Cells and Development, Год журнала: 2025, Номер unknown, С. 204028 - 204028
Опубликована: Апрель 1, 2025
Язык: Английский
Nature Physics, Год журнала: 2025, Номер unknown
Опубликована: Март 11, 2025
Язык: Английский
Процитировано
2
Cell stem cell, Год журнала: 2025, Номер unknown
Опубликована: Апрель 1, 2025
Considerable phenotypic variation under identical culture conditions limits the potential of stem-cell-based embryo models (SEMs) in basic and applied research. The biological processes causing this seemingly stochastic remain unclear. Here, we investigated roots by parallel recording transcriptomic states morphological history individual structures modeling embryonic trunk formation. Machine learning integration time-resolved single-cell RNA sequencing with imaging-based profiling identified early features predictive end states. Leveraging power revealed that imbalance oxidative phosphorylation glycolysis results aberrant morphology a neural lineage bias, which confirmed metabolic measurements. Accordingly, interventions improved Collectively, our work establishes divergent as drivers offers broadly applicable framework to chart predict organoids SEMs. strategy can be used identify control underlying processes, ultimately increasing reproducibility.
Язык: Английский
Процитировано
2
Development, Год журнала: 2023, Номер 150(14)
Опубликована: Июль 4, 2023
ABSTRACT In embryonic stem cell (ESC) models for early development, spatially and temporally varying patterns of signaling types emerge spontaneously. However, mechanistic insight into this dynamic self-organization is limited by a lack methods spatiotemporal control signaling, the relevance signal dynamics cell-to-cell variability to pattern emergence remains unknown. Here, we combine optogenetic stimulation, imaging transcriptomic approaches study human ESCs (hESC) in two-dimensional (2D) culture. Morphogen were controlled via activation canonical Wnt/β-catenin (optoWnt), which drove broad transcriptional changes mesendoderm differentiation at high efficiency (>99% cells). When activated within subpopulations, optoWnt induced distinct epithelial mesenchymal domains, mediated migration, an mesenchymal-like transition TGFβ signaling. Furthermore, demonstrate that such subpopulations can be used uncover feedback mechanisms between neighboring types. These findings reveal Wnt sufficient generate tissue-scale patterning establish hESC model system investigating relevant embryogenesis.
Язык: Английский
Процитировано
25
Nature, Год журнала: 2024, Номер 632(8027), С. 1073 - 1081
Опубликована: Июль 17, 2024
Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction live imaging a biological sample within timeframe interest. Here we demonstrate an alternative paradigm in which such activities stably recorded to genome. Enhancer-driven genomic recording transcriptional multiplex (ENGRAM) is based on signal-dependent production prime editing guide RNAs mediate insertion signal-specific barcodes (symbols) into genomically encoded unit. We show how this strategy can be used for cell-type-specific dozens hundreds cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging pathway-responsive elements, also time- concentration-dependent WNT, NF-κB Tet-On activities. By coupling ENGRAM sequential genome via DNA Typewriter
Язык: Английский
Процитировано
17
Nature Methods, Год журнала: 2024, Номер 21(5), С. 798 - 803
Опубликована: Март 20, 2024
Abstract Multicellular systems grow over the course of weeks from single cells to tissues or even full organisms, making live imaging challenging. To bridge spatiotemporal scales, we present an open-top dual-view and dual-illumination light-sheet microscope dedicated large specimens at single-cell resolution. The configuration objectives together with a customizable multiwell mounting system combines dual view high-throughput multiposition imaging. We use this image wide variety samples highlight its capabilities gain quantitative information in such as mature intestinal organoids gastruloids.
Язык: Английский
Процитировано
12
Cell, Год журнала: 2024, Номер 187(14), С. 3461 - 3495
Опубликована: Июнь 20, 2024
Developmental biology-the study of the processes by which cells, tissues, and organisms develop change over time-has entered a new golden age. After molecular genetics revolution in 80s 90s diversification field early 21st century, we have phase when powerful technologies provide approaches open unexplored avenues. Progress has been accelerated advances genomics, imaging, engineering, computational biology emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary led remarkable progress understanding animal development. describe classic questions gene regulation, pattern formation, morphogenesis, organogenesis, stem cell are being revisited. discuss connections development with evolution, self-organization, metabolism, time, ecology. speculate developmental might evolve an era synthetic biology, artificial intelligence, human engineering.
Язык: Английский
Процитировано
12
Nature Cell Biology, Год журнала: 2024, Номер 26(10), С. 1790 - 1803
Опубликована: Авг. 20, 2024
Abstract Gastruloids are a powerful in vitro model of early human development. However, although elongated and composed all three germ layers, gastruloids do not morphologically resemble post-implantation embryos. Here we show that an pulse retinoic acid (RA), together with later Matrigel, robustly induces posterior embryo-like morphological structures, including neural tube flanked by segmented somites diverse cell types, crest, progenitors, renal progenitors myocytes. Through silico staging based on single-cell RNA sequencing, find RA-gastruloids progress further than other or mouse embryo models, aligning to E9.5 CS11 cynomolgus monkey We leverage chemical genetic perturbations confirm WNT BMP signalling regulate somite formation length the context, while transcription factors TBX6 PAX3 underpin presomitic mesoderm respectively. Looking forward, robust, scalable for decoding embryogenesis.
Язык: Английский
Процитировано
10
Nature Cell Biology, Год журнала: 2024, Номер 26(11), С. 1832 - 1844
Опубликована: Окт. 2, 2024
Язык: Английский
Процитировано
10
Developmental Cell, Год журнала: 2024, Номер unknown
Опубликована: Май 1, 2024
During neural tube (NT) development, the notochord induces an organizer, floorplate, which secretes Sonic Hedgehog (SHH) to pattern progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without notochord, demonstrating that can self-organize inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of marker FOXA2 was initially spatially scattered before resolving into multiple clusters, underwent competition and sorting, resulting a stable "winning" floorplate. We identified BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing receiving while simultaneously expressing BMP-inhibitor NOGGIN, promoting persistence. Noggin mutation perturbed formation NTOs vivo at mid/hindbrain regions, how autonomously notochord. Identifying pathways governing organizer is critical for harnessing developmental plasticity tissue engineering.
Язык: Английский
Процитировано
9
Nature Protocols, Год журнала: 2025, Номер unknown
Опубликована: Март 21, 2025
Язык: Английский
Процитировано
1