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2.5D tubulogenesis

ABSTRACT: Hepatocyte growth factor-induced three-dimensional tubulogenesis (3D) is a simple and highly controllable system for studying epithelial tubule initiation and maintenance. However, due to its limited efficiency and asynchronous development, isolating genes associated with specific morphological changes observed during tubule formation has been unfeasible. Here we report a significantly enhanced in vitro culture method called 2.5-dimensional tubulogenesis (2.5D). Detailed image analysis of 2.5D has revealed morphologically distinct stages -- monolayer, extension, and tubule -- and finds that these stages display in a highly synchronized manner. Using time-course transcriptional profiling, we collected genes whose expression changes specifically associate with extension and tubule stage. Time-course microarrays to identify genes whose temporal regulation is associated with extension and tubule stages. Four biological replicates for each stage (monolayer, extension, and tubule).

ORGANISM(S): Canis lupus familiaris

SUBMITTER: SH Kwon

PROVIDER: E-GEOD-25514 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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2.5D tubulogenesis

Project description:Hepatocyte growth factor-induced three-dimensional tubulogenesis (3D) is a simple and highly controllable system for studying epithelial tubule initiation and maintenance. However, due to its limited efficiency and asynchronous development, isolating genes associated with specific morphological changes observed during tubule formation has been unfeasible. Here we report a significantly enhanced in vitro culture method called 2.5-dimensional tubulogenesis (2.5D). Detailed image analysis of 2.5D has revealed morphologically distinct stages -- monolayer, extension, and tubule -- and finds that these stages display in a highly synchronized manner. Using time-course transcriptional profiling, we collected genes whose expression changes specifically associate with extension and tubule stage.

2010-12-24 | GSE25514 | GEO

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2007-07-06 | E-GEOD-1690 | biostudies-arrayexpress

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Comparative proteomic analysis of kidney distal convoluted tubule and cortical collecting duct cells following long-term hormonal stimulation

Project description:The distal convoluted tubule (DCT) and the cortical collecting ducts (CCD) are portions of renal tubule that are partly responsible for maintaining the systemic concentrations of potassium, sodium, calcium and magnesium. Despite being structurally similar, DCT and CCD cells have different transport capabilities due to a variety of different membrane-associated transport proteins. However, DCT and CCD cells appear to be modulated via the same hormones. The objective of this study was assess the differential response of DCT and CCD cells to long-term exposure to the hormones vasopressin or angiotensin II, both of which modulate DCT and CCD cells differently. Mass spectrometry based quantitative proteomics was used to profile the differential proteome between DCT and CCD.

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Gene expression change in Gata2 conditional knockout mice adult renal collecting duct

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2013-11-19 | E-GEOD-52448 | biostudies-arrayexpress

Canis lupus familiaris

Project description:2.5D tubulogenesis

| PRJNA133765 | ENA

Proteome profiling of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells revealed an unexpected deviation between 2D monolayer and 3D spheroid model cultures.

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2021-11-15 | PXD015410 | Pride

Comparison of spheroid-based 3-dimensional culture to monolayer of larynx carcinoma cell line HLaC78.

Project description:In vitro proliferation and/or invasion tests (such as MTT assay, Boyden Chamber Assay, Scratch assay) using established and well-characterized cell lines can provide easy and reproducible tools to investigate anti-tumour or anti-invasion agents ex vivo. However, in vivo cells in a tissue context interact with neighbouring cells and extracellular matrix components. In 2-dimensional monolayer cultures cells tend to loose tissue-specific properties. 2-D culture models therefore seem unsuitable to mimic the behaviour of cells in a natural, 3-dimensional microenvironment, especially for testing of growth or invasion inhibiting substances. Spheroids on the other hand resemble in many aspects solid, non-vascularized tumour tissue. Within this study the larynx carcinoma cell line HLaC78 was used as a model for comparing overall gene expression in 2D monolayer culture with 72 hrs old HLaC78 multicellular spheroids, providing evidence for extensive restructuring of gene expression in the 3-dimensional context.

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