Diabetic Retinopathy and Laser Therapy in Rats: A Protein-Protein Interaction Network Analysis

Akram Safaei--- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,
Mostafa Rezaei Tavirani--- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,
Mona Zamanian Azodi--- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,
Alireza Lashay--- Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran,
Seyed Farzad Mohammadi--- Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran,
Mohamad Ghasemi Broumand--- Physiotherapy Research Centre, School of Rehabilitation, Shahid Beheshti University of Medical Sciences, Tehran, Iran,
Ali Asghar Peyvandi--- Hearing Disorder Research Center, Shahid Behshti University of Medical Sciences, Tehran, Iran,
Farshad Okhovatian--- Physiotherapy Research Centre, School of Rehabilitation, Shahid Beheshti University of Medical Sciences, Tehran, Iran,
Hassan Peyvandi--- Hearing Disorder Research Center, Shahid Behshti University of Medical Sciences, Tehran, Iran,
Mohammad Rostami Nejad--- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran



Introduction: Diabetic retinopathy (DR) is a serious microvascular complication of diabetes which can cause vision loss or blindness ultimately. Non enzymatic glycation of proteins leads to advanced glycation end products (AGEs) in DR. Since laser therapy is a well-established method, in this study, protein-protein interaction (PPI) network is applied for protein targets in DR disease in rats treated by laser.

Methods: In this study, we focused on articles that investigated and compared the proteome profiles of DR rats with healthy control and also DR rats before and after laser therapy. The networks of related differentially expressed proteins were explored using Cytoscape version 3.3.0, the PPI analysis methods and ClueGO.

Results: Analysis of PPI network of 37 related proteins to DR rats including 108 nodes, introduced 10 hub-bottleneck proteins and 5 concerned biochemical pathways. On the other hand, PPI analysis of related proteins to DR rats before and after laser therapy corresponded to 33 proteins and 2 biological pathways.

Discussion: Centrality and cluster screening identified hub-bottelneck genes, including Aldoa, HSPD1, Pgam2, Mapk3, SLC2A4, Ctnnb1, Ywhab, HSPA8, GAPDH and Actb for DR rats versus healthy control and ENO1, Aldoa, GAPDH for DR samples after laser therapy.
Conclusion: Gene expression analysis of the DR samples treated via laser therapy provides a molecular evidence in support of the therapeutic effect of laser.


Diabetic retinopathy rat; Laser therapy; Protein-protein interaction network (PPI) analysis.

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Cade WT. Diabetes-related microvascular and macrovascular diseases in the physical therapy setting. Physical therapy. 2008;88(11):1322-35.

Grunwald JE, DuPont J, Riva CE. Retinal haemodynamics in patients with early diabetes mellitus. British journal of ophthalmology. 1996;80(4):327-31.

Zorena K, Raczyńska D, Raczyńska K. Immunological risk factors for the development and progression of diabetic retinopathy: INTECH Open Access Publisher; 2012.

Abu El-Asrar AM, Nawaz MI, Kangave D, Mairaj Siddiquei M, Geboes K. Angiogenic and vasculogenic factors in the vitreous from patients with proliferative diabetic retinopathy. Journal of Diabetes Research. 2013;2013.

Bierhaus A, Hofmann MA, Ziegler R, Nawroth PP. AGEs and their interaction with AGE-receptors in vascular disease and diabetes mellitus. I. The AGE concept. Cardiovascular research. 1998;37(3):586-600.

Goh S-Y, Cooper ME. The role of advanced glycation end products in progression and complications of diabetes. The Journal of Clinical Endocrinology & Metabolism. 2008;93(4):1143-52.

Zorena K, Raczyńska D, Raczyńska K. Biomarkers in diabetic retinopathy and the therapeutic implications. Mediators of inflammation. 2013;2013.


Abbaszadeh H-A, Peyvandi AA, Sadeghi Y, Safaei A, Zamanian-Azodi M, Khoramgah MS, et al. Er: YAG Laser and Cyclosporin A Effect on Cell Cycle Regulation of Human Gingival Fibroblast Cells. Journal of Lasers in Medical Sciences. 2017;8(3):143-9.

Ivanov AA, Khuri FR, Fu H. Targeting protein–protein interactions as an anticancer strategy. Trends in pharmacological sciences. 2013;34(7):393-400.

Ideker T, Sharan R. Protein networks in disease. Genome research. 2008;18(4):644-52.

Zamanian-Azodi M, Rezaei-Tavirani M, Nejadi N, Arefi Oskouie A, Zayeri F, Hamdieh M, et al. Serum Proteomic Profiling of Obsessive-Compulsive Disorder, Washing Subtype: A Preliminary Study. Basic and Clinical Neuroscience. 2017;8(4):307-16.

Zamanian–Azodi M, Rezaei-Tavirani M, Rahmati-Rad S, Tavirani MR. Ethanol and cancer induce similar changes on protein expression pattern of human fibroblast cell. Iranian journal of pharmaceutical research: IJPR. 2016;15(Suppl):175.

Goh K-I, Cusick ME, Valle D, Childs B, Vidal M, Barabasi A-L. The human disease network. Proceedings of the National Academy of Sciences. 2007;104(21):8685-90.

Yang X, Deignan JL, Qi H, Zhu J, Qian S, Zhong J, et al. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nature genetics. 2009;41(4):415-23.

Safari-Alighiarloo N, Taghizadeh M, Rezaei-Tavirani M, Goliaei B, Peyvandi AA. Protein-protein interaction networks (PPI) and complex diseases. Gastroenterology and Hepatology from bed to bench. 2014;7(1).

Safaei A, Tavirani MR, Oskouei AA, Azodi MZ, Mohebbi SR, Nikzamir AR. Protein-protein interaction network analysis of cirrhosis liver disease. Gastroenterology and Hepatology from bed to bench. 2016;9(2):114.

Zamanian-Azodi M, Rezaei-Tavirani M, Rahmati-Rad S, Hasanzadeh H, Tavirani MR, Seyyedi SS. Protein-Protein Interaction Network could reveal the relationship between the breast and colon cancer. Gastroenterology and Hepatology from bed to bench. 2015;8(3):215.

Rezaei-Tavirani M, Zamanian-Azodi M, Rajabi S, Masoudi-Nejad A, Rostami-Nejad M, Rahmatirad S. Protein Clustering and Interactome Analysis in Parkinson and Alzheimer's Diseases. Archives of Iranian Medicine (AIM). 2016;19(2).

Neubauer AS, Ulbig MW. Laser treatment in diabetic retinopathy. Ophthalmologica. 2007;221(2):95-102.

Kalantari S, Rutishauser D, Samavat S, Nafar M, Mahmudieh L, Rezaei-Tavirani M, et al. Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography. PloS one. 2013;8(12):e80830.

Zali H, Rezaei-Tavirani M, Kariminia A, Yousefi R, Shokrgozar MA. Evaluation of growth inhibitory and apoptosis inducing activity of human calprotectin on the human gastric cell line (AGS). Iranian Biomedical Journal. 2008;12(1):7-14.

TaviraniPhD MR. Meningioma protein-protein interaction network. Archives of Iranian medicine. 2014;17(4):262.

Marshall J. Thermal and mechanical mechanisms in laser damage to the retina. Investigative ophthalmology & visual science. 1970;9(2):97-115.

Quin GGJ, Len AC, Billson FA, Gillies MC. Proteome map of normal rat retina and comparison with the proteome of diabetic rat retina: new insight in the pathogenesis of diabetic retinopathy. Proteomics. 2007;7(15):2636-50.

Quin GJ, Lyons B, Len AC, Madigan MC, Gillies MC. Proteome changes induced by laser in diabetic retinopathy. Clinical & experimental ophthalmology. 2015;43(2):180-7.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13(11):2498-504.

Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol. 2007;3(4):e59.

Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091-3.

Liu H, Hu ZZ, Wu CH. DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics. 2005;6:201.

Rivera CG, Vakil R, Bader JS. NeMo: Network Module identification in Cytoscape. BMC Bioinformatics. 2010;18(11):1471-2105.

Khuri S, Wuchty S. Essentiality and centrality in protein interaction networks revisited. BMC bioinformatics. 2015;16(1):1.

Yao DC, Tolan DR, Murray MF, Harris DJ, Darras BT, Geva A, et al. Hemolytic anemia and severe rhabdomyolysis caused by compound heterozygous mutations of the gene for erythrocyte/muscle isozyme of aldolase, ALDOA (Arg303X/Cys338Tyr). Blood. 2004;103(6):2401-3.

Mamczur P, Gamian A, Kolodziej J, Dziegiel P, Rakus D. Nuclear localization of aldolase A correlates with cell proliferation. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research. 2013;1833(12):2812-22.

Ahn BY, Song ES, Cho YJ, Kwon OW, Kim JK, Lee NG. Identification of an anti‐aldolase autoantibody as a diagnostic marker for diabetic retinopathy by immunoproteomic analysis. Proteomics. 2006;6(4):1200-9.

Itoh H, Komatsuda A, Ohtani H, Wakui H, Imai H, Sawada Ki, et al. Mammalian HSP60 is quickly sorted into the mitochondria under conditions of dehydration. European Journal of Biochemistry. 2002;269(23):5931-8.

Karnati R, Laurie DE, Laurie GW. Lacritin and the tear proteome as natural replacement therapy for dry eye. Experimental eye research. 2013;117:39-52.

Ganguly A, Shields CL. Differential gene expression profile of retinoblastoma compared to normal retina. 2010.

Colotti C, Cavallini G, Vitale R, Donati A, Maltinti M, Del Ry S, et al. Effects of aging and anti-aging caloric restrictions on carbonyl and heat shock protein levels and expression. Biogerontology. 2005;6(6):397-406.

Tsujino S, Shanske S, Sakoda S, Fenichel G, DiMauro S. The molecular genetic basis of muscle phosphoglycerate mutase (PGAM) deficiency. American journal of human genetics. 1993;52(3):472.

Jiang X, Sun Q, Li H, Li K, Ren X. The role of phosphoglycerate mutase 1 in tumor aerobic glycolysis and its potential therapeutic implications. International journal of cancer. 2014;135(9):1991-6.

Santen RJ, Song RX, McPherson R, Kumar R, Adam L, Jeng M-H, et al. The role of mitogen-activated protein (MAP) kinase in breast cancer. The Journal of steroid biochemistry and molecular biology. 2002;80(2):239-56.

Kawashima I, Mitsumori T, Nozaki Y, Yamamoto T, Shobu-Sueki Y, Nakajima K, et al. Negative regulation of the LKB1/AMPK pathway by ERK in human acute myeloid leukemia cells. Experimental hematology. 2015;43(7):524-33. e1.

Iida M, Towatari M, Nakao A, Iida H, Kiyoi H, Nakano Y, et al. Lack of constitutive activation of MAP kinase pathway in human acute myeloid leukemia cells with N-Ras mutation. Leukemia. 1999;13:585-9.

Ye X, Xu G, Chang Q, Fan J, Sun Z, Qin Y, et al. ERK1/2 signaling pathways involved in VEGF release in diabetic rat retina. Investigative ophthalmology & visual science. 2010;51(10):5226-33.

Kraus C, Liehr T, Hülsken J, Behrens J, Birchmeier W, Grzeschik K-H, et al. Localization of the human β-catenin gene (CTNNB1) to 3p21: a region implicated in tumor development. Genomics. 1994;23(1):272-4.

MacDonald BT, Tamai K, He X. Wnt/β-catenin signaling: components, mechanisms, and diseases. Developmental cell. 2009;17(1):9-26.

Thakur R, Mishra DP. Pharmacological modulation of beta‐catenin and its applications in cancer therapy. Journal of cellular and molecular medicine. 2013;17(4):449-56.

García-Jiménez C, García-Martínez JM, Chocarro-Calvo A, De la Vieja A. A new link between diabetes and cancer: enhanced WNT/β-catenin signaling by high glucose. Journal of molecular endocrinology. 2014;52(1):R51-R66.

Chocarro-Calvo A, García-Martínez JM, Ardila-González S, De la Vieja A, García-Jiménez C. Glucose-induced β-catenin acetylation enhances Wnt signaling in cancer. Molecular cell. 2013;49(3):474-86.

Elghazi L, Gould AP, Weiss AJ, Barker DJ, Callaghan J, Opland D, et al. Importance of β-catenin in glucose and energy homeostasis. Scientific reports. 2012;2:693.

Zhang B, Zhou KK, Ma J-x. Inhibition of connective tissue growth factor overexpression in diabetic retinopathy by SERPINA3K via blocking the WNT/β-catenin pathway. Diabetes. 2010;59(7):1809-16.

Wilker E, Yaffe MB. 14-3-3 proteins—a focus on cancer and human disease. Journal of molecular and cellular cardiology. 2004;37(3):633-42.

Zhang Y, Li M, Wei L, Zhu L, Hu S, Wu S, et al. Differential protein expression in perfusates from metastasized rat livers. Proteome science. 2013;11(1):1.

Almeida MB, do Nascimento JLM, Herculano AM, Crespo-López ME. Molecular chaperones: toward new therapeutic tools. Biomedicine & Pharmacotherapy. 2011;65(4):239-43.

Sziksz E, Pap D, Veres G, Fekete A, Tulassay T, Vannay Á. Involvement of heat shock proteins in gluten-sensitive enteropathy. World Journal of Gastroenterology: WJG. 2014;20(21):6495.

Brehme M, Voisine C, Rolland T, Wachi S, Soper JH, Zhu Y, et al. A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease. Cell reports. 2014;9(3):1135-50.

Rocha-Martins M, Njaine B, Silveira MS. Avoiding pitfalls of internal controls: validation of reference genes for analysis by qRT-PCR and Western blot throughout rat retinal development. PloS one. 2012;7(8):e43028.

Saunders P, Chalecka‐Franaszek E, Chuang DM. Subcellular distribution of glyceraldehyde‐3‐phosphate dehydrogenase in cerebellar granule cells undergoing cytosine arabinoside‐induced apoptosis. Journal of neurochemistry. 1997;69(5):1820-8.

Kanwar M, Kowluru RA. Role of glyceraldehyde 3-phosphate dehydrogenase in the development and progression of diabetic retinopathy. Diabetes. 2009;58(1):227-34.

Chee CS, Chang KM, Loke MF, Loo VPA, Subrayan V. Association of potential salivary biomarkers with diabetic retinopathy and its severity in type-2 diabetes mellitus: a proteomic analysis by mass spectrometry. PeerJ. 2016;4:e2022.

Zhu X, Miao X, Wu Y, Li C, Guo Y, Liu Y, et al. ENO1 promotes tumor proliferation and cell adhesion mediated drug resistance (CAM-DR) in Non-Hodgkin's Lymphomas. Experimental cell research. 2015;335(2):216-23.

Song Y, Luo Q, Long H, Hu Z, Que T, Zhang Xa, et al. Alpha-enolase as a potential cancer prognostic marker promotes cell growth, migration, and invasion in glioma. Molecular cancer. 2014;13(1):1.

Hsiao K-C, Shih N-Y, Fang H-L, Huang T-S, Kuo C-C, Chu P-Y, et al. Surface α-enolase promotes extracellular matrix degradation and tumor metastasis and represents a new therapeutic target. PLoS One. 2013;8(7):e69354.

Li B, Sheng M, Xie L, Liu F, Yan G, Wang W, et al. Tear Proteomic Analysis of Patients With Type 2 Diabetes and Dry Eye Syndrome by Two-Dimensional Nano-Liquid Chromatography Coupled With Tandem Mass SpectrometryNano-Liquid Chromatography/Tandem Mass Spectrometry. Investigative ophthalmology & visual science. 2014;55(1):177-86.

Du S, Guan Z, Hao L, Song Y, Wang L, Gong L, et al. Fructose-bisphosphate aldolase a is a potential metastasis-associated marker of lung squamous cell carcinoma and promotes lung cell tumorigenesis and migration. PloS one. 2014;9(1):e85804.

Walther EU, Dichgans M, Maricich SM, Romito RR, Yang F, Dziennis S, et al. Genomic sequences of aldolase C (Zebrin II) direct lacZ expression exclusively in non-neuronal cells of transgenic mice. Proceedings of the National Academy of Sciences. 1998;95(5):2615-20.

Van den Enden MK, Nyengaard JR, Ostrow E, Burgan JH, Williamson JR. Elevated glucose levels increase retinal glycolysis and sorbitol pathway metabolism. Implications for diabetic retinopathy. Investigative ophthalmology & visual science. 1995;36(8):1675-85.

Krasnov GS, Dmitriev AA, Snezhkina AV, Kudryavtseva AV. Deregulation of glycolysis in cancer: glyceraldehyde-3-phosphate dehydrogenase as a therapeutic target. Expert opinion on therapeutic targets. 2013;17(6):681-93.

Nicholls C, Pinto AR, Li H, Li L, Wang L, Simpson R, et al. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) induces cancer cell senescence by interacting with telomerase RNA component. Proceedings of the National Academy of Sciences. 2012;109(33):13308-13.

Koya D, King GL. Protein kinase C activation and the development of diabetic complications. Diabetes. 1998;47(6):859-66.

Aiello LP, Bursell S-E, Clermont A, Duh E, Ishii H, Takagi C, et al. Vascular endothelial growth factor–induced retinal permeability is mediated by protein kinase C in vivo and suppressed by an orally effective β-isoform–selective inhibitor. Diabetes. 1997;46(9):1473-80.

Madsen-Bouterse S, Mohammad G, Kowluru RA. Glyceraldehyde-3-phosphate dehydrogenase in retinal microvasculature: implications for the development and progression of diabetic retinopathy. Investigative ophthalmology & visual science. 2010;51(3):1765-72.

Reddy VS, Raghu G, Reddy SS, Pasupulati AK, Suryanarayana P, Reddy GB. Response of Small Heat Shock Proteins in Diabetic Rat RetinaExpression of sHsps in Diabetic Retina. Investigative ophthalmology & visual science. 2013;54(12):7674-82.

Abcouwer SF. Angiogenic factors and cytokines in diabetic retinopathy. Journal of clinical & cellular immunology. 2013(11):1.

Semeraro F, Cancarini A, Rezzola S, Romano M, Costagliola C. Diabetic retinopathy: vascular and inflammatory disease. Journal of diabetes research. 2015;2015.

Song MK, Roufogalis BD, Huang TH. Modulation of diabetic retinopathy pathophysiology by natural medicines through PPAR‐γ‐related pharmacology. British journal of pharmacology. 2012;165(1):4-19.

Gray LR, Tompkins SC, Taylor EB. Regulation of pyruvate metabolism and human disease. Cellular and Molecular Life Sciences. 2014;71(14):2577-604.

Zhou Y, Ostenson C-G, Ling Z-C, Grill V. Deficiency of pyruvate dehydrogenase activity in pancreatic islets of diabetic GK rats. Endocrinology. 1995;136(8):3546-51.

Chambers KT, Leone TC, Sambandam N, Kovacs A, Wagg CS, Lopaschuk GD, et al. Chronic inhibition of pyruvate dehydrogenase in heart triggers an adaptive metabolic response. Journal of Biological Chemistry. 2011;286(13):11155-62.

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