Kidney Development

This page serves a placeholder for a future kidney development meeting, which will follow the lung development changes to the ontology.

Suggested GO Terms for Nephrogenesis (Meeting at HGU 22nd June 2009) List from the White Board – All are ‘Biological Process’

• Stem cell maintenance,
• Elective cell death,
• Cell division,
• Leaving the stem cell compartment,
• Mesenchymal cell condensation,
• Chemotaxis in mesenchymal cells,
• Sensing a quorum of cells / control of the number of cells in a cell group,
• Mesenchyme to epithelium transition,
• Formation of tight junctions,
• Formation of zona adherens,
• Formation of basement membrane,
• Epithelial cell polarization (apical/basal polarization),
• Epithelial patterning,
• Differentiation of cell types,
• Morphogenesis of epithelial tubules,
• Oriented mitosis,
• Cell shape change,
• Programmed cell death / apoptosis,
• Formation of renal vesicle,
• Formation of comma-shaped body,
• Formation of s-shaped body,
• Formation of glomerulus,
• Formation of mesangium,
• Formation of … each anatomical structure,
• Signalling to blood vessel-forming cells,
• Connection of nephron tublule to collecting duct,
• Migration of kidney (from pelvis to upper lumbar/ lower thoracic region).

Working list – adapted from the white board list by looking at existing terms in GO using QuickGO (working draft)

Please note that there are many more cell types and anatomical structures to add here, see below under differentiation of …. (cell type) and formation of.. (structure). This is something we should perhaps do soon, but probably working with experts in adult nephron anatomy at least some of whom we already collaborate with and may be able to help, for example Prof. Brigitte Kaissling in Zurich. Of course this is all quite coarse granularity so I expect we will be adding terms for some time.

My aim was simply to get the list to the state where existing GO terms are used where possible and to suggest terms where we think there may be none existing. I think this is worth the small effort since we can probably best judge whether an existing term suits. I don’t plan to go through GO to look for more terms at the moment, so am just using the terms we came up with in the white board list. I have added a few definitions just to see how easy it would be to adapt existing definitions to the case of the nephron.

Now that we have done this, I assume it’s over to Yasmin and colleagues to sort out our suggestions in relation to the GO DAG and GO conventions.

List – DD, JD Thursday, July 2, 2009

• GO:0035019 somatic stem cell maintenance,
• GO:0048864 stem cell development,
• GO:0048863 stem cell differentiation,
• GO:0048103 somatic stem cell division.

• Nephrogenic stem cell differentiation [Defn: The process whereby a relatively unspecialized cell acquires specialized features of a nephrogenic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.]
• Commitment of multipotent stem cells to the nephrogenic lineage [Defn: The initial commitment of cells whereby the developmental fate of a cell becomes restricted such that it will develop into some type of cell in the nephron.]
• Mesenchymal cell condensation involved in nephron development [Defn: the cell adhesion process by which nephron precursor mesenchyme cells adhere to one another to form the pretubular aggregate in the initial stages of nephron development.]
• chemoattraction of in mesenchymal cells involved in nephron development [Defn: I am not sure if there is sufficient evidence for the involvement of chenotaxis in the formation of the pretubular aggregate – Jamie? If not, I presume it should be deleted for the time being?]
• Sensing a quorum of cells / control of the number of cells in a cell group
• GO:0060231 mesenchymal to epithelial transition,
• Mesenchyme to epithelim transition in the metanephric kidney,
• GO:0010717 regulation of epithelial to mesenchymal transition,
• Formation of tight junctions,
• Formation of adherens junctions,
• Formation of basement membrane,
• GO:0045198 establishment of epithelial cell apical/basal polarity,
• Epithelial patterning of the nephron epithelium {Syn: segmentation of the nephron epithelium},
• GO:0002070 epithelial cell maturation,
  • Podocyte differentiation,
  • Proximal tubule cell differentiation,
  • Loop of Henle cell differentiation,
  • Distal tubule cell differentiation,
  • Connecting tubule cell differentiation,
  • ..........Differentiation of all other nephron cell types.
• Formation of renal vesicle,
• Formation of comma-shaped body,
• Formation of s-shaped body,
• Formation of glomerulus,
• Formation of mesangium,
• ..........Formation of each anatomical structure.
• Morphogenesis of epithelial tubules (I think this is not GO:0001838 embryonic epithelial tube formation or GO:0060562 epithelial tube morphogenesis because it is not the formation of the tube but the morphogenesis of its form from a spherical vesicle to a comma shape and thence to an S shape). What is the difference between GO:0001838 embryonic epithelial tube formation and GO:0060562 epithelial tube morphogenesis? The definitions are very similar. Pretty similar also to GO:0035239 Tube morphogenesis. We need something that does not denote the generation and organization of tubes, but their subsequent changes in shape. One possibility would be ‘comma-shaped body morphogenesis’, but it would be good to have a more general ancestor term so that one could link basic processes that occur in the morphogenesis of different forms of epithelial tube.
• Regulation of epithelial tubule diameter (is_a GO:0035296 regulation of tube diameter)
• Oriented mitosis (could not find such a term in GO – not GO:0008356 asymmetric cell division)
• Cell morphogenesis
• GO:0008360 regulation of cell shape,
• GO:0012501 programmed cell death,
• Signalling to blood vessel-forming cells (need to ask Jamie about this – is it GO:0060684 epithelial-mesenchymal cell signaling?)
• Connection of nephron tubule to collecting duct