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Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation.

Foronda M, Morgado-Palacin L, Gómez-López G, Domínguez O, Pisano DG, Blasco MA - Genom Data (2015)

Bottom Line: Besides, Sox4 (cKO) mice are resistant to skin carcinogenesis, thus linking Sox4 to both normal and pathological HFSC activation (Foronda M et al., 2014).Here we provide additional details on the analysis of Sox4-regulated transcriptome in Telogen and Anagen skin.The raw and processed microarray data is deposited in GEO under GSE58155.

View Article: PubMed Central - PubMed

Affiliation: Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), C/ Melchor Fernández Almagro, 3, E-28029, Madrid, Spain.

ABSTRACT
Adult stem cells (ASCs) reside in specific niches in a quiescent state in adult mammals. Upon specific cues they become activated and respond by self-renewing and differentiating into newly generated specialised cells that ensure appropriate tissue fitness. ASC quiescence also serves as a tumour suppression mechanism by hampering cellular transformation and expansion (White AC et al., 2014). Some genes restricted to early embryonic development and adult stem cell niches are often potent modulators of stem cell quiescence, and derailed expression of these is commonly associated to cancer (Vervoort SJ et al., 2013). Among them, it has been shown that recommissioned Sox4 expression facilitates proliferation, survival and migration of malignant cells. By generating a conditional Knockout mouse model in stratified epithelia (Sox4 (cKO) mice), we demonstrated a delayed plucking-induced Anagen in the absence of Sox4. Skin global transcriptome analysis revealed a prominent defect in the induction of transcriptional networks that control hair follicle stem cell (HFSC) activation such as those regulated by Wnt/Ctnnb1, Shh, Myc or Sox9, cell cycle and DNA damage response-associated pathways. Besides, Sox4 (cKO) mice are resistant to skin carcinogenesis, thus linking Sox4 to both normal and pathological HFSC activation (Foronda M et al., 2014). Here we provide additional details on the analysis of Sox4-regulated transcriptome in Telogen and Anagen skin. The raw and processed microarray data is deposited in GEO under GSE58155.

No MeSH data available.


Related in: MedlinePlus

A) Venn's diagram showing the overlap between the significantly enriched pathways in Sox4WT vs Sox4cKO mouse skin in Telogen (green) and Anagen (yellow). Only pathways showing FDR < 0.05 were included for this comparison. Note that most deregulated pathways belong to the Anagen group, reinforcing a role for Sox4 in this condition, and that the overlap is minimal between both categories.B) Enrichment plots for selected pathways, obtained from the NCI repository at FDR < 0.150, where N indicates the number of genes included in each list, and FDR means false discovery rate (q value). The red to blue bar represents the ranked list of genes (red = Sox4WT, blue = Sox4cKO). Genes showing differential expression between genotypes are located at the edges of the bar, and similarly-expressed genes are in the centre. The Y axis represents the enrichment score (ES). Plk1, ATM, nuclear β-catenin, E2F, FoxM1 and TAP63 pathways are shown from left to right and top to bottom.C) Comparison of the values obtained by qPCR and microarray in Sox4WT vs Sox4cKO mouse skin, for the selected DEGs. Fold change relative to Sox4WT (set to 1) is shown. N = 6 mice per genotype.
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f0005: A) Venn's diagram showing the overlap between the significantly enriched pathways in Sox4WT vs Sox4cKO mouse skin in Telogen (green) and Anagen (yellow). Only pathways showing FDR < 0.05 were included for this comparison. Note that most deregulated pathways belong to the Anagen group, reinforcing a role for Sox4 in this condition, and that the overlap is minimal between both categories.B) Enrichment plots for selected pathways, obtained from the NCI repository at FDR < 0.150, where N indicates the number of genes included in each list, and FDR means false discovery rate (q value). The red to blue bar represents the ranked list of genes (red = Sox4WT, blue = Sox4cKO). Genes showing differential expression between genotypes are located at the edges of the bar, and similarly-expressed genes are in the centre. The Y axis represents the enrichment score (ES). Plk1, ATM, nuclear β-catenin, E2F, FoxM1 and TAP63 pathways are shown from left to right and top to bottom.C) Comparison of the values obtained by qPCR and microarray in Sox4WT vs Sox4cKO mouse skin, for the selected DEGs. Fold change relative to Sox4WT (set to 1) is shown. N = 6 mice per genotype.

Mentions: Images were analysed with Agilent Feature Extraction (FE) Software (ver. 10.1.1). FE performs spot quantitation and systematic gradient correction by spatial de-trending algorithms. QC reports provided by FE (which inform on signal qualities, background level and overall sensitivity within well-established acceptance thresholds) were examined for the absence of anomalies. We then performed background subtraction using the normexp method [9]. To normalize the dataset, we performed loess within-array normalization and quantile approach for between-array normalization. Differentially expressed genes were obtained by applying linear models with R limma package [10] (Bioconductor project, http://www.bioconductor.org). To account for multiple hypothesis testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg false discovery rate (FDR) correction [11]. Those genes with FDR < 0.05 were selected as differentially expressed genes (DEGs). Gene set enrichment analysis (GSEA) was studied using annotations from NCI [12], KEGG [13] and Reactome [14] databases. We additionally studied some custom-made gene lists obtained from genomic datasets publicly available [3], [5]. Genes were ranked according to their limma moderated t statistic. After Kolmogorov–Smirnov testing, those gene sets showing FDR < 0.25, a well-established cut-off for the identification of biologically relevant gene sets [15], were considered enriched between Sox4WT vs Sox4cKO mice (Fig. 1A and B).


Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation.

Foronda M, Morgado-Palacin L, Gómez-López G, Domínguez O, Pisano DG, Blasco MA - Genom Data (2015)

A) Venn's diagram showing the overlap between the significantly enriched pathways in Sox4WT vs Sox4cKO mouse skin in Telogen (green) and Anagen (yellow). Only pathways showing FDR < 0.05 were included for this comparison. Note that most deregulated pathways belong to the Anagen group, reinforcing a role for Sox4 in this condition, and that the overlap is minimal between both categories.B) Enrichment plots for selected pathways, obtained from the NCI repository at FDR < 0.150, where N indicates the number of genes included in each list, and FDR means false discovery rate (q value). The red to blue bar represents the ranked list of genes (red = Sox4WT, blue = Sox4cKO). Genes showing differential expression between genotypes are located at the edges of the bar, and similarly-expressed genes are in the centre. The Y axis represents the enrichment score (ES). Plk1, ATM, nuclear β-catenin, E2F, FoxM1 and TAP63 pathways are shown from left to right and top to bottom.C) Comparison of the values obtained by qPCR and microarray in Sox4WT vs Sox4cKO mouse skin, for the selected DEGs. Fold change relative to Sox4WT (set to 1) is shown. N = 6 mice per genotype.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664675&req=5

f0005: A) Venn's diagram showing the overlap between the significantly enriched pathways in Sox4WT vs Sox4cKO mouse skin in Telogen (green) and Anagen (yellow). Only pathways showing FDR < 0.05 were included for this comparison. Note that most deregulated pathways belong to the Anagen group, reinforcing a role for Sox4 in this condition, and that the overlap is minimal between both categories.B) Enrichment plots for selected pathways, obtained from the NCI repository at FDR < 0.150, where N indicates the number of genes included in each list, and FDR means false discovery rate (q value). The red to blue bar represents the ranked list of genes (red = Sox4WT, blue = Sox4cKO). Genes showing differential expression between genotypes are located at the edges of the bar, and similarly-expressed genes are in the centre. The Y axis represents the enrichment score (ES). Plk1, ATM, nuclear β-catenin, E2F, FoxM1 and TAP63 pathways are shown from left to right and top to bottom.C) Comparison of the values obtained by qPCR and microarray in Sox4WT vs Sox4cKO mouse skin, for the selected DEGs. Fold change relative to Sox4WT (set to 1) is shown. N = 6 mice per genotype.
Mentions: Images were analysed with Agilent Feature Extraction (FE) Software (ver. 10.1.1). FE performs spot quantitation and systematic gradient correction by spatial de-trending algorithms. QC reports provided by FE (which inform on signal qualities, background level and overall sensitivity within well-established acceptance thresholds) were examined for the absence of anomalies. We then performed background subtraction using the normexp method [9]. To normalize the dataset, we performed loess within-array normalization and quantile approach for between-array normalization. Differentially expressed genes were obtained by applying linear models with R limma package [10] (Bioconductor project, http://www.bioconductor.org). To account for multiple hypothesis testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg false discovery rate (FDR) correction [11]. Those genes with FDR < 0.05 were selected as differentially expressed genes (DEGs). Gene set enrichment analysis (GSEA) was studied using annotations from NCI [12], KEGG [13] and Reactome [14] databases. We additionally studied some custom-made gene lists obtained from genomic datasets publicly available [3], [5]. Genes were ranked according to their limma moderated t statistic. After Kolmogorov–Smirnov testing, those gene sets showing FDR < 0.25, a well-established cut-off for the identification of biologically relevant gene sets [15], were considered enriched between Sox4WT vs Sox4cKO mice (Fig. 1A and B).

Bottom Line: Besides, Sox4 (cKO) mice are resistant to skin carcinogenesis, thus linking Sox4 to both normal and pathological HFSC activation (Foronda M et al., 2014).Here we provide additional details on the analysis of Sox4-regulated transcriptome in Telogen and Anagen skin.The raw and processed microarray data is deposited in GEO under GSE58155.

View Article: PubMed Central - PubMed

Affiliation: Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), C/ Melchor Fernández Almagro, 3, E-28029, Madrid, Spain.

ABSTRACT
Adult stem cells (ASCs) reside in specific niches in a quiescent state in adult mammals. Upon specific cues they become activated and respond by self-renewing and differentiating into newly generated specialised cells that ensure appropriate tissue fitness. ASC quiescence also serves as a tumour suppression mechanism by hampering cellular transformation and expansion (White AC et al., 2014). Some genes restricted to early embryonic development and adult stem cell niches are often potent modulators of stem cell quiescence, and derailed expression of these is commonly associated to cancer (Vervoort SJ et al., 2013). Among them, it has been shown that recommissioned Sox4 expression facilitates proliferation, survival and migration of malignant cells. By generating a conditional Knockout mouse model in stratified epithelia (Sox4 (cKO) mice), we demonstrated a delayed plucking-induced Anagen in the absence of Sox4. Skin global transcriptome analysis revealed a prominent defect in the induction of transcriptional networks that control hair follicle stem cell (HFSC) activation such as those regulated by Wnt/Ctnnb1, Shh, Myc or Sox9, cell cycle and DNA damage response-associated pathways. Besides, Sox4 (cKO) mice are resistant to skin carcinogenesis, thus linking Sox4 to both normal and pathological HFSC activation (Foronda M et al., 2014). Here we provide additional details on the analysis of Sox4-regulated transcriptome in Telogen and Anagen skin. The raw and processed microarray data is deposited in GEO under GSE58155.

No MeSH data available.


Related in: MedlinePlus