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Zhou Y, Zhou W, Rao Y, He J, Huang Y, Zhao P, Li J. Dysregulated energy and protein homeostasis and the loss of GABAergic amacrine cells in aging retina. Exp Eye Res 2024; 245:109985. [PMID: 38945518 DOI: 10.1016/j.exer.2024.109985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/30/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Aging is a major risk factor for the development or the worsening of retinal degenerative conditions. The intricate network of the neural retina determined that the retinal aging is a complicated process. The aim of this study is to delineate the transcriptomic changes of major retinal neurons during aging in C57BL/6 mice at single-cell level. We analyzed the transcriptional profiles of the photoreceptor, bipolar, amacrine, and Müller glial cells of 1.5-2 and 24-30 months old mice using single-cell RNA sequencing technique. We selectively confirmed the differences in gene expression using immunofluorescence staining and RNA in situ hybridization analysis. We found that each retinal cell type had unique changes upon aging. However, they all showed signs of dysregulated glucose and energy metabolism, and perturbed proteostasis. In particular, old Müller glia exhibited the most profound changes, including the upregulation of cell metabolism, stress-responses, antigen-presentation and immune responses and metal ion homeostasis. The dysregulated gliogenesis and differentiation was confirmed by the presence of Müller glia expressing rod-specific genes in the inner nuclear layer and the outer plexiform layer of the old retina. We further pinpointed the specific loss of GABAergic amacrine cells in old retina. Our study emphasized changes of amacrine and Müller glia during retinal aging, provided resources for further research on the molecular and cellular regulatory mechanisms underlying aging-associated retinal deterioration.
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Affiliation(s)
- Yutong Zhou
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Wenchuan Zhou
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yuqing Rao
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Jincan He
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yue Huang
- Department of Ophthalmology, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Peiquan Zhao
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Jing Li
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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2
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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.
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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.
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3
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Kulshrestha P, Sharma S, Vishwakarma S, Ali MJ, Dave TV, Kaur I. Quality and applicability of cadaveric donor eyes for molecular biology research: An Indian experience. Indian J Ophthalmol 2024; 72:962-967. [PMID: 38454856 DOI: 10.4103/ijo.ijo_2553_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/04/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE Human ocular tissue banking plays an important part in the advancement of translational research for identifying the molecular processes involved in disease etiology and pathogenesis. Timely obtaining a good-quality ocular tissue from a cadaveric donor is exceedingly difficult, especially in remote areas, with a variable transportation time (within 12-24 h), raising concerns about RNA quality and its subsequent applications. Therefore, we assessed the utility of retinal tissues from cadaver donor and enucleated eyes based on the RNA quality and gene expression by real-time polymerase chain reaction (PCR). SETTINGS AND DESIGN Prospective study. METHODS Retina tissues were separated from the donor/enucleated eyes received in the eye bank within 24 h of death (n = 15) and within an hour from OR (n = 3), respectively, and stored immediately at -80 degree. RNA was isolated using trizol, and the quantity and quality were assessed using Qubit and agarose gel electrophoresis, respectively. QPCR was performed for measuring the expression of different retinal-specific genes. The cellular viability of the retina was assessed by establishing explant primary cell cultures. STATISTICAL ANALYSIS The data were calculated as an average of normalised Ct values ± standard error of the mean. RESULTS RNA obtained from cadaveric tissues despite being partially degraded showed a uniform strong gene expression of several retinal-specific genes such as PAX6, RHO, TUBB3, CRX , and ALDH1L1 . The primary cultures established from cadaveric tissues showed viable cells. CONCLUSION The cadaver donor tissues collected within 24 hours of death can be effectively utilized for gene expression profiling.
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Affiliation(s)
- Prerna Kulshrestha
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sarmeela Sharma
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sushma Vishwakarma
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mohammed J Ali
- Govindram Seksaria Institute of Dacryology, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Tarjani V Dave
- Hariram Motumal Nasta and Renu Hariram Nasta Ophthalmic Plastic Surgery Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Inderjeet Kaur
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
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4
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Palko SI, Benoit MR, Yao AY, Mohan R, Yan R. ER-stress response in retinal Müller glia occurs significantly earlier than amyloid pathology in the Alzheimer's mouse brain and retina. Glia 2024; 72:1067-1081. [PMID: 38497356 PMCID: PMC11006574 DOI: 10.1002/glia.24514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 03/19/2024]
Abstract
Alzheimer's Disease (AD) pathogenesis is thought to begin up to 20 years before cognitive symptoms appear, suggesting the need for more sensitive diagnostic biomarkers of AD. In this report, we demonstrated pathological changes in retinal Müller glia significantly earlier than amyloid pathology in AD mouse models. By utilizing the knock-in NLGF mouse model, we surprisingly discovered an increase in reticulon 3 (RTN3) protein levels in the NLGF retina as early as postnatal day 30 (P30). Despite RTN3 being a canonically neuronal protein, this increase was noted in the retinal Müller glia, confirmed by immunohistochemical characterization. Further unbiased transcriptomic assays of the P30 NLGF retina revealed that retinal Müller glia were the most sensitive responding cells in this mouse retina, compared with other cell types including photoreceptor cells and ganglion neurons. Pathway analyses of differentially expressed genes in glia cells showed activation of ER stress response via the upregulation of unfolded protein response (UPR) proteins such as ATF4 and CHOP. Early elevation of RTN3 in response to challenges by toxic Aβ likely facilitated UPR. Altogether, these findings suggest that Müller glia act as a sentinel for AD pathology in the retina and should aid for both intervention and diagnosis.
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Affiliation(s)
| | | | - Annie Y. Yao
- Department of Neuroscience, University of Connecticut Health Center, Farmington CT 06030 USA
| | - Royce Mohan
- Department of Neuroscience, University of Connecticut Health Center, Farmington CT 06030 USA
| | - Riqiang Yan
- Department of Neuroscience, University of Connecticut Health Center, Farmington CT 06030 USA
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Zhong W, Yang Q, Wang F, Lin X, Chen Z, Xue J, Zhao W, Liu X, Rao B, Zhang J. Cell-specific localization of β-synuclein in the mouse retina. Brain Struct Funct 2024; 229:1279-1298. [PMID: 38703218 DOI: 10.1007/s00429-024-02799-z] [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: 12/06/2023] [Accepted: 04/01/2024] [Indexed: 05/06/2024]
Abstract
β-synuclein, a member of the synuclein family, is frequently co-expressed with α-synuclein in the neural system, where it serves to inhibit abnormal aggregation of α-synuclein in neurodegenerative diseases. Beyond its role in pathological conditions, β-synuclein plays various functions independently of α-synuclein. In our investigation, we discovered a broader expression of β-synuclein in the mouse retina compared to α-synuclein. This widespread pattern implies its potential significance in the retina. Through detailed examination via light- and electron-microscopic immunocytochemistry, we identified β-synuclein expression from the inner segment (IS) and outer segment (OS) of photoreceptor cells to the ganglion cell layer (GCL). Our findings unveiled unique features, including β-synuclein immunoreactive IS and OS of cones, higher expression in cone pedicles than in rod spherules, absence in horizontal cells, limited expression in cone bipolar dendrites and somas, higher expression in cone bipolar terminals, presence in most amacrine cells, and expression in almost majority of somas in GCL with an absence in intrinsically photosensitive retinal ganglion cell (ipRGCs) processes. Notably, all cholinergic amacrine cells express high β- but not α-synuclein, while dopaminergic amacrine cells express α-synuclein exclusively. These distinctive expression patterns offer valuable insights for further exploration into the functions of β-synuclein and its potential role in synuclein pathology within the retina.
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Affiliation(s)
- Wenhui Zhong
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China.
| | - Qingwen Yang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Fenglan Wang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Xin Lin
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Zhongqun Chen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Jing Xue
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Wenna Zhao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Xiaoqing Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Bilin Rao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Jun Zhang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- Laboratory of Retinal Physiology and Disease, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China.
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6
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Kim MJ, Kulkarni V, Goode MA, Hernandez J, Graham S, Sivesind TE, Manchadi ML. Utilizing systems genetics to enhance understanding into molecular targets of skin cancer. Exp Dermatol 2024; 33:e15043. [PMID: 38459629 PMCID: PMC11018140 DOI: 10.1111/exd.15043] [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: 12/31/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/10/2024]
Abstract
Despite progress made with immune checkpoint inhibitors and targeted therapies, skin cancer remains a significant public health concern in the United States. The intricacies of the disease, encompassing genetics, immune responses, and external factors, call for a comprehensive approach. Techniques in systems genetics, including transcriptional correlation analysis, functional pathway enrichment analysis, and protein-protein interaction network analysis, prove valuable in deciphering intricate molecular mechanisms and identifying potential diagnostic and therapeutic targets for skin cancer. Recent studies demonstrate the efficacy of these techniques in uncovering molecular processes and pinpointing diagnostic markers for various skin cancer types, highlighting the potential of systems genetics in advancing innovative therapies. While certain limitations exist, such as generalizability and contextualization of external factors, the ongoing progress in AI technologies provides hope in overcoming these challenges. By providing protocols and a practical example involving Braf, we aim to inspire early-career experimental dermatologists to adopt these tools and seamlessly integrate these techniques into their skin cancer research, positioning them at the forefront of innovative approaches in combating this devastating disease.
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Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | | | - Micah A Goode
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Jacob Hernandez
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Sean Graham
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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7
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van Koeverden AK, Afiat BC, Nguyen CT, Bui BV, Lee PY. Understanding how ageing impacts ganglion cell susceptibility to injury in glaucoma. Clin Exp Optom 2024; 107:147-155. [PMID: 37980904 DOI: 10.1080/08164622.2023.2279734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 10/31/2023] [Indexed: 11/21/2023] Open
Abstract
Glaucoma is a leading cause of blindness worldwide, with a marked increase in prevalence with advancing age. Due to the multifactorial nature of glaucoma pathogenesis, dissecting how ageing impacts upon glaucoma risk requires analysis and synthesis of evidence from a vast literature. While there is a wealth of human clinical studies examining glaucoma pathogenesis and why older patients have increased risk, many aspects of the disease such as adaptations of retinal ganglion cells to stress, autophagy and the role of glial cells in glaucoma, require the use of animal models to study the complex cellular processes and interactions. Additionally, the accelerated nature of ageing in rodents facilitates the longitudinal study of changes that would not be feasible in human clinical studies. This review article examines evidence derived predominantly from rodent models on how the ageing process impacts upon various aspects of glaucoma pathology from the retinal ganglion cells themselves, to supporting cells and tissues such as glial cells, connective tissue and vasculature, in addition to oxidative stress and autophagy. An improved understanding of how ageing modifies these factors may lead to the development of different therapeutic strategies that target specific risk factors or processes involved in glaucoma.
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Affiliation(s)
- Anna K van Koeverden
- Department of Optometry and Vision Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Brianna C Afiat
- Department of Optometry and Vision Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Christine To Nguyen
- Department of Optometry and Vision Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Bang V Bui
- Department of Optometry and Vision Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pei Ying Lee
- Department of Optometry and Vision Sciences, The University of Melbourne, Parkville, Victoria, Australia
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8
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Rapp J, Hospach A, Liang P, Schwämmle M, Renz L, Agostini H, Schlunck G, Bucher F. Oncostatin M Reduces Pathological Neovascularization in the Retina Through Müller Cell Activation. Invest Ophthalmol Vis Sci 2024; 65:22. [PMID: 38190125 PMCID: PMC10777876 DOI: 10.1167/iovs.65.1.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 12/01/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose Continuous vision loss due to vasoproliferative eye disease still represents an unsolved issue despite anti-vascular endothelial growth factor (VEGF) therapy. The impact of signal transducer and activator of transcription 3 (STAT3) signaling on retinal angiogenesis and its potential use as a therapeutic target remain controversial. In vitro, oncostatin M (OSM), as a strong STAT3 activator, possesses robust proangiogenic activity. This study investigated to what extent the proangiogenic effects of OSM translate to the in vivo setting of vasoproliferative eye disease. Methods The in vitro effect of OSM on endothelial cells was investigated in the spheroid sprouting assay and through RNA sequencing. The mouse model for oxygen-induced retinopathy (OIR) was used to evaluate the impact of OSM in vivo. Signaling patterns were measured by western blot and retinal cryosections. Primary Müller cell cultures were used to evaluate the effect of OSM on the Müller cell secretome. Murine retinal vascular endothelial cells were isolated from OIR retinas using fluorescence-activated cell sorting (FACS) and were used for RNA sequencing. Results Although OSM induced pro-angiogenic responses in vitro, in the OIR model intravitreal injection of OSM reduced retinal neovascularization by 65.2% and vaso-obliteration by 45.5% in Müller cells. Injecting OSM into the vitreous activated the STAT3 signaling pathway in multiple retinal cell types, including Müller cells. In vitro, OSM treatment increased CXCL10 secretion. RNA sequencing of sorted vascular endothelial cells at OIR P17 following OSM treatment indicated downregulation of angiogenesis- and mitosis-associated genes. Conclusions In vivo, OSM reveals a beneficial angiomodulatory effect by activating Müller cells and changing their secretome. The data highlight contradictions between cytokine-induced effects in vitro and in vivo depending on the cell types mediating the effect.
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Affiliation(s)
- Julian Rapp
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alban Hospach
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Paula Liang
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Schwämmle
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lisa Renz
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hansjürgen Agostini
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Günther Schlunck
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Felicitas Bucher
- Eye Center, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Kellogg CM, Pham K, Ko S, Cox JE, Machalinski AH, Stout MB, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Specificity and efficiency of tamoxifen-mediated Cre induction is equivalent regardless of age. iScience 2023; 26:108413. [PMID: 38058312 PMCID: PMC10696116 DOI: 10.1016/j.isci.2023.108413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/15/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Temporally controlling Cre recombination through tamoxifen (Tam) induction has many advantages for biomedical research. Most studies report early post-natal/juvenile (<2 m.o.) Tam induction, but age-related neurodegeneration and aging studies can require Cre induction in older mice (>12 m.o.). While anecdotally reported as problematic, there are no published comparisons of Tam-mediated Cre induction at early and late ages. Here, microglial-specific Cx3cr1creERT2 mice were crossed to a floxed NuTRAP reporter to compare Cre induction at early (3-6 m.o.) and late (20 m.o.) ages. Specificity and efficiency of microglial labeling at 21-22 m.o. were identical in mice induced with Tam at early and late ages. Age-related microglial translatomic changes were also similar regardless of Tam induction age. Each Cre and flox mouse line should be independently validated, however, these findings demonstrate that Tam-mediated Cre induction can be performed even into older mouse ages and should be generalizable to other inducible Cre models.
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Affiliation(s)
- Collyn M. Kellogg
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sunghwan Ko
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jillian E.J. Cox
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael B. Stout
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Amanda L. Sharpe
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael J. Beckstead
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sarah R. Ocañas
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M. Freeman
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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10
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Kim MJ, Martin CA, Kim J, Jablonski MM. Computational methods in glaucoma research: Current status and future outlook. Mol Aspects Med 2023; 94:101222. [PMID: 37925783 PMCID: PMC10842846 DOI: 10.1016/j.mam.2023.101222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Advancements in computational techniques have transformed glaucoma research, providing a deeper understanding of genetics, disease mechanisms, and potential therapeutic targets. Systems genetics integrates genomic and clinical data, aiding in identifying drug targets, comprehending disease mechanisms, and personalizing treatment strategies for glaucoma. Molecular dynamics simulations offer valuable molecular-level insights into glaucoma-related biomolecule behavior and drug interactions, guiding experimental studies and drug discovery efforts. Artificial intelligence (AI) technologies hold promise in revolutionizing glaucoma research, enhancing disease diagnosis, target identification, and drug candidate selection. The generalized protocols for systems genetics, MD simulations, and AI model development are included as a guide for glaucoma researchers. These computational methods, however, are not separate and work harmoniously together to discover novel ways to combat glaucoma. Ongoing research and progresses in genomics technologies, MD simulations, and AI methodologies project computational methods to become an integral part of glaucoma research in the future.
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Affiliation(s)
- Minjae J Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Cole A Martin
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Jinhwa Kim
- Graduate School of Artificial Intelligence, Graduate School of Metaverse, Department of Management Information Systems, Sogang University, 1 Shinsoo-Dong, Mapo-Gu, Seoul, South Korea.
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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Kellogg CM, Pham K, Ko S, Cox JEJ, Machalinski AH, Stout MB, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Consistent specificity and efficiency of tamoxifen-mediated cre induction across ages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558482. [PMID: 37781585 PMCID: PMC10541132 DOI: 10.1101/2023.09.19.558482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Temporally controlling cre recombination through tamoxifen (Tam) induction has many advantages for biomedical research. Most studies report Tam induction at early post-natal/juvenile (<2 m.o.) mouse ages, but age-related neurodegeneration and aging studies can require cre induction in older mice (>12 m.o.). While anecdotally reported as problematic, there are no published comparisons of Tam mediated cre induction at early and late ages. Here, microglial-specific Cx3cr1 creERT 2 mice were crossed to a floxed NuTRAP reporter to compare cre induction at early (3-6 m.o.) and late (20 m.o.) ages. Specificity and efficiency of microglial labeling at 21-22 m.o. were identical in mice induced with Tam at 3-6 m.o. or 20 m.o. of age. Age-related microglial translatomic changes were also similar regardless of Tam induction age. Each cre and flox mouse line should be validated independently, however, these findings demonstrate that Tam-mediated cre induction can be performed even into older mouse ages.
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Ocañas SR, Isola JVV, Saccon TD, Pham KD, Chucair-Elliott AJ, Schneider A, Freeman WM, Stout MB. Cell-Specific Paired Interrogation of the Mouse Ovarian Epigenome and Transcriptome. J Vis Exp 2023:10.3791/64765. [PMID: 36912526 PMCID: PMC10165884 DOI: 10.3791/64765] [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] [Indexed: 03/14/2023] Open
Abstract
Assessing cell-type-specific epigenomic and transcriptomic changes are key to understanding ovarian aging. To this end, the optimization of the translating ribosome affinity purification (TRAP) method and the isolation of nuclei tagged in specific cell types (INTACT) method was performed for the subsequent paired interrogation of the cell-specific ovarian transcriptome and epigenome using a novel transgenic NuTRAP mouse model. The expression of the NuTRAP allele is under the control of a floxed STOP cassette and can be targeted to specific ovarian cell types using promoter-specific Cre lines. Since recent studies have implicated ovarian stromal cells in driving premature aging phenotypes, the NuTRAP expression system was targeted to stromal cells using a Cyp17a1-Cre driver. The induction of the NuTRAP construct was specific to ovarian stromal fibroblasts, and sufficient DNA and RNA for sequencing studies were obtained from a single ovary. The NuTRAP model and methods presented here can be used to study any ovarian cell type with an available Cre line.
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Affiliation(s)
- Sarah R Ocañas
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation; Genes & Human Disease Research Program, Oklahoma Medical Research Foundation; Oklahoma City Veterans Affairs Medical Center
| | - José V V Isola
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation; Oklahoma City Veterans Affairs Medical Center
| | - Tatiana D Saccon
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation
| | - Kevin D Pham
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation
| | | | | | - Willard M Freeman
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation; Oklahoma City Veterans Affairs Medical Center
| | - Michael B Stout
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation; Oklahoma City Veterans Affairs Medical Center;
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