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Coltrini D, Belleri M, Gambicorti E, Romano D, Morescalchi F, Krishna Chandran AM, Calza S, Semeraro F, Presta M. Gene expression analysis identifies two distinct molecular clusters of idiopatic epiretinal membranes. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165938. [PMID: 32827649 DOI: 10.1016/j.bbadis.2020.165938] [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: 05/22/2020] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022]
Abstract
Idiopathic epiretinal membranes (ERMs) are fibrocellular membranes containing extracellular matrix proteins and epiretinal cells of retinal and extraretinal origin. iERMs lead to decreased visual acuity and their pathogenesis has not been completely defined. Aim of this study was to provide a molecular characterization of iERMs by gene expression analysis. To this purpose, 56 iERMs obtained by pars plana vitrectomy were analyzed for the expression levels of genes encoding biomarkers of the cellular and molecular events occurring in iERMs. RT-qPCR analysis showed significant differences in the levels of cell population, extracellular matrix and cytokine/growth factor biomarkers among the iERMs investigated. Hierarchical clustering of RT-qPCR data identified two distinct iERM clusters, Cluster B samples representing transcriptionally "activated" iERMs when compared to transcriptionally "quiescent" Cluster A specimens. Further, Cluster B could be subdivided in two subgroups, Cluster B1 iERMs, characterized by a marked glial cell activation, and Cluster B2 samples characterized by a more pro-fibrotic phenotype. Preoperative decimal best-corrected visual acuity and post-surgery inner segment/outer grading values were higher in Cluster A patients, that showed a prevalence of fovea-attached type iERMs with near-normal inner retina, than in Cluster B patients, that presented more severe clinical and spectral domain optical coherence tomography (SD-OCT) features. In conclusion, this molecular characterization has identified two major clusters of iERM specimens with distinct transcriptional activities that reflect different clinical and SD-OCT features of iERM patients. This retrospective work paves the way to prospective whole-genome transcriptomic studies to allow a molecular classification of iERMs and for the identification of molecular signature(s) of prognostic and therapeutic significance.
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Affiliation(s)
- Daniela Coltrini
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Mirella Belleri
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Elena Gambicorti
- Eye Clinic, Department of Neurological and Vision Sciences, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Davide Romano
- Eye Clinic, Department of Neurological and Vision Sciences, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Francesco Morescalchi
- Eye Clinic, Department of Neurological and Vision Sciences, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Adwaid Manu Krishna Chandran
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Stefano Calza
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Francesco Semeraro
- Eye Clinic, Department of Neurological and Vision Sciences, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy.
| | - Marco Presta
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
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Stiemke AB, Sah E, Simpson RN, Lu L, Williams RW, Jablonski MM. Systems Genetics of Optic Nerve Axon Necrosis During Glaucoma. Front Genet 2020; 11:31. [PMID: 32174956 PMCID: PMC7056908 DOI: 10.3389/fgene.2020.00031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 01/09/2020] [Indexed: 12/28/2022] Open
Abstract
In this study, we identify genomic regions that modulate the number of necrotic axons in optic nerves of a family of mice, some of which have severe glaucoma, and define a set of high priority positional candidate genes that modulate retinal ganglion cell (RGC) axonal degeneration. A large cohort of the BXD family were aged to greater than 13 months of age. Optic nerves from 74 strains and the DBA/2J (D2) parent were harvested, sectioned, and stained with p-phenylenediamine. Numbers of necrotic axons per optic nerve cross-section were counted from 1 to 10 replicates per genotype. Strain means and standard errors were uploaded into GeneNetwork 2 for mapping and systems genetics analyses (Trait 18614). The number of necrotic axons per nerve ranged from only a few hundred to more than 4,000. Using conventional interval mapping as well as linear mixed model mapping, we identified a single locus on chromosome 12 between 109 and 112.5 Mb with a likelihood ratio statistic (LRS) of ~18.5 (p genome-wide ~0.1). Axon necrosis is not linked to locations of major known glaucoma genes in this family, including Gpnmb, Tyrp1, Cdh11, Pou6f2, and Cacna2d1. This indicates that although these genes contribute to pigmentary dispersion or elevated IOP, none directly modulates axon necrosis. Of 156 positional candidates, eight genes—CDC42 binding protein kinase beta (Cdc42bpb); eukaryotic translation initiation factor 5 (Eif5); BCL2-associated athanogene 5 (Bag5); apoptogenic 1, mitochondrial (Apopt1); kinesin light chain 1 (Klc1); X-ray repair cross complementing 3 (Xrcc3); protein phosphatase 1, regulatory subunit 13B (Ppp1r13b); and transmembrane protein 179 (Tmem179)—passed stringent criteria and are high priority candidates. Several candidates are linked to mitochondria and/or axons, strengthening their plausible role as modulators of ON necrosis. Additional studies are required to validate and/or eliminate plausible candidates. Surprisingly, IOP and ON necrosis are inversely correlated across the BXD family in mice >13 months of age and these two traits share few genes among their top ocular and retinal correlates. These data suggest that the two traits are independently modulated or that a more complex and multifaceted approach is required to reveal their association.
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Affiliation(s)
- Andrew B Stiemke
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Eric Sah
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Raven N Simpson
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
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3
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Violitzi F, Perivolidi VI, Thireou T, Grivas I, Haralambous S, Samiotaki M, Panayotou G, Douni E. Mapping Interactome Networks of DNAJC11, a Novel Mitochondrial Protein Causing Neuromuscular Pathology in Mice. J Proteome Res 2019; 18:3896-3912. [DOI: 10.1021/acs.jproteome.9b00338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Foteini Violitzi
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Fleming 34, 16672, Vari, Greece
| | - Vasiliki-Iris Perivolidi
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Fleming 34, 16672, Vari, Greece
| | - Trias Thireou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Ioannis Grivas
- Transgenic Technology Lab and Inflammation Research Group, Hellenic Pasteur Institute, Vas. Sofias 127, 11521, Athens, Greece
| | - Sylva Haralambous
- Transgenic Technology Lab and Inflammation Research Group, Hellenic Pasteur Institute, Vas. Sofias 127, 11521, Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Fleming 34, 16672, Vari, Greece
| | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Fleming 34, 16672, Vari, Greece
| | - Eleni Douni
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Fleming 34, 16672, Vari, Greece
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Lee J, Choi SH, Kim YB, Jun I, Sung JJ, Lee DR, Kim YI, Cho MS, Byeon SH, Kim DS, Kim DW. Defined Conditions for Differentiation of Functional Retinal Ganglion Cells From Human Pluripotent Stem Cells. Invest Ophthalmol Vis Sci 2019; 59:3531-3542. [PMID: 30025074 DOI: 10.1167/iovs.17-23439] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose We aimed to establish an efficient method for retinal ganglion cell (RGC) differentiation from human pluripotent stem cells (hPSCs) using defined factors. Methods To define the contribution of specific signal pathways to RGC development and optimize the differentiation of hPSCs toward RGCs, we examined RGC differentiation in three stages: (1) eye field progenitors expressing the eye field transcription factors (EFTFs), (2) RGC progenitors expressing MATH5, and (3) RGCs expressing BRN3B and ISLET1. By monitoring the condition that elicited the highest yield of cells expressing stage-specific markers, we determined the optimal concentrations and combinations of signaling pathways required for efficient generation of RGCs from hPSCs. Results Precise modulation of signaling pathways, including Wnt, insulin growth factor-1, and fibroblast growth factor, in combination with mechanical isolation of neural rosette cell clusters significantly enriched RX and PAX6 double-positive eye field progenitors from hPSCs by day 12. Furthermore, Notch signal inhibition facilitated differentiation into MATH5-positive progenitors at 90% efficiency by day 20, and these cells further differentiated to BRN3B and ISLET1 double-positive RGCs at 45% efficiency by day 40. RGCs differentiated via this method were functional as exemplified by their ability to generate action potentials, express microfilament components on neuronal processes, and exhibit axonal transportation of mitochondria. Conclusions This protocol offers highly defined culture conditions for RGC differentiation from hPSCs and in vitro disease model and cell source for transplantation for diseases related to RGCs.
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Affiliation(s)
- Junwon Lee
- Department of Physiology, Yonsei University College of Medicine, Seoul, South Korea.,Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Sang-Hwi Choi
- Department of Physiology, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Young-Beom Kim
- Department of Physiology, Korea University College of Medicine, Seoul, South Korea
| | - Ikhyun Jun
- Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Jin Jea Sung
- Department of Physiology, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongjin R Lee
- Department of Physiology, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Yang In Kim
- Department of Physiology, Korea University College of Medicine, Seoul, South Korea
| | | | - Suk Ho Byeon
- Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Dae-Sung Kim
- Department of Biotechnology, Brain Korea 21 Plus Project for Biotechnology, Korea University, Seoul, South Korea
| | - Dong-Wook Kim
- Department of Physiology, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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5
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Opere CA, Heruye S, Njie-Mbye YF, Ohia SE, Sharif NA. Regulation of Excitatory Amino Acid Transmission in the Retina: Studies on Neuroprotection. J Ocul Pharmacol Ther 2017; 34:107-118. [PMID: 29267132 DOI: 10.1089/jop.2017.0085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Excitotoxicity occurs in neurons due to the accumulation of excitatory amino acids such as glutamate in the synaptic and extrasynaptic locations. In the retina, excessive glutamate concentrations trigger a neurotoxic cascade involving several mechanisms, including the elevation of intracellular calcium (Ca2+) and the activation of α-amino-3-hydroxy 5-methyl-4-iso-xazole-propionic acid/kainate (AMPA/KA) and N-methyl-d-aspartate (NMDA) receptors leading to retinal degeneration. Both ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs) are present in the mammalian retina. Indeed, due to the abundant expression of GluRs, the mammalian retina is highly susceptible to excitotoxic neurodegeneration. Excitotoxicity has been postulated to present a common downstream mechanism for several stimuli, including hypoglycemia, hypoxia, ischemia, and chronic neurodegenerative diseases. Experimental approaches to the study of neuroprotection in the retina have utilized insults that trigger hypoxia, hypoglycemia, or excitotoxicity. Using these experimental approaches, the neuroprotective potential of GluR agents, including the NMDA receptor modulators (MK801, ifenprodil, memantine); AMPA/KA receptor antagonist (CNQX); Group II and III mGluR agonists (LY354740, quisqualate); and Ca2+-channel blockers (diltiazem, lomerizine, verapamil, ω-conotoxin), and others (pituitary adenylate cyclase activating polypeptide, neuropeptide Y, acetylcholine receptor agonists) have been elucidated. In addition to corroborating the exocytotic role of excitatory amino acids in retinal degeneration, these studies affirm that multiple mechanism/s contribute to the prevention of damage caused by excitotoxicity in the retina. Therefore, it is feasible that several pathways are involved in protecting the retina from toxic insults in ocular neurodegenerative conditions such as glaucoma and retinal ischemia. Furthermore, these experimental models are viable tools for evaluating therapeutic candidates in ocular neuropathies.
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Affiliation(s)
- Catherine A Opere
- 1 Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University , Omaha, Nebraska
| | - Segewkal Heruye
- 1 Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University , Omaha, Nebraska
| | - Ya-Fatou Njie-Mbye
- 2 Department of Environmental and Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University , Houston, Texas
| | - Sunny E Ohia
- 2 Department of Environmental and Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University , Houston, Texas
| | - Najam A Sharif
- 2 Department of Environmental and Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University , Houston, Texas.,3 Santen Incorporated , Emeryville, California
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Systems genetics identifies a role for Cacna2d1 regulation in elevated intraocular pressure and glaucoma susceptibility. Nat Commun 2017; 8:1755. [PMID: 29176626 PMCID: PMC5701146 DOI: 10.1038/s41467-017-00837-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 06/28/2017] [Indexed: 12/21/2022] Open
Abstract
Glaucoma is a multi-factorial blinding disease in which genetic factors play an important role. Elevated intraocular pressure is a highly heritable risk factor for primary open angle glaucoma and currently the only target for glaucoma therapy. Our study helps to better understand underlying genetic and molecular mechanisms that regulate intraocular pressure, and identifies a new candidate gene, Cacna2d1, that modulates intraocular pressure and a promising therapeutic, pregabalin, which binds to CACNA2D1 protein and lowers intraocular pressure significantly. Because our study utilizes a genetically diverse population of mice with known sequence variants, we are able to determine that the intraocular pressure-lowering effect of pregabalin is dependent on the Cacna2d1 haplotype. Using human genome-wide association study (GWAS) data, evidence for association of a CACNA2D1 single-nucleotide polymorphism and primary open angle glaucoma is found. Importantly, these results demonstrate that our systems genetics approach represents an efficient method to identify genetic variation that can guide the selection of therapeutic targets. Elevated intraocular pressure (IOP) is a heritable risk factor for primary open angle glaucoma. Using forward mouse genetics, cell biology, pharmacology and human genetic data, the authors identify CACNA2D1 as an IOP risk gene that can be therapeutically targeted by the drug pregabalin in animal models.
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7
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Chintalapudi SR, Jablonski MM. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene. Methods Mol Biol 2017; 1488:391-417. [PMID: 27933535 DOI: 10.1007/978-1-4939-6427-7_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas. We found that chromosome 1 harbors an eQTL that modulates the expression of Sncg in the mouse retina and identified Pfdn2 as the candidate upstream modulator of Sncg expression. Downregulation of Pfdn2 in enriched RGCs causes a concomitant reduction in Sncg. In this chapter, we describe our strategy and methods for identifying and confirming a genetic modulation of a glaucoma-associated gene. A similar method can be applied to other genes expressed in other tissues.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA
| | - Monica M Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Pharmaceutical Sciences, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA.
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8
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Chintalapudi SR, Wang X, Li H, Lau YHC, Williams RW, Jablonski MM. Genetic and immunohistochemical analysis of HSPA5 in mouse and human retinas. Mol Vis 2016; 22:1318-1331. [PMID: 27881906 PMCID: PMC5108462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
PURPOSE Photoreceptor degenerative diseases are among the leading causes of vision loss. Although the causative genetic mutations are often known, mechanisms leading to photoreceptor degeneration remain poorly defined. We have previously demonstrated that the photoreceptor membrane-associated protein XAP-1 antigen is a product of the HSPA5 gene. In this study, we used systems genetic methods, statistical modeling, and immunostaining to identify and analyze candidate genes that modulate Hspa5 expression in the retina. METHODS Quantitative trait locus (QTL) mapping was used to map the genomic region that regulates Hspa5 in the cross between C57BL/6J X DBA/2J mice (BXD) genetic reference panel. The stepwise refinement of candidate genes was based on expression QTL mapping, gene expression correlation analyses (direct and partial), and analysis of regional sequence variants. The subcellular localization of candidate proteins and HSPA5 in mouse and human retinas was evaluated by immunohistochemistry. Differences in the localization of extracellular HSPA5 were assessed between healthy human donor and atrophic age-related macular degeneration (AMD) donor eyes. RESULTS In the eyes of healthy mice, extracellular HSPA5 was confined to the area around the cone photoreceptor outer segments. Mapping variation in Hspa5 mRNA expression levels in the retina revealed a statistically significant trans-acting expression QTL (eQTL) on Chromosome 2 (Chr 2) and a suggestive locus on Chr 15. Sulf2 on Chr 2 was the strongest candidate gene based on partial correlation analysis, Pearson correlation with Hspa5, expression levels in the retina, a missense variant in exon 14, and its reported function in the extracellular matrix and interphotoreceptor matrix. SULF2 is localized to the rod and cone photoreceptors in both human and mouse retinas. In human retinas with no pathology, extracellular HSPA5 was localized around many cones within the macular area. In contrast, fewer HSPA5-immunopositive cones were observed in the retinas from AMD donors. CONCLUSIONS We identified Sulf2 as a candidate gene modulating the Hspa5 expression in the retina. The preferential loss of HSPA5 in the interphotoreceptor matrix around cone photoreceptors in atrophic AMD retinas opens up new avenues for exploring the changes in interphotoreceptor matrix (IPM) that are associated with macular disease.
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Affiliation(s)
- Sumana R. Chintalapudi
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN
| | - XiaoFei Wang
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN
| | - Huiling Li
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN,Department of Ophthalmology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yin H. Chan Lau
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN
| | - Robert W. Williams
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN,Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN
| | - Monica M. Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN,Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, TN
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9
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Lu H, Lu L, Williams RW, Jablonski MM. Iris transillumination defect and its gene modulators do not correlate with intraocular pressure in the BXD family of mice. Mol Vis 2016; 22:224-33. [PMID: 27011731 PMCID: PMC4783577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/02/2016] [Indexed: 11/16/2022] Open
Abstract
PURPOSE Intraocular pressure (IOP) is currently the only treatable phenotype associated with primary open angle glaucoma (POAG). Our group has developed the BXD murine panel for identifying genetic modulators of the various endophenotypes of glaucoma, including pigment dispersion, IOP, and retinal ganglion cell (RGC) death. The BXD family consists of the inbred progeny of crosses between the C57BL/6J (B6) strain and the glaucoma-prone DBA/2J (D2) strain that has mutations in Tyrp1 and Gpnmb. The role of these genes in the iris transillumination defect (TID) has been well documented; however, their possible roles in modulating IOP during glaucoma onset and progression are yet not well understood. METHODS We used the IOP data sets and the Eye M430v2 (Sep08) RMA Database available on GeneNetwork to determine whether mutations in Tyrp1 and Gpnmb or TIDs have a direct role in the elevation of IOP in the BXD family. We also determined whether TIDs and IOP are coregulated. RESULTS As expected, Tyrp1 and Gpnmb expression levels showed a high degree of correlation with TIDs. However, there was no correlation between the expression of these genes and IOP. Moreover, unlike TIDs, IOP did not map to either the Tyrp1 or Gpnmb locus. Although the Tyrp1 and Gpnmb mutations in BXD strains are a prerequisite for the development of TID, they are not required for or associated with elevated IOP. CONCLUSIONS Genetic modulators of IOP thus may be independently identified using the full array of BXD mice without concern for the presence of TIDs or mutations in Typr1 and/or Gpnmb.
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Affiliation(s)
- Hong Lu
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN,Department of Ophthalmology, Nantong Eye Institute, Affiliated Hospital of Nantong University, Nantong, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN,Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN
| | - Monica M. Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN
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10
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Chintalapudi SR, Morales-Tirado VM, Williams RW, Jablonski MM. Multipronged approach to identify and validate a novel upstream regulator of Sncg in mouse retinal ganglion cells. FEBS J 2016; 283:678-93. [PMID: 26663874 DOI: 10.1111/febs.13620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/22/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Mechanistic studies on RGCs are hindered by the lack of sufficient primary cells and consensus regarding their signature markers. Recently, γ-synuclein (SNCG) has been shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the role of Sncg in RGCs, we used a novel systems genetics approach to identify a gene that modulates Sncg expression, followed by confirmatory studies in both healthy and diseased retinae. We found that chromosome 1 harbors an expression quantitative trait locus that modulates Sncg expression in the mouse retina, and identified the prefoldin-2 (PFDN2) gene as the candidate upstream modulator of Sncg expression. Our immunohistochemical analyses revealed similar expression patterns in both mouse and human healthy retinae, with PFDN2 colocalizing with SNCG in RGCs and their axons. In contrast, in retinae from glaucoma subjects, SNCG levels were significantly reduced, although PFDN2 levels were maintained. Using a novel flow cytometry-based RGC isolation method, we obtained viable populations of murine RGCs. Knocking down Pfdn2 expression in primary murine RGCs significantly reduced Sncg expression, confirming that Pfdn2 regulates Sncg expression in murine RGCs. Gene Ontology analysis indicated shared mitochondrial function associated with Sncg and Pfdn2. These data solidify the relationship between Sncg and Pfdn2 in RGCs, and provide a novel mechanism for maintaining RGC health.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vanessa M Morales-Tirado
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W Williams
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
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11
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Chaum E, Winborn CS, Bhattacharya S. Genomic regulation of senescence and innate immunity signaling in the retinal pigment epithelium. Mamm Genome 2015; 26:210-21. [PMID: 25963977 DOI: 10.1007/s00335-015-9568-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/02/2015] [Indexed: 01/04/2023]
Abstract
The tumor suppressor p53 is a major regulator of genes important for cell cycle arrest, senescence, apoptosis, and innate immunity, and has recently been implicated in retinal aging. In this study we sought to identify the genetic networks that regulate p53 function in the retina using quantitative trait locus (QTL) analysis. First we examined age-associated changes in the activation and expression levels of p53; known p53 target proteins and markers of innate immune system activation in primary retinal pigment epithelial (RPE) cells that were harvested from young and aged human donors. We observed increased expression of p53, activated caspase-1, CDKN1A, CDKN2A (p16INK4a), TLR4, and IFNα in aged primary RPE cell lines. We used the Hamilton Eye Institute (HEI) retinal dataset ( www.genenetwork.org ) to identify genomic loci that modulate expression of genes in the p53 pathway in recombinant inbred BXD mouse strains using a QTL systems biology-based approach. We identified a significant trans-QTL on chromosome 1 (region 172-177 Mb) that regulates the expression of Cdkn1a. Many of the genes in this QTL locus are involved in innate immune responses, including Fc receptors, interferon-inducible family genes, and formin 2. Importantly, we found an age-related increase in FCGR3A and FMN2 and a decrease in IFI16 levels in RPE cultures. There is a complex multigenic innate immunity locus that controls expression of genes in the p53 pathway in the RPE, which may play an important role in modulating age-related changes in the retina.
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Affiliation(s)
- Edward Chaum
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA,
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An Introduction to Pain Pathways and Pain “Targets”. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 131:1-30. [DOI: 10.1016/bs.pmbts.2015.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Swaminathan S, Lu H, Williams RW, Lu L, Jablonski MM. Genetic modulation of the iris transillumination defect: a systems genetics analysis using the expanded family of BXD glaucoma strains. Pigment Cell Melanoma Res 2013; 26:487-98. [PMID: 23582180 PMCID: PMC3752936 DOI: 10.1111/pcmr.12106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 04/10/2013] [Indexed: 11/29/2022]
Abstract
We investigated the contributions of Tyrp1 and Gpnmb to the iris transillumination defect (TID) in five age cohorts of BXD mice. Using systems genetics, we also evaluated the role of other known pigmentation genes (PGs). Mapping studies indicate that Tyrp1 contributes to the phenotype at all ages, yet the TID maps to Gpnmb only in the oldest cohort. Composite interval mapping reveals secondary loci viz. Oca2, Myo5a, Prkcz, and Zbtb20 that modulate the phenotype in the age groups up to 10–13 months. The contributions of Tyrp1 and Gpnmb were highly significant in all age cohorts. Moreover, in young mice, all six gene candidates had substantial interactions in our model. Our model accounted for 71–88% of the explained variance of the TID phenotype across the age bins. These results demonstrate that along with Tyrp1 and Gpnmb, Oca2, Myo5a, Prkcz, and Zbtb20 modulate the TID in an age-dependent manner.
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Affiliation(s)
- Shankar Swaminathan
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, USA
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Ishikawa M. Abnormalities in glutamate metabolism and excitotoxicity in the retinal diseases. SCIENTIFICA 2013; 2013:528940. [PMID: 24386591 PMCID: PMC3872404 DOI: 10.1155/2013/528940] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/17/2013] [Indexed: 05/14/2023]
Abstract
In the physiological condition, glutamate acts as an excitatory neurotransmitter in the retina. However, excessive glutamate can be toxic to retinal neurons by overstimulation of the glutamate receptors. Glutamate excess is primarily attributed to perturbation in the homeostasis of the glutamate metabolism. Major pathway of glutamate metabolism consists of glutamate uptake by glutamate transporters followed by enzymatic conversion of glutamate to nontoxic glutamine by glutamine synthetase. Glutamate metabolism requires energy supply, and the energy loss inhibits the functions of both glutamate transporters and glutamine synthetase. In this review, we describe the present knowledge concerning the retinal glutamate metabolism under the physiological and pathological conditions.
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Affiliation(s)
- Makoto Ishikawa
- Department of Ophthalmology, Akita Graduate University Faculty of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
- *Makoto Ishikawa:
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Parikh N, Zollanvari A, Alterovitz G. An automated bayesian framework for integrative gene expression analysis and predictive medicine. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2012; 2012:95-104. [PMID: 22779059 PMCID: PMC3392067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
MOTIVATION This work constructs a closed loop Bayesian Network framework for predictive medicine via integrative analysis of publicly available gene expression findings pertaining to various diseases. RESULTS An automated pipeline was successfully constructed. Integrative models were made based on gene expression data obtained from GEO experiments relating to four different diseases using Bayesian statistical methods. Many of these models demonstrated a high level of accuracy and predictive ability. The approach described in this paper can be applied to any complex disorder and can include any number and type of genome-scale studies.
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Affiliation(s)
- Neena Parikh
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
| | - Amin Zollanvari
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA
- Children’s Hospital Informatics Program at Harvard-MIT Division of Health Science, Boston, MA
| | - Gil Alterovitz
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA
- Children’s Hospital Informatics Program at Harvard-MIT Division of Health Science, Boston, MA
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Lu H, Li L, Watson ER, Williams RW, Geisert EE, Jablonski MM, Lu L. Complex interactions of Tyrp1 in the eye. Mol Vis 2011; 17:2455-68. [PMID: 21976956 PMCID: PMC3185026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/12/2011] [Indexed: 11/20/2022] Open
Abstract
PURPOSE To use a systems genetics approach to construct and analyze co-expression networks that are causally linked to mutations in a key pigementation gene, tyrosinase-related protein 1 (Tyrp1), that is associated both with oculocutaneous albinism type 3 (OCA3) in humans and with glaucoma in mice. METHODS Gene expression patterns were measured in whole eyes of a large family of BXD recombinant inbred (RI) mice derived from parental lines that encode for wildtype (C57BL/6J) and mutant (DBA/2J) Tyrp1. Protein levels of Tyrp1 were measured in whole eyes and isolated irides. Bioinformatics analyses were performed on the expression data along with our archived sequence data. Separate data sets were generated which were comprised of strains that harbor either wildtype or mutant Tyrp1 and each was mined individually to identify gene networks that covary significantly with each isoform of Tyrp1. Ontology trees and network graphs were generated to probe essential function and statistical significance of covariation. Genes with strong covariance in wildtype mice were assembled into genome-wide heatmaps for cohorts carrying either wildtype or mutant Tyrp1. RESULTS Single nucleotide polymorphism (SNP) analysis verified the presence of the Tyrp1b mutation in the Tyrp1 gene. Message levels were greater in BXD strains with the mutant Tyrp1. Interval mapping of these BXD mice revealed a strong expression quantitative trait locus (eQTL) on Chr 4 at the location of the gene itself. Composite mapping revealed a suggestive eQTL on Chr 9 at the location of myosin-Va (Myo5a), mutations in which are known as dilute. Enriched biologic processes associated with wildtype Tyrp1 included pigmentation, melanin biosynthetic process, and mesenchymal cell development, while associations with the mutant gene included categories of neural crest cell development, protein metabolic processes and glycoprotein metabolic processes. Genome-wide heatmaps revealed strong candidate cis-eQTLs on Chr 4 at Tyrp1 and on Chr 9 at Myo5a in all mice. In the wildtype data set, Tyrp1 was an upstream regulator of six pigmentation and two mesenchyme genes. In addition, five genes, including Tyrp1, were at least partially regulated by Myo5a. Analyses of the strains harboring the mutant gene revealed significant loss of correlation to traditional genes and gain of correlation to genes with little or no functional relationship. CONCLUSIONS These findings indicate that the Tyrp1(b) mutation modifies the pathways and gene networks in which Tyrp1 functions. Our results also indicate direct and indirect regulatory control of Tyrp1 and other pigmentation and mesenchymal genes by Myo5a. Lastly, we find that the mutations reduce the ability of Tyrp1 to regulate expression of other genes that participate in pigmentation metabolism.
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Affiliation(s)
- Hong Lu
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN,Department of Ophthalmology, Affiliated Hospital of Nantong University, Nantong, China
| | - Liyuan Li
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN
| | - Edmond R. Watson
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN
| | - Robert W. Williams
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN
| | - Eldon E. Geisert
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN,Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN
| | - Monica M. Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN,Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN
| | - Lu Lu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN,Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
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Ishikawa M, Yoshitomi T, Zorumski CF, Izumi Y. Downregulation of glutamine synthetase via GLAST suppression induces retinal axonal swelling in a rat ex vivo hydrostatic pressure model. Invest Ophthalmol Vis Sci 2011; 52:6604-16. [PMID: 21775659 DOI: 10.1167/iovs.11-7375] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE. High levels of glutamate can be toxic to retinal GCs. Thus, effective buffering of extracellular glutamate is important in preserving retinal structure and function. GLAST, a major glutamate transporter in the retina, and glutamine synthetase (GS) regulate extracellular glutamate accumulation and prevent excitotoxicity. This study was an examination of changes in function and expression of GLAST and GS in ex vivo rat retinas exposed to acute increases in ambient pressure. METHODS. Ex vivo rat retinas were exposed to elevated hydrostatic pressure for 24 hours. The expression of GLAST and GS were examined using immunochemistry and real-time PCR analysis. Also examined were the effects of (2S,3S)-3-[3-[4-(trifluoromethyl) benzoylamino] benzyloxy] aspartate (TFB-TBOA), an inhibitor of glutamate transporters, and l-methionine-S-sulfoximine (MSO), an inhibitor of GS. RESULTS. In this acute model, Western blot and real-time RT-PCR analyses revealed that substantially (75 mm Hg), but not moderately (35 mm Hg), elevated pressure depressed GLAST expression, diminished GS activity, and induced axonal swelling between the GC layer and the inner limiting membrane. However, at the moderately elevated pressure (35 mm Hg), administration of either TFB-TBOA or MSO also induced axonal swelling and excitotoxic neuronal damage. MSO did not depress GLAST expression but TFB-TBOA significantly suppressed GS, suggesting that downregulation of GS during pressure loading may result from impaired GLAST expression. CONCLUSIONS. The retina is at risk during acute intraocular pressure elevation due to downregulation of GS activity resulting from depressed GLAST expression.
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Affiliation(s)
- Makoto Ishikawa
- Department of Ophthalmology, Akita University School of Medicine, Japan.
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Lu H, Wang X, Pullen M, Guan H, Chen H, Sahu S, Zhang B, Chen H, Williams RW, Geisert EE, Lu L, Jablonski MM. Genetic dissection of the Gpnmb network in the eye. Invest Ophthalmol Vis Sci 2011; 52:4132-42. [PMID: 21398278 DOI: 10.1167/iovs.10-6493] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
PURPOSE To use a systematic genetics approach to investigate the regulation of Gpnmb, a gene that contributes to pigmentary dispersion syndrome (PDS) and pigmentary glaucoma (PG) in the DBA/2J (D2) mouse. METHODS Global patterns of gene expression were studied in whole eyes of a large family of BXD mouse strains (n = 67) generated by crossing the PDS- and PG-prone parent (DBA/2J) with a resistant strain (C57BL/6J). Quantitative trait locus (eQTL) mapping methods and gene set analysis were used to evaluate Gpnmb coexpression networks in wild-type and mutant cohorts. RESULTS The level of Gpnmb expression was associated with a highly significant cis-eQTL at the location of the gene itself. This autocontrol of Gpnmb is likely to be a direct consequence of the known premature stop codon in exon 4. Both gene ontology and coexpression network analyses demonstrated that the mutation in Gpnmb radically modified the set of genes with which Gpnmb expression is correlated. The covariates of wild-type Gpnmb are involved in biological processes including melanin synthesis and cell migration, whereas the covariates of mutant Gpnmb are involved in the biological processes of posttranslational modification, stress activation, and sensory processing. CONCLUSIONS These results demonstrated that a systematic genetics approach provides a powerful tool for constructing coexpression networks that define the biological process categories within which similarly regulated genes function. The authors showed that the R150X mutation in Gpnmb dramatically modified its list of genetic covariates, which may explain the associated ocular pathology.
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Affiliation(s)
- Hong Lu
- Department of Ophthalmology, Affiliated Hospital of Nantong University, Nantong, China
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Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE. Genetic networks in the mouse retina: growth associated protein 43 and phosphatase tensin homolog network. Mol Vis 2011; 17:1355-72. [PMID: 21655357 PMCID: PMC3108897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 05/21/2011] [Indexed: 10/26/2022] Open
Abstract
PURPOSE The present study examines the structure and covariance of endogenous variation in gene expression across the recently expanded family of C57BL/6J (B) X DBA/2J (D) Recombinant Inbred (BXD RI) strains of mice. This work is accompanied by a highly interactive database that can be used to generate and test specific hypotheses. For example, we define the genetic network regulating growth associated protein 43 (Gap43) and phosphatase tensin homolog (Pten). METHODS The Hamilton Eye Institute (HEI) Retina Database within GeneNetwork features the data analysis of 346 Illumina Sentrix BeadChip Arrays (mouse whole genome-6 version 2). Eighty strains of mice are presented, including 75 BXD RI strains, the parental strains (C57BL/6J and DBA/2J), the reciprocal crosses, and the BALB/cByJ mice. Independent biologic samples for at least two animals from each gender were obtained with a narrow age range (48 to 118 days). Total RNA was prepared followed by the production of biotinylated cRNAs, which were pipetted into the Mouse WG-6V2 arrays. The data was globally normalized with rank invariant and stabilization (2z+8). RESULTS The HEI Retina Database is located on the GeneNetwork website. The database was used to extract unique transcriptome signatures for specific cell types in the retina (retinal pigment epithelial, amacrine, and retinal ganglion cells). Two genes associated with axonal outgrowth (Gap43 and Pten) were used to display the power of this new retina database. Bioinformatic tools located within GeneNetwork in conjunction with the HEI Retina Database were used to identify the unique signature Quantitative Trait Loci (QTLs) for Gap43 and Pten on chromosomes 1, 2, 12, 15, 16, and 19. Gap43 and Pten possess networks that are similar to ganglion cell networks that may be associated with axonal growth in the mouse retina. This network involves high correlations of transcription factors (SRY sex determining region Y-box 2 [Sox2], paired box gene 6 [Pax6], and neurogenic differentiation 1 [Neurod1]), and genes involved in DNA binding (proliferating cell nuclear antigen [Pcna] and zinc finger, BED-type containing 4 [Zbed4]), as well as an inhibitor of DNA binding (inhibitor of DNA binding 2, dominant negative helix-loop-helix protein [Id2]). Furthermore, we identified the potential upstream modifiers on chromosome 2 (teashirt zinc finger homeobox 2 [Tshz2], RNA export 1 homolog [Rae1] and basic helix-loop-helix domain contatining, class B4 [Bhlhb4]) on chromosome 15 (RAB, member of RAS oncogene family-like 2a [Rabl2a], phosphomannomutase 1 [Pmm1], copine VIII [Cpne8], and fibulin 1 [Fbln1]). CONCLUSIONS The endogenous variation in mRNA levels among BXD RI strains can be used to explore and test expression networks underlying variation in retina structure, function, and disease susceptibility. The Gap43 and Pten network highlights the covariance of gene expression and forms a molecular network associated with axonal outgrowth in the adult retina.
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Affiliation(s)
| | | | - William E. Orr
- Department of Ophthalmology and Center for Vision Research, Memphis, TN
| | - Lu Lu
- Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN
| | - Robert W. Williams
- Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN
| | - Eldon E. Geisert
- Department of Ophthalmology and Center for Vision Research, Memphis, TN
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