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

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.

The aim of regenerative medicine as the primary process involved in cell growth and organ reconstruction is to return the main cell functions and recovery of the damaged tissue or organ via its replacing or regenerating.In fact, there are three solutions for patients having organ impairment based on the severity of the destruction: graft implantation, substitution, and restoration. Graft implantation has an extensive waiting list candidates all around the world; for example, the organ transplantation waiting list is updated every 15 min in the United States of America. The ultimate prospect of tissue engineering is creating and providing tissues that are preferably autologous in organ substitutions through cells and biomaterials utilization simultaneously.Besides, tissue engineering has been determined as an efficient method to assist in rescuing lives and improving the quality of life. Considering the major components for tissue engineering, that is, scaffolds, cells, and growth factors and a variety of their available options would highlight the fact that selecting the most appropriate ones to fabricate an engineered tissue demands an optimization system. In fact, a wide range of biomaterials can be used as scaffolds; polymers and hydrogels are the most commonly used materials in this field.[5–7] Selecting the appropriate material is in close relation with the destination tissue. Poly-lactide-co-glycolide (PLGA), poly-caprolactone (PCL), poly-glycerol sebacate (PGS), and polymethyl methacrylate (PMMA) are some of the high consumption polymers in retinal tissue engineering. In addition to scaffolds, growth factors play an essential role in tissue engineering.[8] Growth factors are generally the regulators of substances, namely proteins or hormones that can stimulate cell proliferation and differentiation. Growth factors play an important role in the healing and regeneration of the retina. Retinal disorders directly affect vision; therefore, retinal tissue engineering is fundamental.To understand the effective mechanisms in this process, it is better to compare growth factors’ interaction with each other and then select the most appropriate one. Looking at the literature, retinal regeneration and retinal tissue engineering have been studied by several researchers.Liu et alstudied the application of hyaluronic acid (HA) hydrogels in retinal progenitor cell transplantation. Their reason for selecting HA was its role as a feeder layer in stem cell cultures. In addition, the relative ease with which various parameters could be controlled (e.g., hydrogel architecture, mechanics, and degradation) was effective in choosing the HA hydrogel. They concluded that HA hydrogels, with their developmentally relevant composition and malleable physical properties, provide a unique microenvironment for self-renewal and differentiation of the retinal progenitor cells (RPCs) for retinal repair. Furthermore, Fausett et al showed that in the damaged zebrafish retina, the Muller glia re-enter the cell cycle, increase α1tubulin (α1T) promoter activity, and generate new neurons and glia for retinal repair. They suggested that the achaete-scute family bHLH transcription factor 1a (ASCL1a) is required to convert the quiescent Muller glia into the actively dividing retinal progenitors, and that ASCL1a is a key regulator in initiating the retinal regeneration. Kador and Goldberg studied the delivery of cell transplants for retinal degeneration. Focusing on the photoreceptor and progenitordirected approaches, the authors reviewed how advances in tissue engineering and cell scaffold design were enhancing cell therapies for retinal degeneration. Furthermore, Yao et alreviewed the current literature on synthetic polymer scaffolds used for stem cell transplantation, especially RPCs. The advantages and disadvantages of different polymer scaffolds, the role of different surface modifications on cell attachment and differentiation, and the controlled drug delivery were discussed in their paper. Tao and Klassen have also presented a wide range of practical biomaterials in retinal tissue engineering. They studied the role of stem cells in retinal repair, and then focused on the material side, followed by considering cells and materials in combination. They also examined the current status of retinal tissue engineering and looked ahead to the challenges that investigators are involved within this field. In addition, Bainbridge et al published their preliminary results of gene therapy for retinal degeneration. In their study, the patients were enrolled in trials of recombinant adeno-associated viral delivery of the retinoid isomerohydrolase , which was administered as a subretinal injection during vitrectomy. The preliminary results from their investigations suggested that the procedure was safe in the short term, and their data were suggestive of efficacy. Furthermore, Nelson et al found out that signal transducer and activator of transcription 3 (STAT3) expression was observed in all Muller glia, whereas ASCL1a expression was restricted to only the mitotic ones. They suggested that while ASCL1a and Lin-28 homolog A (LIN28a) are required for Muller glia proliferation, STAT3 is necessary for the maximal number of Muller glia to proliferate during regeneration of the damaged zebrafish retina. In another study, Spence et al[28] worked on the fibroblast growth factor (FGF)– hedgehog (SHH) interdependence during retinal regeneration. Their results support a model where the FGF and SHH pathways work together to stimulate retinal regeneration. Recently, Singh et al reviewed retinal tissue engineering from the pluripotent stem cells and summarized the progress in cell therapies of the retina, with a focus on the human pluripotent stem cell-derived retinal tissue, and critically evaluated the potential of retinal organoid approaches to solve a major unmet clinically needed retinal repair and vision restoration in conditions caused by retinal degeneration and traumatic ocular injuries. Based on the published works, it can be concluded that there is no comprehensive study on the retinal growth factors that can draw up the existing relation among them. In addition, to the best of our knowledge, there is no insilico study of retinal tissue engineering. In fact, in retinal regeneration, several proteins are used therapeutically. If the interaction between them would be clear, and the biological function of each one is determined, they can be used as growth factors in retinal tissue engineering. In order to get the best results from the in-vitro and in-vivo tests, it is needed to select the best growth factors based on previous experiments and existing data. However, there are many reports about the effects of using each growth factor without any coherence and correlation among them. It seems that describing the interactions among growth factors is a critical fact that would lighten up the retinal tissue engineering path, that is, possible effects of increasing the amount of a growth factor on other growth factors’ functions. One of the least expensive methods for detecting this kind of facts is evaluating them with an in-silico study. In this work, retinal growth factors interactions have been studied via creating their interaction network. By creating this network, the influence of each growth factor on the biological processes can be determined. The higher degree in this network leads to higher interactions among them and causes much more effect. The main goal of this study is to find out which kind of retinal growth factor should be used to have the highest effect on the desired biological process.1


. Hierarchical layout of the PPI network performed by STRING App in Cytoscape 3.7.2. This network presents GO analysis of retina regeneration effective growth. Each circle provides a schematic drawing of protein structure. The colors are set randomly, and the connection line’s thickness illustrates the relation of power. Also, a thicker line presents much more evidence and documents to approve the connectivity.
. Hierarchical layout of the PPI network performed by STRING App in Cytoscape 3.7.2. This network presents GO analysis of retina regeneration effective growth. Each circle provides a schematic drawing of protein structure. The colors are set randomly, and the connection line’s thickness illustrates the relation of power. Also, a thicker line presents much more evidence and documents to approve the connectivity.

1.Beheshtizadeh N, Baradaran-Rafii A, Sistani MS, Azami M. An In-Silico Study on the Most Effective Growth Factors in Retinal Regeneration Utilizing Tissue Engineering Concepts. J Ophthalmic Vis Res 2021;16:56–67.