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Systematic Analysis of Protein Interaction Network Associated with Azoospermia

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Systematic Analysis of Protein Interaction Network Associated with Azoospermia International Journal of Molecular Sciences Article Systematic Analysis of Protein Interaction Network Associated with Azoospermia Soudabeh Sabetian * and Mohd Shahir Shamsir Department of Biological and Health Sciences, Faculty of Bioscience & Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor, Malaysia; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +60-7555-7526; Fax: +60-7553-1279 Academic Editors: Tatyana Karabencheva-Christova and Christo Z. Christov Received: 27 July 2016; Accepted: 1 November 2016; Published: 10 November 2016 Abstract: Non-obstructive azoospermia is a severe infertility factor. Currently, the etiology of this condition remains elusive with several possible molecular pathway disruptions identified in the post-meiotic spermatozoa. In the presented study, in order to identify all possible candidate genes associated with azoospermia and to map their relationship, we present the first protein-protein interaction network related to azoospermia and analyze the complex effects of the related genes systematically. Using Online Mendelian Inheritance in Man, the Human Protein Reference Database and Cytoscape, we created a novel network consisting of 209 protein nodes and 737 interactions. Mathematical analysis identified three proteins, ar, dazap2, and esr1, as hub nodes and a bottleneck protein within the network. We also identified new candidate genes, CREBBP and BCAR1, which may play a role in azoospermia. The gene ontology analysis suggests a genetic link between azoospermia and liver disease. The KEGG analysis also showed 45 statistically important pathways with 31 proteins associated with colorectal, pancreatic, chronic myeloid leukemia and prostate cancer. Two new genes and associated diseases are promising for further experimental validation. Keywords: azoospermia; gene ontology; infertility; protein interaction network 1. Introduction Male factor infertility is involved in over 50% of couples trying to conceive [1]. The increasing role of the male factor in cases of couples’ infertility has been identified due to the increased evaluation of male reproductive function and the development of new diagnostic tools [2,3]. Despite this, azoospermia is always taken as a matter of serious interest while treating the issues related to infertility [4]. Non-obstructive azoospermia (NOA) is considered to be a severe male infertility factor due to the impaired spermatogenesis with the consequent absence of spermatozoa in the ejaculate [5]. Although intracytoplasmic sperm injection (ICSI) as an assisted reproductive technology is an efficient therapy for severe male infertility, the success rate for NOA cases following ICSI therapy is around 36% [6]. Previous research has studied the medical treatment to improve the sperm quality of the patients before carrying out ICSI cycles [7]. Therefore, while understanding the overall mechanism of azoospermia is very important to improve the medical therapy, the underlying etiology and mechanism(s) remain elusive [4,7]. The presence of androgens is necessary for the production of normal sperm. It has been found that defective spermatogenesis is caused by lowering the levels of intratesticular androgens [8]. Recent research has established a new relationship of the androgen receptor gene with azoospermia [9] where most patients suffering from idiopathic azoospermia have normal levels of serum androgen, which indicates that the etiology of this condition might be due to the faults in the androgen response pathway [8]. Chromosome disorders are considered as the most common genetic defect in NOA [10]. Int. J. Mol. Sci. 2016, 17, 1857; doi:10.3390/ijms17111857 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2016, 17, 1857 2 of 10 androgen response pathway [8]. Chromosome disorders are considered as the most common genetic defect in NOA [10]. In order to identify the candidate genes which are associated with NOA, several techniques have been adopted. It has been determined if the men suffering from azoospermia have an increased risk of cancer; however, most of the conducted research has not extensively taken the molecular biological pathways or the systematic interactions between the components into consideration [11– 13]. InInt. this J. Mol. study, Sci. 2016 construction, 17, 1857 and analysis of a protein-protein interaction network were2 of 10 applied in order to extensively consider all the cell functions of the proteins associated with the azoospermia and the molecular biological pathways of the genetic links between azoospermia and other diseases. In order to identify the candidate genes which are associated with NOA, several techniques have been adopted. It has been determined if the men suffering from azoospermia have an increased risk of 2. Resultscancer; and however, Discussion most of the conducted research has not extensively taken the molecular biological pathways or the systematic interactions between the components into consideration [11–13]. In this 2.1. Constructionstudy, construction and Parameters and analysis of Protein-Protein of a protein-protein Interaction interaction Protein-Protein network were appliedInteraction in order (PPI to Network) extensively consider all the cell functions of the proteins associated with the azoospermia and the Themolecular initial biological selection pathways of proteins of the genetic from links the between Online azoospermia Mendelian and Inheritance other diseases. in Man (OMIM) database produced 86 proteins associated with azoospermia (refer to supplementary file). Examination2. Results of andthe Discussion identified proteins in Protein-Protein Interaction (PPI) data from the Human Protein2.1. Reference Construction Database and Parameters (HPRD of Protein-Protein database) Interactionshowed Protein-Proteinthat there are Interaction 209 related (PPI Network) proteins with 737 links (referThe to initial the selectionsupplementary of proteins fromfile). the The Online retr Mendelianieved data Inheritance were inentered Man (OMIM) into databaseCytoscape 2.8 to constructproduced the PPI 86 proteinsnetwork. associated The R withpackage azoospermia was used (refer to to calculate supplementary the topological file). Examination parameters. of The mean thedegree identified value proteins of the in protein Protein-Protein nodes Interactionis 7.05. Th (PPI)e shortest data from path the analysis Human Protein of the Reference network showed that anyDatabase two randomly (HPRD database) selected showed nodes that on there the are network 209 related were proteins connected with 737 via links 2.85 (refer links. to the The degree exponentsupplementary value is lower file). The than retrieved 3 [14], data which were entered is similar into Cytoscape to the other 2.8 to constructnetworks the following PPI network. a scale-free The R package was used to calculate the topological parameters. The mean degree value of the protein distributionnodes is and 7.05. similar The shortest to values path analysis of other of the human network protein showed networks that any two [15]. randomly A histogram selected nodes is used to plot the distributionon the network of the were shortest connected paths via 2.85 (Figure links. The 1A). degree exponent value is lower than 3 [14], which is similar to the other networks following a scale-free distribution and similar to values of other human 2.2. Theprotein Key Nodes networks of the [15 ].PPI A histogram Network is used to plot the distribution of the shortest paths (Figure1A). In2.2. a scale-free The Key Nodes distribution, of the PPI Network the presence of a small number of highly connected nodes known as hubs is moreIn a scale-freeimportant distribution, than lesser the presenceconnected of a smallnodes, number which of highlyis one connected of the important nodes known features of networksas hubs [14,16]. is more The important hub nodes than lesserplay connectedan important nodes, role which in isthe one survival of the important of cells featuresbecause of if the hub nodes networksare attacked [14,16 ].in The a network, hub nodes the play network an important can role be inbroken the survival into ofpieces cells because [17]. The if the nodes hub nodes that possess a degreeare or attacked a Betweenness in a network, Centrality the network can(BC) be brokenvalue intolarger pieces than [17]. Thethe nodesmean that were possess selected a degree (Table 1). or a Betweenness Centrality (BC) value larger than the mean were selected (Table1). Twenty-two of Twenty-twothe nodes of inthe the nodes network in are the proteins network that are have protei been associatedns that have with been azoospermia. associated with azoospermia. A Figure 1. Cont. Int. J. Mol. Sci. 2016, 17, 1857 3 of 10 Int. J. Mol. Sci. 2016, 17, 1857 3 of 10 B FigureFigure 1.1.( A(A)) Histogram Histogram showing showing distribution distribution of theof the shortest shortest path. path. Two Two randomly randomly selected selected nodes nodes were connectedwere connected via 2.85 via links; 2.85 (links;B) The (B small) The (simplified)small (simplified) network network of the Protein-Proteinof the Protein-Protein Interactions Interactions (PPIs) of(PPIs) azoospermia. of azoospermia. The identified The identifi importanted important nodes nodes and theirand their interconnected interconnected nodes nodes were were extracted extracted to constructto construct a new a new small small PPI PPI network. network. This This new new network network consists consists of of 46 46 nodes nodes and and
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