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Shoji JY, Davis RP, Mummery CL, Krauss S. Global Literature Analysis of Organoid and Organ-on-Chip Research. Adv Healthc Mater 2024; 13:e2301067. [PMID: 37479227 DOI: 10.1002/adhm.202301067] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/14/2023] [Indexed: 07/23/2023]
Abstract
Organoids and cells in organ-on-chip platforms replicate higher-level anatomical, physiological, or pathological states of tissues and organs. These technologies are widely regarded by academia, the pharmacological industry and regulators as key biomedical developments. To map advances in this emerging field, a literature analysis of 16,000 article metadata based on a quality-controlled text-mining algorithm is performed. The analysis covers titles, keywords, and abstracts of categorized academic publications in the literature and preprint databases published after 2010. The algorithm identifies and tracks 149 and 107 organs or organ substructures modeled as organoids and organ-on-chip, respectively, stem cell sources, as well as 130 diseases, and 16 groups of organisms other than human and mouse in which organoid/organ-on-chip technology is applied. The analysis illustrates changing diversity and focus in organoid/organ-on-chip research and captures its geographical distribution. The downloadable dataset provided is a robust framework for researchers to interrogate with their own questions.
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Affiliation(s)
- Jun-Ya Shoji
- Hybrid Technology Hub, Center of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, 0372, Norway
| | - Richard P Davis
- Department of Anatomy & Embryology, Leiden University Medical Center, Leiden, 2300RC, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, 2300RC, the Netherlands
| | - Christine L Mummery
- Department of Anatomy & Embryology, Leiden University Medical Center, Leiden, 2300RC, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, 2300RC, the Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, Enschede, 7522NB, the Netherlands
| | - Stefan Krauss
- Hybrid Technology Hub, Center of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, 0372, Norway
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Buck SA, Rubin SA, Kunkhyen T, Treiber CD, Xue X, Fenno LE, Mabry SJ, Sundar VR, Yang Z, Shah D, Ketchesin KD, Becker-Krail DD, Vasylieva I, Smith MC, Weisel FJ, Wang W, Erickson-Oberg MQ, O’Leary EI, Aravind E, Ramakrishnan C, Kim YS, Wu Y, Quick M, Coleman JA, MacDonald WA, Elbakri R, De Miranda BR, Palladino MJ, McCabe BD, Fish KN, Seney ML, Rayport S, Mingote S, Deisseroth K, Hnasko TS, Awatramani R, Watson AM, Waddell S, Cheetham CEJ, Logan RW, Freyberg Z. Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560584. [PMID: 37873436 PMCID: PMC10592912 DOI: 10.1101/2023.10.02.560584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Parkinson's disease (PD) targets some dopamine (DA) neurons more than others. Sex differences offer insights, with females more protected from DA neurodegeneration. The mammalian vesicular glutamate transporter VGLUT2 and Drosophila ortholog dVGLUT have been implicated as modulators of DA neuron resilience. However, the mechanisms by which VGLUT2/dVGLUT protects DA neurons remain unknown. We discovered DA neuron dVGLUT knockdown increased mitochondrial reactive oxygen species in a sexually dimorphic manner in response to depolarization or paraquat-induced stress, males being especially affected. DA neuron dVGLUT also reduced ATP biosynthetic burden during depolarization. RNA sequencing of VGLUT+ DA neurons in mice and flies identified candidate genes that we functionally screened to further dissect VGLUT-mediated DA neuron resilience across PD models. We discovered transcription factors modulating dVGLUT-dependent DA neuroprotection and identified dj-1β as a regulator of sex-specific DA neuron dVGLUT expression. Overall, VGLUT protects DA neurons from PD-associated degeneration by maintaining mitochondrial health.
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Affiliation(s)
- Silas A. Buck
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sophie A. Rubin
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Tenzin Kunkhyen
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Christoph D. Treiber
- Centre for Neural Circuits & Behaviour, University of Oxford, Oxford OX1 3TA, UK
| | - Xiangning Xue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Lief E. Fenno
- Departments of Psychiatry and Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel J. Mabry
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Varun R. Sundar
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Zilu Yang
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Divia Shah
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kyle D. Ketchesin
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Darius D. Becker-Krail
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Iaroslavna Vasylieva
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Megan C. Smith
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Florian J. Weisel
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wenjia Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - M. Quincy Erickson-Oberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Emma I. O’Leary
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Eshan Aravind
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yanying Wu
- Centre for Neural Circuits & Behaviour, University of Oxford, Oxford OX1 3TA, UK
| | - Matthias Quick
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Department of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Jonathan A. Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | - Rania Elbakri
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Briana R. De Miranda
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael J. Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Pittsburgh Institute of Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Brian D. McCabe
- Brain Mind Institute, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Kenneth N. Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Marianne L. Seney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Stephen Rayport
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Department of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Susana Mingote
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Department of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Neuroscience Initiative, Advanced Science Research Center, Graduate Center of The City University of New York, New York, NY 10031, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Thomas S. Hnasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | | | - Alan M. Watson
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Scott Waddell
- Centre for Neural Circuits & Behaviour, University of Oxford, Oxford OX1 3TA, UK
| | | | - Ryan W. Logan
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Oun A, Sabogal-Guaqueta AM, Galuh S, Alexander A, Kortholt A, Dolga AM. The multifaceted role of LRRK2 in Parkinson's disease: From human iPSC to organoids. Neurobiol Dis 2022; 173:105837. [PMID: 35963526 DOI: 10.1016/j.nbd.2022.105837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/21/2022] [Accepted: 08/06/2022] [Indexed: 11/28/2022] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease affecting elderly people. Pathogenic mutations in Leucine-Rich Repeat Kinase 2 (LRRK2) are the most common cause of autosomal dominant PD. LRRK2 activity is enhanced in both familial and idiopathic PD, thereby studies on LRRK2-related PD research are essential for understanding PD pathology. Finding an appropriate model to mimic PD pathology is crucial for revealing the molecular mechanisms underlying disease progression, and aiding drug discovery. In the last few years, the use of human-induced pluripotent stem cells (hiPSCs) grew exponentially, especially in studying neurodegenerative diseases like PD, where working with brain neurons and glial cells was mainly possible using postmortem samples. In this review, we will discuss the use of hiPSCs as a model for PD pathology and research on the LRRK2 function in both neuronal and immune cells, together with reviewing the recent advances in 3D organoid models and microfluidics.
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Affiliation(s)
- Asmaa Oun
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands; Department of Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology (GBB), University of Groningen, Groningen, the Netherlands; Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Angelica Maria Sabogal-Guaqueta
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands
| | - Sekar Galuh
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands
| | - Anastasia Alexander
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands
| | - Arjan Kortholt
- Department of Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology (GBB), University of Groningen, Groningen, the Netherlands; YETEM-Innovative Technologies Application and Research Centre Suleyman Demirel University, Isparta, Turkey.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands.
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Kim H, Sim H, Lee JE, Seo MK, Lim J, Bang Y, Nam D, Lee SY, Chung SK, Choi HJ, Park SW, Son I, Kim J, Seol W. Ciliogenesis is Not Directly Regulated by LRRK2 Kinase Activity in Neurons. Exp Neurobiol 2021; 30:232-243. [PMID: 34230223 PMCID: PMC8278138 DOI: 10.5607/en21003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/28/2021] [Accepted: 05/14/2021] [Indexed: 11/19/2022] Open
Abstract
Mutations in the Leucine-rich repeat kinase 2 (LRRK2) gene are the most prevalent cause of familial Parkinson’s disease (PD). The increase in LRRK2 kinase activity observed in the pathogenic G2019S mutation is important for PD development. Several studies have reported that increased LRRK2 kinase activity and treatment with LRRK2 kinase inhibitors decreased and increased ciliogenesis, respectively, in mouse embryonic fibroblasts (MEFs) and retinal pigment epithelium (RPE) cells. In contrast, treatment of SH-SY5Y dopaminergic neuronal cells with PD-causing chemicals increased ciliogenesis. Because these reports were somewhat contradictory, we tested the effect of LRRK2 kinase activity on ciliogenesis in neurons. In SH-SY5Y cells, LRRK2 inhibitor treatment slightly increased ciliogenesis, but serum starvation showed no increase. In rat primary neurons, LRRK2 inhibitor treatment repeatedly showed no significant change. Little difference was observed between primary cortical neurons prepared from wild-type (WT) and G2019S+/- mice. However, a significant increase in ciliogenesis was observed in G2019S+/- compared to WT human fibroblasts, and this pattern was maintained in neural stem cells (NSCs) differentiated from the induced pluripotent stem cells (iPSCs) prepared from the same WT/G2019S fibroblast pair. NSCs differentiated from G2019S and its gene-corrected WT counterpart iPSCs were also used to test ciliogenesis in an isogenic background. The results showed no significant difference between WT and G2019S regardless of kinase inhibitor treatment and B27-deprivation-mimicking serum starvation. These results suggest that LRRK2 kinase activity may be not a direct regulator of ciliogenesis and ciliogenesis varies depending upon the cell type or genetic background.
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Affiliation(s)
- Hyejung Kim
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| | - Hyuna Sim
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Korea
| | - Joo-Eun Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Mi Kyoung Seo
- Paik Institute for Clinical Research, Inje University College of Medicine, Busan 47392, Korea
| | - Juhee Lim
- College of Pharmacy, CHA University, Seongnam 13496, Korea
| | - Yeojin Bang
- College of Pharmacy, CHA University, Seongnam 13496, Korea
| | - Daleum Nam
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| | - Seo-Young Lee
- Division of Clinical Medicine, Korea Institute of Oriental Medicine, Daejeon 34054, Korea
| | - Sun-Ku Chung
- Division of Herbal Medicine Research, Korea Institute of Oriental Medicine, Daejeon 34054, Korea
| | - Hyun Jin Choi
- College of Pharmacy, CHA University, Seongnam 13496, Korea
| | - Sung Woo Park
- Paik Institute for Clinical Research, Inje University College of Medicine, Busan 47392, Korea.,Department of Convergence Biomedical Science, Inje University College of Medicine, Busan 47392, Korea
| | - Ilhong Son
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea.,Department of Neurology, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| | - Janghwan Kim
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Korea
| | - Wongi Seol
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
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