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Defects in cytochrome c oxidase expression induce a metabolic shift to glycolysis and carcinogenesis.

Dong DW, Srinivasan S, Guha M, Avadhani NG - Genom Data (2015)

Bottom Line: These results suggest that a defect in CcO complex initiates a retrograde signaling which can induce tumor progression.Physiological studies of these cells and esophageal tumors from human patients support these results.GEO accession number = GSE68525.

View Article: PubMed Central - PubMed

Affiliation: The Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, PA, United States ; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, PA, United States.

ABSTRACT
Mitochondrial metabolic dysfunction is often seen in cancers. This paper shows that the defect in a mitochondrial electron transport component, the cytochrome c oxidase (CcO), leads to increased glycolysis and carcinogenesis. Using whole genome microarray expression analysis we show that genetic silencing of the CcO subunit Cox4i1 in mouse C2C12 myoblasts resulted in metabolic shift to glycolysis, activated a retrograde stress signaling, and induced carcinogenesis. In the knockdown cells, the expression of Cox4i1 was less than 5% of the control and the expression of the irreversible glycolytic enzymes (Hk1, Pfkm and Pkm) increased two folds, facilitating metabolic shift to glycolysis. The expression of Ca (2+) sensitive Calcineurin (Ppp3ca) and the expression of PI3-kinase (Pik3r4 and Pik3cb) increased by two folds. This Ca (2+)/Calcineurin/PI3K retrograde stress signaling induced the up-regulation of many nuclear genes involved in tumor progression. Overall, we found 1047 genes with 2-folds expression change (with p-value less than 0.01) between the knockdown and the control, among which were 35 up-regulated genes in pathways in cancer (enrichment p-value less than 10(- 5)). Functional analysis revealed that the up-regulated genes in pathways in cancer were dominated by genes in signal transduction, regulation of transcription and PI3K signaling pathway. These results suggest that a defect in CcO complex initiates a retrograde signaling which can induce tumor progression. Physiological studies of these cells and esophageal tumors from human patients support these results. GEO accession number = GSE68525.

No MeSH data available.


Related in: MedlinePlus

Quality control for data analysis. The array expression data (from all 41,345 probes) of each sample are projected to the first two components of PCA, P1 and P2 in a, showing the separation of 6 samples into three groups. This separation is also shown in the 6 × 6 matrix of the correlation coefficients between samples (b). The plot in (c) shows the selection criteria for significant fold change in individual gene expression: the absolute fold change has to be bigger than 20.5 (red and blue dots), and the p-value has to be smaller than 0.05. For functional analysis, the selected genes are ranked by p-value and are further selected by Benjamini-Hocheberg method to limit FDR (d).
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f0005: Quality control for data analysis. The array expression data (from all 41,345 probes) of each sample are projected to the first two components of PCA, P1 and P2 in a, showing the separation of 6 samples into three groups. This separation is also shown in the 6 × 6 matrix of the correlation coefficients between samples (b). The plot in (c) shows the selection criteria for significant fold change in individual gene expression: the absolute fold change has to be bigger than 20.5 (red and blue dots), and the p-value has to be smaller than 0.05. For functional analysis, the selected genes are ranked by p-value and are further selected by Benjamini-Hocheberg method to limit FDR (d).

Mentions: The data were processed by Affymetrix Expression Console using Probeset-Summarize-Engine with default setting of the robust multi-array average (RMA, [1]) method to calculate the expression level for each probeset of the array (in log2 unit, online file: rma-gene-full.summary.txt). For quality control, we performed principal component analysis (PCA) based on RMA expression levels of the samples. The projection to the most dominant two components is shown in Fig. 1a. The control samples formed a single cluster separable from the knockdown. However, the knockdown samples are further branched into two groups. The grouping is also clearly shown (Fig. 1b) by the correlation coefficient value (with each probe mean over all samples removed) between two samples: if the two samples come from the same group, the value is high (above 0.6); if they come from different groups, the value is low or negative. Further investigation of the biological samples showed that C4KD1 and C4KD2 cells contained nearly 90% reduced Cox4i1 mRNA and protein as compared to control cells [2], while in C4KD3 cells the reduction was not as much (probably due to a less effective population selection by antibiotic resulting a mixture of knockdown and non-knockdown cells). This is consistent with microarray results: for both C4KD1 and C4KD2 the reduction were ~ 20 folds, for C4KD3 only ~ 2 folds. In the following analysis, C4KD3 was excluded.


Defects in cytochrome c oxidase expression induce a metabolic shift to glycolysis and carcinogenesis.

Dong DW, Srinivasan S, Guha M, Avadhani NG - Genom Data (2015)

Quality control for data analysis. The array expression data (from all 41,345 probes) of each sample are projected to the first two components of PCA, P1 and P2 in a, showing the separation of 6 samples into three groups. This separation is also shown in the 6 × 6 matrix of the correlation coefficients between samples (b). The plot in (c) shows the selection criteria for significant fold change in individual gene expression: the absolute fold change has to be bigger than 20.5 (red and blue dots), and the p-value has to be smaller than 0.05. For functional analysis, the selected genes are ranked by p-value and are further selected by Benjamini-Hocheberg method to limit FDR (d).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664720&req=5

f0005: Quality control for data analysis. The array expression data (from all 41,345 probes) of each sample are projected to the first two components of PCA, P1 and P2 in a, showing the separation of 6 samples into three groups. This separation is also shown in the 6 × 6 matrix of the correlation coefficients between samples (b). The plot in (c) shows the selection criteria for significant fold change in individual gene expression: the absolute fold change has to be bigger than 20.5 (red and blue dots), and the p-value has to be smaller than 0.05. For functional analysis, the selected genes are ranked by p-value and are further selected by Benjamini-Hocheberg method to limit FDR (d).
Mentions: The data were processed by Affymetrix Expression Console using Probeset-Summarize-Engine with default setting of the robust multi-array average (RMA, [1]) method to calculate the expression level for each probeset of the array (in log2 unit, online file: rma-gene-full.summary.txt). For quality control, we performed principal component analysis (PCA) based on RMA expression levels of the samples. The projection to the most dominant two components is shown in Fig. 1a. The control samples formed a single cluster separable from the knockdown. However, the knockdown samples are further branched into two groups. The grouping is also clearly shown (Fig. 1b) by the correlation coefficient value (with each probe mean over all samples removed) between two samples: if the two samples come from the same group, the value is high (above 0.6); if they come from different groups, the value is low or negative. Further investigation of the biological samples showed that C4KD1 and C4KD2 cells contained nearly 90% reduced Cox4i1 mRNA and protein as compared to control cells [2], while in C4KD3 cells the reduction was not as much (probably due to a less effective population selection by antibiotic resulting a mixture of knockdown and non-knockdown cells). This is consistent with microarray results: for both C4KD1 and C4KD2 the reduction were ~ 20 folds, for C4KD3 only ~ 2 folds. In the following analysis, C4KD3 was excluded.

Bottom Line: These results suggest that a defect in CcO complex initiates a retrograde signaling which can induce tumor progression.Physiological studies of these cells and esophageal tumors from human patients support these results.GEO accession number = GSE68525.

View Article: PubMed Central - PubMed

Affiliation: The Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, PA, United States ; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, PA, United States.

ABSTRACT
Mitochondrial metabolic dysfunction is often seen in cancers. This paper shows that the defect in a mitochondrial electron transport component, the cytochrome c oxidase (CcO), leads to increased glycolysis and carcinogenesis. Using whole genome microarray expression analysis we show that genetic silencing of the CcO subunit Cox4i1 in mouse C2C12 myoblasts resulted in metabolic shift to glycolysis, activated a retrograde stress signaling, and induced carcinogenesis. In the knockdown cells, the expression of Cox4i1 was less than 5% of the control and the expression of the irreversible glycolytic enzymes (Hk1, Pfkm and Pkm) increased two folds, facilitating metabolic shift to glycolysis. The expression of Ca (2+) sensitive Calcineurin (Ppp3ca) and the expression of PI3-kinase (Pik3r4 and Pik3cb) increased by two folds. This Ca (2+)/Calcineurin/PI3K retrograde stress signaling induced the up-regulation of many nuclear genes involved in tumor progression. Overall, we found 1047 genes with 2-folds expression change (with p-value less than 0.01) between the knockdown and the control, among which were 35 up-regulated genes in pathways in cancer (enrichment p-value less than 10(- 5)). Functional analysis revealed that the up-regulated genes in pathways in cancer were dominated by genes in signal transduction, regulation of transcription and PI3K signaling pathway. These results suggest that a defect in CcO complex initiates a retrograde signaling which can induce tumor progression. Physiological studies of these cells and esophageal tumors from human patients support these results. GEO accession number = GSE68525.

No MeSH data available.


Related in: MedlinePlus