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Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches

  • Authors:
    • Guiming Wang
    • Dong Kuai
    • Yudong Yang
    • Gaochao Yang
    • Zhigang Wei
    • Wenbo Zhao
  • View Affiliations / Copyright

    Affiliations: Department of Surgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China, Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
    Copyright: © Wang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 2039-2048
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    Published online on: March 1, 2017
       https://doi.org/10.3892/mmr.2017.6273
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Abstract

The present study aimed to investigate potential gene markers for predicting the formation of carotid atheroma plaques using high‑throughput bioinformatics methods. The GSE43292 gene expression profile was downloaded from the Gene Expression Omnibus database. Following data processing, differentially expressed genes (DEGs) were screened using a paired t‑test in the Linear Models for Microarray Data package with the criteria of a false discovery rate of P<0.05 and |log2 fold‑change| ≥0.58, followed by functional enrichment, protein‑protein interaction (PPI) network construction, key node and module analysis, and prediction of transcription factors (TFs) targeting genes in the significant modules. The results revealed that the gene expression profiles from 32 paired samples of carotid atheroma plaque tissue and macroscopically intact tissue were obtained, based on which 886 DEGs, including 513 upregulated genes and 373 downregulated genes, were identified. The upregulated and downregulated gene sets were enriched in 24 and 13 pathways, respectively. The PPI network constructed with these DEGs comprised 35 key nodes with degrees ≥20, among which spleen tyrosine kinase (SYK), LYN and phosphatidylinositol‑4,5‑bisphosphate 3‑kinase catalytic subunit γ (PIK3CG) were the three highest. A significant module was mined in the PPI network, which consisted of 29 DEGs targeted by 11 TFs. The DEGs between the carotid atheroma plaque and macroscopically intact tissue samples may be involved in carotid atherogenesis. Key nodes in the PPI network constructed from these DEGs and the genes involved in the significant module, including SYK, LYN and PIK3CG, are promising for the prediction of carotid plaque formation.
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1 

Fatahzadeh M and Glick M: Stroke: Epidemiology, classification, risk factors, complications, diagnosis, prevention and medical and dental management. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 102:180–191. 2006. View Article : Google Scholar : PubMed/NCBI

2 

Friedlander AH and Baker JD: Panoramic radiography: An aid in detecting patients at risk of cerebrovascular accident. J Am Dent Assoc. 125:1598–1603. 1994. View Article : Google Scholar : PubMed/NCBI

3 

Foulkes MA, Wolf PA, Price TR, Mohr JP and Hier DB: The Stroke data bank: Design, methods, and baseline characteristics. Stroke. 19:547–554. 1988. View Article : Google Scholar : PubMed/NCBI

4 

Beckstrom BW, Horsley SH, Scheetz JP, Khan Z, Silveira AM, Clark SJ, Greenwell H and Farman AG: Correlation between carotid area calcifications and periodontitis: A retrospective study of digital panoramic radiographic findings in pretreatment cancer patients. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 103:359–366. 2007. View Article : Google Scholar : PubMed/NCBI

5 

Kappelle LJ: Symptomatic carotid artery stenosis. J Neurol. 249:254–259. 2002. View Article : Google Scholar : PubMed/NCBI

6 

Ayari H and Bricca G: Identification of two genes potentially associated in iron-heme homeostasis in human carotid plaque using microarray analysis. J Biosci. 38:311–315. 2013. View Article : Google Scholar : PubMed/NCBI

7 

Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al: NCBI GEO: Archive for functional genomics data sets-update. Nucleic Acids Res. 41(Database issue): D991–D995. 2013. View Article : Google Scholar : PubMed/NCBI

8 

Stary HC, Chandler AB, Dinsmore RE, Fuster V, Glagov S, Insull W Jr, Rosenfeld ME, Schwartz CJ, Wagner WD and Wissler RW: A definition of advanced types of atherosclerotic lesions and a histological classification of atherosclerosis. A report from the committee on vascular lesions of the council on arteriosclerosis, American heart association. Arterioscler Thromb Vasc Biol. 15:1512–1531. 1995. View Article : Google Scholar : PubMed/NCBI

9 

Carvalho BS and Irizarry RA: A framework for oligonucleotide microarray preprocessing. Bioinformatics. 26:2363–2367. 2010. View Article : Google Scholar : PubMed/NCBI

10 

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W and Smyth GK: limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43:e472015. View Article : Google Scholar : PubMed/NCBI

11 

Benjamini Y, Drai D, Elmer G, Kafkafi N and Golani I: Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 125:279–284. 2001. View Article : Google Scholar : PubMed/NCBI

12 

Diboun I, Wernisch L, Orengo CA and Koltzenburg M: Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics. 7:2522006. View Article : Google Scholar : PubMed/NCBI

13 

Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC and Lempicki RA: The DAVID gene functional classification tool: A novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8:R1832007. View Article : Google Scholar : PubMed/NCBI

14 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI

15 

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T and Yamanishi Y: KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36(Database issue): D480–D484. 2008.PubMed/NCBI

16 

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, et al: STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43(Database issue): D447–D452. 2015. View Article : Google Scholar : PubMed/NCBI

17 

Smoot ME, Ono K, Ruscheinski J, Wang PL and Ideker T: Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics. 27:431–432. 2011. View Article : Google Scholar : PubMed/NCBI

18 

Janky R, Verfaillie A, Imrichová H, Van De Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Sanchez M Naval, Potier D, et al: iRegulon: From a gene list to a gene regulatory network using large motif and track collections. PLoS Comput Biol. 10:e10037312014. View Article : Google Scholar : PubMed/NCBI

19 

Koton S, Schneider AL, Rosamond WD, Shahar E, Sang Y, Gottesman RF and Coresh J: Stroke incidence and mortality trends in US communities, 1987 to 2011. JAMA. 312:259–268. 2014. View Article : Google Scholar : PubMed/NCBI

20 

Wakhloo AK, Lieber BB, Seong J, Sadasivan C, Gounis MJ, Miskolczi L and Sandhu JS: Hemodynamics of carotid artery atherosclerotic occlusive disease. J Vasc Interv Radiol. 15:S111–S121. 2004. View Article : Google Scholar : PubMed/NCBI

21 

Attila M, Jürgen R and Tybulewicz VL: The SYK tyrosine kinase: A crucial player in diverse biological functions. Nat Rev Immunol. 10:387–402. 2010. View Article : Google Scholar : PubMed/NCBI

22 

Mallat Z, Hugel B, Ohan J, Lesèche G, Freyssinet JM and Tedgui A: Shed membrane microparticles with procoagulant potential in human atherosclerotic plaques: A role for apoptosis in plaque thrombogenicity. Circulation. 99:348–353. 1999. View Article : Google Scholar : PubMed/NCBI

23 

Ait-Oufella H, Pouresmail V, Simon T, Blanc-Brude O, Kinugawa K, Merval R, Offenstadt G, Lesèche G, Cohen PL, Tedgui A and Mallat Z: Defective mer receptor tyrosine kinase signaling in bone marrow cells promotes apoptotic cell accumulation and accelerates atherosclerosis. Arterioscler Thromb Vasc Biol. 28:1429–1431. 2008. View Article : Google Scholar : PubMed/NCBI

24 

Choi SH, Yin H, Ravandi A, Armando A, Dumlao D, Kim J, Almazan F, Taylor AM, McNamara CA, Tsimikas S, et al: Polyoxygenated cholesterol ester hydroperoxide activates TLR4 and SYK dependent signaling in macrophages. PLoS One. 8:e831452013. View Article : Google Scholar : PubMed/NCBI

25 

Hilgendorf I, Eisele S, Remer I, Schmitz J, Zeschky K, Colberg C, Stachon P, Wolf D, Willecke F, Buchner M, et al: The oral spleen tyrosine kinase inhibitor fostamatinib attenuates inflammation and atherogenesis in low-density lipoprotein receptor-deficient mice. Arterioscler Thromb Vasc Biol. 31:1991–1999. 2011. View Article : Google Scholar : PubMed/NCBI

26 

Saito YD, Jensen AR, Salgia R and Posadas EM: Fyn: A novel molecular target in cancer. Cancer. 116:1629–1637. 2010. View Article : Google Scholar : PubMed/NCBI

27 

Toubiana J, Rossi A-L, Belaidouni N, Grimaldi D, Pene F, Chafey P, Comba B, Camoin L, Bismuth G, et al: Src-family-tyrosine kinase Lyn is critical for TLR2-mediated NF-κB activation through the PI 3-kinase signaling pathway. Innate immunity. 21:685–697. 2015. View Article : Google Scholar : PubMed/NCBI

28 

Horiuchi M: Anti-inflammatory effect of nifedipine and vasculoprotection. Drugs. 66:28–30. 2006. View Article : Google Scholar : PubMed/NCBI

29 

Sawczuk M, Maciejewska-Karłowska A, Skotarczak B and Pawlik A: Association between single nucleotide polymorphism rs342286 near the PIK3CG gene and acute coronary syndromes. Pol Arch Med Wewn. 124:210–212. 2014.PubMed/NCBI

30 

Wain LV, Verwoert GC, O'Reilly PF, Shi G, Johnson T, Johnson AD, Bochud M, Rice KM, Henneman P, Smith AV, et al: Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure. Nat Genet. 43:1005–1011. 2011. View Article : Google Scholar : PubMed/NCBI

31 

Bis JC, Kavousi M, Franceschini N, Isaacs A, Abecasis GR, Schminke U, Post WS, Smith AV, Cupples LA, Markus HS, et al: Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque. Nat Genet. 43:940–947. 2011. View Article : Google Scholar : PubMed/NCBI

32 

Adams JN, Raffield LM, Freedman BI, Langefeld CD, Ng MC, Carr JJ, Cox AJ and Bowden DW: Analysis of common and coding variants with cardiovascular disease in the diabetes heart study. Cardiovasc Diabetol. 13:772014. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Wang G, Kuai D, Yang Y, Yang G, Wei Z and Zhao W: Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches. Mol Med Rep 15: 2039-2048, 2017.
APA
Wang, G., Kuai, D., Yang, Y., Yang, G., Wei, Z., & Zhao, W. (2017). Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches. Molecular Medicine Reports, 15, 2039-2048. https://doi.org/10.3892/mmr.2017.6273
MLA
Wang, G., Kuai, D., Yang, Y., Yang, G., Wei, Z., Zhao, W."Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches". Molecular Medicine Reports 15.4 (2017): 2039-2048.
Chicago
Wang, G., Kuai, D., Yang, Y., Yang, G., Wei, Z., Zhao, W."Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches". Molecular Medicine Reports 15, no. 4 (2017): 2039-2048. https://doi.org/10.3892/mmr.2017.6273
Copy and paste a formatted citation
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Spandidos Publications style
Wang G, Kuai D, Yang Y, Yang G, Wei Z and Zhao W: Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches. Mol Med Rep 15: 2039-2048, 2017.
APA
Wang, G., Kuai, D., Yang, Y., Yang, G., Wei, Z., & Zhao, W. (2017). Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches. Molecular Medicine Reports, 15, 2039-2048. https://doi.org/10.3892/mmr.2017.6273
MLA
Wang, G., Kuai, D., Yang, Y., Yang, G., Wei, Z., Zhao, W."Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches". Molecular Medicine Reports 15.4 (2017): 2039-2048.
Chicago
Wang, G., Kuai, D., Yang, Y., Yang, G., Wei, Z., Zhao, W."Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches". Molecular Medicine Reports 15, no. 4 (2017): 2039-2048. https://doi.org/10.3892/mmr.2017.6273
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