty-five differentially expressed genes (DEGs) from both groups were identified and the expression of selected corresponding secreted proteins were validated using ELISA and Western blot. Several biomarkers, including CCN2, THBS1, NPPA, and NPPB, were identified, which showed significant overexpressions in the hypertrophic samples in both the cardiac biopsies and in the endothelin-1-treated cells, both at gene and protein levels. The protein-interaction network analysis revealed CCN2 as a central node among the 25 overlapping DEGs, suggesting that this gene might play an important role in the development of cardiac hypertrophy. GO-enrichment analysis of the 25 DEGs revealed many biological processes associated with cardiac function and the development of cardiac hypertrophy. In conclusion, we identified important similarities between ET-1-stimulated human-stem-cell-derived cardiomyocytes and human hypertrophic cardiac tissue. Novel putative cardiac hypertrophy biomarkers were identified and validated on the protein level, lending support for further investigations to assess their potential for future clinical applications.
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Affiliation(s)
- Markus Johansson
- Systems Biology Research Center, School of Bioscience, University of Skövde, SE-541 28 Skövde, Sweden; (S.H.-H.); (P.S.); (J.S.)
- Department of Molecular and Clinical Medicine, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, SE-413 45 Gothenburg, Sweden;
- Correspondence: (M.J.); (B.T.)
| | - Benyapa Tangruksa
- Systems Biology Research Center, School of Bioscience, University of Skövde, SE-541 28 Skövde, Sweden; (S.H.-H.); (P.S.); (J.S.)
- Correspondence: (M.J.); (B.T.)
| | - Sepideh Heydarkhan-Hagvall
- Systems Biology Research Center, School of Bioscience, University of Skövde, SE-541 28 Skövde, Sweden; (S.H.-H.); (P.S.); (J.S.)
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, SE-413 83 Gothenburg, Sweden
| | - Anders Jeppsson
- Department of Molecular and Clinical Medicine, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, SE-413 45 Gothenburg, Sweden;
- Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden
| | - Peter Sartipy
- Systems Biology Research Center, School of Bioscience, University of Skövde, SE-541 28 Skövde, Sweden; (S.H.-H.); (P.S.); (J.S.)
| | - Jane Synnergren
- Systems Biology Research Center, School of Bioscience, University of Skövde, SE-541 28 Skövde, Sweden; (S.H.-H.); (P.S.); (J.S.)
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11
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Application of the water-insoluble, temperature-responsive block polymer poly(butyl methacrylate-block-N-isopropylacrylamide) for pluripotent stem cell culture and cell-selective detachment. J Biosci Bioeng 2022; 133:502-508. [PMID: 35246394 DOI: 10.1016/j.jbiosc.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/21/2022]
Abstract
Induced pluripotent stem (iPS) cells have been widely studied in regenerative medicine, pathology modeling, and drug screening. Stable mass culture of iPS cells is essential for these applications. iPS cells can spontaneously differentiate into other cells during culture, and removal of these differentiated cells is necessary. Herein, a cost-effective culture method suitable for mass culture and a detailed analysis of the selective detachment of iPS cells are presented. A simple method for coating the water-insoluble thermoresponsive polymer poly (butyl methacrylate-block-N-isopropylacrylamide) on commercially available polystyrene dishes was employed. Analysis of the effects of the polymer composition, coating thickness, and surface structure on iPS cell culture/detachment showed that a coating thickness of approximately 10-40 nm using a polymer with a high poly (N-isopropylacrylamide) content was suitable for iPS cell detachment. Moreover, an interesting change in surface morphology was observed following temperature variation, thereby affecting laminin adsorption. Second, selective detachment in cocultures of iPS cells and differentiated cells enabled collection of iPS cells with more than 98% purity. Finally, long-term iPS cell culture was conducted using temperature-responsive cell detachment. Overall, long-term maintenance-free culture of iPS cells was possible without manual removal of differentiated cells.
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12
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Induced Pluripotent Stem Cells (iPSCs) Provide a Potentially Unlimited T Cell Source for CAR-T Cell Development and Off-the-Shelf Products. Pharm Res 2021; 38:931-945. [PMID: 34114161 DOI: 10.1007/s11095-021-03067-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/24/2021] [Indexed: 12/28/2022]
Abstract
Chimeric antigen receptor T (CAR-T) cell therapy has been increasingly conducted for cancer patients in clinical settings. Progress in this therapeutic approach is hampered by the lack of a solid manufacturing process, T lymphocytes, and tumor-specific antigens. T cell source used in CAR-T cell therapy is derived predominantly from the patient's own T lymphocytes, which makes this approach impracticable to patients with progressive diseases and T leukemia. The generation of autologous CAR-T cells is time-consuming due to the lack of readily available T lymphocytes and is not applicable for third-party patients. Pluripotent stem cells, such as human induced pluripotent stem cells (hiPSCs), can provide an unlimited T cell source for CAR-T cell development with the potential of generating off-the-shelf T cell products. T-iPSCs (iPSC-derived T cells) are phenotypically defined, expandable, and as functional as physiological T cells. The combination of iPSC and CAR technologies provides an exciting opportunity to oncology and greatly facilitates cell-based therapy for cancer patients. However, T-iPSCs, in combination with CARs, are at the early stage of development and need further pre-clinical and clinical studies. This review will critically discuss the progress made in iPSC-derived T cells and provides a roadmap for the development of CAR iPSC-derived T cells and off-the-shelf T-iPSCs.
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13
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Piotrowski T, Rippel O, Elanzew A, Nießing B, Stucken S, Jung S, König N, Haupt S, Stappert L, Brüstle O, Schmitt R, Jonas S. Deep-learning-based multi-class segmentation for automated, non-invasive routine assessment of human pluripotent stem cell culture status. Comput Biol Med 2020; 129:104172. [PMID: 33352307 DOI: 10.1016/j.compbiomed.2020.104172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) are capable of differentiating into a variety of human tissue cells. They offer new opportunities for personalized medicine and drug screening. This requires large quantities of high quality hiPSCs, obtainable only via automated cultivation. One of the major requirements of an automated cultivation is a regular, non-invasive analysis of the cell condition, e.g. by whole-well microscopy. However, despite the urgency of this requirement, there are currently no automatic, image-processing-based solutions for multi-class routine quantification of this nature. This paper describes a method to fully automate the cell state recognition based on phase contrast microscopy and deep-learning. This approach can be used for in process control during an automated hiPSC cultivation. The U-Net based algorithm is capable of segmenting important parameters of hiPSC colony formation and can discriminate between the classes hiPSC colony, single cells, differentiated cells and dead cells. The model achieves more accurate results for the classes hiPSC colonies, differentiated cells, single hiPSCs and dead cells than visual estimation by a skilled expert. Furthermore, parameters for each hiPSC colony are derived directly from the classification result such as roundness, size, center of gravity and inclusions of other cells. These parameters provide localized information about the cell state and enable well based treatment of the cell culture in automated processes. Thus, the model can be exploited for routine, non-invasive image analysis during an automated hiPSC cultivation. This facilitates the generation of high quality hiPSC derived products for biomedical purposes.
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Affiliation(s)
- Tobias Piotrowski
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany.
| | - Oliver Rippel
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - Andreas Elanzew
- Life & Brain GmbH, Cellomics Unit, Bonn, Germany; Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty &University Hospital Bonn, Bonn, Germany
| | - Bastian Nießing
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | | | - Sven Jung
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - Niels König
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - Simone Haupt
- Life & Brain GmbH, Cellomics Unit, Bonn, Germany
| | | | - Oliver Brüstle
- Life & Brain GmbH, Cellomics Unit, Bonn, Germany; Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty &University Hospital Bonn, Bonn, Germany
| | - Robert Schmitt
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany; Laboratory for Machine Tools and Production (WZL), RWTH Aachen, Germany
| | - Stephan Jonas
- Department of Medical Informatics, RWTH Aachen University, Germany
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14
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Wang AYL, Loh CYY. Episomal Induced Pluripotent Stem Cells: Functional and Potential Therapeutic Applications. Cell Transplant 2019; 28:112S-131S. [PMID: 31722555 PMCID: PMC7016470 DOI: 10.1177/0963689719886534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The term episomal induced pluripotent stem cells (EiPSCs) refers to somatic cells that are reprogrammed into induced pluripotent stem cells (iPSCs) using non-integrative episomal vector methods. This reprogramming process has a better safety profile compared with integrative methods using viruses. There is a current trend toward using episomal plasmid reprogramming to generate iPSCs because of the improved safety profile. Clinical reports of potential human cell sources that have been successfully reprogrammed into EiPSCs are increasing, but no review or summary has been published. The functional applications of EiPSCs and their potential uses in various conditions have been described, and these may be applicable to clinical scenarios. This review summarizes the current direction of EiPSC research and the properties of these cells with the aim of explaining their potential role in clinical applications and functional restoration.
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Affiliation(s)
- Aline Yen Ling Wang
- Center for Vascularized Composite Allotransplantation, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,*Both the authors contributed equally to this article
| | - Charles Yuen Yung Loh
- St Andrew's Center for Burns and Plastic Surgery, Chelmsford, United Kingdom.,*Both the authors contributed equally to this article
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15
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Fernandes CFDL, Iglesia RP, Melo-Escobar MI, Prado MB, Lopes MH. Chaperones and Beyond as Key Players in Pluripotency Maintenance. Front Cell Dev Biol 2019; 7:150. [PMID: 31428613 PMCID: PMC6688531 DOI: 10.3389/fcell.2019.00150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022] Open
Abstract
Pluripotency is orchestrated by distinct players and chaperones and their partners have emerged as pivotal molecules in proteostasis control to maintain stemness. The proteostasis network consists of diverse interconnected pathways that function dynamically according to the needs of the cell to quality control and maintain protein homeostasis. The proteostasis machinery of pluripotent stem cells (PSCs) is finely adjusted in response to distinct stimuli during cell fate commitment to determine successful organism development. Growing evidence has shown different classes of chaperones regulating crucial cellular processes in PSCs. Histones chaperones promote proper nucleosome assembly and modulate the epigenetic regulation of factors involved in PSCs’ rapid turnover from pluripotency to differentiation. The life cycle of pluripotency proteins from synthesis and folding, transport and degradation is finely regulated by chaperones and co-factors either to maintain the stemness status or to cell fate commitment. Here, we summarize current knowledge of the chaperone network that govern stemness and present the versatile role of chaperones in stem cells resilience. Elucidation of the intricate regulation of pluripotency, dissecting in detail molecular determinants and drivers, is fundamental to understanding the properties of stem cells in order to provide a reliable foundation for biomedical research and regenerative medicine.
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Affiliation(s)
- Camila Felix de Lima Fernandes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rebeca Piatniczka Iglesia
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria Isabel Melo-Escobar
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mariana Brandão Prado
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marilene Hohmuth Lopes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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16
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Ferreira AF, Ferreira FU, Costa PNMD, Catelli LF, Favarin Macedo MDC, Santos TPMD, Leopoldino AM, Picanço-Castro V, Kashima S, Covas DT. Generation of integration-free induced pluripotent stem cells from blood-derived cells isolated from patient with severe haemophilia A. Haemophilia 2019; 25:e195-e199. [PMID: 30866120 DOI: 10.1111/hae.13716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/11/2019] [Accepted: 01/30/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Aline Fernanda Ferreira
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Fernanda Ursoli Ferreira
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Péricles Natan Mendes da Costa
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lucas Ferrioli Catelli
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Maria do Carmo Favarin Macedo
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Tálita P M Dos Santos
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Virgínia Picanço-Castro
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Simone Kashima
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Dimas Tadeu Covas
- Center for Cell based Therapy, Regional Blood Center, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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17
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Panepucci RA, de Souza Lima IM. Arrayed functional genetic screenings in pluripotency reprogramming and differentiation. Stem Cell Res Ther 2019; 10:24. [PMID: 30635073 PMCID: PMC6330485 DOI: 10.1186/s13287-018-1124-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Thoroughly understanding the molecular mechanisms responsible for the biological properties of pluripotent stem cells, as well as for the processes involved in reprograming, differentiation, and transition between Naïve and Primed pluripotent states, is of great interest in basic and applied research. Although pluripotent cells have been extensively characterized in terms of their transcriptome and miRNome, a comprehensive understanding of how these gene products specifically impact their biology, depends on gain- or loss-of-function experimental approaches capable to systematically interrogate their function. We review all studies carried up to date that used arrayed screening approaches to explore the function of these genetic elements on those biological contexts, using focused or genome-wide genetic libraries. We further discuss the limitations and advantages of approaches based on assays with population-level primary readouts, derived from single-parameter plate readers, or cell-level primary readouts, obtained using multiparametric flow cytometry or quantitative fluorescence microscopy (i.e., high-content screening). Finally, we discuss technical limitation and future perspectives, highlighting how the integration of screening data may lead to major advances in the field of stem cell research and therapy.
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Affiliation(s)
- Rodrigo Alexandre Panepucci
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP CEP: 14051-140 Brazil
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP Brazil
| | - Ildercílio Mota de Souza Lima
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP CEP: 14051-140 Brazil
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP Brazil
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