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Wang M, Hong Y, Fu X, Sun X. Advances and applications of biomimetic biomaterials for endogenous skin regeneration. Bioact Mater 2024; 39:492-520. [PMID: 38883311 PMCID: PMC11179177 DOI: 10.1016/j.bioactmat.2024.04.011] [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: 12/08/2023] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 06/18/2024] Open
Abstract
Endogenous regeneration is becoming an increasingly important strategy for wound healing as it facilitates skin's own regenerative potential for self-healing, thereby avoiding the risks of immune rejection and exogenous infection. However, currently applied biomaterials for inducing endogenous skin regeneration are simplistic in their structure and function, lacking the ability to accurately mimic the intricate tissue structure and regulate the disordered microenvironment. Novel biomimetic biomaterials with precise structure, chemical composition, and biophysical properties offer a promising avenue for achieving perfect endogenous skin regeneration. Here, we outline the recent advances in biomimetic materials induced endogenous skin regeneration from the aspects of structural and functional mimicry, physiological process regulation, and biophysical property design. Furthermore, novel techniques including in situ reprograming, flexible electronic skin, artificial intelligence, single-cell sequencing, and spatial transcriptomics, which have potential to contribute to the development of biomimetic biomaterials are highlighted. Finally, the prospects and challenges of further research and application of biomimetic biomaterials are discussed. This review provides reference to address the clinical problems of rapid and high-quality skin regeneration.
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Affiliation(s)
- Mengyang Wang
- Research Center for Tissue Repair and Regeneration Affiliated to the Medical Innovation Research Department, PLA General Hospital and PLA Medical College, Beijing, 100853, PR China
- PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100089, PR China
| | - Yiyue Hong
- Research Center for Tissue Repair and Regeneration Affiliated to the Medical Innovation Research Department, PLA General Hospital and PLA Medical College, Beijing, 100853, PR China
- PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100089, PR China
| | - Xiaobing Fu
- Research Center for Tissue Repair and Regeneration Affiliated to the Medical Innovation Research Department, PLA General Hospital and PLA Medical College, Beijing, 100853, PR China
- PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100089, PR China
- Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, PR China
| | - Xiaoyan Sun
- Research Center for Tissue Repair and Regeneration Affiliated to the Medical Innovation Research Department, PLA General Hospital and PLA Medical College, Beijing, 100853, PR China
- PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100089, PR China
- Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, PR China
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2
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Filippi M, Mekkattu M, Katzschmann RK. Sustainable biofabrication: from bioprinting to AI-driven predictive methods. Trends Biotechnol 2024:S0167-7799(24)00180-X. [PMID: 39069377 DOI: 10.1016/j.tibtech.2024.07.002] [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: 04/15/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
Biofabrication is potentially an inherently sustainable manufacturing process of bio-hybrid systems based on biomaterials embedded with cell communities. These bio-hybrids promise to augment the sustainability of various human activities, ranging from tissue engineering and robotics to civil engineering and ecology. However, as routine biofabrication practices are laborious and energetically disadvantageous, our society must refine production and validation processes in biomanufacturing. This opinion highlights the research trends in sustainable material selection and biofabrication techniques. By modeling complex biosystems, the computational prediction will allow biofabrication to shift from an error-trial method to an efficient, target-optimized approach with minimized resource and energy consumption. We envision that implementing bionomic rationality in biofabrication will render bio-hybrid products fruitful for greening human activities.
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Affiliation(s)
- Miriam Filippi
- Soft Robotics Laboratory, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland.
| | - Manuel Mekkattu
- Soft Robotics Laboratory, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Robert K Katzschmann
- Soft Robotics Laboratory, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland.
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3
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Jia S, Liang R, Chen J, Liao S, Lin J, Li W. Emerging technology has a brilliant future: the CRISPR-Cas system for senescence, inflammation, and cartilage repair in osteoarthritis. Cell Mol Biol Lett 2024; 29:64. [PMID: 38698311 PMCID: PMC11067114 DOI: 10.1186/s11658-024-00581-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024] Open
Abstract
Osteoarthritis (OA), known as one of the most common types of aseptic inflammation of the musculoskeletal system, is characterized by chronic pain and whole-joint lesions. With cellular and molecular changes including senescence, inflammatory alterations, and subsequent cartilage defects, OA eventually leads to a series of adverse outcomes such as pain and disability. CRISPR-Cas-related technology has been proposed and explored as a gene therapy, offering potential gene-editing tools that are in the spotlight. Considering the genetic and multigene regulatory mechanisms of OA, we systematically review current studies on CRISPR-Cas technology for improving OA in terms of senescence, inflammation, and cartilage damage and summarize various strategies for delivering CRISPR products, hoping to provide a new perspective for the treatment of OA by taking advantage of CRISPR technology.
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Affiliation(s)
- Shicheng Jia
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shantou University Medical College, Shantou, 515041, China
| | - Rongji Liang
- Shantou University Medical College, Shantou, 515041, China
| | - Jiayou Chen
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shantou University Medical College, Shantou, 515041, China
| | - Shuai Liao
- Department of Bone and Joint, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Jianjing Lin
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| | - Wei Li
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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4
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Grath A, Dai G. SOX17/ETV2 improves the direct reprogramming of adult fibroblasts to endothelial cells. CELL REPORTS METHODS 2024; 4:100732. [PMID: 38503291 PMCID: PMC10985233 DOI: 10.1016/j.crmeth.2024.100732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/07/2023] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
Abstract
An autologous source of vascular endothelial cells (ECs) is valuable for vascular regeneration and tissue engineering without the concern of immune rejection. The transcription factor ETS variant 2 (ETV2) has been shown to directly convert patient fibroblasts into vascular EC-like cells. However, reprogramming efficiency is low and there are limitations in EC functions, such as eNOS expression. In this study, we directly reprogram adult human dermal fibroblasts into reprogrammed ECs (rECs) by overexpressing SOX17 in conjunction with ETV2. We find several advantages to rEC generation using this approach, including improved reprogramming efficiency, increased enrichment of EC genes, formation of large blood vessels carrying blood from the host, and, most importantly, expression of eNOS in vivo. From these results, we present an improved method to reprogram adult fibroblasts into functional ECs and posit ideas for the future that could potentially further improve the reprogramming process.
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Affiliation(s)
- Alexander Grath
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Guohao Dai
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
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5
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Song Y, Soto J, Wong SY, Wu Y, Hoffman T, Akhtar N, Norris S, Chu J, Park H, Kelkhoff DO, Ang CE, Wernig M, Kasko A, Downing TL, Poo MM, Li S. Biphasic regulation of epigenetic state by matrix stiffness during cell reprogramming. SCIENCE ADVANCES 2024; 10:eadk0639. [PMID: 38354231 PMCID: PMC10866547 DOI: 10.1126/sciadv.adk0639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
We investigate how matrix stiffness regulates chromatin reorganization and cell reprogramming and find that matrix stiffness acts as a biphasic regulator of epigenetic state and fibroblast-to-neuron conversion efficiency, maximized at an intermediate stiffness of 20 kPa. ATAC sequencing analysis shows the same trend of chromatin accessibility to neuronal genes at these stiffness levels. Concurrently, we observe peak levels of histone acetylation and histone acetyltransferase (HAT) activity in the nucleus on 20 kPa matrices, and inhibiting HAT activity abolishes matrix stiffness effects. G-actin and cofilin, the cotransporters shuttling HAT into the nucleus, rises with decreasing matrix stiffness; however, reduced importin-9 on soft matrices limits nuclear transport. These two factors result in a biphasic regulation of HAT transport into nucleus, which is directly demonstrated on matrices with dynamically tunable stiffness. Our findings unravel a mechanism of the mechano-epigenetic regulation that is valuable for cell engineering in disease modeling and regenerative medicine applications.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jennifer Soto
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sze Yue Wong
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yifan Wu
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Tyler Hoffman
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Navied Akhtar
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92617, USA
| | - Sam Norris
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Julia Chu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hyungju Park
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Structure and Function of Neural Network, Korea Brain Research Institute (KBRI), Daegu 41068, South Korea
| | - Douglas O. Kelkhoff
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cheen Euong Ang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Pathology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Andrea Kasko
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Timothy L. Downing
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92617, USA
| | - Mu-ming Poo
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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6
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Hamano M, Nakamura T, Ito R, Shimada Y, Iwata M, Takeshita JI, Eguchi R, Yamanishi Y. DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion. Bioinformatics 2024; 40:btae048. [PMID: 38273708 PMCID: PMC10868337 DOI: 10.1093/bioinformatics/btae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
MOTIVATION Direct reprogramming (DR) is a process that directly converts somatic cells to target cells. Although DR via small molecules is safer than using transcription factors (TFs) in terms of avoidance of tumorigenic risk, the determination of DR-inducing small molecules is challenging. RESULTS Here we present a novel in silico method, DIRECTEUR, to predict small molecules that replace TFs for DR. We extracted DR-characteristic genes using transcriptome profiles of cells in which DR was induced by TFs, and performed a variant of simulated annealing to explore small molecule combinations with similar gene expression patterns with DR-inducing TFs. We applied DIRECTEUR to predicting combinations of small molecules that convert fibroblasts into neurons or cardiomyocytes, and were able to reproduce experimentally verified and functionally related molecules inducing the corresponding conversions. The proposed method is expected to be useful for practical applications in regenerative medicine. AVAILABILITY AND IMPLEMENTATION The code and data are available at the following link: https://github.com/HamanoLaboratory/DIRECTEUR.git.
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Affiliation(s)
- Momoko Hamano
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Toru Nakamura
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Ryoku Ito
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Yuki Shimada
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Jun-ichi Takeshita
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8569, Japan
| | - Ryohei Eguchi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
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7
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Çakmak A, Fuerkaiti S, Karagüzel D, Karaaslan Ç, Gümüşderelioğlu M. Enhanced Osteogenic Potential of Noggin Knockout C2C12 Cells on BMP-2 Releasing Silk Scaffolds. ACS Biomater Sci Eng 2023; 9:6175-6185. [PMID: 37796024 PMCID: PMC10646847 DOI: 10.1021/acsbiomaterials.3c00506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023]
Abstract
The CRISPR/Cas9 mechanism offers promising therapeutic approaches for bone regeneration by stimulating or suppressing critical signaling pathways. In this study, we aimed to increase the activity of BMP-2 signaling through knockout of Noggin, thereby establishing a synergistic effect on the osteogenic activity of cells in the presence of BMP-2. Since Noggin is an antagonist expressed in skeletal tissues and binds to subunits of bone morphogenetic proteins (BMPs) to inhibit osteogenic differentiation, here Noggin expression was knocked out using the CRISPR/Cas9 system. In accordance with this purpose, C2C12 (mouse myoblast) cells were transfected with CRISPR/Cas9 plasmids. Transfection was achieved with Lipofectamine and confirmed with intense fluorescent signals in microscopic images and deletion in target sequence in Sanger sequencing analysis. Thus, Noggin knockout cells were identified as a new cell source for tissue engineering studies. Then, the transfected cells were seeded on highly porous silk scaffolds bearing BMP-2-loaded silk nanoparticles (30 ng BMP-2/mg silk nanoparticle) in the size of 288 ± 62 nm. BMP-2 is released from the scaffolds in a controlled manner for up to 60 days. The knockout of Noggin by CRISPR/Cas9 was found to synergistically promote osteogenic differentiation in the presence of BMP-2 through increased Coll1A1 and Ocn expression and mineralization. Gene editing of Noggin and BMP-2 increased almost 2-fold Col1A1 expression and almost 3-fold Ocn expression compared to the control group. Moreover, transfected cells produced extracellular matrix (ECM) containing collagen fibers on the scaffolds and mineral-like structures were formed on the fibers. In addition, mineralization characterized by intense Alizarin red staining was detected in transfected cells cultured in the presence of BMP-2, while the other groups did not exhibit any mineralized areas. As has been demonstrated in this study, the CRISPR/Cas9 mechanism has great potential for obtaining new cell sources to be used in tissue engineering studies.
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Affiliation(s)
- Anıl
Sera Çakmak
- Department
of Chemical Engineering, Hacettepe University, 06800 Ankara, Turkey
| | - Sümeyra Fuerkaiti
- Division
of Bioengineering, Graduate School of Science and Engineering, Hacettepe University, 06800 Ankara, Turkey
| | - Dilara Karagüzel
- Department
of Biology, Molecular Biology Section, Hacettepe
University, 06800 Ankara, Turkey
| | - Çağatay Karaaslan
- Division
of Bioengineering, Graduate School of Science and Engineering, Hacettepe University, 06800 Ankara, Turkey
- Department
of Biology, Molecular Biology Section, Hacettepe
University, 06800 Ankara, Turkey
| | - Menemşe Gümüşderelioğlu
- Department
of Chemical Engineering, Hacettepe University, 06800 Ankara, Turkey
- Division
of Bioengineering, Graduate School of Science and Engineering, Hacettepe University, 06800 Ankara, Turkey
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8
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Dubey AK, Mostafavi E. Biomaterials-mediated CRISPR/Cas9 delivery: recent challenges and opportunities in gene therapy. Front Chem 2023; 11:1259435. [PMID: 37841202 PMCID: PMC10568484 DOI: 10.3389/fchem.2023.1259435] [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: 07/15/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023] Open
Abstract
The use of biomaterials in delivering CRISPR/Cas9 for gene therapy in infectious diseases holds tremendous potential. This innovative approach combines the advantages of CRISPR/Cas9 with the protective properties of biomaterials, enabling accurate and efficient gene editing while enhancing safety. Biomaterials play a vital role in shielding CRISPR/Cas9 components, such as lipid nanoparticles or viral vectors, from immunological processes and degradation, extending their effectiveness. By utilizing the flexibility of biomaterials, tailored systems can be designed to address specific genetic diseases, paving the way for personalized therapeutics. Furthermore, this delivery method offers promising avenues in combating viral illnesses by precisely modifying pathogen genomes, and reducing their pathogenicity. Biomaterials facilitate site-specific gene modifications, ensuring effective delivery to infected cells while minimizing off-target effects. However, challenges remain, including optimizing delivery efficiency, reducing off-target effects, ensuring long-term safety, and establishing scalable production techniques. Thorough research, pre-clinical investigations, and rigorous safety evaluations are imperative for successful translation from the laboratory to clinical applications. In this review, we discussed how CRISPR/Cas9 delivery using biomaterials revolutionizes gene therapy and infectious disease treatment, offering precise and safe editing capabilities with the potential to significantly improve human health and quality of life.
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Affiliation(s)
- Ankit Kumar Dubey
- Global Research and Publishing Foundation, New Delhi, India
- Institute of Scholars, Bengaluru, Karnataka, India
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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9
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Punjani N, Deska-Gauthier D, Hachem LD, Abramian M, Fehlings MG. Neuroplasticity and regeneration after spinal cord injury. NORTH AMERICAN SPINE SOCIETY JOURNAL 2023; 15:100235. [PMID: 37416090 PMCID: PMC10320621 DOI: 10.1016/j.xnsj.2023.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
Spinal cord injury (SCI) is a debilitating condition with significant personal, societal, and economic burden. The highest proportion of traumatic injuries occur at the cervical level, which results in severe sensorimotor and autonomic deficits. Following the initial physical damage associated with traumatic injuries, secondary pro-inflammatory, excitotoxic, and ischemic cascades are initiated further contributing to neuronal and glial cell death. Additionally, emerging evidence has begun to reveal that spinal interneurons undergo subtype specific neuroplastic circuit rearrangements in the weeks to months following SCI, contributing to or hindering functional recovery. The current therapeutic guidelines and standards of care for SCI patients include early surgery, hemodynamic regulation, and rehabilitation. Additionally, preclinical work and ongoing clinical trials have begun exploring neuroregenerative strategies utilizing endogenous neural stem/progenitor cells, stem cell transplantation, combinatorial approaches, and direct cell reprogramming. This review will focus on emerging cellular and noncellular regenerative therapies with an overview of the current available strategies, the role of interneurons in plasticity, and the exciting research avenues enhancing tissue repair following SCI.
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Affiliation(s)
- Nayaab Punjani
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Dylan Deska-Gauthier
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Laureen D. Hachem
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Surgery, Division of Neurosurgery and Spine Program, University of Toronto, Toronto, ON, Canada
| | - Madlene Abramian
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Michael G. Fehlings
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Surgery, Division of Neurosurgery and Spine Program, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Krembil Neuroscience Centre, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
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10
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Wang F, Li R, Zhang L, Nie X, Wang L, Chen L. Cell Transdifferentiation: A Challenging Strategy with Great Potential. Cell Reprogram 2023; 25:154-161. [PMID: 37471050 DOI: 10.1089/cell.2023.0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
With the discovery and development of somatic cell nuclear transfer, cell fusion, and induced pluripotent stem cells, cell transdifferentiation research has presented unique advantages and stimulated a heated discussion worldwide. Cell transdifferentiation is a phenomenon by which a cell changes its lineage and acquires the phenotype of other cell types when exposed to certain conditions. Indeed, many adult stem cells and differentiated cells were reported to change their phenotype and transform into other lineages. This article reviews the differentiation of stem cells and classification of transdifferentiation, as well as the advantages, challenges, and prospects of cell transdifferentiation. This review discusses new research directions and the main challenges in the use of transdifferentiation in human cells and molecular replacement therapy. Overall, such knowledge is expected to provide a deep understanding of cell fate and regulation, which can change through differentiation, dedifferentiation, and transdifferentiation, with multiple applications.
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Affiliation(s)
- Fuping Wang
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Runting Li
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou China
| | - Limeng Zhang
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou China
| | - Xiaoning Nie
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou China
| | - Linqing Wang
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou China
| | - Longxin Chen
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou China
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11
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Son D, Zheng J, Kim IY, Kang PJ, Park K, Priscilla L, Hong W, Yoon BS, Park G, Yoo JE, Song G, Lee JB, You S. Human induced neural stem cells support functional recovery in spinal cord injury models. Exp Mol Med 2023; 55:1182-1192. [PMID: 37258581 PMCID: PMC10318049 DOI: 10.1038/s12276-023-01003-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/16/2023] [Accepted: 03/08/2023] [Indexed: 06/02/2023] Open
Abstract
Spinal cord injury (SCI) is a clinical condition that leads to permanent and/or progressive disabilities of sensory, motor, and autonomic functions. Unfortunately, no medical standard of care for SCI exists to reverse the damage. Here, we assessed the effects of induced neural stem cells (iNSCs) directly converted from human urine cells (UCs) in SCI rat models. We successfully generated iNSCs from human UCs, commercial fibroblasts, and patient-derived fibroblasts. These iNSCs expressed various neural stem cell markers and differentiated into diverse neuronal and glial cell types. When transplanted into injured spinal cords, UC-derived iNSCs survived, engrafted, and expressed neuronal and glial markers. Large numbers of axons extended from grafts over long distances, leading to connections between host and graft neurons at 8 weeks post-transplantation with significant improvement of locomotor function. This study suggests that iNSCs have biomedical applications for disease modeling and constitute an alternative transplantation strategy as a personalized cell source for neural regeneration in several spinal cord diseases.
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Affiliation(s)
- Daryeon Son
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jie Zheng
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - In Yong Kim
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Phil Jun Kang
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Kyoungmin Park
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Lia Priscilla
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Wonjun Hong
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Byung Sun Yoon
- Institute of Regenerative Medicine, STEMLAB, Inc., Seoul, 02841, Republic of Korea
| | - Gyuman Park
- Institute of Future Medicine, STEMLAB, Inc., Seoul, 02841, Republic of Korea
| | - Jeong-Eun Yoo
- Institute of Future Medicine, STEMLAB, Inc., Seoul, 02841, Republic of Korea
| | - Gwonhwa Song
- Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - Jang-Bo Lee
- Department of Neurosurgery, College of Medicine, Korea University Anam Hospital, Seoul, 02841, Republic of Korea.
| | - Seungkwon You
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
- Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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12
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Mou Q, Bai Y, Xu M, Lv D, Deng J, Hu N, Yang J. Microarray Chip and Method for Simultaneous and Highly Consistent Electroporation of Multiple Cells of Different Sizes. Anal Chem 2023. [PMID: 37230941 DOI: 10.1021/acs.analchem.3c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cell electroporation is an important cell manipulation technology to artificially transfer specific extracellular components into cells. However, the consistency of substance transport during the electroporation process is still an issue due to the wide size distribution of the natural cells. In this study, a cell electroporation microfluidic chip based on a microtrap array is proposed. The microtrap structure was optimized for single-cell capture and electric field focusing. The effects of the cell size on the cell electroporation in the microchip were investigated through simulation and experiment methods using the giant unilamellar vesicle as the simplified cell model, and a numerical model of a uniform electric field was used as a comparison. Compared with the uniform electric field, a lower threshold electric field is required to induce electroporation and produces a higher transmembrane voltage on the cell under a specific electric field in the microchip, showing an improvement in cell viability and electroporation efficiency. The larger perforated area produced on the cells in the microchip under a specific electric field allows a higher substance transfer efficiency, and the electroporation results are less affected by the cell size, which is beneficial for improving substance transfer consistency. Furthermore, the relative perforation area increases with the decrease of the cell diameter in the microchip, which is exactly opposite to that in a uniform electric field. By manipulating the electric field applied to the microtrap individually, a consistent proportion of substance transfer during electroporation of cells with different sizes can be achieved.
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Affiliation(s)
- Qiongyao Mou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Yaqi Bai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Mengli Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Dan Lv
- Key Laboratory of Biorheological Science and Technology, Ministry of Education and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Jinan Deng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Jun Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education and Bioengineering College, Chongqing University, Chongqing 400044, China
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13
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Seah C, Huckins LM, Brennand KJ. Stem Cell Models for Context-Specific Modeling in Psychiatric Disorders. Biol Psychiatry 2023; 93:642-650. [PMID: 36658083 DOI: 10.1016/j.biopsych.2022.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 01/21/2023]
Abstract
Genome-wide association studies reveal the complex polygenic architecture underlying psychiatric disorder risk, but there is an unmet need to validate causal variants, resolve their target genes(s), and explore their functional impacts on disorder-related mechanisms. Disorder-associated loci regulate transcription of target genes in a cell type- and context-specific manner, which can be measured through expression quantitative trait loci. In this review, we discuss methods and insights from context-specific modeling of genetically and environmentally regulated expression. Human induced pluripotent stem cell-derived cell type and organoid models have uncovered context-specific psychiatric disorder associations by investigating tissue-, cell type-, sex-, age-, and stressor-specific genetic regulation of expression. Techniques such as massively parallel reporter assays and pooled CRISPR (clustered regularly interspaced short palindromic repeats) screens make it possible to functionally fine-map genome-wide association study loci and validate their target genes at scale. Integration of disorder-associated contexts with these patient-specific human induced pluripotent stem cell models makes it possible to uncover gene by environment interactions that mediate disorder risk, which will ultimately improve our ability to diagnose and treat psychiatric disorders.
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Affiliation(s)
- Carina Seah
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
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14
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Missinato MA, Murphy S, Lynott M, Yu MS, Kervadec A, Chang YL, Kannan S, Loreti M, Lee C, Amatya P, Tanaka H, Huang CT, Puri PL, Kwon C, Adams PD, Qian L, Sacco A, Andersen P, Colas AR. Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells. Nat Commun 2023; 14:1709. [PMID: 36973293 PMCID: PMC10043290 DOI: 10.1038/s41467-023-37256-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
Defining the mechanisms safeguarding cell fate identity in differentiated cells is crucial to improve 1) - our understanding of how differentiation is maintained in healthy tissues or altered in a disease state, and 2) - our ability to use cell fate reprogramming for regenerative purposes. Here, using a genome-wide transcription factor screen followed by validation steps in a variety of reprogramming assays (cardiac, neural and iPSC in fibroblasts and endothelial cells), we identified a set of four transcription factors (ATF7IP, JUNB, SP7, and ZNF207 [AJSZ]) that robustly opposes cell fate reprogramming in both lineage and cell type independent manners. Mechanistically, our integrated multi-omics approach (ChIP, ATAC and RNA-seq) revealed that AJSZ oppose cell fate reprogramming by 1) - maintaining chromatin enriched for reprogramming TF motifs in a closed state and 2) - downregulating genes required for reprogramming. Finally, KD of AJSZ in combination with MGT overexpression, significantly reduced scar size and improved heart function by 50%, as compared to MGT alone post-myocardial infarction. Collectively, our study suggests that inhibition of barrier to reprogramming mechanisms represents a promising therapeutic avenue to improve adult organ function post-injury.
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Affiliation(s)
- Maria A Missinato
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sean Murphy
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Michael S Yu
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yu-Ling Chang
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mafalda Loreti
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Christopher Lee
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Prashila Amatya
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Hiroshi Tanaka
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Chun-Teng Huang
- Viral Vector Core Facility Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Peter D Adams
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Li Qian
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alessandra Sacco
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter Andersen
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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15
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Silva-Pedrosa R, Salgado AJ, Ferreira PE. Revolutionizing Disease Modeling: The Emergence of Organoids in Cellular Systems. Cells 2023; 12:930. [PMID: 36980271 PMCID: PMC10047824 DOI: 10.3390/cells12060930] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cellular models have created opportunities to explore the characteristics of human diseases through well-established protocols, while avoiding the ethical restrictions associated with post-mortem studies and the costs associated with researching animal models. The capability of cell reprogramming, such as induced pluripotent stem cells (iPSCs) technology, solved the complications associated with human embryonic stem cells (hESC) usage. Moreover, iPSCs made significant contributions for human medicine, such as in diagnosis, therapeutic and regenerative medicine. The two-dimensional (2D) models allowed for monolayer cellular culture in vitro; however, they were surpassed by the three-dimensional (3D) cell culture system. The 3D cell culture provides higher cell-cell contact and a multi-layered cell culture, which more closely respects cellular morphology and polarity. It is more tightly able to resemble conditions in vivo and a closer approach to the architecture of human tissues, such as human organoids. Organoids are 3D cellular structures that mimic the architecture and function of native tissues. They are generated in vitro from stem cells or differentiated cells, such as epithelial or neural cells, and are used to study organ development, disease modeling, and drug discovery. Organoids have become a powerful tool for understanding the cellular and molecular mechanisms underlying human physiology, providing new insights into the pathogenesis of cancer, metabolic diseases, and brain disorders. Although organoid technology is up-and-coming, it also has some limitations that require improvements.
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Affiliation(s)
- Rita Silva-Pedrosa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.J.S.); (P.E.F.)
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - António José Salgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.J.S.); (P.E.F.)
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Pedro Eduardo Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.J.S.); (P.E.F.)
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
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16
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Dennison R, Usuga E, Chen H, Paul JZ, Arbelaez CA, Teng YD. Direct Cell Reprogramming and Phenotypic Conversion: An Analysis of Experimental Attempts to Transform Astrocytes into Neurons in Adult Animals. Cells 2023; 12:618. [PMID: 36831283 PMCID: PMC9954435 DOI: 10.3390/cells12040618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Central nervous system (CNS) repair after injury or disease remains an unresolved problem in neurobiology research and an unmet medical need. Directly reprogramming or converting astrocytes to neurons (AtN) in adult animals has been investigated as a potential strategy to facilitate brain and spinal cord recovery and advance fundamental biology. Conceptually, AtN strategies rely on forced expression or repression of lineage-specific transcription factors to make endogenous astrocytes become "induced neurons" (iNs), presumably without re-entering any pluripotent or multipotent states. The AtN-derived cells have been reported to manifest certain neuronal functions in vivo. However, this approach has raised many new questions and alternative explanations regarding the biological features of the end products (e.g., iNs versus neuron-like cells, neural functional changes, etc.), developmental biology underpinnings, and neurobiological essentials. For this paper per se, we proposed to draw an unconventional distinction between direct cell conversion and direct cell reprogramming, relative to somatic nuclear transfer, based on the experimental methods utilized to initiate the transformation process, aiming to promote a more in-depth mechanistic exploration. Moreover, we have summarized the current tactics employed for AtN induction, comparisons between the bench endeavors concerning outcome tangibility, and discussion of the issues of published AtN protocols. Lastly, the urgency to clearly define/devise the theoretical frameworks, cell biological bases, and bench specifics to experimentally validate primary data of AtN studies was highlighted.
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Affiliation(s)
- Rachel Dennison
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA 02129, USA
- Laboratory of SCI, Stem Cell and Recovery Neurobiology Research, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Mass General Brigham, and Harvard Medical School, Boston, MA 02115, USA
| | - Esteban Usuga
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA 02129, USA
- Laboratory of SCI, Stem Cell and Recovery Neurobiology Research, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Mass General Brigham, and Harvard Medical School, Boston, MA 02115, USA
| | - Harriet Chen
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA 02129, USA
- Laboratory of SCI, Stem Cell and Recovery Neurobiology Research, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Mass General Brigham, and Harvard Medical School, Boston, MA 02115, USA
| | - Jacob Z. Paul
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA 02129, USA
- Laboratory of SCI, Stem Cell and Recovery Neurobiology Research, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Mass General Brigham, and Harvard Medical School, Boston, MA 02115, USA
| | - Christian A. Arbelaez
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA 02129, USA
- Laboratory of SCI, Stem Cell and Recovery Neurobiology Research, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Mass General Brigham, and Harvard Medical School, Boston, MA 02115, USA
| | - Yang D. Teng
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA 02129, USA
- Laboratory of SCI, Stem Cell and Recovery Neurobiology Research, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Mass General Brigham, and Harvard Medical School, Boston, MA 02115, USA
- Neurotrauma Recovery Research, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Mass General Brigham, and Harvard Medical School, Boston, MA 02115, USA
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17
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Sramkó B, Földes A, Kádár K, Varga G, Zsembery Á, Pircs K. The Wisdom in Teeth: Neuronal Differentiation of Dental Pulp Cells. Cell Reprogram 2023; 25:32-44. [PMID: 36719998 PMCID: PMC9963504 DOI: 10.1089/cell.2022.0102] [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] [Indexed: 02/02/2023] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are found in almost all postnatal organs. Under appropriate environmental cues, multipotency enables MSCs to serve as progenitors for several lineage-specific, differentiated cell types. In vitro expansion and differentiation of MSCs give the opportunity to obtain hardly available somatic cells, such as neurons. The neurogenic potential of MSCs makes them a promising, autologous source to restore damaged tissue and as such, they have received much attention in the field of regenerative medicine. Several stem cell pool candidates have been studied thus far, but only a few of them showed neurogenic differentiation potential. Due to their embryonic ontology, stem cells residing in the stroma of the dental pulp chamber are an exciting source for in vitro neural cell differentiation. In this study, we review the key properties of dental pulp stem cells (DPSCs), with a particular focus on their neurogenic potential. Moreover, we summarize the various presently available methods used for neural differentiation of human DPSCs also emphasizing the difficulties in reproducibly high production of such cells. We postulate that because DPSCs are stem cells with very close ontology to neurogenic lineages, they may serve as excellent targets for neuronal differentiation in vitro and even for direct reprogramming.
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Affiliation(s)
- Bendegúz Sramkó
- HCEMM-SU Neurobiology and Neurodegenerative Diseases Research Group, Budapest, Hungary.,Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Anna Földes
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Kristóf Kádár
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Gábor Varga
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Ákos Zsembery
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Karolina Pircs
- HCEMM-SU Neurobiology and Neurodegenerative Diseases Research Group, Budapest, Hungary.,Institute of Translational Medicine, Semmelweis University, Budapest, Hungary.,Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
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18
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Su C, Pang J. Target Control of Asynchronous Boolean Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:707-719. [PMID: 34882560 DOI: 10.1109/tcbb.2021.3133608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We study the target control of asynchronous Boolean networks, to identify interventions that can drive the dynamics of a given Boolean network from any initial state to the desired target attractor. Based on the application time, the control can be realised with three types of perturbations, including instantaneous, temporary and permanent perturbations. We develop efficient methods to compute the target control for a given target attractor with these three types of perturbations. We compare our methods with the stable motif-based control method on a variety of real-life biological networks to evaluate their performance. We show that our methods scale well for large Boolean networks and they are able to identify a rich set of solutions with a small number of perturbations.
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19
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Verma AH, Haldavnekar R, Venkatakrishnan K, Tan B. Dual-Purpose 3D-Silica Nanostructure Matrix for Rapid Epigenetic Reprogramming of Tumor Cell to Cancer Stem Cell Spheroid. SMALL METHODS 2023; 7:e2200798. [PMID: 36424183 DOI: 10.1002/smtd.202200798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Cancer stem cells (CSCs), a rare subpopulation responsible for tumorigenesis and therapeutic resistance, are difficult to characterize and isolate. Conventional method of growing CSCs takes up to 2-8 weeks inhibiting the rate of research. Therefore, rapid reprogramming (RR) of tumor cells into CSCs is crucial to accelerate the stem cell oncology research. The current RR techniques cannot be utilized for CSC RR due to many limitations posed due to isolation requirements resulting in loss of vital data. Hence, a technique that can induce CSC RR without the need for isolation procedures is needed. Here, fabrication of a 3D-silica nanostructured extracellular matrix for RR and in situ monitoring is reported. The RR is tested using three preclinical cancer models. The 3D matrix and a zeta potential study confirm an intense material-cellular interaction resulting in the enhanced expressions of surface and epigenetic biomarkers. Cancer cells require only 3-day period to form CSC spheroids with 3D-silica extracellular matrix. Real-time single-cell monitoring of the methylene blue-induced photodynamic demonstrates the dual functionality. To the authors' knowledge, this is the first study to demonstrate a CSC epigenetic reprogramming using nanostructures. These findings may pave the path for accelerating the stem cell research in oncology.
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Affiliation(s)
- Anish Hiresha Verma
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON, M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Rupa Haldavnekar
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON, M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON, M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON, M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
- Nano-characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
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20
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Patel I, Parchem RJ. Regulation of Oct4 in stem cells and neural crest cells. Birth Defects Res 2022; 114:983-1002. [PMID: 35365980 PMCID: PMC9525453 DOI: 10.1002/bdr2.2007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 12/30/2022]
Abstract
During embryonic development, cells gradually restrict their developmental potential as they exit pluripotency and differentiate into various cell types. The POU transcription factor Oct4 (encoded by Pou5f1) lies at the center of the pluripotency machinery that regulates stemness and differentiation in stem cells, and is required for reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). Several studies have revealed that Oct4 and other stemness genes are also expressed in multipotent cell populations such as neural crest cells (NCCs), and are required to expand the NCC developmental potential. Transcriptional regulation of Oct4 has been studied extensively in stem cells during early embryonic development and reprogramming, but not in NCCs. Here, we review how Oct4 is regulated in pluripotent stem cells, and address some of the gaps in knowledge about regulation of the pluripotency network in NCCs.
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Affiliation(s)
- Ivanshi Patel
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTexasUSA,Stem Cells and Regenerative Medicine Center, Center for Cell and Gene TherapyBaylor College of MedicineHoustonTexasUSA,Dan L Duncan Comprehensive Cancer CenterBaylor College of MedicineHoustonTexasUSA
| | - Ronald J. Parchem
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTexasUSA,Stem Cells and Regenerative Medicine Center, Center for Cell and Gene TherapyBaylor College of MedicineHoustonTexasUSA,Dan L Duncan Comprehensive Cancer CenterBaylor College of MedicineHoustonTexasUSA
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21
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Nakamura T, Iwata M, Hamano M, Eguchi R, Takeshita JI, Yamanishi Y. Small compound-based direct cell conversion with combinatorial optimization of pathway regulations. Bioinformatics 2022; 38:ii99-ii105. [PMID: 36124791 DOI: 10.1093/bioinformatics/btac475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Direct cell conversion, direct reprogramming (DR), is an innovative technology that directly converts source cells to target cells without bypassing induced pluripotent stem cells. The use of small compounds (e.g. drugs) for DR can help avoid carcinogenic risk induced by gene transfection; however, experimentally identifying small compounds remains challenging because of combinatorial explosion. RESULTS In this article, we present a new computational method, COMPRENDRE (combinatorial optimization of pathway regulations for direct reprograming), to elucidate the mechanism of small compound-based DR and predict new combinations of small compounds for DR. We estimated the potential target proteins of DR-inducing small compounds and identified a set of target pathways involving DR. We identified multiple DR-related pathways that have not previously been reported to induce neurons or cardiomyocytes from fibroblasts. To overcome the problem of combinatorial explosion, we developed a variant of a simulated annealing algorithm to identify the best set of compounds that can regulate DR-related pathways. Consequently, the proposed method enabled to predict new DR-inducing candidate combinations with fewer compounds and to successfully reproduce experimentally verified compounds inducing the direct conversion from fibroblasts to neurons or cardiomyocytes. The proposed method is expected to be useful for practical applications in regenerative medicine. AVAILABILITY AND IMPLEMENTATION The code supporting the current study is available at the http://labo.bio.kyutech.ac.jp/~yamani/comprendre. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Toru Nakamura
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Momoko Hamano
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Ryohei Eguchi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Jun-Ichi Takeshita
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8569, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
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22
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Human-Induced Pluripotent Stem Cell Technology: Toward the Future of Personalized Psychiatry. J Pers Med 2022; 12:jpm12081340. [PMID: 36013289 PMCID: PMC9410334 DOI: 10.3390/jpm12081340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The polygenic and multifactorial nature of many psychiatric disorders has hampered implementation of the personalized medicine approach in clinical practice. However, induced pluripotent stem cell (iPSC) technology has emerged as an innovative tool for patient-specific disease modeling to expand the pathophysiology knowledge and treatment perspectives in the last decade. Current technologies enable adult human somatic cell reprogramming into iPSCs to generate neural cells and direct neural cell conversion to model organisms that exhibit phenotypes close to human diseases, thereby effectively representing relevant aspects of neuropsychiatric disorders. In this regard, iPSCs reflect patient pathophysiology and pharmacological responsiveness, particularly when cultured under conditions that emulate spatial tissue organization in brain organoids. Recently, the application of iPSCs has been frequently associated with gene editing that targets the disease-causing gene to deepen the illness pathophysiology and to conduct drug screening. Moreover, gene editing has provided a unique opportunity to repair the putative causative genetic lesions in patient-derived cells. Here, we review the use of iPSC technology to model and potentially treat neuropsychiatric disorders by illustrating the key studies on a series of mental disorders, including schizophrenia, major depressive disorder, bipolar disorder, and autism spectrum disorder. Future perspectives will involve the development of organ-on-a-chip platforms that control the microenvironmental conditions so as to reflect individual pathophysiological by adjusting physiochemical parameters according to personal health data. This strategy could open new ways by which to build a disease model that considers individual variability and tailors personalized treatments.
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23
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Ren R, Fan Y, Peng Z, Wang S, Jiang Y, Fu L, Cao J, Zhao S, Wang H. Characterization and perturbation of CTCF-mediated chromatin interactions for enhancing myogenic transdifferentiation. Cell Rep 2022; 40:111206. [PMID: 35977522 DOI: 10.1016/j.celrep.2022.111206] [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: 04/23/2021] [Revised: 06/21/2022] [Accepted: 07/22/2022] [Indexed: 11/03/2022] Open
Abstract
Expression of key transcription factors can induce transdifferentiation in somatic cells; however, this conversion is usually incomplete due to undefined intrinsic barriers. Here, we employ MyoD-induced transdifferentiation of fibroblasts as a model to illustrate the chromatin structures that impede the cell-fate transition. Focusing on the three-dimensional (3D) chromatin interactions, we show that MyoD directly establishes chromatin loops to activate myogenic transcriptional program. Similarly, dynamic changes of CTCF-mediated chromatin interactions are favorable for fibroblast-to-myoblast conversion. However, a substantial portion of CTCF-mediated chromatin interactions remain stable, and the associated genes are steady in expression and enriched for fibroblast function that may restrict cell-identity transformation. Temporal CTCF depletion can interrupt the resistant chromatin loops to enhance myogenic transdifferentiation in mice, pig, and chicken fibroblasts. Therefore, during induced transdifferentiation, the transcription factor can directly reorganize the 3D chromatin interactions, and perturbation of CTCF-mediated genome topology may resolve the limitations of cell fate transitions.
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Affiliation(s)
- Ruimin Ren
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Yu Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhelun Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sheng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yunqi Jiang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liangliang Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianhua Cao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Heng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; College of Animal Science and Technology, Shandong Agricultural University, Taian, China.
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24
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Kim H, Park HJ, Chang HW, Back JH, Lee SJ, Park YE, Kim EH, Hong Y, Kwak G, Kwon IC, Lee JE, Lee YS, Kim SY, Yang Y, Kim SH. Exosome-guided direct reprogramming of tumor-associated macrophages from protumorigenic to antitumorigenic to fight cancer. Bioact Mater 2022; 25:527-540. [PMID: 37056267 PMCID: PMC10087080 DOI: 10.1016/j.bioactmat.2022.07.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/29/2022] [Accepted: 07/19/2022] [Indexed: 11/02/2022] Open
Abstract
Highly immunosuppressive tumor microenvironment containing various protumoral immune cells accelerates malignant transformation and treatment resistance. In particular, tumor-associated macrophages (TAMs), as the predominant infiltrated immune cells in a tumor, play a pivotal role in regulating the immunosuppressive tumor microenvironment. As a potential therapeutic strategy to counteract TAMs, here we explore an exosome-guided in situ direct reprogramming of tumor-supportive M2-polarized TAMs into tumor-attacking M1-type macrophages. Exosomes derived from M1-type macrophages (M1-Exo) promote a phenotypic switch from anti-inflammatory M2-like TAMs toward pro-inflammatory M1-type macrophages with high conversion efficiency. Reprogrammed M1 macrophages possessing protein-expression profiles similar to those of classically activated M1 macrophages display significantly increased phagocytic function and robust cross-presentation ability, potentiating antitumor immunity surrounding the tumor. Strikingly, these M1-Exo also lead to the conversion of human patient-derived TAMs into M1-like macrophages that highly express MHC class II, offering the clinical potential of autologous and allogeneic exosome-guided direct TAM reprogramming for arming macrophages to join the fight against cancer.
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25
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Ribosomes and Ribosomal Proteins Promote Plasticity and Stemness Induction in Glioma Cells via Reprogramming. Cells 2022; 11:cells11142142. [PMID: 35883585 PMCID: PMC9323835 DOI: 10.3390/cells11142142] [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: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Glioblastoma multiforme (GBM) is a lethal tumor that develops in the adult brain. Despite advances in therapeutic strategies related to surgical resection and chemo-radiotherapy, the overall survival of patients with GBM remains unsatisfactory. Genetic research on mutation, amplification, and deletion in GBM cells is important for understanding the biological aggressiveness, diagnosis, and prognosis of GBM. However, the efficacy of drugs targeting the genetic abnormalities in GBM cells is limited. Investigating special microenvironments that induce chemo-radioresistance in GBM cells is critical to improving the survival and quality of life of patients with GBM. GBM cells acquire and maintain stem-cell-like characteristics via their intrinsic potential and extrinsic factors from their special microenvironments. The acquisition of stem-cell-like phenotypes and aggressiveness may be referred to as a reprogramming of GBM cells. In addition to protein synthesis, deregulation of ribosome biogenesis is linked to several diseases including cancer. Ribosomal proteins possess both tumor-promotive and -suppressive functions as extra-ribosomal functions. Incorporation of ribosomes and overexpression of ribosomal protein S6 reprogram and induce stem-cell-like phenotypes in GBM cells. Herein, we review recent literature and our published data on the acquisition of aggressiveness by GBM and discuss therapeutic options through reprogramming.
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26
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Kuang J, Huang T, Pei D. The Art of Reprogramming for Regenerative Medicine. Front Cell Dev Biol 2022; 10:927555. [PMID: 35846373 PMCID: PMC9280648 DOI: 10.3389/fcell.2022.927555] [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: 04/24/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional pharmaceuticals in the forms of small chemical compounds or macromolecules such as proteins or RNAs have provided lifesaving solutions to many acute and chronic conditions to date. However, there are still many unmet medical needs, especially those of degenerative nature. The advent of cell-based therapy holds the promise to meet these challenges. In this review, we highlight a relatively new paradigm for generating or regenerating functional cells for replacement therapy against conditions such as type I diabetes, myocardial infarction, neurodegenerative diseases and liver fibrosis. We focus on the latest progresses in cellular reprogramming for generating diverse functional cell types. We will also discuss the mechanisms involved and conclude with likely general principles underlying reprogramming.
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Affiliation(s)
- Junqi Kuang
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Tao Huang
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Duanqing Pei
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- *Correspondence: Duanqing Pei,
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27
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Arnan C, Ullrich S, Pulido-Quetglas C, Nurtdinov R, Esteban A, Blanco-Fernandez J, Aparicio-Prat E, Johnson R, Pérez-Lluch S, Guigó R. Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages. BMC Genomics 2022; 23:402. [PMID: 35619054 PMCID: PMC9137126 DOI: 10.1186/s12864-022-08612-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify protein-coding (pc) and non-coding genes playing a role along different processes. In particular, the usage of a nuclease active Cas9 coupled to a single gRNA has proven to efficiently impair the expression of pc-genes by generating deleterious frameshifts. Here, we first demonstrate that targeting the same gene simultaneously with two guide RNAs (paired guide RNAs, pgRNAs) synergistically enhances the capacity of the CRISPR-Cas9 system to knock out pc-genes. We next design a library to target, in parallel, pc-genes and lncRNAs known to change expression during the transdifferentiation from pre-B cells to macrophages. We show that this system is able to identify known players in this process, and also predicts 26 potential novel ones, of which we select four (two pc-genes and two lncRNAs) for deeper characterization. Our results suggest that in the case of the candidate lncRNAs, their impact in transdifferentiation may be actually mediated by enhancer regions at the targeted loci, rather than by the lncRNA transcripts themselves. The CRISPR-Cas9 coupled to a pgRNAs system is, therefore, a suitable tool to simultaneously target pc-genes and lncRNAs for genomic perturbation assays.
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Affiliation(s)
- Carme Arnan
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Sebastian Ullrich
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Carlos Pulido-Quetglas
- Department of Medical Oncology, Bern University Hospital, University of Bern, Inselspital, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Alexandre Esteban
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Present address: Department of Research and Innovation, "la Caixa" Foundation, Barcelona, Catalonia, Spain
| | - Joan Blanco-Fernandez
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Present address: Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Estel Aparicio-Prat
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Rory Johnson
- Department of Medical Oncology, Bern University Hospital, University of Bern, Inselspital, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Sílvia Pérez-Lluch
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain.
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28
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Eguchi R, Hamano M, Iwata M, Nakamura T, Oki S, Yamanishi Y. TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. Bioinformatics 2022; 38:2839-2846. [PMID: 35561200 DOI: 10.1093/bioinformatics/btac209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Direct reprogramming involves the direct conversion of fully differentiated mature cell types into various other cell types while bypassing an intermediate pluripotent state (e.g. induced pluripotent stem cells). Cell differentiation by direct reprogramming is determined by two types of transcription factors (TFs): pioneer factors (PFs) and cooperative TFs. PFs have the distinct ability to open chromatin aggregations, assemble a collective of cooperative TFs and activate gene expression. The experimental determination of two types of TFs is extremely difficult and costly. RESULTS In this study, we developed a novel computational method, TRANSDIRE (TRANS-omics-based approach for DIrect REprogramming), to predict the TFs that induce direct reprogramming in various human cell types using multiple omics data. In the algorithm, potential PFs were predicted based on low signal chromatin regions, and the cooperative TFs were predicted through a trans-omics analysis of genomic data (e.g. enhancers), transcriptome data (e.g. gene expression profiles in human cells), epigenome data (e.g. chromatin immunoprecipitation sequencing data) and interactome data. We applied the proposed methods to the reconstruction of TFs that induce direct reprogramming from fibroblasts to six other cell types: hepatocytes, cartilaginous cells, neurons, cardiomyocytes, pancreatic cells and Paneth cells. We demonstrated that the methods successfully predicted TFs for most cell conversions with high accuracy. Thus, the proposed methods are expected to be useful for various practical applications in regenerative medicine. AVAILABILITY AND IMPLEMENTATION The source code and data are available at the following website: http://figshare.com/s/b653781a5b9e6639972b. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ryohei Eguchi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Momoko Hamano
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Toru Nakamura
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
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29
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Figueiredo C, Blasczyk R. Generation of HLA Universal Megakaryocytes and Platelets by Genetic Engineering. Front Immunol 2021; 12:768458. [PMID: 34777386 PMCID: PMC8579098 DOI: 10.3389/fimmu.2021.768458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Patelet transfusion refractoriness remains a relevant hurdle in the treatment of severe alloimmunized thrombocytopenic patients. Antibodies specific for the human leukocyte antigens (HLA) class I are considered the major immunological cause for PLT transfusion refractoriness. Due to the insufficient availability of HLA-matched PLTs, the development of new technologies is highly desirable to provide an adequate management of thrombocytopenia in immunized patients. Blood pharming is a promising strategy not only to generate an alternative to donor blood products, but it may offer the possibility to optimize the therapeutic effect of the produced blood cells by genetic modification. Recently, enormous technical advances in the field of in vitro production of megakaryocytes (MKs) and PLTs have been achieved by combining progresses made at different levels including identification of suitable cell sources, cell pharming technologies, bioreactors and application of genetic engineering tools. In particular, use of RNA interference, TALEN and CRISPR/Cas9 nucleases or nickases has allowed for the generation of HLA universal PLTs with the potential to survive under refractoriness conditions. Genetically engineered HLA-silenced MKs and PLTs were shown to be functional and to have the capability to survive cell- and antibody-mediated cytotoxicity using in vitro and in vivo models. This review is focused on the methods to generate in vitro genetically engineered MKs and PLTs with the capacity to evade allogeneic immune responses.
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Affiliation(s)
- Constanca Figueiredo
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Rainer Blasczyk
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
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30
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Li B, Hon GC. Single-Cell Genomics: Catalyst for Cell Fate Engineering. Front Bioeng Biotechnol 2021; 9:748942. [PMID: 34733831 PMCID: PMC8558416 DOI: 10.3389/fbioe.2021.748942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
As we near a complete catalog of mammalian cell types, the capability to engineer specific cell types on demand would transform biomedical research and regenerative medicine. However, the current pace of discovering new cell types far outstrips our ability to engineer them. One attractive strategy for cellular engineering is direct reprogramming, where induction of specific transcription factor (TF) cocktails orchestrates cell state transitions. Here, we review the foundational studies of TF-mediated reprogramming in the context of a general framework for cell fate engineering, which consists of: discovering new reprogramming cocktails, assessing engineered cells, and revealing molecular mechanisms. Traditional bulk reprogramming methods established a strong foundation for TF-mediated reprogramming, but were limited by their small scale and difficulty resolving cellular heterogeneity. Recently, single-cell technologies have overcome these challenges to rapidly accelerate progress in cell fate engineering. In the next decade, we anticipate that these tools will enable unprecedented control of cell state.
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Affiliation(s)
- Boxun Li
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, United States
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31
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Cellular Models for Primary CoQ Deficiency Pathogenesis Study. Int J Mol Sci 2021; 22:ijms221910211. [PMID: 34638552 PMCID: PMC8508219 DOI: 10.3390/ijms221910211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/07/2023] Open
Abstract
Primary coenzyme Q10 (CoQ) deficiency includes a heterogeneous group of mitochondrial diseases characterized by low mitochondrial levels of CoQ due to decreased endogenous biosynthesis rate. These diseases respond to CoQ treatment mainly at the early stages of the disease. The advances in the next generation sequencing (NGS) as whole-exome sequencing (WES) and whole-genome sequencing (WGS) have increased the discoveries of mutations in either gene already described to participate in CoQ biosynthesis or new genes also involved in this pathway. However, these technologies usually provide many mutations in genes whose pathogenic effect must be validated. To functionally validate the impact of gene variations in the disease’s onset and progression, different cell models are commonly used. We review here the use of yeast strains for functional complementation of human genes, dermal skin fibroblasts from patients as an excellent tool to demonstrate the biochemical and genetic mechanisms of these diseases and the development of human-induced pluripotent stem cells (hiPSCs) and iPSC-derived organoids for the study of the pathogenesis and treatment approaches.
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32
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Choi DH, Lee KE, Park J, Park YJ, Lee JY, Park YS. Cell-Permeable Oct4 Gene Delivery Enhances Stem Cell-like Properties of Mouse Embryonic Fibroblasts. Int J Mol Sci 2021; 22:9357. [PMID: 34502264 PMCID: PMC8430778 DOI: 10.3390/ijms22179357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Direct conversion of one cell type into another is a trans-differentiation process. Recent advances in fibroblast research revealed that epithelial cells can give rise to fibroblasts by epithelial-mesenchymal transition. Conversely, fibroblasts can also give rise to epithelia by undergoing a mesenchymal to epithelial transition. To elicit stem cell-like properties in fibroblasts, the Oct4 transcription factor acts as a master transcriptional regulator for reprogramming somatic cells. Notably, the production of gene complexes with cell-permeable peptides, such as low-molecular-weight protamine (LMWP), was proposed to induce reprogramming without cytotoxicity and genomic mutation. We designed a complex with non-cytotoxic LMWP to prevent the degradation of Oct4 and revealed that the positively charged cell-permeable LMWP helped condense the size of the Oct4-LMWP complexes (1:5 N:P ratio). When the Oct4-LMWP complex was delivered into mouse embryonic fibroblasts (MEFs), stemness-related gene expression increased while fibroblast intrinsic properties decreased. We believe that the Oct4-LMWP complex developed in this study can be used to reprogram terminally differentiated somatic cells or convert them into stem cell-like cells without risk of cell death, improving the stemness level and stability of existing direct conversion techniques.
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Affiliation(s)
- Da Hyeon Choi
- Department of Biological Sciences and Biotechnology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea; (D.H.C.); (K.E.L.); (J.P.)
| | - Kyeong Eun Lee
- Department of Biological Sciences and Biotechnology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea; (D.H.C.); (K.E.L.); (J.P.)
| | - Jiwon Park
- Department of Biological Sciences and Biotechnology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea; (D.H.C.); (K.E.L.); (J.P.)
| | - Yoon Jeong Park
- Department of Dental Regenerative Bioengineering and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea;
- Central Research Institute, Nano Intelligent Biomedical Engineering Corporation (NIBEC), School of Dentistry, Seoul National University, Seoul 03080, Korea;
| | - Jue-Yeon Lee
- Central Research Institute, Nano Intelligent Biomedical Engineering Corporation (NIBEC), School of Dentistry, Seoul National University, Seoul 03080, Korea;
| | - Yoon Shin Park
- Department of Biological Sciences and Biotechnology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea; (D.H.C.); (K.E.L.); (J.P.)
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33
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Hywood JD, Sadeghipour S, Clayton ZE, Yuan J, Stubbs C, Wong JWT, Cooke JP, Patel S. Induced endothelial cells from peripheral arterial disease patients and neonatal fibroblasts have comparable angiogenic properties. PLoS One 2021; 16:e0255075. [PMID: 34375370 PMCID: PMC8354451 DOI: 10.1371/journal.pone.0255075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/11/2021] [Indexed: 12/05/2022] Open
Abstract
Induced endothelial cells (iECs) generated from neonatal fibroblasts via transdifferentiation have been shown to have pro-angiogenic properties and are a potential therapy for peripheral arterial disease (PAD). It is unknown if iECs can be generated from fibroblasts collected from PAD patients and whether these cells are pro-angiogenic. In this study fibroblasts were collected from four PAD patients undergoing carotid endarterectomies. These cells, and neonatal fibroblasts, were transdifferentiated into iECs using modified mRNA. Endothelial phenotype and pro-angiogenic cytokine secretion were investigated. NOD-SCID mice underwent surgery to induce hindlimb ischaemia in a murine model of PAD. Mice received intramuscular injections with either control vehicle, or 1 × 106 neonatal-derived or 1 × 106 patient-derived iECs. Recovery in perfusion to the affected limb was measured using laser Doppler scanning. Perfusion recovery was enhanced in mice treated with neonatal-derived iECs and in two of the three patient-derived iEC lines investigated in vivo. Patient-derived iECs can be successfully generated from PAD patients and for specific patients display comparable pro-angiogenic properties to neonatal-derived iECs.
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Affiliation(s)
- Jack D. Hywood
- Heart Research Institute, Newtown, NSW, Australia
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | | | - Zoe E. Clayton
- Heart Research Institute, Newtown, NSW, Australia
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Jun Yuan
- Heart Research Institute, Newtown, NSW, Australia
| | - Colleen Stubbs
- RNACore, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Jack W. T. Wong
- School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - John P. Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Sanjay Patel
- Heart Research Institute, Newtown, NSW, Australia
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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34
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Basu A, Tiwari VK. Epigenetic reprogramming of cell identity: lessons from development for regenerative medicine. Clin Epigenetics 2021; 13:144. [PMID: 34301318 PMCID: PMC8305869 DOI: 10.1186/s13148-021-01131-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/13/2021] [Indexed: 12/17/2022] Open
Abstract
Epigenetic mechanisms are known to define cell-type identity and function. Hence, reprogramming of one cell type into another essentially requires a rewiring of the underlying epigenome. Cellular reprogramming can convert somatic cells to induced pluripotent stem cells (iPSCs) that can be directed to differentiate to specific cell types. Trans-differentiation or direct reprogramming, on the other hand, involves the direct conversion of one cell type into another. In this review, we highlight how gene regulatory mechanisms identified to be critical for developmental processes were successfully used for cellular reprogramming of various cell types. We also discuss how the therapeutic use of the reprogrammed cells is beginning to revolutionize the field of regenerative medicine particularly in the repair and regeneration of damaged tissue and organs arising from pathological conditions or accidents. Lastly, we highlight some key challenges hindering the application of cellular reprogramming for therapeutic purposes.
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Affiliation(s)
- Amitava Basu
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany.
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, BT9 7BL, UK.
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35
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Reprogramming Restores Vision in Mice by Changing DNA Methylation. Neurosci Bull 2021; 37:1526-1528. [PMID: 34097224 DOI: 10.1007/s12264-021-00729-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022] Open
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36
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Su C, Pang J. CABEAN: a software for the control of asynchronous Boolean networks. Bioinformatics 2021; 37:879-881. [PMID: 32845335 DOI: 10.1093/bioinformatics/btaa752] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/04/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Direct cell reprogramming, also called transdifferentiation, has great potential for tissue engineering and regenerative medicine. Boolean networks, a popular modelling framework for gene regulatory networks, make it possible to identify intervention targets for direct cell reprogramming with computational methods. In this work, we present our software, CABEAN, for the control of asynchronous Boolean networks. CABEAN identifies efficacious nodes, whose perturbations can drive the dynamics of a network from a source attractor (the initial cell type) to a target attractor (the desired cell type). CABEAN provides several control methods integrating practical constraints. Thus, it has the ability to provide a rich set of control sets, such that biologists can select suitable ones for validation based on specific experimental settings. AVAILABILITY AND IMPLEMENTATION The executable binary and the user guide of the software are publicly available at https://satoss.uni.lu/software/CABEAN/.
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Affiliation(s)
- Cui Su
- Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Jun Pang
- Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
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37
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Postnatal Pluripotent Cells: Quarter of a Century of Research. Bull Exp Biol Med 2021; 170:515-521. [PMID: 33713237 DOI: 10.1007/s10517-021-05099-2] [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: 10/09/2020] [Indexed: 10/21/2022]
Abstract
Almost quarter of a century long studies aimed at identification, isolation, culturing, and use of postnatal pluripotent cells for the development of cell-based technologies have not met with success and failed to provide reliable and reproducible protocols of cell isolation, identification, and culturing. At the same time, experimental data in this field suggest that postnatal pluripotent cells are not the copies of embryonic cells and, therefore, the tests routinely used for identification of embryonic pluripotent cells are not fully adequate for characterization of their postnatal analogues. Therefore, cell lineage tracing methods showing the differentiation routes of the studied cells in human or animal body after birth should be developed and used.
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38
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Jung S, Appleton E, Ali M, Church GM, Del Sol A. A computer-guided design tool to increase the efficiency of cellular conversions. Nat Commun 2021; 12:1659. [PMID: 33712564 PMCID: PMC7954801 DOI: 10.1038/s41467-021-21801-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Human cell conversion technology has become an important tool for devising new cell transplantation therapies, generating disease models and testing gene therapies. However, while transcription factor over-expression-based methods have shown great promise in generating cell types in vitro, they often endure low conversion efficiency. In this context, great effort has been devoted to increasing the efficiency of current protocols and the development of computational approaches can be of great help in this endeavor. Here we introduce a computer-guided design tool that combines a computational framework for prioritizing more efficient combinations of instructive factors (IFs) of cellular conversions, called IRENE, with a transposon-based genomic integration system for efficient delivery. Particularly, IRENE relies on a stochastic gene regulatory network model that systematically prioritizes more efficient IFs by maximizing the agreement of the transcriptional and epigenetic landscapes between the converted and target cells. Our predictions substantially increased the efficiency of two established iPSC-differentiation protocols (natural killer cells and melanocytes) and established the first protocol for iPSC-derived mammary epithelial cells with high efficiency.
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Affiliation(s)
- Sascha Jung
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain
| | - Evan Appleton
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Muhammad Ali
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Maastricht University School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Antonio Del Sol
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain.
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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39
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Mollinari C, Merlo D. Direct Reprogramming of Somatic Cells to Neurons: Pros and Cons of Chemical Approach. Neurochem Res 2021; 46:1330-1336. [PMID: 33666839 PMCID: PMC8084785 DOI: 10.1007/s11064-021-03282-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Accepted: 02/20/2021] [Indexed: 12/11/2022]
Abstract
Translating successful preclinical research in neurodegenerative diseases into clinical practice has been difficult. The preclinical disease models used for testing new drugs not always appear predictive of the effects of the agents in the human disease state. Human induced pluripotent stem cells, obtained by reprogramming of adult somatic cells, represent a powerful system to study the molecular mechanisms of the disease onset and pathogenesis. However, these cells require a long time to differentiate into functional neural cells and the resetting of epigenetic information during reprogramming, might miss the information imparted by age. On the contrary, the direct conversion of somatic cells to neuronal cells is much faster and more efficient, it is safer for cell therapy and allows to preserve the signatures of donors’ age. Direct reprogramming can be induced by lineage-specific transcription factors or chemical cocktails and represents a powerful tool for modeling neurological diseases and for regenerative medicine. In this Commentary we present and discuss strength and weakness of several strategies for the direct cellular reprogramming from somatic cells to generate human brain cells which maintain age‐related features. In particular, we describe and discuss chemical strategy for cellular reprogramming as it represents a valuable tool for many applications such as aged brain modeling, drug screening and personalized medicine.
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Affiliation(s)
- Cristiana Mollinari
- Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere 100, 00133, Rome, Italy. .,Department of Neuroscience, Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy.
| | - Daniela Merlo
- Department of Neuroscience, Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy
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40
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Cai Q, Liao W, Xue F, Wang X, Zhou W, Li Y, Zeng W. Selection of different endothelialization modes and different seed cells for tissue-engineered vascular graft. Bioact Mater 2021; 6:2557-2568. [PMID: 33665496 PMCID: PMC7887299 DOI: 10.1016/j.bioactmat.2020.12.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Tissue-engineered vascular grafts (TEVGs) have enormous potential for vascular replacement therapy. However, thrombosis and intimal hyperplasia are important problems associated with TEVGs especially small diameter TEVGs (<6 mm) after transplantation. Endothelialization of TEVGs is a key point to prevent thrombosis. Here, we discuss different types of endothelialization and different seed cells of tissue-engineered vascular grafts. Meanwhile, endothelial heterogeneity is also discussed. Based on it, we provide a new perspective for selecting suitable types of endothelialization and suitable seed cells to improve the long-term patency rate of tissue-engineered vascular grafts with different diameters and lengths. The material, diameter and length of tissue-engineered vascular graft are all key factors affecting its long-term patency. Endothelialization strategies should consider the different diameters and lengths of tissue-engineered vascular grafts. Cell heterogeneity and tissue heterogeneity should be considered in the application of seed cells.
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Affiliation(s)
- Qingjin Cai
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China
| | - Wanshan Liao
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China
| | - Fangchao Xue
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China
| | - Xiaochen Wang
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China
| | - Weiming Zhou
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China
| | - Yanzhao Li
- State Key Laboratory of Trauma, Burn and Combined Injury, Chongqing, China
| | - Wen Zeng
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China.,State Key Laboratory of Trauma, Burn and Combined Injury, Chongqing, China.,Departments of Neurology, Southwest Hospital, Third Military Medical University, Chongqing, China
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41
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Xu B, Siehr A, Shen W. Functional skeletal muscle constructs from transdifferentiated human fibroblasts. Sci Rep 2020; 10:22047. [PMID: 33328524 PMCID: PMC7744552 DOI: 10.1038/s41598-020-78987-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Transdifferentiation of human non-muscle cells directly into myogenic cells by forced expression of MyoD represents one route to obtain highly desirable human myogenic cells. However, functional properties of the tissue constructs derived from these transdifferentiated cells have been rarely studied. Here, we report that three-dimensional (3D) tissue constructs engineered with iMyoD-hTERT-NHDFs, normal human dermal fibroblasts transduced with genes encoding human telomerase reverse transcriptase and doxycycline-inducible MyoD, generate detectable contractile forces in response to electrical stimuli upon MyoD expression. Withdrawal of doxycycline in the middle of 3D culture results in 3.05 and 2.28 times increases in twitch and tetanic forces, respectively, suggesting that temporally-controlled MyoD expression benefits functional myogenic differentiation of transdifferentiated myoblast-like cells. Treatment with CHIR99021, a Wnt activator, and DAPT, a Notch inhibitor, leads to further enhanced contractile forces. The ability of these abundant and potentially patient-specific and disease-specific cells to develop into functional skeletal muscle constructs makes them highly valuable for many applications, such as disease modeling.
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Affiliation(s)
- Bin Xu
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Allison Siehr
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wei Shen
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
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42
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Dotson GA, Ryan CW, Chen C, Muir L, Rajapakse I. Cellular reprogramming: Mathematics meets medicine. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 13:e1515. [PMID: 33289324 PMCID: PMC8867497 DOI: 10.1002/wsbm.1515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/11/2022]
Abstract
Generating needed cell types using cellular reprogramming is a promising strategy for restoring tissue function in injury or disease. A common method for reprogramming is addition of one or more transcription factors that confer a new function or identity. Advancements in transcription factor selection and delivery have culminated in successful grafting of autologous reprogrammed cells, an early demonstration of their clinical utility. Though cellular reprogramming has been successful in a number of settings, identification of appropriate transcription factors for a particular transformation has been challenging. Computational methods enable more sophisticated prediction of relevant transcription factors for reprogramming by leveraging gene expression data of initial and target cell types, and are built on mathematical frameworks ranging from information theory to control theory. This review highlights the utility and impact of these mathematical frameworks in the field of cellular reprogramming. This article is categorized under: Reproductive System Diseases > Reproductive System Diseases>Genetics/Genomics/Epigenetics Reproductive System Diseases > Reproductive System Diseases>Stem Cells and Development Reproductive System Diseases > Reproductive System Diseases>Computational Models.
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Affiliation(s)
- Gabrielle A. Dotson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Charles W. Ryan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Can Chen
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Lindsey Muir
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, 48109, USA
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43
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Huang D, Gibeley SB, Xu C, Xiao Y, Celik O, Ginsberg HN, Leong KW. Engineering liver microtissues for disease modeling and regenerative medicine. ADVANCED FUNCTIONAL MATERIALS 2020; 30:1909553. [PMID: 33390875 PMCID: PMC7774671 DOI: 10.1002/adfm.201909553] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 05/08/2023]
Abstract
The burden of liver diseases is increasing worldwide, accounting for two million deaths annually. In the past decade, tremendous progress has been made in the basic and translational research of liver tissue engineering. Liver microtissues are small, three-dimensional hepatocyte cultures that recapitulate liver physiology and have been used in biomedical research and regenerative medicine. This review summarizes recent advances, challenges, and future directions in liver microtissue research. Cellular engineering approaches are used to sustain primary hepatocytes or produce hepatocytes derived from pluripotent stem cells and other adult tissues. Three-dimensional microtissues are generated by scaffold-free assembly or scaffold-assisted methods such as macroencapsulation, droplet microfluidics, and bioprinting. Optimization of the hepatic microenvironment entails incorporating the appropriate cell composition for enhanced cell-cell interactions and niche-specific signals, and creating scaffolds with desired chemical, mechanical and physical properties. Perfusion-based culture systems such as bioreactors and microfluidic systems are used to achieve efficient exchange of nutrients and soluble factors. Taken together, systematic optimization of liver microtissues is a multidisciplinary effort focused on creating liver cultures and on-chip models with greater structural complexity and physiological relevance for use in liver disease research, therapeutic development, and regenerative medicine.
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Affiliation(s)
- Dantong Huang
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Sarah B. Gibeley
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Cong Xu
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Ozgenur Celik
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Henry N. Ginsberg
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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44
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Jiang L, Liang J, Huang W, Wu Z, Paul C, Wang Y. Strategies and Challenges to Improve Cellular Programming-Based Approaches for Heart Regeneration Therapy. Int J Mol Sci 2020; 21:E7662. [PMID: 33081233 PMCID: PMC7589611 DOI: 10.3390/ijms21207662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/29/2022] Open
Abstract
Limited adult cardiac cell proliferation after cardiovascular disease, such as heart failure, hampers regeneration, resulting in a major loss of cardiomyocytes (CMs) at the site of injury. Recent studies in cellular reprogramming approaches have provided the opportunity to improve upon previous techniques used to regenerate damaged heart. Using these approaches, new CMs can be regenerated from differentiation of iPSCs (similar to embryonic stem cells), the direct reprogramming of fibroblasts [induced cardiomyocytes (iCMs)], or induced cardiac progenitors. Although these CMs have been shown to functionally repair infarcted heart, advancements in technology are still in the early stages of development in research laboratories. In this review, reprogramming-based approaches for generating CMs are briefly introduced and reviewed, and the challenges (including low efficiency, functional maturity, and safety issues) that hinder further translation of these approaches into a clinical setting are discussed. The creative and combined optimal methods to address these challenges are also summarized, with optimism that further investigation into tissue engineering, cardiac development signaling, and epigenetic mechanisms will help to establish methods that improve cell-reprogramming approaches for heart regeneration.
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Affiliation(s)
- Lin Jiang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267-0529, USA
| | - Jialiang Liang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267-0529, USA
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267-0529, USA
| | - Zhichao Wu
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267-0529, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267-0529, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267-0529, USA
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45
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Milichko V, Dyachuk V. Novel Glial Cell Functions: Extensive Potency, Stem Cell-Like Properties, and Participation in Regeneration and Transdifferentiation. Front Cell Dev Biol 2020; 8:809. [PMID: 33015034 PMCID: PMC7461986 DOI: 10.3389/fcell.2020.00809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
Glial cells are the most abundant cells in both the peripheral and central nervous systems. During the past decade, a subpopulation of immature peripheral glial cells, namely, embryonic Schwann cell-precursors, have been found to perform important functions related to development. These cells have properties resembling those of the neural crest and, depending on their location in the body, can transform into several different cell types in peripheral tissues, including autonomic neurons. This review describes the multipotent properties of Schwann cell-precursors and their importance, together with innervation, during early development. The heterogeneity of Schwann cells, as revealed using single-cell transcriptomics, raises a question on whether some glial cells in the adult peripheral nervous system retain their stem cell-like properties. We also discuss how a deeper insight into the biology of both embryonic and adult Schwann cells might lead to an effective treatment of the damage of both neural and non-neural tissues, including the damage caused by neurodegenerative diseases. Furthermore, understanding the potential involvement of Schwann cells in the regulation of tumor development may reveal novel targets for cancer treatment.
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Affiliation(s)
- Valentin Milichko
- Department of Nanophotonics and Metamaterials, ITMO University, St. Petersburg, Russia
| | - Vyacheslav Dyachuk
- Department of Nanophotonics and Metamaterials, ITMO University, St. Petersburg, Russia.,National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
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46
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Jadczyk T, Caluori G, Wojakowski W, Starek Z. Nanotechnology and stem cells in vascular biology. VASCULAR BIOLOGY 2020; 1:H103-H109. [PMID: 32923961 PMCID: PMC7439937 DOI: 10.1530/vb-19-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/03/2022]
Abstract
Nanotechnology and stem cells are one of the most promising strategies for clinical medicine applications. The article provides an up-to-date view on advances in the field of regenerative and targeted vascular therapies describing a molecular design (propulsion mechanism, composition, target identification) and applications of nanorobots. Stem cell paragraph presents current clinical application of various cell types involved in vascular biology including mesenchymal stem cells, very small embryonic-like stem cells, induced pluripotent stem cells, mononuclear stem cells, amniotic fluid-derived stem cells and endothelial progenitor cells. A possible bridging between the two fields is also envisioned, where bio-inspired, safe, long-lasting nanorobots can fully target the cellular specific cues and even drive vascular process in a timely manner.
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Affiliation(s)
- Tomasz Jadczyk
- Department of Cardiology and Structural Heart Diseases, Medical University of Silesia, Katowice, Poland.,Interventional Cardiac Electrophysiology Group, International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Guido Caluori
- Department of Cardiology and Structural Heart Diseases, Medical University of Silesia, Katowice, Poland.,Nanobiotechnology, CEITEC-MU, Brno, Czech Republic
| | - Wojciech Wojakowski
- Department of Cardiology and Structural Heart Diseases, Medical University of Silesia, Katowice, Poland
| | - Zdenek Starek
- Interventional Cardiac Electrophysiology Group, International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic.,First Department of Internal Medicine, Cardioangiology, St. Anne's University Hospital Brno, Masaryk University, Brno, Czech Republic
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47
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Durko AP, Yacoub MH, Kluin J. Tissue Engineered Materials in Cardiovascular Surgery: The Surgeon's Perspective. Front Cardiovasc Med 2020; 7:55. [PMID: 32351975 PMCID: PMC7174659 DOI: 10.3389/fcvm.2020.00055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/20/2020] [Indexed: 12/13/2022] Open
Abstract
In cardiovascular surgery, reconstruction and replacement of cardiac and vascular structures are routinely performed. Prosthetic or biological materials traditionally used for this purpose cannot be considered ideal substitutes as they have limited durability and no growth or regeneration potential. Tissue engineering aims to create materials having normal tissue function including capacity for growth and self-repair. These advanced materials can potentially overcome the shortcomings of conventionally used materials, and, if successfully passing all phases of product development, they might provide a better option for both the pediatric and adult patient population requiring cardiovascular interventions. This short review article overviews the most important cardiovascular pathologies where tissue engineered materials could be used, briefly summarizes the main directions of development of these materials, and discusses the hurdles in their clinical translation. At its beginnings in the 1980s, tissue engineering (TE) was defined as “an interdisciplinary field that applies the principles of engineering and the life sciences toward the development of biological substitutes that restore, maintain, or improve tissue function” (1). Currently, the utility of TE products and materials are being investigated in several fields of human medicine, ranging from orthopedics to cardiovascular surgery (2–5). In cardiovascular surgery, reconstruction and replacement of cardiac and vascular structures are routinely performed. Considering the shortcomings of traditionally used materials, the need for advanced materials that can “restore, maintain or improve tissue function” are evident. Tissue engineered substitutes, having growth and regenerative capacity, could fundamentally change the specialty (6). This article overviews the most important cardiovascular pathologies where TE materials could be used, briefly summarizes the main directions of development of TE materials along with their advantages and shortcomings, and discusses the hurdles in their clinical translation.
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Affiliation(s)
- Andras P Durko
- Department of Cardiothoracic Surgery, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Magdi H Yacoub
- Imperial College London, National Heart and Lung Institute, London, United Kingdom
| | - Jolanda Kluin
- Department of Cardiothoracic Surgery, Amsterdam University Medical Center, Amsterdam, Netherlands
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48
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Pareja E, Gómez-Lechón MJ, Tolosa L. Induced pluripotent stem cells for the treatment of liver diseases: challenges and perspectives from a clinical viewpoint. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:566. [PMID: 32775367 PMCID: PMC7347783 DOI: 10.21037/atm.2020.02.164] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The only curative treatment for severe end-stage liver disease (ESLD) is liver transplantation (LT) but it is limited by the shortage of organ donors. The increase of the incidence of liver disease has led to develop new therapeutic approaches such as liver cell transplantation. Current challenges that limit a wider application of this therapy include a limited cell source and the poor engraftment in the host liver of cryopreserved hepatocytes after thawing. Induced pluripotent stem cells (iPSCs) that can be differentiated into hepatocyte-like cells (HLCs) are being widely explored as an alternative to human hepatocytes because of their unlimited proliferation capacity and their potential ability to avoid the immune system. Their large-scale production could provide a new tool to produce enough HLCs for treating patients with metabolic diseases, acute liver failure (ALF), those with ESLD or patients not considered for organ transplantation. In this review we discuss current challenges for generating differentiated cells compatible with human application as well as in-depth safety evaluation. This analysis highlights the uncertainties and deficiencies that should be addressed before their clinical use but also points out the potential benefits that will produce a great impact in the field of hepatology.
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Affiliation(s)
- Eugenia Pareja
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,Unidad Hepatobiliopancreáctica, Hospital Universitario Doctor Peset, Valencia, Spain
| | - M José Gómez-Lechón
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,CIBERehd, ISCIII, Madrid, Spain
| | - Laia Tolosa
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
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49
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Liu K, Ma W, Li C, Li J, Zhang X, Liu J, Liu W, Wu Z, Zang C, Liang Y, Guo J, Li L. Advances in Transcription Factors Related to Neuroglial Cell Reprogramming. Transl Neurosci 2020; 11:17-27. [PMID: 32161682 PMCID: PMC7053399 DOI: 10.1515/tnsci-2020-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/07/2020] [Indexed: 11/27/2022] Open
Abstract
Neuroglial cells have a high level of plasticity, and many types of these cells are present in the nervous system. Neuroglial cells provide diverse therapeutic targets for neurological diseases and injury repair. Cell reprogramming technology provides an efficient pathway for cell transformation during neural regeneration, while transcription factor-mediated reprogramming can facilitate the understanding of how neuroglial cells mature into functional neurons and promote neurological function recovery.
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Affiliation(s)
- Kuangpin Liu
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Wei Ma
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Chunyan Li
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Junjun Li
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Xingkui Zhang
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Jie Liu
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Wei Liu
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Zheng Wu
- Second Department of General Surgery, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Chenghao Zang
- Second Department of General Surgery, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yu Liang
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
| | - Jianhui Guo
- Second Department of General Surgery, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Liyan Li
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
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50
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Zhang Q, Zhang X, Truskey GA. Vascular Microphysiological Systems to Model Diseases. CELL & GENE THERAPY INSIGHTS 2020; 6:93-102. [PMID: 32431950 PMCID: PMC7236815 DOI: 10.18609/cgti.2020.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human vascular microphysiological systems (MPS) represent promising three-dimensional in vitro models of normal and diseased vascular tissue. These systems build upon advances in tissue engineering, microfluidics, and stem cell differentiation and replicate key functional units of organs and tissues. Vascular models have been developed for the microvasculature as well as medium-size arterioles. Key functions of the vascular system have been reproduced and stem cells offer the potential to model genetic diseases and population variation in genes that may increase individual risk for cardiovascular disease. Such systems can be used to evaluate new therapeutics options.
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Affiliation(s)
- Qiao Zhang
- Department of Biomedical Engineering, Duke University, 1427 CIEMAS, 101 Science Drive, Durham, NC 27708-0281, USA
| | - Xu Zhang
- Department of Biomedical Engineering, Duke University, 1427 CIEMAS, 101 Science Drive, Durham, NC 27708-0281, USA
| | - George A. Truskey
- Department of Biomedical Engineering, Duke University, 1427 CIEMAS, 101 Science Drive, Durham, NC 27708-0281, USA
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