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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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Mfge8 deficiency does not impair apoptotic cell engulfment in the SED. (A) Heavy cytoplasmic inclusions of MEG-E8 (green) and E-cadherin (red) were detected within MNP within the SED (arrows). (B) In the SED of WT and Mfge8−/− mice, strong cytoplasmic inclusions of E-cadherin (red) were detected within CD11c+ MNP (green) indicative of the uptake of apoptotic epithelial cells (arrows). (C and D) Apoptotic cells (TUNEL+, green) and CD11c+ MNP (red) were detected by IHC in the SED (C) and B cell follicles (D) of Peyer's patches from WT and Mfge8−/− mice. Bar charts show the mean number of MNP-bound apoptotic cells in the SED (C) and B cell follicles (D) of Peyer's patches of WT (open bars) and Mfge8−/− mice (closed bars). FO, follicle. Each bar represents data from the analysis of 100–300 MNP from each mouse strain.
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DSS022F7: Mfge8 deficiency does not impair apoptotic cell engulfment in the SED. (A) Heavy cytoplasmic inclusions of MEG-E8 (green) and E-cadherin (red) were detected within MNP within the SED (arrows). (B) In the SED of WT and Mfge8−/− mice, strong cytoplasmic inclusions of E-cadherin (red) were detected within CD11c+ MNP (green) indicative of the uptake of apoptotic epithelial cells (arrows). (C and D) Apoptotic cells (TUNEL+, green) and CD11c+ MNP (red) were detected by IHC in the SED (C) and B cell follicles (D) of Peyer's patches from WT and Mfge8−/− mice. Bar charts show the mean number of MNP-bound apoptotic cells in the SED (C) and B cell follicles (D) of Peyer's patches of WT (open bars) and Mfge8−/− mice (closed bars). FO, follicle. Each bar represents data from the analysis of 100–300 MNP from each mouse strain.

Mentions: MFG-E8 aids the phagocytic clearance of apoptotic cells by mononuclear phagocytes.12,25 The mononuclear phagocytes in Peyer's patches comprise a heterogeneous population of classical DC and macrophages, and our data show that the majority of those in the FAE and B cell follicles (including tingible body macrophages) express CD11c.26 In the SED of Peyer's patches, cytoplasmic inclusions of MFG-E8 and the epithelial cell marker E-cadherin were detected in mononuclear phagocytes implying the uptake of apoptotic epithelial cells (Fig. 7A and B, arrows). We therefore determined whether the expression of MFG-E8 by the FAE was important for the engulfment of apoptotic cells by mononuclear phagocytes in the underlying SED by comparing the number of phagocyte-associated apoptotic cells in the Peyer's patches of WT and Mfge8−/− mice. In the SED, the mean number of phagocyte-bound apoptotic cells was similar in Peyer's patches from each group of mice indicating that the engulfment of apoptic cells was unaffected in the absence of MGF-E8 (Fig. 7C). In contrast, the apoptotic cell load of phagocytes in the B cell follicles was significantly higher in Peyer's patches from Mfge8−/− mice (Fig. 7D) consistent with previous data.25 These data show that MFG-E8 expression in the FAE does not regulate the engulfment of apoptotic cells by mononuclear phagocytes within the SED.Figure 7.


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)

Mfge8 deficiency does not impair apoptotic cell engulfment in the SED. (A) Heavy cytoplasmic inclusions of MEG-E8 (green) and E-cadherin (red) were detected within MNP within the SED (arrows). (B) In the SED of WT and Mfge8−/− mice, strong cytoplasmic inclusions of E-cadherin (red) were detected within CD11c+ MNP (green) indicative of the uptake of apoptotic epithelial cells (arrows). (C and D) Apoptotic cells (TUNEL+, green) and CD11c+ MNP (red) were detected by IHC in the SED (C) and B cell follicles (D) of Peyer's patches from WT and Mfge8−/− mice. Bar charts show the mean number of MNP-bound apoptotic cells in the SED (C) and B cell follicles (D) of Peyer's patches of WT (open bars) and Mfge8−/− mice (closed bars). FO, follicle. Each bar represents data from the analysis of 100–300 MNP from each mouse strain.
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Related In: Results  -  Collection

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DSS022F7: Mfge8 deficiency does not impair apoptotic cell engulfment in the SED. (A) Heavy cytoplasmic inclusions of MEG-E8 (green) and E-cadherin (red) were detected within MNP within the SED (arrows). (B) In the SED of WT and Mfge8−/− mice, strong cytoplasmic inclusions of E-cadherin (red) were detected within CD11c+ MNP (green) indicative of the uptake of apoptotic epithelial cells (arrows). (C and D) Apoptotic cells (TUNEL+, green) and CD11c+ MNP (red) were detected by IHC in the SED (C) and B cell follicles (D) of Peyer's patches from WT and Mfge8−/− mice. Bar charts show the mean number of MNP-bound apoptotic cells in the SED (C) and B cell follicles (D) of Peyer's patches of WT (open bars) and Mfge8−/− mice (closed bars). FO, follicle. Each bar represents data from the analysis of 100–300 MNP from each mouse strain.
Mentions: MFG-E8 aids the phagocytic clearance of apoptotic cells by mononuclear phagocytes.12,25 The mononuclear phagocytes in Peyer's patches comprise a heterogeneous population of classical DC and macrophages, and our data show that the majority of those in the FAE and B cell follicles (including tingible body macrophages) express CD11c.26 In the SED of Peyer's patches, cytoplasmic inclusions of MFG-E8 and the epithelial cell marker E-cadherin were detected in mononuclear phagocytes implying the uptake of apoptotic epithelial cells (Fig. 7A and B, arrows). We therefore determined whether the expression of MFG-E8 by the FAE was important for the engulfment of apoptotic cells by mononuclear phagocytes in the underlying SED by comparing the number of phagocyte-associated apoptotic cells in the Peyer's patches of WT and Mfge8−/− mice. In the SED, the mean number of phagocyte-bound apoptotic cells was similar in Peyer's patches from each group of mice indicating that the engulfment of apoptic cells was unaffected in the absence of MGF-E8 (Fig. 7C). In contrast, the apoptotic cell load of phagocytes in the B cell follicles was significantly higher in Peyer's patches from Mfge8−/− mice (Fig. 7D) consistent with previous data.25 These data show that MFG-E8 expression in the FAE does not regulate the engulfment of apoptotic cells by mononuclear phagocytes within the SED.Figure 7.

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