Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Oncology Letters
      • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Biomedical Reports
      • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • Information for Authors
    • Information for Reviewers
    • Information for Librarians
    • Information for Advertisers
    • Conferences
  • Language Editing
Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • For Authors
    • For Reviewers
    • For Librarians
    • For Advertisers
    • Conferences
  • Language Editing
Login Register Submit
  • This site uses cookies
  • You can change your cookie settings at any time by following the instructions in our Cookie Policy. To find out more, you may read our Privacy Policy.

    I agree
Search articles by DOI, keyword, author or affiliation
Search
Advanced Search
presentation
Molecular Medicine Reports
Join Editorial Board Propose a Special Issue
Print ISSN: 1791-2997 Online ISSN: 1791-3004
Journal Cover
April-2018 Volume 17 Issue 4

Full Size Image

Sign up for eToc alerts
Recommend to Library

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

Medicine International

An International Open Access Journal Devoted to General Medicine.

Journal Cover
April-2018 Volume 17 Issue 4

Full Size Image

Sign up for eToc alerts
Recommend to Library

  • Article
  • Citations
    • Cite This Article
    • Download Citation
    • Create Citation Alert
    • Remove Citation Alert
    • Cited By
  • Similar Articles
    • Related Articles (in Spandidos Publications)
    • Similar Articles (Google Scholar)
    • Similar Articles (PubMed)
  • Download PDF
  • Download XML
  • View XML
Article Open Access

Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease

  • Authors:
    • Peng Zhao
    • Jiansheng Li
    • Liping Yang
    • Ya Li
    • Yange Tian
    • Suyun Li
  • View Affiliations / Copyright

    Affiliations: Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P.R. China, Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P.R. China
    Copyright: © Zhao et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 5247-5257
    |
    Published online on: January 25, 2018
       https://doi.org/10.3892/mmr.2018.8480
  • Expand metrics +
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )
Cited By (CrossRef): 0 citations Loading Articles...

This article is mentioned in:



Abstract

Bufei Yishen formula (BYF) is a traditional Chinese medicine formula, which has long been used as a therapeutic agent for the treatment of chronic obstructive pulmonary disease (COPD). Systems pharmacology has previously been used to identify the potential targets of BYF, and an experimental study has demonstrated that BYF is able to prevent COPD. In addition, the transcriptomic and metabolomic profiles of lung tissues from rats with COPD and BYF‑treated rats have been characterized. The present study aimed to determine the therapeutic mechanisms underlying the effects of BYF on COPD treatment by integrating transcriptomics, proteomics and metabolomics, together with systems pharmacology datasets. Initially, the proteomic profiles of rats with COPD and BYF‑treated rats were analyzed. Subsequently, pathway and network analyses were conducted to integrate three‑omics data; the results demonstrated that the genes, proteins and metabolites were predominantly associated with oxidoreductase activity, antioxidant activity, focal adhesion and lipid metabolism. Finally, a comprehensive analysis of systems pharmacology, transcriptomic, proteomic and metabolomic datasets was performed, and numerous genes, proteins and metabolites were found to be regulated in BYF‑treated rats; the potential target proteins of BYF were involved in lipid metabolism, inflammatory response, oxidative stress and focal adhesion. In conclusion, BYF exerted beneficial effects against COPD, potentially by modulating lipid metabolism, the inflammatory response, oxidative stress and cell junction pathways at the system level.
View Figures

Figure 1

Figure 2

Figure 3

Figure 4

View References

1 

Vestbo J, Hurd SS, Agustí AG, Jones PW, Vogelmeier C, Anzueto A, Barnes PJ, Fabbri LM, Martinez FJ, Nishimura M, et al: Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease GOLD executive summary. Am J Respir Crit Care Med. 187:347–365. 2013. View Article : Google Scholar : PubMed/NCBI

2 

Beran D, Zar HJ, Perrin C, Menezes AM and Burney P; Forum of International Respiratory Societies working group collaboration, : Burden of asthma and chronic obstructive pulmonary disease and access to essential medicines in low-income and middle-income countries. Lancet Resp Med. 3:159–170. 2015. View Article : Google Scholar

3 

Gan WQ, Man SF, Senthilselvan A and Sin DD: Association between chronic obstructive pulmonary disease and systemic inflammation: A systematic review and a meta-analysis. Thorax. 59:574–580. 2004. View Article : Google Scholar : PubMed/NCBI

4 

Li SY, Li JS, Wang MH, Xie Y, Yu XQ, Sun ZK, Ma LJ, Zhang W, Zhang HL, Cao F and Pan YC: Effects of comprehensive therapy based on traditional Chinese medicine patterns in stable chronic obstructive pulmonary disease: A four-center, open-label, randomized, controlled study. BMC Complement Altern Med. 12:1972012. View Article : Google Scholar : PubMed/NCBI

5 

Li J, Zhao P, Li Y, Tian Y and Wang Y: Systems pharmacology-based dissection of mechanisms of Chinese medicinal formula Bufei Yishen as an effective treatment for chronic obstructive pulmonary disease. Sci Rep. 5:152902015. View Article : Google Scholar : PubMed/NCBI

6 

Su G, Burant CF, Beecher CW, Athey BD and Meng F: Integrated metabolome and transcriptome analysis of the NCI60 dataset. BMC Bioinformatics. 12 Suppl 1:S362011. View Article : Google Scholar : PubMed/NCBI

7 

Vogel C and Marcotte EM: Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet. 13:227–232. 2012. View Article : Google Scholar : PubMed/NCBI

8 

Tan KC, Ipcho SV, Trengove RD, Oliver RP and Solomon PS: Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology. Mol Plant Pathol. 10:703–715. 2009. View Article : Google Scholar : PubMed/NCBI

9 

Wilmes A, Limonciel A, Aschauer L, Moenks K, Bielow C, Leonard MO, Hamon J, Carpi D, Ruzek S, Handler A, et al: Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress. J Proteomics. 79:180–194. 2013. View Article : Google Scholar : PubMed/NCBI

10 

Meierhofer D, Weidner C and Sauer S: Integrative analysis of transcriptomics, proteomics, and metabolomics data of white adipose and liver tissue of high-fat diet and rosiglitazone-treated insulin-resistant mice identified pathway alterations and molecular hubs. J Proteome Res. 13:5592–5602. 2014. View Article : Google Scholar : PubMed/NCBI

11 

Li J, Yang L, Yao Q, Li Y, Tian Y, Li S, Jiang S, Wang Y, Li X and Guo Z: Effects and mechanism of bufei yishen formula in a rat chronic obstructive pulmonary disease model. Evid Based Complement Alternat Med. 2014:3819762014. View Article : Google Scholar : PubMed/NCBI

12 

Yang LP, Li JS, Li Y, Tian Y, Li S, Jiang S, Wang Y and Song X: Identification of metabolites and metabolic pathways related to treatment with Bufei Yishen formula in a Rat COPD model using HPLC Q-TOF/MS. Evid-Based Complement Alternat Med. 2015:9567502015. View Article : Google Scholar : PubMed/NCBI

13 

Li Y, Li SY, Li JS, Deng L, Tian YG, Jiang SL, Wang Y and Wang YY: A rat model for stable chronic obstructive pulmonary disease induced by cigarette smoke inhalation and repetitive bacterial infection. Biol Pharm Bull. 35:1752–1760. 2012. View Article : Google Scholar : PubMed/NCBI

14 

Maere S, Heymans K and Kuiper M: BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 21:3448–3449. 2005. View Article : Google Scholar : PubMed/NCBI

15 

Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z and Galon J: ClueGO: A Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 25:1091–1093. 2009. View Article : Google Scholar : PubMed/NCBI

16 

Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, et al: Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics. 28:373–380. 2012. View Article : Google Scholar : PubMed/NCBI

17 

Santus P, Sola A, Carlucci P, Fumagalli F, Di Gennaro A, Mondoni M, Carnini C, Centanni S and Sala A: Lipid peroxidation and 5-lipoxygenase activity in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 171:838–843. 2005. View Article : Google Scholar : PubMed/NCBI

18 

Tulah AS, Parker SG, Moffatt MF, Wardlaw AJ, Connolly MJ and Sayers I: The role of ALOX5AP, LTA4H and LTB4R polymorphisms in determining baseline lung function and COPD susceptibility in UK smokers. BMC Med Genet. 12:1732011. View Article : Google Scholar : PubMed/NCBI

19 

Barnes PJ: Cellular and molecular mechanisms of chronic obstructive pulmonary disease. Clin Chest Med. 35:71–86. 2014. View Article : Google Scholar : PubMed/NCBI

20 

Sunnetcioglu A, Alp HH, Sertogullarindan B, Balaharoglu R and Gunbatar H: Evaluation of oxidative damage and antioxidant mechanisms in COPD, lung cancer, and obstructive sleep apnea syndrome. Respir Care. 61:205–211. 2016. View Article : Google Scholar : PubMed/NCBI

21 

Lakhdar R, Denden S, Mouhamed MH, Chalgoum A, Leban N, Knani J, Lefranc G, Miled A, Ben Chibani J and Khelil AH: Correlation of EPHX1, GSTP1, GSTM1, and GSTT1 genetic polymorphisms with antioxidative stress markers in chronic obstructive pulmonary disease. Exp Lung Res. 37:195–204. 2011. View Article : Google Scholar : PubMed/NCBI

22 

Escribano A, Amor M, Pastor S, Castillo S, Sanz F, Codoñer-Franch P and Dasí F: Decreased glutathione and low catalase activity contribute to oxidative stress in children with α-1 antitrypsin deficiency. Thorax. 70:82–83. 2015. View Article : Google Scholar : PubMed/NCBI

23 

Rahman I and MacNee W: Antioxidant pharmacological therapies for COPD. Curr Opin Pharmacol. 12:256–265. 2012. View Article : Google Scholar : PubMed/NCBI

24 

Harju T, Kaarteenaho-Wiik R, Sirvio R, Sirviö R, Pääkkö P, Crapo JD, Oury TD, Soini Y and Kinnula VL: Manganese superoxide dismutase is increased in the airways of smokers' lungs. Eur Respir J. 24:765–771. 2004. View Article : Google Scholar : PubMed/NCBI

25 

Dong X, Liu Y, Du M, Wang Q, Yu CT and Fan X: P38 mitogen-activated protein kinase inhibition attenuates pulmonary inflammatory response in a rat cardiopulmonary bypass model. Eur J Cardiothorac Surg. 30:77–84. 2006. View Article : Google Scholar : PubMed/NCBI

26 

Huang Y, Meng XM, Jiang GL, Yang YR, Liu J, Lv XW and Li J: Studies on mitogen-activated protein kinase signaling pathway in the alveolar macrophages of chronic bronchitis rats. Mol Cell Biochem. 400:97–105. 2015. View Article : Google Scholar : PubMed/NCBI

27 

Kida Y, Kobayashi M, Suzuki T, Takeshita A, Okamatsu Y, Hanazawa S, Yasui T and Hasegawa K: Interleukin-1 stimulates cytokines, prostaglandin E2 and matrix metalloproteinase-1 production via activation of MAPK/AP-1 and NF-kappaB in human gingival fibroblasts. Cytokine. 29:159–168. 2005. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Zhao P, Li J, Yang L, Li Y, Tian Y and Li S: Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease. Mol Med Rep 17: 5247-5257, 2018.
APA
Zhao, P., Li, J., Yang, L., Li, Y., Tian, Y., & Li, S. (2018). Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease. Molecular Medicine Reports, 17, 5247-5257. https://doi.org/10.3892/mmr.2018.8480
MLA
Zhao, P., Li, J., Yang, L., Li, Y., Tian, Y., Li, S."Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease". Molecular Medicine Reports 17.4 (2018): 5247-5257.
Chicago
Zhao, P., Li, J., Yang, L., Li, Y., Tian, Y., Li, S."Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease". Molecular Medicine Reports 17, no. 4 (2018): 5247-5257. https://doi.org/10.3892/mmr.2018.8480
Copy and paste a formatted citation
x
Spandidos Publications style
Zhao P, Li J, Yang L, Li Y, Tian Y and Li S: Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease. Mol Med Rep 17: 5247-5257, 2018.
APA
Zhao, P., Li, J., Yang, L., Li, Y., Tian, Y., & Li, S. (2018). Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease. Molecular Medicine Reports, 17, 5247-5257. https://doi.org/10.3892/mmr.2018.8480
MLA
Zhao, P., Li, J., Yang, L., Li, Y., Tian, Y., Li, S."Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease". Molecular Medicine Reports 17.4 (2018): 5247-5257.
Chicago
Zhao, P., Li, J., Yang, L., Li, Y., Tian, Y., Li, S."Integration of transcriptomics, proteomics, metabolomics and systems pharmacology data to reveal the therapeutic mechanism underlying Chinese herbal Bufei Yishen formula for the treatment of chronic obstructive pulmonary disease". Molecular Medicine Reports 17, no. 4 (2018): 5247-5257. https://doi.org/10.3892/mmr.2018.8480
Follow us
  • Twitter
  • LinkedIn
  • Facebook
About
  • Spandidos Publications
  • Careers
  • Cookie Policy
  • Privacy Policy
How can we help?
  • Help
  • Live Chat
  • Contact
  • Email to our Support Team