EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways

Nature Methods, Год журнала: 2023, Номер 20(6), С. 815 - 823

Опубликована: Май 8, 2023

Abstract Evolutionarily conserved signaling pathways are essential for early embryogenesis, and reducing or abolishing their activity leads to characteristic developmental defects. Classification of phenotypic defects can identify the underlying mechanisms, but this requires expert knowledge classification schemes have not been standardized. Here we use a machine learning approach automated phenotyping train deep convolutional neural network, EmbryoNet, accurately zebrafish mutants in an unbiased manner. Combined with model time-dependent trajectories, identifies classifies high precision caused by loss function seven major relevant vertebrate development. Our algorithms wide applications biology robustly evolutionarily distant species. Furthermore, using high-throughput drug screens, show that EmbryoNet resolve mechanism action pharmaceutical substances. As part work, freely provide more than 2 million images were used test EmbryoNet.

Язык: Английский

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Context-dependent TGFβ family signalling in cell fate regulation

Nature Reviews Molecular Cell Biology, Год журнала: 2023, Номер 24(12), С. 876 - 894

Опубликована: Авг. 18, 2023

Язык: Английский

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An improved Erk biosensor detects oscillatory Erk dynamics driven by mitotic erasure during early development

Developmental Cell, Год журнала: 2023, Номер 58(23), С. 2802 - 2818.e5

Опубликована: Сен. 15, 2023

Extracellular signal-regulated kinase (Erk) signaling dynamics elicit distinct cellular responses in a variety of contexts. The early zebrafish embryo is an ideal model to explore the role Erk vivo, as gradient activated diphosphorylated (P-Erk) induced by fibroblast growth factor (Fgf) at blastula margin. Here, we describe improved Erk-specific biosensor, which term modified translocation reporter (modErk-KTR). We demonstrate utility this biosensor vitro and developing Drosophila embryos. Moreover, show that Fgf/Erk dynamic coupled tissue during both development. activity rapidly extinguished just prior mitosis, refer mitotic erasure, inducing periods inactivity, thus providing source heterogeneity asynchronously dividing tissue. Our transgenic lines represent important resource for interrogating vivo.

Язык: Английский

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Combinatorial interpretation of BMP and WNT controls the decision between primitive streak and extraembryonic fates

Cell Systems, Год журнала: 2024, Номер 15(5), С. 445 - 461.e4

Опубликована: Апрель 30, 2024

Язык: Английский

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Optogenetic control of Nodal signaling patterns

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 12, 2024

Abstract A crucial step in early embryogenesis is the establishment of spatial patterns signaling activity. Tools to perturb morphogen signals with high resolution space and time can help reveal how embryonic cells decode these make appropriate fate decisions. Here, we present new optogenetic reagents an experimental pipeline for creating designer Nodal live zebrafish embryos. receptors were fused light-sensitive heterodimerizing pair Cry2/CIB1N, Type II receptor was sequestered cytosol. The improved optoNodal2 eliminate dark activity improve response kinetics, without sacrificing dynamic range. We adapted ultra-widefield microscopy platform parallel light patterning up 36 embryos demonstrated precise control over downstream gene expression. Patterned activation drove precisely controlled internalization endodermal precursors. Further, used patterned illumination generate synthetic mutants, rescuing several characteristic developmental defects. This study establishes toolkit systematic exploration

Язык: Английский

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A geometrical model of cell fate specification in the mouse blastocyst

Development, Год журнала: 2024, Номер 151(8)

Опубликована: Апрель 2, 2024

The lineage decision that generates the epiblast and primitive endoderm from inner cell mass (ICM) is a paradigm for fate specification. Recent mathematics has formalized Waddington's landscape metaphor proven decisions in detailed gene network models must conform to small list of low-dimensional stereotypic changes called bifurcations. most plausible bifurcation ICM so-called heteroclinic flip we define elaborate here. Our re-analysis recent data suggests there sufficient movement so FGF signal, which drives decision, can be treated as spatially uniform. We thus extend model single entire by means self-consistently defined time-dependent signal. This consistent with available propose additional dynamic experiments test it further. demonstrates simplified, quantitative intuitively transparent descriptions are possible when attention shifted specific genes lineages. very any situation where embryo needs control over relative proportions two fates morphogen feedback.

Язык: Английский

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c-JUN: a chromatin repressor that limits mesoderm differentiation in human pluripotent stem cells

Nucleic Acids Research, Год журнала: 2025, Номер 53(3)

Опубликована: Янв. 24, 2025

Abstract Cell fate determination at the chromatin level is not fully comprehended. Here, we report that c-JUN acts on loci to limit mesoderm cell specification as cells exit pluripotency. Although widely expressed across various types in early embryogenesis, it essential for maintaining Instead, functions a repressor constrain development while having negligible impact ectoderm differentiation. interacts with MBD3–NuRD complex, which helps maintain low accessibility state mesoderm-related genes during differentiation of human pluripotent stem into mesoderm. Furthermore, specifically inhibits activation key factors, such EOMES and GATA4. Knocking out or inhibiting JNK inhibitor can alleviate this suppression, promoting Consistently, knockdown MBD3 enhances generation, whereas overexpression impedes it. Overexpressing redirects toward fibroblast-like lineage. Collectively, our findings suggest regulator restrict fate.

Язык: Английский

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Small Molecules and Epigenetic Modifiers in Facilitating Pancreatic β-cell Formation: A Comprehensive Insight

Advances in experimental medicine and biology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

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Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo

Development, Год журнала: 2023, Номер 150(17)

Опубликована: Авг. 21, 2023

Positional information in development often manifests as stripes of gene expression, but how form remains incompletely understood. Here, we use optogenetics and live-cell biosensors to investigate the posterior brachyenteron (byn) stripe early Drosophila embryos. This depends on interpretation an upstream ERK activity gradient expression two target genes, tailless (tll) huckebein (hkb), that exert antagonistic control over byn. We find high or low doses signaling produce transient sustained byn respectively. Although tll transcription is always rapidly induced, hkb converts graded inputs into a variable time delay. Nuclei thus interpret amplitude through relative timing transcription. Antagonistic regulatory paths acting different timescales are hallmarks incoherent feedforward loop, which sufficient explain dynamics adds temporal complexity steady-state model formation. further show 'blurring' all-or-none stimulus intracellular diffusion non-locally produces stripe. Overall, provide blueprint for using dissect developmental signal space time.

Язык: Английский

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A geometrical model of cell fate specification in the mouse blastocyst

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Окт. 25, 2023

Abstract The lineage decision that generates the epiblast and primitive endoderm from inner cell mass (ICM) is a paradigm for fate specification. Recent mathematics has formalized Waddington’s landscape metaphor proven decisions in detailed gene network models must conform to small list of low dimensional stereotypic changes called bifurcations. most plausible bifurcation ICM so-called heteroclinic flip we define elaborate here. Our reanalysis recent data suggests there sufficient movement so FGF signal, which drives decision, can be treated as spatially uniform. We thus extend model single entire by means self-consistently defined time-dependent signal. This consistent with available propose additional dynamic experiments test it further. demonstrates simplified, quantitative, intuitively transparent descriptions are possible when attention shifted specific genes lineages. very any situation where embryo needs control over relative proportions two fates morphogen feedback.

Язык: Английский

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