A dynamic and expandable Digital 3D-Atlas MAKER for monitoring the temporal changes in tissue growth during hindbrain morphogenesis
Abstract
Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-atlas to monitor the changes in the growth of the neuronal differentiation domain in the zebrafish hindbrain upon time. DAMAKER integrates spatial and temporal data of cell populations, neuronal differentiation and brain morphogenesis, through in vivo imaging techniques paired with image analyses and segmentation tools. First, we generated a 3D-reference from several imaged hindbrains and segmented them using a trainable tool; these were aligned using rigid registration, revealing distribution of neuronal differentiation growth patterns along the axes. Second, we quantified the dynamic growth of the neuronal differentiation domain by in vivo neuronal birthdating experiments. We generated digital neuronal birthdating 3D-maps and revealed that the temporal order of neuronal differentiation prefigured the spatial distribution of neurons in the tissue, with an inner-outer differentiation gradient. Last, we applied it to specific differentiated neuronal populations such as glutamatergic and GABAergic neurons, as proof-of-concept that the digital birthdating 3D-maps could be used as a proxy to infer neuronal birthdate. As this protocol uses open-access tools and algorithms, it can be shared for standardized, accessible, tissue-wide cell population atlas construction.
Data availability
All data generated or analysed during this study are included in the manuscript or in the supplementary files.All code is available in https://github.com/cristinapujades/Blanc-et-al.-2022.
Article and author information
Author details
Funding
Agencia Estatal de Investigación (PGC2018-095663-B-I00)
- Cristina Pujades
Agencia Estatal de Investigación (PGC2018-101643-B-I00)
- Frederic Udina
Agencia Estatal de Investigación (CEX2018-000792-M)
- Matthias Blanc
- Cristina Pujades
Institució Catalana de Recerca i Estudis Avançats
- Cristina Pujades
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: Zebrafish (Dario rerio) were treated according to the Spanish/European regulations for the handling of animals in research. All protocols were approved by the Institutional Animal Care and Use Ethic Committee (Comitè Etica en Experimentació Animal, PRBB) and the Generalitat of Catalonia (Departament de Territori i Sostenibilitat), and they were implemented according to European regulations. The Project Licenses covering the proposed work (Ref 10642, Ref 10477, GC) pay particular attention to the 3Rs (Replacement, Reduction, Refinement).
Copyright
© 2022, Blanc et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 937
- views
-
- 186
- downloads
-
- 0
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Developmental Biology
- Neuroscience
Two major ligand-receptor signaling axes – endothelin Edn3 and its receptor Ednrb, and glial-derived neurotrophic factor (GDNF) and its receptor Ret – are required for migration of enteric nervous system (ENS) progenitors to the hindgut. Mutations in either component cause colonic aganglionosis, also called Hirschsprung disease. Here, we have used Wnt1Cre and Pax2Cre in mice to show that these driver lines label distinct ENS lineages during progenitor migration and in their terminal hindgut fates. Both Cre lines result in Hirschsprung disease when combined with conditional Ednrb or conditional Ret alleles. In vitro explant assays and analysis of lineage-labeled mutant embryos show that GDNF but not Edn3 is a migration cue for cells of both lineages. Instead, Edn3-Ednrb function is required in both for GDNF responsiveness albeit in different ways: by expanding the Ret+ population in the Pax2Cre lineage, and by supporting Ret function in Wnt1Cre-derived cells. Our results demonstrate that two distinct lineages of progenitors give rise to the ENS, and that these divergently utilize endothelin signaling to support migration to the hindgut.
-
- Developmental Biology
Maternal obesity has deleterious effects on the process of establishing oocyte DNA methylation; yet the underlying mechanisms remain unclear. Here, we found that maternal obesity disrupted the genomic methylation of oocytes using a high-fat diet (HFD) induced mouse model, at least a part of which was transmitted to the F2 oocytes and livers via females. We further examined the metabolome of serum and found that the serum concentration of melatonin was reduced. Exogenous melatonin treatment significantly reduced the hyper-methylation of HFD oocytes, and the increased expression of DNMT3a and DNMT1 in HFD oocytes was also decreased. These suggest that melatonin may play a key role in the disrupted genomic methylation in the oocytes of obese mice. To address how melatonin regulates the expression of DNMTs, the function of melatonin was inhibited or activated upon oocytes. Results revealed that melatonin may regulate the expression of DNMTs via the cAMP/PKA/CREB pathway. These results suggest that maternal obesity induces genomic methylation alterations in oocytes, which can be partly transmitted to F2 in females, and that melatonin is involved in regulating the hyper-methylation of HFD oocytes by increasing the expression of DNMTs via the cAMP/PKA/CREB pathway.