1
|
Chucair-Elliott AJ, Ocañas SR, Pham K, Machalinski A, Plafker S, Stout MB, Elliott MH, Freeman WM. Age- and sex- divergent translatomic responses of the mouse retinal pigmented epithelium. Neurobiol Aging 2024; 140:41-59. [PMID: 38723422 PMCID: PMC11173338 DOI: 10.1016/j.neurobiolaging.2024.04.012] [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: 10/24/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Aging is the main risk factor for age-related macular degeneration (AMD), a retinal neurodegenerative disease that leads to irreversible blindness, particularly in people over 60 years old. Retinal pigmented epithelium (RPE) atrophy is an AMD hallmark. Genome-wide chromatin accessibility, DNA methylation, and gene expression studies of AMD and control RPE demonstrate epigenomic/transcriptomic changes occur during AMD onset and progression. However, mechanisms by which molecular alterations of normal aging impair RPE function and contribute to AMD pathogenesis are unclear. Here, we specifically interrogate the RPE translatome with advanced age and across sexes in a novel RPE reporter mouse model. We find differential age- and sex- associated transcript expression with overrepresentation of pathways related to inflammation in the RPE. Concordant with impaired RPE function, the phenotypic changes in the aged translatome suggest that aged RPE becomes immunologically active, in both males and females, with some sex-specific signatures, which supports the need for sex representation for in vivo studies.
Collapse
Affiliation(s)
- Ana J Chucair-Elliott
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
| | - Sarah R Ocañas
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Adeline Machalinski
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Scott Plafker
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael B Stout
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael H Elliott
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
| |
Collapse
|
2
|
Li HZ, Pike ACW, Lotsaris I, Chi G, Hansen JS, Lee SC, Rödström KEJ, Bushell SR, Speedman D, Evans A, Wang D, He D, Shrestha L, Nasrallah C, Burgess-Brown NA, Vandenberg RJ, Dafforn TR, Carpenter EP, Sauer DB. Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2. Nat Commun 2024; 15:5503. [PMID: 38951531 PMCID: PMC11217458 DOI: 10.1038/s41467-024-48921-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 05/16/2024] [Indexed: 07/03/2024] Open
Abstract
Proline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and regulates the kinetics of signaling proteins. To understand the structural basis of proline import, we solved the structure of the proline transporter SIT1 in complex with the COVID-19 viral receptor ACE2 by cryo-electron microscopy. The structure of pipecolate-bound SIT1 reveals the specific sequence requirements for proline transport in the SLC6 family and how this protein excludes amino acids with extended side chains. By comparing apo and substrate-bound SIT1 states, we also identify the structural changes that link substrate release and opening of the cytoplasmic gate and provide an explanation for how a missense mutation in the transporter causes iminoglycinuria.
Collapse
Affiliation(s)
- Huanyu Z Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ashley C W Pike
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Irina Lotsaris
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Karin E J Rödström
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon R Bushell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Speedman
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Evans
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dong Wang
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Didi He
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leela Shrestha
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chady Nasrallah
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert J Vandenberg
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia.
| | | | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
3
|
Abcouwer SF, Miglioranza Scavuzzi B, Kish PE, Kong D, Shanmugam S, Le XA, Yao J, Hager H, Zacks DN. The mouse retinal pigment epithelium mounts an innate immune defense response following retinal detachment. J Neuroinflammation 2024; 21:74. [PMID: 38528525 PMCID: PMC10964713 DOI: 10.1186/s12974-024-03062-2] [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: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
The retinal pigment epithelium (RPE) maintains photoreceptor viability and function, completes the visual cycle, and forms the outer blood-retinal barrier (oBRB). Loss of RPE function gives rise to several monogenic retinal dystrophies and contributes to age-related macular degeneration. Retinal detachment (RD) causes separation of the neurosensory retina from the underlying RPE, disrupting the functional and metabolic relationships between these layers. Although the retinal response to RD is highly studied, little is known about how the RPE responds to loss of this interaction. RNA sequencing (RNA-Seq) was used to compare normal and detached RPE in the C57BL6/J mouse. The naïve mouse RPE transcriptome was compared to previously published RPE signature gene lists and from the union of these 14 genes (Bmp4, Crim1, Degs1, Gja1, Itgav, Mfap3l, Pdpn, Ptgds, Rbp1, Rnf13, Rpe65, Slc4a2, Sulf1 and Ttr) representing a core signature gene set applicable across rodent and human RPE was derived. Gene ontology enrichment analysis (GOEA) of the mouse RPE transcriptome identified expected RPE features and functions, such as pigmentation, phagocytosis, lysosomal and proteasomal degradation of proteins, and barrier function. Differentially expressed genes (DEG) at 1 and 7 days post retinal detachment (dprd) were defined as mRNA with a significant (padj≤0.05) fold change (FC) of 0.67 ≥ FC ≥ 1.5 in detached versus naïve RPE. The RPE transcriptome exhibited dramatic changes at 1 dprd, with 2297 DEG identified. The KEGG pathways and biological process GO groups related to innate immune responses were significantly enriched. Lipocalin 2 (Lcn2) and several chemokines were upregulated, while numerous genes related to RPE functions, such as pigment synthesis, visual cycle, phagocytosis, and tight junctions were downregulated at 1 dprd. The response was largely transient, with only 18 significant DEG identified at 7 dprd, including upregulation of complement gene C4b. Validation studies confirmed RNA-Seq results. Thus, the RPE quickly downregulates cell-specific functions and mounts an innate immune defense response following RD. Our data demonstrate that the RPE contributes to the inflammatory response to RD and may play a role in attraction of immune cells to the subretinal space.
Collapse
Affiliation(s)
- Steven F Abcouwer
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA.
| | - Bruna Miglioranza Scavuzzi
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Phillip E Kish
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Dejuan Kong
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Sumathi Shanmugam
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Xuan An Le
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Jingyu Yao
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Heather Hager
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - David N Zacks
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medicine, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| |
Collapse
|
4
|
Farjood F, Manos JD, Wang Y, Williams AL, Zhao C, Borden S, Alam N, Prusky G, Temple S, Stern JH, Boles NC. Identifying biomarkers of heterogeneity and transplantation efficacy in retinal pigment epithelial cells. J Exp Med 2023; 220:e20230913. [PMID: 37728563 PMCID: PMC10510736 DOI: 10.1084/jem.20230913] [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: 05/26/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Transplantation of retinal pigment epithelial (RPE) cells holds great promise for patients with retinal degenerative diseases, such as age-related macular degeneration. In-depth characterization of RPE cell product identity and critical quality attributes are needed to enhance efficacy and safety of replacement therapy strategies. Here, we characterized an adult RPE stem cell-derived (RPESC-RPE) cell product using bulk and single-cell RNA sequencing (scRNA-seq), assessing functional cell integration in vitro into a mature RPE monolayer and in vivo efficacy by vision rescue in the Royal College of Surgeons rats. scRNA-seq revealed several distinct subpopulations in the RPESC-RPE product, some with progenitor markers. We identified RPE clusters expressing genes associated with in vivo efficacy and increased cell integration capability. Gene expression analysis revealed lncRNA (TREX) as a predictive marker of in vivo efficacy. TREX knockdown decreased cell integration while overexpression increased integration in vitro and improved vision rescue in the RCS rats.
Collapse
Affiliation(s)
| | | | - Yue Wang
- Neural Stem Cell Institute, Rensselaer, NY, USA
| | | | | | | | - Nazia Alam
- Burke Neurological Institute at Weill Cornell Medicine, White Plains, NY, USA
| | - Glen Prusky
- Burke Neurological Institute at Weill Cornell Medicine, White Plains, NY, USA
| | | | | | | |
Collapse
|
5
|
Mullin NK, Voigt AP, Boese EA, Liu X, Stone EM, Tucker BA, Mullins RF. Transcriptomic and Chromatin Accessibility Analysis of the Human Macular and Peripheral Retinal Pigment Epithelium at the Single-Cell Level. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1750-1761. [PMID: 36775060 PMCID: PMC10616710 DOI: 10.1016/j.ajpath.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/12/2023]
Abstract
Some human retinal diseases are characterized by pathology that is restricted to specific cell types and to specific regions of the eye. Several disease entities either selectively affect or spare the macula, the retina region at the center of the posterior pole. Photoreceptor cells in the macula are involved in high-acuity vision and require metabolic support from non-neuronal cell types. Some macular diseases involve the retinal pigment epithelium (RPE), an epithelial cell layer with several metabolic-support functions essential for the overlying photoreceptors. In the current study, the ways in which RPE confers region-specific disease susceptibility were determined by examining heterogeneity within RPE tissue from human donors. RPE nuclei from the macular and peripheral retina were profiled using joint single-nucleus RNA and ATAC sequencing. The expression of several genes differed between macular and peripheral RPE. Region-specific ATAC peaks were found, suggesting regulatory elements used exclusively by macular or peripheral RPE. Across anatomic regions, subpopulations of RPE were identified that appeared to have differential levels of expression of visual cycle genes. Finally, loci associated with age-related macular degeneration were examined for a better understanding of RPE-specific disease phenotypes. These findings showed variations in the regulation of gene expression in the human RPE by region and subpopulation, and provide a source for a better understanding of the molecular basis of macular disease.
Collapse
Affiliation(s)
- Nathaniel K Mullin
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Andrew P Voigt
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Erin A Boese
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Xiuying Liu
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Edwin M Stone
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Budd A Tucker
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Robert F Mullins
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa.
| |
Collapse
|
6
|
Nam U, Lee S, Jeon JS. Generation of a 3D Outer Blood-Retinal Barrier with Advanced Choriocapillaris and Its Application in Diabetic Retinopathy in a Microphysiological System. ACS Biomater Sci Eng 2023; 9:4929-4939. [PMID: 37494673 DOI: 10.1021/acsbiomaterials.3c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The outer blood-retinal barrier (oBRB) provides an optimal environment for the function of the photoreceptor by regulating the exchange of molecules between subretinal space and the choriocapillaris, and its dysfunction could impair the photoreceptor's function and vision. The existing in vitro models have limitations in reproducing the barrier function or physiological characteristics of oBRB and choriocapillaris. Here, we engineered a microphysiological system-based oBRB-choriocapillaris model that simultaneously incorporates the desired physiological characteristics and is simple to fabricate. First, we generated microvascular networks to mimic choriocapillaris and investigated the role of fibroblasts in vasculogenesis. By adding retinal pigment epithelial cells to one side of blood vessels formed with endothelial cells and fibroblasts and optimizing their culture medium conditions, we established an oBRB-choriocapillaris model. To verify the physiological similarity of our oBRB-choriocapillaris model, we identified the polarization and expression of the tight junction of the retinal pigment epithelium, Bruch's membrane, and the fenestral diaphragm of choriocapillaris. Finally, we tried to recapitulate the diabetes mellitus environment in our model with hyperglycemia and diabetes-related cytokines. This induced a decrease in tight junction integrity, loss of barrier function, and shrinkage of blood vessels, similar to the in vivo pathological changes observed in the oBRB and choriocapillaris. The oBRB-choriocapillaris model developed using a microphysiological system is expected to offer a valuable in vitro platform for retinal and choroidal vascular diseases in preclinical applications.
Collapse
Affiliation(s)
- Ungsig Nam
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Seokhun Lee
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jessie S Jeon
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| |
Collapse
|
7
|
Zhu S, Xu R, Engel AL, Wang Y, McNeel R, Hurley JB, Chao JR, Du J. Proline provides a nitrogen source in the retinal pigment epithelium to synthesize and export amino acids for the neural retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537355. [PMID: 37131780 PMCID: PMC10153141 DOI: 10.1101/2023.04.18.537355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is known that metabolic defects in the retinal pigment epithelium (RPE) can cause degeneration of its neighboring photoreceptors in the retina, leading to retinal degenerative diseases such as age-related macular degeneration. However, how RPE metabolism supports the health of the neural retina remains unclear. The retina requires exogenous nitrogen sources for protein synthesis, neurotransmission, and energy metabolism. Using 15N tracing coupled with mass spectrometry, we found human RPE can utilize the nitrogen in proline to produce and export 13 amino acids, including glutamate, aspartate, glutamine, alanine and serine. Similarly, we found this proline nitrogen utilization in the mouse RPE/choroid but not in the neural retina of explant cultures. Co-culture of human RPE with the retina showed that the retina can take up the amino acids, especially glutamate, aspartate and glutamine, generated from proline nitrogen in the RPE. Intravenous delivery of 15N proline in vivo demonstrated 15N-derived amino acids appear earlier in the RPE before the retina. We also found proline dehydrogenase (PRODH), the key enzyme in proline catabolism is highly enriched in the RPE but not the retina. The deletion of PRODH blocks proline nitrogen utilization in RPE and the import of proline nitrogen-derived amino acids in the retina. Our findings highlight the importance of RPE metabolism in supporting nitrogen sources for the retina, providing insight into understanding the mechanisms of the retinal metabolic ecosystem and RPE-initiated retinal degenerative diseases.
Collapse
Affiliation(s)
- Siyan Zhu
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506
- Department of Pharmaceutical and Pharmacological Sciences, West Virginia University, Morgantown, WV 26506
| | - Rong Xu
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506
| | - Abbi L. Engel
- Department of Ophthalmology, University of Washington, Seattle, WA 98109
| | - Yekai Wang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506
| | - Rachel McNeel
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506
| | - James B. Hurley
- Department of Ophthalmology, University of Washington, Seattle, WA 98109
- Department of Biochemistry, University of Washington, Seattle, WA 98109
| | - Jennifer R. Chao
- Department of Ophthalmology, University of Washington, Seattle, WA 98109
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506
| |
Collapse
|
8
|
Emri E, Cappa O, Kelly C, Kortvely E, SanGiovanni JP, McKay BS, Bergen AA, Simpson DA, Lengyel I. Zinc Supplementation Induced Transcriptional Changes in Primary Human Retinal Pigment Epithelium: A Single-Cell RNA Sequencing Study to Understand Age-Related Macular Degeneration. Cells 2023; 12:773. [PMID: 36899910 PMCID: PMC10000409 DOI: 10.3390/cells12050773] [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: 02/05/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Zinc supplementation has been shown to be beneficial to slow the progression of age-related macular degeneration (AMD). However, the molecular mechanism underpinning this benefit is not well understood. This study used single-cell RNA sequencing to identify transcriptomic changes induced by zinc supplementation. Human primary retinal pigment epithelial (RPE) cells could mature for up to 19 weeks. After 1 or 18 weeks in culture, we supplemented the culture medium with 125 µM added zinc for one week. RPE cells developed high transepithelial electrical resistance, extensive, but variable pigmentation, and deposited sub-RPE material similar to the hallmark lesions of AMD. Unsupervised cluster analysis of the combined transcriptome of the cells isolated after 2, 9, and 19 weeks in culture showed considerable heterogeneity. Clustering based on 234 pre-selected RPE-specific genes divided the cells into two distinct clusters, we defined as more and less differentiated cells. The proportion of more differentiated cells increased with time in culture, but appreciable numbers of cells remained less differentiated even at 19 weeks. Pseudotemporal ordering identified 537 genes that could be implicated in the dynamics of RPE cell differentiation (FDR < 0.05). Zinc treatment resulted in the differential expression of 281 of these genes (FDR < 0.05). These genes were associated with several biological pathways with modulation of ID1/ID3 transcriptional regulation. Overall, zinc had a multitude of effects on the RPE transcriptome, including several genes involved in pigmentation, complement regulation, mineralization, and cholesterol metabolism processes associated with AMD.
Collapse
Affiliation(s)
- Eszter Emri
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
- Section Ophthalmogenetics, Department of Human Genetics, Queen Emma Centre for Precision Medicine, Amsterdam UMC, Location AMC, 1105AZ Amsterdam, The Netherlands
| | - Oisin Cappa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Caoimhe Kelly
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Elod Kortvely
- Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - John Paul SanGiovanni
- Biosciences Research Laboratories, BIO5 Institute, University of Arizona, 1230 North Cherry Avenue, Tucson, AZ 85724, USA
| | - Brian S. McKay
- Department of Ophthalmology and Vision Science, University of Arizona, 1656 E. Mabel Street, Tucson, AZ 85724, USA
| | - Arthur A. Bergen
- Section Ophthalmogenetics, Department of Human Genetics, Queen Emma Centre for Precision Medicine, Amsterdam UMC, Location AMC, 1105AZ Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), 1105AZ Amsterdam, The Netherlands
| | - David A. Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Imre Lengyel
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| |
Collapse
|
9
|
Yednock T, Fong DS, Lad EM. C1q and the classical complement cascade in geographic atrophy secondary to age-related macular degeneration. Int J Retina Vitreous 2022; 8:79. [PMID: 36348407 PMCID: PMC9641935 DOI: 10.1186/s40942-022-00431-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Geographic atrophy (GA) secondary to age-related macular degeneration (AMD) is a retinal neurodegenerative disorder. Human genetic data support the complement system as a key component of pathogenesis in AMD, which has been further supported by pre-clinical and recent clinical studies. However, the involvement of the different complement pathways (classical, lectin, alternative), and thus the optimal complement inhibition target, has yet to be fully defined. There is evidence that C1q, the initiating molecule of the classical pathway, is a key driver of complement activity in AMD. C1q is expressed locally by infiltrating phagocytic cells and C1q-activating ligands are present at disease onset and continue to accumulate with disease progression. The accumulation of C1q on photoreceptor synapses with age and disease is consistent with its role in synapse elimination and neurodegeneration that has been observed in other neurodegenerative disorders. Furthermore, genetic deletion of C1q, local pharmacologic inhibition within the eye, or genetic deletion of downstream C4 prevents photoreceptor cell damage in mouse models. Hence, targeting the classical pathway in GA could provide a more specific therapeutic approach with potential for favorable efficacy and safety.
Collapse
Affiliation(s)
- Ted Yednock
- Annexon Biosciences, 1400 Sierra Point Parkway Building C, 2nd Floor, Brisbane, CA, 94005, USA
| | - Donald S Fong
- Annexon Biosciences, 1400 Sierra Point Parkway Building C, 2nd Floor, Brisbane, CA, 94005, USA.
| | - Eleonora M Lad
- Department of Ophthalmology, Duke University Medical Center, 2351 Erwin Rd, Durham, NC, 27705, USA
| |
Collapse
|
10
|
Subramanian R, Sahoo D. Boolean implication analysis of single-cell data predicts retinal cell type markers. BMC Bioinformatics 2022; 23:378. [PMID: 36114457 PMCID: PMC9482279 DOI: 10.1186/s12859-022-04915-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022] Open
Abstract
Background The retina is a complex tissue containing multiple cell types that are essential for vision. Understanding the gene expression patterns of various retinal cell types has potential applications in regenerative medicine. Retinal organoids (optic vesicles) derived from pluripotent stem cells have begun to yield insights into the transcriptomics of developing retinal cell types in humans through single cell RNA-sequencing studies. Previous methods of gene reporting have relied upon techniques in vivo using microarray data, or correlational and dimension reduction methods for analyzing single cell RNA-sequencing data computationally. We aimed to develop a state-of-the-art Boolean method that filtered out noise, could be applied to a wide variety of datasets and lent insight into gene expression over differentiation. Results Here, we present a bioinformatic approach using Boolean implication to discover genes which are retinal cell type-specific or involved in retinal cell fate. We apply this approach to previously published retina and retinal organoid datasets and improve upon previously published correlational methods. Our method improves the prediction accuracy of marker genes of retinal cell types and discovers several new high confidence cone and rod-specific genes. Conclusions The results of this study demonstrate the benefits of a Boolean approach that considers asymmetric relationships. We have shown a statistically significant improvement from correlational, symmetric methods in the prediction accuracy of retinal cell-type specific genes. Furthermore, our method contains no cell or tissue-specific tuning and hence could impact other areas of gene expression analyses in cancer and other human diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04915-4.
Collapse
|
11
|
Pandey RS, Krebs MP, Bolisetty MT, Charette JR, Naggert JK, Robson P, Nishina PM, Carter GW. Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium. Int J Mol Sci 2022; 23:10419. [PMID: 36142331 PMCID: PMC9499471 DOI: 10.3390/ijms231810419] [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: 06/18/2022] [Revised: 08/09/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Transcriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease. However, available evidence points to RPE cell heterogeneity within native tissue, which adds complexity to global transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2667 and 2846 RPE cells. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell populations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1-2% of total cells) exhibited the hallmarks of stem and/or progenitor (SP) cells. Placing C1-6 along a pseudotime axis suggested a relative decrease in melanogenesis and SP gene expression and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means clustering of all detected transcripts identified additional expression patterns that may advance the understanding of RPE SP cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.
Collapse
Affiliation(s)
- Ravi S. Pandey
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Mark P. Krebs
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mohan T. Bolisetty
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | | | | | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Patsy M. Nishina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | |
Collapse
|
12
|
DeVera C, Dixon J, Chrenek MA, Baba K, Le YZ, Iuvone PM, Tosini G. The Circadian Clock in the Retinal Pigment Epithelium Controls the Diurnal Rhythm of Phagocytic Activity. Int J Mol Sci 2022; 23:5302. [PMID: 35628111 PMCID: PMC9141420 DOI: 10.3390/ijms23105302] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
The diurnal peak of phagocytosis by the retinal pigment epithelium (RPE) of photoreceptor outer segments (POS) is under circadian control and believed that this process involves interactions from the retina and RPE. Previous studies have demonstrated that a functional circadian clock exists within multiple retinal cell types and RPE. Thereby, the aim of this study was to determine whether the clock in the retina or RPE controls the diurnal phagocytic peak and whether disruption of the circadian clock in the RPE would affect cellular function and the viability during aging. To that, we generated and validated an RPE tissue-specific KO of the essential clock gene, Bmal1, and then determined the daily rhythm in phagocytic activity by the RPE in mice lacking a functional circadian clock in the retina or RPE. Then, using electroretinography, spectral domain-optical coherence tomography, and optomotor response of visual function we determined the effect of Bmal1 removal in young (6 months) and old (18 months) mice. RPE morphology and lipofuscin accumulation was determined in young and old mice. Our data shows that the clock in the RPE, rather than the retina clock, controls the diurnal phagocytic peak. Surprisingly, absence of a functional RPE clock and phagocytic peak does not result in any detectable age-related degenerative phenotype in the retina or RPE. Thus, our results demonstrate that the circadian clock in the RPE controls the daily peak of phagocytic activity. However, the absence of the clock in the RPE does not result in deterioration of photoreceptors or the RPE during aging.
Collapse
Affiliation(s)
- Christopher DeVera
- Department of Pharmacology & Toxicology and Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA; (C.D.); (K.B.)
| | - Jendayi Dixon
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
| | - Micah A. Chrenek
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
| | - Kenkichi Baba
- Department of Pharmacology & Toxicology and Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA; (C.D.); (K.B.)
| | - Yun Z. Le
- Departments of Medicine, Cell Biology, and Ophthalmology and Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - P. Michael Iuvone
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gianluca Tosini
- Department of Pharmacology & Toxicology and Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA; (C.D.); (K.B.)
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
| |
Collapse
|
13
|
Kanda P, Gupta A, Gottlieb C, Karanjia R, Coupland SG, Bal MS. Pathophysiology of central serous chorioretinopathy: a literature review with quality assessment. Eye (Lond) 2022; 36:941-962. [PMID: 34654892 PMCID: PMC9046392 DOI: 10.1038/s41433-021-01808-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 09/15/2021] [Accepted: 10/01/2021] [Indexed: 01/31/2023] Open
Abstract
The pathogenesis of central serous chorioretinopathy (CSCR), a pachychoroid disease, is poorly understood. While choroid hyperpermeability and retinal pigment epithelium dysfunction are cornerstones for developing CSCR, the mechanisms at the retinal, vascular, retinal pigment epithelium, and cellular level continue to be an enigma. A few preclinical studies and the development of small-sized, poorly controlled clinical trials have resulted in limited insight into the disease mechanism. Effective treatments for CSCR are still lacking as current trials have produced inconsistent results for functional and structural gains. Thus, critically evaluating the literature to explore disease mechanisms and provide an up-to-date understanding of pathophysiology can provide valuable information and avenues to new treatments. In this study, a comprehensive summary of the mechanistic insight into CSCR is presented while highlighting the shortcomings of current literature. The mechanism was divided into seven sub-categories including mechanical obstruction, inflammation, oxidative stress, paracrine factors, autonomic dysfunction, mineralocorticoid receptors activation, and medications. We implemented validated tools like the JBI and CAMARADES to objectively analyze the quality of both clinical and preclinical studies, respectively. Overall, our analysis of the literature showed that no single mechanism was populated with a large number of sufficiently sized and good-quality studies. However, compiling these studies gave hints not only to CSCR pathogenesis but also pachychoroid disease in general while providing suggestions for future exploration.
Collapse
Affiliation(s)
- Pushpinder Kanda
- grid.28046.380000 0001 2182 2255Department of Ophthalmology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada ,grid.412687.e0000 0000 9606 5108University of Ottawa Eye Institute, The Ottawa Hospital, Ottawa, ON Canada
| | - Arnav Gupta
- grid.28046.380000 0001 2182 2255Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Chloe Gottlieb
- grid.28046.380000 0001 2182 2255Department of Ophthalmology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada ,grid.412687.e0000 0000 9606 5108University of Ottawa Eye Institute, The Ottawa Hospital, Ottawa, ON Canada ,grid.412687.e0000 0000 9606 5108Ottawa Hospital Research Institute, Ottawa, ON Canada
| | - Rustum Karanjia
- grid.28046.380000 0001 2182 2255Department of Ophthalmology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada ,grid.412687.e0000 0000 9606 5108University of Ottawa Eye Institute, The Ottawa Hospital, Ottawa, ON Canada ,grid.412687.e0000 0000 9606 5108Ottawa Hospital Research Institute, Ottawa, ON Canada ,grid.280881.b0000 0001 0097 5623Doheny Eye Institute, Los Angeles, CA 90033 USA ,grid.19006.3e0000 0000 9632 6718Doheny Eye Centers UCLA, Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA 91105 USA
| | - Stuart G. Coupland
- grid.28046.380000 0001 2182 2255Department of Ophthalmology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada ,grid.412687.e0000 0000 9606 5108University of Ottawa Eye Institute, The Ottawa Hospital, Ottawa, ON Canada ,grid.28046.380000 0001 2182 2255Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Manpartap Singh Bal
- grid.511274.4Queen’s University School of Medicine, Department of Ophthalmology, Kingston Health Science Centre, Kingston, ON Canada
| |
Collapse
|
14
|
Millo T, Rivera A, Obolensky A, Marks-Ohana D, Xu M, Li Y, Wilhelm E, Gopalakrishnan P, Gross M, Rosin B, Hanany M, Webster A, Tracewska AM, Koenekoop RK, Chen R, Arno G, Schueler-Furman O, Roosing S, Banin E, Sharon D. Identification of autosomal recessive novel genes and retinal phenotypes in members of the solute carrier (SLC) superfamily. Genet Med 2022; 24:1523-1535. [PMID: 35486108 DOI: 10.1016/j.gim.2022.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022] Open
Abstract
PURPOSE This study aimed to investigate the clinical and genetic aspects of solute carrier (SLC) genes in inherited retinal diseases (IRDs). METHODS Exome sequencing data were filtered to identify pathogenic variants in SLC genes. Analysis of transcript and protein expression was performed on fibroblast cell lines and retinal sections. RESULTS Comprehensive analysis of 433 SLC genes in 913 exome sequencing IRD samples revealed homozygous pathogenic variants in 6 SLC genes, including 2 candidate novel genes, which were 2 variants in SLC66A1, causing autosomal recessive retinitis pigmentosa (ARRP), and a variant in SLC39A12, causing autosomal recessive mild widespread retinal degeneration with marked macular involvement. In addition, we present 4 families with ARRP and homozygous null variants in SLC37A3 that were previously suggested to cause retinitis pigmentosa, 2 of which cause exon skipping. The recently reported SLC4A7- c.2007dup variant was found in 2 patients with ARRP resulting in the absence of protein. Finally, variants in SLC24A1 were found in 4 individuals with either ARRP or congenital stationary night blindness. CONCLUSION We report on SLC66A1 and SLC39A12 as candidate novel IRD genes, establish SLC37A3 pathogenicity, and provide further evidence of SLC4A7 as IRD genes. We extend the phenotypic spectrum of SLC24A1 and suggest that its ARRP phenotype may be more common than previously reported.
Collapse
Affiliation(s)
- Talya Millo
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Antonio Rivera
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexey Obolensky
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Devora Marks-Ohana
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mingchu Xu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Yumei Li
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Enosh Wilhelm
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prakadeeswari Gopalakrishnan
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Menachem Gross
- Department of Otolaryngology/Head and Neck Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Boris Rosin
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mor Hanany
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andrew Webster
- University College London, Institute of Ophthalmology, London, United Kingdom; Moorfields Eye Hospital, NHS Foundation Trust, London, United Kingdom
| | - Anna Maria Tracewska
- Łukasiewicz Research Network - PORT Polish Center for Technology Development, Stabłowicka, Wrocław, Poland
| | - Robert K Koenekoop
- Department of Paediatric surgery, Human Genetics and Ophthalmology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Gavin Arno
- University College London, Institute of Ophthalmology, London, United Kingdom; Moorfields Eye Hospital, NHS Foundation Trust, London, United Kingdom
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Susanne Roosing
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Eyal Banin
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Dror Sharon
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
15
|
Brandli A, Khong FL, Kong RCK, Kelly DJ, Fletcher EL. Transcriptomic analysis of choroidal neovascularization reveals dysregulation of immune and fibrosis pathways that are attenuated by a novel anti-fibrotic treatment. Sci Rep 2022; 12:859. [PMID: 35039609 PMCID: PMC8764037 DOI: 10.1038/s41598-022-04845-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/15/2021] [Indexed: 02/05/2023] Open
Abstract
Neovascular AMD (nAMD) leads to vision loss and is a leading cause of visual impairment in the industrialised world. Current treatments that target blood vessel growth have not been able to treat subretinal fibrosis and nAMD patients continue to lose vision. The molecular mechanisms involved in the development of fibrotic lesions in nAMD are not well understood. The aim of this study was to further understand subretinal fibrosis in the laser photocoagulation model of choroidal neovascularization (CNV) by studying the whole transcriptome of the RPE/choroid following CNV and the application of an anti-fibrotic following CNV. Seven days after laser induced CNV, RPE and choroid tissue was separated and underwent RNAseq. Differential expression analysis and pathway analysis revealed an over representation of immune signalling and fibrotic associated pathways in CNV compared to control RPE/choroid tissue. Comparisons between the mouse CNV model to human CNV revealed an overlap in upregulated expression for immune genes (Ccl2, Ccl8 and Cxcl9) and extracellular matrix remodeling genes (Comp, Lrcc15, Fndc1 and Thbs2). Comparisons between the CNV model and other fibrosis models showed an overlap of over 60% of genes upregulated in either lung or kidney mouse models of fibrosis. Treatment of CNV using a novel cinnamoyl anthranilate anti-fibrotic (OCX063) in the laser induced CNV model was selected as this class of drugs have previously been shown to target fibrosis. CNV lesion leakage and fibrosis was found to be reduced using OCX063 and gene expression of genes within the TGF-beta signalling pathway. Our findings show the presence of fibrosis gene expression pathways present in the laser induced CNV mouse model and that anti-fibrotic treatments offer the potential to reduce subretinal fibrosis in AMD.
Collapse
Affiliation(s)
- Alice Brandli
- Department of Anatomy and Physiology, The University of Melbourne, Grattan St, Parkville, VIC, 3010, Australia
| | - Fay L Khong
- Department of Medicine, The University of Melbourne, St Vincent's Hospital, Fitzroy, VIC, 3065, Australia
- Occurx Pty Ltd, 31 Queen St, Melbourne, VIC, 3000, Australia
| | - Roy C K Kong
- Department of Medicine, The University of Melbourne, St Vincent's Hospital, Fitzroy, VIC, 3065, Australia
- Occurx Pty Ltd, 31 Queen St, Melbourne, VIC, 3000, Australia
| | - Darren J Kelly
- Department of Medicine, The University of Melbourne, St Vincent's Hospital, Fitzroy, VIC, 3065, Australia
| | - Erica L Fletcher
- Department of Anatomy and Physiology, The University of Melbourne, Grattan St, Parkville, VIC, 3010, Australia.
| |
Collapse
|
16
|
Little K, Llorián-Salvador M, Scullion S, Hernández C, Simó-Servat O, Del Marco A, Bosma E, Vargas-Soria M, Carranza-Naval MJ, Van Bergen T, Galbiati S, Viganò I, Musi CA, Schlingemann R, Feyen J, Borsello T, Zerbini G, Klaassen I, Garcia-Alloza M, Simó R, Stitt AW. Common pathways in dementia and diabetic retinopathy: understanding the mechanisms of diabetes-related cognitive decline. Trends Endocrinol Metab 2022; 33:50-71. [PMID: 34794851 DOI: 10.1016/j.tem.2021.10.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/06/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Type 2 diabetes (T2D) is associated with multiple comorbidities, including diabetic retinopathy (DR) and cognitive decline, and T2D patients have a significantly higher risk of developing Alzheimer's disease (AD). Both DR and AD are characterized by a number of pathological mechanisms that coalesce around the neurovascular unit, including neuroinflammation and degeneration, vascular degeneration, and glial activation. Chronic hyperglycemia and insulin resistance also play a significant role, leading to activation of pathological mechanisms such as increased oxidative stress and the accumulation of advanced glycation end-products (AGEs). Understanding these common pathways and the degree to which they occur simultaneously in the brain and retina during diabetes will provide avenues to identify T2D patients at risk of cognitive decline.
Collapse
Affiliation(s)
- Karis Little
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - María Llorián-Salvador
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Sarah Scullion
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Cristina Hernández
- Vall d'Hebron Research Institute and CIBERDEM (ISCIII), Barcelona, Spain
| | - Olga Simó-Servat
- Vall d'Hebron Research Institute and CIBERDEM (ISCIII), Barcelona, Spain
| | - Angel Del Marco
- Division of Physiology, School of Medicine, Instituto de Investigacion Biomedica de Cadiz (INIBICA), Universidad de Cadiz, Cadiz, Spain
| | - Esmeralda Bosma
- Ocular Angiogenesis Group, University of Amsterdam, Amsterdam, The Netherlands
| | - Maria Vargas-Soria
- Division of Physiology, School of Medicine, Instituto de Investigacion Biomedica de Cadiz (INIBICA), Universidad de Cadiz, Cadiz, Spain
| | - Maria Jose Carranza-Naval
- Division of Physiology, School of Medicine, Instituto de Investigacion Biomedica de Cadiz (INIBICA), Universidad de Cadiz, Cadiz, Spain
| | | | - Silvia Galbiati
- Complications of Diabetes Unit, Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ilaria Viganò
- Complications of Diabetes Unit, Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Clara Alice Musi
- Università Degli Studi di Milano and Istituto di Ricerche Farmacologiche Mario Negri- IRCCS, Milano, Italy
| | - Reiner Schlingemann
- Ocular Angiogenesis Group, University of Amsterdam, Amsterdam, The Netherlands; Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Lausanne, Switzerland
| | | | - Tiziana Borsello
- Università Degli Studi di Milano and Istituto di Ricerche Farmacologiche Mario Negri- IRCCS, Milano, Italy
| | - Gianpaolo Zerbini
- Complications of Diabetes Unit, Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ingeborg Klaassen
- Ocular Angiogenesis Group, University of Amsterdam, Amsterdam, The Netherlands
| | - Monica Garcia-Alloza
- Division of Physiology, School of Medicine, Instituto de Investigacion Biomedica de Cadiz (INIBICA), Universidad de Cadiz, Cadiz, Spain
| | - Rafael Simó
- Vall d'Hebron Research Institute and CIBERDEM (ISCIII), Barcelona, Spain.
| | - Alan W Stitt
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK.
| | | |
Collapse
|
17
|
Markitantova YV, Simirskii VN. The Role of the Purinergic Signaling System in the Control of Histogenesis, Homeostasis, and Pathogenesis of the Vertebrate Retina. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Landowski M, Bowes Rickman C. Targeting Lipid Metabolism for the Treatment of Age-Related Macular Degeneration: Insights from Preclinical Mouse Models. J Ocul Pharmacol Ther 2021; 38:3-32. [PMID: 34788573 PMCID: PMC8817708 DOI: 10.1089/jop.2021.0067] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Age-related macular degeneration (AMD) is a major leading cause of irreversible visual impairment in the world with limited therapeutic interventions. Histological, biochemical, genetic, and epidemiological studies strongly implicate dysregulated lipid metabolism in the retinal pigmented epithelium (RPE) in AMD pathobiology. However, effective therapies targeting lipid metabolism still need to be identified and developed for this blinding disease. To test lipid metabolism-targeting therapies, preclinical AMD mouse models are needed to establish therapeutic efficacy and the role of lipid metabolism in the development of AMD-like pathology. In this review, we provide a comprehensive overview of current AMD mouse models available to researchers that could be used to provide preclinical evidence supporting therapies targeting lipid metabolism for AMD. Based on previous studies of AMD mouse models, we discuss strategies to modulate lipid metabolism as well as examples of studies evaluating lipid-targeting therapeutics to restore lipid processing in the RPE. The use of AMD mouse models may lead to worthy lipid-targeting candidate therapies for clinical trials to prevent the blindness caused by AMD.
Collapse
Affiliation(s)
- Michael Landowski
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Catherine Bowes Rickman
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, USA.,Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| |
Collapse
|
19
|
Hsp90-associated DNA replication checkpoint protein and proteasome-subunit components are involved in the age-related macular degeneration. Chin Med J (Engl) 2021; 134:2322-2332. [PMID: 34629418 PMCID: PMC8510006 DOI: 10.1097/cm9.0000000000001773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: Age-related macular degeneration (AMD) is the leading cause of vision loss worldwide. However, the mechanisms involved in the development and progression of AMD are poorly delineated. We aimed to explore the critical genes involved in the progression of AMD. Methods: The differentially expressed genes (DEGs) in AMD retinal pigment epithelial (RPE)/choroid tissues were identified using the microarray datasets GSE99248 and GSE125564, which were downloaded from the gene expression omnibus database. The overlapping DEGs from the two datasets were screened to identify DEG-related biological pathways using gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The hub genes were identified from these DEGs through protein-protein interaction network analyses. The expression levels of hub genes were evaluated by quantitative real-time polymerase chain reaction following the induction of senescence in ARPE-19 with FK866. Following the identification of AMD-related key genes, the potential small molecule compounds targeting the key genes were predicted by PharmacoDB. Finally, a microRNA-gene interaction network was constructed. Results: Microarray analyses identified 174 DEGs in the AMD RPE compared to the healthy RPE samples. These DEGs were primarily enriched in the pathways involved in the regulation of DNA replication, cell cycle, and proteasome-mediated protein polyubiquitination. Among the top ten hub genes, HSP90AA1, CHEK1, PSMA4, PSMD4, and PSMD8 were upregulated in the senescent ARPE-19 cells. Additionally, the drugs targeting HSP90AA1, CHEK1, and PSMA4 were identified. We hypothesize that Hsa-miR-16-5p might target four out of the five key DEGs in the AMD RPE. Conclusions: Based on our findings, HSP90AA1 is likely to be a central gene controlling the DNA replication and proteasome-mediated polyubiquitination during the RPE senescence observed in the progression of AMD. Targeting HSP90AA1, CHEK1, PSMA4, PSMD4, and/or PSMD8 genes through specific miRNAs or small molecules might potentially alleviate the progression of AMD through attenuating RPE senescence.
Collapse
|
20
|
Du J, Zhu S, Lim RR, Chao JR. Proline metabolism and transport in retinal health and disease. Amino Acids 2021; 53:1789-1806. [PMID: 33871679 PMCID: PMC8054134 DOI: 10.1007/s00726-021-02981-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/10/2021] [Indexed: 12/11/2022]
Abstract
The retina is one of the most energy-demanding tissues in the human body. Photoreceptors in the outer retina rely on nutrient support from the neighboring retinal pigment epithelium (RPE), a monolayer of epithelial cells that separate the retina and choroidal blood supply. RPE dysfunction or cell death can result in photoreceptor degeneration, leading to blindness in retinal degenerative diseases including some inherited retinal degenerations and age-related macular degeneration (AMD). In addition to having ready access to rich nutrients from blood, the RPE is also supplied with lactate from adjacent photoreceptors. Moreover, RPE can phagocytose lipid-rich outer segments for degradation and recycling on a daily basis. Recent studies show RPE cells prefer proline as a major metabolic substrate, and they are highly enriched for the proline transporter, SLC6A20. In contrast, dysfunctional or poorly differentiated RPE fails to utilize proline. RPE uses proline to fuel mitochondrial metabolism, synthesize amino acids, build the extracellular matrix, fight against oxidative stress, and sustain differentiation. Remarkably, the neural retina rarely imports proline directly, but it uptakes and utilizes intermediates and amino acids derived from proline catabolism in the RPE. Mutations of genes in proline metabolism are associated with retinal degenerative diseases, and proline supplementation is reported to improve RPE-initiated vision loss. This review will cover proline metabolism in RPE and highlight the importance of proline transport and utilization in maintaining retinal metabolism and health.
Collapse
Affiliation(s)
- Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV, 26506, USA. .,Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA. .,One Medical Center Dr, WVU Eye Institute, PO Box 9193, Morgantown, WV, 26505, USA.
| | - Siyan Zhu
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV, 26506, USA.,Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Rayne R Lim
- Department of Ophthalmology, University of Washington, Seattle, WA, 98109, USA
| | - Jennifer R Chao
- Department of Ophthalmology, University of Washington, Seattle, WA, 98109, USA
| |
Collapse
|
21
|
Louer EMM, Yi G, Carmone C, Robben J, Stunnenberg HG, den Hollander AI, Deen PMT. Genes Involved in Energy Metabolism Are Differentially Expressed During the Day-Night Cycle in Murine Retinal Pigment Epithelium. Invest Ophthalmol Vis Sci 2020; 61:49. [PMID: 32460311 PMCID: PMC7405837 DOI: 10.1167/iovs.61.5.49] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose The functional interaction between photoreceptors and retinal pigment epithelium (RPE) cells is essential for vision. Phagocytosis of photoreceptor outer segments (POSs) by the RPE follows a circadian pattern; however, it remains unknown whether other RPE processes follow a daily rhythm. Therefore, our aim was to identify RPE processes following a daily rhythm. Methods Murine RPE was isolated at Zeitgeber time (ZT) 0, 2, 4, 9, 14, and 19 (n = 5 per time point), after which RNA was isolated and sequenced. Genes with a significant difference in expression between time points (P < 0.05) were subjected to EnrichR pathway analysis to identify daily rhythmic processes. Results Pathway enrichment revealed 13 significantly enriched KEGG pathways (P < 0.01), including the metabolic pathway (P = 0.002821). Analysis of the metabolic pathway differentially expressed genes revealed that genes involved in adenosine triphosphate production, glycolysis, glycogenolysis, and glycerophospholipid were low at ZT0 (light onset) and high at ZT19 (night). Genes involved in fatty acid degradation and cholesterol synthesis were high at light onset and low at night. Conclusions Our transcriptome data suggest that the highest energy demand of RPE cells is at night, whereas POS phagocytosis and degradation take place in the morning. Furthermore, we identified genes involved in fatty acid and glycerophospholipid synthesis that are upregulated at night, possibly playing a role in generating building blocks for membrane synthesis.
Collapse
|
22
|
Identification of Key Genes and Pathways Associated with Age-Related Macular Degeneration. J Ophthalmol 2020; 2020:2714746. [PMID: 32904543 PMCID: PMC7456487 DOI: 10.1155/2020/2714746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/16/2020] [Accepted: 07/28/2020] [Indexed: 01/27/2023] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of severe, permanent vision loss among the elderly in the developed world. The cellular and molecular pathogenesis of initiation and development of AMD remain poorly delineated. The limited resources of the human AMD RPE/choroid tissues impeded the extensive study of the disease. To better understand the molecular and pathway changes in human AMD RPE/choroid tissues, we searched the literature and found three independent studies using high-throughput technology to analyze gene expression in 54 human AMD RPE/choroid tissues and 46 age-matched healthy controls. We downloaded these data, pooled them together, and reanalyzed the difference between molecular and pathways by the Ingenuity Pathway Analysis (IPA) database. Totally, 353 differentially expressed genes (DEGs) were identified, among which 181 genes were downregulated and 172 genes were upregulated in RPE/choroid of AMD patients. Furthermore, several significantly enriched biological processes, including cancer, organismal injury and abnormalities, and ophthalmic disease, were identified associated with these DEGs. By analysis of canonical pathway, the phototransduction pathway and atherosclerosis signaling were the top two significant canonical pathways altered in RPE/choroid tissues in human AMD. As expected, several ophthalmic disease-related molecules, including RHO, PDE6A, 3',5'-cyclic-GMP phosphodiesterase, and G protein alpha, were in the central nodes of disease network. The bioinformatics technology combined with the existing high-throughput data was applied to evaluate the underlying key genes and pathways in human AMD tissues, which may predict downstream and upstream biological processes and identify potential therapeutic intervention targets in human AMD.
Collapse
|
23
|
Markitantova YV, Simirskii VN. Role of the Redox System in Initiation of a Regenerative Response of Neural Eye Tissues in Vertebrates. Russ J Dev Biol 2020. [DOI: 10.1134/s106236042001004x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
24
|
Baradaran-Rafii A, Sarvari M, Alavi-Moghadam S, Payab M, Goodarzi P, Aghayan HR, Larijani B, Rezaei-Tavirani M, Biglar M, Arjmand B. Cell-based approaches towards treating age-related macular degeneration. Cell Tissue Bank 2020; 21:339-347. [PMID: 32157501 DOI: 10.1007/s10561-020-09826-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022]
Abstract
Age-related macular degeneration as one of the most common causes of worldwide vision loss needs a proper approach for treatment. Therein, cell therapy and regenerative medicine can hold a great promise to be an effective approach. Accordingly, some preclinical and clinical studies were conducted to search around the therapeutic influence of stem cells in Age-related macular degeneration models and subjects. Hereupon, the purpose of the current review is to discuss the mechanisms of age-related macular degeneration, appropriate animal models along with suitable dosage and route of stem cell administration for its treatment.
Collapse
Affiliation(s)
- Alireza Baradaran-Rafii
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Sarvari
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Aghayan
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mahmood Biglar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
25
|
Markitantova Y, Simirskii V. Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes. Int J Mol Sci 2020; 21:E1602. [PMID: 32111086 PMCID: PMC7084737 DOI: 10.3390/ijms21051602] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Retinal development is under the coordinated control of overlapping networks of signaling pathways and transcription factors. The paper was conceived as a review of the data and ideas that have been formed to date on homeobox genes mutations that lead to the disruption of eye organogenesis and result in inherited eye/retinal diseases. Many of these diseases are part of the same clinical spectrum and have high genetic heterogeneity with already identified associated genes. We summarize the known key regulators of eye development, with a focus on the homeobox genes associated with monogenic eye diseases showing retinal manifestations. Recent advances in the field of genetics and high-throughput next-generation sequencing technologies, including single-cell transcriptome analysis have allowed for deepening of knowledge of the genetic basis of inherited retinal diseases (IRDs), as well as improve their diagnostics. We highlight some promising avenues of research involving molecular-genetic and cell-technology approaches that can be effective for IRDs therapy. The most promising neuroprotective strategies are aimed at mobilizing the endogenous cellular reserve of the retina.
Collapse
|
26
|
DeVera C, Tosini G. Circadian analysis of the mouse retinal pigment epithelium transcriptome. Exp Eye Res 2020; 193:107988. [PMID: 32105725 DOI: 10.1016/j.exer.2020.107988] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
The presence of a phagocytic peak of photoreceptor outer segments by the retinal pigment epithelium (RPE) one or 2 h after the onset of light has been reported for several diurnal and nocturnal species. This peak in phagocytic activity also persists under constant lighting conditions (i.e., constant light or dark) thus demonstrating that the timing of this peak is driven by a circadian clock. The aim of this study was to investigate the change in RPE whole transcriptome at two different circadian times (CT; 1 h before (CT23) and 1 h after (CT1) subjective light onset). C57BL/6J male mice were maintained in constant dark conditions for three days and euthanized under red light (<1 lux) at CT23 and CT1. RPE was isolated from whole eyes for RNA library preparation and sequencing on an Illumina HiSeq4000 platform. 14,083 mouse RPE transcripts were detected in common between CT23 and CT1. 12,005 were protein coding transcripts and 2078 were non-protein coding transcripts. 2421 protein coding transcripts were significantly upregulated whereas only 3 transcripts were significantly downregulated and 12 non-protein coding transcripts were significantly upregulated and 31 non-protein coding transcripts were significantly downregulated at CT1 when compared to CT23 (p < 0.05, fold change ≥ ±2.0). Of the protein coding transcripts, most of them were characterized as: enzymes, kinases, and transcriptional regulators with a large majority of activity in the cytoplasm, nucleus, and plasma membrane. Non-protein coding transcripts included biotypes such as long-non coding RNAs and pseudogenes. Gene ontology analysis and ingenuity pathway analysis revealed that differentially expressed transcripts were associated with integrin signaling, oxidative phosphorylation, protein phosphorylation, and actin cytoskeleton remodeling suggesting that these previously identified phagocytic pathways are under circadian control. Our analysis identified new pathways (e.g., increased mitochondrial respiration via increased oxidative phosphorylation) that may be involved in the circadian control of phagocytic activity. In addition, our dataset suggests a possible regulatory role for the identified non-protein coding transcripts in mediating the complex function of RPE phagocytosis. Finally, our results also indicate, as seen in other tissues, about 20% of the whole RPE transcriptome may be under circadian clock regulation.
Collapse
Affiliation(s)
- Christopher DeVera
- Department of Pharmacology and Toxicology, Atlanta, GA, USA, 30310; Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA, USA, 30310
| | - Gianluca Tosini
- Department of Pharmacology and Toxicology, Atlanta, GA, USA, 30310; Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA, USA, 30310.
| |
Collapse
|
27
|
Yam M, Engel AL, Wang Y, Zhu S, Hauer A, Zhang R, Lohner D, Huang J, Dinterman M, Zhao C, Chao JR, Du J. Proline mediates metabolic communication between retinal pigment epithelial cells and the retina. J Biol Chem 2019; 294:10278-10289. [PMID: 31110046 PMCID: PMC6664195 DOI: 10.1074/jbc.ra119.007983] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/16/2019] [Indexed: 01/16/2023] Open
Abstract
The retinal pigment epithelium (RPE) is a monolayer of pigmented cells between the choroid and the retina. RPE dysfunction underlies many retinal degenerative diseases, including age-related macular degeneration, the leading cause of age-related blindness. To perform its various functions in nutrient transport, phagocytosis of the outer segment, and cytokine secretion, the RPE relies on an active energy metabolism. We previously reported that human RPE cells prefer proline as a nutrient and transport proline-derived metabolites to the apical, or retinal, side. In this study, we investigated how RPE utilizes proline in vivo and why proline is a preferred substrate. By using [13C]proline labeling both ex vivo and in vivo, we found that the retina rarely uses proline directly, whereas the RPE utilizes it at a high rate, exporting proline-derived mitochondrial intermediates for use by the retina. We observed that in primary human RPE cell culture, proline is the only amino acid whose uptake increases with cellular maturity. In human RPE, proline was sufficient to stimulate de novo serine synthesis, increase reductive carboxylation, and protect against oxidative damage. Blocking proline catabolism in RPE impaired glucose metabolism and GSH production. Notably, in an acute model of RPE-induced retinal degeneration, dietary proline improved visual function. In conclusion, proline is an important nutrient that supports RPE metabolism and the metabolic demand of the retina.
Collapse
Affiliation(s)
- Michelle Yam
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Abbi L Engel
- the Department of Ophthalmology, University of Washington, Seattle, Washington 98109
| | - Yekai Wang
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Siyan Zhu
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Allison Hauer
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Rui Zhang
- From the Departments of Ophthalmology and
- the Save Sight Institute, University of Sydney, 8 Macquarie Street, Sydney, New South Wales 2000, Australia
| | - Daniel Lohner
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Jiancheng Huang
- From the Departments of Ophthalmology and
- the Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China, and
- the Department of Ophthalmology, State Key Laboratory of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Marlee Dinterman
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Chen Zhao
- the Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China, and
| | - Jennifer R Chao
- the Department of Ophthalmology, University of Washington, Seattle, Washington 98109,
| | - Jianhai Du
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| |
Collapse
|
28
|
Liu B, Calton MA, Abell NS, Benchorin G, Gloudemans MJ, Chen M, Hu J, Li X, Balliu B, Bok D, Montgomery SB, Vollrath D. Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. Commun Biol 2019; 2:186. [PMID: 31123710 PMCID: PMC6527609 DOI: 10.1038/s42003-019-0430-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023] Open
Abstract
The retinal pigment epithelium (RPE) serves vital roles in ocular development and retinal homeostasis but has limited representation in large-scale functional genomics datasets. Understanding how common human genetic variants affect RPE gene expression could elucidate the sources of phenotypic variability in selected monogenic ocular diseases and pinpoint causal genes at genome-wide association study (GWAS) loci. We interrogated the genetics of gene expression of cultured human fetal RPE (fRPE) cells under two metabolic conditions and discovered hundreds of shared or condition-specific expression or splice quantitative trait loci (e/sQTLs). Co-localizations of fRPE e/sQTLs with age-related macular degeneration (AMD) and myopia GWAS data suggest new candidate genes, and mechanisms by which a common RDH5 allele contributes to both increased AMD risk and decreased myopia risk. Our study highlights the unique transcriptomic characteristics of fRPE and provides a resource to connect e/sQTLs in a critical ocular cell type to monogenic and complex eye disorders.
Collapse
Affiliation(s)
- Boxiang Liu
- Department of Biology, Stanford University, Stanford, CA 94305 USA
| | - Melissa A. Calton
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Nathan S. Abell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Gillie Benchorin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael J. Gloudemans
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, 94305 CA USA
| | - Ming Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Jane Hu
- Department of Ophthalmology, Jules Stein Eye Institute, UCLA, Los Angeles, 90095 CA USA
| | - Xin Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Brunilda Balliu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Dean Bok
- Department of Ophthalmology, Jules Stein Eye Institute, UCLA, Los Angeles, 90095 CA USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Douglas Vollrath
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| |
Collapse
|
29
|
Donato L, Scimone C, Nicocia G, D'Angelo R, Sidoti A. Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. Cell Cycle 2018; 18:84-104. [PMID: 30569795 DOI: 10.1080/15384101.2018.1558873] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is a very heterogeneous inherited ocular disorder group characterized by progressive retinal disruption. Retinal pigment epithelium (RPE) degeneration, due to oxidative stress which arrests the metabolic support to photoreceptors, represents one of the principal causes of RP. Here, the role of oxidative stress in RP onset and progression was analyzed by a comparative whole transcriptome analysis of human RPE cells, treated with 100 µg/ml of oxLDL and untreated, at different time points. Experiment was thrice repeated and performed on Ion ProtonTM sequencing system. Data analysis, including low quality reads trimming and gene expression quantification, was realized by CLC Genomics Workbench software. The whole analysis highlighted 14 clustered "macro-pathways" and many sub-pathways, classified by selection of 5271 genes showing the highest alteration of expression. Among them, 23 genes were already known to be RP causative ones (15 over-expressed and 8 down-expressed), and their enrichment and intersection analyses highlighted new 77 candidate related genes (49 over-expressed and 28 down-expressed). A final filtering analysis then highlighted 29 proposed candidate genes. This data suggests that many new genes, not yet associated with RP, could influence its etiopathogenesis.
Collapse
Affiliation(s)
- Luigi Donato
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Concetta Scimone
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Giacomo Nicocia
- c Department of Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | - Rosalia D'Angelo
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Antonina Sidoti
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| |
Collapse
|
30
|
Foltz LP, Howden SE, Thomson JA, Clegg DO. Functional Assessment of Patient-Derived Retinal Pigment Epithelial Cells Edited by CRISPR/Cas9. Int J Mol Sci 2018; 19:E4127. [PMID: 30572641 PMCID: PMC6321630 DOI: 10.3390/ijms19124127] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa is the most common form of inherited blindness and can be caused by a multitude of different genetic mutations that lead to similar phenotypes. Specifically, mutations in ubiquitously expressed splicing factor proteins are known to cause an autosomal dominant form of the disease, but the retina-specific pathology of these mutations is not well understood. Fibroblasts from a patient with splicing factor retinitis pigmentosa caused by a missense mutation in the PRPF8 splicing factor were used to produce three diseased and three CRISPR/Cas9-corrected induced pluripotent stem cell (iPSC) clones. We differentiated each of these clones into retinal pigment epithelial (RPE) cells via directed differentiation and analyzed the RPE cells in terms of gene and protein expression, apicobasal polarity, and phagocytic ability. We demonstrate that RPE cells can be produced from patient-derived and corrected cells and they exhibit morphology and functionality similar but not identical to wild-type RPE cells in vitro. Functionally, the RPE cells were able to establish apicobasal polarity and phagocytose photoreceptor outer segments at the same capacity as wild-type cells. These data suggest that patient-derived iPSCs, both diseased and corrected, are able to differentiate into RPE cells with a near normal phenotype and without differences in phagocytosis, a result that differs from previous mouse models. These RPE cells can now be studied to establish a disease-in-a-dish system relevant to retinitis pigmentosa.
Collapse
Affiliation(s)
- Leah P Foltz
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Sara E Howden
- Murdoch Children's Research Institute, University of Melbourne, Parkville 3052, Australia.
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - James A Thomson
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Dennis O Clegg
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
| |
Collapse
|
31
|
On the origin of proteins in human drusen: The meet, greet and stick hypothesis. Prog Retin Eye Res 2018; 70:55-84. [PMID: 30572124 DOI: 10.1016/j.preteyeres.2018.12.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/12/2022]
Abstract
Retinal drusen formation is not only a clinical hallmark for the development of age-related macular degeneration (AMD) but also for other disorders, such as Alzheimer's disease and renal diseases. The initiation and growth of drusen is poorly understood. Attention has focused on lipids and minerals, but relatively little is known about the origin of drusen-associated proteins and how they are retained in the space between the basal lamina of the retinal pigment epithelium and the inner collagenous layer space (sub-RPE-BL space). While some authors suggested that drusen proteins are mainly derived from cellular debris from processed photoreceptor outer segments and the RPE, others suggest a choroidal cell or blood origin. Here, we reviewed and supplemented the existing literature on the molecular composition of the retina/choroid complex, to gain a more complete understanding of the sources of proteins in drusen. These "drusenomics" studies showed that a considerable proportion of currently identified drusen proteins is uniquely originating from the blood. A smaller, but still large fraction of drusen proteins comes from both blood and/or RPE. Only a small proportion of drusen proteins is uniquely derived from the photoreceptors or choroid. We next evaluated how drusen components may "meet, greet and stick" to each other and/or to structures like hydroxyapatite spherules to form macroscopic deposits in the sub-RPE-BL space. Finally, we discuss implications of our findings with respect to the previously proposed homology between drusenogenesis in AMD and plaque formation in atherosclerosis.
Collapse
|
32
|
Korkka I, Viheriälä T, Juuti-Uusitalo K, Uusitalo-Järvinen H, Skottman H, Hyttinen J, Nymark S. Functional Voltage-Gated Calcium Channels Are Present in Human Embryonic Stem Cell-Derived Retinal Pigment Epithelium. Stem Cells Transl Med 2018; 8:179-193. [PMID: 30394009 PMCID: PMC6344904 DOI: 10.1002/sctm.18-0026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 08/24/2018] [Accepted: 09/07/2018] [Indexed: 11/25/2022] Open
Abstract
Retinal pigment epithelium (RPE) performs important functions for the maintenance of photoreceptors and vision. Malfunctions within the RPE are implicated in several retinal diseases for which transplantations of stem cell‐derived RPE are promising treatment options. Their success, however, is largely dependent on the functionality of the transplanted cells. This requires correct cellular physiology, which is highly influenced by the various ion channels of RPE, including voltage‐gated Ca2+ (CaV) channels. This study investigated the localization and functionality of CaV channels in human embryonic stem cell (hESC)‐derived RPE. Whole‐cell patch‐clamp recordings from these cells revealed slowly inactivating L‐type currents comparable to freshly isolated mouse RPE. Some hESC‐RPE cells also carried fast transient T‐type resembling currents. These findings were confirmed by immunostainings from both hESC‐ and mouse RPE that showed the presence of the L‐type Ca2+ channels CaV1.2 and CaV1.3 as well as the T‐type Ca2+ channels CaV3.1 and CaV3.2. The localization of the major subtype, CaV1.3, changed during hESC‐RPE maturation co‐localizing with pericentrin to the base of the primary cilium before reaching more homogeneous membrane localization comparable to mouse RPE. Based on functional assessment, the L‐type Ca2+ channels participated in the regulation of vascular endothelial growth factor secretion as well as in the phagocytosis of photoreceptor outer segments in hESC‐RPE. Overall, this study demonstrates that a functional machinery of voltage‐gated Ca2+ channels is present in mature hESC‐RPE, which is promising for the success of transplantation therapies. stem cells translational medicine2019;8:179&15
Collapse
Affiliation(s)
- Iina Korkka
- Faculty of Biomedical Sciences and Engineering, BioMediTech, Tampere University of Technology, Tampere, Finland
| | - Taina Viheriälä
- Faculty of Biomedical Sciences and Engineering, BioMediTech, Tampere University of Technology, Tampere, Finland.,Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere, Finland
| | - Kati Juuti-Uusitalo
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere, Finland
| | - Hannele Uusitalo-Järvinen
- Eye Centre, Tampere University Hospital, Tampere, Finland.,Faculty of Medicine and Life Sciences, Department of Ophthalmology, University of Tampere, Tampere, Finland
| | - Heli Skottman
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere, Finland
| | - Jari Hyttinen
- Faculty of Biomedical Sciences and Engineering, BioMediTech, Tampere University of Technology, Tampere, Finland
| | - Soile Nymark
- Faculty of Biomedical Sciences and Engineering, BioMediTech, Tampere University of Technology, Tampere, Finland
| |
Collapse
|
33
|
Bennis A, Jacobs JG, Catsburg LAE, Ten Brink JB, Koster C, Schlingemann RO, van Meurs J, Gorgels TGMF, Moerland PD, Heine VM, Bergen AA. Stem Cell Derived Retinal Pigment Epithelium: The Role of Pigmentation as Maturation Marker and Gene Expression Profile Comparison with Human Endogenous Retinal Pigment Epithelium. Stem Cell Rev Rep 2018; 13:659-669. [PMID: 28730556 PMCID: PMC5602068 DOI: 10.1007/s12015-017-9754-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In age-related macular degeneration (AMD) the retinal pigment epithelium (RPE) deteriorates, leading to photoreceptor decay and severe vision loss. New therapeutic strategies aim at RPE replacement by transplantation of pluripotent stem cell (PSC)-derived RPE. Several protocols to generate RPE have been developed where appearance of pigmentation is commonly used as indicator of RPE differentiation and maturation. It is, however, unclear how different pigmentation stages reflect developmental stages and functionality of PSC-derived RPE cells. We generated human embryonic stem cell-derived RPE (hESC-RPE) cells and investigated their gene expression profiles at early pigmentation (EP) and late pigmentation (LP) stages. In addition, we compared the hESC-RPE samples with human endogenous RPE. We used a common reference design microarray (44 K). Our analysis showed that maturing hESC-RPE, upon acquiring pigmentation, expresses markers specific for human RPE. Interestingly, our analysis revealed that EP and LP hESC-RPE do not differ much in gene expression. Our data further showed that pigmented hESC-RPE has a significant lower expression than human endogenous RPE in the visual cycle and oxidative stress pathways. In contrast, we observed a significantly higher expression of pathways related to the process adhesion-to-polarity model that is typical of developing epithelial cells. We conclude that, in vitro, the first appearance of pigmentation hallmarks differentiated RPE. However, further increase in pigmentation does not result in much significant gene expression changes and does not add important RPE functionalities. Consequently, our results suggest that the time span for obtaining differentiated hESC-RPE cells, that are suitable for transplantation, may be greatly reduced.
Collapse
Affiliation(s)
- A Bennis
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - J G Jacobs
- Department of Pediatrics/Child Neurology, VU University Medical Center, Amsterdam, The Netherlands
| | - L A E Catsburg
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - J B Ten Brink
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - C Koster
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - R O Schlingemann
- Ocular Angiogenesis Group, AMC, Amsterdam, The Netherlands.,Department of Ophthalmology, AMC, Amsterdam, The Netherlands.,Department of Cell Biology and Histology, AMC, Amsterdam, The Netherlands
| | - J van Meurs
- Rotterdam Eye Hospital, Amsterdam, The Netherlands
| | - T G M F Gorgels
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.,University Eye Clinic Maastricht, MUMC+, Amsterdam, The Netherlands
| | - P D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, AMC, Amsterdam, The Netherlands
| | - V M Heine
- Department of Pediatrics/Child Neurology, VU University Medical Center, Amsterdam, The Netherlands. .,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands.
| | - A A Bergen
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands. .,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands. .,Department of Ophthalmology, AMC, Amsterdam, The Netherlands.
| |
Collapse
|
34
|
Chiang CK, Tworak A, Kevany BM, Xu B, Mayne J, Ning Z, Figeys D, Palczewski K. Quantitative phosphoproteomics reveals involvement of multiple signaling pathways in early phagocytosis by the retinal pigmented epithelium. J Biol Chem 2017; 292:19826-19839. [PMID: 28978645 DOI: 10.1074/jbc.m117.812677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/22/2017] [Indexed: 12/12/2022] Open
Abstract
One of the major biological functions of the retinal pigmented epithelium (RPE) is the clearance of shed photoreceptor outer segments (POS) through a multistep process resembling phagocytosis. RPE phagocytosis helps maintain the viability of photoreceptors that otherwise could succumb to the high metabolic flux and photo-oxidative stress associated with visual processing. The regulatory mechanisms underlying phagocytosis in the RPE are not fully understood, although dysfunction of this process contributes to the pathogenesis of multiple human retinal degenerative disorders, including age-related macular degeneration. Here, we present an integrated transcriptomic, proteomic, and phosphoproteomic analysis of phagocytosing RPE cells, utilizing three different experimental models: the human-derived RPE-like cell line ARPE-19, cultured murine primary RPE cells, and RPE samples from live mice. Our combined results indicated that early stages of phagocytosis in the RPE are mainly characterized by pronounced changes in the protein phosphorylation level. Global phosphoprotein enrichment analysis revealed involvement of PI3K/Akt, mechanistic target of rapamycin (mTOR), and MEK/ERK pathways in the regulation of RPE phagocytosis, confirmed by immunoblot analyses and in vitro phagocytosis assays. Most strikingly, phagocytosis of POS by cultured RPE cells was almost completely blocked by pharmacological inhibition of phosphorylation of Akt. Our findings, along with those of previous studies, indicate that these phosphorylation events allow the RPE to integrate multiple signals instigated by shed POS at different stages of the phagocytic process.
Collapse
Affiliation(s)
- Cheng-Kang Chiang
- From the Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada.,the Department of Chemistry, National Dong Hwa University, No. 1 Sec. 2 Da Hsueh Road, Shoufeng, Hualien 97401, Taiwan
| | | | | | - Bo Xu
- From the Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Janice Mayne
- From the Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Zhibin Ning
- From the Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Daniel Figeys
- From the Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada, .,the Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada
| | - Krzysztof Palczewski
- the Department of Pharmacology and .,the Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, and
| |
Collapse
|
35
|
Shao Z, Wang H, Zhou X, Guo B, Gao X, Xiao Z, Liu M, Sha J, Jiang C, Luo Y, Liu Z, Li S. Spontaneous generation of a novel foetal human retinal pigment epithelium (RPE) cell line available for investigation on phagocytosis and morphogenesis. Cell Prolif 2017; 50. [PMID: 28924976 PMCID: PMC6529143 DOI: 10.1111/cpr.12386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/18/2017] [Indexed: 12/16/2022] Open
Abstract
Objectives Primary retinal pigment epithelium (RPE) cells have a limited capacity to re‐establish epithelial morphology and to maintain native RPE function in vitro, and all commercially available RPE cell lines have drawbacks of morphology or function; therefore, the establishment of new RPE cell lines with typical characteristics of RPE would be helpful in further understanding of their physiological and pathological mechanisms. Here, we firstly report a new spontaneously generated RPE line, fhRPE‐13A, from a 13‐week aborted foetus. We aimed to investigate its availability as a RPE model. Materials and methods RNA‐seq data were mapped to the human genome assembly hg19. Global transcriptional data were analysed by Weighted Gene Co‐expression Network Analysis (WGCNA) and differentially expressed genes (DEGs). The morphology and molecular characteristics were examined by immunofluorescence, transmission electron micrographs, PCR and western blot. Photoreceptor outer segments (POS) phagocytosis assay and transepithelial resistance measurement (TER) were performed to assess phagocytic activity and barrier function, respectively. Results The fhRPE‐13A cells showed typical polygonal morphology and normal biological processes of RPE. Meanwhile they were capable of POS phagocytosis in vitro, and the expression level of TYR and TYRP1 were significantly higher than that in ARPE‐19 cells. Conclusions The foetal human RPE line fhRPE‐13A is a valuable system for researching phagocytosis and morphogenesis of RPE in vitro.
Collapse
Affiliation(s)
- Zhihua Shao
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haiyun Wang
- Shanghai First Maternity and Infant Health Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuejian Zhou
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Baosen Guo
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Xuehu Gao
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Zengrong Xiao
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Meng Liu
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Jihong Sha
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Chunlian Jiang
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Yuping Luo
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhixue Liu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Siguang Li
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
36
|
Au ED, Fernandez-Godino R, Kaczynksi TJ, Sousa ME, Farkas MH. Characterization of lincRNA expression in the human retinal pigment epithelium and differentiated induced pluripotent stem cells. PLoS One 2017; 12:e0183939. [PMID: 28837677 PMCID: PMC5570510 DOI: 10.1371/journal.pone.0183939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/14/2017] [Indexed: 11/29/2022] Open
Abstract
Long intervening non-coding RNAs (lincRNAs) are increasingly being implicated as important factors in many aspects of cellular development, function, and disease, but remain poorly understood. In this study, we examine the human retinal pigment epithelium (RPE) lincRNA transcriptome using RNA-Seq data generated from human fetal RPE (fRPE), RPE derived from human induced pluripotent stem cells (iPS-RPE), and undifferentiated iPS (iPS). In addition, we determine the suitability of iPS-RPE, from a transcriptome standpoint, as a model for use in future studies of lincRNA structure and function. A comparison of gene and isoform expression across the whole transcriptome shows only minimal differences between all sample types, though fRPE and iPS-RPE show higher concordance than either shows with iPS. Notably, RPE signature genes show the highest degree of fRPE to iPS-RPE concordance, indicating that iPS-RPE cells provide a suitable model for use in future studies. An analysis of lincRNAs demonstrates high concordance between fRPE and iPS-RPE, but low concordance between either RPE and iPS. While most lincRNAs are expressed at low levels (RPKM < 10), there is a high degree of concordance among replicates within each sample type, suggesting the expression is consistent, even at levels subject to high variability. Finally, we identified and annotated 180 putative novel genes in the fRPE samples, a majority of which are also expressed in the iPS-RPE. Overall, this study represents the first characterization of lincRNA expression in the human RPE, and provides a model for studying the role lincRNAs play in RPE development, function, and disease.
Collapse
Affiliation(s)
- Elizabeth D. Au
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
| | - Rosario Fernandez-Godino
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States of America
| | - Tadeusz J. Kaczynksi
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
| | - Maria E. Sousa
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
| | - Michael H. Farkas
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- * E-mail:
| |
Collapse
|
37
|
Bennis A, ten Brink JB, Moerland PD, Heine VM, Bergen AA. Comparative gene expression study and pathway analysis of the human iris- and the retinal pigment epithelium. PLoS One 2017; 12:e0182983. [PMID: 28827822 PMCID: PMC5565104 DOI: 10.1371/journal.pone.0182983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/27/2017] [Indexed: 11/25/2022] Open
Abstract
Background The retinal pigment epithelium (RPE) is a neural monolayer lining the back of the eye. Degeneration of the RPE leads to severe vision loss in, so far incurable, diseases such as age-related macular degeneration and some forms of retinitis pigmentosa. A promising future replacement therapy may be autologous iris epithelial cell transdifferentiation into RPE in vitro and, subsequently, transplantation. In this study we compared the gene expression profiles of the iris epithelium (IE) and the RPE. Methods We collected both primary RPE- and IE cells from 5 freshly frozen human donor eyes, using respectively laser dissection microscopy and excision. We performed whole-genome expression profiling using 44k Agilent human microarrays. We investigated the gene expression profiles on both gene and functional network level, using R and the knowledge database Ingenuity. Results The major molecular pathways related to the RPE and IE were quite similar and yielded basic neuro-epithelial cell functions. Nonetheless, we also found major specific differences: For example, genes and molecular pathways, related to the visual cycle and retinol biosynthesis are significantly higher expressed in the RPE than in the IE. Interestingly, Wnt and aryl hydrocarbon receptor (AhR-) signaling pathways are much higher expressed in the IE than in the RPE, suggesting, respectively, a possible pluripotent and high detoxification state of the IE. Conclusions This study provides a valuation of the similarities and differences between the expression profiles of the RPE and IE. Our data combined with that of the literature, represent a most comprehensive perspective on transcriptional variation, which may support future research in the development of therapeutic transplantation of IE.
Collapse
Affiliation(s)
- Anna Bennis
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Vivi M. Heine
- Department of Pediatrics / Child Neurology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Centre, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
38
|
Hughes AE, Bridgett S, Meng W, Li M, Curcio CA, Stambolian D, Bradley DT. Sequence and Expression of Complement Factor H Gene Cluster Variants and Their Roles in Age-Related Macular Degeneration Risk. Invest Ophthalmol Vis Sci 2017; 57:2763-9. [PMID: 27196323 PMCID: PMC4884056 DOI: 10.1167/iovs.15-18744] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Purpose To investigate how potentially functional genetic variants are coinherited on each of four common complement factor H (CFH) and CFH-related gene haplotypes and to measure expression of these genes in eye and liver tissues. Methods We sequenced the CFH region in four individuals (one homozygote for each of four common CFH region haplotypes) to identify all genetic variants. We studied associations between the haplotypes and AMD phenotypes in 2157 cases and 1150 controls. We examined RNA-seq profiles in macular and peripheral retina and retinal pigment epithelium/choroid/sclera (RCS) from eight eye donors and three liver samples. Results The haplotypic coinheritance of potentially functional variants (including missense variants, novel splice sites, and the CFHR3–CFHR1 deletion) was described for the four common haplotypes. Expression of the short and long CFH transcripts differed markedly between the retina and liver. We found no expression of any of the five CFH-related genes in the retina or RCS, in contrast to the liver, which is the main source of the circulating proteins. Conclusions We identified all genetic variants on common CFH region haplotypes and described their coinheritance. Understanding their functional effects will be key to developing and stratifying AMD therapies. The small scale of our expression study prevented us from investigating the relationships between CFH region haplotypes and their expression, and it will take time and collaboration to develop epidemiologic-scale studies. However, the striking difference between systemic and ocular expression of complement regulators shown in this study suggests important implications for the development of intraocular and systemic treatments.
Collapse
Affiliation(s)
- Anne E Hughes
- Formerly of Centre for Public Health Queen's University Belfast, Belfast, United Kingdom
| | - Stephen Bridgett
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Weihua Meng
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Christine A Curcio
- Department of Ophthalmology, University of Alabama, Birmingham, Alabama, United States
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Declan T Bradley
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| |
Collapse
|
39
|
Csincsi ÁI, Szabó Z, Bánlaki Z, Uzonyi B, Cserhalmi M, Kárpáti É, Tortajada A, Caesar JJE, Prohászka Z, Jokiranta TS, Lea SM, Rodríguez de Córdoba S, Józsi M. FHR-1 Binds to C-Reactive Protein and Enhances Rather than Inhibits Complement Activation. THE JOURNAL OF IMMUNOLOGY 2017; 199:292-303. [PMID: 28533443 DOI: 10.4049/jimmunol.1600483] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/21/2017] [Indexed: 01/28/2023]
Abstract
Factor H-related protein (FHR) 1 is one of the five human FHRs that share sequence and structural homology with the alternative pathway complement inhibitor FH. Genetic studies on disease associations and functional analyses indicate that FHR-1 enhances complement activation by competitive inhibition of FH binding to some surfaces and immune proteins. We have recently shown that FHR-1 binds to pentraxin 3. In this study, our aim was to investigate whether FHR-1 binds to another pentraxin, C-reactive protein (CRP), analyze the functional relevance of this interaction, and study the role of FHR-1 in complement activation and regulation. FHR-1 did not bind to native, pentameric CRP, but it bound strongly to monomeric CRP via its C-terminal domains. FHR-1 at high concentration competed with FH for CRP binding, indicating possible complement deregulation also on this ligand. FHR-1 did not inhibit regulation of solid-phase C3 convertase by FH and did not inhibit terminal complement complex formation induced by zymosan. On the contrary, by binding C3b, FHR-1 allowed C3 convertase formation and thereby enhanced complement activation. FHR-1/CRP interactions increased complement activation via the classical and alternative pathways on surfaces such as the extracellular matrix and necrotic cells. Altogether, these results identify CRP as a ligand for FHR-1 and suggest that FHR-1 enhances, rather than inhibits, complement activation, which may explain the protective effect of FHR-1 deficiency in age-related macular degeneration.
Collapse
Affiliation(s)
- Ádám I Csincsi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zsóka Szabó
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zsófia Bánlaki
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Barbara Uzonyi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Immunology Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Marcell Cserhalmi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Éva Kárpáti
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Agustín Tortajada
- Departamento Medicina Celular y Molecular, Centro de Investigaciones Biológicas, 28040 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28040 Madrid, Spain
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Zoltán Prohászka
- Research Laboratory, 3rd Department of Internal Medicine, Semmelweis University, H-1125 Budapest, Hungary; and
| | - T Sakari Jokiranta
- Research Programs Unit, Immunobiology, Haartman Institute, University of Helsinki, FI-00014 Helsinki, Finland
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Santiago Rodríguez de Córdoba
- Departamento Medicina Celular y Molecular, Centro de Investigaciones Biológicas, 28040 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28040 Madrid, Spain
| | - Mihály Józsi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary;
| |
Collapse
|
40
|
Wegscheid ML, Anastasaki C, Gutmann DH. Human stem cell modeling in neurofibromatosis type 1 (NF1). Exp Neurol 2017; 299:270-280. [PMID: 28392281 DOI: 10.1016/j.expneurol.2017.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/15/2017] [Accepted: 04/05/2017] [Indexed: 01/03/2023]
Abstract
The future of precision medicine is heavily reliant on the use of human tissues to identify the key determinants that account for differences between individuals with the same disorder. This need is exemplified by the neurofibromatosis type 1 (NF1) neurogenetic condition. As such, individuals with NF1 are born with a germline mutation in the NF1 gene, but may develop numerous distinct neurological problems, ranging from autism and attention deficit to brain and peripheral nerve sheath tumors. Coupled with accurate preclinical mouse models, the availability of NF1 patient-derived induced pluripotent stem cells (iPSCs) provides new opportunities to define the critical factors that underlie NF1-associated nervous system disease pathogenesis and progression. In this review, we discuss the generation and potential applications of iPSC technology to the study of NF1.
Collapse
Affiliation(s)
- Michelle L Wegscheid
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Corina Anastasaki
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States.
| |
Collapse
|