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Analysis of gene expression changes in Trichophyton rubrum after skin interaction.

Liu T, Xu X, Leng W, Xue Y, Dong J, Jin Q - J. Med. Microbiol. (2014)

Bottom Line: Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses.In this study, T. rubrum infection was modelled by adding human skin sections to a limited medium containing glucose and cDNA microarrays were used to monitor T. rubrum gene expression patterns on a global level.We observed that exposure to human skin resulted in upregulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation, metabolism and secondary transport, the stress response, and signalling pathways.

View Article: PubMed Central - PubMed

Affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China.

ABSTRACT
Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses. In this study, T. rubrum infection was modelled by adding human skin sections to a limited medium containing glucose and cDNA microarrays were used to monitor T. rubrum gene expression patterns on a global level. We observed that exposure to human skin resulted in upregulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation, metabolism and secondary transport, the stress response, and signalling pathways. These results provide a reference set of T. rubrum genes whose expression patterns change upon infection and reveal previously unknown genes that most likely correspond to proteins that should be considered as virulence factor candidates and potential new drug targets for T. rubrum infection.

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KMC clustering of microarray data and identification of genes with similar transcriptional profiles. (a) A total of 768 genes were clustered on the basis of their expression profiles when cultured with human skin sections relative to their expression profiles when cultured in LM across five time points. Each gene belonged to one of the four KMC clusters. Each gene’s expression values were standardized to have a median of 0 and an sd of 1 across the time points from 0 to 12 h. The lighter colour in the cluster dendrogram is correlated with a higher expression level. (b) Mean expression profiles of the genes within each cluster. To obtain each profile, a sum of the expression values across the five time points for each gene was standardized to 1. Next, the time-course values for all genes in each cluster were summed and the summed value for the five time points for each cluster was scaled to 1. log2(H/C): for each gene in KMC clusters, log2(H/C) refers to log2 (expression level cultured in human skin sections/expression level cultured in LM).
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f1: KMC clustering of microarray data and identification of genes with similar transcriptional profiles. (a) A total of 768 genes were clustered on the basis of their expression profiles when cultured with human skin sections relative to their expression profiles when cultured in LM across five time points. Each gene belonged to one of the four KMC clusters. Each gene’s expression values were standardized to have a median of 0 and an sd of 1 across the time points from 0 to 12 h. The lighter colour in the cluster dendrogram is correlated with a higher expression level. (b) Mean expression profiles of the genes within each cluster. To obtain each profile, a sum of the expression values across the five time points for each gene was standardized to 1. Next, the time-course values for all genes in each cluster were summed and the summed value for the five time points for each cluster was scaled to 1. log2(H/C): for each gene in KMC clusters, log2(H/C) refers to log2 (expression level cultured in human skin sections/expression level cultured in LM).

Mentions: To assess gene expression patterns during the infection process, the mycelia of a T. rubrum isolate were grown in a human skin suspension medium and equal amounts of mycelia were introduced into LM as a control. During the 12 h culture process, the growth of the mycelia in these two media showed no obvious differences. The skin sections in the medium were also not consumed visibly. Changes in gene expression were monitored from 0 to 12 h using a cDNA microarray. A total of 2452 genes were selected based on the significant changes in expression by ANOVA (P<0.01) during this period. Using ANOVA (P<0.01) by TIGR MeV software (Saeed et al., 2003), the expression patterns of the 2452 selected genes were compared with the corresponding data from the control LM culture. Of these 2452 genes, the expression changes of 1258 genes were confirmed as due mainly to human skin induction, rather than simply being time-dependent. Of these 1258 genes, 768 demonstrated changes in expression levels exceeding a twofold difference and were used for further analysis to identify genes whose expression levels were altered dramatically in response to human skin induction (for detailed results, see Table S2). To verify the microarray results, the relative expression levels of 15 genes were estimated by quantitative real-time RT-PCR. The results showed a strong positive correlation between the two techniques (Table 1). These 768 genes were then subjected to KMC analysis using TIGR MeV software to evaluate the relative expression pattern of T. rubrum cultured in skin suspension medium (Saeed et al., 2003). Each of these 768 genes belonged to one of four KMC clusters (Fig. 1).


Analysis of gene expression changes in Trichophyton rubrum after skin interaction.

Liu T, Xu X, Leng W, Xue Y, Dong J, Jin Q - J. Med. Microbiol. (2014)

KMC clustering of microarray data and identification of genes with similar transcriptional profiles. (a) A total of 768 genes were clustered on the basis of their expression profiles when cultured with human skin sections relative to their expression profiles when cultured in LM across five time points. Each gene belonged to one of the four KMC clusters. Each gene’s expression values were standardized to have a median of 0 and an sd of 1 across the time points from 0 to 12 h. The lighter colour in the cluster dendrogram is correlated with a higher expression level. (b) Mean expression profiles of the genes within each cluster. To obtain each profile, a sum of the expression values across the five time points for each gene was standardized to 1. Next, the time-course values for all genes in each cluster were summed and the summed value for the five time points for each cluster was scaled to 1. log2(H/C): for each gene in KMC clusters, log2(H/C) refers to log2 (expression level cultured in human skin sections/expression level cultured in LM).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4042497&req=5

f1: KMC clustering of microarray data and identification of genes with similar transcriptional profiles. (a) A total of 768 genes were clustered on the basis of their expression profiles when cultured with human skin sections relative to their expression profiles when cultured in LM across five time points. Each gene belonged to one of the four KMC clusters. Each gene’s expression values were standardized to have a median of 0 and an sd of 1 across the time points from 0 to 12 h. The lighter colour in the cluster dendrogram is correlated with a higher expression level. (b) Mean expression profiles of the genes within each cluster. To obtain each profile, a sum of the expression values across the five time points for each gene was standardized to 1. Next, the time-course values for all genes in each cluster were summed and the summed value for the five time points for each cluster was scaled to 1. log2(H/C): for each gene in KMC clusters, log2(H/C) refers to log2 (expression level cultured in human skin sections/expression level cultured in LM).
Mentions: To assess gene expression patterns during the infection process, the mycelia of a T. rubrum isolate were grown in a human skin suspension medium and equal amounts of mycelia were introduced into LM as a control. During the 12 h culture process, the growth of the mycelia in these two media showed no obvious differences. The skin sections in the medium were also not consumed visibly. Changes in gene expression were monitored from 0 to 12 h using a cDNA microarray. A total of 2452 genes were selected based on the significant changes in expression by ANOVA (P<0.01) during this period. Using ANOVA (P<0.01) by TIGR MeV software (Saeed et al., 2003), the expression patterns of the 2452 selected genes were compared with the corresponding data from the control LM culture. Of these 2452 genes, the expression changes of 1258 genes were confirmed as due mainly to human skin induction, rather than simply being time-dependent. Of these 1258 genes, 768 demonstrated changes in expression levels exceeding a twofold difference and were used for further analysis to identify genes whose expression levels were altered dramatically in response to human skin induction (for detailed results, see Table S2). To verify the microarray results, the relative expression levels of 15 genes were estimated by quantitative real-time RT-PCR. The results showed a strong positive correlation between the two techniques (Table 1). These 768 genes were then subjected to KMC analysis using TIGR MeV software to evaluate the relative expression pattern of T. rubrum cultured in skin suspension medium (Saeed et al., 2003). Each of these 768 genes belonged to one of four KMC clusters (Fig. 1).

Bottom Line: Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses.In this study, T. rubrum infection was modelled by adding human skin sections to a limited medium containing glucose and cDNA microarrays were used to monitor T. rubrum gene expression patterns on a global level.We observed that exposure to human skin resulted in upregulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation, metabolism and secondary transport, the stress response, and signalling pathways.

View Article: PubMed Central - PubMed

Affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China.

ABSTRACT
Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses. In this study, T. rubrum infection was modelled by adding human skin sections to a limited medium containing glucose and cDNA microarrays were used to monitor T. rubrum gene expression patterns on a global level. We observed that exposure to human skin resulted in upregulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation, metabolism and secondary transport, the stress response, and signalling pathways. These results provide a reference set of T. rubrum genes whose expression patterns change upon infection and reveal previously unknown genes that most likely correspond to proteins that should be considered as virulence factor candidates and potential new drug targets for T. rubrum infection.

Show MeSH
Related in: MedlinePlus