[NTR] subepithelial intestinal fibroblast and subclasses

[Caroline-99]

Please check that the term does not already exist by using the ontology search tool OLS:
https://www.ebi.ac.uk/ols4/ontologies/cl

Preferred term label
subepithelial intestinal fibroblast

Synonyms (add reference(s), please)
S2 mesenchymal cells (related synonym) PMID: 33916891
S2 fibroblast (related synonym)

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)
A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts of intestine. This cell is characterized by expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. This cell secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation.
PMID: 30270042
PMID: 33430285
PMID: 33916891
PMID: 37080817

comments
The S2 fibroblast population is located near the intestinal epithelial lining and can be can be divided into S2a and S2b subtypes, with S2a being associated with the differentiation process. S2b is pericryptic (around the crypts) and regulates intestinal stem cell proliferation, niche establishment, and wound healing.
PMID: 30270042
PMID: 33916891

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)
fibroblast

Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)
adjacent to intestinal epithelium

Your ORCID

Additional notes or concerns
Suggestions from gut cell atlas:

• AA - suggestion: split into colonic and intestinal variants as quite different based on location?
• VG: Also refered to as S2 fibroblasts. Depending on the annotation level, we can also split by top (S2b - NRG1, NPY) and bottom (S2a - VSTM2A) fibroblasts

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Preferred term label
crypt-bottom Fibroblast

Synonyms (add reference(s), please)

CBFs (related synonym) https://doi.org/10.1371/journal.pbio.3001032
bottom pericryptic--associated fibroblasts (related synonym) PMID: [33916891]
(https://pubmed.ncbi.nlm.nih.gov/33916891)

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)
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.

PMID: 33916891
https://doi.org/10.1371/journal.pbio.3001032

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)
subepithelial intestinal fibroblast

Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)
adjacent to the base of the crypt of Lieberkuhn

Your ORCID

Additional notes or concerns

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Preferred term label
crypt-top Fibroblast

Synonyms (add reference(s), please)
S2b fibroblast (related synonym) PMID: 37495570
top pericryptic fibroblast (related synonym) PMID: 33916891
S2b pericryptal fibroblasts (related synonym) PMID: 37495570

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)
A subepithelial intestinal fibroblast that is located at the top of the crypt of Lieberkuhn. These fibroblasts secrete a range of cell-cell signaling factors (WNTs and BMPs) that promote epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation.

PMID: 33916891
https://doi.org/10.1371/journal.pbio.3001032

Comments
S2b fibroblasts were found to be located at the top of the crypt and express NRG1 and NPY.
PMID: 37495570 - Supplementary figure 6

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)
subepithelial intestinal fibroblast

Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)
adjacent to top of the crypt of Lieberkuhn (New uberon term needed)
Currently: adjacent to epithelium of crypt of Lieberkuhn could be used ?

Your ORCID

Additional notes or concerns

[dosumis]

Needs a better name. Make sure definition is very clearly distinct from submucosal