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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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The dendrogram of the hierarchical cluster analysis. The genes with over fivefold change or less than 0.2-fold between AS and ASAC were listed at the right side of the graph. Abbreviations of the seven up-regulated genes: Fxyd3: FXYD domain-containing ion transport regulator 3; Col6a2: procollagen, type VI, alpha 2; Uba52: ubiquitin A-52 residue ribosomal protein fusion product 1; Tm9sf2: transmembrane 9 superfamily member 2; CD24: CD24 antigen; Mgp: matrix Gla protein; Rpl31: ribosomal protein L31. Abbreviations of the four down-regulated genes: Ap1m1: Adaptor-related protein complex AP-1, mu subunit; Mgst2: Microsomal glutathione S-transferase 2; Atp1b1: ATPase, Na+/K+ transporting, beta 1 polypeptide; Ywhaq: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide.
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Figure 3: The dendrogram of the hierarchical cluster analysis. The genes with over fivefold change or less than 0.2-fold between AS and ASAC were listed at the right side of the graph. Abbreviations of the seven up-regulated genes: Fxyd3: FXYD domain-containing ion transport regulator 3; Col6a2: procollagen, type VI, alpha 2; Uba52: ubiquitin A-52 residue ribosomal protein fusion product 1; Tm9sf2: transmembrane 9 superfamily member 2; CD24: CD24 antigen; Mgp: matrix Gla protein; Rpl31: ribosomal protein L31. Abbreviations of the four down-regulated genes: Ap1m1: Adaptor-related protein complex AP-1, mu subunit; Mgst2: Microsomal glutathione S-transferase 2; Atp1b1: ATPase, Na+/K+ transporting, beta 1 polypeptide; Ywhaq: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide.

Mentions: Based on the global expression matrix, the dendrogram clearly identified CK from the other 3 libraries, while AS and ASAC displayed more similar patterns than CKAC on the gene expression profiles (Figure 3). The genes with over fivefold change or less than 0.2-fold between AS and ASAC were listed at the right side of the hierarchical clustering dendrogram. Seven genes were ranked with an expression over 5-fold increase: Fxyd3 (Rn.3896), Col6a2 (Rn.11889), Uba52 (Rn.4300), Tm9sf2 (Rn.11839), CD24 (Rn.6007), Mgp (Rn.2379), and ribosomal protein L31 (Rpl31, Rn.1101). Four genes were listed with an expression over 5-fold decrease: Ap1m1 (Rn.139185), Mgst2 (Rn.7854), Atp1b1 (Rn.8925), and Ywhaq (Rn.2502).


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)

The dendrogram of the hierarchical cluster analysis. The genes with over fivefold change or less than 0.2-fold between AS and ASAC were listed at the right side of the graph. Abbreviations of the seven up-regulated genes: Fxyd3: FXYD domain-containing ion transport regulator 3; Col6a2: procollagen, type VI, alpha 2; Uba52: ubiquitin A-52 residue ribosomal protein fusion product 1; Tm9sf2: transmembrane 9 superfamily member 2; CD24: CD24 antigen; Mgp: matrix Gla protein; Rpl31: ribosomal protein L31. Abbreviations of the four down-regulated genes: Ap1m1: Adaptor-related protein complex AP-1, mu subunit; Mgst2: Microsomal glutathione S-transferase 2; Atp1b1: ATPase, Na+/K+ transporting, beta 1 polypeptide; Ywhaq: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The dendrogram of the hierarchical cluster analysis. The genes with over fivefold change or less than 0.2-fold between AS and ASAC were listed at the right side of the graph. Abbreviations of the seven up-regulated genes: Fxyd3: FXYD domain-containing ion transport regulator 3; Col6a2: procollagen, type VI, alpha 2; Uba52: ubiquitin A-52 residue ribosomal protein fusion product 1; Tm9sf2: transmembrane 9 superfamily member 2; CD24: CD24 antigen; Mgp: matrix Gla protein; Rpl31: ribosomal protein L31. Abbreviations of the four down-regulated genes: Ap1m1: Adaptor-related protein complex AP-1, mu subunit; Mgst2: Microsomal glutathione S-transferase 2; Atp1b1: ATPase, Na+/K+ transporting, beta 1 polypeptide; Ywhaq: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide.
Mentions: Based on the global expression matrix, the dendrogram clearly identified CK from the other 3 libraries, while AS and ASAC displayed more similar patterns than CKAC on the gene expression profiles (Figure 3). The genes with over fivefold change or less than 0.2-fold between AS and ASAC were listed at the right side of the hierarchical clustering dendrogram. Seven genes were ranked with an expression over 5-fold increase: Fxyd3 (Rn.3896), Col6a2 (Rn.11889), Uba52 (Rn.4300), Tm9sf2 (Rn.11839), CD24 (Rn.6007), Mgp (Rn.2379), and ribosomal protein L31 (Rpl31, Rn.1101). Four genes were listed with an expression over 5-fold decrease: Ap1m1 (Rn.139185), Mgst2 (Rn.7854), Atp1b1 (Rn.8925), and Ywhaq (Rn.2502).

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