[NTR] border associated macrophage

dosumis commented 7 months ago

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

border associated macrophage

Synonyms (add reference(s), please)

BAM https://doi.org/10.1038/s41586-023-06808-9.

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

A type of macrophage with an elongated cell body with numerous processes that extend along the borders of the CNS - in the choroid plexus, meningeal and perivascular spaces This distinctive morphology allows them to interact with various components of the CNS vasculature and meninges, as well as participate in immune surveillance and regulation of the blood-brain barrier.

(Note - def partly derived from LLM content. Please check against references!)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10217436/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10452120/

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

macrophage

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

choroid plexus, meningeal and perivascular spaces

Please check Uberon for some suitable collective term to cover these.

Your ORCID

Additional notes or concerns

dosumis commented 7 months ago

@AvolaAmg - this is a term needed for mouse brain annotation. Might be useful to follow along with fixes.

lubianat commented 6 months ago

Maybe relevant: https://www.sciencedirect.com/science/article/pii/S1074761318300323

"we revealed that microglia, several subsets of border-associated macrophages and dendritic cells coexist in the CNS at steady state and exhibit disease-specific transformations in the immune microenvironment during aging and in models of Alzheimer’s disease and multiple sclerosis."

Just to note here that maybe subdivisions of BAMs will be needed in the future.

Also relevant from https://www.annualreviews.org/doi/10.1146/annurev-immunol-093019-110159

"Tissue macrophages in the CNS come in two flavors: Microglia are located in the parenchyma (their name pointing to their small cell body of around 7–10 μm), and CNS-associated macrophages (CAMs) are found in CNS interfaces including the meninges, perivascular space, and choroid plexus (Figure 1). CAMs are also known as border-associated macrophages (BAMs) and encompass perivascular macrophages (PVMs), subdural leptomeningeal macrophages (MMs), and choroid plexus macrophages (3–7)."

lubianat commented 6 months ago

@dosumis Maybe we need to create "brain border" in Uberon first.

A subclass of regional part of brain, perhaps?

It is a complex modelling, as "perivascular space" is an immaterial entity and "choroid plexus" is a material entity. Nevertheless, it is an important concept to model. General ref:

https://www.nature.com/articles/s41586-022-05474-7

dosumis commented 6 months ago

"CAMs are also known as border-associated macrophages (BAMs) and encompass perivascular macrophages (PVMs), subdural leptomeningeal macrophages (MMs), and choroid plexus macrophages (3–7)."

Given this, it's probably worth making the subclasses at the same time.

lubianat commented 6 months ago

I checked and we have some of the subclasses in CL already

It would be a matter of putting the border associated macrophage between the CNS macrophage and the subclasses, I guess.

AvolaAmg commented 6 months ago

I had a look at the central nervous system macrophages and this is what I think we should add/modify. Let me know what you think

new term request border associated macrophage

Preferred term label border associated macrophage

Definition A central nervous system macrophage that is resident in the choroid plexus, meningeal and perivascular spaces. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier. databasa_cross_refence PMID:37232741 PMID:37626977

synonym BAM database_cross_reference PMID:36945367

synonym: CAM Database_cross_reference: PMID:33556248

synonym: CNS-associated macrophage Database_cross_reference: PMID:37232741

comment A border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169

database_cross_reference PMID:29426702 PMID:37232741

parent cell term: central nervous system macrophage

Add synonyms for meningeal macrophage and revise cell definition:

label meningeal macrophage

definition: A central nervous system macrophage resident in the meninges. This macrophage types is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation. The cell body of this macrophage is elongated and amoeboid spindle-shaped with limited mobility.

database_cross_reference <-- these need to be added to the ones that are already present in CL PMID:37232741 PMID:24078900 PMID:24078900

synonym subdural leptomeningeal macrophages

database_cross_reference: PMID:33556248

synonym subdural meningeal macrophages

database_cross_reference: PMID:28323268

synonym MM

database_cross_reference: PMID:33556248

synonym MnMΦ

database_cross_reference:  PMID:38347231

parent cell term: border associated macrophage

 Add synonym of choroid plexus macrophage and modify the definition:

definition A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage expresses scavenger receptors, has a star-like shaped body.

database_cross_reference PMID:37232741

synonym  cpMΦ database_cross_reference PMID:37232741

Add synonym of perivascular macrophage and modify definition

perivascular macrophage definition  A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14, CD16, CD163. In homeostatic conditions, this central nervous system macrophage has a Non-motile cell body with extending and retracting projections through the blood vessel wall.

database_cross_reference PMID:37232741

synonym  pvMΦ database_cross_reference PMID:37232741

parent cell term: border associated macrophage

New Term Request choroid epiplexus macrophage

label choroid epiplexus macrophage

definition A choroid plexus macrophage that is located in the apical surface of the choroid plexus epithelium. This macrophage has a star-like shaped body.

database_cross_reference PMID:37232741 PMID:31061494

synonym Kolmer’s cell database_cross_refence PMID:31433571

synonym cpepiMΦ database_cross_reference PMID:38347231

synonym epiplexus cpMΦ database_cross_reference PMID:38347231

parent cell term: choroid plexus macrophage

New Term Request stromal choroid macrophage

label stromal choroid plexus macrophage

definition A choroid plexus macrophage that is located in the choroid plexus stroma.

database_cross_reference PMID:38347231

synonym stromal cpMΦ

database_cross_reference PMID:38347231

parent cell term: choroid plexus macrophage

New Term Request dural macrophage

label dural macrophage

definition A central nervous system macrophage which is part of the dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis.

database_cross_reference PMID:31061494

synonym dmMΦ database_cross_reference PMID:37232741

parent cell term: Border Associated Macrophage

I feel that the microglia should also be revised, I will have a quick read around to make sure that everything is in place, but this should be a separate ticket

aleixpuigb commented 6 months ago

Thank you Alida for your literature reseaarch. I have some comments:

borderline associated macrophage

In the literature there seems to be a preference for "border associated macrophage" or "border-associated macrophage". Is there a reason for calling it borderline. I can't see it in the references that have been provided. Please, use lower-case letters.

A macrophage that has an elongated cell body with dynamic processes

In one of the references provided (PMID:37232741), we have the following statements about different morphologies depending the subclass:

The subpopulations of BAMs generally vary in morphology, motility, and function.
The BAM subpopulations and microglia generally vary in morphology. Meningeal macrophages are flat, spindle-shaped cells with a few thick membrane projections from their cell body residing close to meningeal vessels . Although sdΜΦ appeared elongated with a more amoeboid morphology than microglia, dmΜΦ was also suggested to be pleomorphic and dendriform-like cells . In the same context, the pvΜΦ had elongated cell bodies permitting the embedding within vessel walls . Regarding the choroid plexus, cpΜΦ display a star-like shape, while cpepiΜΦ seem more phenotypically diverse, varying from round to bipolar to stellate.

I am missing some synonyms. If the preferred label is Borderline associated macrophage, I would also add as exact synonyms: "border associated macrophage", "border-associated macrophage" and "CNS-associated macrophage". All these synonyms can be found in PMID:37232741.

meningeal macrophage

Please use lower case and singular form for synonyms. In one of the publications provided there is another synonym (MM) PMID:33556248

sdMΦ

The reference seems to be wrong. This abbreviation is used in PMID:37232741

choroid-plexus macrophage

It might have two subclasses: stromal and epiplexus:

Once within their niche, microglia, MnMΦ, PvMΦ, and epiplexus cpMΦ are long-lived and self-maintain, thereby, retaining their YS origin, while dmMΦ and stromal cpMΦ are slowly replaced by circulating cells

obophenotype / cell-ontology