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Article Open Access

Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network

  • Authors:
    • Chi Zhang
    • Yan Wang
    • Chun-Lei Zhang
    • Hua-Rong Wu
  • View Affiliations / Copyright

    Affiliations: Department of Orthopaedics, The First Rehabilitation Hospital of Shanghai, Shanghai 200090, P.R. China, Medical Laboratory Diagnosis Center, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China, Department of Clinical Laboratory, The People's Hospital of Gaotang, Gaotang, Shandong 252800, P.R. China, Department of Spinal Bone, General Hospital of Xingtai Coal Mineral Company, Jizhong Energy Resource, Xingtai, Hebei 054000, P.R. China
    Copyright: © Zhang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 3155-3161
    |
    Published online on: February 26, 2019
       https://doi.org/10.3892/etm.2019.7310
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Abstract

Risk metabolites of postmenopausal osteoporosis (PO) were explored to offer a theoretical basis for future therapy. The data E-GEOD-7429 were downloaded from ArrayExpress database. In total 20 samples deprived from postmenopausal women having low or high bone mineral density (BMD) were covered in this expression profile. After screening of diffe- rentially expressed genes (DEGs), gene-gene network was constructed taking the intersection between the DEGs and genes in the seed protein-protein interaction network. Then, the other five networks were established, including metabolite, phenotype, gene-metabolite, phenotype-gene, and phenotype-metabolite networks. Next, these 6 networks were integrated into one weighted multi-omics network to further identify the candidate metabolites using random walk with restart based on the PO-related seed genes, seed metabolites and phenotype. Using the score among nodes of the weighted composite network, the top 50 metabolites, and the top 100 co-expressed genes interacting with the top 50 metabolites were detected. A set of 601 DEGs between low BMD and high BMD samples were selected. Significantly, the top 5 metabolites were respectively glucosylgalactosyl hydroxylysine, all-trans-5,6-epoxyretinoic acid, tretinoin, colecalciferol, and rocaltrol. Moreover, 3 metabolites (estraderm, triphosadenine, and tretinoin) had a degree >50 in the co-expression network. Tretinoin was the member of the top 5 metabolites, and estraderm was a metabolite with the seventh interaction score. A series of metabolites, tretinoin and estraderm might be closely associa- ted with the onset and progression of PO.
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1 

Marcus R: Post-menopausal osteoporosis. Best Pract Res Clin Obstet Gynaecol. 16:309–327. 2002. View Article : Google Scholar : PubMed/NCBI

2 

Seibel MJ, Dunstan CR, Zhou H, Allan CM and Handelsman DJ: Sex steroids, not FSH, influence bone mass. Cell. 127(1079): author reply. 1080–1081. 2006.

3 

Kiel DP, Demissie S, Dupuis J, Lunetta KL, Murabito JM and Karasik D: Genome-wide association with bone mass and geometry in the Framingham Heart Study. BMC Med Genet. 8 (Suppl 1):S142007. View Article : Google Scholar : PubMed/NCBI

4 

Xiao SM, Gao Y, Cheung CL, Bow CH, Lau KS, Sham PC, Tan KCB and Kung AWC: Association of CDX1 binding site of periostin gene with bone mineral density and vertebral fracture risk. Osteoporos Int. 23:1877–1887. 2012. View Article : Google Scholar : PubMed/NCBI

5 

Chen Y and Xia RG: Screening and functional microarray analysis of differentially expressed genes related to osteoporosis. Genet Mol Res. 13:3228–3236. 2014. View Article : Google Scholar : PubMed/NCBI

6 

Jemtland R, Holden M, Reppe S, Olstad OK, Reinholt FP, Gautvik VT, Refvem H, Frigessi A, Houston B and Gautvik KM: Molecular disease map of bone characterizing the postmenopausal osteoporosis phenotype. J Bone Miner Res. 26:1793–1801. 2011. View Article : Google Scholar : PubMed/NCBI

7 

Xiao P, Chen Y, Jiang H, Liu YZ, Pan F, Yang TL, Tang ZH, Larsen JA, Lappe JM, Recker RR, et al: In vivo genome-wide expression study on human circulating B cells suggests a novel ESR1 and MAPK3 network for postmenopausal osteoporosis. J Bone Miner Res. 23:644–654. 2008. View Article : Google Scholar : PubMed/NCBI

8 

Ma M, Chen X, Lu L, Yuan F, Zeng W, Luo S, Yin F and Cai J: Identification of crucial genes related to postmenopausal osteoporosis using gene expression profiling. Aging Clin Exp Res. 28:1067–1074. 2016. View Article : Google Scholar : PubMed/NCBI

9 

Fiehn O: Metabolomics - the link between genotypes and phenotypes. Plant Mol Biol. 48:155–171. 2002. View Article : Google Scholar : PubMed/NCBI

10 

Nicholson JK and Lindon JC: Systems biology: Metabonomics. Nature. 455:1054–1056. 2008. View Article : Google Scholar : PubMed/NCBI

11 

Nicholson JK and Wilson ID: Opinion: understanding ‘global’ systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov. 2:668–676. 2003. View Article : Google Scholar : PubMed/NCBI

12 

Yao Q, Xu Y, Yang H, Shang D, Zhang C, Zhang Y, Sun Z, Shi X, Feng L, Han J, et al: Global prioritization of disease candidate metabolites based on a multi-omics composite network. Sci Rep. 5:172012015. View Article : Google Scholar : PubMed/NCBI

13 

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

14 

Xia J and Wishart DS: MSEA: A web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res 38 (Web Server). W71–7. 2010. View Article : Google Scholar

15 

Jewison T, Su Y, Disfany FM, Liang Y, Knox C, Maciejewski A, Poelzer J, Huynh J, Zhou Y, Arndt D, et al: SMPDB 2.0: Big improvements to the Small Molecule Pathway Database. Nucleic Acids Res. 42(D1): D478–D484. 2014. View Article : Google Scholar : PubMed/NCBI

16 

Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A and Bork P: STITCH 2: An interaction network database for small molecules and proteins. Nucleic Acids Res. 38 (Suppl_1):D552–D556. 2010. View Article : Google Scholar : PubMed/NCBI

17 

van Driel MA, Bruggeman J, Vriend G, Brunner HG and Leunissen JA: A text-mining analysis of the human phenome. Eur J Hum Genet. 14:535–542. 2006. View Article : Google Scholar : PubMed/NCBI

18 

Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, et al: HMDB: A knowledgebase for the human metabolome. Nucleic Acids Res 37 (Database). D603–D610. 2009. View Article : Google Scholar

19 

Amberger JS, Bocchini CA, Schiettecatte F, Scott AF and Hamosh A: OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 43(D1): D789–D798. 2015. View Article : Google Scholar : PubMed/NCBI

20 

Wu X, Jiang R, Zhang MQ and Li S: Network-based global inference of human disease genes. Mol Syst Biol. 4:1892008. View Article : Google Scholar : PubMed/NCBI

21 

Paul TV, Thomas N, Seshadri MS, Oommen R, Jose A and Mahendri NV: Prevalence of osteoporosis in ambulatory postmenopausal women from a semiurban region in Southern India: relationship to calcium nutrition and vitamin D status. Endocr Pract. 14:665–671. 2008. View Article : Google Scholar : PubMed/NCBI

22 

Feng Z, Liu C, Guan X and Mor V: China's rapidly aging population creates policy challenges in shaping a viable long-term care system. Health Aff (Millwood). 31:2764–2773. 2012. View Article : Google Scholar : PubMed/NCBI

23 

Ahmed N, Sammons J, Khokher MA and Hassan HT: Retinoic acid suppresses interleukin 6 production in normal human osteoblasts. Cytokine. 12:289–293. 2000. View Article : Google Scholar : PubMed/NCBI

24 

Xu P, Guo X, Yao JF, Cai QK and Li YF: The effect and the mechanism of osteoporotic model female rats induced by retinoic acid. Orthopedic J China. 10:995–998. 2001.(In Chinese).

25 

Shiraishi A, Takeda S, Masaki T, Higuchi Y, Uchiyama Y, Kubodera N, Sato K, Ikeda K, Nakamura T, Matsumoto T, et al: Alfacalcidol inhibits bone resorption and stimulates formation in an ovariectomized rat model of osteoporosis: Distinct actions from estrogen. J Bone Miner Res. 15:770–779. 2000. View Article : Google Scholar : PubMed/NCBI

26 

Ma Y, Xu Y and Qian Z: The changes of hepcidin in tretinoin-induced osteoporosis in rats. Jiangsu Med J. 8:0272008.

27 

Chen Q, Xiong Y, Wang Z, Xue L and Wang L: Osteoporosis model of rats caused by tretinoin acid and experimental study on effects of gallium salts on apoptosis, contents of DNA, molecular weight of DNA and lipid peroxidation. Zhong Guo Di Fang Bing Fang Zhi Za Zhi. 19:68–70. 2003.(In Chinese).

28 

Dai X, Xiong Y, Wang Z, Lei Y, Zuo H and Xue L: Experimental study on effect of gallium salt and estradiol on bone metabolism in tretinoin-induced osteoporosis of rats. J Xi'an Med University. 3:215–217. 2001.(In Chinese).

29 

Yu S-J, Huang XY, Wang CH, Shan WL, Zhu GX and Liu HC: Effect of low-concentration estradiol on proliferation and differentiation of osteoblasts from jaws of osteoporotic rats. Chin J Prosthodontics. 1:17–21. 2016.(In Chinese).

30 

Lindsay R, Bush TL, Grady D, Speroff L and Lobo RA: Therapeutic controversy: Estrogen replacement in menopause. J Clin Endocrinol Metab. 81:3829–3838. 1996. View Article : Google Scholar : PubMed/NCBI

31 

Haines CJ, Chung TK, Leung PC, Hsu SY and Leung DH: Calcium supplementation and bone mineral density in postmenopausal women using estrogen replacement therapy. Bone. 16:529–531. 1995. View Article : Google Scholar : PubMed/NCBI

32 

Nowson CA, Green RM, Hopper JL, Sherwin AJ, Young D, Kaymakci B, Guest CS, Smid M, Larkins RG and Wark JD: A co-twin study of the effect of calcium supplementation on bone density during adolescence. Osteoporos Int. 7:219–225. 1997. View Article : Google Scholar : PubMed/NCBI

33 

Nieves JW, Golden AL, Siris E, Kelsey JL and Lindsay R: Teenage and current calcium intake are related to bone mineral density of the hip and forearm in women aged 30–39 years. Am J Epidemiol. 141:342–351. 1995. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Zhang C, Wang Y, Zhang C and Wu H: Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network. Exp Ther Med 17: 3155-3161, 2019.
APA
Zhang, C., Wang, Y., Zhang, C., & Wu, H. (2019). Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network. Experimental and Therapeutic Medicine, 17, 3155-3161. https://doi.org/10.3892/etm.2019.7310
MLA
Zhang, C., Wang, Y., Zhang, C., Wu, H."Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network". Experimental and Therapeutic Medicine 17.4 (2019): 3155-3161.
Chicago
Zhang, C., Wang, Y., Zhang, C., Wu, H."Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network". Experimental and Therapeutic Medicine 17, no. 4 (2019): 3155-3161. https://doi.org/10.3892/etm.2019.7310
Copy and paste a formatted citation
x
Spandidos Publications style
Zhang C, Wang Y, Zhang C and Wu H: Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network. Exp Ther Med 17: 3155-3161, 2019.
APA
Zhang, C., Wang, Y., Zhang, C., & Wu, H. (2019). Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network. Experimental and Therapeutic Medicine, 17, 3155-3161. https://doi.org/10.3892/etm.2019.7310
MLA
Zhang, C., Wang, Y., Zhang, C., Wu, H."Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network". Experimental and Therapeutic Medicine 17.4 (2019): 3155-3161.
Chicago
Zhang, C., Wang, Y., Zhang, C., Wu, H."Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network". Experimental and Therapeutic Medicine 17, no. 4 (2019): 3155-3161. https://doi.org/10.3892/etm.2019.7310
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