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Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations.

Kobayashi A, Donaldson DS, Kanaya T, Fukuda S, Baillie JK, Freeman TC, Ohno H, Williams IR, Mabbott NA - DNA Res. (2012)

Bottom Line: The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium.This study provides new insight into the FAE transcriptome.Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.

ABSTRACT
The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium. Using a meta-analysis approach, we identified a transcriptional signature that distinguished the FAE from a large collection of mouse cells and tissues. A co-expressed cluster of 21 FAE-specific genes was identified, and the analysis of the transcription factor binding site motifs in their promoter regions indicated that these genes shared an underlying transcriptional programme. This cluster contained known FAE- (Anxa10, Ccl20, Psg18 and Ubd) and M-cell-specific (Gp2) genes, suggesting that the others were novel FAE-specific genes. Some of these novel candidate genes were expressed highly by the FAE and M cells (Calcb, Ces3b, Clca2 and Gjb2), and others only by the FAE (Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl). We also identified a subset of novel FAE-related genes that were induced in the intestinal epithelium after receptor activator of nuclear factor (NF)-κB ligand stimulation. These included Mfge8 which was specific to FAE enterocytes. This study provides new insight into the FAE transcriptome. Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.

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Expression profiles of the genes within cluster 65. (A) The mean expression profile of the probe set intensities within cluster 65 over the 130 samples. The red-boxed area indicates the Peyer's patch M cell data sets; the blue-boxed area indicates the FAE data sets. The cluster 65 nodes derived from the network graph are also shown. (B) Heat map showing the mean expression of all probe sets within cluster 65 in samples from enriched Peyer's patch M cells (PP M cells), CT-stimulated villous epithelium (CT-stim. villous epith.), ileum epithelial cells (ileum IEC), FAE, SI epithelium (SI epith.), ileum and NALT. Each column represents the mean (log2) probe set intensity for all samples from each source (n = 2–4). P-values for those genes which were expressed significantly within the FAE at levels >2.0-fold when compared with the villous epithelium (ileum IEC, SI epithelium, ileum) are indicated. (C) IHC confirmation of the expression of proteins encoded by FAE-related genes (CCL20 and ubiquitin D, red) and M cell-related (GP2+ cells, green, arrows) in mouse Peyer's patches. SED, subepithelial dome. Dotted line indicates the luminal surface of the FAE.
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DSS022F4: Expression profiles of the genes within cluster 65. (A) The mean expression profile of the probe set intensities within cluster 65 over the 130 samples. The red-boxed area indicates the Peyer's patch M cell data sets; the blue-boxed area indicates the FAE data sets. The cluster 65 nodes derived from the network graph are also shown. (B) Heat map showing the mean expression of all probe sets within cluster 65 in samples from enriched Peyer's patch M cells (PP M cells), CT-stimulated villous epithelium (CT-stim. villous epith.), ileum epithelial cells (ileum IEC), FAE, SI epithelium (SI epith.), ileum and NALT. Each column represents the mean (log2) probe set intensity for all samples from each source (n = 2–4). P-values for those genes which were expressed significantly within the FAE at levels >2.0-fold when compared with the villous epithelium (ileum IEC, SI epithelium, ileum) are indicated. (C) IHC confirmation of the expression of proteins encoded by FAE-related genes (CCL20 and ubiquitin D, red) and M cell-related (GP2+ cells, green, arrows) in mouse Peyer's patches. SED, subepithelial dome. Dotted line indicates the luminal surface of the FAE.

Mentions: Our main aim was to use this clustering approach to gain further insights into the biology of the FAE. Cluster 65 contained 29 probe sets encoding 21 annotated genes and the mean expression profile of this cluster was restricted to the FAE and M cells (Fig. 4A). The mean expression level of these genes in the FAE samples was significantly higher when compared with the villous epithelium [ileum epithelial cells, small intestine (SI) epithelium and ileum samples; Fig. 4B]. Several of these genes had previously been reported to be expressed highly throughout the FAE (Anxa10, Ccl20, Psg18 and Ubd), whereas Gp2 is specifically expressed by the M cells within it.2,4,13–15 The expression of CCL20, ubiquitin D and GP2 in the FAE is shown in Fig. 4C. By using the principle of ‘guilt-by-association’, these data suggested that the remaining genes in cluster 65 were also related to FAE function. Analysis of the expression profiles of these potentially novel genes across the different data sets indicated that Calcb, Ces3b, Clca2 and Gjb2 were expressed at highly significant levels within the FAE and Peyer's patch M cell samples when compared with the villous epithelium. Others including Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl were expressed in the FAE, but not by M cells (Fig. 4B).Figure 4.


Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations.

Kobayashi A, Donaldson DS, Kanaya T, Fukuda S, Baillie JK, Freeman TC, Ohno H, Williams IR, Mabbott NA - DNA Res. (2012)

Expression profiles of the genes within cluster 65. (A) The mean expression profile of the probe set intensities within cluster 65 over the 130 samples. The red-boxed area indicates the Peyer's patch M cell data sets; the blue-boxed area indicates the FAE data sets. The cluster 65 nodes derived from the network graph are also shown. (B) Heat map showing the mean expression of all probe sets within cluster 65 in samples from enriched Peyer's patch M cells (PP M cells), CT-stimulated villous epithelium (CT-stim. villous epith.), ileum epithelial cells (ileum IEC), FAE, SI epithelium (SI epith.), ileum and NALT. Each column represents the mean (log2) probe set intensity for all samples from each source (n = 2–4). P-values for those genes which were expressed significantly within the FAE at levels >2.0-fold when compared with the villous epithelium (ileum IEC, SI epithelium, ileum) are indicated. (C) IHC confirmation of the expression of proteins encoded by FAE-related genes (CCL20 and ubiquitin D, red) and M cell-related (GP2+ cells, green, arrows) in mouse Peyer's patches. SED, subepithelial dome. Dotted line indicates the luminal surface of the FAE.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473373&req=5

DSS022F4: Expression profiles of the genes within cluster 65. (A) The mean expression profile of the probe set intensities within cluster 65 over the 130 samples. The red-boxed area indicates the Peyer's patch M cell data sets; the blue-boxed area indicates the FAE data sets. The cluster 65 nodes derived from the network graph are also shown. (B) Heat map showing the mean expression of all probe sets within cluster 65 in samples from enriched Peyer's patch M cells (PP M cells), CT-stimulated villous epithelium (CT-stim. villous epith.), ileum epithelial cells (ileum IEC), FAE, SI epithelium (SI epith.), ileum and NALT. Each column represents the mean (log2) probe set intensity for all samples from each source (n = 2–4). P-values for those genes which were expressed significantly within the FAE at levels >2.0-fold when compared with the villous epithelium (ileum IEC, SI epithelium, ileum) are indicated. (C) IHC confirmation of the expression of proteins encoded by FAE-related genes (CCL20 and ubiquitin D, red) and M cell-related (GP2+ cells, green, arrows) in mouse Peyer's patches. SED, subepithelial dome. Dotted line indicates the luminal surface of the FAE.
Mentions: Our main aim was to use this clustering approach to gain further insights into the biology of the FAE. Cluster 65 contained 29 probe sets encoding 21 annotated genes and the mean expression profile of this cluster was restricted to the FAE and M cells (Fig. 4A). The mean expression level of these genes in the FAE samples was significantly higher when compared with the villous epithelium [ileum epithelial cells, small intestine (SI) epithelium and ileum samples; Fig. 4B]. Several of these genes had previously been reported to be expressed highly throughout the FAE (Anxa10, Ccl20, Psg18 and Ubd), whereas Gp2 is specifically expressed by the M cells within it.2,4,13–15 The expression of CCL20, ubiquitin D and GP2 in the FAE is shown in Fig. 4C. By using the principle of ‘guilt-by-association’, these data suggested that the remaining genes in cluster 65 were also related to FAE function. Analysis of the expression profiles of these potentially novel genes across the different data sets indicated that Calcb, Ces3b, Clca2 and Gjb2 were expressed at highly significant levels within the FAE and Peyer's patch M cell samples when compared with the villous epithelium. Others including Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl were expressed in the FAE, but not by M cells (Fig. 4B).Figure 4.

Bottom Line: The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium.This study provides new insight into the FAE transcriptome.Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.

ABSTRACT
The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium. Using a meta-analysis approach, we identified a transcriptional signature that distinguished the FAE from a large collection of mouse cells and tissues. A co-expressed cluster of 21 FAE-specific genes was identified, and the analysis of the transcription factor binding site motifs in their promoter regions indicated that these genes shared an underlying transcriptional programme. This cluster contained known FAE- (Anxa10, Ccl20, Psg18 and Ubd) and M-cell-specific (Gp2) genes, suggesting that the others were novel FAE-specific genes. Some of these novel candidate genes were expressed highly by the FAE and M cells (Calcb, Ces3b, Clca2 and Gjb2), and others only by the FAE (Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl). We also identified a subset of novel FAE-related genes that were induced in the intestinal epithelium after receptor activator of nuclear factor (NF)-κB ligand stimulation. These included Mfge8 which was specific to FAE enterocytes. This study provides new insight into the FAE transcriptome. Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.

Show MeSH
Related in: MedlinePlus