1
|
Ma J, Chu TK, Polo Prieto M, Park Y, Li Y, Chen R, Mardon G, Frankfort BJ, Tran NM. Sample multiplexing for retinal single-cell RNA-sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.589797. [PMID: 38712294 PMCID: PMC11071429 DOI: 10.1101/2024.04.23.589797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Rare cell populations can be challenging to characterize using microfluidic single-cell RNA sequencing (scRNA-seq) platforms. Typically, the population of interest must be enriched and pooled from multiple biological specimens for efficient collection. However, these practices preclude the resolution of sample origin together with phenotypic data and are problematic in experiments in which biological or technical variation is expected to be high (e.g., disease models, genetic perturbation screens, or human samples). One solution is sample multiplexing whereby each sample is tagged with a unique sequence barcode that is resolved bioinformatically. We have established a scRNA-seq sample multiplexing pipeline for mouse retinal ganglion cells using cholesterol-modified-oligos and utilized the enhanced precision to investigate cell type distribution and transcriptomic variance across retinal samples. As single cell transcriptomics are becoming more widely used to research development and disease, sample multiplexing represents a useful method to enhance the precision of scRNA-seq analysis.
Collapse
|
2
|
Ashok A, Tai WL, Lennikov A, Chang K, Chen J, Li B, Cho KS, Utheim TP, Chen DF. Electrical stimulation alters DNA methylation and promotes neurite outgrowth. J Cell Biochem 2023; 124:1530-1545. [PMID: 37642194 DOI: 10.1002/jcb.30462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
Electrical stimulation (ES) influences neural regeneration and functionality. We here investigate whether ES regulates DNA demethylation, a critical epigenetic event known to influence nerve regeneration. Retinal ganglion cells (RGCs) have long served as a standard model for central nervous system neurons, whose growth and disease development are reportedly affected by DNA methylation. The current study focuses on the ability of ES to rescue RGCs and preserve vision by modulating DNA demethylation. To evaluate DNA demethylation pattern during development, RGCs from mice at different stages of development, were analyzed using qPCR for ten-eleven translocation (TETs) and immunostained for 5 hydroxymethylcytosine (5hmc) and 5 methylcytosine (5mc). To understand the effect of ES on neurite outgrowth and DNA demethylation, cells were subjected to ES at 75 µAmp biphasic ramp for 20 min and cultured for 5 days. ES increased TETs mediated neurite outgrowth, DNA demethylation, TET1 and growth associated protein 43 levels significantly. Immunostaining of PC12 cells following ES for histone 3 lysine 9 trimethylation showed cells attained an antiheterochromatin configuration. Cultured mouse and human retinal explants stained with β-III tubulin exhibited increased neurite growth following ES. Finally, mice subjected to optic nerve crush injury followed by ES exhibited improved RGCs function and phenotype as validated using electroretinogram and immunohistochemistry. Our results point to a possible therapeutic regulation of DNA demethylation by ES in neurons.
Collapse
Affiliation(s)
- Ajay Ashok
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Wai Lydia Tai
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Anton Lennikov
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Karen Chang
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Julie Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Boyuan Li
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Kin-Sang Cho
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Tor Paaske Utheim
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Dong Feng Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
3
|
Perez R, Park Y, Hirano A, Brecha N, Frankfort B, Zuniga-Sanchez E. Modeling subcellular specificity in the developing retina. RESEARCH SQUARE 2023:rs.3.rs-3214285. [PMID: 37609217 PMCID: PMC10441513 DOI: 10.21203/rs.3.rs-3214285/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The precise wiring of the nervous system relies on neurons extending their processes at the right time and place to find their appropriate synaptic partner. The mechanisms that determine when and where neurons extend their neurites during synaptogenesis remains a central question in the field. In the present study, we developed a cell culture system coupled with live imaging to investigate the wiring mechanisms in the developing nervous system. We focused on horizontal cells which are interneurons in the mammalian outer retina known to synapse selectively to distinct photoreceptors. Our data shows cultured horizontal cells extend neurites in a similar manner as in vivo with horizontal cells isolated from young mice extending more complex processes compared to those from adult retinas. In addition, horizontal cells cultured alone do not extend neurites and require other retinal cells for neurite extension suggesting that there must be extrinsic cues that promote neurite outgrowth. Moreover, these extrinsic cues do not appear to be solely secreted factors as supernatant from wild-type retinas is not sufficient to promote neurite outgrowth. In summary, we established a new system that can be used to decipher the mechanisms involved in neuronal wiring of the developing central nervous system.
Collapse
|
4
|
Riordan SM, Aladdad AM, McLoughlin KJ, Kador KE. Purification of Retinal Ganglion Cells from Differentiation Through Adult via Immunopanning and Low-Pressure Flow Cytometry. Methods Mol Biol 2023; 2708:11-24. [PMID: 37558955 DOI: 10.1007/978-1-0716-3409-7_2] [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] [Indexed: 08/11/2023]
Abstract
The isolation and culturing of rodent retinal ganglion cells (RGC) is a key step in studying the function and cellular response of this crucial cell type. Typical methods used for isolation of RGCs include immunopanning or magnetic bead separation with antibodies targeting RGC specific protein markers. However, in developmental research, many of the most common markers, such as Thy-1, are not expressed in early stages of development. To help study these crucial early stage RGCs, we have developed a novel method that utilizes a transgenic mouse with a GFP tag on the protein BRN3 and a low-pressure fluorescence-activated cell sorter (FACS) system.
Collapse
Affiliation(s)
- Sean M Riordan
- Department of Ophthalmology and Department of Biomedical Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Afnan M Aladdad
- Department of Ophthalmology and Department of Biomedical Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Kiran J McLoughlin
- Department of Ophthalmology and Department of Biomedical Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Karl E Kador
- Department of Ophthalmology and Department of Biomedical Sciences, University of Missouri-Kansas City, Kansas City, MO, USA.
| |
Collapse
|
5
|
Pitale PM, Shen G, Sigireddi RR, Polo-Prieto M, Park YH, Gibson SE, Westenskow PD, Channa R, Frankfort BJ. Selective vulnerability of the intermediate retinal capillary plexus precedes retinal ganglion cell loss in ocular hypertension. Front Cell Neurosci 2022; 16:1073786. [PMID: 36545655 PMCID: PMC9760765 DOI: 10.3389/fncel.2022.1073786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/15/2022] [Indexed: 12/08/2022] Open
Abstract
Introduction: Glaucoma, a disease of retinal ganglion cell (RGC) injury and potentially devastating vision loss, is associated with both ocular hypertension (OHT) and reduced ocular blood flow. However, the relationship between OHT and retinal capillary architecture is not well understood. In this project, we studied microvasculature damage in mice exposed to mild levels of induced OHT. Methods: Mild OHT was induced with the microbead model for 2 weeks. At this time point, some retinas were immunostained with CD31 (endothelium), Collagen IV (basement membrane), and RBPMS (RGCs) for z-stack confocal microscopy. We processed these confocal images to distinguish the three retinal capillary plexi (superficial, intermediate, and deep). We manually counted RGC density, analyzed vascular complexity, and identified topographical and spatial vascular features of the retinal capillaries using a combination of novel manual and automated workflows. Other retinas were dissociated and immunopanned to isolate RGCs and amacrine cells (ACs) for hypoxia gene array analysis. Results: RGC counts were normal but there was decreased overall retinal capillary complexity. This reduced complexity could be explained by abnormalities in the intermediate retinal capillary plexus (IRCP) that spared the other plexi. Capillary junction density, vessel length, and vascular area were all significantly reduced, and the number of acellular capillaries was dramatically increased. ACs, which share a neurovascular unit (NVU) with the IRCP, displayed a marked increase in the relative expression of many hypoxia-related genes compared to RGCs from the same preparations. Discussion: We have discovered a rapidly occurring, IRCP-specific, OHT-induced vascular phenotype that precedes RGC loss. AC/IRCP NVU dysfunction may be a mechanistic link for early vascular remodeling in glaucoma.
Collapse
Affiliation(s)
- Priyamvada M. Pitale
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Guofu Shen
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Rohini R. Sigireddi
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Maria Polo-Prieto
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Yong H. Park
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Solomon E. Gibson
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States,Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Peter D. Westenskow
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Roomasa Channa
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Benjamin J. Frankfort
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States,Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Benjamin J. Frankfort
| |
Collapse
|
6
|
Lesslich HM, Klapal L, Wilke J, Haak A, Dietzel ID. Adjusting the neuron to astrocyte ratio with cytostatics in hippocampal cell cultures from postnatal rats: A comparison of cytarabino furanoside (AraC) and 5-fluoro-2'-deoxyuridine (FUdR). PLoS One 2022; 17:e0265084. [PMID: 35263366 PMCID: PMC8906639 DOI: 10.1371/journal.pone.0265084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/22/2022] [Indexed: 01/29/2023] Open
Abstract
Cell culture studies offer the unique possibility to investigate the influence of pharmacological treatments with quantified dosages applied for defined time durations on survival, morphological maturation, protein expression and function as well as the mutual interaction of various cell types. Cultures obtained from postnatal rat brain contain a substantial number of glial cells that further proliferate with time in culture leading to an overgrowth of neurons with glia, especially astrocytes and microglia. A well-established method to decrease glial proliferation in vitro is to apply low concentrations of cytosine arabinoside (AraC). While AraC primarily effects dividing cells, it has been reported repeatedly that it is also neurotoxic, which is the reason why most protocols limit its application to concentrations of up to 5 μM for a duration of 24 h. Here, we investigated 5-fluoro-2'-deoxyuridine (FUdR) as a possible substitute for AraC. We applied concentrations of both cytostatics ranging from 4 μM to 75 μM and compared cell composition and cell viability in cultures prepared from 0-2- and 3-4-day old rat pups. Using FUdR as proliferation inhibitor, higher ratios of neurons to glia cells were obtained with a maximal neuron to astrocyte ratio of up to 10:1, which could not be obtained using AraC in postnatal cultures. Patch-clamp recordings revealed no difference in the amplitudes of voltage-gated Na+ currents in neurons treated with FUdR compared with untreated control cells suggesting replacement of AraC by FUdR as glia proliferation inhibitor if highly neuron-enriched postnatal cultures are desired.
Collapse
Affiliation(s)
- Heiko M. Lesslich
- Department of Biochemistry II, Ruhr-Universität Bochum, Bochum, Germany
- * E-mail:
| | - Lars Klapal
- Department of Biochemistry II, Ruhr-Universität Bochum, Bochum, Germany
| | - Justus Wilke
- Department of Biochemistry II, Ruhr-Universität Bochum, Bochum, Germany
| | - Annika Haak
- Nanoscopy Group, RUBION, Ruhr-Universität Bochum, Bochum, Germany
| | | |
Collapse
|
7
|
Eldred KC, Reh TA. Human retinal model systems: Strengths, weaknesses, and future directions. Dev Biol 2021; 480:114-122. [PMID: 34529997 DOI: 10.1016/j.ydbio.2021.09.001] [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: 01/31/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The retina is a complex neuronal structure that converts light energy into visual perception. Many specialized aspects of the primate retina, including a cone rich macula for high acuity vision, ocular size, and cell type diversity are not found in other animal models. In addition, the unique morphologies and distinct laminar positions of cell types found in the retina make this model system ideal for the study of neuronal cell fate specification. Many key early events of human retinal development are inaccessible to investigation as they occur during gestation. For these reasons, it has been necessary to develop retinal model systems to gain insight into human-specific retinal development and disease. Recent advances in culturing retinal tissue have generated new systems for retinal research and have moved us closer to generating effective regenerative therapies for vision loss. Here, we describe the strengths, weaknesses, and future directions for different human retinal model systems including dissociated primary tissue, explanted primary tissue, retinospheres, and stem cell-derived retinal organoids.
Collapse
Affiliation(s)
- Kiara C Eldred
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
8
|
Molinari C, Ruga S, Farghali M, Galla R, Fernandez-Godino R, Clemente N, Uberti F. Effects of a New Combination of Natural Extracts on Glaucoma-Related Retinal Degeneration. Foods 2021; 10:1885. [PMID: 34441662 PMCID: PMC8391439 DOI: 10.3390/foods10081885] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glaucoma is currently the leading cause of irreversible blindness; it is a neuropathy characterized by structural alterations of the optic nerve, leading to visual impairments. The aim of this work is to develop a new oral formulation able to counteract the early changes connected to glaucomatous degeneration. The composition is based on gastrodin and vitamin D3 combined with vitamin C, blackcurrant, and lycopene. METHODS Cells and tissues of the retina were used to study biological mechanisms involved in glaucoma, to slow down the progression of the disease. Experiments mimicking the conditions of glaucoma were carried out to examine the etiology of retinal degeneration. RESULTS Our results show a significant ability to restore glaucoma-induced damage, by counteracting ROS production and promoting cell survival by inhibiting apoptosis. These effects were confirmed by the intracellular mechanism that was activated following administration of the compound, either before or after the glaucoma induction. In particular, the main results were obtained as a preventive action of glaucoma, showing a beneficial action on all selected markers, both on cells and on eyecup preparations. It is therefore possible to hypothesize both the preventive and therapeutic use of this formulation, in the presence of risk factors, and due to its ability to inhibit the apoptotic cycle and to stimulate cell survival mechanisms, respectively. CONCLUSION This formulation has exhibited an active role in the prevention or restoration of glaucoma damage for the first time.
Collapse
Affiliation(s)
- Claudio Molinari
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy; (C.M.); (S.R.); (M.F.); (R.G.)
| | - Sara Ruga
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy; (C.M.); (S.R.); (M.F.); (R.G.)
| | - Mahitab Farghali
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy; (C.M.); (S.R.); (M.F.); (R.G.)
| | - Rebecca Galla
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy; (C.M.); (S.R.); (M.F.); (R.G.)
| | - Rosario Fernandez-Godino
- Ocular Genomics Institute-Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA;
| | - Nausicaa Clemente
- Dipartimento di Scienze della Salute, Interdisciplinary Research Center of Autoimmune Diseases-IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy;
| | - Francesca Uberti
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy; (C.M.); (S.R.); (M.F.); (R.G.)
| |
Collapse
|