An In-Silico Study on the Most Effective Growth Factors in Retinal Regeneration Utilizing Tissue Engineering Concepts


Purpose: Considering the significance of retinal disorders and the growing need to employ tissue engineering in this field, in-silico studies can be used to establish a cost-effective method. This in-silico study was performed to find the most effective growth factors contributing to retinal tissue engineering.

Methods: In this study, a regeneration gene database was used. All 21 protein-coding genes participating in retinal regeneration were considered as a protein–protein interaction (PPI) network via the “STRING App” in “Cytoscape 3.7.2” software. The resultant graph possessed 21 nodes as well as 37 edges. Gene ontology (GO) analysis, as well as the centrality analysis, revealed the most effective proteins in retinal regeneration.

Results: According to the biological processes and the role of each protein in different pathways, selecting the correct one is possible through the information that the network provides. Eye development, detection of the visible light, visual perception, photoreceptor cell differentiation, camera-type eye development, eye morphogenesis, and angiogenesis are the major biological processes in retinal regeneration. Based on the GO analysis, SHH, STAT3, FGFR1, OPN4, ITGAV, RAX, and RPE65 are effective in retinal regeneration via the biological processes. In addition, based on the centrality analysis, four proteins have the greatest influence on retinal regeneration: SHH, IGF1, STAT3, and ASCL1.

Conclusion: With the intention of applying the most impressive growth factors in retinal engineering, it seems logical to pay attention to SHH, STAT3, and RPE65. Utilizing these proteins can lead to fabricate high efficiency engineered retina via all aforementioned biological processes.


Effective Growth Factors, In-silico Study, Regenerative Medicine, Retinal Tissue Engineering, Systems Biology

1. Mason C, Dunnill P. A brief definition of regenerative medicine. Regen Med 2008;3:1–5.

2. Abouna GM. Organ shortage crisis: problems and possible solutions. Transplant Proc 2008;40:34–38.

3. Mao AS, Mooney DJ. Regenerative medicine: current therapies and future directions. Proc Natl Acad Sci USA 2015;112:14452–14459.

4. Beheshtizadeh N, Lotfibakhshaiesh N, Pazhouhnia Z, Hoseinpour M, Nafari M. A review of 3D bio-printing for bone and skin tissue engineering: a commercial approach. J Mater Sci 2020;55:3729–3749.

5. Khan F, Tanaka M. Designing smart biomaterials for tissue engineering. Int J Mol Sci 2017;19:17.

6. Lee EJ, Kasper FK, Mikos AG. Biomaterials for tissue engineering. Ann Biomed Eng 2014;42:323–337.

7. Sudhakar CK, Upadhyay N, Verma A, Jain A, Narayana Charyulu R, Jain S. Nanomedicine and Tissue Engineering. In: Thomas S, Grohens Y, Ninan N, editors. Nanotechnology applications for tissue engineering. Oxford: William Andrew Publishing; 2015:1–19.

8. Vasita R, Katti DS. Growth factor-delivery systems for tissue engineering: a materials perspective. Expert Rev Med Devices 2006;3:29–47.

9. Cervelló I, Medrano JV, Simón C. Regenerative medicine and tissue engineering in reproductive medicine: future clinical applications in human infertility. In: Laurence J, editor. Translating regenerative medicine to the clinic. Boston: Academic Press; 2016:139–151.

10. Dzobo K, Thomford NE, Senthebane DA, Shipanga H, Rowe A, Dandara C, et al. Advances in regenerative medicine and tissue engineering: innovation and transformation of medicine. Stem Cells Int 2018;2018:24.

11. Schwartz SD, Pan CK, Klimanskaya I, Lanza R. Retinal Degeneration. In: Lanza R, Langer R, Vacanti J, editors. Principles of tissue engineering. 4th edition. Boston: Academic Press; 2014:1427–1440.

12. Abedin Zadeh M, Khoder M, Al-Kinani AA, Younes HM, Alany RG. Retinal cell regeneration using tissue engineered polymeric scaffolds. Drug Discov Today 2019;24:1669–1678.

13. Goldman D. Müller glial cell reprogramming and retina regeneration. Nat Rev Neurosci 2014;15:431–442.

14. Hamon A, Roger JE, Yang X-J, Perron M. Müller glial celldependent regeneration of the neural retina: an overview across vertebrate model systems. Dev Dyn 2016;245:727–738.

15. Kim HS, Kim D, Jeong YW, Choi MJ, Lee GW, Thangavelu M, et al. Engineering retinal pigment epithelial cells regeneration for transplantation in regenerative medicine using PEG/Gellan gum hydrogels. Int J Biol Macromol 2019;130:220–228.

16. Lenkowski JR, Raymond PA. Müller glia: stem cells for generation and regeneration of retinal neurons in teleost fish. Prog Retin Eye Res 2014;40:94–123.

17. Soleimannejad M, Ebrahimi-Barough S, Nadri S, Riazi- Esfahani M, Soleimani M, Tavangar SM, et al. Retina tissue engineering by conjunctiva mesenchymal stem cells encapsulated in fibrin gel: hypotheses on novel approach to retinal diseases treatment. Med Hypotheses 2017;101:75–77.

18. Tao SL, Klassen H. 12 – Biomaterials for retinal tissue engineering. In: Chirila TV, Harkin DG, editors. Biomaterials and regenerative medicine in ophthalmology. 2nd ed. Cambridge: Woodhead Publishing; 2016:291– 308.

19. Wang P, Li X, Zhu W, Zhong Z, Moran A, Wang W, et al. 3D bioprinting of hydrogels for retina cell culturing. Bioprinting 2018;12:e00029.

20. White DT, Sengupta S, Saxena MT, Xu Q, Hanes J, Ding D, et al. Immunomodulation-accelerated neuronal regeneration following selective rod photoreceptor cell ablation in the zebrafish retina. Proc Natl Acad Sci USA 2017;11:E3719–E3728.

21. Zhu J, Luz-Madrigal A, Haynes T, Zavada J, Burke AK, Del Rio-Tsonis K. β-Catenin inactivation is a pre-requisite for chick retina regeneration. PLOS ONE 2014;9:e101748– e101748.

22. Liu Y, Wang R, Zarembinski TI, Doty N, Jiang C, Regatieri C, et al. The application of hyaluronic acid hydrogels to retinal progenitor cell transplantation. Tissue Eng Part A 2013;19:135–142.

23. Fausett BV, Gumerson JD, Goldman D. The proneural basic helix-loop-helix gene ascl1a is required for retina regeneration. J Neurosci 2008;28:1109–1117.

24. Kador KE, Goldberg JL. Scaffolds and stem cells: delivery of cell transplants for retinal degenerations. Expert Rev Ophthalmol 2012;7:459–470.

25. Yao J, Tao SL, Young MJ. Synthetic polymer scaffolds for stem cell transplantation in retinal tissue engineering. Polymers 2011;3:899.

26. Bainbridge JW, Smith AJ, Barker SS, Robbie S, Henderson R, Balaggan K, et al. Effect of gene therapy on visual function in leber’s congenital amaurosis. N Engl J Med 2008;358:2231–2239.

27. Nelson CM, Gorsuch RA, Bailey TJ, Ackerman KM, Kassen SC, Hyde DR. Stat3 defines three populations of Muller glia and is required for initiating maximal muller glia proliferation in the regenerating zebrafish retina. J Comp Neurol 2012;520:4294–4311.

28. Spence JR, Aycinena JC, Del Rio-Tsonis K. Fibroblast growth factor-hedgehog interdependence during retina regeneration. Dev Dyn 2007;236:1161–1174.

29. Singh R, Cuzzani O, Binette F, Sternberg H, West MD, Nasonkin IO. Pluripotent stem cells for retinal tissue engineering: current status and future prospects. Stem Cell Rev 2018;14:463–483.

30. Zhao M, Rotgans B, Wang T, Cummins SF. REGene: an online gene resource for animal regeneration with literature evidence. Sci Rep 2016;6:23167.

31. Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. Cytoscape STRINGApp: network analysis and visualization of proteomics data. bioRxiv 2018:438192.

32. Consortium TGO. The Gene Ontology project in 2008. Nucleic Acids Res 2007;36:D440–D444.

33. The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res 2019;47:D330–D338.

34. Homma K, Koriyama Y, Mawatari K, Higuchi Y, Kosaka J, Kato S. Early downregulation of IGF-I decides the fate of rat retinal ganglion cells after optic nerve injury. Neurochem Int 2007;50:741–748.

35. Pola R, Ling LE, Silver M, Corbley MJ, Kearney M, Blake Pepinsky R, et al. The morphogen Sonic hedgehog is an indirect angiogenic agent upregulating two families of angiogenic growth factors. Nat Med 2001;7:706–711.

36. Rousseau B, Larrieu-Lahargue F, Bikfalvi A, Javerzat S. Involvement of fibroblast growth factors in choroidal angiogenesis and retinal vascularization. Exp Eye Res 2003;77:147–156.

37. Morandi EM, Verstappen R, Zwierzina ME, Geley S, Pierer G, Ploner C. ITGAV and ITGA5 diversely regulate proliferation and adipogenic differentiation of human adipose derived stem cells. Sci Rep 2016;6:28889.

38. Jauregui R, Park KS, Tsang SH. Two-year progression analysis of RPE65 autosomal dominant retinitis pigmentosa. Ophthalmic Genet 2018;39:544–549.

39. Nissila JS, Manttari SK, Sarkioja TT, Tuominen HJ, Takala TE, Kiviniemi VJ, et al. The distribution of melanopsin (OPN4) protein in the human brain. Chronobiol Int 2017;34:37–44.

40. Voronina VA, Kozhemyakina EA, O’Kernick CM, Kahn ND, Wenger SL, Linberg JV, et al. Mutations in the human RAX homeobox gene in a patient with anophthalmia and sclerocornea. Hum Mol Genet 2004;13:315–322.

41. Hicks D, Courtois Y. Fibroblast growth factor stimulates photoreceptor differentiation in vitro. J Neurosci 1992;12:2022–2033.

42. Osakada F, Ikeda H, Mandai M, Wataya T, Watanabe K, Yoshimura N, et al. Toward the generation of rod and cone photoreceptors from mouse, monkey and human embryonic stem cells. Nat Biotechnol 2008;26:215–224.

43. Osakada F, Ikeda H, Sasai Y, Takahashi M. Stepwise differentiation of pluripotent stem cells into retinal cells. Nat Protoc 2009;4:811–824.

44. Enzmann V, Yolcu E, Kaplan HJ, Ildstad ST. Stem cells as tools in regenerative therapy for retinal degeneration. Arch Ophthalmol 2009;127:563–571.

45. Akrami H, Soheili ZS, Sadeghizadeh M, Khalooghi K, Ahmadieh H, Kanavi MR, et al. Evaluation of RPE65, CRALBP, VEGF, CD68, and tyrosinase gene expression in human retinal pigment epithelial cells cultured on amniotic membrane. Biochem Genet 2011;49:313–322.

46. Regent F, Morizur L, Lesueur L, Habeler W, Plancheron A, Ben M’Barek K, et al. Automation of human pluripotent stem cell differentiation toward retinal pigment epithelial cells for large-scale productions. Sci Rep 2019;9:10646.

47. Patel AK, Syeda S, Hackam AS. Signal transducer and activator of transcription 3 (STAT3) signaling in retinal pigment epithelium cells. JAKSTAT 2013;2:e25434– e25434.