Kidney - Agenda for Kidney Development Ontology Content Meeting

Please suggest agenda items, relevant papers and other information relating to kidney development GO terms that you would like discussed at this workshop, to enable us to form an agenda.

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Participants

GO annotators	GO Editors	Kidney Development Experts
Dr Yasmin Alam-Faruque (GOA/EBI) Dr Emily Dimmer (GOA/EBI) Dr Rachael Huntley (GOA/EBI) Dr Rebecca Foulger (UniProt/Xenopus/EBI) Dr Susan Tweedie (Flybase/EBI) Dr Doug Howe (ZFIN/USA) (via Skype)	Dr David Hill (Jax/USA) Dr Midori Harris (EBI) Dr Jane Lomax (EBI)	Professor Adrian Woolf (ICH) Dr Duncan Davidson (GUDMAP) Professor Randall Thomas (IBISC CNRS) Professor Jamie Davies (GUDMAP) (available pm via phone/email if needed) Dr Bernard de Bono (Virtual Physiological Human, EBI)

Location

EMBL-EBI, Room C202/203 - shared facilities, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD. Date: Monday 25th January 2010, 9:30am to 5pm

• Travel instructions to the EBI, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD [1]
• Further information about the on-site accommodation [2]

Programme

9:15am	Tea/ Coffee and Cookies
9:30am	Welcome and introduction	Yasmin
9:35am	Introduction to GO	David Hill
9:45am	Kidney precursor cells and tissues (segmentation) * Development of kidney field * Nephrogenic stem cell differentiation. * Sensing a quorum of cells / control of the number of cells in a cell group * (Mesonephric/metanephric) mesenchyme-epithelial transition * Formation of tight junctions/ adherens junctions/ basement membrane, * formation of pronephric-, mesonephric-, metanephric-specific terms? * SF 2859892: specification of kidney anlage *PMID 18715948 * SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600 * SF 2916204: mesenchymal cell differentiation involved in kidney development *PMID 12399320 and SF 2929915 mesenchymal cell differentiation involved in urinary tract development *PMID 17442697 * SF 2926832: metanephric + nephrogenic mesenchyme morphogenesis PMID 15342483
11am	Coffee break
11:20am	Kidney morphogenesis - Kidney structure formation * Cell morphogenesis * Formation of renal vesicle, * Formation of comma-shaped body/ S-shaped body/ glomerulus * Formation of mesangium, * Macula densa formation/ development * Oriented mitosis * SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600 * SF 2903833: kidney glomus development *PMID 10572058 * SF 2905937: Glomerular mesangium PMID 8910451 and PMID 10077614 * SF 2928268: specification of renal capsule PMID 15634693
12:30pm	Lunch @ on-site campus restaurant
1:30pm	Anatomical structure development/ formation * Epithelial patterning of the nephron epithelium: proximal/distal nephron tubule patterning/ specification/ identity/ development * Regulation of epithelial tubule diameter (is_a GO:0035296 regulation of tube diameter) * Morphogenesis of epithelial tubules * mesonephric tubule (anterior and posterior in mouse) * new children of GO:0002070 epithelial cell maturation: podocyte/ proximal tubule/ loop of Henle/ distal tubule/ connecting tubule cell differentiation (and other nephron cell types) * nephric duct/ tubule specification/ differentiation/ morphogenesis * Collecting duct system development/ formation/ differentiation * Connection of nephron tubule to collecting duct * Connecting tubule development; * SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385 * SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600 * SF 2907403 Podocyte development/ differentiation PMID 19050011
3pm	Coffee break
3:20pm	Continue with Anatomical structure development/ formation * kidney proximal tubule development/ specification; proximal convoluted tubule; * kidney intermediate tubule development/ identity/ specification:- thin descending limb; thin ascending limb; thick ascending limb; * kidney distal tubule development/ specification; distal convoluted tubule * Signalling to blood vessel-forming cells/ renal vasculature development (GO:0060684 epithelial-mesenchymal cell signaling?) * renal smooth muscle cell differentiation * SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385 * SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600 * SF 2903833: kidney glomus development *PMID 10572058 * SF 2929817 Ureter development *PMID 17442697 * SF 2930545 Glomerular capillary formation *PMID 18272846
5pm	Close

KDM Minutes

KDM Minutes

Current Kidney Development Ontology Terms

The currently available kidney development process ontology (November 2009) [[3]]
GO:0001656 GO:0001657 GO:0001658 GO:0001822 GO:0001823 GO:0032835 GO:0032836 GO:0034671 GO:0034672 GO:0048793 GO:0060675 GO:0060676 GO:0060677 GO:0060678 GO:0060679 GO:0060680 GO:0060681 GO:0060682

• chart [4]

Relevant papers and other resources

• Kidney Development Review Papers:
  • Mammalian reviews:
    • PMID 19906853 Advances in early kidney specification, development and patterning. Dressler M 2009. Talks about the essential roles of intrinsic nuclear factors and secreted signaling molecules in specifying renal epithelial stem cells and their self-renewal, in driving the complex dynamics of epithelial cell branching morphogenesis, and in nephron patterning.
    • PMID 15554941 Transcriptional control of kidney development. Bouchard M. 2004. Talks about genes involved in nephric lineage specification (Pax2/Pax8/Lim1/Bmp4/Wt1/GDNF1/Eya1/Foxc1); metanephros development - UB positioning, induction, nephron induction, ureter branching, Stromal cell differentiation(Gdnf1/Eya1/Foxc1/2/Slit2/Robo2/Bmp4/Pax2/Hox11(HoxA11/C11/D11)/ Sall1/Wt1/Six1/Wnt4/Emx2/Gata3/BF2/Pod1/Pbx21.
    • PMID 15380247 Recent genetic studies of mouse kidney development. Yu J, McMahon AP, Valerius MT. 2004. Has a nice diagram of the stages of nephron formation on p.551. Also lists genes investigated with particular molecular regulation of outgrowth of the uteric bud and regulation of tubulogenesis (Table 1; p552 - Gdf1, Six1, Slit2/Robo2, Wnt1, Fras1+Grip1, Pod1, Pbx1, Brn1, Psen1/2).
    • PMID 16760375 Role of transcriptional networks in coordinating early events during kidney development. Boyle S, de Caestecker Mark. 2006. Has nice diagrams of stages of early mammalian kidney development. Reviews transcription factors in mesenephric mesenchyme: Eya1/ Foxc1/2/ Hoxa/c/d11/ Pax2/ Pbx1/ Rar-alpha/beta2/ Sall1/ Six1/ Wt1.
    • PMID 12094231 Coordinating early kidney development: lessons from gene targeting. Vainio S, Lin Y. 2002. Nice diagrams of kidney development. List of genes essential for early kidney development (Transcription Factors: Emx2/Eya1/Foxc1/Foxd1/Pax2/Rara,Rarb/Sall1/Wt1; Growth factors: Bmp4/Bmp7/Fgf7/Gdnf/Wnt4; Growth factors/receptors: Gfra1/Notch2/Ret; Proteoglycans and their biosynthetic enzymes: Hs2st/Gpc3).

• Other resources:
  • Kidney Development Websites:
    • Mouse Anatomy Browser - [5]
    • FMA human anatomy browser- [6]
    • GUDMAP browser - [7]
      • Metanephros [8]
      • renal vesicle [9]
  • Kidney Development GO wiki [10]
  • Loop of Henle GO Cocuration wiki [11]

Notes

• Added KDM acronym to any NTR via SF relating to kidney development

• All KDM requests currently in SF [12]

• Related terms recently requested:
  • SF 2932119 -ive regn of GO:0060681 PMID 17118062
  • SF 2929886 BMP signaling involved in urinary tract segmentation PMID 17442697
  • SF 2929817 ureter development/differentiation/morphogenesis PMID 17442697
  • SF 2928381 ureteric peristalsis PMID 18776146

• Recently committed NTR nephrogenesis-related GO terms
  • (SF 2884040 metanephric mesenchyme to epithelial transition terms *PMID 15843474) (November 2009).
  • (SF 2907000 *PMID 10021330) Addition of 'Nephrogenesis' as a 'related' synonym of 'Kidney Development'. BMP4 (human) Induction of nephrogenesis: NTR: "nephric duct morphogenesis" and NTR "positive regulation of kidney development".(December 2009)
  • (SF 2914121 +ive and -ive regulation of branching involved in ureteric bud morphogenesis and +ive and -ive regulation of glomerulus development PMID 12141440) (December 2009)
  • SF 2930642 cellular response to dexamethasone stimulus PMID 17537984 (January 2010)

• GO:0060677 ureteric bud elongation (Def: The process by which the ureteric bud grows along its axis) - does this term cover ureteric bud invasion? (the initial key step of metanephros devpt, the ureteric bud invades the mesenchyme and induces epithelialization and differentiation of the mesenchyme into the glomeruli, the Loop of Henle and the proximal and distal tubules - see PMID 18470945|PMID 11688560). If so, need to improve definition.

• Keep an eye on definition compatability across species/taxa

Ontology Editing

Midori Harris and David Hill are working through terms added during the meeting and the SF items. The first changes from the meeting were committed to the live GO on February 8, 2010, in gene_ontology_write.obo revision 1.1010.

The changes committed are summarized below and in the CVS log, and shown in detail in two diff files, one generated by the obodiff utility and the other by the UNIX diff utility.

February 8, 2010

2010-02-08

confirmed definition of 'kidney development' GO:0001822; adjusted parentage

definition adjustments:
 GO:0001759	induction of an organ
 GO:0061005	cell differentiation involved in kidney development

added synonyms:
  GO:0061004	pattern specification involved in kidney development

new terms:
  GO:0072001	renal system development
  GO:0072002	Malpighian tubule development
  GO:0072003	kidney rudiment formation
  GO:0072004	kidney field specification
  GO:0072005	maintenance of kidney identity
  GO:0072006	nephron development
  GO:0072007	mesangial cell differentiation
  GO:0072008	glomerular mesangial cell differentiation
  GO:0072009	nephron epithelium development
  GO:0072010	glomerular epithelium development
  GO:0072011	glomerular endothelium development
  GO:0072012	glomerulus vasculature development
  GO:0072013	glomus development
  GO:0072014	proximal tubule development
  GO:0072015	glomerular visceral epithelial cell development
  GO:0072016	glomerular parietal epithelial cell development
  GO:0072017	distal tubule development
  GO:0072018	intermediate tubule development
  GO:0072019	proximal convoluted tubule development
  GO:0072020	proximal straight tubule development
  GO:0072021	ascending thin limb development
  GO:0072022	descending thin limb development
  GO:0072023	thick ascending limb development
  GO:0072024	macula densa development
  GO:0072025	distal convoluted tubule development
  GO:0072026	distal straight tubule development
  GO:0072027	connecting tubule development
  GO:0072028	nephron morphogenesis
  GO:0072029	long nephron development
  GO:0072030	short nephron development
  GO:0072031	S1 development
  GO:0072032	S2 development
  GO:0072033	renal vesicle formation
  GO:0072034	positive regulation of renal vesicle formation
  GO:0072035	pre-tubular aggregate formation
  GO:0072036	mesenchymal to epithelial transition involved in renal vesicle formation
  GO:0072037	mesenchymal stem cell differentiation involved in nephron morphogenesis
  GO:0072038	mesenchymal stem cell maintenance involved in nephron morphogenesis
  GO:0072039	regulation of mesenchymal stem cell apoptosis involved in nephron morphogenesis
  GO:0072040	negative regulation of mesenchymal stem cell apoptosis involved in nephron morphogenesis
  GO:0072041	positive regulation of mesenchymal stem cell apoptosis involved in nephron morphogenesis
  GO:0072042	regulation of mesenchymal stem cell proliferation involved in nephron morphogenesis
  GO:0072043	regulation of pre-tubular aggregate formation by cell-cell signaling
  GO:0072044	collecting duct development
  GO:0072045	convergent extension involved in nephron morphogenesis
  GO:0072046	establishment of planar polarity involved in nephron morphogenesis
  GO:0072047	proximal/distal pattern formation involved in nephron development
  GO:0072048	renal system pattern specification
  GO:0072049	comma-shaped body morphogenesis
  GO:0072050	S-shaped body morphogenesis
  GO:0072051	juxtaglomerular apparatus development
  GO:0072052	juxtaglomerulus cell differentiation
  GO:0072053	renal inner medulla development
  GO:0072054	renal outer medulla development
  GO:0072055	renal cortex development
  GO:0072056	pyramids development
  GO:0072057	inner stripe development
  GO:0072058	outer stripe development
  GO:0072059	cortical collecting duct development
  GO:0072060	outer medullary collecting duct development
  GO:0072061	inner medullary collecting duct development
  GO:0072062	S1 cell differentiation
  GO:0072063	short descending thin limb development
  GO:0072064	long descending thin limb development
  GO:0072065	long descending thin limb bend development
  GO:0072066	prebend segment development
  GO:0072067	early distal convoluted tubule development
  GO:0072068	late distal convoluted tubule development
  GO:0072069	DCT cell differentiation
  GO:0072070	loop of Henle development
  GO:0072071	interstitial cell differentiation
  GO:0072072	kidney stroma development
  GO:0072073	kidney epithelium development
  GO:0072074	kidney mesenchyme development
  GO:0072075	metanephric mesenchyme development
  GO:0072076	nephrogenic mesenchyme development
  GO:0072077	renal vesicle morphogenesis
  GO:0072078	nephron tubule morphogenesis
  GO:0072079	nephron tubule formation
  GO:0072080	nephron tubule development
  GO:0072081	specification of nephron tubule identity
  GO:0072082	specification of proximal tubule identity
  GO:0072083	specification of intermediate tubule identity
  GO:0072084	specification of distal tubule identity
  GO:0072085	specification of connecting tubule identity
  GO:0072086	specification of loop of Henle identity
  GO:0072087	renal vesicle development
  GO:0072088	nephron epithelium morphogenesis
  GO:0072089	stem cell proliferation
  GO:0072090	mesenchymal stem cell proliferation involved in nephron morphogenesis
  GO:0072091	regulation of stem cell proliferation

February 22, 2010

Added new terms for these SF items (more information in comments):

• Glomerular mesangium
• Podocyte development/ differentiation
• head kidney development
• specification of renal capsule
• metanephric + nephrogenic mesenchyme morphogenesis
• mesenchymal cell proliferation involved in kidney