Insights into the suitability of utilizing brown rats (Rattus norvegicus) as a model for healing spinal cord injury with epidermal growth factor and fibroblast growth factor-II by predicting protein-protein interactions

The stimulation of the proliferation and differentiation of neural stem cells (NSCs) offers the possibility of a renewable source of replacement cells to treat numerous neurological diseases including spinal cord injury, traumatic brain injury and stroke. Epidermal growth factor (EGF) and fibroblast growth factor-2 (FGF-2) have been used to stimulate NSCs to renew, expand, and produce precursors for neural repair within an adult brown rat (Rattus norvegicus). To provide greater insight into the interspecies protein-protein interactions between human FGF-2 and EGF proteins and native R. norvegicus proteins, we have utilized the Massively Parallel Protein-Protein Interaction Prediction Engine (MP-PIPE) in an attempt to computationally shed light on the pathways potentially driving neurosphere proliferation. This study determined similar and differing protein interaction pathways between the two growth factors and the proteins in R. norvegicus compared with the proteins in H. sapiens. The protein-protein interactions predicted that EGF and FGF-2 may behave differently in rats than in humans. The identification and improved understanding of these differences may help to improve the clinical translation of NSC therapies from rats to humans.

[1]  M. Nugent,et al.  Fibroblast growth factor-2. , 2000, The international journal of biochemistry & cell biology.

[2]  B. Stokes,et al.  Cellular inflammatory response after spinal cord injury in sprague‐dawley and lewis rats , 1997, The Journal of comparative neurology.

[3]  Juwen Shen,et al.  Predicting protein–protein interactions based only on sequences information , 2007, Proceedings of the National Academy of Sciences.

[4]  Shao-Chun Wang,et al.  Epidermal Growth Factor Receptor Protects Proliferating Cell Nuclear Antigen from Cullin 4A Protein-mediated Proteolysis* , 2012, The Journal of Biological Chemistry.

[5]  Zihan Lou,et al.  A comparative study to evaluate the efficacy of EGF, FGF-2, and 0.3% (w/v) ofloxacin drops on eardrum regeneration , 2017, Medicine.

[6]  Ashkan Golshani,et al.  Uncharacterized ORF HUR1 influences the efficiency of non-homologous end-joining repair in Saccharomyces cerevisiae. , 2018, Gene.

[7]  August B. Smit,et al.  Neurotrophic Actions of a Novel Molluscan Epidermal Growth Factor , 2000, The Journal of Neuroscience.

[8]  J. R. Green,et al.  Global investigation of protein–protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences , 2008, Nucleic acids research.

[9]  Richard J Bodnar,et al.  Epidermal Growth Factor and Epidermal Growth Factor Receptor: The Yin and Yang in the Treatment of Cutaneous Wounds and Cancer. , 2013, Advances in wound care.

[10]  Jean-Loup Faulon,et al.  Predicting protein-protein interactions using signature products , 2005, Bioinform..

[11]  Albert Chan,et al.  PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs , 2006, BMC Bioinformatics.

[12]  Shaun K Olsen,et al.  Receptor Specificity of the Fibroblast Growth Factor Family , 2006, Journal of Biological Chemistry.

[13]  Peter Tontonoz,et al.  The E3 Ubiquitin Ligase IDOL Induces the Degradation of the Low Density Lipoprotein Receptor Family Members VLDLR and ApoER2* , 2010, The Journal of Biological Chemistry.

[14]  Antonio Ibarra,et al.  Lewis, Fischer 344, and Sprague-Dawley Rats Display Differences in Lipid Peroxidation, Motor Recovery, and Rubrospinal Tract Preservation after Spinal Cord Injury , 2015, Front. Neurol..

[15]  Bryan Kolb,et al.  Growth Factor-Stimulated Generation of New Cortical Tissue and Functional Recovery after Stroke Damage to the Motor Cortex of Rats , 2007, Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism.

[16]  Yanzhi Guo,et al.  Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences , 2008, Nucleic acids research.

[17]  Philip Stanier,et al.  FGF signalling and SUMO modification: new players in the aetiology of cleft lip and/or palate. , 2007, Trends in genetics : TIG.

[18]  Da-wei Zhang,et al.  Characterization of the role of EGF-A of low density lipoprotein receptor in PCSK9 binding , 2013, Journal of Lipid Research.

[19]  F. Deák,et al.  The matrilins: a novel family of oligomeric extracellular matrix proteins. , 1999, Matrix biology : journal of the International Society for Matrix Biology.

[20]  C. MacArthur,et al.  Receptor Specificity of the Fibroblast Growth Factor Family* , 1996, The Journal of Biological Chemistry.

[21]  A. Salgado,et al.  From basics to clinical: A comprehensive review on spinal cord injury , 2014, Progress in Neurobiology.

[22]  Eyal Oren,et al.  Global, regional, and national burden of neurological disorders, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016 , 2017, The Lancet. Neurology.

[23]  Pier Paolo Di Fiore,et al.  Human USP3 Is a Chromatin Modifier Required for S Phase Progression and Genome Stability , 2007, Current Biology.

[24]  S. Vandenberg,et al.  Epidermal growth factor differentially regulates low density lipoprotein receptor–related protein gene expression in neoplastic and fetal human astrocytes , 1999, Glia.

[25]  Ashkan Golshani,et al.  Designing Anti-Zika Virus Peptides Derived from Predicted Human-Zika Virus Protein-Protein Interactions , 2017, bioRxiv.

[26]  Mustafa B. A. Djamgoz,et al.  Regulation of voltage-gated sodium channel expression in cancer: hormones, growth factors and auto-regulation , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[27]  J. Chai,et al.  Crystal Structure of Human Epidermal Growth Factor and Its Dimerization* , 2001, The Journal of Biological Chemistry.

[28]  Ashkan Golshani,et al.  Positome: A method for improving protein-protein interaction quality and prediction accuracy , 2017, 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

[29]  Tzu-Chi Chen,et al.  Using an in situ proximity ligation assay to systematically profile endogenous protein-protein interactions in a pathway network. , 2014, Journal of proteome research.

[30]  Yungki Park,et al.  Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences , 2009, BMC Bioinformatics.

[31]  Ashkan Golshani,et al.  Phosphatase Complex Pph3/Psy2 Is Involved in Regulation of Efficient Non-Homologous End-Joining Pathway in the Yeast Saccharomyces cerevisiae , 2014, PloS one.

[32]  Hui Wang,et al.  Efficient prediction of human protein-protein interactions at a global scale , 2014, BMC Bioinformatics.

[33]  Ashkan Golshani,et al.  Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean , 2017, Theoretical and Applied Genetics.

[34]  Charlotte Wiberg,et al.  Matrilin-2 interacts with itself and with other extracellular matrix proteins. , 2002, The Biochemical journal.

[35]  Jaclyn R. Gareau,et al.  The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition , 2010, Nature Reviews Molecular Cell Biology.

[36]  Michiie Sakamoto,et al.  Characterization of High‐Molecular‐Mass Forms of Basic Fibroblast Growth Factor Produced by Hepatocellular Carcinoma Cells: Possible Involvement of Basic Fibroblast Growth Factor in Hepatocarcinogenesis , 1991, Japanese journal of cancer research : Gann.

[37]  Xiaokun Li,et al.  High-level expression and purification of human epidermal growth factor with SUMO fusion in Escherichia coli. , 2006, Protein and peptide letters.