A snail tale and the chicken embryo

Nieto, M. Ángela

doi:10.1387/ijdb.170301mn

Cited by 5 publications

(4 citation statements)

References 53 publications

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“…By contrast, a number of comparative studies performed in several group of animals (chordates, insects, nematodes…) have revealed that development is flexible and that formation of homologous characters may rely on different mechanisms, a process known as developmental system drift (DSD) (3,(7)(8)(9)(10)(11)(12)(13)(14). In some cases, key GRN nodes have changed (for example the role of Snail/Slug genes in vertebrate neural crest (15)). Focusing on GRN edgesgene expression regulationvarious situations have been described, and conservation of CRM sequence at the DNA level does not necessarily correlate with conservation of activity.…”

Section: Introductionmentioning

confidence: 99%

Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos

Coulcher

Roure

Chowdhury

et al. 2020

eLife

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Ascidians with very similar embryos but highly divergent genomes are thought to have undergone extensive developmental system drift. We compared, in four species (Ciona and Phallusia for Phlebobranchia, Molgula and Halocynthia for Stolidobranchia), gene expression and gene regulation for a network of six transcription factors regulating peripheral nervous system (PNS) formation in Ciona. All genes, but one in Molgula, were expressed in the PNS with some differences correlating with phylogenetic distance. Cross-species transgenesis indicated strong levels of conservation, except in Molgula, in gene regulation despite lack of sequence conservation of the enhancers. Developmental system drift in ascidians is thus higher for gene regulation than for gene expression and is impacted not only by phylogenetic distance, but also in a clade-specific manner and unevenly within a network. Finally, considering that Molgula is divergent in our analyses, this suggests deep conservation of developmental mechanisms in ascidians after 390 My of separate evolution.

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Section: Introductionmentioning

confidence: 99%

Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos

Coulcher

Roure

Chowdhury

et al. 2020

eLife

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“…2 D). The first group includes genes that are associated between NC and a closely-related cell type in only one organism (e.g., NC and neural plate in frog: sox2, sox3 (neural plate markers [ 26 ]), snai2 (neural crest marker [ 27 ]) , hes1, zic1 (neural border markers [ 20 ]); NC and midhindbrain in mice: fodx3, gadd45a (neural crest marker [ 28 ]) , mdk, ptn (neural crest-derived neurons markers [ 29 ])). If this gene expression signature was the consequence of the evolutionary divergence of function, this could be studied using the scRNA-seq of the ancestor organisms.…”

Section: Resultsmentioning

confidence: 99%

scEvoNet: a gradient boosting-based method for prediction of cell state evolution

2023

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Background Exploring the function or the developmental history of cells in various organisms provides insights into a given cell type's core molecular characteristics and putative evolutionary mechanisms. Numerous computational methods now exist for analyzing single-cell data and identifying cell states. These methods mostly rely on the expression of genes considered as markers for a given cell state. Yet, there is a lack of scRNA-seq computational tools to study the evolution of cell states, particularly how cell states change their molecular profiles. This can include novel gene activation or the novel deployment of programs already existing in other cell types, known as co-option. Results Here we present scEvoNet, a Python tool for predicting cell type evolution in cross-species or cancer-related scRNA-seq datasets. ScEvoNet builds the confusion matrix of cell states and a bipartite network connecting genes and cell states. It allows a user to obtain a set of genes shared by the characteristic signature of two cell states even between distantly-related datasets. These genes can be used as indicators of either evolutionary divergence or co-option occurring during organism or tumor evolution. Our results on cancer and developmental datasets indicate that scEvoNet is a helpful tool for the initial screening of such genes as well as for measuring cell state similarities. Conclusion The scEvoNet package is implemented in Python and is freely available from https://github.com/monsoro/scEvoNet. Utilizing this framework and exploring the continuum of transcriptome states between developmental stages and species will help explain cell state dynamics.

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“…Researchers in the field of EMP have employed various animal models, including as C. elegans, Drosophila Melanogaster, chick embryos, zebrafish and mice to study the in vivo dynamics of phenotypic plasticity in developmental EMT and cancer EMP (Jimenez et al, 2016;Gómez-Cuadrado et al, 2017;Nieto, 2018;Stuelten et al, 2018;Campbell et al, 2019). Genetically engineered mouse models and patient-derived xenografts (PDXs) have been observed to recapitulate metastatic and organ homing properties similar to clinical specimens (Sikandar et al, 2017).…”

Section: Current Modalities To Investigate Plasticitymentioning

confidence: 99%

New Insights Into the Role of Phenotypic Plasticity and EMT in Driving Cancer Progression

Bhatia

Wang

Toh

et al. 2020

Front. Mol. Biosci.

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Tumor cells demonstrate substantial plasticity in their genotypic and phenotypic characteristics. Epithelial-mesenchymal plasticity (EMP) can be characterized into dynamic intermediate states and can be orchestrated by many factors, either intercellularly via epigenetic reprograming, or extracellularly via growth factors, inflammation and/or hypoxia generated by the tumor stromal microenvironment. EMP has the capability to alter phenotype and produce heterogeneity, and thus by changing the whole cancer landscape can attenuate oncogenic signaling networks, invoke antiapoptotic features, defend against chemotherapeutics and reprogram angiogenic and immune recognition functions. We discuss here the role of phenotypic plasticity in tumor initiation, progression and metastasis and provide an update of the modalities utilized for the molecular characterization of the EMT states and attributes of cellular behavior, including cellular metabolism, in the context of EMP. We also summarize recent findings in dynamic EMP studies that provide new insights into the phenotypic plasticity of EMP flux in cancer and propose therapeutic strategies to impede the metastatic outgrowth of phenotypically heterogeneous tumors.

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A snail tale and the chicken embryo

Cited by 5 publications

References 53 publications

Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos

Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos

scEvoNet: a gradient boosting-based method for prediction of cell state evolution

New Insights Into the Role of Phenotypic Plasticity and EMT in Driving Cancer Progression

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