Assessing the Relative Contributions of Mosaic and Regulatory Developmental Modes from Single-Cell Trajectories DOI Creative Commons

Solène Song,

Paul Villoutreix

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

Опубликована: Июль 25, 2024

Abstract Development is a highly complex process consisting of coordinated cell proliferation, differentiation and spatial organization. Classically, two ways to specify types during development are hypothesized : mosaic regulative modes. In the mode, particular isolated from rest embryo will nevertheless give rise cells with fate identical ones expected in normal development, thus relying on lineage-inherited factors. depends its interactions environment, relies space-dependant Both modes often coexist given animal. We propose quantify their respective contributions single-cell trajectories. C. elegans provides unique opportunity elaborate such an approach. Indeed, invariant lineage enables integration positions, relationships protein expression data. Using single profile as readout state, we relate following measurable quantities. The contribution or quantified by strength relationship between cell-cell distance . Similarly, context-dependent context measures similarity neighborhoods based gene profiles neighbours. assess significance these comparing empirical results obtained data artificial models generated using simple rules. With measures, show co-existence relative varies across different tissues time. particular, see skin tissue that early mode dominates while at later stages, dominates, suggesting convergence These general can be applied other datasets made available progress transcriptomics lineage-tracing, paving way for quantitative, unbiased perturbation-free study fundamental concepts developmental biology.

Язык: Английский

STP: single-cell partition for subcellular spatially-resolved transcriptomics DOI Creative Commons
Haoyang Li, Qinan Hu, Zhaowen Qiu

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Май 20, 2025

Spatially-resolved transcriptomics (SRT) technologies now allow exploration of gene expression with spatial context. Recent advances achieving subcellular resolution provide richer data but also introduce challenges, such as aggregating spots into individual cells, which is a task distinct from traditional deconvolution. Existing methods often grid SRT predefined squares, unrealistic for accurately capturing cellular boundaries. We propose method, STP, that integrates nuclei-stained images to partition cells. STP first segments nuclei and maps their masks onto the data, then uses simulated-annealing-inspired approach expand nuclear boundaries full level. Evaluated on datasets Drosophila embryos at multiple developmental stages mouse large field-of-view, demonstrated accurate single-cell partitioning, unveiling significant tissue patterns identifying undetected cell types beyond previous methods.

Язык: Английский

Процитировано

0
Assessing the Relative Contributions of Mosaic and Regulatory Developmental Modes from Single-Cell Trajectories DOI Creative Commons

Solène Song,

Paul Villoutreix

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

Опубликована: Июль 25, 2024

Abstract Development is a highly complex process consisting of coordinated cell proliferation, differentiation and spatial organization. Classically, two ways to specify types during development are hypothesized : mosaic regulative modes. In the mode, particular isolated from rest embryo will nevertheless give rise cells with fate identical ones expected in normal development, thus relying on lineage-inherited factors. depends its interactions environment, relies space-dependant Both modes often coexist given animal. We propose quantify their respective contributions single-cell trajectories. C. elegans provides unique opportunity elaborate such an approach. Indeed, invariant lineage enables integration positions, relationships protein expression data. Using single profile as readout state, we relate following measurable quantities. The contribution or quantified by strength relationship between cell-cell distance . Similarly, context-dependent context measures similarity neighborhoods based gene profiles neighbours. assess significance these comparing empirical results obtained data artificial models generated using simple rules. With measures, show co-existence relative varies across different tissues time. particular, see skin tissue that early mode dominates while at later stages, dominates, suggesting convergence These general can be applied other datasets made available progress transcriptomics lineage-tracing, paving way for quantitative, unbiased perturbation-free study fundamental concepts developmental biology.

Язык: Английский

Процитировано

0