In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins
Abstract Organisms are far greater than the sum of their differentiated cells, as the function of most cell types emerges from their organisation into three-dimensional tissues. Yet, the mechanisms underlying architectural diversity remain poorly understood, partly due to a lack of methods for direc...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62127-9 |
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| _version_ | 1849343832626298880 |
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| author | Max Brambach Jana Wittmann Marvin Albert Jérôme Julmi Robert Bill Darren Gilmour |
| author_facet | Max Brambach Jana Wittmann Marvin Albert Jérôme Julmi Robert Bill Darren Gilmour |
| author_sort | Max Brambach |
| collection | DOAJ |
| description | Abstract Organisms are far greater than the sum of their differentiated cells, as the function of most cell types emerges from their organisation into three-dimensional tissues. Yet, the mechanisms underlying architectural diversity remain poorly understood, partly due to a lack of methods for directly comparing different tissue organisations. Here we establish nuQLOUD, an efficient imaging and computational framework that reduces complex tissues to clouds of nuclear positions, enabling the extraction of cell-type agnostic architectural features. Applying nuQLOUD to whole zebrafish embryos reveals that global tissue diversity can be efficiently reduced to two archetypes, termed ‘amorphous’ and ‘crystalline’. We investigate the role of cadherin cell adhesion molecules in controlling organisational diversity and demonstrate that their expression segregates along tissue-archetypal lines. Targeted perturbations identify N-cadherin as a general driver of the amorphous archetype. This organisation-centric approach provides a way to conceptualise tissue diversification and investigate the underlying mechanisms within a standardised, quantitative framework. |
| format | Article |
| id | doaj-art-2d3aabdd3cd84692823d9187de62233d |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-2d3aabdd3cd84692823d9187de62233d2025-08-20T03:42:52ZengNature PortfolioNature Communications2041-17232025-07-0116111510.1038/s41467-025-62127-9In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherinsMax Brambach0Jana Wittmann1Marvin Albert2Jérôme Julmi3Robert Bill4Darren Gilmour5Department of Molecular Life Sciences, University of ZurichDepartment of Molecular Life Sciences, University of ZurichDepartment of Molecular Life Sciences, University of ZurichDepartment of Molecular Life Sciences, University of ZurichDepartment of Molecular Life Sciences, University of ZurichDepartment of Molecular Life Sciences, University of ZurichAbstract Organisms are far greater than the sum of their differentiated cells, as the function of most cell types emerges from their organisation into three-dimensional tissues. Yet, the mechanisms underlying architectural diversity remain poorly understood, partly due to a lack of methods for directly comparing different tissue organisations. Here we establish nuQLOUD, an efficient imaging and computational framework that reduces complex tissues to clouds of nuclear positions, enabling the extraction of cell-type agnostic architectural features. Applying nuQLOUD to whole zebrafish embryos reveals that global tissue diversity can be efficiently reduced to two archetypes, termed ‘amorphous’ and ‘crystalline’. We investigate the role of cadherin cell adhesion molecules in controlling organisational diversity and demonstrate that their expression segregates along tissue-archetypal lines. Targeted perturbations identify N-cadherin as a general driver of the amorphous archetype. This organisation-centric approach provides a way to conceptualise tissue diversification and investigate the underlying mechanisms within a standardised, quantitative framework.https://doi.org/10.1038/s41467-025-62127-9 |
| spellingShingle | Max Brambach Jana Wittmann Marvin Albert Jérôme Julmi Robert Bill Darren Gilmour In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins Nature Communications |
| title | In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins |
| title_full | In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins |
| title_fullStr | In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins |
| title_full_unstemmed | In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins |
| title_short | In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins |
| title_sort | in toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins |
| url | https://doi.org/10.1038/s41467-025-62127-9 |
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