TrajectoryGeometry suggests cell fate decisions can involve branches rather than bifurcations DOI Creative Commons
Anna Laddach, Vassilis Pachnis, Michael Shapiro

и другие.

NAR Genomics and Bioinformatics, Год журнала: 2024, Номер 6(4)

Опубликована: Июль 2, 2024

Abstract Differentiation of multipotential progenitor cells is a key process in the development any multi-cellular organism and often continues throughout its life. It assumed that bi-potential develops along (relatively) straight trajectory until it reaches decision point where bifurcates. At this one two directions chosen, each direction representing unfolding new transcriptional programme. However, we have lacked quantitative means for testing model. Accordingly, developed R package TrajectoryGeometry. Applying to published data find several examples where, rather than bifurcate, developmental pathways branch. That is, bipotential relatively leading potential fates. A second branches off from towards other fate. In sense only branch follow make ‘decision’. Our methods give precise descriptions genes cellular involved these trajectories. We speculate branching may be more common behaviour advantages control-theoretic viewpoint.

Язык: Английский

Spatiotemporal dynamics exhibited by horizontal basal cells reveal a pro-neurogenic pathway during injury-induced olfactory epithelium regeneration DOI Creative Commons
Jonathan D. Louie, Camila M. Barrios-Camacho,

Benjamin H. Bromberg

и другие.

iScience, Год журнала: 2024, Номер 27(5), С. 109600 - 109600

Опубликована: Март 27, 2024

Horizontal basal cells (HBCs) mediate olfactory epithelium (OE) regeneration following severe tissue injury. The dynamism of the post-injury environment is well illustrated by

Язык: Английский

Процитировано

2
An in vitro model of acute horizontal basal cell activation reveals gene regulatory networks underlying the nascent activation phase DOI Creative Commons
Camila M. Barrios-Camacho, Matthew J. Zunitch, Jonathan D. Louie

и другие.

Stem Cell Reports, Год журнала: 2024, Номер 19(8), С. 1156 - 1171

Опубликована: Июль 25, 2024

While horizontal basal cells (HBCs) make minor contributions to olfactory epithelium (OE) regeneration during homeostatic conditions, they possess a potent, latent capacity activate and subsequently regenerate the OE following severe injury. Activation requires, is mediated by, downregulation of transcription factor (TF) TP63. In this paper, we describe cellular processes that drive nascent stages HBC activation. The compound phorbol 12-myristate 13-acetate (PMA) induces rapid loss in TP63 protein enrichment HOPX nuclear translocation RELA, previously identified as components Using bulk RNA sequencing (RNA-seq), find PMA-treated HBCs pass through various activation identifiable by transcriptional regulatory signatures mimic vivo. These temporal are associated with varying degrees engraftment differentiation potential transplantation assays. Together, these data show our vitro system models physiologically relevant features vivo identifies new candidates for mechanistic testing.

Язык: Английский

Процитировано

2
Trajectorygeometry suggests cell fate decisions involve branches rather than bifurcations DOI Creative Commons
Anna Laddach, Michael Shapiro

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

Опубликована: Фев. 28, 2024

A bstract Differentiation of multipotential progenitor cells is a key process in the development any multi-cellular organism and often continues throughout its life. It assumed that bi-potential develops along (relatively) straight trajectory until it reaches decision point where bifurcates. At this one two directions chosen, each direction representing unfolding new transcriptomic programme. However, we have lacked quantitative means for testing model. Accordingly, developed R package TrajectoryGeometry. Applying to published data find several examples where, rather than bifurcate, developmental pathways branch . That is, bipotential relatively leading potential fates. second branches off from towards other fate. In sense only follow make “decision”. Our methods give precise descriptions genes cellular involved these trajectories. We speculate branching may be more common behaviour advantages control-theoretic viewpoint.

Язык: Английский

Процитировано

0
Two decades on: Special issue on olfaction celebrating Axel and Buck's Nobel Prize DOI Open Access
Paolo E. Forni, C. Ron Yu

genesis, Год журнала: 2024, Номер 62(4)

Опубликована: Июль 26, 2024

Язык: Английский

Процитировано

0
TrajectoryGeometry suggests cell fate decisions can involve branches rather than bifurcations DOI Creative Commons
Anna Laddach, Vassilis Pachnis, Michael Shapiro

и другие.

NAR Genomics and Bioinformatics, Год журнала: 2024, Номер 6(4)

Опубликована: Июль 2, 2024

Abstract Differentiation of multipotential progenitor cells is a key process in the development any multi-cellular organism and often continues throughout its life. It assumed that bi-potential develops along (relatively) straight trajectory until it reaches decision point where bifurcates. At this one two directions chosen, each direction representing unfolding new transcriptional programme. However, we have lacked quantitative means for testing model. Accordingly, developed R package TrajectoryGeometry. Applying to published data find several examples where, rather than bifurcate, developmental pathways branch. That is, bipotential relatively leading potential fates. A second branches off from towards other fate. In sense only branch follow make ‘decision’. Our methods give precise descriptions genes cellular involved these trajectories. We speculate branching may be more common behaviour advantages control-theoretic viewpoint.

Язык: Английский

Процитировано

0