1
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Li D, Mei Q, Li G. scQA: A dual-perspective cell type identification model for single cell transcriptome data. Comput Struct Biotechnol J 2024; 23:520-536. [PMID: 38235363 PMCID: PMC10791572 DOI: 10.1016/j.csbj.2023.12.021] [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] [Received: 10/13/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Single-cell RNA sequencing technologies have been pivotal in advancing the development of algorithms for clustering heterogeneous cell populations. Existing methods for utilizing scRNA-seq data to identify cell types tend to neglect the beneficial impact of dropout events and perform clustering focusing solely on quantitative perspective. Here, we introduce a novel method named scQA, notable for its ability to concurrently identify cell types and cell type-specific key genes from both qualitative and quantitative perspectives. In contrast to other methods, scQA not only identifies cell types but also extracts key genes associated with these cell types, enabling bidirectional clustering for scRNA-seq data. Through an iterative process, our approach aims to minimize the number of landmarks to approximately a dozen while maximizing the inclusion of quasi-trend-preserved genes with dropouts both qualitatively and quantitatively. It then clusters cells by employing an ingenious label propagation strategy, obviating the requirement for a predetermined number of cell types. Validated on 20 publicly available scRNA-seq datasets, scQA consistently outperforms other salient tools. Furthermore, we confirm the effectiveness and potential biological significance of the identified key genes through both external and internal validation. In conclusion, scQA emerges as a valuable tool for investigating cell heterogeneity due to its distinctive fusion of qualitative and quantitative facets, along with bidirectional clustering capabilities. Furthermore, it can be seamlessly integrated into border scRNA-seq analyses. The source codes are publicly available at https://github.com/LD-Lyndee/scQA.
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Affiliation(s)
- Di Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
| | - Qinglin Mei
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Guojun Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
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2
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Dorgau B, Collin J, Rozanska A, Zerti D, Unsworth A, Crosier M, Hussain R, Coxhead J, Dhanaseelan T, Patel A, Sowden JC, FitzPatrick DR, Queen R, Lako M. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina. Nat Commun 2024; 15:3567. [PMID: 38670973 PMCID: PMC11053058 DOI: 10.1038/s41467-024-47933-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: 07/11/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids.
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Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Darin Zerti
- Biosciences Institute, Newcastle University, Newcastle, UK
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Moira Crosier
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Aara Patel
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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3
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Dorgau B, Collin J, Rozanska A, Boczonadi V, Moya-Molina M, Unsworth A, Hussain R, Coxhead J, Dhanaseelan T, Armstrong L, Queen R, Lako M. Deciphering the spatiotemporal transcriptional and chromatin accessibility of human retinal organoid development at the single-cell level. iScience 2024; 27:109397. [PMID: 38510120 PMCID: PMC10952046 DOI: 10.1016/j.isci.2024.109397] [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] [Received: 08/23/2023] [Revised: 11/28/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Molecular information on the early stages of human retinal development remains scarce due to limitations in obtaining early human eye samples. Pluripotent stem cell-derived retinal organoids (ROs) provide an unprecedented opportunity for studying early retinogenesis. Using a combination of single cell RNA-seq and spatial transcriptomics we present for the first-time a single cell spatiotemporal transcriptome of RO development. Our data demonstrate that ROs recapitulate key events of retinogenesis including optic vesicle/cup formation, presence of a putative ciliary margin zone, emergence of retinal progenitor cells and their orderly differentiation to retinal neurons. Combining the scRNA- with scATAC-seq data, we were able to reveal cell-type specific transcription factor binding motifs on accessible chromatin at each stage of organoid development, and to show that chromatin accessibility is highly correlated to the developing human retina, but with some differences in the temporal emergence and abundance of some of the retinal neurons.
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Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Veronika Boczonadi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Marina Moya-Molina
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
- Newcells Biotech, Newcastle upon Tyne NE4 5BX, UK
| | - Adrienne Unsworth
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Rafiqul Hussain
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Jonathan Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Tamil Dhanaseelan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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4
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Yuan M, Jin S, Tan G, Song S, Liu Y, Wang H, Shen Y. A Non-canonical Excitatory PV RGC-PV SC Visual Pathway for Mediating the Looming-evoked Innate Defensive Response. Neurosci Bull 2024; 40:310-324. [PMID: 37302108 PMCID: PMC10912393 DOI: 10.1007/s12264-023-01076-z] [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] [Received: 02/23/2023] [Accepted: 05/04/2023] [Indexed: 06/13/2023] Open
Abstract
Parvalbumin-positive retinal ganglion cells (PV+ RGCs) are an essential subset of RGCs found in various species. However, their role in transmitting visual information remains unclear. Here, we characterized PV+ RGCs in the retina and explored the functions of the PV+ RGC-mediated visual pathway. By applying multiple viral tracing strategies, we investigated the downstream of PV+ RGCs across the whole brain. Interestingly, we found that the PV+ RGCs provided direct monosynaptic input to PV+ excitatory neurons in the superficial layers of the superior colliculus (SC). Ablation or suppression of SC-projecting PV+ RGCs abolished or severely impaired the flight response to looming visual stimuli in mice without affecting visual acuity. Furthermore, using transcriptome expression profiling of individual cells and immunofluorescence colocalization for RGCs, we found that PV+ RGCs are predominant glutamatergic neurons. Thus, our findings indicate the critical role of PV+ RGCs in an innate defensive response and suggest a non-canonical subcortical visual pathway from excitatory PV+ RGCs to PV+ SC neurons that regulates looming visual stimuli. These results provide a potential target for intervening and treating diseases related to this circuit, such as schizophrenia and autism.
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Affiliation(s)
- Man Yuan
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Sen Jin
- The Brain Cognition and Brain Disease Institute, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, National Medical Products Administration Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen, 518055, China
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, 430071, China
| | - Gao Tan
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Siyuan Song
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, 77030, USA
| | - Yizong Liu
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Huadong Wang
- The Brain Cognition and Brain Disease Institute, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, National Medical Products Administration Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen, 518055, China
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, 430071, China
| | - Yin Shen
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China.
- Frontier Science Center of Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China.
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5
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Xi G, Feng P, Zhang X, Wu S, Zhang J, Wang X, Xiang A, Xu W, Wang N, Zhu W. iPSC-derived cells stimulate ABCG2 + /NES + endogenous trabecular meshwork cell proliferation and tissue regeneration. Cell Prolif 2024:e13611. [PMID: 38356373 DOI: 10.1111/cpr.13611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
A major risk factor for glaucoma, the first leading cause of irreversible blindness worldwide, is the decellularisation of the trabecular meshwork (TM) in the conventional outflow pathway. Stem cell-based therapy, particularly the utilisation of induced pluripotent stem cells (iPSCs), presents an enticing potential for tissue regeneration and intraocular pressure (IOP) maintenance in glaucoma. We have previously observed that differentiated iPSCs can stimulate endogenous cell proliferation in the TM, a pivotal factor in TM regeneration and aqueous humour outflow restoration. In this study, we investigated the response of TM cells in vivo after interacting with iPSC-derived cells and identified two subpopulations responsible for this relatively long-term tissue regeneration: ATP Binding Cassette Subfamily G Member 2 (ABCG2)-positive cells and Nestin (NES)-positive cells. We further uncovered that alterations of these responsive cells are linked to ageing and different glaucoma etiologies, suggesting that ABCG2+ subpopulation decellularization could serve as a potential risk factor for TM decellularization in glaucoma. Taken together, our findings illustrated the proliferative subpopulations in the conventional outflow pathway when stimulated with iPSC-derived cells and defined them as TM precursors, which may be applied to develop novel therapeutic approaches for glaucoma.
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Affiliation(s)
- Gaiping Xi
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Pengchao Feng
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Xiaoyan Zhang
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Shen Wu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
| | - Jingxue Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
| | - Xiangji Wang
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Ailing Xiang
- Qingdao Xikai Biotechnology Co., Ltd, Qingdao, China
| | - Wenhua Xu
- Department of Inspection, Qingdao University, Qingdao, China
| | - Ningli Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
- Advanced Innovation Center for Big Data-Based Precision Medicine, Beijing University of Aeronautics and Astronautics-Capital Medical University, Beijing, China
| | - Wei Zhu
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
- Advanced Innovation Center for Big Data-Based Precision Medicine, Beijing University of Aeronautics and Astronautics-Capital Medical University, Beijing, China
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6
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Li M, Guo H, Wang B, Han Z, Wu S, Liu J, Huang H, Zhu J, An F, Lin Z, Mo K, Tan J, Liu C, Wang L, Deng X, Li G, Ji J, Ouyang H. The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation. Nat Commun 2024; 15:256. [PMID: 38177186 PMCID: PMC10766623 DOI: 10.1038/s41467-023-44471-w] [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: 08/16/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Proper differentiation of corneal epithelial cells (CECs) from limbal stem/progenitor cells (LSCs) is required for maintenance of ocular homeostasis and clear vision. Here, using a single-cell transcriptomic atlas, we delineate the comprehensive and refined molecular regulatory dynamics during human CEC development and differentiation. We find that RORA is a CEC-specific molecular switch that initiates and drives LSCs to differentiate into mature CECs by activating PITX1. RORA dictates CEC differentiation by establishing CEC-specific enhancers and chromatin interactions between CEC gene promoters and distal regulatory elements. Conversely, RORA silences LSC-specific promoters and disrupts promoter-anchored chromatin loops to turn off LSC genes. Collectively, our work provides detailed and comprehensive insights into the transcriptional dynamics and RORA-mediated epigenetic remodeling underlying human corneal epithelial differentiation.
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Affiliation(s)
- Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Bofeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zhuo Han
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Jin Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Fengjiao An
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zesong Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Chunqiao Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, 999077, China
| | - Guigang Li
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jianping Ji
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
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7
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Wang B, Guo H, Han Z, Wu S, Liu J, Lin Z, An F, Zhu J, Li M. NRG1 Regulates Proliferation, Migration and Differentiation of Human Limbal Epithelial Stem Cells. Curr Issues Mol Biol 2023; 45:10121-10130. [PMID: 38132478 PMCID: PMC10742012 DOI: 10.3390/cimb45120632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Limbal epithelial stem/progenitor cells (LESCs) proliferate, migrate and differentiate into mature corneal epithelium cells (CECs) that cover the ocular surface. LESCs play a crucial role in the maintenance and regeneration of the corneal epithelium, and their dysfunction can lead to various corneal diseases. Neuregulin 1 (NRG1) is a member of the epidermal growth factor family that regulates the growth and differentiation of epithelial tissues. Here, we depicted the dynamic transcriptomic profiles during human CEC differentiation, identifying six gene co-expression modules that were specific to different differentiation stages. We found that the expression of NRG1 was high in human LESCs and decreased dramatically upon differentiation. Knockdown of NRG1 significantly inhibited LESC proliferation and upregulated the expression of the terminal differentiation marker genes KRT3, KRT12 and CLU. In addition, the scratch wound closure assay showed that knockdown of NRG1 attenuated wound closure of LESCs over 24 h. Together, we dissected the transcriptional regulatory dynamics during CEC differentiation and identified NRG1 as a key regulator that promoted LESC proliferation and migration and maintained the undifferentiated state.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China; (B.W.); (Z.H.)
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8
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Ahsanuddin S, Wu AY. Single-cell transcriptomics of the ocular anterior segment: a comprehensive review. Eye (Lond) 2023; 37:3334-3350. [PMID: 37138096 PMCID: PMC10156079 DOI: 10.1038/s41433-023-02539-3] [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: 11/21/2022] [Revised: 03/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Elucidating the cellular and genetic composition of ocular tissues is essential for uncovering the pathophysiology of ocular diseases. Since the introduction of single-cell RNA sequencing (scRNA-seq) in 2009, vision researchers have performed extensive single-cell analyses to better understand transcriptome complexity and heterogeneity of ocular structures. This technology has revolutionized our ability to identify rare cell populations and to make cross-species comparisons of gene expression in both steady state and disease conditions. Importantly, single-cell transcriptomic analyses have enabled the identification of cell-type specific gene markers and signalling pathways between ocular cell populations. While most scRNA-seq studies have been conducted on retinal tissues, large-scale transcriptomic atlases pertaining to the ocular anterior segment have also been constructed in the past three years. This timely review provides vision researchers with an overview of scRNA-seq experimental design, technical limitations, and clinical applications in a variety of anterior segment-related ocular pathologies. We review open-access anterior segment-related scRNA-seq datasets and illustrate how scRNA-seq can be an indispensable tool for the development of targeted therapeutics.
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Affiliation(s)
- Sofia Ahsanuddin
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, New York City, NY, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Albert Y Wu
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Wolf J, Rasmussen DK, Sun YJ, Vu JT, Wang E, Espinosa C, Bigini F, Chang RT, Montague AA, Tang PH, Mruthyunjaya P, Aghaeepour N, Dufour A, Bassuk AG, Mahajan VB. Liquid-biopsy proteomics combined with AI identifies cellular drivers of eye aging and disease in vivo. Cell 2023; 186:4868-4884.e12. [PMID: 37863056 PMCID: PMC10720485 DOI: 10.1016/j.cell.2023.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/26/2023] [Accepted: 09/13/2023] [Indexed: 10/22/2023]
Abstract
Single-cell analysis in living humans is essential for understanding disease mechanisms, but it is impractical in non-regenerative organs, such as the eye and brain, because tissue biopsies would cause serious damage. We resolve this problem by integrating proteomics of liquid biopsies with single-cell transcriptomics from all known ocular cell types to trace the cellular origin of 5,953 proteins detected in the aqueous humor. We identified hundreds of cell-specific protein markers, including for individual retinal cell types. Surprisingly, our results reveal that retinal degeneration occurs in Parkinson's disease, and the cells driving diabetic retinopathy switch with disease stage. Finally, we developed artificial intelligence (AI) models to assess individual cellular aging and found that many eye diseases not associated with chronological age undergo accelerated molecular aging of disease-specific cell types. Our approach, which can be applied to other organ systems, has the potential to transform molecular diagnostics and prognostics while uncovering new cellular disease and aging mechanisms.
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Affiliation(s)
- Julian Wolf
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Ditte K Rasmussen
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Young Joo Sun
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Jennifer T Vu
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Elena Wang
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fabio Bigini
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Robert T Chang
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Artis A Montague
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Peter H Tang
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; Retina Consultants of Minnesota, Edina, MN 55435, USA
| | - Prithvi Mruthyunjaya
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine Dufour
- Departments of Physiology and Pharmacology & Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alexander G Bassuk
- Departments of Pediatrics and Neurology, The Iowa Neuroscience Institute (INI), University of Iowa, Iowa City, IA 52242, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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10
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Lyu P, Zhai Y, Li T, Qian J. CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server. Bioinformatics 2023; 39:btad521. [PMID: 37610325 PMCID: PMC10477937 DOI: 10.1093/bioinformatics/btad521] [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: 03/21/2023] [Revised: 07/17/2023] [Accepted: 08/22/2023] [Indexed: 08/24/2023] Open
Abstract
MOTIVATION Single-cell sequencing technology has become a routine in studying many biological problems. A core step of analyzing single-cell data is the assignment of cell clusters to specific cell types. Reference-based methods are proposed for predicting cell types for single-cell clusters. However, the scalability and lack of preprocessed reference datasets prevent them from being practical and easy to use. RESULTS Here, we introduce a reference-based cell annotation web server, CellAnn, which is super-fast and easy to use. CellAnn contains a comprehensive reference database with 204 human and 191 mouse single-cell datasets. These reference datasets cover 32 organs. Furthermore, we developed a cluster-to-cluster alignment method to transfer cell labels from the reference to the query datasets, which is superior to the existing methods with higher accuracy and higher scalability. Finally, CellAnn is an online tool that integrates all the procedures in cell annotation, including reference searching, transferring cell labels, visualizing results, and harmonizing cell annotation labels. Through the user-friendly interface, users can identify the best annotation by cross-validating with multiple reference datasets. We believe that CellAnn can greatly facilitate single-cell sequencing data analysis. AVAILABILITY AND IMPLEMENTATION The web server is available at www.cellann.io, and the source code is available at https://github.com/Pinlyu3/CellAnn_shinyapp.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Yijie Zhai
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218, United States
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
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11
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Swamy VS, Batz ZA, McGaughey DM. PLAE Web App Enables Powerful Searching and Multiple Visualizations Across One Million Unified Single-Cell Ocular Transcriptomes. Transl Vis Sci Technol 2023; 12:18. [PMID: 37747415 PMCID: PMC10578359 DOI: 10.1167/tvst.12.9.18] [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] [Received: 11/01/2022] [Accepted: 07/02/2023] [Indexed: 09/26/2023] Open
Abstract
Purpose To create a high-performance reactive web application to query single-cell gene expression data across cell type, species, study, and other factors. Methods We updated the content and structure of the underlying data (single cell Eye in a Disk [scEiaD]) and wrote the web application PLAE (https://plae.nei.nih.gov) to visualize and explore the data. Results The new portal provides quick visualization of over a million individual cells from vertebrate eye and body transcriptomes encompassing four species, 60 cell types, six ocular tissues, and 23 body tissues across 35 publications. To demonstrate the value of this unified pan-eye dataset, we replicated known neurogenic and cone macula markers in addition to proposing six new cone human region markers. Conclusions The PLAE web application offers the eye community a powerful and quick means to test hypotheses related to gene expression across a highly diverse, community-derived database. Translational Relevance The PLAE resource enables any researcher or clinician to study and research gene expression patterning across a wide variety of curated ocular cell types with a responsive web app.
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Affiliation(s)
- Vinay S Swamy
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Zachary A Batz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - David M McGaughey
- Bioinformatics Group, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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12
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Hamashima K, Wong KW, Sam TW, Teo JHJ, Taneja R, Le MTN, Li QJ, Hanna JH, Li H, Loh YH. Single-nucleus multiomic mapping of m 6A methylomes and transcriptomes in native populations of cells with sn-m6A-CT. Mol Cell 2023; 83:S1097-2765(23)00649-4. [PMID: 37657444 PMCID: PMC10895704 DOI: 10.1016/j.molcel.2023.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/21/2023] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
N6-methyladenosine (m6A) RNA modification plays important roles in the governance of gene expression and is temporally regulated in different cell states. In contrast to global m6A profiling in bulk sequencing, single-cell technologies for analyzing m6A heterogeneity are not extensively established. Here, we developed single-nucleus m6A-CUT&Tag (sn-m6A-CT) for simultaneous profiling of m6A methylomes and transcriptomes within a single nucleus using mouse embryonic stem cells (mESCs). m6A-CT is capable of enriching m6A-marked RNA molecules in situ, without isolating RNAs from cells. We adapted m6A-CT to the droplet-based single-cell omics platform and demonstrated high-throughput performance in analyzing nuclei isolated from thousands of cells from various cell types. We show that sn-m6A-CT profiling is sufficient to determine cell identity and allows the generation of cell-type-specific m6A methylome landscapes from heterogeneous populations. These indicate that sn-m6A-CT provides additional dimensions to multimodal datasets and insights into epitranscriptomic landscape in defining cell fate identity and states.
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Affiliation(s)
- Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
| | - Ka Wai Wong
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Tsz Wing Sam
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore
| | - Jia Hao Jackie Teo
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore
| | - Minh T N Le
- Department of Pharmacology and Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; Department of Surgery, Immunology Program, Cancer Program, and Nanomedicine Translational Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore; Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Graduate School's Integrative Sciences and Engineering Programme, National University of Singapore, 28 Medical Drive, Singapore, Singapore.
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13
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Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye. Proc Natl Acad Sci U S A 2023; 120:e2306153120. [PMID: 37566633 PMCID: PMC10450437 DOI: 10.1073/pnas.2306153120] [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: 04/16/2023] [Accepted: 06/29/2023] [Indexed: 08/13/2023] Open
Abstract
Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here, we used high-throughput single-nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in six extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases-for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ~151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the data presented here complete a "Version 1" cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as the neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
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Affiliation(s)
- Aboozar Monavarfeshani
- Center for Brain Science, Harvard University, Cambridge, MA02138
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Christian Pappas
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Kenechukwu A. Odenigbo
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA02142
| | - Tavé van Zyl
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT065101
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Joshua R. Sanes
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
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14
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Katsura M, Urade Y, Nansai H, Kobayashi M, Taguchi A, Ishikawa Y, Ito T, Fukunaga H, Tozawa H, Chikaoka Y, Nakaki R, Echigo A, Kohro T, Sone H, Wada Y. Low-dose radiation induces unstable gene expression in developing human iPSC-derived retinal ganglion organoids. Sci Rep 2023; 13:12888. [PMID: 37558727 PMCID: PMC10412642 DOI: 10.1038/s41598-023-40051-6] [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] [Received: 01/16/2023] [Accepted: 08/03/2023] [Indexed: 08/11/2023] Open
Abstract
The effects of low-dose radiation on undifferentiated cells carry important implications. However, the effects on developing retinal cells remain unclear. Here, we analyzed the gene expression characteristics of neuronal organoids containing immature human retinal cells under low-dose radiation and predicted their changes. Developing retinal cells generated from human induced pluripotent stem cells (iPSCs) were irradiated with either 30 or 180 mGy on days 4-5 of development for 24 h. Genome-wide gene expression was observed until day 35. A knowledge-based pathway analysis algorithm revealed fluctuations in Rho signaling and many other pathways. After a month, the levels of an essential transcription factor of eye development, the proportion of paired box 6 (PAX6)-positive cells, and the proportion of retinal ganglion cell (RGC)-specific transcription factor POU class 4 homeobox 2 (POU4F2)-positive cells increased with 30 mGy of irradiation. In contrast, they decreased after 180 mGy of irradiation. Activation of the "development of neurons" pathway after 180 mGy indicated the dedifferentiation and development of other neural cells. Fluctuating effects after low-dose radiation exposure suggest that developing retinal cells employ hormesis and dedifferentiation mechanisms in response to stress.
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Affiliation(s)
- Mari Katsura
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Reiwa Eye Clinic, Hatsukaichi, Hiroshima, Japan
| | - Yoshihiro Urade
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Hiroko Nansai
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mika Kobayashi
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Akashi Taguchi
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Yukiko Ishikawa
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Ito
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Hisako Fukunaga
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideto Tozawa
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yoko Chikaoka
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | | | | | - Takahide Kohro
- Department of Clinical Informatics, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hideko Sone
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan.
- Environmental Health and Prevention Research Unit, Yokohama University of Pharmacy, Yokohama, Japan.
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo, Japan.
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
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15
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Araujo-Silva CA, Marinho PM, Marcos AAA, Branco AMC, Sakamoto V, Matuoka ML, Moraes NF, Tierno PFGMM, Mourad WM, Nascimento H, Burnier M, de Souza W, Belfort R. Postmortem Ultrastructural Analysis of the Retina from COVID-19 Deceased Patients. Ocul Immunol Inflamm 2023:1-9. [PMID: 37552861 DOI: 10.1080/09273948.2023.2238817] [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: 04/21/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023]
Abstract
PURPOSE COVID-19 (coronavirus disease 2019) is an infectious disease caused by SARS-CoV-2, first reported in 2019 in Wuhan, China. Among the common complications is a pro-inflammatory and hypercoagulative response that compromises the vasculature among various organs. METHODS In this report, we present the postmortem retinal findings of five patients observed by means of optical microscopy and transmission and scanning electron microscopy techniques. RESULTS Clinical manifestations such as retinal hemorrhages and exacerbated inflammatory infiltrate, altered ultra structure with swollen mitochondria and pyknotic cells in both layers of the retina were observed in all analyzed eyes. CONCLUSION Our data point to the fragility of this tissue in cases of severe COVID-19.
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Affiliation(s)
- Carlla A Araujo-Silva
- Laboratório de Ultraestrutura Celular Hertha Meyer, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens - INBEB, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagens - CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paula M Marinho
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Alléxya A A Marcos
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Ana M C Branco
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Victoria Sakamoto
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Mateus L Matuoka
- Hospital Municipal de Barueri Dr. Francisco Moran, São Paulo, Brazil
| | - Nara F Moraes
- Hospital Municipal de Barueri Dr. Francisco Moran, São Paulo, Brazil
| | | | - Walid M Mourad
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
| | - Heloisa Nascimento
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
- Hospital Municipal de Barueri Dr. Francisco Moran, São Paulo, Brazil
| | - Miguel Burnier
- Department of Ophthalmology, McGill University, Montreal, Quebec, Canada
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens - INBEB, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagens - CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rubens Belfort
- São Paulo Hospital, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Instituto Paulista de Estudos e Pesquisas em Oftalmologia - IPEPO, São Paulo, Brazil
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16
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Arts JA, Laberthonnière C, Lima Cunha D, Zhou H. Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease. Cells 2023; 12:1808. [PMID: 37443842 PMCID: PMC10340756 DOI: 10.3390/cells12131808] [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: 06/02/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease.
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Affiliation(s)
- Julian A. Arts
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Camille Laberthonnière
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Dulce Lima Cunha
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Huiqing Zhou
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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17
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Vöcking O, Famulski JK. Single cell transcriptome analyses of the developing zebrafish eye- perspectives and applications. Front Cell Dev Biol 2023; 11:1213382. [PMID: 37457291 PMCID: PMC10346855 DOI: 10.3389/fcell.2023.1213382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
Within a relatively short period of time, single cell transcriptome analyses (SCT) have become increasingly ubiquitous with transcriptomic research, uncovering plentiful details that boost our molecular understanding of various biological processes. Stemming from SCT analyses, the ever-growing number of newly assigned genetic markers increases our understanding of general function and development, while providing opportunities for identifying genes associated with disease. SCT analyses have been carried out using tissue from numerous organisms. However, despite the great potential of zebrafish as a model organism, other models are still preferably used. In this mini review, we focus on eye research as an example of the advantages in using zebrafish, particularly its usefulness for single cell transcriptome analyses of developmental processes. As studies have already shown, the unique opportunities offered by zebrafish, including similarities to the human eye, in combination with the possibility to analyze and extract specific cells at distinct developmental time points makes the model a uniquely powerful one. Particularly the practicality of collecting large numbers of embryos and therefore isolation of sufficient numbers of developing cells is a distinct advantage compared to other model organisms. Lastly, the advent of highly efficient genetic knockouts methods offers opportunities to characterize target gene function in a more cost-efficient way. In conclusion, we argue that the use of zebrafish for SCT approaches has great potential to further deepen our molecular understanding of not only eye development, but also many other organ systems.
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Affiliation(s)
| | - Jakub K. Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
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18
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Liang Q, Cheng X, Wang J, Owen L, Shakoor A, Lillvis JL, Zhang C, Farkas M, Kim IK, Li Y, DeAngelis M, Chen R. A multi-omics atlas of the human retina at single-cell resolution. CELL GENOMICS 2023; 3:100298. [PMID: 37388908 PMCID: PMC10300490 DOI: 10.1016/j.xgen.2023.100298] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/22/2023] [Accepted: 03/17/2023] [Indexed: 07/01/2023]
Abstract
Cell classes in the human retina are highly heterogeneous with their abundance varying by several orders of magnitude. Here, we generated and integrated a multi-omics single-cell atlas of the adult human retina, including more than 250,000 nuclei for single-nuclei RNA-seq and 137,000 nuclei for single-nuclei ATAC-seq. Cross-species comparison of the retina atlas among human, monkey, mice, and chicken revealed relatively conserved and non-conserved types. Interestingly, the overall cell heterogeneity in primate retina decreases compared with that of rodent and chicken retina. Through integrative analysis, we identified 35,000 distal cis-element-gene pairs, constructed transcription factor (TF)-target regulons for more than 200 TFs, and partitioned the TFs into distinct co-active modules. We also revealed the heterogeneity of the cis-element-gene relationships in different cell types, even from the same class. Taken together, we present a comprehensive single-cell multi-omics atlas of the human retina as a resource that enables systematic molecular characterization at individual cell-type resolution.
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Affiliation(s)
- Qingnan Liang
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuesen Cheng
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Wang
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leah Owen
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - Akbar Shakoor
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - John L. Lillvis
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Charles Zhang
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - Michael Farkas
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Yumei Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Rui Chen
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Sun D, Shi WY, Dou SQ. Single-cell RNA sequencing in cornea research: Insights into limbal stem cells and their niche regulation. World J Stem Cells 2023; 15:466-475. [PMID: 37342216 PMCID: PMC10277966 DOI: 10.4252/wjsc.v15.i5.466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/26/2023] Open
Abstract
The corneal epithelium is composed of stratified squamous epithelial cells on the outer surface of the eye, which acts as a protective barrier and is critical for clear and stable vision. Its continuous renewal or wound healing depends on the proliferation and differentiation of limbal stem cells (LSCs), a cell population that resides at the limbus in a highly regulated niche. Dysfunction of LSCs or their niche can cause limbal stem cell deficiency, a disease that is manifested by failed epithelial wound healing or even blindness. Nevertheless, compared to stem cells in other tissues, little is known about the LSCs and their niche. With the advent of single-cell RNA sequencing, our understanding of LSC characteristics and their microenvironment has grown considerably. In this review, we summarized the current findings from single-cell studies in the field of cornea research and focused on important advancements driven by this technology, including the heterogeneity of the LSC population, novel LSC markers and regulation of the LSC niche, which will provide a reference for clinical issues such as corneal epithelial wound healing, ocular surface reconstruction and interventions for related diseases.
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Affiliation(s)
- Di Sun
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266000, Shandong Province, China
| | - Wei-Yun Shi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Eye Hospital of Shandong First Medical University, Jinan 250000, Shandong Province, China
- School of Ophthalmology, Shandong First Medical University, Qingdao 266000, Shandong Province, China
| | - Sheng-Qian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266000, Shandong Province, China
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20
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Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Transcriptomic Analysis of the Ocular Posterior Segment Completes a Cell Atlas of the Human Eye. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538447. [PMID: 37162855 PMCID: PMC10168356 DOI: 10.1101/2023.04.26.538447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here we used high-throughput single nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in the extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases - for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ∼151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the new data complete a "Version 1" cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
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Affiliation(s)
- Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Equal contributions
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Equal contributions
| | - Christian Pappas
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Kenechukwu A. Odenigbo
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Tavé van Zyl
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Present address: Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT 06510
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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21
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Vöcking O, Famulski JK. A temporal single cell transcriptome atlas of zebrafish anterior segment development. Sci Rep 2023; 13:5656. [PMID: 37024546 PMCID: PMC10079958 DOI: 10.1038/s41598-023-32212-4] [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: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Anterior segment dysgenesis (ASD), resulting in vision impairment, stems from maldevelopment of anterior segment (AS) tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells (POM). POM cells specify into anterior segment mesenchyme (ASM) cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS. Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development, Tg[foxc1b:GFP], we isolated GFP+ ASM cells at several developmental timepoints (48-144 hpf) and performed single cell RNA sequencing. Clustering analysis indicates subdifferentiation of ASM as early as 48 hpf and subsequent diversification into corneal epithelium/endothelium/stroma, or annular ligament (AL) lineages. Tracking individual clusters reveals common developmental pathways, up to 72 hpf, for the AL and corneal endothelium/stroma and distinct pathways for corneal epithelium starting at 48 hpf. Spatiotemporal validation of over 80 genes found associated with AS development demonstrates a high degree of conservation with mammalian trabecular meshwork and corneal tissues. In addition, we characterize thirteen novel genes associated with annular ligament and seven with corneal development. Overall, the data provide a molecular verification of the long-standing hypothesis that POM derived ASM give rise to AS tissues and highlight the high degree of conservation between zebrafish and mammals.
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Affiliation(s)
- Oliver Vöcking
- Department of Biology, University of Kentucky, Lexington, USA
| | - J K Famulski
- Department of Biology, University of Kentucky, Lexington, USA.
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22
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Kuepfer L, Fuellen G, Stahnke T. Quantitative systems pharmacology of the eye: Tools and data for ocular QSP. CPT Pharmacometrics Syst Pharmacol 2023; 12:288-299. [PMID: 36708082 PMCID: PMC10014063 DOI: 10.1002/psp4.12918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 12/21/2022] [Accepted: 01/02/2023] [Indexed: 01/29/2023] Open
Abstract
Good eyesight belongs to the most-valued attributes of health, and diseases of the eye are a significant healthcare burden. Case numbers are expected to further increase in the next decades due to an aging society. The development of drugs in ophthalmology, however, is difficult due to limited accessibility of the eye, in terms of drug administration and in terms of sampling of tissues for drug pharmacokinetics (PKs) and pharmacodynamics (PDs). Ocular quantitative systems pharmacology models provide the opportunity to describe the distribution of drugs in the eye as well as the resulting drug-response in specific segments of the eye. In particular, ocular physiologically-based PK (PBPK) models are necessary to describe drug concentration levels in different regions of the eye. Further, ocular effect models using molecular data from specific cellular systems are needed to develop dose-response correlations. We here describe the current status of PK/PBPK as well as PD models for the eyes and discuss cellular systems, data repositories, as well as animal models in ophthalmology. The application of the various concepts is highlighted for the development of new treatments for postoperative fibrosis after glaucoma surgery.
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Affiliation(s)
- Lars Kuepfer
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Aging Research (IBIMA), Rostock University Medical Center, Rostock, Germany
| | - Thomas Stahnke
- Institute for ImplantTechnology and Biomaterials e.V., Rostock, Germany.,Department of Ophthalmology, Rostock University Medical Center, Rostock, Germany
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23
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Narta K, Teltumbade MR, Vishal M, Sadaf S, Faruq M, Jama H, Waseem N, Rao A, Sen A, Ray K, Mukhopadhyay A. Whole Exome Sequencing Reveals Novel Candidate Genes in Familial Forms of Glaucomatous Neurodegeneration. Genes (Basel) 2023; 14:495. [PMID: 36833422 PMCID: PMC9957298 DOI: 10.3390/genes14020495] [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: 12/22/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Glaucoma is the largest cause of irreversible blindness with a multifactorial genetic etiology. This study explores novel genes and gene networks in familial forms of primary open angle glaucoma (POAG) and primary angle closure glaucoma (PACG) to identify rare mutations with high penetrance. Thirty-one samples from nine MYOC-negative families (five POAG and four PACG) underwent whole-exome sequencing and analysis. A set of prioritized genes and variations were screened in an independent validation cohort of 1536 samples and the whole-exome data from 20 sporadic patients. The expression profiles of the candidate genes were analyzed in 17 publicly available expression datasets from ocular tissues and single cells. Rare, deleterious SNVs in AQP5, SRFBP1, CDH6 and FOXM1 from POAG families and in ACACB, RGL3 and LAMA2 from PACG families were found exclusively in glaucoma cases. AQP5, SRFBP1 and CDH6 also revealed significant altered expression in glaucoma in expression datasets. Single-cell expression analysis revealed enrichment of identified candidate genes in retinal ganglion cells and corneal epithelial cells in POAG; whereas for PACG families, retinal ganglion cells and Schwalbe's Line showed enriched expression. Through an unbiased exome-wide search followed by validation, we identified novel candidate genes for familial cases of POAG and PACG. The SRFBP1 gene found in a POAG family is located within the GLC1M locus on Chr5q. Pathway analysis of candidate genes revealed enrichment of extracellular matrix organization in both POAG and PACG.
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Affiliation(s)
- Kiran Narta
- Genomics & Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road (Near Sukhdev Vihar), New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Manoj Ramesh Teltumbade
- Genomics & Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road (Near Sukhdev Vihar), New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mansi Vishal
- Genomics & Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road (Near Sukhdev Vihar), New Delhi 110025, India
- CSIR-Indian Institute of Chemical Biology, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Samreen Sadaf
- Genomics & Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road (Near Sukhdev Vihar), New Delhi 110025, India
| | - Mohd. Faruq
- Genomics & Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road (Near Sukhdev Vihar), New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Hodan Jama
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Naushin Waseem
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Aparna Rao
- L. V. Prasad Eye Institute, Bhubaneswar 751024, India
| | | | - Kunal Ray
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- CSIR-Indian Institute of Chemical Biology, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Arijit Mukhopadhyay
- Genomics & Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road (Near Sukhdev Vihar), New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Translational Medicine Unit, Biomedical Research & Innovation Centre, University of Salford, Salford M5 4WT, UK
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24
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Burger A, Baldock RA, Adams DJ, Din S, Papatheodorou I, Glinka M, Hill B, Houghton D, Sharghi M, Wicks M, Arends MJ. Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC Med Inform Decis Mak 2023; 23:36. [PMID: 36793076 PMCID: PMC9933383 DOI: 10.1186/s12911-023-02111-9] [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] [Received: 06/30/2022] [Accepted: 01/13/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND The Human Cell Atlas resource will deliver single cell transcriptome data spatially organised in terms of gross anatomy, tissue location and with images of cellular histology. This will enable the application of bioinformatics analysis, machine learning and data mining revealing an atlas of cell types, sub-types, varying states and ultimately cellular changes related to disease conditions. To further develop the understanding of specific pathological and histopathological phenotypes with their spatial relationships and dependencies, a more sophisticated spatial descriptive framework is required to enable integration and analysis in spatial terms. METHODS We describe a conceptual coordinate model for the Gut Cell Atlas (small and large intestines). Here, we focus on a Gut Linear Model (1-dimensional representation based on the centreline of the gut) that represents the location semantics as typically used by clinicians and pathologists when describing location in the gut. This knowledge representation is based on a set of standardised gut anatomy ontology terms describing regions in situ, such as ileum or transverse colon, and landmarks, such as ileo-caecal valve or hepatic flexure, together with relative or absolute distance measures. We show how locations in the 1D model can be mapped to and from points and regions in both a 2D model and 3D models, such as a patient's CT scan where the gut has been segmented. RESULTS The outputs of this work include 1D, 2D and 3D models of the human gut, delivered through publicly accessible Json and image files. We also illustrate the mappings between models using a demonstrator tool that allows the user to explore the anatomical space of the gut. All data and software is fully open-source and available online. CONCLUSIONS Small and large intestines have a natural "gut coordinate" system best represented as a 1D centreline through the gut tube, reflecting functional differences. Such a 1D centreline model with landmarks, visualised using viewer software allows interoperable translation to both a 2D anatomogram model and multiple 3D models of the intestines. This permits users to accurately locate samples for data comparison.
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Affiliation(s)
- Albert Burger
- Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK.
| | - Richard A. Baldock
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
| | - David J. Adams
- grid.10306.340000 0004 0606 5382Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Shahida Din
- grid.39489.3f0000 0001 0388 0742Edinburgh IBD Unit Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Irene Papatheodorou
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge, UK
| | - Michael Glinka
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
| | - Bill Hill
- grid.9531.e0000000106567444Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Derek Houghton
- grid.9531.e0000000106567444Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Mehran Sharghi
- grid.9531.e0000000106567444Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Michael Wicks
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
| | - Mark J. Arends
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
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25
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Yi Y, Zeng Y, Sam TW, Hamashima K, Tan RJR, Warrier T, Phua JX, Taneja R, Liou YC, Li H, Xu J, Loh YH. Ribosomal proteins regulate 2-cell-stage transcriptome in mouse embryonic stem cells. Stem Cell Reports 2023; 18:463-474. [PMID: 36638791 PMCID: PMC9968990 DOI: 10.1016/j.stemcr.2022.12.007] [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: 04/07/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
A rare sub-population of mouse embryonic stem cells (mESCs), the 2-cell-like cell, is defined by the expression of MERVL and 2-cell-stage-specific transcript (2C transcript). Here, we report that the ribosomal proteins (RPs) RPL14, RPL18, and RPL23 maintain the identity of mESCs and regulate the expression of 2C transcripts. Disregulation of the RPs induces DUX-dependent expression of 2C transcripts and alters the chromatin landscape. Mechanically, knockdown (KD) of RPs triggers the binding of RPL11 to MDM2, an interaction known to prevent P53 protein degradation. Increased P53 protein upon RP KD further activates its downstream pathways, including DUX. Our study delineates the critical roles of RPs in 2C transcript activation, ascribing a novel function to these essential proteins.
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Affiliation(s)
- Yao Yi
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tsz Wing Sam
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Rachel Jun Rou Tan
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Tushar Warrier
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Jun Xiang Phua
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore; Joint Center for Single Cell Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, Singapore 119077, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore.
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26
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Tribble JR, Hagström A, Jusseaume K, Lardner E, Wong RCB, Stålhammar G, Williams PA. NAD salvage pathway machinery expression in normal and glaucomatous retina and optic nerve. Acta Neuropathol Commun 2023; 11:18. [PMID: 36681854 PMCID: PMC9867855 DOI: 10.1186/s40478-023-01513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023] Open
Abstract
Glaucoma is the leading cause of irreversible blindness and is a major health and economic burden. Current treatments do not address the neurodegenerative component of glaucoma. In animal models of glaucoma, the capacity to maintain retinal nicotinamide adenine dinucleotide (NAD) pools declines early during disease pathogenesis. Treatment with nicotinamide, an NAD precursor through the NAD salvage pathway, robustly protects against neurodegeneration in a number of glaucoma models and improves vision in existing glaucoma patients. However, it remains unknown in humans what retinal cell types are able to process nicotinamide to NAD and how these are affected in glaucoma. To address this, we utilized publicly available RNA-sequencing data (bulk, single cell, and single nucleus) and antibody labelling in highly preserved enucleated human eyes to identify expression of NAD synthesizing enzyme machinery. This identifies that the neural retina favors expression of the NAD salvage pathway, and that retinal ganglion cells are particularly enriched for these enzymes. NMNAT2, a key terminal enzyme in the salvage pathway, is predominantly expressed in retinal ganglion cell relevant layers of the retina and declines in glaucoma. These findings suggest that human retinal ganglion cells can directly utilize nicotinamide and could maintain a capacity to do so in glaucoma, showing promise for ongoing clinical trials.
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Affiliation(s)
- James R Tribble
- Division of Eye and Vision, Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hagström
- Division of Eye and Vision, Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kenza Jusseaume
- Division of Eye and Vision, Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lardner
- Division of Eye and Vision, Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Raymond Ching-Bong Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery (Ophthalmology), The University of Melbourne, Melbourne, Australia
| | - Gustav Stålhammar
- Division of Eye and Vision, Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Pete A Williams
- Division of Eye and Vision, Department of Clinical Neuroscience, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden.
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27
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Wang B, Guo H, Liu D, Wu S, Liu J, Lan X, Huang H, An F, Zhu J, Ji J, Wang L, Ouyang H, Li M. ETS1-HMGA2 Axis Promotes Human Limbal Epithelial Stem Cell Proliferation. Invest Ophthalmol Vis Sci 2023; 64:12. [PMID: 36652264 PMCID: PMC9855287 DOI: 10.1167/iovs.64.1.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Purpose This study aimed to investigate the role and molecular mechanism of ETS1 in the proliferation and differentiation of human limbal epithelial stem cells (LESCs). Methods RNA-seq and quantitative real-time PCR were used to determine gene expression changes when ETS1 and HMGA2 was knocked down using short-hairpin RNAs or overexpressed by lentivirus. Immunofluorescence and flow cytometry experiments were performed to assess the roles of ETS1 and HMGA2 in LESC proliferation. ETS1-bound cis-regulatory elements and target genes in LESCs were identified using chromatin immunoprecipitation sequencing. The epigenetic features of ETS1-binding sites were assessed by the published histone modification and chromatin accessibility profiles. Results ETS1 was robustly expressed in LESCs but dramatically reduced on differentiation into corneal epithelial cells (CECs). ETS1 knockdown in LESCs inhibited cellular proliferation and activated CEC markers (KRT3, KRT12, CLU, and ALDH3A1). When ETS1 was overexpressed during CEC differentiation, LESC-associated genes were upregulated while CEC-associated genes were downregulated. The genome-wide binding profile of ETS1 was identified in LESCs. ETS1 occupied H3K4me3-marked promoters and H3K27ac/H3K4me1-marked enhancers. ETS1-binding sites were also enriched for chromatin accessibility signal. HMGA2 showed a consistent expression pattern with ETS1. ETS1 activates HMAG2 by binding to its promoter. Knockdown and overexpression experiments suggested that HMGA2 can promote LESC proliferation and inhibits its differentiation. Conclusions ETS1 promotes LESC proliferation and inhibits its differentiation via activating HMGA2.
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Affiliation(s)
- Bofeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dongmei Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xihong Lan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Fengjiao An
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jin Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jianping Ji
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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Kong S, Li R, Tian Y, Zhang Y, Lu Y, Ou Q, Gao P, Li K, Zhang Y. Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Front Genet 2023; 13:1100016. [PMID: 36685871 PMCID: PMC9846559 DOI: 10.3389/fgene.2022.1100016] [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] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.
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Affiliation(s)
- Siyuan Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
| | - Rongrong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yunhan Tian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yaqiu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuhui Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoer Ou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peiwen Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,College of Life Science and Engineering, Foshan University, Foshan, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
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Lundstrom K, Hromić-Jahjefendić A, Bilajac E, Aljabali AAA, Baralić K, Sabri NA, Shehata EM, Raslan M, Ferreira ACBH, Orlandi L, Serrano-Aroca Á, Tambuwala MM, Uversky VN, Azevedo V, Alzahrani KJ, Alsharif KF, Halawani IF, Alzahrani FM, Redwan EM, Barh D. COVID-19 signalome: Pathways for SARS-CoV-2 infection and impact on COVID-19 associated comorbidity. Cell Signal 2023; 101:110495. [PMID: 36252792 PMCID: PMC9568271 DOI: 10.1016/j.cellsig.2022.110495] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic has been the focus of research the past two years. The major breakthrough was made by discovering pathways related to SARS-CoV-2 infection through cellular interaction by angiotensin-converting enzyme (ACE2) and cytokine storm. The presence of ACE2 in lungs, intestines, cardiovascular tissues, brain, kidneys, liver, and eyes shows that SARS-CoV-2 may have targeted these organs to further activate intracellular signalling pathways that lead to cytokine release syndrome. It has also been reported that SARS-CoV-2 can hijack coatomer protein-I (COPI) for S protein retrograde trafficking to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), which, in turn, acts as the assembly site for viral progeny. In infected cells, the newly synthesized S protein in endoplasmic reticulum (ER) is transported first to the Golgi body, and then from the Golgi body to the ERGIC compartment resulting in the formation of specific a motif at the C-terminal end. This review summarizes major events of SARS-CoV-2 infection route, immune response following host-cell infection as an important factor for disease outcome, as well as comorbidity issues of various tissues and organs arising due to COVID-19. Investigations on alterations of host-cell machinery and viral interactions with multiple intracellular signaling pathways could represent a major factor in more effective disease management.
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Affiliation(s)
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka Cesta 15, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Esma Bilajac
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka Cesta 15, 71000 Sarajevo, Bosnia and Herzegovina
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, P.O. Box 566, Irbid 21163, Jordan.
| | - Katarina Baralić
- Department of Toxicology "Akademik Danilo Soldatović", University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11221 Belgrade, Serbia.
| | - Nagwa A Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo 11865, Egypt.
| | - Eslam M Shehata
- Drug Research Center, Clinical Research and Bioanalysis Department, Cairo 11865, Egypt.
| | - Mohamed Raslan
- Drug Research Center, Clinical Research and Bioanalysis Department, Cairo 11865, Egypt.
| | - Ana Cláudia B H Ferreira
- Campinas State University, Campinas, São Paulo, Brazil; University Center of Lavras (UNILAVRAS), Lavras, Minas Gerais, Brazil.
| | - Lidiane Orlandi
- University Center of Lavras (UNILAVRAS), Lavras, Minas Gerais, Brazil.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Laboratory, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain.
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Khalaf F Alsharif
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Ibrahim F Halawani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Fuad M Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
| | - Debmalya Barh
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, India.
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Deng Y, Zhang Y, Cai T, Wang Q, Zhang W, Chen Z, Luo X, Su G, Yang P. Transcriptomic profiling of iris tissue highlights LCK signaling and T cell-mediated immunity in Behcet's uveitis. J Autoimmun 2022; 133:102920. [PMID: 36191467 DOI: 10.1016/j.jaut.2022.102920] [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: 07/22/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 12/13/2022]
Abstract
Uveitis is the most common form of ocular lesions in Behcet's disease, severely affecting visual function. Molecular pathological changes of ocular lesions in patients with Behcet's uveitis (BU) are largely unknown. In this study, we performed the first comprehensive transcriptomic profiling of iris specimens from BU patients and healthy donors to provide an insight into intraocular immunopathogenesis. The mRNA sequencing identified 1633 differentially expressed genes (DEGs) between the BU group and healthy controls. GO functional enrichment analysis on DEGs showed that T cell activation was the most significantly enriched biological process. KEGG analysis of DEGs also revealed several prominently enriched T cell-related pathways, including the T cell receptor signaling pathway, Th17 cell differentiation, and Th1 and Th2 cell differentiation. The lymphocyte-specific protein tyrosine kinase (LCK) was identified as the key hub gene in the protein interaction network of DEGs. Western blot analysis further showed increased expression of active LCK in the BU group, suggesting activation of LCK signaling. Using publicly accessible single-cell RNA-sequencing data of the healthy iris, LCK was found to be expressed in clusters of activated T cells but not in other iris cell clusters, suggesting an overt association between LCK upregulation and T cell-mediated immune dysregulation. Additionally, 16 drugs were predicted to be potential inhibitors of LCK. Overall, these findings not only highlighted the central role of T cell-mediated immunity and previously unreported LCK signaling in intraocular immunopathogenesis but also revealed the potential value of LCK as a new therapeutic target for BU patients.
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Affiliation(s)
- Yang Deng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Yinan Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Tao Cai
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Qingfeng Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Wanyun Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Zhijun Chen
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Xiang Luo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China.
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31
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Sonam S, Bangru S, Perry KJ, Chembazhi UV, Kalsotra A, Henry JJ. Cellular and molecular profiles of larval and adult Xenopus corneal epithelia resolved at the single-cell level. Dev Biol 2022; 491:13-30. [PMID: 36049533 PMCID: PMC10241109 DOI: 10.1016/j.ydbio.2022.08.007] [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: 01/20/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022]
Abstract
Corneal Epithelial Stem Cells (CESCs) and their proliferative progeny, the Transit Amplifying Cells (TACs), are responsible for homeostasis and maintaining corneal transparency. Owing to our limited knowledge of cell fates and gene activity within the cornea, the search for unique markers to identify and isolate these cells remains crucial for ocular surface reconstruction. We performed single-cell RNA sequencing of corneal cells from larval and adult stages of Xenopus. Our results indicate that as the cornea develops and matures, there is an increase in cellular diversity, which is accompanied by a substantial shift in transcriptional profile, gene regulatory network and cell-cell communication dynamics. Our data also reveals several novel genes expressed in corneal cells and changes in gene expression during corneal differentiation at both developmental time-points. Importantly, we identify specific basal cell clusters in both the larval and adult cornea that comprise a relatively undifferentiated cell type and express distinct stem cell markers, which we propose are the putative larval and adult CESCs, respectively. This study offers a detailed atlas of single-cell transcriptomes in the frog cornea. In the future, this work will be useful to elucidate the function of novel genes in corneal epithelial homeostasis, wound healing and regeneration.
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Affiliation(s)
- Surabhi Sonam
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA
| | - Kimberly J Perry
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Ullas V Chembazhi
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA.
| | - Jonathan J Henry
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, USA.
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32
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Gül FC, Timurkaan ES. Evaluation of choroidal thickness with OCT in COVID-19 patients with high D-dimer levels. Sci Rep 2022; 12:16826. [PMID: 36258025 PMCID: PMC9579170 DOI: 10.1038/s41598-022-21579-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022] Open
Abstract
To evaluate retinal and choroidal thickness with optical coherence tomography (OCT) to detect retinal and choroidal pathologies in coronavirus disease 2019 (COVID-19) patients with high D-dimer levels. Thirty patients who were hospitalized in the intensive care unit due to severe acute respiratory syndrome coronavirus 2 and whose D-dimer levels were high during this period, who applied to the internal medicine outpatient clinic between 15 and 30 days after discharge, and 30 healthy volunteers with similar age and gender as the control group was included in the study. After full ophthalmological examination, central foveal and choroidal thicknesses were evaluated using optical coherence tomography. Statistical analysis of the study data demonstrated that there was no significant difference between the groups in terms of age or gender (p > 0.05). There was also no statistically significant difference between the groups in terms of central foveal thickness, central choroidal thickness, or nasal 500, nasal 1500, temporal 500, or temporal 500 micron distances (p > 0.05 for all parameters). Choroidal and retinal vascular thicknesses were not affected in the short term in COVID-19 patients hospitalized in the intensive care unit.
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Affiliation(s)
- Fatih Cem Gül
- Universal Eye Center, Ophthalmology Clinic, Elazig, Turkey.
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33
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Mulfaul K, Russell JF, Voigt AP, Stone EM, Tucker BA, Mullins RF. The Essential Role of the Choriocapillaris in Vision: Novel Insights from Imaging and Molecular Biology. Annu Rev Vis Sci 2022; 8:33-52. [PMID: 36108103 PMCID: PMC9668353 DOI: 10.1146/annurev-vision-100820-085958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
The choriocapillaris, a dense capillary network located at the posterior pole of the eye, is essential for supporting normal vision, supplying nutrients, and removing waste products from photoreceptor cells and the retinal pigment epithelium. The anatomical location, heterogeneity, and homeostatic interactions with surrounding cell types make the choroid complex to study both in vivo and in vitro. Recent advances in single-cell RNA sequencing, in vivo imaging, and in vitro cell modeling are vastly improving our knowledge of the choroid and its role in normal health and in age-related macular degeneration (AMD). Histologically, loss of endothelial cells (ECs) of the choriocapillaris occurs early in AMD concomitant with elevated formation of the membrane attack complex of complement. Advanced imaging has allowed us to visualize early choroidal blood flow changes in AMD in living patients, supporting histological findings of loss of choroidal ECs. Single-cell RNA sequencing is being used to characterize choroidal cell types transcriptionally and discover their altered patterns of gene expression in aging and disease. Advances in induced pluripotent stem cell protocols and 3D cultures will allow us to closely mimic the in vivo microenvironment of the choroid in vitro to better understand the mechanism leading to choriocapillaris loss in AMD.
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Affiliation(s)
- Kelly Mulfaul
- Department of Ophthalmology and Visual Sciences and the Institute for Vision Research, The University of Iowa, Iowa City, Iowa, USA;
| | - Jonathan F Russell
- Department of Ophthalmology and Visual Sciences and the Institute for Vision Research, The University of Iowa, Iowa City, Iowa, USA;
| | - Andrew P Voigt
- Department of Ophthalmology and Visual Sciences and the Institute for Vision Research, The University of Iowa, Iowa City, Iowa, USA;
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences and the Institute for Vision Research, The University of Iowa, Iowa City, Iowa, USA;
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences and the Institute for Vision Research, The University of Iowa, Iowa City, Iowa, USA;
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences and the Institute for Vision Research, The University of Iowa, Iowa City, Iowa, USA;
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34
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Lambert P, de Bodt C, Verleysen M, Lee JA. SQuadMDS: A lean Stochastic Quartet MDS improving global structure preservation in neighbor embedding like t-SNE and UMAP. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2022.06.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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35
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Suo L, Dai W, Qin X, Li G, Zhang D, Cheng T, Yao T, Zhang C. Screening of primary open-angle glaucoma diagnostic markers based on immune-related genes and immune infiltration. BMC Genom Data 2022; 23:67. [PMID: 36002796 PMCID: PMC9400315 DOI: 10.1186/s12863-022-01072-8] [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: 04/01/2022] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Primary open-angle glaucoma (POAG) continues to be a poorly understood disease. Although there were multiple researches on the identification of POAG biomarkers, few studies systematically revealed the immune-related cells and immune infiltration of POAG. Bioinformatics analyses of optic nerve (ON) and trabecular meshwork (TM) gene expression data were performed to further elucidate the immune-related genes of POAG and identify candidate target genes for treatment.
Methods
We performed a gene analysis of publicly available microarray data, namely, the GSE27276-GPL2507, GSE2378-GPL8300, GSE9944-GPL8300, and GSE9944-GPL571 datasets from the Gene Expression Omnibus database. The obtained datasets were used as input for parallel pathway analyses. Based on random forest and support vector machine (SVM) analysis to screen the key genes, significantly changed pathways were clustered into functional categories, and the results were further investigated. CIBERSORT was used to evaluate the infiltration of immune cells in POAG tissues. A network visualizing the differences between the data in the POAG and normal groups was created. GO and KEGG enrichment analyses were performed using the Metascape database. We divided the differentially expressed mRNAs into upregulated and downregulated groups and predicted the drug targets of the differentially expressed genes through the Connectivity Map (CMap) database.
Results
A total of 49 differentially expressed genes, including 19 downregulated genes and 30 upregulated genes, were detected. Five genes ((Keratin 14) KRT14, (Hemoglobin subunit beta) HBB, (Acyl-CoA Oxidase 2) ACOX2, (Hephaestin) HEPH and Keratin 13 (KRT13)) were significantly changed. The results showed that the expression profiles of drug disturbances, including those for avrainvillamide-analysis-3, cytochalasin-D, NPI-2358, oxymethylone and vinorelbine, were negatively correlated with the expression profiles of disease disturbances. This finding indicated that these drugs may reduce or even reverse the POAG disease state.
Conclusion
This study provides an overview of the processes involved in the molecular pathogenesis of POAG in the ON and TM. The findings provide a new understanding of the molecular mechanism of POAG from the perspective of immunology.
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van den Bosch QCC, Nguyen JQN, Brands T, van den Bosch TPP, Verdijk RM, Paridaens D, Naus NC, de Klein A, Kiliç E, Brosens E. FOXD1 Is a Transcription Factor Important for Uveal Melanocyte Development and Associated with High-Risk Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14153668. [PMID: 35954332 PMCID: PMC9367502 DOI: 10.3390/cancers14153668] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Despite successful treatment of primary uveal melanoma (UM), metastases still occur in approximately 50% of the patients. Unfortunately, little is known about the mechanism behind metastasized UM. By reanalyzing publicly available single-cell RNA sequencing data of embryonic zebrafish larvae and validating the results with UM data, we have identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. The most significant finding is FOXD1, which is nearly exclusively expressed in high-risk UM and is associated with poor survival. FOXD1 is a novel gene which could be involved in the metastatic capability of UM. Elucidating its function and role in metastatic UM could help to understand and develop treatment for UM. Abstract Uveal melanoma (UM) is a deadly ocular malignancy, originating from uveal melanocytes. Although much is known regarding prognostication in UM, the exact mechanism of metastasis is mostly unknown. Metastatic tumor cells are known to express a more stem-like RNA profile which is seen often in cell-specific embryonic development to induce tumor progression. Here, we identified novel transcription regulators by reanalyzing publicly available single cell RNA sequencing experiments. We identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. Our most significant finding is FOXD1, as this gene is nearly exclusively expressed in high-risk UM and its expression is associated with a poor prognosis. Even within the BAP1-mutated UM, the expression of FOXD1 is correlated with poor survival. FOXD1 is a novel factor which could potentially be involved in the metastatic capacity of high-risk UM. Elucidating the function of FOXD1 in UM could provide insight into the malignant transformation of uveal melanocytes, especially in high-risk UM.
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Affiliation(s)
- Quincy C. C. van den Bosch
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Thierry P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dion Paridaens
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
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van Zyl T, Yan W, McAdams AM, Monavarfeshani A, Hageman GS, Sanes JR. Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types. Proc Natl Acad Sci U S A 2022; 119:e2200914119. [PMID: 35858321 PMCID: PMC9303934 DOI: 10.1073/pnas.2200914119] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
The anterior segment of the eye consists of the cornea, iris, ciliary body, crystalline lens, and aqueous humor outflow pathways. Together, these tissues are essential for the proper functioning of the eye. Disorders of vision have been ascribed to defects in all of them; some disorders, including glaucoma and cataract, are among the most prevalent causes of blindness in the world. To characterize the cell types that compose these tissues, we generated an anterior segment cell atlas of the human eye using high-throughput single-nucleus RNA sequencing (snRNAseq). We profiled 195,248 nuclei from nondiseased anterior segment tissues of six human donors, identifying >60 cell types. Many of these cell types were discrete, whereas others, especially in the lens and cornea, formed continua corresponding to known developmental transitions that persist in adulthood. Having profiled each tissue separately, we performed an integrated analysis of the entire anterior segment, revealing that some cell types are unique to a single structure, whereas others are shared across tissues. The integrated cell atlas was then used to investigate cell type-specific expression patterns of more than 900 human ocular disease genes identified through either Mendelian inheritance patterns or genome-wide association studies.
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Affiliation(s)
- Tavé van Zyl
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Alexi M. McAdams
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Aboozar Monavarfeshani
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Boston Children’s Hospital, F.M. Kirby Neurobiology Center, Boston, MA 02115
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84132
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132
| | - Joshua R. Sanes
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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38
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Correia C, Weiskittel TM, Ung CY, Villasboas Bisneto JC, Billadeau DD, Kaufmann SH, Li H. Uncovering Pharmacological Opportunities for Cancer Stem Cells-A Systems Biology View. Front Cell Dev Biol 2022; 10:752326. [PMID: 35359437 PMCID: PMC8962639 DOI: 10.3389/fcell.2022.752326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/10/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer stem cells (CSCs) represent a small fraction of the total cancer cell population, yet they are thought to drive disease propagation, therapy resistance and relapse. Like healthy stem cells, CSCs possess the ability to self-renew and differentiate. These stemness phenotypes of CSCs rely on multiple molecular cues, including signaling pathways (for example, WNT, Notch and Hedgehog), cell surface molecules that interact with cellular niche components, and microenvironmental interactions with immune cells. Despite the importance of understanding CSC biology, our knowledge of how neighboring immune and tumor cell populations collectively shape CSC stemness is incomplete. Here, we provide a systems biology perspective on the crucial roles of cellular population identification and dissection of cell regulatory states. By reviewing state-of-the-art single-cell technologies, we show how innovative systems-based analysis enables a deeper understanding of the stemness of the tumor niche and the influence of intratumoral cancer cell and immune cell compositions. We also summarize strategies for refining CSC systems biology, and the potential role of this approach in the development of improved anticancer treatments. Because CSCs are amenable to cellular transitions, we envision how systems pharmacology can become a major engine for discovery of novel targets and drug candidates that can modulate state transitions for tumor cell reprogramming. Our aim is to provide deeper insights into cancer stemness from a systems perspective. We believe this approach has great potential to guide the development of more effective personalized cancer therapies that can prevent CSC-mediated relapse.
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Affiliation(s)
- Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Taylor M Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | | | - Daniel D Billadeau
- Department of Immunology, Mayo Clinic, Rochester, MN, United States,Division of Oncology Research, Mayo Clinic, Rochester, MN, United States
| | - Scott H Kaufmann
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, United States,Division of Oncology Research, Mayo Clinic, Rochester, MN, United States
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,*Correspondence: Hu Li,
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