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. 2016 Nov 5;11(1):148.
doi: 10.1186/s13023-016-0531-y.

Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation

Meena Kumari Kotni  1 , Mingzhu Zhao  2 , Dong-Qing Wei  1
Affiliations

Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation

Meena Kumari Kotni et al. Orphanet J Rare Dis. .

Abstract

Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that involves the death of neurons. ALS is associated with many gene mutations as previously studied. In order to explore the molecular mechanisms underlying ALS with C9orf72 mutation, gene expression profiles of ALS fibroblasts and control fibroblasts were subjected to bioinformatics analysis. Genes with critical functional roles can be detected by a measure of node centrality in biological networks. In gene co-expression networks, highly connected genes called as candidate hubs have been associated with key disease-related pathways. Herein, this method was applied to find the hub genes related to ALS disease.

Methods: Illumina HiSeq microarray gene expression dataset GSE51684 was retrieved from Gene Expression Omnibus (GEO) database which included four Sporadic ALS, twelve Familial ALS and eight control samples. Differentially Expressed Genes (DEGs) were identified using the Student's t test statistical method and gene co-expression networking. Gene ontology (GO) function and KEGG pathway enrichment analysis of DEGs were performed using the DAVID online tool. Protein-protein interaction (PPI) networks were constructed by mapping the DEGs onto protein-protein interaction data from publicly available databases to identify the pathways where DEGs are involved in. PPI interaction network was divided into subnetworks using MCODE algorithm and was analyzed using Cytoscape.

Results: The results revealed that the expression of DEGs was mainly involved in cell adhesion, cell-cell signaling, Extra cellular matrix region GO processes and focal adhesion, neuroactive ligand receptor interaction, Extracellular matrix receptor interaction. Tumor necrosis factor (TNF), Endothelin 1 (EDN1), Angiotensin (AGT) and many cell adhesion molecules (CAM) were detected as hub genes that can be targeted as novel therapeutic targets for ALS disease.

Conclusion: These analyses and findings enhance the understanding of ALS pathogenesis and provide references for ALS therapy.

Keywords: Amyotrophic lateral sclerosis; C9orf72 mutation; Hub genes; Protein-protein interaction network.

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Figures

Fig. 1
Fig. 1
PPI network constructed from DEGs on the basis of human interactome (Nodes with higher degree values (hubs) are depicted with large shape and red colour with continuous gradient mapping to green colour with lower degree value)
Fig. 2
Fig. 2
Subnetworks identified from PPI of DEGs. Nodes in violet color are upregulated genes, yellow nodes are downregulated genes and blue lines are interactions between nodes
See this image and copyright information in PMC

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References

    1. de Carvalho M. Tackling diagnostic delays in ALS. Lancet Neurol. 2015;14(5):457–458. doi: 10.1016/S1474-4422(15)00020-4. - DOI - PubMed
    1. Kiernan MC. ALS and neuromuscular disease: in search of the Holy Grail. Lancet Neurol. 2014;13(1):13–14. doi: 10.1016/S1474-4422(13)70226-6. - DOI - PubMed
    1. Ling SC, Polymenidou M, Cleveland DW. Converging Mechanisms in ALS and FTD: Disrupted RNA and Protein Homeostasis. Neuron. 2013;79(3):416–438. doi: 10.1016/j.neuron.2013.07.033. - DOI - PMC - PubMed
    1. Beleza-Meireles A, AL-Chalabi A. Genetic studies of Amyotrophic lateral sclerosis: controversies and perspectives. Amyotroph Lateral Scler. 2009;10(1):1–14. doi: 10.1080/17482960802585469. - DOI - PubMed
    1. Oh YK, Shin KS, Yuan J, Kang SJ. Superoxide dismutase 1 mutants related to amyotrophic lateral sclerosis induce endoplasmic stress in neuro2a cells. J Neurochem. 2008;104(4):993–1005. doi: 10.1111/j.1471-4159.2007.05053.x. - DOI - PubMed

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