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Laminin enterocyte of colon #2609

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Laminin enterocyte of colon #2609

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d8ce6fb
import
JABelfiore Sep 24, 2024
616718a
merged import
JABelfiore Sep 24, 2024
ea4bcff
def, refs
JABelfiore Sep 24, 2024
ed39985
Merge branch 'master' into 2583-ntr-laminin-enterocyte-of-colon
JABelfiore Sep 26, 2024
a568169
Merge branch 'master' into 2583-ntr-laminin-enterocyte-of-colon
JABelfiore Oct 22, 2024
2603c50
name change, subclass update
JABelfiore Oct 22, 2024
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10 changes: 10 additions & 0 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3076,6 +3076,7 @@ Declaration(Class(obo:CL_4047007))
Declaration(Class(obo:CL_4047011))
Declaration(Class(obo:CL_4047012))
Declaration(Class(obo:CL_4047019))
Declaration(Class(obo:CL_4047021))
Declaration(Class(obo:CL_4047051))
Declaration(Class(obo:CL_4047052))
Declaration(Class(obo:CL_4052001))
Expand Down Expand Up @@ -32547,6 +32548,15 @@ AnnotationAssertion(terms:date obo:CL_4047019 "2024-09-24T12:11:09Z"^^xsd:dateTi
AnnotationAssertion(rdfs:label obo:CL_4047019 "early enterocyte"@en)
EquivalentClasses(obo:CL_4047019 ObjectIntersectionOf(obo:CL_0000584 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0013740)))

# Class: obo:CL_4047021 (laminin enterocyte of colon)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:14585148") Annotation(oboInOwl:hasDbXref "PMID:35101094") obo:IAO_0000115 obo:CL_4047021 "An enterocyte located in the epithelium of the large intestine. This cell expresses and interacts with specific laminin isoforms, particularly laminin-332 (composed of α3, β3, and γ2 chains) and laminin-511 (composed of α5, β1, and γ1 chains). Laminin enterocytes of the colon are attached to the basement membrane via hemidesmosomes containing α6β4 integrin, which binds to laminins. This cell exhibits differential expression of laminin chains along the crypt-surface axis")
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These references are not relevant - new references are needed to support the definition.

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@JABelfiore - https://pubmed.ncbi.nlm.nih.gov/35101094/ - still needs updating.

I couldn't get hold of the other paper - but it is quite old - way before the single cell transciptomics era. Might be useful for cross-referencing location of lamins that are markers for these cell types

From GCA:

VG: not sure if we'll see these in the integrated dataset, but we repeatedly see this cluster of colonocytes that express these laminin genes, particularly LAMA3. Unfortunately, we haven't validate them yet by ISH or IF

Sounds like this is a transcriptomically distinct subset of colonocytes. Might be worth asking VG for reference.

AnnotationAssertion(terms:contributor obo:CL_4047021 <https://orcid.org/0009-0005-7919-4905>)
AnnotationAssertion(terms:date obo:CL_4047021 "2024-09-24T14:36:31Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4047021 "laminin enterocyte of colon"@en)
EquivalentClasses(obo:CL_4047021 ObjectIntersectionOf(obo:CL_1000347 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0013740)))
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This defines the cell type as
"Any colonocyte that is part of the crypt or Lieberkuhn" probably too strong. If so, use SubClassOf

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updated

SubClassOf(obo:CL_4047021 obo:CL_1000347)

# Class: obo:CL_4047051 (small intestine BEST4+ enterocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047051 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium.")
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