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Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture.

Yin LM, Jiang GH, Wang Y, Wang Y, Liu YY, Jin WR, Xu YD, Zhang QH, Yang YQ - J. Biomed. Sci. (2009)

Bottom Line: By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC).Totally 3 same KEGG pathways were found among the three groups.Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, PR China. collegeylm@hotmail.com

ABSTRACT

Background: Asthma has become an important public health issue and approximately 300 million people have suffered from the disease worldwide. Nowadays, the use of acupuncture in asthma is increasing. This study intended to systematically analyze and compare the gene expression profiles between the asthmatic and acupuncture-treated asthmatic rat lung, and tried to gain insight into the molecular mechanism underlying the early airway response (EAR) phase of asthma treated by acupuncture.

Methods: Four tag libraries of serial analysis of gene expression (SAGE) were established from lung tissues of control rats (CK), asthmatic rats (AS), asthmatic rats treated by acupuncture (ASAC), and control rats treated by acupuncture (CKAC). Bioinformatic analyses were carried out by using the methods including unsupervised hierarchical clustering, functional annotation tool of the database for annotation, visualization, and integrated discovery (DAVID), gene ontology (GO) tree machine, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis.

Results: There were totally 186 differentially expressed tags (P < 0.05, P(CK/AS)) between the libraries of CK and AS, 130 differentially expressed tags between libraries of AS/ASAC (P < 0.05, P(AS/ASAC)), and 144 differentially expressed tags between libraries of CK/CKAC (P < 0.05, P(CK/CKAC)). The gene expression profiles of AS and ASAC were more similar than other libraries via unsupervised SAGE clustering. By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC). Totally 3 same KEGG pathways were found among the three groups. Moreover, 21 specific tags of the acupuncture in treating asthma were detected using Venn diagrams.

Conclusion: Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

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Real-time PCR confirmation of differentially regulated genes of interest predicted by SAGE. * meant the expression levels were up-regulated more than 2 folds compared with CK, # meant the expression levels were down-regulated more than 0.5 fold compared with AS. The expression levels of the three genes of CKAS were up-regulated less than 2 folds compared with CK.
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Figure 2: Real-time PCR confirmation of differentially regulated genes of interest predicted by SAGE. * meant the expression levels were up-regulated more than 2 folds compared with CK, # meant the expression levels were down-regulated more than 0.5 fold compared with AS. The expression levels of the three genes of CKAS were up-regulated less than 2 folds compared with CK.

Mentions: To confirm the expression profiles among the four SAGE libraries, three differentially expressed genes of interest were chosen and their expression levels were evaluated by qRT-PCR. Dusp1 encodes a protein that catalyzes the dephosphorylation and inactivation of MAP kinase. S100A9 is a calcium binding protein that may be associated with acute inflammatory processes. MT-2 has a high content of cysteine residues that bind various heavy metals and could be transcriptionally regulated by both heavy metals and glucocorticoids. The results indicate that the expression profiles of representative genes in qRT-PCR analysis correspond to the SAGE data (Figure 2), which supports the validation of our quantitative data for further bioinformatic analysis.


Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture.

Yin LM, Jiang GH, Wang Y, Wang Y, Liu YY, Jin WR, Xu YD, Zhang QH, Yang YQ - J. Biomed. Sci. (2009)

Real-time PCR confirmation of differentially regulated genes of interest predicted by SAGE. * meant the expression levels were up-regulated more than 2 folds compared with CK, # meant the expression levels were down-regulated more than 0.5 fold compared with AS. The expression levels of the three genes of CKAS were up-regulated less than 2 folds compared with CK.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2698896&req=5

Figure 2: Real-time PCR confirmation of differentially regulated genes of interest predicted by SAGE. * meant the expression levels were up-regulated more than 2 folds compared with CK, # meant the expression levels were down-regulated more than 0.5 fold compared with AS. The expression levels of the three genes of CKAS were up-regulated less than 2 folds compared with CK.
Mentions: To confirm the expression profiles among the four SAGE libraries, three differentially expressed genes of interest were chosen and their expression levels were evaluated by qRT-PCR. Dusp1 encodes a protein that catalyzes the dephosphorylation and inactivation of MAP kinase. S100A9 is a calcium binding protein that may be associated with acute inflammatory processes. MT-2 has a high content of cysteine residues that bind various heavy metals and could be transcriptionally regulated by both heavy metals and glucocorticoids. The results indicate that the expression profiles of representative genes in qRT-PCR analysis correspond to the SAGE data (Figure 2), which supports the validation of our quantitative data for further bioinformatic analysis.

Bottom Line: By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC).Totally 3 same KEGG pathways were found among the three groups.Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, PR China. collegeylm@hotmail.com

ABSTRACT

Background: Asthma has become an important public health issue and approximately 300 million people have suffered from the disease worldwide. Nowadays, the use of acupuncture in asthma is increasing. This study intended to systematically analyze and compare the gene expression profiles between the asthmatic and acupuncture-treated asthmatic rat lung, and tried to gain insight into the molecular mechanism underlying the early airway response (EAR) phase of asthma treated by acupuncture.

Methods: Four tag libraries of serial analysis of gene expression (SAGE) were established from lung tissues of control rats (CK), asthmatic rats (AS), asthmatic rats treated by acupuncture (ASAC), and control rats treated by acupuncture (CKAC). Bioinformatic analyses were carried out by using the methods including unsupervised hierarchical clustering, functional annotation tool of the database for annotation, visualization, and integrated discovery (DAVID), gene ontology (GO) tree machine, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis.

Results: There were totally 186 differentially expressed tags (P < 0.05, P(CK/AS)) between the libraries of CK and AS, 130 differentially expressed tags between libraries of AS/ASAC (P < 0.05, P(AS/ASAC)), and 144 differentially expressed tags between libraries of CK/CKAC (P < 0.05, P(CK/CKAC)). The gene expression profiles of AS and ASAC were more similar than other libraries via unsupervised SAGE clustering. By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC). Totally 3 same KEGG pathways were found among the three groups. Moreover, 21 specific tags of the acupuncture in treating asthma were detected using Venn diagrams.

Conclusion: Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

Show MeSH
Related in: MedlinePlus