Retinal proteomics of experimental glaucoma model reveal intraocular pressure-induced mediators of neurodegenerative changes
Corresponding Author
Mehdi Mirzaei
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
Correspondence Mehdi Mirzaei, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Vivek K. Gupta, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Vivek K. Gupta
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Correspondence Mehdi Mirzaei, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Vivek K. Gupta, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Search for more papers by this authorNitin Chitranshi
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorLiting Deng
Search for more papers by this authorKanishka Pushpitha
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorMojdeh Abbasi
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorJoel M. Chick
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
Search for more papers by this authorRashi Rajput
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorYunqi Wu
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
Search for more papers by this authorMatthew J. McKay
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
Search for more papers by this authorGhasem H. Salekdeh
Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
Search for more papers by this authorVeer B. Gupta
School of Medicine, Deakin University, Melbourne, Australia
Search for more papers by this authorPaul A. Haynes
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Search for more papers by this authorStuart L. Graham
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorCorresponding Author
Mehdi Mirzaei
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
Correspondence Mehdi Mirzaei, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Vivek K. Gupta, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Vivek K. Gupta
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Correspondence Mehdi Mirzaei, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Vivek K. Gupta, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
Email: [email protected]
Search for more papers by this authorNitin Chitranshi
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorLiting Deng
Search for more papers by this authorKanishka Pushpitha
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorMojdeh Abbasi
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorJoel M. Chick
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
Search for more papers by this authorRashi Rajput
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorYunqi Wu
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
Search for more papers by this authorMatthew J. McKay
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
Search for more papers by this authorGhasem H. Salekdeh
Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
Search for more papers by this authorVeer B. Gupta
School of Medicine, Deakin University, Melbourne, Australia
Search for more papers by this authorPaul A. Haynes
Department of Molecular Sciences, Macquarie University, Sydney, Australia
Search for more papers by this authorStuart L. Graham
Department of Clinical Medicine, Macquarie University, Sydney, Australia
Search for more papers by this authorMehdi Mirzaei, Vivek K. Gupta, and Nitin Chitranshi contributed equally to this study.
Abstract
Current evidence suggests that exposure to chronically induced intraocular pressure (IOP) leads to neurodegenerative changes in the inner retina. This study aimed to determine retinal proteomic alterations in a rat model of glaucoma and compared findings with human retinal proteomics changes in glaucoma reported previously. We developed an experimental glaucoma rat model by subjecting the rats to increased IOP (9.3 ± 0.1 vs 20.8 ± 1.6 mm Hg) by weekly microbead injections into the eye (8 weeks). The retinal tissues were harvested from control and glaucomatous eyes and protein expression changes analysed using a multiplexed quantitative proteomics approach (TMT-MS3). Immunofluorescence was performed for selected protein markers for data validation. Our study identified 4304 proteins in the rat retinas. Out of these, 139 proteins were downregulated (≤0.83) while the expression of 109 proteins was upregulated (≥1.2-fold change) under glaucoma conditions (P ≤ .05). Computational analysis revealed reduced expression of proteins associated with glutathione metabolism, mitochondrial dysfunction/oxidative phosphorylation, cytoskeleton, and actin filament organisation, along with increased expression of proteins in coagulation cascade, apoptosis, oxidative stress, and RNA processing. Further functional network analysis highlighted the differential modulation of nuclear receptor signalling, cellular survival, protein synthesis, transport, and cellular assembly pathways. Alterations in crystallin family, glutathione metabolism, and mitochondrial dysfunction associated proteins shared similarities between the animal model of glaucoma and the human disease condition. In contrast, the activation of the classical complement pathway and upregulation of cholesterol transport proteins were exclusive to human glaucoma. These findings provide insights into the neurodegenerative mechanisms that are specifically affected in the retina in response to chronically elevated IOP.
CONFLICT OF INTERESTS
The authors declare that there are no conflict of interests.
Open Research
DATA AVAILABILITY STATEMENT
The data that support the findings of this study is available freely at https://data.mendeley.com/datasets/mhmvnm5wwg/1
Supporting Information
| Filename | Description |
|---|---|
| jcb29822-sup-0001-Table_1.xlsx663 KB | Supporting information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1Chitranshi N, Dheer Y, Abbasi M, You Y, Graham SL, Gupta V. Glaucoma pathogenesis and neurotrophins: focus on the molecular and genetic basis for therapeutic prospects. Curr Neuropharmacol. 2018; 16: 1018-1035.
- 2McMonnies CW. Glaucoma history and risk factors. J Optom. 2017; 10: 71-78.
- 3Kass MA, Heuer DK, Higginbotham EJ, et al. The ocular hypertension treatment study: a randomized trial determines that topical ocular hypotensive medication delays or prevents the onset of primary open-angle glaucoma. Arch Ophthalmol. 2002; 120: 701-713.
- 4Mirzaei M, Gupta VB, Chick JM, et al. Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Sci Rep. 2017; 7:12685.
- 5Bhattacharya SK, Crabb JS, Bonilha VL, Gu X, Takahara H, Crabb JW. Proteomics implicates peptidyl arginine deiminase 2 and optic nerve citrullination in glaucoma pathogenesis. Invest Ophthalmol Vis Sci. 2006; 47: 2508-2514.
- 6Tezel G, Yang X, Cai J. Proteomic identification of oxidatively modified retinal proteins in a chronic pressure-induced rat model of glaucoma. Invest Ophthalmol Vis Sci. 2005; 46: 3177-3187.
- 7Tezel G. A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration. Prog Retin Eye Res. 2013; 35: 18-43.
- 8Tezel G. A decade of proteomics studies of glaucomatous neurodegeneration. Proteomics Clin Appl. 2014; 8: 154-167.
- 9Funke S, Perumal N, Beck S, et al. Glaucoma related proteomic alterations in human retina samples. Sci Rep. 2016; 6:29759.
- 10Stowell C, Arbogast B, Cioffi G, Burgoyne C, Zhou A. Retinal proteomic changes following unilateral optic nerve transection and early experimental glaucoma in non-human primate eyes. Exp Eye Res. 2011; 93: 13-28.
- 11Anders F, Teister J, Funke S, et al. Proteomic profiling reveals crucial retinal protein alterations in the early phase of an experimental glaucoma model. Graefes Arch Clin Exp Ophthalmol. 2017; 255: 1395-1407.
- 12You Y, Thie J, Klistorner A, Gupta VK, Graham SL. Normalization of visual evoked potentials using underlying electroencephalogram levels improves amplitude reproducibility in rats. Invest Ophthalmol Vis Sci. 2012; 53: 1473-1478.
- 13Gupta V, Mirzaei M, Gupta VB, et al. Glaucoma is associated with plasmin proteolytic activation mediated through oxidative inactivation of neuroserpin. Sci Rep. 2017; 7:8412.
- 14Gupta V, You Y, Li J, et al. BDNF impairment is associated with age-related changes in the inner retina and exacerbates experimental glaucoma. Biochimica et Biophysica Acta. 2014; 1842: 1567-1578.
- 15You Y, Gupta VK, Li JC, Al-Adawy N, Klistorner A, Graham SL. FTY720 protects retinal ganglion cells in experimental glaucoma FTY720 protects RGCs. Invest Ophthalmol Vis Sci. 2014; 55: 3060-3066.
- 16Chitranshi N, Dheer Y, Mirzaei M, et al. Loss of Shp2 rescues BDNF/TrkB signaling and contributes to improved retinal ganglion cell neuroprotection. Mol Ther. 2019; 27: 424-441.
- 17Gupta V, Chitranshi N, You Y, Gupta V, Klistorner A, Graham S. Brain derived neurotrophic factor is involved in the regulation of glycogen synthase kinase 3beta (GSK3beta) signalling. Biochem Biophys Res Commun. 2014; 454: 381-386.
- 18Mirzaei M, Pushpitha K, Deng L, et al. Upregulation of proteolytic pathways and altered protein biosynthesis underlie retinal pathology in a mouse model of Alzheimer's disease. Mol Neurobiol. 2019; 56: 6017-6034.
- 19Wessel D, Flügge UI. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem. 1984; 138: 141-143.
- 20Gupta VK, Gowda LR. Alpha-1-proteinase inhibitor is a heparin binding serpin: molecular interactions with the Lys rich cluster of helix-F domain. Biochimie. 2008; 90: 749-761.
- 21Kulak NA, Pichler G, Paron I, Nagaraj N, Mann M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nature Methods. 2014; 11: 319-324.
- 22McAlister GC, Nusinow DP, Jedrychowski MP, et al. MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal Chem. 2014; 86: 7150-7158.
- 23Huttlin EL, Ting L, Bruckner RJ, et al. The BioPlex network: a systematic exploration of the human interactome. Cell. 2015; 162: 425-440.
- 24Elias JE, Gygi SP. Target-Decoy search strategy for mass spectrometry-based proteomics. In: SJ Hubbard, AR Jones, eds. Proteome Bioinformatics. Totowa, NJ: Humana Press; 2010: 55-71.
10.1007/978-1-60761-444-9_5 Google Scholar
- 25McAlister GC, Huttlin EL, Haas W, et al. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal Chem. 2012; 84: 7469-7478.
- 26Chick JM, Munger SC, Simecek P, et al. Defining the consequences of genetic variation on a proteome-wide scale. Nature. 2016; 534: 500-505.
- 27Mirzaei M, Pascovici D, Wu JX, et al. TMT one-stop shop: From reliable sample preparation to computational analysis platform. In: S Keerthikumar, S Mathivanan, eds. Proteome Bioinformatics. New York, NY: Springer; 2017: 45-66.
10.1007/978-1-4939-6740-7_5 Google Scholar
- 28Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015; 43: D447-D452.
- 29Basavarajappa DK, Gupta VK, Dighe R, Rajala A, Rajala RV. Phosphorylated Grb14 is an endogenous inhibitor of retinal protein tyrosine phosphatase 1B, and light-dependent activation of Src phosphorylates Grb14. Mol Cell Biol. 2011; 31: 3975-3987.
- 30Chitranshi N, Dheer Y, Kumar S, Graham SL, Gupta V. Molecular docking, dynamics, and pharmacology studies on bexarotene as an agonist of ligand-activated transcription factors, retinoid X receptors. J Cell Biochem. 2019; 120: 11745-11760.
- 31Lee S, Van Bergen NJ, Kong GY, et al. Mitochondrial dysfunction in glaucoma and emerging bioenergetic therapies. Exp Eye Res. 2011; 93: 204-212.
- 32Hüttemann M, Lee I, Samavati L, Yu H, Doan JW. Regulation of mitochondrial oxidative phosphorylation through cell signaling. Biochimica et Biophysica Acta. 2007; 1773: 1701-1720.
- 33Kong GYX, Van Bergen NJ, Trounce IA, Crowston JG. Mitochondrial dysfunction and glaucoma. J Glaucoma. 2009; 18: 93-100.
- 34Moreno MC, Campanelli J, Sande P, Sáenz DA, Keller Sarmiento MI, Rosenstein RE. Retinal oxidative stress induced by high intraocular pressure. Free Radic Biol Med. 2004; 37: 803-812.
- 35Clark AF, Miggans ST, Wilson K, Browder S, McCartney MD. Cytoskeletal changes in cultured human glaucoma trabecular meshwork cells. J Glaucoma. 1995; 4: 183-188.
- 36Hoare MJ, Grierson I, Brotchie D, Pollock N, Cracknell K, Clark AF. Cross-linked actin networks (CLANs) in the trabecular meshwork of the normal and glaucomatous human eye in situ. Invest Ophthalmol Vis Sci. 2009; 50: 1255-1263.
- 37Job R, Raja V, Grierson I, et al. Cross-linked actin networks (CLANs) are present in lamina cribrosa cells. Br J Ophthalmol. 2010; 94: 1388-1392.
- 38Launay N, Goudeau B, Kato K, Vicart P, Lilienbaum A. Cell signaling pathways to alphaB-crystallin following stresses of the cytoskeleton. Exp Cell Res. 2006; 312: 3570-3584.
- 39Jacobsen AV, Murphy JM. The secret life of kinases: insights into non-catalytic signalling functions from pseudokinases. Biochem Soc Trans. 2017; 45: 665-681.
- 40Liu Y, Allingham RR, Qin X, et al. Gene expression profile in human trabecular meshwork from patients with primary open-angle glaucoma. Invest Ophthalmol Vis Sci. 2013; 54: 6382-6389.
- 41Komatsu M, Wang QJ, Holstein GR, et al. Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration. Proc Natl Acad Sci USA. 2007; 104: 14489-14494.
- 42Wang DY, Ray A, Rodgers K, et al. Global gene expression changes in rat retinal ganglion cells in experimental glaucoma. Invest Ophthalmol Vis Sci. 2010; 51: 4084-4095.
- 43Ishikawa K, Yoshida S, Kadota K, et al. Gene expression profile of hyperoxic and hypoxic retinas in a mouse model of oxygen-induced retinopathy. Invest Ophthalmol Vis Sci. 2010; 51: 4307-4319.
- 44Manca F, Pincet F, Truskinovsky L, Rothman JE, Foret L, Caruel M. SNARE machinery is optimized for ultrafast fusion. Proc Natl Acad Sci USA. 2019; 116: 2435-2442.
- 45McKay BS, Congrove NR, Johnson AA, Dismuke WM, Bowen TJ, Stamer WD. A role for myocilin in receptor-mediated endocytosis. PLoS One. 2013; 8:e82301.
- 46Dismuke WM, McKay BS, Stamer WD. Myocilin, a component of a membrane-associated protein complex driven by a homologous Q-SNARE domain. Biochemistry. 2012; 51: 3606-3613.
- 47Liang XH, Sun H, Nichols JG, et al. COPII vesicles can affect the activity of antisense oligonucleotides by facilitating the release of oligonucleotides from endocytic pathways. Nucleic Acids Res. 2018; 46: 10225-10245.
- 48Alqawlaq S, Huzil JT, Ivanova MV, Foldvari M. Challenges in neuroprotective nanomedicine development: progress towards noninvasive gene therapy of glaucoma. Nanomedicine. 2012; 7: 1067-1083.
- 49Frost LS, Mitchell CH, Boesze-Battaglia K. Autophagy in the eye: implications for ocular cell health. Exp Eye Res. 2014; 124: 56-66.
- 50Porter K, Nallathambi J, Lin Y, Liton PB. Lysosomal basification and decreased autophagic flux in oxidatively stressed trabecular meshwork cells: implications for glaucoma pathogenesis. Autophagy. 2013; 9: 581-94.
- 51Swarup G, Sayyad Z. Altered functions and interactions of glaucoma-associated mutants of optineurin. Front Immunol. 2018; 9: 1287.
- 52Dheer Y, Chitranshi N, Gupta V, et al. Retinoid x receptor modulation protects against ER stress response and rescues glaucoma phenotypes in adult mice. Exp Neurol. 2019; 314: 111-125.
- 53Liedtke T, Schwamborn JC, Schröer U, Thanos S. Elongation of axons during regeneration involves retinal crystallin β b2 (crybb2). Mol Cell Proteomics. 2007; 6: 895-907.
- 54Piri N, Song M, Kwong JMK, Caprioli J. Modulation of alpha and beta crystallin expression in rat retinas with ocular hypertension-induced ganglion cell degeneration. Brain Res. 2007; 1141: 1-9.
- 55Prokosch V, Schallenberg M, Thanos S. Crystallins are regulated biomarkers for monitoring topical therapy of glaucomatous optic neuropathy. PLoS One. 2013; 8:e49730.
- 56Tezel G, Seigel GM, Wax MB. Autoantibodies to small heat shock proteins in glaucoma. Invest Ophthalmol Vis Sci. 1998; 39: 2277-2287.
- 57Tian H, Wang L, Cai R, Zheng L, Guo L. Identification of protein network alterations upon retinal ischemia-reperfusion injury by quantitative proteomics using a Rattus norvegicus model. PLoS One. 2014; 9:e116453.
- 58Levi M, van der Poll T. Inflammation and coagulation. Crit Care Med. 2010; 38: S26-S34.
- 59Chrysostomou V, Rezania F, Trounce IA, Crowston JG. Oxidative stress and mitochondrial dysfunction in glaucoma. Curr Opin Pharmacol. 2013; 13: 12-15.
- 60Munemasa Y, Kitaoka Y, Kuribayashi J, Ueno S. Modulation of mitochondria in the axon and soma of retinal ganglion cells in a rat glaucoma model. J Neurochem. 2010; 115: 1508-1519.
- 61Kim KY, Perkins GA, Shim MS, et al. DRP1 inhibition rescues retinal ganglion cells and their axons by preserving mitochondrial integrity in a mouse model of glaucoma. Cell Death Dis. 2015; 6:e1839.
- 62Lee D, Kim KY, Shim MS, et al. Coenzyme Q10 ameliorates oxidative stress and prevents mitochondrial alteration in ischemic retinal injury. Apoptosis. 2014; 19: 603-614.
- 63Williams PA, Harder JM, Foxworth NE, et al. Vitamin B3 modulates mitochondrial vulnerability and prevents glaucoma in aged mice. Science. 2017; 355: 756-760.
- 64Horita S, Simsek E, Simsek T, et al. SLC4A4 compound heterozygous mutations in exon-intron boundary regions presenting with severe proximal renal tubular acidosis and extrarenal symptoms coexisting with Turner's syndrome: a case report. BMC Med Genet. 2018; 19: 103.
- 65Cai X, Du J, Liu Y, et al. Identification and characterization of receptor-interacting protein 2 as a TNFR-associated factor 3 binding partner. Gene. 2013; 517: 205-211.
- 66Yu DH, Zhang X, Wang H, et al. The essential role of TNIK gene amplification in gastric cancer growth. Oncogenesis. 2014; 2:e89.
- 67Zagajewska K, Piatkowska M, Goryca K, et al. GWAS links variants in neuronal development and actin remodeling related loci with pseudoexfoliation syndrome without glaucoma. Exp Eye Res. 2018; 168: 138-148.
- 68Mirzaei M, Deng L, Gupta VB, Graham S, Gupta V. Complement pathway in Alzheimer's pathology and retinal neurodegenerative disorders—the road ahead. Neural Regen Res. 2020; 15: 257-258.
Citing Literature
