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Osaki D, Ouji Y, Sakagami M, Kitamura T, Misu M, Kitahara T, Yoshikawa M. Culture of organoids with vestibular cell-derived factors promotes differentiation of embryonic stem cells into inner ear vestibular hair cells. J Biosci Bioeng 2023; 135:143-150. [PMID: 36503871 DOI: 10.1016/j.jbiosc.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Abstract
Vestibular hair cells (V-HCs) residing in the inner ear have important roles related to balance. Although differentiation of pluripotent stem cells into HCs has been shown, an effective method has yet to be established. We previously reported that use of vestibular cell-derived conditioned medium (V-CM) was helpful to induce embryonic stem (ES) cells to differentiate into V-HC-like cells in two-dimensional (2D) cultures of ES-derived embryoid bodies (EBs). In the present report, V-CM was used with three-dimensional (3D) cultures of EBs, which resulted in augmented expression of V-HC-related markers (Math1, Myosin6, Brn3c, Dnah5), but not of the cochlear HC-related marker Lmod3. Gene expression analyses of both 2D and 3D EBs cultured for two weeks revealed a greater level of augmented induction of HC-related markers in the 3D-cultured EBs. These results indicate that a 3D culture in combination with use of V-CM is an effective method for producing V-HCs.
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Affiliation(s)
- Daisuke Osaki
- Department of Pathogen, Infection and Immunity, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; Department of Otolaryngology - Head and Neck Surgery, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
| | - Yukiteru Ouji
- Department of Pathogen, Infection and Immunity, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
| | - Masaharu Sakagami
- Department of Pathogen, Infection and Immunity, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; Department of Otolaryngology - Head and Neck Surgery, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
| | - Tomotaka Kitamura
- Department of Pathogen, Infection and Immunity, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
| | - Masayasu Misu
- Department of Pathogen, Infection and Immunity, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
| | - Tadashi Kitahara
- Department of Otolaryngology - Head and Neck Surgery, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
| | - Masahide Yoshikawa
- Department of Pathogen, Infection and Immunity, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan.
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2
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Völkner M, Wagner F, Kurth T, Sykes AM, Del Toro Runzer C, Ebner LJA, Kavak C, Alexaki VI, Cimalla P, Mehner M, Koch E, Karl MO. Modeling inducible neuropathologies of the retina with differential phenotypes in organoids. Front Cell Neurosci 2023; 17:1106287. [PMID: 37213216 PMCID: PMC10196395 DOI: 10.3389/fncel.2023.1106287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/06/2023] [Indexed: 05/23/2023] Open
Abstract
Neurodegenerative diseases remain incompletely understood and therapies are needed. Stem cell-derived organoid models facilitate fundamental and translational medicine research. However, to which extent differential neuronal and glial pathologic processes can be reproduced in current systems is still unclear. Here, we tested 16 different chemical, physical, and cell functional manipulations in mouse retina organoids to further explore this. Some of the treatments induce differential phenotypes, indicating that organoids are competent to reproduce distinct pathologic processes. Notably, mouse retina organoids even reproduce a complex pathology phenotype with combined photoreceptor neurodegeneration and glial pathologies upon combined (not single) application of HBEGF and TNF, two factors previously associated with neurodegenerative diseases. Pharmacological inhibitors for MAPK signaling completely prevent photoreceptor and glial pathologies, while inhibitors for Rho/ROCK, NFkB, and CDK4 differentially affect them. In conclusion, mouse retina organoids facilitate reproduction of distinct and complex pathologies, mechanistic access, insights for further organoid optimization, and modeling of differential phenotypes for future applications in fundamental and translational medicine research.
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Affiliation(s)
- Manuela Völkner
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
| | - Felix Wagner
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
| | - Thomas Kurth
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform Core Facility Electron Microscopy and Histology, Dresden, Germany
| | - Alex M. Sykes
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Lynn J. A. Ebner
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
| | - Cagri Kavak
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
| | - Vasileia Ismini Alexaki
- Technische Universität Dresden, Institute of Clinical Chemistry and Laboratory Medicine, University Clinic Carl Gustav Carus, Dresden, Germany
| | - Peter Cimalla
- Technische Universität Dresden, Carl Gustav Carus Faculty of Medicine, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, Dresden, Germany
| | - Mirko Mehner
- Technische Universität Dresden, Carl Gustav Carus Faculty of Medicine, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, Dresden, Germany
| | - Edmund Koch
- Technische Universität Dresden, Carl Gustav Carus Faculty of Medicine, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, Dresden, Germany
| | - Mike O. Karl
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
- *Correspondence: Mike O. Karl, ,
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3
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Xue Y, Lin B, Chen JT, Tang WC, Browne AW, Seiler MJ. The Prospects for Retinal Organoids in Treatment of Retinal Diseases. Asia Pac J Ophthalmol (Phila) 2022; 11:314-327. [PMID: 36041146 PMCID: PMC9966053 DOI: 10.1097/apo.0000000000000538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/22/2022] [Indexed: 12/28/2022] Open
Abstract
Retinal degeneration (RD) is a significant cause of incurable blindness worldwide. Photoreceptors and retinal pigmented epithelium are irreversibly damaged in advanced RD. Functional replacement of photoreceptors and/or retinal pigmented epithelium cells is a promising approach to restoring vision. This paper reviews the current status and explores future prospects of the transplantation therapy provided by pluripotent stem cell-derived retinal organoids (ROs). This review summarizes the status of rodent RD disease models and discusses RO culture and analytical tools to evaluate RO quality and function. Finally, we review and discuss the studies in which RO-derived cells or sheets were transplanted. In conclusion, methods to derive ROs from pluripotent stem cells have significantly improved and become more efficient in recent years. Meanwhile, more novel technologies are applied to characterize and validate RO quality. However, opportunity remains to optimize tissue differentiation protocols and achieve better RO reproducibility. In order to screen high-quality ROs for downstream applications, approaches such as noninvasive and label-free imaging and electrophysiological functional testing are promising and worth further investigation. Lastly, transplanted RO-derived tissues have allowed improvements in visual function in several RD models, showing promises for clinical applications in the future.
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Affiliation(s)
- Yuntian Xue
- Biomedical Engineering, University of California, Irvine, CA
- Stem Cell Research Center, University of California, Irvine, CA
| | - Bin Lin
- Stem Cell Research Center, University of California, Irvine, CA
| | - Jacqueline T. Chen
- Stem Cell Research Center, University of California, Irvine, CA
- Gavin Herbert Eye Institute Ophthalmology, University of California, Irvine, CA
| | - William C. Tang
- Biomedical Engineering, University of California, Irvine, CA
| | - Andrew W. Browne
- Biomedical Engineering, University of California, Irvine, CA
- Gavin Herbert Eye Institute Ophthalmology, University of California, Irvine, CA
- Institute for Clinical and Translational Science, University of California, Irvine, CA
| | - Magdalene J. Seiler
- Stem Cell Research Center, University of California, Irvine, CA
- Gavin Herbert Eye Institute Ophthalmology, University of California, Irvine, CA
- Department of Physical Medicine and Rehabilitation, University of California, Irvine, CA
- Department of Anatomy and Neurobiology, University of California, Irvine, CA
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4
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Chen T, Zou L, Wang D, Li W, Yang Y, Liu X, Cao X, Chen J, Zhang Y, Fu J. Metabolomics study of Angelica sinensis (Oliv.) Diels on the abnormal uterine bleeding rats by ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry analysis. Food Sci Nutr 2021; 9:6596-6609. [PMID: 34925789 PMCID: PMC8645739 DOI: 10.1002/fsn3.2605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/11/2022] Open
Abstract
The objective of this study was to explore the effects and underlying intervention mechanisms of Angelica water extract (AWE) on abnormal uterine bleeding (AUB) based on serum metabolomics. Firstly, the concentration of main active substances in AWE was determined and the chemical components were identified by UPLC-Q-Exactive Orbitrap-MS/MS. A drug-induced abortion model was established by mifepristone and misoprostol. After administration AWE (2.16 g/kg) for 7 days, the coagulation function, serum hormone levels, H&E staining, and immunohistochemistry observation of uterus were detected. In addition, serum metabolites profiles were performed on ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS). The contents of ferulic acid, senkyunolide A, and ligustilide in AWE were 0.7276, 0.0868, and 1.9908 mg/g, respectively. Twenty-six compounds were identified in AWE. It was found that AWE was effective in regulation of coagulation function and promoting endometrial recovery. Meanwhile, the levels of E2, Pg, and HCG and the expression of ERα, Erβ, and PR were down-regulated in AUB model and up-regulated by the treatment of AWE. Twenty-one potential biomarkers were eventually identified by multivariate statistical analysis. Study indicated that glycerophospholipid, sphingolipid, amino acids, retinol metabolism and primary bile acid biosynthesis were the main related metabolic pathways involved for the treatment of AUB by AWE. The results showed that AWE has potential therapeutic effect on AUB by altering the metabolic aberrations.
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Affiliation(s)
- Ting‐Ting Chen
- Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduChina
- School of PharmacyDali UniversityDaliChina
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural AffairsSchool of Food and Biological EngineeringChengdu UniversityChengduChina
| | - Di Wang
- School of PharmacyChengdu University of Traditional Chinese MedicineChengduChina
| | - Wei Li
- School of Preclinical MedicineChengdu UniversityChengduChina
| | - Yong Yang
- School of Preclinical MedicineChengdu UniversityChengduChina
| | | | - Xin Cao
- School of Preclinical MedicineChengdu UniversityChengduChina
| | - Jia‐Rong Chen
- School of Preclinical MedicineChengdu UniversityChengduChina
| | - Yan Zhang
- School of Preclinical MedicineChengdu UniversityChengduChina
| | - Jia Fu
- Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduChina
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5
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Massengill MT, Lewin AS. Gene Therapy for Rhodopsin-associated Autosomal Dominant Retinitis Pigmentosa. Int Ophthalmol Clin 2021; 61:79-96. [PMID: 34584046 PMCID: PMC8478325 DOI: 10.1097/iio.0000000000000383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Stone NE, Voigt AP, Mullins RF, Sulchek T, Tucker BA. Microfluidic processing of stem cells for autologous cell replacement. Stem Cells Transl Med 2021; 10:1384-1393. [PMID: 34156760 PMCID: PMC8459636 DOI: 10.1002/sctm.21-0080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/10/2021] [Accepted: 05/15/2021] [Indexed: 12/18/2022] Open
Abstract
Autologous photoreceptor cell replacement is one of the most promising approaches currently under development for the treatment of inherited retinal degenerative blindness. Unlike endogenous stem cell populations, induced pluripotent stem cells (iPSCs) can be differentiated into both rod and cone photoreceptors in high numbers, making them ideal for this application. That said, in addition to photoreceptor cells, state of the art retinal differentiation protocols give rise to all of the different cell types of the normal retina, the majority of which are not required and may in fact hinder successful photoreceptor cell replacement. As such, following differentiation photoreceptor cell enrichment will likely be required. In addition, to prevent the newly generated photoreceptor cells from suffering the same fate as the patient's original cells, correction of the patient's disease‐causing genetic mutations will be necessary. In this review we discuss literature pertaining to the use of different cell sorting and transfection approaches with a focus on the development and use of novel next generation microfluidic devices. We will discuss how gold standard strategies have been used, the advantages and disadvantages of each, and how novel microfluidic platforms can be incorporated into the clinical manufacturing pipeline to reduce the complexity, cost, and regulatory burden associated with clinical grade production of photoreceptor cells for autologous cell replacement.
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Affiliation(s)
- Nicholas E. Stone
- The George W. Woodruff School of Mechanical EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Andrew P. Voigt
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Robert F. Mullins
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Todd Sulchek
- The George W. Woodruff School of Mechanical EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Budd A. Tucker
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
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7
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TGF-β2 upregulates tyrosinase activity via Opsin3 in human skin melanocytes in vitro. J Invest Dermatol 2021; 141:2679-2689. [PMID: 34029574 DOI: 10.1016/j.jid.2021.01.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/12/2021] [Accepted: 01/25/2021] [Indexed: 01/17/2023]
Abstract
Opsin3 (OPN3) is a potential key regulator of human melanocyte melanogenesis. How OPN3-mediated regulation of melanocyte melanogenesis is triggered is largely unclear. Transforming growth factor-β (TGF-β) can inhibit the growth of human melanocytes and reduce melanin synthesis in melanocytes. However, whether TGF-β2 can modulate pigmentation in normal human primary melanocytes via OPN3 is entirely unknown. Here, we constructed a co-culture model with human epidermal melanocytes and keratinocytes. Higher OPN3, tyrosinase (TYR), tyrosinase-related protein (TRP)-1, and TRP-2 expression and higher tyrosinase activity were detected in co-cultured cells than in mono-cultured cells. Moreover, elevated levels of TGF-β2 were detected in the culture supernatant of melanocytes co-cultured with keratinocytes. OPN3 inhibition in melanocytes decreased TYR, TRP-1, and TRP-2 expression and downregulated tyrosinase activity. Our findings indicate that TGF-β2 upregulates TYR, TRP-1 and TRP-2 expression in human melanocytes via OPN3 and downstream calcium-dependent G protein-coupled signalling pathways to induce melanogenesis. Interestingly, treatment with the TGF-β2 receptor inhibitor LY2109761 (10 μM) did not inhibit TGF-β2-induced melanocyte melanogenesis via OPN3. Collectively, our data suggest that TGF-β2 upregulates tyrosinase activity via OPN3 through a TGF-β2R-independent and calcium-dependent G protein-coupled signalling pathway.
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8
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Völkner M, Kurth T, Schor J, Ebner LJA, Bardtke L, Kavak C, Hackermüller J, Karl MO. Mouse Retinal Organoid Growth and Maintenance in Longer-Term Culture. Front Cell Dev Biol 2021; 9:645704. [PMID: 33996806 PMCID: PMC8114082 DOI: 10.3389/fcell.2021.645704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/11/2021] [Indexed: 12/14/2022] Open
Abstract
Using retinal organoid systems, organ-like 3D tissues, relies implicitly on their robustness. However, essential key parameters, particularly retinal growth and longer-term culture, are still insufficiently defined. Here, we hypothesize that a previously optimized protocol for high yield of evenly-sized mouse retinal organoids with low variability facilitates assessment of such parameters. We demonstrate that these organoids reliably complete retinogenesis, and can be maintained at least up to 60 days in culture. During this time, the organoids continue to mature on a molecular and (ultra)structural level: They develop photoreceptor outer segments and synapses, transiently maintain its cell composition for about 5-10 days after completing retinogenesis, and subsequently develop pathologic changes - mainly of the inner but also outer retina and reactive gliosis. To test whether this organoid system provides experimental access to the retina during and upon completion of development, we defined and stimulated organoid growth by activating sonic hedgehog signaling, which in patients and mice in vivo with a congenital defect leads to enlarged eyes. Here, a sonic hedgehog signaling activator increased retinal epithelia length in the organoid system when applied during but not after completion of development. This experimentally supports organoid maturation, stability, and experimental reproducibility in this organoid system, and provides a potential enlarged retina pathology model, as well as a protocol for producing larger organoids. Together, our study advances the understanding of retinal growth, maturation, and maintenance, and further optimizes the organoid system for future utilization.
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Affiliation(s)
- Manuela Völkner
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Thomas Kurth
- Center for Molecular and Cellular Bioengineering, Technology Platform, Electron Microscopy and Histology Facility, Technische Universität Dresden, Dresden, Germany
| | - Jana Schor
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lynn J A Ebner
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Lara Bardtke
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Cagri Kavak
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Jörg Hackermüller
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Mike O Karl
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany.,CRTD - Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
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9
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Stone NE, Voigt AP, Cooke JA, Giacalone JC, Hanasoge S, Mullins RF, Tucker BA, Sulchek T. Label-free microfluidic enrichment of photoreceptor cells. Exp Eye Res 2020; 199:108166. [PMID: 32771499 DOI: 10.1016/j.exer.2020.108166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/20/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022]
Abstract
Inherited retinal degenerative disorders such as retinitis pigmentosa and Usher syndrome are characterized by progressive death of photoreceptor cells. To restore vision to patients blinded by these diseases, a stem cell-based photoreceptor cell replacement strategy will likely be required. Although retinal stem cell differentiation protocols suitable for generating photoreceptor cells exist, they often yield a rather heterogenous mixture of cell types. To enrich the donor cell population for one or a few cell types, scientists have traditionally relied upon the use of antibody-based selection approaches. However, these strategies are quite labor intensive and require animal derived reagents and equipment that are not well suited to current good manufacturing practices (cGMP). The purpose of this study was to develop and evaluate a microfluidic cell sorting device capable of exploiting the physical and mechanical differences between retinal cell types to enrich specific donor cell populations such as Retinal Pigment Epithelial (RPE) cells and photoreceptor cells. Using this device, we were able to separate a mixture of RPE and iPSC-derived photoreceptor precursor cell lines into two substantially enriched fractions. The enrichment factor of the RPE fraction was 2 and that of the photoreceptor precursor cell fraction was 2.7. Similarly, when human retina, obtained from 3 independent donors, was dissociated and passed through the sorting device, the heterogeneous mixture could be reliably sorted into RPE and photoreceptor cell rich fractions. In summary, microfluidic cell sorting is a promising approach for antibody free enrichment of retinal cell populations.
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Affiliation(s)
- Nicholas E Stone
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew P Voigt
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Jessica A Cooke
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Joseph C Giacalone
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Srinivas Hanasoge
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Robert F Mullins
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Budd A Tucker
- Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Todd Sulchek
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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10
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Kegeles E, Naumov A, Karpulevich EA, Volchkov P, Baranov P. Convolutional Neural Networks Can Predict Retinal Differentiation in Retinal Organoids. Front Cell Neurosci 2020; 14:171. [PMID: 32719585 PMCID: PMC7350982 DOI: 10.3389/fncel.2020.00171] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
Abstract
We have developed a deep learning-based computer algorithm to recognize and predict retinal differentiation in stem cell-derived organoids based on bright-field imaging. The three-dimensional "organoid" approach for the differentiation of pluripotent stem cells (PSC) into retinal and other neural tissues has become a major in vitro strategy to recapitulate development. We decided to develop a universal, robust, and non-invasive method to assess retinal differentiation that would not require chemical probes or reporter gene expression. We hypothesized that basic-contrast bright-field (BF) images contain sufficient information on tissue specification, and it is possible to extract this data using convolutional neural networks (CNNs). Retina-specific Rx-green fluorescent protein mouse embryonic reporter stem cells have been used for all of the differentiation experiments in this work. The BF images of organoids have been taken on day 5 and fluorescent on day 9. To train the CNN, we utilized a transfer learning approach: ImageNet pre-trained ResNet50v2, VGG19, Xception, and DenseNet121 CNNs had been trained on labeled BF images of the organoids, divided into two categories (retina and non-retina), based on the fluorescent reporter gene expression. The best-performing classifier with ResNet50v2 architecture showed a receiver operating characteristic-area under the curve score of 0.91 on a test dataset. A comparison of the best-performing CNN with the human-based classifier showed that the CNN algorithm performs better than the expert in predicting organoid fate (84% vs. 67 ± 6% of correct predictions, respectively), confirming our original hypothesis. Overall, we have demonstrated that the computer algorithm can successfully recognize and predict retinal differentiation in organoids before the onset of reporter gene expression. This is the first demonstration of CNN's ability to classify stem cell-derived tissue in vitro.
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Affiliation(s)
- Evgenii Kegeles
- Department of Ophthalmology, The Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
- Genome Technologies and Bioinformatics Research Centre, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Anton Naumov
- Department of Information Systems, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
| | - Evgeny A. Karpulevich
- Genome Technologies and Bioinformatics Research Centre, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Department of Information Systems, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Pavel Volchkov
- Genome Technologies and Bioinformatics Research Centre, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Endocrinology Research Centre, Institute for Personalized Medicine, Moscow, Russia
| | - Petr Baranov
- Department of Ophthalmology, The Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
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11
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Fligor CM, Huang KC, Lavekar SS, VanderWall KB, Meyer JS. Differentiation of retinal organoids from human pluripotent stem cells. Methods Cell Biol 2020; 159:279-302. [PMID: 32586447 DOI: 10.1016/bs.mcb.2020.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human pluripotent stem cells (hPSCs) possess the remarkable ability to differentiate into any cell type of the body, including those of the retina. Through the differentiation of these cells as retinal organoids, it is now possible to model the spatial and temporal development of the human retina using hPSCs, in which retinal progenitor cells produce the entire repertoire of retinal cells, first differentiating into retinal ganglion cells and ending with mature photoreceptors, bipolar cells, and Müller glia. Importantly, retinal organoids self-assemble into laminated structures that recapitulate the layering of the human retina with a retinal ganglion cell layer lining the inner layer and a distinctly separate photoreceptor layer occupying the outer layers. This organoid technology has provided access to human tissue for developmental and disease modeling, as well as translational applications such as high throughput drug screening and cell replacement therapies. However, the differentiation of retinal organoids does require some expertise and multiple strategies produce inconsistent results. Here, we describe in detail a well-established and relatively simple method for the generation of retinal organoids.
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Affiliation(s)
- Clarisse M Fligor
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Kang-Chieh Huang
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Sailee S Lavekar
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Kirstin B VanderWall
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Jason S Meyer
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Ophthalmology, Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN, United States; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States.
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12
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Shrestha A, Allen BN, Wiley LA, Tucker BA, Worthington KS. Development of High-Resolution Three-Dimensional-Printed Extracellular Matrix Scaffolds and Their Compatibility with Pluripotent Stem Cells and Early Retinal Cells. J Ocul Pharmacol Ther 2019; 36:42-55. [PMID: 31414943 DOI: 10.1089/jop.2018.0146] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Purpose: Widely used approaches for retinal disease modeling and in vitro therapeutic testing can be augmented by using tissue-engineered scaffolds with a precise 3-dimensional structure. However, the materials currently used for these scaffolds are poorly matched to the biochemical and mechanical properties of the in vivo retina. Here, we create biopolymer-based scaffolds with a structure that is amenable to retinal tissue engineering and modeling. Methods: Optimal two-photon polymerization (TPP) settings, including laser power and scanning speed, are identified for 4 methacrylated biopolymer formulations: collagen, gelatin, hyaluronic acid (HA), and a 50/50 mixture of gelatin/HA, each with methylene blue as a photoinitiator. For select formulations, fabrication accuracy and swelling are determined and biocompatibility is evaluated by using human induced pluripotent stem cells and rat postnatal retinal cells. Results: TPP is feasible for each biopolymer formulation, but it is the most reliable for mixtures containing gelatin and the least reliable for HA alone. The mean size of microscaffold pores is within several microns of the intended value but the overall structure size is several times greater than the modeled volume. The addition of HA to gelatin scaffolds increases cell viability and promotes neuronal phenotype, including Tuj-1 expression and characteristic morphology. Conclusion: We successfully determined a useful range of TPP settings for 4 methacrylated biopolymer formulations. When crosslinked, these extracellular matrix-derived molecules support the growth and attachment of retinal cells. We anticipate that when combined with existing patient-specific approaches, this technique will enable more efficient and accurate retinal disease modeling and therapeutic testing in vitro than current techniques allow.
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Affiliation(s)
- Arwin Shrestha
- Roy J. Carver Department of Biomedical Engineering, College of Engineering, The University of Iowa, Iowa City, Iowa.,Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Roy J. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Brittany N Allen
- Roy J. Carver Department of Biomedical Engineering, College of Engineering, The University of Iowa, Iowa City, Iowa
| | - Luke A Wiley
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Roy J. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Budd A Tucker
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Roy J. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Kristan S Worthington
- Roy J. Carver Department of Biomedical Engineering, College of Engineering, The University of Iowa, Iowa City, Iowa.,Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Roy J. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
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Sekiya S, Kikuchi T, Shimizu T. Perfusion culture maintained with an air-liquid interface to stimulate epithelial cell organization in renal organoids in vitro. BMC Biomed Eng 2019; 1:15. [PMID: 32903332 PMCID: PMC7422605 DOI: 10.1186/s42490-019-0017-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/06/2019] [Indexed: 11/10/2022] Open
Abstract
Background Organoids derived from induced pluripotent stem (iPS) or embryonic stem (ES) cells have been evaluated as in vitro models of development and disease. However, maintaining these cells under long-term static culture conditions is difficult because of nutrition shortages and waste accumulation. To overcome these issues, perfusion culture systems are required for organoid technology. A system with a stable microenvironment, nutrient availability, and waste removal will accelerate organoid generation. The aim of this study was to develop a novel perfusion system for renal organoids by maintaining the air-liquid interface with a device fabricated using a 3D printer. Results Our results revealed slow flow at the organoid cultivation area based on microbead movement on the membrane, which depended on the perfusion rate under the membrane. Moreover, the perfused culture medium below the organoids via a porous membrane diffused throughout the organoids, maintaining the air-liquid interface. The diffusion rates within organoids were increased according to the flow rate of the culture medium under the membrane. The perfused culture medium also stimulated cytoskeletal and basement membrane re-organization associated with promotion tubular formation under 2.5 μL/min flow culture. In contrast, tubules in organoids were diminished at a flow rate of 10 μL/min. Conclusions Our liquid-air interface perfusion system accelerated organization of the renal organoids. These results suggest that suitable perfusion conditions can accelerate organization of epithelial cells and tissues in renal organoids in vitro.
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Affiliation(s)
- Sachiko Sekiya
- Institute of Advanced Biomedical and Engineering Science, Tokyo Women's Medical University, Kawada-cho 8-1 TWIns, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Tetsutaro Kikuchi
- Institute of Advanced Biomedical and Engineering Science, Tokyo Women's Medical University, Kawada-cho 8-1 TWIns, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Tatsuya Shimizu
- Institute of Advanced Biomedical and Engineering Science, Tokyo Women's Medical University, Kawada-cho 8-1 TWIns, Shinjuku-ku, Tokyo, 162-8666 Japan
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Correction of NR2E3 Associated Enhanced S-cone Syndrome Patient-specific iPSCs using CRISPR-Cas9. Genes (Basel) 2019; 10:genes10040278. [PMID: 30959774 PMCID: PMC6523438 DOI: 10.3390/genes10040278] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/24/2022] Open
Abstract
Enhanced S-cone syndrome (ESCS) is caused by recessive mutations in the photoreceptor cell transcription factor NR2E3. Loss of NR2E3 is characterized by repression of rod photoreceptor cell gene expression, over-expansion of the S-cone photoreceptor cell population, and varying degrees of M- and L-cone photoreceptor cell development. In this study, we developed a CRISPR-based homology-directed repair strategy and corrected two different disease-causing NR2E3 mutations in patient-derived induced pluripotent stem cells (iPSCs) generated from two affected individuals. In addition, one patient’s iPSCs were differentiated into retinal cells and NR2E3 transcription was evaluated in CRISPR corrected and uncorrected clones. The patient’s c.119-2A>C mutation caused the inclusion of a portion of intron 1, the creation of a frame shift, and generation of a premature stop codon. In summary, we used a single set of CRISPR reagents to correct different mutations in iPSCs generated from two individuals with ESCS. In doing so we demonstrate the advantage of using retinal cells derived from affected patients over artificial in vitro model systems when attempting to demonstrate pathophysiologic mechanisms of specific mutations.
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15
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Casadei E, Salinas I. Comparative models for human nasal infections and immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:212-222. [PMID: 30513304 PMCID: PMC7102639 DOI: 10.1016/j.dci.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 05/09/2023]
Abstract
The human olfactory system is a mucosal surface and a major portal of entry for respiratory and neurotropic pathogens into the body. Understanding how the human nasopharynx-associated lymphoid tissue (NALT) halts the progression of pathogens into the lower respiratory tract or the central nervous system is key for developing effective cures. Although traditionally mice have been used as the gold-standard model for the study of human nasal diseases, mouse models present important caveats due to major anatomical and functional differences of the human and murine olfactory system and NALT. We summarize the NALT anatomy of different animal groups that have thus far been used to study host-pathogen interactions at the olfactory mucosa and to test nasal vaccines. The goal of this review is to highlight the strengths and limitations of each animal model of nasal immunity and to identify the areas of research that require further investigation to advance human health.
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Affiliation(s)
- Elisa Casadei
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA.
| | - Irene Salinas
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA
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