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Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction.

Cheng KC, Huang HC, Chen JH, Hsu JW, Cheng HC, Ou CH, Yang WB, Chen ST, Wong CH, Juan HF - BMC Genomics (2007)

Bottom Line: In previous studies, F3, the active component of the polysaccharide extract, was found to activate various cytokines such as IL-1, IL-6, IL-12, and TNF-alpha.The apoptosis induction through the DR3 and DR4/5 death receptors was found to be one of the most significant pathways and play a key role in THP-1 cells after F3 treatment.Our results showed that F3 may induce death receptor ligands to initiate signaling via receptor oligomerization, recruitment of specialized adaptor proteins and activation of caspase cascades.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Science, National Taiwan University, Taipei 106, Taiwan. jerekcheng@gmail.com

ABSTRACT

Background: Ganoderma lucidum has been widely used as a herbal medicine for promoting health and longevity in China and other Asian countries. Polysaccharide extracts from Ganoderma lucidum have been reported to exhibit immuno-modulating and anti-tumor activities. In previous studies, F3, the active component of the polysaccharide extract, was found to activate various cytokines such as IL-1, IL-6, IL-12, and TNF-alpha. This gave rise to our investigation on how F3 stimulates immuno-modulating or anti-tumor effects in human leukemia THP-1 cells.

Results: Here, we integrated time-course DNA microarray analysis, quantitative PCR assays, and bioinformatics methods to study the F3-induced effects in THP-1 cells. Significantly disturbed pathways induced by F3 were identified with statistical analysis on microarray data. The apoptosis induction through the DR3 and DR4/5 death receptors was found to be one of the most significant pathways and play a key role in THP-1 cells after F3 treatment. Based on time-course gene expression measurements of the identified pathway, we reconstructed a plausible regulatory network of the involved genes using reverse-engineering computational approach.

Conclusion: Our results showed that F3 may induce death receptor ligands to initiate signaling via receptor oligomerization, recruitment of specialized adaptor proteins and activation of caspase cascades.

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Related in: MedlinePlus

The flow chart for the microarray data analysis. We used Affymetrix HG-U133A chip GeneChip oligonucleotide microarray. Initial data analysis was performed using Affymetrix Microarray Suite v5.0 software, setting the scaling of all probe sets to a constant value of 500 for each GeneChip. Additional data analysis was performed using GeneSpring v 5.1 (Silicon Genetics Inc., Redwood City, California). Genes with a 2-fold change in differential expression between THP-1 control and F3- or LPS-treated THP-1 cells were selected for mapping significantly disturbed biological pathways. The pathway of apoptosis induction through the DR3 and DR4/5 death receptors was shown to be very significant in F3-treated THP-1 cells. F3–6 h and F3–24 h indicate the F3-treated THP1 cells after 6 hours and 24 hours, respectively. LPS-24 h indicates the LPS-treated THP1 cells after 24 hours. C-0 h and C-6 h indicate the control THP1 cells (without any treatment) in 0 hour and 6 hours, respectively.
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Figure 4: The flow chart for the microarray data analysis. We used Affymetrix HG-U133A chip GeneChip oligonucleotide microarray. Initial data analysis was performed using Affymetrix Microarray Suite v5.0 software, setting the scaling of all probe sets to a constant value of 500 for each GeneChip. Additional data analysis was performed using GeneSpring v 5.1 (Silicon Genetics Inc., Redwood City, California). Genes with a 2-fold change in differential expression between THP-1 control and F3- or LPS-treated THP-1 cells were selected for mapping significantly disturbed biological pathways. The pathway of apoptosis induction through the DR3 and DR4/5 death receptors was shown to be very significant in F3-treated THP-1 cells. F3–6 h and F3–24 h indicate the F3-treated THP1 cells after 6 hours and 24 hours, respectively. LPS-24 h indicates the LPS-treated THP1 cells after 24 hours. C-0 h and C-6 h indicate the control THP1 cells (without any treatment) in 0 hour and 6 hours, respectively.

Mentions: In order to identify patterns of gene expression associated with apoptotic effect in THP-1 cells induced by F3, we performed a transcriptomic analysis on the THP-1 control and F3-treated or LPS-treated THP-1 cells by oligonucleotide microarray. In Figure 3, we observed clear separation of control (0 and 6 hours) and F3-treated (6 and 24 hours) samples after performing principle component analysis on the gene expression profiles measured by microarray experiments. Figure 4 shows the flow chart for our microarray data analysis. In Figure 5, the intensities of gene expression of one experiment were plotted on the x axis and the intensities of the other experiment on the y axis. A single dot represents one gene as shown in the scatter plots. The upper three scatter plots showed no difference between the control experiments for 0 hour and 6 hours. These results showed the consistency of our duplicate microarray experiments.


Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction.

Cheng KC, Huang HC, Chen JH, Hsu JW, Cheng HC, Ou CH, Yang WB, Chen ST, Wong CH, Juan HF - BMC Genomics (2007)

The flow chart for the microarray data analysis. We used Affymetrix HG-U133A chip GeneChip oligonucleotide microarray. Initial data analysis was performed using Affymetrix Microarray Suite v5.0 software, setting the scaling of all probe sets to a constant value of 500 for each GeneChip. Additional data analysis was performed using GeneSpring v 5.1 (Silicon Genetics Inc., Redwood City, California). Genes with a 2-fold change in differential expression between THP-1 control and F3- or LPS-treated THP-1 cells were selected for mapping significantly disturbed biological pathways. The pathway of apoptosis induction through the DR3 and DR4/5 death receptors was shown to be very significant in F3-treated THP-1 cells. F3–6 h and F3–24 h indicate the F3-treated THP1 cells after 6 hours and 24 hours, respectively. LPS-24 h indicates the LPS-treated THP1 cells after 24 hours. C-0 h and C-6 h indicate the control THP1 cells (without any treatment) in 0 hour and 6 hours, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2211495&req=5

Figure 4: The flow chart for the microarray data analysis. We used Affymetrix HG-U133A chip GeneChip oligonucleotide microarray. Initial data analysis was performed using Affymetrix Microarray Suite v5.0 software, setting the scaling of all probe sets to a constant value of 500 for each GeneChip. Additional data analysis was performed using GeneSpring v 5.1 (Silicon Genetics Inc., Redwood City, California). Genes with a 2-fold change in differential expression between THP-1 control and F3- or LPS-treated THP-1 cells were selected for mapping significantly disturbed biological pathways. The pathway of apoptosis induction through the DR3 and DR4/5 death receptors was shown to be very significant in F3-treated THP-1 cells. F3–6 h and F3–24 h indicate the F3-treated THP1 cells after 6 hours and 24 hours, respectively. LPS-24 h indicates the LPS-treated THP1 cells after 24 hours. C-0 h and C-6 h indicate the control THP1 cells (without any treatment) in 0 hour and 6 hours, respectively.
Mentions: In order to identify patterns of gene expression associated with apoptotic effect in THP-1 cells induced by F3, we performed a transcriptomic analysis on the THP-1 control and F3-treated or LPS-treated THP-1 cells by oligonucleotide microarray. In Figure 3, we observed clear separation of control (0 and 6 hours) and F3-treated (6 and 24 hours) samples after performing principle component analysis on the gene expression profiles measured by microarray experiments. Figure 4 shows the flow chart for our microarray data analysis. In Figure 5, the intensities of gene expression of one experiment were plotted on the x axis and the intensities of the other experiment on the y axis. A single dot represents one gene as shown in the scatter plots. The upper three scatter plots showed no difference between the control experiments for 0 hour and 6 hours. These results showed the consistency of our duplicate microarray experiments.

Bottom Line: In previous studies, F3, the active component of the polysaccharide extract, was found to activate various cytokines such as IL-1, IL-6, IL-12, and TNF-alpha.The apoptosis induction through the DR3 and DR4/5 death receptors was found to be one of the most significant pathways and play a key role in THP-1 cells after F3 treatment.Our results showed that F3 may induce death receptor ligands to initiate signaling via receptor oligomerization, recruitment of specialized adaptor proteins and activation of caspase cascades.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Science, National Taiwan University, Taipei 106, Taiwan. jerekcheng@gmail.com

ABSTRACT

Background: Ganoderma lucidum has been widely used as a herbal medicine for promoting health and longevity in China and other Asian countries. Polysaccharide extracts from Ganoderma lucidum have been reported to exhibit immuno-modulating and anti-tumor activities. In previous studies, F3, the active component of the polysaccharide extract, was found to activate various cytokines such as IL-1, IL-6, IL-12, and TNF-alpha. This gave rise to our investigation on how F3 stimulates immuno-modulating or anti-tumor effects in human leukemia THP-1 cells.

Results: Here, we integrated time-course DNA microarray analysis, quantitative PCR assays, and bioinformatics methods to study the F3-induced effects in THP-1 cells. Significantly disturbed pathways induced by F3 were identified with statistical analysis on microarray data. The apoptosis induction through the DR3 and DR4/5 death receptors was found to be one of the most significant pathways and play a key role in THP-1 cells after F3 treatment. Based on time-course gene expression measurements of the identified pathway, we reconstructed a plausible regulatory network of the involved genes using reverse-engineering computational approach.

Conclusion: Our results showed that F3 may induce death receptor ligands to initiate signaling via receptor oligomerization, recruitment of specialized adaptor proteins and activation of caspase cascades.

Show MeSH
Related in: MedlinePlus