Apoptosis via the B cell antigen receptor

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Hi Paula

For the annotation of PMID: 15214043 Apoptosis via the B cell antigen receptor requires Bax translocation and involves mitochondrial depolarization, cytochrome C release, and caspase-9 activation I think there should be a GO term extrinsic apoptotic signaling pathway via B cell antigen receptor Which would need extrinsic apoptotic signaling pathway via BCR alias And part of links to GO:0001783 B cell apoptotic process or possibly more appropriate would be to be a part of GO:0002516 B cell deletion

As the BCR is a protein complex I think this would be a useful term, Note that the TCR probably induces apoptosis in a similar way, we have the T cell term GO:0045058 T cell selection, but not T cell apoptosis or T cell deletion, see PMID:22235227, PMID:23046121 I wonder if it would be appropriate to have some grouping term too so we have GO:0030098 lymphocyte differentiation maybe there should be the term lymphocyte selection/apoptosis/deletion as it is possible that there are genes in common to both cell pathways

Thanks

Ruth

Reported by: RLovering

Original Ticket: geneontology/ontology-requests/10194

[gocentral]

• assigned_to: Ruth --> Paola Roncaglia

Original comment by: paolaroncaglia

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Hi Ruth, thanks for your suggestions. To start with:

Becky, would you agree with a term GO:NEW extrinsic apoptotic signaling pathway via B cell receptor is_a extrinsic apoptotic signaling pathway is_a B cell receptor signaling pathway

We could even have a grouping term GO:NEW extrinsic apoptotic signaling pathway via antigen receptor is_a extrinsic apoptotic signaling pathway is_a antigen receptor-mediated signaling pathway with children GO:NEW extrinsic apoptotic signaling pathway via B cell receptor GO:NEW extrinsic apoptotic signaling pathway via T cell receptor (linking to GO:0050852 T cell receptor signaling pathway)

For the cell-type specific apoptotic process terms, I'd wait till we have the appropriate template in TG, and I'd need to check with Alex about selection/deletion terms.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hello,

I don't like 'via' in the wording since the pathway starts with ligand-receptor binding. Better would be: B cell receptor apoptotic signaling pathway ; GO:NEW is_a: B cell receptor signaling pathway ; GO:0050853 is_a: extrinsic apoptotic signaling pathway ; GO:0097191

Let me know if you want me to do any edits Paola. Thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

Hi Ruth,

I've added this term so you can annotate PMID: 15214043:

[Term] id: GO:1990117 name: B cell receptor apoptotic signaling pathway namespace: biological_process def: "An extrinsic apoptotic signaling pathway initiated by the cross-linking of an antigen receptor on a B cell." [GOC:BHF, GOC:rl, PMID:15214043] synonym: "B cell receptor extrinsic apoptotic signaling pathway" EXACT [] synonym: "extrinsic apoptotic signaling pathway via B cell antigen receptor" RELATED [] synonym: "extrinsic apoptotic signaling pathway via BCR" RELATED [] is_a: GO:0050853 ! B cell receptor signaling pathway is_a: GO:0097191 ! extrinsic apoptotic signaling pathway relationship: part_of GO:0001783 ! B cell apoptotic process

I'd like to ask Alex about the link to 'B cell deletion' and about the processes you mention in the second paragraph - just because I'm not an expert in this area. Thanks for your patience!

Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> open-accepted

Original comment by: paolaroncaglia

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• status: open-accepted --> pending-accepted

Original comment by: paolaroncaglia

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Set to pending - waiting for Alex Diehl to comment.

Original comment by: paolaroncaglia

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Hi Ruth,

I haven't had any feedback yet on the pending questions of 'B cell deletion' and the processes you mention in the second paragraph of your original request. Since the term you needed to annotate has been added anyway, I'm closing this ticket. If the same or similar issues come up again, we'll look into them, but right now, I'd leave things as they are.

Thanks and best, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: pending-accepted --> closed-accepted

Original comment by: paolaroncaglia