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Added subepithelial intestinal fibroblast and two subclasses
Added textual and logical defs
Added synonyms and references
Note:
For crypt top fibroblast - the current logical defs: adjacent to epithelium of crypt of Lieberkuhn - This will change to adjacent to top of the crypt of Lieberkuhn (new uberon term needed - top of the crypt of Lieberkuhn)
This is Victoria's response to S2 fibroblasts. Based on that I have added S2 fibroblast as a related synonym to subepithelial intestinal fibroblast and S2b as a related synonym to cry-top fibroblasts but have not included S2a fibroblast.
These fibroblasts were described in the paper from Kinchen et al (DOI: 10.1016/j.cell.2018.08.067). They don’t mention about location, but in the supplementary table 4 there are the DEGs between these two clusters.
Regarding the spatial location, this is something we saw ourselves with CosMx (DOI: 10.1038/s41467-023-40156-6, supplementary figure 6). S2b are expressed at the top of the crypt. We also have stainings for NRG1 and NPY, markers of S2b, and they show a clear apical location. However, regarding S2a, while they are not as apical as S2b, their bottom location is not that clear. So maybe, unlike S2b which could be refer to as “top-crypt”, it might not be 100% correct to refer to S2a as “bottom-crypt”…
Maybe the DEGs signature from Kinchen’s paper is enough, without getting into location?
crypt-bottom fibroblastdefinition "A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis."
crypt-top fibroblastdefinition "A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation."
subepithelial intestinal fibroblastcomment "The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing."
subepithelial intestinal fibroblastdefinition "A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation."
crypt-bottom fibroblastdefinition "A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis."
crypt-top fibroblastdefinition "A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation."
subepithelial intestinal fibroblastcomment "The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing."
subepithelial intestinal fibroblastdefinition "A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation."
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Caroline-99
deleted the
2567-ntr-subepithelial-intestinal-fibroblast-and-subclasses
branch
Added subepithelial intestinal fibroblast and two subclasses
Note: