Protein-protein interaction network analysis of major depression disorder via proteomic approach from cerebrospinal fluid sample

authors:

avatar Majid Rezaei Tavirani , avatar Reza Vafaei , avatar Vahid Mansouri , avatar Mona Zamanian Azodi ORCID , *

Koomesh: Vol.19, issue 3; 577-583
published online: September 02, 2017
article type: Research Article
received: July 01, 2016
accepted: January 02, 2017

how to cite: Rezaei Tavirani M, Vafaei R, Mansouri V, Zamanian Azodi M. Protein-protein interaction network analysis of major depression disorder via proteomic approach from cerebrospinal fluid sample. koomesh. 2017;19(3):e152903. 

Abstract

Introduction: As the major depression disorder (MDD) is one of the prevalent psychiatric conditions, molecular characteristic is important to gain a better understanding of its complex nature. In this study, the protein-protein interaction network analysis is carried out in order to have a better understanding the molecular mechanism of MDD. Materials and Methods: The MDD differentially expressed proteins of cerebral fluid were extracted from the literature. Cytoscape Software was used for the network construction of 39 retrieved proteins. In addition, Cytoscape plug-ins, MCODE and ClueGO+CluePedia identified the protein complexes and biological processes, respectively. Results: The MDD map centrality analysis identified 15 hub proteins. This network comprises of four protein complexes and seven significant biological processes. Conclusion: In this study, some of the central proteins, protein complexes, and biological processes related to MDD are introduced. The further investigations can help validating possible drug targets and diagnostic biomarkers

References

  • 1.

    Ghorbani R. Effects of cognitive therapy, drug therapy and combined therapy in improvement of major depression. Koomesh 2011; 13: 114-119.

  • 2.

    Bot M, Chan MK, Jansen R, Lamers F, Vogelzangs N, Steiner J, et al. Serum proteomic profiling of major depressive disorder. Transl Psychiatry 2015; 5: 1-9.

  • 3.

    Martins-de-Souza D, Guest P, Harris L, Vanattou-Saifoudine N, Webster M, Rahmoune H, Bahn S. Identification of proteomic signatures associated with depression and psychotic depression in post-mortem brains from major depression patients. Transl Psychiatry 2012; 2: 1-13.

  • 4.

    Hamet P, Tremblay J. Genetics and genomics of depression. Metabolism 2005; 54: 10-15.

  • 5.

    Mirmohammadkhani M. Vitamin D serum levels in nurses in Semnan educational hospitals and its association with depression. Koomesh 2016; 17: 313-322.

  • 6.

    Zamanian-Azodi M, Mortazavi-Tabatabaei SA, Mansouri V, Vafaee R. Metabolite-protein interaction (MPI) network analysis of obsessive-compulsive disorder (OCD) from reported metabolites. Arvand J Health Med Sci 2016; 2: 112-120.

  • 7.

    Rezaei-Tavirani M, Rahmati-Rad S, Rezaei-Tavirani M. Ethanol and cancer induce similar changes on protein expression pattern of human fibroblast cell. Iran J Pharmac Res 2016; 15: 175-184. (Persian).

  • 8.

    Zali H, Zamanian-Azodi M, Tavirani MR, Baghban AA-z. Protein drug targets of lavandula angustifolia on treatment of rat Alzheimer's disease. Iran J Pharmac Res 2015; 14: 291-302.

  • 9.

    Rezaie-Tavirani M, Fayazfar S, Heydari-Keshel S, Rezaee MB, Zamanian-Azodi M, Rezaei-Tavirani M, Khodarahmi R. Effect of essential oil of Rosa Damascena on human colon cancer cell line SW742. Gastroenterol Hepatol Bed Bench 2013; 6: 25-31.

  • 10.

    Tohyama M, Miyata S, Hattori T, Shimizu S, Matsuzaki S. Molecular basis of major psychiatric diseases such as schizophrenia and depression. Anat Sci Int 2015; 90: 137-143.

  • 11.

    Stelzhammer V, Haenisch F, Chan MK, Cooper JD, Steiner J, Steeb H, et al. Proteomic changes in serum of first onset, antidepressant drug-nave major depression patients. Int J Neuropsychopharmacol 2014; 17: 1599-1608.

  • 12.

    Ditzen C, Tang N, Jastorff AM, Teplytska L, Yassouridis A, Maccarrone G, et al. Cerebrospinal fluid biomarkers for major depression confirm relevance of associated pathophysiology. Neuropsychopharmacology 2012; 37: 1013-1025.

  • 13.

    Schutzer SE, Liu T, Natelson BH, Angel TE, Schepmoes AA, Purvine SO, et al. Establishing the proteome of normal human cerebrospinal fluid. PLoS One 2010; 5: e10980.

  • 14.

    Zamanian-Azodi M, Rezaei-Tavirani M, Rahmati-Rad S, Hasanzadeh H, Rezaei Tavirani M, Seyyedi SS. Protein-protein interaction network could reveal the relationship between the breast and colon cancer. Gastroenterol Hepatol Bed Bench 2015; 8: 215-224.

  • 15.

    Ranjbar MM, Ahmadi NA, Ghorban K, Ghalyanchi Langeroudi A, Dadmanesh M, Amini H-R, Sedighi Moghaddam B. Immnoinformatics: novel view in understanding of immune system function, databases and prediction of immunogenic epitopes. Koomesh 2015; 17: 18-26.

  • 16.

    Safaei A, Rezaei Tavirani M, Arefi Oskouei A, Zamanian Azodi M, Mohebbi SR, Nikzamir AR. Protein-protein interaction network analysis of cirrhosis liver disease. Gastroenterol Hepatol Bed Bench 2016; 9: 114-123.

  • 17.

    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 Res 2003; 13: 2498-2504.

  • 18.

    Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al. STRING v10: proteinprotein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015; 43: D447-452.

  • 19.

    Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003; 4: 1-27.

  • 20.

    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: 1091-1093.

  • 21.

    Bindea G, Galon J, Mlecnik B. Cluepedia cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics 2013; 29: 661-663.

  • 22.

    Sayehmiri K. Is there a relationship between metabolic syndrome and depression? A systematic review and meta-analysis. Koomesh 2015; 16: 488-494.

  • 23.

    Puchades M, Hansson SF, Nilsson CL, Andreasen N, Blennow K, Davidsson P. Proteomic studies of potential cerebrospinal fluid protein markers for Alzheimer's disease. Brain Res Mol Brain Res 2003; 118: 140-146.

  • 24.

    Lim J, Hao T, Shaw C, Patel AJ, Szab G, Rual JF, et al. A proteinprotein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 2006; 125: 801-814.

  • 25.

    Lage K, Karlberg EO, Strling ZM, Olason PI, Pedersen AG, Rigina O, et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nature Biotechnol 2007; 25: 309-316.

  • 26.

    Yang Y, Wan C, Li H, Zhu H, La Y, Xi Z, et al. Altered levels of acute phase proteins in the plasma of patients with schizophrenia. Anal Chem 2006; 78: 3571-3576.

  • 27.

    Small SA, Petsko GA. Retromer in Alzheimer disease, parkinson disease and other neurological disorders. Nat Rev Neurosci 2015; 16: 126-132.

  • 28.

    Harold D, Abraham R, Hollingworth P, Sims R, Gerrish A, Hamshere ML, et al. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nature Genet 2009; 41: 1088-1093.

  • 29.

    Zamanian-Azodi M, Rezaei-Tavirani M, Nejadi N, Arefi Oskouie A, Zayeri F, Hamdieh M, et al. Serum proteomic profiling of obsessive-compulsive disorder (OCD), washing subtype: a preliminary study. Basic Clin Neur J (Persian)##.