KDM NTR: metanephric glomerular mesangium cell migration

[gocentral]

Hi,

for annotation of PDGFB_RAT( Q05028) and ADIPOQ_MOUSE (Q60994) in PMID:19450854 I will need the following new terms:

For PDGFB_RAT( Q05028) GO:0072223 metanephric glomerular mesangium development --< GO:NEW metanephric glomerular mesangium cell migration --< GO:NEW regulation of metanephric glomerular mesangium cell migration --< GO:NEW positive regulation of metanephric glomerular mesangium cell migration (IDA) --< GO:NEW negative regulation of metanephric glomerular mesangium cell migration

For ADIPOQ_MOUSE (Q60994) GO:0010642 negative regulation of platelet-derived growth factor receptor signaling pathway --< GO:NEW negative regulation of platelet-derived growth factor receptor signaling pathway involved in metanephric glomerular mesangium cell migration (IDA)

Thanks, Yasmin

Reported by: yafaruque

Original Ticket: geneontology/ontology-requests/8214

[gocentral]

• assigned_to: nobody --> rfoulger

Original comment by: rebeccafoulger

[gocentral]

PMID should be 19460854

Original comment by: yafaruque

[gocentral]

Hi Yasmin,

After my email this morning, I had a chat to David about these. He agrees that the MC migration isn't part of development, but rather happens during a disease process (see PMID:19460854). Therefore in GO we shouldn't be capturing: positive regulation of cell migration by PDGFR signaling pathway ; GO:NEW (PDGF) or negative regulation of cell migration by negative regulation of PDGFR signaling pathway ; GO:NEW (adiponectin)

Are there any papers which describe PDGF-induced cell migration in a 'normal' state? If so, I can add terms in for that.

thanks, Becky

For my future reference: i. PDGF induces cell migration (which contributes to chronic kidney disease) ii. Adiponectin binds PDGF, inhibiting the interaction of PDGF with its receptor. iii. Adiponectin therefore counteracts the increased cell migration induced by PDGF.

Original comment by: rebeccafoulger

[gocentral]

Hi Becky,

I am currently trying to annotate the paper PMID:19019919 'PDGF receptor-{beta} modulates metanephric mesenchyme chemotaxis induced by PDGF AA in which the authors are performing migration experiments on normal and mutant (PDGFR-b -/-) embryonic mesenchymal mesangial cells to chow that PDGFB induces cell migration. (the 1st line of the introduction mentions that cell migration does occur in kidney development). Hence I still require the terms I asked for in the original request. In addition I will require the term : for annotation of PDGFB: GO:0010641 positive regulation of platelet-derived growth factor receptor signaling pathway --< GO:NEW positive regulation of platelet-derived growth factor receptor signaling pathway involved in metanephric glomerular mesangium cell migration (IDA) Thanks, Yasmin

Original comment by: yafaruque

[gocentral]

Also: PMID:10734101 shows embryonic metanephric mesenchyme cell migration in response to PDGFBB so I will require the new term GO:0072075 metanephric mesenchyme development --GO:NEW metanephric mesenchyme cell migration involved in metanephros development (IDA) thanks Y

Original comment by: yafaruque

[gocentral]

Hi Yasmin,

I'm doing this one in parts, so I can use TermGenie. I have added:

cell migration involved in kidney development ; GO:0035787 cell migration involved in metanephros development ; GO:0035788 metanephric mesenchymal cell migration ; GO:0035789 platelet-derived growth factor receptor-alpha signaling pathway ; GO:0035790 platelet-derived growth factor receptor-beta signaling pathway ; GO:0035791

I have added 'metanephric mesenchymal cell chemotaxis' as a narrow synonym for GO:0035789.

I will use TermGenie to add in regulation terms, then will connect them up with a term:

positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway ; GO:NEW

Both PGFR-beta and PGF-B are part of the signaling pathway so can be annotated directly to this term. Because in wild-type cells, PDGFR-beta suppresses signaling from PDGFR-alpha, I don't think it's correct to add a '+ve regulation of MMC migration by PGFR-alpha signaling pathway' because it doesn't get this far. Therefore, I would annotate PGFR-beta to just 'negative regulation of PGFR-alpha signaling pathway ; GO:NEW'. Let me know if you disagree tho.

Will update with IDs from TermGenie.

Thanks, Becky

A couple of notes: Both PMID:19019919 and PMID: 10734101 discuss migration of the metanephric mesenchymal cells (MMCs) rather than migration of the derived mesangial cells. Therefore I've just added the migration term in for the precursors.

For my future reference: 1/ Mesangial cells derive from metanephric mesenchymal cells (MMCs). 2/ Undifferentiated MMCs migrate from the mesenchyme into the cleft of the maturing glomerulus. Once in the developing glomerular cleft, they can proliferate.

Original comment by: rebeccafoulger

[gocentral]

Second of 3 parts:

Added via TermGenie: id: GO:2000584 name: negative regulation of platelet-derived growth factor receptor-alpha signaling pathway

id: GO:2000591 name: positive regulation of metanephric mesenchymal cell migration

(I've also added alll the other regulation terms for completeness).

Will connect up the terms when the regulation terms are in the live ontology, with: positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway ; GO:NEW

Original comment by: rebeccafoulger

[gocentral]

Finally, the term you've been waiting for is......

positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway ; GO:0035793

phew... I can close this SF now. thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-works-for-me

Original comment by: rebeccafoulger

[gocentral]

Hi Becky, I think for annotation of ADIPOQ_MOUSE (Q60994) I really needed the term GO:NEW negative regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway ; would you be able to create this term for me - I have just created this regulation term in TermGenie (ID: GO:1900238 Label: regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway) but don't know how to create the negative regulation term (not sure if we I am going about this the right way)

Yasmin

Original comment by: yafaruque

[gocentral]

• status: closed-works-for-me --> open-works-for-me

Original comment by: yafaruque

[gocentral]

sorry Becky, Please ignore this last comment! I had this as an outstanding SF request in P2GO and I just read through the previous comment sand your suggestion to use GO:2000584 name: negative regulation of platelet-derived growth factor receptor-alpha signaling pathway instead!

Original comment by: yafaruque

[gocentral]

• status: open-works-for-me --> closed-works-for-me

Original comment by: rebeccafoulger