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Gastrointestinal Fibroblasts Have Specialized, Diverse Transcriptional Phenotypes: A Comprehensive Gene Expression Analysis of Human Fibroblasts.

Higuchi Y, Kojima M, Ishii G, Aoyagi K, Sasaki H, Ochiai A - PLoS ONE (2015)

Bottom Line: The signature genes that discriminated GIFs from non-GIFs, SMFs from SPFs, and the fibroblasts of one organ from another organ consisted of genes associated with transcriptional regulation, signaling ligands, and extracellular matrix remodeling.In addition, the anatomical site- and organ-dependent diversity of GIFs was also discovered.These features of GIFs contribute to their specific physiological function and homeostatic maintenance, and create a functional diversity of the gastrointestinal tract.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cancer Biology, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

ABSTRACT

Background: Fibroblasts are the principal stromal cells that exist in whole organs and play vital roles in many biological processes. Although the functional diversity of fibroblasts has been estimated, a comprehensive analysis of fibroblasts from the whole body has not been performed and their transcriptional diversity has not been sufficiently explored. The aim of this study was to elucidate the transcriptional diversity of human fibroblasts within the whole body.

Methods: Global gene expression analysis was performed on 63 human primary fibroblasts from 13 organs. Of these, 32 fibroblasts from gastrointestinal organs (gastrointestinal fibroblasts: GIFs) were obtained from a pair of 2 anatomical sites: the submucosal layer (submucosal fibroblasts: SMFs) and the subperitoneal layer (subperitoneal fibroblasts: SPFs). Using hierarchical clustering analysis, we elucidated identifiable subgroups of fibroblasts and analyzed the transcriptional character of each subgroup.

Results: In unsupervised clustering, 2 major clusters that separate GIFs and non-GIFs were observed. Organ- and anatomical site-dependent clusters within GIFs were also observed. The signature genes that discriminated GIFs from non-GIFs, SMFs from SPFs, and the fibroblasts of one organ from another organ consisted of genes associated with transcriptional regulation, signaling ligands, and extracellular matrix remodeling.

Conclusions: GIFs are characteristic fibroblasts with specific gene expressions from transcriptional regulation, signaling ligands, and extracellular matrix remodeling related genes. In addition, the anatomical site- and organ-dependent diversity of GIFs was also discovered. These features of GIFs contribute to their specific physiological function and homeostatic maintenance, and create a functional diversity of the gastrointestinal tract.

No MeSH data available.


The Expression of Anatomical Site and Organ Signature Genes in Human Tissue.(A-D) The mRNA expression of anatomical and organ signature genes in human mesenchymal tissue (n = 3). SPFs signature: MSX1 (A), SMFs signature: PITX1 (B), colon fibroblasts signature: HOXA10 (C), stomach fibroblasts signature: HOXB8 (D). (E) Immunofluorescence staining of MSX1 in human colonic tissue. Arrow heads show vimentin-positive, spindle-shaped fibroblastic cells. (F) Semi-quantitative value of nuclear MSX1 expression in human colonic and gastric tissue (n = 3).
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pone.0129241.g006: The Expression of Anatomical Site and Organ Signature Genes in Human Tissue.(A-D) The mRNA expression of anatomical and organ signature genes in human mesenchymal tissue (n = 3). SPFs signature: MSX1 (A), SMFs signature: PITX1 (B), colon fibroblasts signature: HOXA10 (C), stomach fibroblasts signature: HOXB8 (D). (E) Immunofluorescence staining of MSX1 in human colonic tissue. Arrow heads show vimentin-positive, spindle-shaped fibroblastic cells. (F) Semi-quantitative value of nuclear MSX1 expression in human colonic and gastric tissue (n = 3).

Mentions: Finally, we confirmed the expression of anatomical site and organ signature genes in human colonic and gastric mesenchymal tissue. Using qRT-PCR, we confirmed that the gene expression of MSX1, HOXA10, and HOXB8 in human mesenchymal tissue was correlated with their expression in vitro, whereas we failed to confirm the gene expression of PITX1 (Fig 6A–6D). Furthermore, using immunofluorescence staining, we observed the protein expression of SPFs signature gene MSX1 in human tissue. We calculated the nuclear protein expression of MSX1 in vimentin-positive, spindle-shaped fibroblastic cells, and confirmed that SPFs showed higher expression of MSX1 than SMFs in vivo (Fig 6E and 6F, S6 Fig).


Gastrointestinal Fibroblasts Have Specialized, Diverse Transcriptional Phenotypes: A Comprehensive Gene Expression Analysis of Human Fibroblasts.

Higuchi Y, Kojima M, Ishii G, Aoyagi K, Sasaki H, Ochiai A - PLoS ONE (2015)

The Expression of Anatomical Site and Organ Signature Genes in Human Tissue.(A-D) The mRNA expression of anatomical and organ signature genes in human mesenchymal tissue (n = 3). SPFs signature: MSX1 (A), SMFs signature: PITX1 (B), colon fibroblasts signature: HOXA10 (C), stomach fibroblasts signature: HOXB8 (D). (E) Immunofluorescence staining of MSX1 in human colonic tissue. Arrow heads show vimentin-positive, spindle-shaped fibroblastic cells. (F) Semi-quantitative value of nuclear MSX1 expression in human colonic and gastric tissue (n = 3).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4457624&req=5

pone.0129241.g006: The Expression of Anatomical Site and Organ Signature Genes in Human Tissue.(A-D) The mRNA expression of anatomical and organ signature genes in human mesenchymal tissue (n = 3). SPFs signature: MSX1 (A), SMFs signature: PITX1 (B), colon fibroblasts signature: HOXA10 (C), stomach fibroblasts signature: HOXB8 (D). (E) Immunofluorescence staining of MSX1 in human colonic tissue. Arrow heads show vimentin-positive, spindle-shaped fibroblastic cells. (F) Semi-quantitative value of nuclear MSX1 expression in human colonic and gastric tissue (n = 3).
Mentions: Finally, we confirmed the expression of anatomical site and organ signature genes in human colonic and gastric mesenchymal tissue. Using qRT-PCR, we confirmed that the gene expression of MSX1, HOXA10, and HOXB8 in human mesenchymal tissue was correlated with their expression in vitro, whereas we failed to confirm the gene expression of PITX1 (Fig 6A–6D). Furthermore, using immunofluorescence staining, we observed the protein expression of SPFs signature gene MSX1 in human tissue. We calculated the nuclear protein expression of MSX1 in vimentin-positive, spindle-shaped fibroblastic cells, and confirmed that SPFs showed higher expression of MSX1 than SMFs in vivo (Fig 6E and 6F, S6 Fig).

Bottom Line: The signature genes that discriminated GIFs from non-GIFs, SMFs from SPFs, and the fibroblasts of one organ from another organ consisted of genes associated with transcriptional regulation, signaling ligands, and extracellular matrix remodeling.In addition, the anatomical site- and organ-dependent diversity of GIFs was also discovered.These features of GIFs contribute to their specific physiological function and homeostatic maintenance, and create a functional diversity of the gastrointestinal tract.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cancer Biology, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

ABSTRACT

Background: Fibroblasts are the principal stromal cells that exist in whole organs and play vital roles in many biological processes. Although the functional diversity of fibroblasts has been estimated, a comprehensive analysis of fibroblasts from the whole body has not been performed and their transcriptional diversity has not been sufficiently explored. The aim of this study was to elucidate the transcriptional diversity of human fibroblasts within the whole body.

Methods: Global gene expression analysis was performed on 63 human primary fibroblasts from 13 organs. Of these, 32 fibroblasts from gastrointestinal organs (gastrointestinal fibroblasts: GIFs) were obtained from a pair of 2 anatomical sites: the submucosal layer (submucosal fibroblasts: SMFs) and the subperitoneal layer (subperitoneal fibroblasts: SPFs). Using hierarchical clustering analysis, we elucidated identifiable subgroups of fibroblasts and analyzed the transcriptional character of each subgroup.

Results: In unsupervised clustering, 2 major clusters that separate GIFs and non-GIFs were observed. Organ- and anatomical site-dependent clusters within GIFs were also observed. The signature genes that discriminated GIFs from non-GIFs, SMFs from SPFs, and the fibroblasts of one organ from another organ consisted of genes associated with transcriptional regulation, signaling ligands, and extracellular matrix remodeling.

Conclusions: GIFs are characteristic fibroblasts with specific gene expressions from transcriptional regulation, signaling ligands, and extracellular matrix remodeling related genes. In addition, the anatomical site- and organ-dependent diversity of GIFs was also discovered. These features of GIFs contribute to their specific physiological function and homeostatic maintenance, and create a functional diversity of the gastrointestinal tract.

No MeSH data available.