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Balasubramanian R, Kizhatil K, Li T, Tolman N, Bhandari A, Clark G, Bupp-Chickering V, Kelly RA, Zhou S, Peregrin J, Simón M, Montgomery C, Stamer WD, Qian J, John SWM. Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.31.555823. [PMID: 37886472 PMCID: PMC10602040 DOI: 10.1101/2023.08.31.555823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Schlemm's canal (SC) is central in intraocular pressure regulation but requires much characterization. It has distinct inner and outer walls, each composed of Schlemm's canal endothelial cells (SECs) with different morphologies and functions. Recent transcriptomic studies of the anterior segment added important knowledge, but were limited in power by SEC numbers or did not focus on SC. To gain a more comprehensive understanding of SC biology, we performed bulk RNA sequencing on C57BL/6J SC, blood vessel, and lymphatic endothelial cells from limbal tissue (∼4500 SECs). We also analyzed mouse limbal tissues by single-cell and single-nucleus RNA sequencing (C57BL/6J and 129/Sj strains), successfully sequencing 903 individual SECs. Together, these datasets confirm that SC has molecular characteristics of both blood and lymphatic endothelia with a lymphatic phenotype predominating. SECs are enriched in pathways that regulate cell-cell junction formation pointing to the importance of junctions in determining SC fluid permeability. Importantly, and for the first time, our analyses characterize 3 molecular classes of SECs, molecularly distinguishing inner wall from outer wall SECs and discovering two inner wall cell states that likely result from local environmental differences. Further, and based on ligand and receptor expression patterns, we document key interactions between SECs and cells of the adjacent trabecular meshwork (TM) drainage tissue. Also, we present cell type expression for a collection of human glaucoma genes. These data provide a new molecular foundation that will enable the functional dissection of key homeostatic processes mediated by SECs as well as the development of new glaucoma therapeutics. Significance statement Schlemm's canal is a critical ocular drainage structure that maintains intraocular pressure with important consequences for glaucoma. Despite this, Schlemm's canal has been relatively understudied with the molecular process that mediate its function, maintain its health, or that are compromised in glaucoma needing much deeper characterization. This study is important as it provides the most comprehensive molecular characterization of Schlemm's canal cells to date providing a wealth of molecular details. In addition to highlighting important biological pathways, this information will guide studies to develop new treatments against glaucoma.
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Upreti A, Padula SL, Weaver JM, Wagner BD, Kneller AM, Petulla AL, Lachke SA, Robinson ML. A Transcriptomics Analysis of the Regulation of Lens Fiber Cell Differentiation in the Absence of FGFRs and PTEN. Cells 2024; 13:1222. [PMID: 39056803 PMCID: PMC11274593 DOI: 10.3390/cells13141222] [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: 04/24/2024] [Revised: 06/28/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Adding 50% vitreous humor to the media surrounding lens explants induces fiber cell differentiation and a significant immune/inflammatory response. While Fgfr loss blocks differentiation in lens epithelial explants, this blockage is partially reversed by deleting Pten. To investigate the functions of the Fgfrs and Pten during lens fiber cell differentiation, we utilized a lens epithelial explant system and conducted RNA sequencing on vitreous humor-exposed explants lacking Fgfrs, or Pten or both Fgfrs and Pten. We found that Fgfr loss impairs both vitreous-induced differentiation and inflammation while the additional loss of Pten restores these responses. Furthermore, transcriptomic analysis suggested that PDGFR-signaling in FGFR-deficient explants is required to mediate the rescue of vitreous-induced fiber differentiation in explants lacking both Fgfrs and Pten. The blockage of β-crystallin induction in explants lacking both Fgfrs and Pten in the presence of a PDGFR inhibitor supports this hypothesis. Our findings demonstrate that a wide array of genes associated with fiber cell differentiation are downstream of FGFR-signaling and that the vitreous-induced immune responses also depend on FGFR-signaling. Our data also demonstrate that many of the vitreous-induced gene-expression changes in Fgfr-deficient explants are rescued in explants lacking both Fgfrs and Pten.
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Affiliation(s)
- Anil Upreti
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA; (A.U.); (S.L.P.); (J.M.W.)
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA; (B.D.W.); (A.M.K.); (A.L.P.)
| | - Stephanie L. Padula
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA; (A.U.); (S.L.P.); (J.M.W.)
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA; (B.D.W.); (A.M.K.); (A.L.P.)
| | - Jacob M. Weaver
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA; (A.U.); (S.L.P.); (J.M.W.)
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA; (B.D.W.); (A.M.K.); (A.L.P.)
| | - Brad D. Wagner
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA; (B.D.W.); (A.M.K.); (A.L.P.)
| | - Allison M. Kneller
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA; (B.D.W.); (A.M.K.); (A.L.P.)
| | - Anthony L. Petulla
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA; (B.D.W.); (A.M.K.); (A.L.P.)
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Michael L. Robinson
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA; (A.U.); (S.L.P.); (J.M.W.)
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA; (B.D.W.); (A.M.K.); (A.L.P.)
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Lin JB, Pepple KL, Concepcion C, Korshunova Y, Paley MA, Paley GL, Laurent J, Apte RS, Hassman LM. Aqueous Macrophages Contribute to Conserved CCL2 and CXCL10 Gradients in Uveitis. OPHTHALMOLOGY SCIENCE 2024; 4:100453. [PMID: 38650614 PMCID: PMC11033188 DOI: 10.1016/j.xops.2023.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 04/25/2024]
Abstract
Purpose Uveitis is a heterogenous group of inflammatory eye disease for which current cytokine-targeted immune therapies are effective for only a subset of patients. We hypothesized that despite pathophysiologic nuances that differentiate individual disease states, all forms of eye inflammation might share common mechanisms for immune cell recruitment. Identifying these mechanisms is critical for developing novel, broadly acting therapeutic strategies. Design Experimental study. Subjects Biospecimens from patients with active or inactive uveitis and healthy controls. Methods Protein concentration and single cell gene expression were assessed in aqueous fluid biopsies and plasma samples from deidentified patients with uveitis or healthy controls. Main Outcome Measures The concentration of 31 inflammatory proteins was measured in all aqueous samples, as well as plasma samples from patients with active uveitis. Chemokine and cytokine ligand and receptor expression were assessed in individual cell types from aqueous biopsies obtained from patients with active uveitis. Results We identified 6 chemokines that were both elevated in active uveitis compared with controls and enriched in aqueous compared with plasma during active uveitis (C-C motif chemokine ligand [CCL]2, C-X-C motif chemokine ligand [CXCL]10, CXCL9, CXCL8, CCL3, and CCL14), forming potential gradients for migration of immune cells from the blood to the eye. Of these, CCL2 and CXCL10 were consistently enriched in the aqueous of all patients in our cohort, as well as in a larger cohort of patients from a previously published study. These data suggest that CCL2 and CXCL10 are key mediators in immune cell migration to the eye during uveitis. Next, single cell RNA sequencing suggested that macrophages contribute to aqueous enrichment of CCL2 and CXCL10 during human uveitis. Finally, using chemokine ligand and receptor expression mapping, we identified a broad signaling network for macrophage-derived CCL2 and CXCL10 in human uveitis. Conclusions These data suggest that ocular macrophages may play a central role, via CCL2 and CXCL10 production, in recruiting inflammatory cells to the eye in patients with uveitis. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Joseph B. Lin
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
- Neurosciences Graduate Program, Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Kathryn L. Pepple
- Department of Ophthalmology, Roger and Angie Karalis Johnson Retina Center, University of Washington, Seattle, Washington
| | - Christian Concepcion
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Yulia Korshunova
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Michael A. Paley
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Grace L. Paley
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer Laurent
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Rajendra S. Apte
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Lynn M. Hassman
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
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Sun W, Xiong D, Ouyang J, Xiao X, Jiang Y, Wang Y, Li S, Xie Z, Wang J, Tang Z, Zhang Q. Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia. Nat Commun 2024; 15:5048. [PMID: 38871723 DOI: 10.1038/s41467-024-49376-w] [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: 06/06/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
Despite the advent of genomic sequencing, molecular diagnosis remains unsolved in approximately half of patients with Mendelian disorders, largely due to unclarified functions of noncoding regions and the difficulty in identifying complex structural variations. In this study, we map a unique form of central iris hypoplasia in a large family to 6q15-q23.3 and 18p11.31-q12.1 using a genome-wide linkage scan. Long-read sequencing reveals a balanced translocation t(6;18)(q22.31;p11.22) with intergenic breakpoints. By performing Hi-C on induced pluripotent stem cells from a patient, we identify two chromatin topologically associating domains spanning across the breakpoints. These alterations lead the ectopic chromatin interactions between APCDD1 on chromosome 18 and enhancers on chromosome 6, resulting in upregulation of APCDD1. Notably, APCDD1 is specifically localized in the iris of human eyes. Our findings demonstrate that noncoding structural variations can lead to Mendelian diseases by disrupting the 3D genome structure and resulting in altered gene expression.
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Affiliation(s)
- Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Shiqiang 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
| | - Ziying Xie
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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Takezawa Y, Kamon M, Hiraki-Kamon K, Mitani A, Shiraishi A, Kato H. Experimental interventions attenuate a conjunctival epidermal metaplasia model. Exp Eye Res 2024; 243:109916. [PMID: 38679224 DOI: 10.1016/j.exer.2024.109916] [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: 12/01/2023] [Revised: 01/22/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
The conjunctiva is a non-keratinized, stratified columnar epithelium with characteristics different from the cornea and eyelid epidermis. From development to adulthood, a distinguishing feature of ocular versus epidermal epithelia is the expression of the master regulator PAX6. A conditionally immortalized conjunctival epithelial cell line (iHCjEC) devoid of stromal or immune cells established in our laboratory spontaneously manifested epidermal metaplasia and upregulated expression of the keratinization-related genes SPRR1A/B and the epidermal cytokeratins KRT1 and KRT10 at the expense of the conjunctival trait. In addition, iHCjEC indicated a significant decrease in PAX6 expression. Dry eye syndrome (DES) and severe ocular surface diseases, such as Sjögren's syndrome and Stevens-Johnson syndrome, cause the keratinization of the entire ocular surface epithelia. We used iHCjECs as a conjunctiva epidermal metaplasia model to test PAX6, serum, and glucocorticoid interventions. Reintroducing PAX6 to iHCjECs resulted in upregulating genes related to cell adhesion and tight junctions, including MIR200CHG and CLDN1. The administration of glucocorticoids or serum resulted in the downregulation of epidermal genes (DSG1, SPRR1A/B, and KRT1) and partially corrected epidermal metaplasia. Our results using an isolated conjunctival epidermal metaplasia model point toward the possibility of rationally "repurposing" clinical interventions, such as glucocorticoid, serum, or PAX6 administration, for treating epidermal metaplasia of the conjunctiva.
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Affiliation(s)
- Yuki Takezawa
- Department of Ophthalmology, Graduate School of Medicine, Ehime University, Toon, Japan.
| | - Masayoshi Kamon
- Department of Developmental Biology and Functional Genomics, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Keiko Hiraki-Kamon
- Department of Developmental Biology and Functional Genomics, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Arisa Mitani
- Department of Ophthalmology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Atsushi Shiraishi
- Department of Ophthalmology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Hidemasa Kato
- Department of Developmental Biology and Functional Genomics, Graduate School of Medicine, Ehime University, Toon, Japan.
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Amirkashani D, Talebi S, Vafaei shahi M, Zekri A, Abdi P, Mehramiz M. Pseudodendritic keratitis in citrullinemia; a report of an unusual and novel ocular finding in this metabolic disorder. Am J Ophthalmol Case Rep 2024; 34:102044. [PMID: 38601192 PMCID: PMC11004497 DOI: 10.1016/j.ajoc.2024.102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Purpose To report a 15 year old girl with citrullinemia type 1 and 2 accompanied by neurologic signs and symptoms and a novel ocular complaint in cornea like tyrosinemia type 2. Observations A 15 year old female was admitted with decreased consciousness and neurologic signs and symptoms. Citrulinemia was discovered through metabolic testing. Later genetic studies revealed mutations in both ASS1 and SLC25A13 genes. Two years after the first presentation, the patient was re-admitted with complaints of bilateral photophobia and tearing. Biomicroscopic examination revealed bilateral corneal haziness with pseudodendritic lesions like tyrosinemia type 2 that were subsided with protein restriction and the use of urea cycle disease (UCD) formula. Conclusions and importance Citrullinemia is the inherited autosomal recessive disorder of urea cycle that leads to ammonia and accumulation of other toxic substances in the blood. Two types of Citrullinemia have been defined. Citrullinemia type 1, caused by deficiency or reduction in argininosuccinate synthetase enzyme activity due to damaging mutation in ASS1 gene. Citrullinemia type 2 as another subtype is caused by the absence or dysfunction of the mitochondrial membrane carrier protein (SLC25A13), also called CITRIN. Pseudodendritic keratitis is a rare condition that may be seen with tyrosinemia type 2. The association of this ocular complaint with citrullinemia has not been described previously. Awareness of this phenomenon may improve the diagnosis and management of citrullinemia patients.
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Affiliation(s)
- Davoud Amirkashani
- Department of Pediatric Endocrinology, Aliasghar Children's Hospital, Aliasghar Clinical Research Development Center, Iran University of Medical Sciences, Tehran, Iran
| | - Saeid Talebi
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vafaei shahi
- Pediatric Growth and Development Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Zekri
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Parisa Abdi
- Translational Ophthalmology Research Center (TORC), Farabi Eye Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdokht Mehramiz
- Department of Pediatric Endocrinology, Aliasghar Children's Hospital, Aliasghar Clinical Research Development Center, Iran University of Medical Sciences, Tehran, Iran
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Koçak G, Uyulgan S, Polatlı E, Sarı V, Kahveci B, Bursali A, Binokay L, Reçber T, Nemutlu E, Mardinoğlu A, Karakülah G, Utine CA, Güven S. Generation of Anterior Segment of the Eye Cells from hiPSCs in Microfluidic Platforms. Adv Biol (Weinh) 2024; 8:e2400018. [PMID: 38640945 DOI: 10.1002/adbi.202400018] [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: 01/10/2024] [Revised: 03/10/2024] [Indexed: 04/21/2024]
Abstract
Ophthalmic diseases affect many people, causing partial or total loss of vision and a reduced quality of life. The anterior segment of the eye accounts for nearly half of all visual impairment that can lead to blindness. Therefore, there is a growing demand for ocular research and regenerative medicine that specifically targets the anterior segment to improve vision quality. This study aims to generate a microfluidic platform for investigating the formation of the anterior segment of the eye derived from human induced pluripotent stem cells (hiPSC) under various spatial-mechanoresponsive conditions. Microfluidic platforms are developed to examine the effects of dynamic conditions on the generation of hiPSCs-derived ocular organoids. The differentiation protocol is validated, and mechanoresponsive genes are identified through transcriptomic analysis. Several culture strategies is implemented for the anterior segment of eye cells in a microfluidic chip. hiPSC-derived cells showed anterior eye cell characteristics in mRNA and protein expression levels under dynamic culture conditions. The expression levels of yes-associated protein and transcriptional coactivator PDZ binding motif (YAP/TAZ) and PIEZO1, varied depending on the differentiation and growth conditions of the cells, as well as the metabolomic profiles under dynamic culture conditions.
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Affiliation(s)
- Gamze Koçak
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Sude Uyulgan
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Elifsu Polatlı
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Vedat Sarı
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Burak Kahveci
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Ahmet Bursali
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
| | - Leman Binokay
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Tuba Reçber
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara, 06100, Türkiye
| | - Emirhan Nemutlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara, 06100, Türkiye
| | - Adil Mardinoğlu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Canan Aslı Utine
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Department of Ophthalmology, Dokuz Eylül University Hospital, Dokuz Eylül University, Izmir, 35340, Türkiye
| | - Sinan Güven
- Izmir Biomedicine and Genome Center, Izmir, 35340, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, 35340, Türkiye
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, Izmir, 35340, Türkiye
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Cui W, Chen S, Hu T, Zhou T, Qiu C, Jiang L, Cheng X, Ji J, Yao K, Han H. Nanoceria-Mediated Cyclosporin A Delivery for Dry Eye Disease Management through Modulating Immune-Epithelial Crosstalk. ACS NANO 2024; 18:11084-11102. [PMID: 38632691 DOI: 10.1021/acsnano.3c11514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Dry eye disease (DED) affects a substantial worldwide population with increasing frequency. Current single-targeting DED management is severely hindered by the existence of an oxidative stress-inflammation vicious cycle and complicated intercellular crosstalk within the ocular microenvironment. Here, a nanozyme-based eye drop, namely nanoceria loading cyclosporin A (Cs@P/CeO2), is developed, which possesses long-term antioxidative and anti-inflammatory capacities due to its regenerative antioxidative activity and sustained release of cyclosporin A (CsA). In vitro studies showed that the dual-functional Cs@P/CeO2 not only inhibits cellular reactive oxygen species production, sequentially maintaining mitochondrial integrity, but also downregulates inflammatory processes and repolarizes macrophages. Moreover, using flow cytometric and single-cell sequencing data, the in vivo therapeutic effect of Cs@P/CeO2 was systemically demonstrated, which rebalances the immune-epithelial communication in the corneal microenvironment with less inflammatory macrophage polarization, restrained oxidative stress, and enhanced epithelium regeneration. Collectively, our data proved that the antioxidative and anti-inflammatory Cs@P/CeO2 may provide therapeutic insights into DED management.
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Affiliation(s)
- Wenyu Cui
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Sheng Chen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, P. R. China
| | - Tianyi Hu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, P. R. China
| | - Tinglian Zhou
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Chen Qiu
- MOE Laboratory of Biosystems Homeostasis & Protection and iCell Biotechnology Regenerative Biomedicine Laboratory of College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Luyang Jiang
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Xiaoyu Cheng
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ke Yao
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
| | - Haijie Han
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou 310009, P. R. China
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9
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Liu Z, Liu K, Shi S, Chen X, Gu X, Wang W, Mao K, Yibulayi R, Wu W, Zeng L, Zhou W, Lin X, Zhang F, Lou B. Alkali injury-induced pathological lymphangiogenesis in the iris facilitates the infiltration of T cells and ocular inflammation. JCI Insight 2024; 9:e175479. [PMID: 38587075 PMCID: PMC11128208 DOI: 10.1172/jci.insight.175479] [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: 09/05/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
Inflammatory lymphangiogenesis is intimately linked to immune regulation and tissue homeostasis. However, current evidence has suggested that classic lymphatic vessels are physiologically absent in intraocular structures. Here, we show that neolymphatic vessels were induced in the iris after corneal alkali injury (CAI) in a VEGFR3-dependent manner. Cre-loxP-based lineage tracing revealed that these lymphatic endothelial cells (LECs) originate from existing Prox1+ lymphatic vessels. Notably, the ablation of iridial lymphangiogenesis via conditional deletion of VEGFR3 alleviated the ocular inflammatory response and pathological T cell infiltration. Our findings demonstrate that iridial neolymphatics actively participate in pathological immune responses following injury and suggest intraocular lymphangiogenesis as a valuable therapeutic target for the treatment of ocular inflammation.
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Affiliation(s)
- Zheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Keli Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shunhua Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xun Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xinyu Gu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Weifa Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Keli Mao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Rukeye Yibulayi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wanwen Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Lei Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Weibin Zhou
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Feng Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Bingsheng Lou
- 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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10
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Ghosh S, Herberg S. ECM biomaterials for modeling of outflow cell biology in health and disease. BIOMATERIALS AND BIOSYSTEMS 2024; 13:100091. [PMID: 38528909 PMCID: PMC10961487 DOI: 10.1016/j.bbiosy.2024.100091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/18/2024] [Accepted: 03/01/2024] [Indexed: 03/27/2024] Open
Abstract
This review highlights the importance of extracellular matrix (ECM) biomaterials in understanding the biology of human trabecular meshwork (TM) and Schlemm's canal (SC) cells under normal and simulated glaucoma-like conditions. We provide an overview of recent progress in the development and application of state-of-the-art 3D ECM biomaterials including cell-derived ECM, ECM scaffolds, Matrigel, and ECM hydrogels for studies of TM and SC cell (patho)biology. Such bioengineered platforms enable accurate and reliable modeling of tissue-like cell-cell and cell-ECM interactions. They bridge the gap between conventional 2D approaches and in vivo/ex vivo models, and have the potential to aid in the identification of the causal mechanism(s) for outflow dysfunction in ocular hypertensive glaucoma. We discuss each model's benefits and limitations, and close with an outlook on future directions.
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Affiliation(s)
- Souvik Ghosh
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Samuel Herberg
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
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11
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Zhang Y, Deng Y, Jing S, Su G, Li N, Huang Z, Zhang W, Chen Z, Yang P. Proteomic profiling of aqueous humor-derived exosomes in Vogt-Koyanagi-Harada disease and Behcet's uveitis. Clin Immunol 2024; 259:109895. [PMID: 38185270 DOI: 10.1016/j.clim.2024.109895] [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: 09/26/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Vogt-Koyanagi-Harada (VKH) disease and Behcet's uveitis (BU) are the two major vision-threatening uveitis entities. This study performed the first label-free quantitative proteomics on aqueous humor-derived exosomes from 84 patients with VKH or BU to determine their potential roles. Sixty-five differentially expressed proteins (DEPs) and 40 DEPs were detected in the VKH and BU groups, respectively. GO and KEGG analysis showed that DEPs were mainly enriched in the complement-related pathways. The complement C1q subcomponent subunit B (C1QB) was identified as a key exosomal protein, and its expression was significantly increased by western blotting in both diseases. Additionally, the integrated analysis based on the published scRNA-seq data showed that C1QB-containing exosomes were mainly produced by mononuclear macrophages in the anterior segment tissue. Overall, our proteomic profiling highlights that complement-related pathways may be actively involved in the pathogenesis of these two diseases. These pathways may also serve as treatment targets for both diseases.
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Affiliation(s)
- Yinan Zhang
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Yang Deng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Shixiang Jing
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Na Li
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China
| | - Ziqian Huang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Wanyun Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Zhijun Chen
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Peizeng Yang
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China; The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China.
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12
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Mah JL, Dunn CW. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nat Ecol Evol 2024; 8:325-338. [PMID: 38182680 DOI: 10.1038/s41559-023-02281-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/16/2023] [Indexed: 01/07/2024]
Abstract
The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons because we lack approaches to build cell phylogenies using model-based approaches. Here we approach the challenges of applying explicit phylogenetic methods to single-cell data by using principal components as phylogenetic characters. We infer a cell phylogeny from a large, comparative single-cell dataset of eye cells from five distantly related mammals. Robust cell type clades enable us to provide a phylogenetic, rather than phenetic, definition of cell type, allowing us to forgo marker genes and phylogenetically classify cells by topology. We further observe evolutionary relationships between diverse vessel endothelia and identify the myelinating and non-myelinating Schwann cells as sister cell types. Finally, we examine principal component loadings and describe the gene expression dynamics underlying the function and identity of cell type clades that have been conserved across the five species. A cell phylogeny provides a rigorous framework towards investigating the evolutionary history of cells and will be critical to interpret comparative single-cell datasets that aim to ask fundamental evolutionary questions.
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Affiliation(s)
- Jasmine L Mah
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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13
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Hamel AR, Yan W, Rouhana JM, Monovarfeshani A, Jiang X, Mehta PA, Advani J, Luo Y, Liang Q, Rajasundaram S, Shrivastava A, Duchinski K, Mantena S, Wang J, van Zyl T, Pasquale LR, Swaroop A, Gharahkhani P, Khawaja AP, MacGregor S, Chen R, Vitart V, Sanes JR, Wiggs JL, Segrè AV. Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma. Nat Commun 2024; 15:396. [PMID: 38195602 PMCID: PMC10776627 DOI: 10.1038/s41467-023-44380-y] [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: 05/11/2022] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
Primary open-angle glaucoma (POAG), characterized by retinal ganglion cell death, is a leading cause of irreversible blindness worldwide. However, its molecular and cellular causes are not well understood. Elevated intraocular pressure (IOP) is a major risk factor, but many patients have normal IOP. Colocalization and Mendelian randomization analysis of >240 POAG and IOP genome-wide association study (GWAS) loci and overlapping expression and splicing quantitative trait loci (e/sQTLs) in 49 GTEx tissues and retina prioritizes causal genes for 60% of loci. These genes are enriched in pathways implicated in extracellular matrix organization, cell adhesion, and vascular development. Analysis of single-nucleus RNA-seq of glaucoma-relevant eye tissues reveals that the POAG and IOP colocalizing genes and genome-wide associations are enriched in specific cell types in the aqueous outflow pathways, retina, optic nerve head, peripapillary sclera, and choroid. This study nominates IOP-dependent and independent regulatory mechanisms, genes, and cell types that may contribute to POAG pathogenesis.
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Affiliation(s)
- Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Wenjun Yan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - John M Rouhana
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aboozar Monovarfeshani
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Xinyi Jiang
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MA, USA
| | - Yuyang Luo
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Qingnan Liang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Skanda Rajasundaram
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Centre for Evidence-Based Medicine, University of Oxford, Oxford, UK
- Faculty of Medicine, Imperial College London, London, UK
| | - Arushi Shrivastava
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Katherine Duchinski
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics (BIG) PhD Program, Harvard Medical School, Boston, MA, USA
| | - Sreekar Mantena
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Jiali Wang
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Tavé van Zyl
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Ophthalmology and Visual Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MA, USA
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4029, Australia
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4029, Australia
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Janey L Wiggs
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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14
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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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15
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Wei S, Liao D, Hu J. Inhibition of miR-144-3p/FOXO1 Attenuates Diabetic Keratopathy Via Modulating Autophagy and Apoptosis. Invest Ophthalmol Vis Sci 2024; 65:1. [PMID: 38165707 PMCID: PMC10768711 DOI: 10.1167/iovs.65.1.1] [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: 09/01/2023] [Accepted: 12/05/2023] [Indexed: 01/04/2024] Open
Abstract
Purpose Diabetic keratopathy (DK) is a vision-threatening disease that occurs in people with diabetes. Mounting evidence indicates that microRNAs (miRNAs) are indispensable in nerve regeneration within DK. Herein, the role of miRNAs associated with DK, especially focusing on autophagy and apoptosis regulation, was investigated. Methods To identify differentially expressed miRNAs, we performed miRNA sequencing on trigeminal ganglion (TG) tissues derived from streptozotocin-induced type 1 diabetic mellitus (T1DM) and normal mice. MiR-144-3p was chosen for the subsequent experiments. To explore the regulatory role of miR-144-3p in DK, miRNA antagomir was utilized to inhibit miR-144-3p expression. Bioinformatic tools were used to predict the target genes of miR-144-3p, and a dual-luciferase reporter assay was then applied for validation. Autophagy and apoptosis activities were measured utilizing TUNEL staining, immunofluorescence staining, and Western blotting. Results Overall, 56 differentially expressed miRNAs were detected in diabetic versus control mice. In the diabetic mouse TG tissue, miR-144-3p expression was aberrantly enhanced, whereas decreasing its expression contributed to improved diabetic corneal re-epithelialization and nerve regeneration. Fork-head Box O1 (FOXO1) was validated as a target gene of miR-144-3p. Overexpression of FOXO1 could prevent both inadequate autophagy and excessive apoptosis in DK. Consistently, a specific miR-144-3p inhibition enhanced autophagy and prevented apoptosis in DK. Conclusions In this study, our research confirmed the target binding relationship between miR-144-3p and FOXO1. Inhibiting miR-144-3p might modulate autophagy and apoptosis, which could generate positive outcomes for corneal nerves via targeting FOXO1 in DK.
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Affiliation(s)
- Shijia Wei
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Danling Liao
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jianzhang Hu
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, China
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16
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Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Del Rio-Tsonis K. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. Development 2024; 151:dev202249. [PMID: 38180241 PMCID: PMC10906490 DOI: 10.1242/dev.202249] [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: 08/09/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataracts. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq and CUT&RUN-seq to discover previously unreported mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Furthermore, we identify an epigenetic paradigm of cellular differentiation, defined by progressive loss of the H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
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Affiliation(s)
- Jared A. Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Sofia M. Rebull
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jacob M. Weaver
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Stacy Bendezu-Sayas
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Michael L. Robinson
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
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17
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Wang W, Wang H. Understanding the complex genetics and molecular mechanisms underlying glaucoma. Mol Aspects Med 2023; 94:101220. [PMID: 37856931 DOI: 10.1016/j.mam.2023.101220] [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: 06/29/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
Glaucoma is the leading cause of irreversible blindness worldwide. Currently the only effective treatment for glaucoma is to reduce the intraocular pressure, which can halt the progression of the disease. Highlighting the importance of identifying individuals at risk of developing glaucoma and those with early-stage glaucoma will help patients receive treatment before sight loss. However, some cases of glaucoma do not have raised intraocular pressure. In fact, glaucoma is caused by a variety of different mechanisms and has a wide range of different subtypes. Understanding other risk factors, the underlying mechanisms, and the pathology of glaucoma might lead to novel treatments and treatment of underlying diseases. In this review we present the latest research into glaucoma including the genetics and molecular basis of the disease.
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Affiliation(s)
- Weiwei Wang
- Shaanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated People's Hospital, Northwest University, Xi'an, 710004, Shaanxi Province, China.
| | - Huaizhou Wang
- Department of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
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18
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Rajasundaram S, Zebardast N, Mehta P, Khawaja AP, Warwick A, Duchinski K, Burgess S, Gill D, Segrè AV, Wiggs J. TIE1 and TEK signalling, intraocular pressure, and primary open-angle glaucoma: a Mendelian randomization study. J Transl Med 2023; 21:847. [PMID: 37996923 PMCID: PMC10668387 DOI: 10.1186/s12967-023-04737-9] [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: 06/01/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND In primary open-angle glaucoma (POAG), lowering intraocular pressure (IOP) is the only proven way of slowing vision loss. Schlemm's canal (SC) is a hybrid vascular and lymphatic vessel that mediates aqueous humour drainage from the anterior ocular chamber. Animal studies support the importance of SC endothelial angiopoietin-TEK signalling, and more recently TIE1 signalling, in maintaining normal IOP. However, human genetic support for a causal role of TIE1 and TEK signalling in lowering IOP is currently lacking. METHODS GWAS summary statistics were obtained for plasma soluble TIE1 (sTIE1) protein levels (N = 35,559), soluble TEK (sTEK) protein levels (N = 35,559), IOP (N = 139,555) and POAG (Ncases = 16,677, Ncontrols = 199,580). Mendelian randomization (MR) was performed to estimate the association of genetically proxied TIE1 and TEK protein levels with IOP and POAG liability. Where significant MR estimates were obtained, genetic colocalization was performed to assess the probability of a shared causal variant (PPshared) versus distinct (PPdistinct) causal variants underlying TIE1/TEK signalling and the outcome. Publicly available single-nucleus RNA-sequencing data were leveraged to investigate differential expression of TIE1 and TEK in the human ocular anterior segment. RESULTS Increased genetically proxied TIE1 signalling and TEK signalling associated with a reduction in IOP (- 0.21 mmHg per SD increase in sTIE1, 95% CI = - 0.09 to - 0.33 mmHg, P = 6.57 × 10-4, and - 0.14 mmHg per SD decrease in sTEK, 95% CI = - 0.03 to - 0.25 mmHg, P = 0.011), but not with POAG liability. Colocalization analysis found that the probability of a shared causal variant was greater for TIE1 and IOP than for TEK and IOP (PPshared/(PPdistinct + PPshared) = 0.98 for TIE1 and 0.30 for TEK). In the anterior segment, TIE1 and TEK were preferentially expressed in SC, lymphatic, and vascular endothelium. CONCLUSIONS This study provides novel human genetic support for a causal role of both TIE1 and TEK signalling in regulating IOP. Here, combined evidence from cis-MR and colocalization analyses provide stronger support for TIE1 than TEK as a potential IOP-lowering therapeutic target.
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Affiliation(s)
- Skanda Rajasundaram
- Faculty of Medicine, Imperial College London, London, UK.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
| | - Nazlee Zebardast
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
| | - Puja Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
- UCL Institute of Cardiovascular Science, London, UK
| | | | - Alasdair Warwick
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Katherine Duchinski
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Ayellet V Segrè
- Faculty of Medicine, Imperial College London, London, UK
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
| | - Janey Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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19
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Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z, Colborn SLZ, Cortez BS, Owen LA, Tran NM, Shekhar K, Sanes JR, Stout JT, Chen S, Li Y, DeAngelis MM, Theis FJ, Chen R. Integrated multi-omics single cell atlas of the human retina. RESEARCH SQUARE 2023:rs.3.rs-3471275. [PMID: 38014002 PMCID: PMC10680922 DOI: 10.21203/rs.3.rs-3471275/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here, we present an integrated multimodal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types. Engaging the retina community, we annotated each cluster, refined the Cell Ontology for the retina, identified distinct marker genes, and characterized cis-regulatory elements and gene regulatory networks (GRNs) for these cell types. Our analysis uncovered intriguing differences in transcriptome, chromatin, and GRNs across cell types. In addition, we modeled changes in gene expression and chromatin openness across gender and age. This integrated atlas also enabled the fine-mapping of GWAS and eQTL variants. Accessible through interactive browsers, this multimodal cross-donor and cross-lab HRCA, can facilitate a better understanding of retinal function and pathology.
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Affiliation(s)
- Jin Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Jun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Ignacio L Ibarra
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Malte D Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Lung Health & Immunity, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Jiaxiong Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States
| | - Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States
| | - Zhen Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | | | | | - Leah A Owen
- John A. Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States
| | - Nicholas M Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Center for Computational Biology; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California, United States
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - J Timothy Stout
- Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, Texas, United States
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, United States
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Margaret M DeAngelis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, United States
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States
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20
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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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21
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Zhu Y, Garcia-Sanchez J, Dalal R, Sun Y, Kapiloff MS, Goldberg JL, Liu WW. Differential expression of PIEZO1 and PIEZO2 mechanosensitive channels in ocular tissues implicates diverse functional roles. Exp Eye Res 2023; 236:109675. [PMID: 37820892 PMCID: PMC10843266 DOI: 10.1016/j.exer.2023.109675] [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: 10/05/2023] [Revised: 10/08/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
PIEZO1 and PIEZO2 are mechanosensitive ion channels that regulate many important physiological processes including vascular blood flow, touch, and proprioception. As the eye is subject to mechanical stress and is highly perfused, these channels may play important roles in ocular function and intraocular pressure regulation. PIEZO channel expression in the eye has not been well defined, in part due to difficulties in validating available antibodies against PIEZO1 and PIEZO2 in ocular tissues. It is also unclear if PIEZO1 and PIEZO2 are differentially expressed. To address these questions, we used single-molecule fluorescence in situ hybridization (smFISH) together with transgenic reporter mice expressing PIEZO fusion proteins under the control of their endogenous promoters to compare the expression and localization of PIEZO1 and PIEZO2 in mouse ocular tissues relevant to glaucoma. We detected both PIEZO1 and PIEZO2 expression in the trabecular meshwork, ciliary body, and in the ganglion cell layer (GCL) of the retina. Piezo1 mRNA was more abundantly expressed than Piezo2 mRNA in these ocular tissues. Piezo1 but not Piezo2 mRNA was detected in the inner nuclear layer and outer nuclear layer of the retina. Our results suggest that PIEZO1 and PIEZO2 are differentially expressed and may have distinct roles as mechanosensors in glaucoma-relevant ocular tissues.
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Affiliation(s)
- Ying Zhu
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Julian Garcia-Sanchez
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Roopa Dalal
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Yang Sun
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael S Kapiloff
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jeffrey L Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Wendy W Liu
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA.
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22
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Zhu M, Hu W, Lin L, Yang Q, Zhang L, Xu J, Xu Y, Liu J, Zhang M, Tong X, Zhu K, Feng K, Feng Y, Su J, Huang X, Li J. Single-cell RNA sequencing reveals new subtypes of lens superficial tissue in humans. Cell Prolif 2023; 56:e13477. [PMID: 37057399 PMCID: PMC10623935 DOI: 10.1111/cpr.13477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/15/2023] Open
Abstract
Although the cell atlas of the human ocular anterior segment of the human eye was revealed by single-nucleus RNA sequencing, whether subtypes of lens stem/progenitor cells exist among epithelial cells and the molecular characteristics of cell differentiation of the human lens remain unclear. Single-cell RNA sequencing is a powerful tool to analyse the heterogeneity of tissues at the single cell level, leading to a better understanding of the processes of cell differentiation. By profiling 18,596 cells in human lens superficial tissue through single-cell sequencing, we identified two subtypes of lens epithelial cells that specifically expressed C8orf4 and ADAMTSL4 with distinct spatial localization, a new type of fibre cells located directly adjacent to the epithelium, and a subpopulation of ADAMTSL4+ cells that might be lens epithelial stem/progenitor cells. We also found two trajectories of lens epithelial cell differentiation and changes of some important genes during differentiation.
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Affiliation(s)
- Meng‐Chao Zhu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Wei Hu
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, Brain Science Collaborative Innovation Center, State Key Laboratory of Medical Neurobiology, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative MedicineFudan UniversityShanghaiChina
| | - Lei Lin
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Qing‐Wen Yang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Lu Zhang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Jia‐Lin Xu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Yi‐Tong Xu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Jia‐Sheng Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Meng‐Di Zhang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Xiao‐Yu Tong
- Zhejiang Provincial Clinical Research Center for Pediatric DiseaseThe Second Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Kai‐Yi Zhu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Ke Feng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Yi Feng
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, Brain Science Collaborative Innovation Center, State Key Laboratory of Medical Neurobiology, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative MedicineFudan UniversityShanghaiChina
| | - Jian‐Zhong Su
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
| | - Xiu‐Feng Huang
- Zhejiang Provincial Clinical Research Center for Pediatric DiseaseThe Second Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Jin Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Ocular Diseases, Eye HospitalWenzhou Medical UniversityWenzhouChina
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23
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Wu YF, Chang NW, Chu LA, Liu HY, Zhou YX, Pai YL, Yu YS, Kuan CH, Wu YC, Lin SJ, Tan HY. Single-Cell Transcriptomics Reveals Cellular Heterogeneity and Complex Cell-Cell Communication Networks in the Mouse Cornea. Invest Ophthalmol Vis Sci 2023; 64:5. [PMID: 37792336 PMCID: PMC10565710 DOI: 10.1167/iovs.64.13.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/30/2023] [Indexed: 10/05/2023] Open
Abstract
Purpose To generate a single-cell RNA-sequencing (scRNA-seq) map and construct cell-cell communication networks of mouse corneas. Methods C57BL/6 mouse corneas were dissociated to single cells and subjected to scRNA-seq. Cell populations were clustered and annotated for bioinformatic analysis using the R package "Seurat." Differential expression patterns were validated and spatially mapped with whole-mount immunofluorescence staining. Global intercellular signaling networks were constructed using CellChat. Results Unbiased clustering of scRNA-seq transcriptomes of 14,732 cells from 40 corneas revealed 17 cell clusters of six major cell types: nine epithelial cell, three keratocyte, two corneal endothelial cell, and one each of immune cell, vascular endothelial cell, and fibroblast clusters. The nine epithelial cell subtypes included quiescent limbal stem cells, transit-amplifying cells, and differentiated cells from corneas and two minor conjunctival epithelial clusters. CellChat analysis provided an atlas of the complex intercellular signaling communications among all cell types. Conclusions We constructed a complete single-cell transcriptomic map and the complex signaling cross-talk among all cell types of the cornea, which can be used as a foundation atlas for further research on the cornea. This study also deepens the understanding of the cellular heterogeneity and heterotypic cell-cell interaction within corneas.
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Affiliation(s)
- Yueh-Feng Wu
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Nai-Wen Chang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-An Chu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsin-Yu Liu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Ophthalmology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Yu-Xian Zhou
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Yun-Lin Pai
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Sheng Yu
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Chen-Hsiang Kuan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Plastic Surgery, Department of Surgery, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Ching Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Jan Lin
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Hsin-Yuan Tan
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
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24
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Li W, Gurdziel K, Pitchaikannu A, Gupta N, Hazlett LD, Xu S. The miR-183/96/182 cluster is a checkpoint for resident immune cells and shapes the cellular landscape of the cornea. Ocul Surf 2023; 30:17-41. [PMID: 37536656 PMCID: PMC10834862 DOI: 10.1016/j.jtos.2023.07.012] [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: 01/30/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
PURPOSE The conserved miR-183/96/182 cluster (miR-183C) regulates both corneal sensory innervation and corneal resident immune cells (CRICs). This study is to uncover its role in CRICs and in shaping the corneal cellular landscape at a single-cell (sc) level. METHODS Corneas of naïve, young adult [2 and 6 months old (mo)], female miR-183C knockout (KO) mice and wild-type (WT) littermates were harvested and dissociated into single cells. Dead cells were removed using a Dead Cell Removal kit. CD45+ CRICs were enriched by Magnetic Activated Cell Sorting (MACS). scRNA libraries were constructed and sequenced followed by comprehensive bioinformatic analyses. RESULTS The composition of major cell types of the cornea stays relatively stable in WT mice from 2 to 6 mo, however the compositions of subtypes of corneal cells shift with age. Inactivation of miR-183C disrupts the stability of the major cell-type composition and age-related transcriptomic shifts of subtypes of corneal cells. The diversity of CRICs is enhanced with age. Naïve mouse cornea contains previously-unrecognized resident fibrocytes and neutrophils. Resident macrophages (ResMφ) adopt cornea-specific function by expressing abundant extracellular matrix (ECM) and ECM organization-related genes. Naïve cornea is endowed with partially-differentiated proliferative ResMφ and contains microglia-like Mφ. Resident lymphocytes, including innate lymphoid cells (ILCs), NKT and γδT cells, are the major source of innate IL-17a. miR-183C limits the diversity and polarity of ResMφ. CONCLUSION miR-183C serves as a checkpoint for CRICs and imposes a global regulation of the cellular landscape of the cornea.
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Affiliation(s)
- Weifeng Li
- Predoctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Department of Genetic Medicine, USA; Wilmer Eye Institute, School of Medicine, The Johns Hopkins University, Baltimore, MD, USA
| | | | - Ahalya Pitchaikannu
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Naman Gupta
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Linda D Hazlett
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Shunbin Xu
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI, USA.
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25
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Zhao M, Toma K, Kinde B, Li L, Patel AK, Wu KY, Lum MR, Tan C, Hooper JE, Kriegstein AR, La Torre A, Liao YJ, Welsbie DS, Hu Y, Han Y, Duan X. Osteopontin drives retinal ganglion cell resiliency in glaucomatous optic neuropathy. Cell Rep 2023; 42:113038. [PMID: 37624696 PMCID: PMC10591811 DOI: 10.1016/j.celrep.2023.113038] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/28/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Chronic neurodegeneration and acute injuries lead to neuron losses via diverse processes. We compared retinal ganglion cell (RGC) responses between chronic glaucomatous conditions and the acute injury model. Among major RGC subclasses, αRGCs and intrinsically photosensitive RGCs (ipRGCs) preferentially survive glaucomatous conditions, similar to findings in the retina subject to axotomy. Focusing on an αRGC intrinsic factor, Osteopontin (secreted phosphoprotein 1 [Spp1]), we found an ectopic neuronal expression of Osteopontin (Spp1) in other RGCs subject to glaucomatous conditions. This contrasted with the Spp1 downregulation subject to axotomy. αRGC-specific Spp1 elimination led to significant αRGC loss, diminishing their resiliency. Spp1 overexpression led to robust neuroprotection of susceptible RGC subclasses under glaucomatous conditions. In contrast, Spp1 overexpression did not significantly protect RGCs subject to axotomy. Additionally, SPP1 marked adult human RGC subsets with large somata and SPP1 expression in the aqueous humor correlated with glaucoma severity. Our study reveals Spp1's role in mediating neuronal resiliency in glaucoma.
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Affiliation(s)
- Mengya Zhao
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kenichi Toma
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Benyam Kinde
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Liang Li
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Amit K Patel
- Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA 92037, USA
| | - Kong-Yan Wu
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew R Lum
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Chengxi Tan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jody E Hooper
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Arnold R Kriegstein
- Department of Neurology and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA 95616, USA
| | - Yaping Joyce Liao
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Derek S Welsbie
- Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA 92037, USA
| | - Yang Hu
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
| | - Ying Han
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Xin Duan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94158, USA.
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26
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Martínez-Carrasco R, Argüeso P. Characterization of Cell Surface Glycan Profiles in Human and Mouse Corneas Using Lectin Microarrays. Cells 2023; 12:2356. [PMID: 37830569 PMCID: PMC10572028 DOI: 10.3390/cells12192356] [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: 08/04/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
The advent of high-throughput sequencing technologies has facilitated the profiling of glycosylation genes at a single-cell level in complex biological systems, but the significance of these gene signatures to the composition of the glycocalyx remains ambiguous. Here, we used lectin microarrays to characterize the composition of cell surface glycans in human and mouse corneas and determine its relationship to single-cell transcriptomic data. Our results identify a series of cell surface glycan signatures that are unique to the different cell types of the human cornea and that correlate, to a certain extent, with the transcriptional expression of glycosylation genes. These include pathways involved in the biosynthesis of O-glycans in epithelial cells and core fucose on stromal and endothelial cell surfaces. Moreover, we show that human and mouse corneas display some structural differences in terms of cell surface glycan composition. These results could provide insights into the specialized function of individual cell types in the cornea and foster the identification of novel cornea-specific biomarkers.
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Affiliation(s)
| | - Pablo Argüeso
- Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02114, USA
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27
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Liu WW, Kinzy TG, Cooke Bailey JN, Xu Z, Hysi P, Wiggs JL. Mechanosensitive ion channel gene survey suggests potential roles in primary open angle glaucoma. Sci Rep 2023; 13:15871. [PMID: 37741866 PMCID: PMC10517927 DOI: 10.1038/s41598-023-43072-3] [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: 05/22/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023] Open
Abstract
Although glaucoma is a disease modulated by eye pressure, the mechanisms of pressure sensing in the eye are not well understood. Here, we investigated associations between mechanosensitive ion channel gene variants and primary open-angle glaucoma (POAG). Common (minor allele frequency > 5%) single nucleotide polymorphisms located within the genomic regions of 20 mechanosensitive ion channel genes in the K2P, TMEM63, PIEZO and TRP channel families were assessed using genotype data from the NEIGHBORHOOD consortium of 3853 cases and 33,480 controls. Rare (minor allele frequency < 1%) coding variants were assessed using exome array genotyping data for 2606 cases and 2606 controls. Association with POAG was analyzed using logistic regression adjusting for age and sex. Two rare PIEZO1 coding variants with protective effects were identified in the NEIGHBOR dataset: R1527H, (OR 0.17, P = 0.0018) and a variant that alters a canonical splice donor site, g.16-88737727-C-G Hg38 (OR 0.38, P = 0.02). Both variants showed similar effects in the UK Biobank and the R1527H also in the FinnGen database. Several common variants also reached study-specific thresholds for association in the NEIGHBORHOOD dataset. These results identify novel variants in several mechanosensitive channel genes that show associations with POAG, suggesting that these channels may be potential therapeutic targets.
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Affiliation(s)
- Wendy W Liu
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, 2370 Watson Court, Palo Alto, CA, 94303, USA.
| | - Tyler G Kinzy
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Zihe Xu
- Department of Ophthalmology, King's College London, St. Thomas' Hospital, London, UK
| | - Pirro Hysi
- Department of Ophthalmology, King's College London, St. Thomas' Hospital, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, UK
| | - Janey L Wiggs
- Massachusetts Eye and Ear, Harvard Medical School Boston, Boston, MA, USA
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Madadi Y, Monavarfeshani A, Chen H, Stamer WD, Williams RW, Yousefi S. Artificial Intelligence Models for Cell Type and Subtype Identification Based on Single-Cell RNA Sequencing Data in Vision Science. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2837-2852. [PMID: 37294649 PMCID: PMC10631573 DOI: 10.1109/tcbb.2023.3284795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various tissues. However, scRNA-seq based identification of discrete cell-types is still labor intensive and depends on prior molecular knowledge. Artificial intelligence has provided faster, more accurate, and user-friendly approaches for cell-type identification. In this review, we discuss recent advances in cell-type identification methods using artificial intelligence techniques based on single-cell and single-nucleus RNA sequencing data in vision science. The main purpose of this review paper is to assist vision scientists not only to select suitable datasets for their problems, but also to be aware of the appropriate computational tools to perform their analysis. Developing novel methods for scRNA-seq data analysis remains to be addressed in future studies.
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29
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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: 6] [Impact Index Per Article: 6.0] [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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30
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Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Rio-Tsonis KD. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548451. [PMID: 37502967 PMCID: PMC10369908 DOI: 10.1101/2023.07.10.548451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Further, we divulge a conserved epigenetic paradigm of cellular differentiation, defined by progressive loss of H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
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Affiliation(s)
- Jared A Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Sofia M Rebull
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
| | - Jacob M Weaver
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Stacy Bendezu-Sayas
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Michael L Robinson
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
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31
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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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32
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Oikawa K, Torne O, Sun D, Moon AKB, Kiland JA, Trane RM, McLellan GJ. Aqueous Humor TGF-β2 and Its Association With Intraocular Pressure in a Naturally Occurring Large Animal Model of Glaucoma. Invest Ophthalmol Vis Sci 2023; 64:18. [PMID: 37459065 PMCID: PMC10362923 DOI: 10.1167/iovs.64.10.18] [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: 01/26/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
Purpose Transforming growth factor (TGF)-β2 has been widely implicated in human glaucoma pathology. The purpose of this study was to determine the source of TGF-β2 in aqueous humor (AH) and its relationship with intraocular pressure (IOP) in an inherited large animal model of glaucoma. Methods Sixty-six glaucomatous cats homozygous for LTBP2 mutation, and 42 normal cats were studied. IOP was measured weekly by rebound tonometry. AH was collected by anterior chamber paracentesis from each eye under general anesthesia, and serum samples collected from venous blood concurrently. Concentrations of total, active and latent TGF-β2 in AH and serum samples were measured by quantitative sandwich immunoassay. For comparisons between groups, unpaired t-test or Mann Whitney test were used, with P < 0.05 considered significant. The relationships between TGF-β2 concentrations and IOP values were examined by Pearson's correlation coefficient and generalized estimating equation. Results IOP and AH TGF-β2 concentrations were significantly higher in glaucomatous than in normal cats. AH TGF-β2 showed a significant, robust positive correlation with IOP in glaucomatous cats (r = 0.83, R2 = 0.70, P < 0.0001). Serum TGF-β2 did not correlate with AH TGF-β2 and was not significantly different between groups. TGF-β2 mRNA and protein expression were significantly increased in local ocular tissues in glaucomatous cats. Conclusions Enhanced, local ocular production of TGF-β2 with a robust positive association with IOP was identified in this spontaneous feline glaucoma model, providing a foundation for preclinical testing of novel therapeutics to limit disease-associated AH TGF-β2 elevation and signaling in glaucoma.
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Affiliation(s)
- Kazuya Oikawa
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- McPherson Eye Research Institute, Madison, Wisconsin, United States
| | - Odalys Torne
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- McPherson Eye Research Institute, Madison, Wisconsin, United States
| | - David Sun
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Alaina K. B. Moon
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Julie A. Kiland
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Ralph Møller Trane
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Gillian J. McLellan
- Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
- McPherson Eye Research Institute, Madison, Wisconsin, United States
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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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Tsedilina TR, Sharova E, Iakovets V, Skorodumova LO. Systematic review of SLC4A11, ZEB1, LOXHD1, and AGBL1 variants in the development of Fuchs' endothelial corneal dystrophy. Front Med (Lausanne) 2023; 10:1153122. [PMID: 37441688 PMCID: PMC10333596 DOI: 10.3389/fmed.2023.1153122] [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: 01/28/2023] [Accepted: 03/30/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction The pathogenic role of variants in TCF4 and COL8A2 in causing Fuchs' endothelial corneal dystrophy (FECD) is not controversial and has been confirmed by numerous studies. The causal role of other genes, SLC4A11, ZEB1, LOXHD1, and AGBL1, which have been reported to be associated with FECD, is more complicated and less obvious. We performed a systematic review of the variants in the above-mentioned genes in FECD cases, taking into account the currently available population frequency information, transcriptomic data, and the results of functional studies to assess their pathogenicity. Methods Search for articles published in 2005-2022 was performed manually between July 2022 and February 2023. We searched for original research articles in peer-reviewed journals, written in English. Variants in the genes of interest identified in patients with FECD were extracted for the analysis. We classified each presented variant by pathogenicity status according to the ACMG criteria implemented in the Varsome tool. Diagnosis, segregation data, presence of affected relatives, functional analysis results, and gene expression in the corneal endothelium were taken into account. Data on the expression of genes of interest in the corneal endothelium were extracted from articles in which transcriptome analysis was performed. The identification of at least one variant in a gene classified as pathogenic or significantly associated with FECD was required to confirm the causal role of the gene in FECD. Results The analysis included 34 articles with 102 unique ZEB1 variants, 20 articles with 64 SLC4A11 variants, six articles with 26 LOXHD1 variants, and five articles with four AGBL1 variants. Pathogenic status was confirmed for seven SLC4A11 variants found in FECD. No variants in ZEB1, LOXHD1, and AGBL1 genes were classified as pathogenic for FECD. According to the transcriptome data, AGBL1 and LOXHD1 were not expressed in the corneal endothelium. Functional evidence for the association of LOXHD1, and AGBL1 with FECD was conflicting. Conclusion Our analysis confirmed the causal role of SLC4A11 variants in the development of FECD. The causal role of ZEB1, LOXHD1, and AGBL1 variants in FECD has not been confirmed. Further evidence from familial cases and functional analysis is needed to confirm their causal roles in FECD.
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Affiliation(s)
- Tatiana Romanovna Tsedilina
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elena Sharova
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valeriia Iakovets
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Liubov Olegovna Skorodumova
- Laboratory of Human Molecular Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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35
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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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Liu J, Zhu M, Xu Y, Zhang M, Sun H, Wang Y, Yang Q, Li J. Autophagy-prominent cell clusters among human lens epithelial cells: integrated single-cell RNA-sequencing analysis. BMC Ophthalmol 2023; 23:168. [PMID: 37081480 PMCID: PMC10116761 DOI: 10.1186/s12886-023-02910-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Autophagy is an important process that maintains the quality of intracellular proteins and organelles. There is extensive evidence that autophagy has an important role in the lens. Human lens epithelial cells (HLECs) play a key role in the internal homeostasis of the lens. HLEC subtypes have been identified, but autophagy-prominent cell clusters among HLECs have not been characterized. PURPOSE To explore the existence of autophagy-prominent cell clusters in HLECs. METHODS Three donated lenses (HLECs from two whole lenses and HLECs from one lens without the anterior central 6-mm zone) were used for single-cell RNA sequencing (scRNA-seq). AUCell and AddModuleScore analysis were used to identify potential autophagy-prominent cell clusters. Transmission electron microscopy (TEM) was used to confirm the results. RESULTS High-quality transcripts from 18,120 cells were acquired by scRNA-seq of the two intact lenses. Unsupervised clustering classified the cells into four clusters. AUCell and AddModuleScore analysis revealed cluster 1 is autophagy-prominent. scRNA-seq analysis of HLECs from the lens capsule lacking the central zone confirmed the cluster 1 HLECs was located in the central capsule zone. The TEM result showed that greater autophagy activity was observed in the HLECs in central capsule zone, which further supported the above conclusions based on scRNA-seq analysis that autophagy was prominent in the central zone where the cluster 1 HLECs located. CONCLUSIONS We identified an autophagy-prominent cell cluster among HLECs and revealed that it was localized in the central zone of the lens capsule. Our findings will aid investigations of autophagy in HLECs and provide insights to guide related research.
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Affiliation(s)
- Jiasheng Liu
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China
| | - Mengchao Zhu
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China
| | - Yitong Xu
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China
| | - Mengdi Zhang
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China
| | - Haisen Sun
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China
| | - Yaqi Wang
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China
| | - Qingwen Yang
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China.
| | - Jin Li
- Department of Cataract, Eye Hospital of Wenzhou Medical University, 270# West Xueyuan Road, Wenzhou, 325000, Zhejiang, China.
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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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38
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Benhar I, Ding J, Yan W, Whitney IE, Jacobi A, Sud M, Burgin G, Shekhar K, Tran NM, Wang C, He Z, Sanes JR, Regev A. Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury. Nat Immunol 2023; 24:700-713. [PMID: 36807640 DOI: 10.1038/s41590-023-01437-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/13/2023] [Indexed: 02/22/2023]
Abstract
Non-neuronal cells are key to the complex cellular interplay that follows central nervous system insult. To understand this interplay, we generated a single-cell atlas of immune, glial and retinal pigment epithelial cells from adult mouse retina before and at multiple time points after axonal transection. We identified rare subsets in naive retina, including interferon (IFN)-response glia and border-associated macrophages, and delineated injury-induced changes in cell composition, expression programs and interactions. Computational analysis charted a three-phase multicellular inflammatory cascade after injury. In the early phase, retinal macroglia and microglia were reactivated, providing chemotactic signals concurrent with infiltration of CCR2+ monocytes from the circulation. These cells differentiated into macrophages in the intermediate phase, while an IFN-response program, likely driven by microglia-derived type I IFN, was activated across resident glia. The late phase indicated inflammatory resolution. Our findings provide a framework to decipher cellular circuitry, spatial relationships and molecular interactions following tissue injury.
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Affiliation(s)
- Inbal Benhar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jiarui Ding
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenjun Yan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Irene E Whitney
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Anne Jacobi
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Malika Sud
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace Burgin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karthik Shekhar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemical and Biomolecular Engineering, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas M Tran
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
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Upreti A, Padula SL, Tangeman JA, Wagner BD, O’Connell MJ, Jaquish TJ, Palko RK, Mantz CJ, Anand D, Lovicu FJ, Lachke SA, Robinson ML. Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response. Cells 2023; 12:501. [PMID: 36766843 PMCID: PMC9914805 DOI: 10.3390/cells12030501] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Lens epithelial explants are comprised of lens epithelial cells cultured in vitro on their native basement membrane, the lens capsule. Biologists have used lens epithelial explants to study many different cellular processes including lens fiber cell differentiation. In these studies, fiber differentiation is typically measured by cellular elongation and the expression of a few proteins characteristically expressed by lens fiber cells in situ. Chromatin and RNA was collected from lens epithelial explants cultured in either un-supplemented media or media containing 50% bovine vitreous humor for one or five days. Chromatin for ATAC-sequencing and RNA for RNA-sequencing was prepared from explants to assess regions of accessible chromatin and to quantitatively measure gene expression, respectively. Vitreous humor increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and, surprisingly, an immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had little effect on the accessibility of the genes highly expressed in the lens epithelium despite dramatic reductions in their mRNA transcripts. An unbiased analysis of differentially accessible regions revealed an enrichment of cis-regulatory motifs for RUNX, SOX and TEAD transcription factors that may drive differential gene expression in response to vitreous.
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Affiliation(s)
- Anil Upreti
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Stephanie L. Padula
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jared A. Tangeman
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Brad D. Wagner
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | | | - Tycho J. Jaquish
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Raye K. Palko
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Courtney J. Mantz
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Frank J. Lovicu
- Molecular and Cellular Biomedicine, School of Medical Sciences, and Save Sight Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Michael L. Robinson
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
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40
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PAX6 Expression Patterns in the Adult Human Limbal Stem Cell Niche. Cells 2023; 12:cells12030400. [PMID: 36766742 PMCID: PMC9913671 DOI: 10.3390/cells12030400] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 01/24/2023] Open
Abstract
Paired box 6 (PAX6), a nuclear transcription factor, determines the fate of limbal epithelial progenitor cells (LEPC) and maintains epithelial cell identity. However, the expression of PAX6 in limbal niche cells, primarily mesenchymal stromal cells (LMSC), and melanocytes is scarce and not entirely clear. To distinctly assess the PAX6 expression in limbal niche cells, fresh and organ-cultured human corneoscleral tissues were stained immunohistochemically. Furthermore, the expression of PAX6 in cultured limbal cells was investigated. Immunostaining revealed the presence of PAX6-negative cells which were positive for vimentin and the melanocyte markers Melan-A and human melanoma black-45 in the basal layer of the limbal epithelium. PAX6 staining was not observed in the limbal stroma. Moreover, the expression of PAX6 was observed by Western blot in cultured LEPC but not in cultured LMSC or LM. These data indicate a restriction of PAX6 expression to limbal epithelial cells at the limbal stem cell niche. These observations warrant further studies for the presence of other PAX isoforms in the limbal stem cell niche.
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Abstract
The trabecular meshwork (TM) of the eye serves as an essential tissue in controlling aqueous humor (AH) outflow and intraocular pressure (IOP) homeostasis. However, dysfunctional TM cells and/or decreased TM cellularity is become a critical pathogenic cause for primary open-angle glaucoma (POAG). Consequently, it is particularly valuable to investigate TM characteristics, which, in turn, facilitates the development of new treatments for POAG. Since 2006, the advancement in induced pluripotent stem cells (iPSCs) provides a new tool to (1) model the TM in vitro and (2) regenerate degenerative TM in POAG. In this context, we first summarize the current approaches to induce the differentiation of TM-like cells from iPSCs and compare iPSC-derived TM models to the conventional in vitro TM models. The efficacy of iPSC-derived TM cells for TM regeneration in POAG models is also discussed. Through these approaches, iPSCs are becoming essential tools in glaucoma modeling and for developing personalized treatments for TM regeneration.
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Affiliation(s)
- Wei Zhu
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, China.
| | - Xiaoyan Zhang
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Shen Wu
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital Eye Center, Capital Medical University, Beijing, China
| | - Ningli Wang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, China
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital Eye Center, Capital Medical University, Beijing, China
| | - Markus H Kuehn
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
- Center for the Prevention and Treatment of Visual Loss, Iowa City Veterans Affairs Medical Center, Iowa City, IA, USA
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42
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Gao XR, Chiariglione M, Arch AJ. Whole-exome sequencing study identifies rare variants and genes associated with intraocular pressure and glaucoma. Nat Commun 2022; 13:7376. [PMID: 36450729 PMCID: PMC9712679 DOI: 10.1038/s41467-022-35188-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
Elevated intraocular pressure (IOP) is a major risk factor for glaucoma, the leading cause of irreversible blindness worldwide. IOP is also the only modifiable risk factor for glaucoma. Previous genome-wide association studies have established the contribution of common genetic variants to IOP. The role of rare variants for IOP was unknown. Using whole exome sequencing data from 110,260 participants in the UK Biobank (UKB), we conducted the largest exome-wide association study of IOP to date. In addition to confirming known IOP genes, we identified 40 novel rare-variant genes for IOP, such as BOD1L1, ACAD10 and HLA-B, demonstrating the power of including and aggregating rare variants in gene discovery. About half of these IOP genes are also associated with glaucoma phenotypes in UKB and the FinnGen cohort. Six of these genes, i.e. ADRB1, PTPRB, RPL26, RPL10A, EGLN2, and MTOR, are drug targets that are either established for clinical treatment or in clinical trials. Furthermore, we constructed a rare-variant polygenic risk score and showed its significant association with glaucoma in independent participants (n = 312,825). We demonstrated the value of rare variants to enhance our understanding of the biological mechanisms regulating IOP and uncovered potential therapeutic targets for glaucoma.
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Affiliation(s)
- Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, 43210, USA. .,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA. .,Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA. .,Ohio State University Physicians Inc., Columbus, OH, USA.
| | - Marion Chiariglione
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Alexander J Arch
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, 43210, USA
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Cvekl A, Camerino MJ. Generation of Lens Progenitor Cells and Lentoid Bodies from Pluripotent Stem Cells: Novel Tools for Human Lens Development and Ocular Disease Etiology. Cells 2022; 11:cells11213516. [PMID: 36359912 PMCID: PMC9658148 DOI: 10.3390/cells11213516] [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: 09/28/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In vitro differentiation of human pluripotent stem cells (hPSCs) into specialized tissues and organs represents a powerful approach to gain insight into those cellular and molecular mechanisms regulating human development. Although normal embryonic eye development is a complex process, generation of ocular organoids and specific ocular tissues from pluripotent stem cells has provided invaluable insights into the formation of lineage-committed progenitor cell populations, signal transduction pathways, and self-organization principles. This review provides a comprehensive summary of recent advances in generation of adenohypophyseal, olfactory, and lens placodes, lens progenitor cells and three-dimensional (3D) primitive lenses, "lentoid bodies", and "micro-lenses". These cells are produced alone or "community-grown" with other ocular tissues. Lentoid bodies/micro-lenses generated from human patients carrying mutations in crystallin genes demonstrate proof-of-principle that these cells are suitable for mechanistic studies of cataractogenesis. Taken together, current and emerging advanced in vitro differentiation methods pave the road to understand molecular mechanisms of cataract formation caused by the entire spectrum of mutations in DNA-binding regulatory genes, such as PAX6, SOX2, FOXE3, MAF, PITX3, and HSF4, individual crystallins, and other genes such as BFSP1, BFSP2, EPHA2, GJA3, GJA8, LIM2, MIP, and TDRD7 represented in human cataract patients.
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Affiliation(s)
- Aleš Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: ; Tel.: +1-718-430-3217; Fax: +1-718-430-8778
| | - Michael John Camerino
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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