Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches
This work demonstrates the efficiency of the software IVEN (Internal Versus External Neighbourhood) in describing the dynamic changes in neighbourhoods of all cell lineages in the mammalian blastocyst. In the mouse model, the primitive endoderm (PrE)/epiblast (Epi) dichotomy is established during bl...
| Autores: | , |
|---|---|
| Formato: | artículo |
| Fecha de publicación: | 2025 |
| País: | España |
| Recursos: | Universidad Autónoma de Madrid |
| Repositorio: | Biblos-e Archivo. Repositorio Institucional de la UAM |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.uam.es:10486/743520 |
| Acesso em linha: | https://hdl.handle.net/10486/743520 https://dx.doi.org/10.2478/aspr-2025-0024 |
| Access Level: | acceso abierto |
| Palavra-chave: | Blastocyst neighbourhood classification distance primitive endoderm epiblast cavity Biología y Biomedicina / Biología |
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Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approachesde la Fuente, RobertoForsyth, Jessica E.Blastocystneighbourhoodclassificationdistanceprimitive endodermepiblastcavityBiología y Biomedicina / BiologíaThis work demonstrates the efficiency of the software IVEN (Internal Versus External Neighbourhood) in describing the dynamic changes in neighbourhoods of all cell lineages in the mammalian blastocyst. In the mouse model, the primitive endoderm (PrE)/epiblast (Epi) dichotomy is established during blastocyst formation, which results in a seemingly random distribution of cells from both lineages within the ICM (‘salt and pepper’ model). Nevertheless, differences in cell potency, plasticity and distribution suggest that specific cell traits, such as environment, might be defining the ultimate fate acquisition. We have tested the new functionalities in the latest IVEN version and its efficiency to explore the changes in cell distribution within cell lineages and sub-populations. For this purpose, we have developed pipelines that combine functionalities from the imaging software (IMARIS) with IVEN internal algorithms to provide an insight into the dynamic cell neighbourhood within the early blastocyst. IVEN returns detailed reconstructions and numerical arrays that can be interpreted to describe the evolution of cell neighbourhoods within and between lineages. Thus, we have been able to identify specific subsets of cells within the TE and the ICM lineages depending on their relative position to the blastocyst cavity and revealed distinct neighbourhood features. IVEN analyses were essential to provide quantitative understanding of the intrinsic dynamics of the mouse blastocyst. Our approach demonstrates the accuracy of IVEN as a descriptive analytical tool and offers the possibility of applying it on to other systems to uncover differences between speciesThe authors wish to thank Dr. Berenika Plusa for her insights and helpful discussions of the analyses presented in this study. R.d.l.F. was supported by NCN 2021/05/X/NZ3/00704Institute of Genetics and Animal Biotechnology of the Polish Academy of SciencesDepartamento de BiologíaFacultad de Ciencias20252025-10-07research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10486/743520https://dx.doi.org/10.2478/aspr-2025-0024reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/7435202026-06-23T12:46:27Z |
| dc.title.none.fl_str_mv |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches |
| title |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches |
| spellingShingle |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches de la Fuente, Roberto Blastocyst neighbourhood classification distance primitive endoderm epiblast cavity Biología y Biomedicina / Biología |
| title_short |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches |
| title_full |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches |
| title_fullStr |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches |
| title_full_unstemmed |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches |
| title_sort |
Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches |
| dc.creator.none.fl_str_mv |
de la Fuente, Roberto Forsyth, Jessica E. |
| author |
de la Fuente, Roberto |
| author_facet |
de la Fuente, Roberto Forsyth, Jessica E. |
| author_role |
author |
| author2 |
Forsyth, Jessica E. |
| author2_role |
author |
| dc.contributor.none.fl_str_mv |
Departamento de Biología Facultad de Ciencias |
| dc.subject.none.fl_str_mv |
Blastocyst neighbourhood classification distance primitive endoderm epiblast cavity Biología y Biomedicina / Biología |
| topic |
Blastocyst neighbourhood classification distance primitive endoderm epiblast cavity Biología y Biomedicina / Biología |
| description |
This work demonstrates the efficiency of the software IVEN (Internal Versus External Neighbourhood) in describing the dynamic changes in neighbourhoods of all cell lineages in the mammalian blastocyst. In the mouse model, the primitive endoderm (PrE)/epiblast (Epi) dichotomy is established during blastocyst formation, which results in a seemingly random distribution of cells from both lineages within the ICM (‘salt and pepper’ model). Nevertheless, differences in cell potency, plasticity and distribution suggest that specific cell traits, such as environment, might be defining the ultimate fate acquisition. We have tested the new functionalities in the latest IVEN version and its efficiency to explore the changes in cell distribution within cell lineages and sub-populations. For this purpose, we have developed pipelines that combine functionalities from the imaging software (IMARIS) with IVEN internal algorithms to provide an insight into the dynamic cell neighbourhood within the early blastocyst. IVEN returns detailed reconstructions and numerical arrays that can be interpreted to describe the evolution of cell neighbourhoods within and between lineages. Thus, we have been able to identify specific subsets of cells within the TE and the ICM lineages depending on their relative position to the blastocyst cavity and revealed distinct neighbourhood features. IVEN analyses were essential to provide quantitative understanding of the intrinsic dynamics of the mouse blastocyst. Our approach demonstrates the accuracy of IVEN as a descriptive analytical tool and offers the possibility of applying it on to other systems to uncover differences between species |
| publishDate |
2025 |
| dc.date.none.fl_str_mv |
2025 2025-10-07 |
| dc.type.none.fl_str_mv |
research article http://purl.org/coar/resource_type/c_2df8fbb1 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/10486/743520 https://dx.doi.org/10.2478/aspr-2025-0024 |
| url |
https://hdl.handle.net/10486/743520 https://dx.doi.org/10.2478/aspr-2025-0024 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ |
| dc.rights.openaire.fl_str_mv |
info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
| dc.publisher.none.fl_str_mv |
Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences |
| publisher.none.fl_str_mv |
Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences |
| dc.source.none.fl_str_mv |
reponame:Biblos-e Archivo. Repositorio Institucional de la UAM instname:Universidad Autónoma de Madrid |
| instname_str |
Universidad Autónoma de Madrid |
| reponame_str |
Biblos-e Archivo. Repositorio Institucional de la UAM |
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Biblos-e Archivo. Repositorio Institucional de la UAM |
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| repository.mail.fl_str_mv |
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1869413221346050048 |
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15.811543 |