Computational approaches to analysing high-throughput imaging datasets in vitro iPSC-derived presomitic mesoderm
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
Somitogenesis occurs when segments of the presomitic mesoderm, one of the three primary germ layer tissues, buds off sequentially to form somites. These somites are the precursors to the bones, skeleton-associated muscles, and parts of the dermis. Somitogenesis is regulated by three main signalling pathways: Wnt, FGF, and Notch.
Notch signalling plays a crucial role in the timing of somitogenesis; it synchronises molecular oscillations of neighbouring cells. The Notch pathway is activated via a cell-to-cell interaction between the ligand, delta/jagged, and Notch receptor. When this interaction occurs, the notch intracellular domain is cleaved and translocated into the nucleus to co-activate various target genes. Notch abnormalities have been linked to various types of cancerous and non-cancerous diseases, including T-cell acute lymphoblastic leukaemia.
The Dale Lab has generated various human-induced pluripotent cell lines that contain either wild-type or mutant Notch carrying a serine-to-alanine mutation at residue 2513. These cell lines are used to generate organoids and 2D monolayers to study the effects of this mutation.
These models can be observed using techniques like confocal microscopy and time-lapse imaging and analysed with image analysis software like Fiji. Due to the scale of the datasets, manual analysis has become impractical, making automated approaches necessary for managing and analysing the data.
Therefore, during my PhD, I aim to :
Develop metrics to describe Notch's role in pattern formation in iPS-derived presomitic mesoderm and investigate whether these metrics can be applied to wild-type versus Notch mutant. I will employ time-lapse analysis to characterise the somitoid phenotype and establish metrics to detail somitoid morphology. Furthermore, I will refine techniques using a 2D immunofluorescence monolayer system to enhance 3D subcellular localisation and classify the presomitic mesoderm cell cycle phase.
Notch signalling plays a crucial role in the timing of somitogenesis; it synchronises molecular oscillations of neighbouring cells. The Notch pathway is activated via a cell-to-cell interaction between the ligand, delta/jagged, and Notch receptor. When this interaction occurs, the notch intracellular domain is cleaved and translocated into the nucleus to co-activate various target genes. Notch abnormalities have been linked to various types of cancerous and non-cancerous diseases, including T-cell acute lymphoblastic leukaemia.
The Dale Lab has generated various human-induced pluripotent cell lines that contain either wild-type or mutant Notch carrying a serine-to-alanine mutation at residue 2513. These cell lines are used to generate organoids and 2D monolayers to study the effects of this mutation.
These models can be observed using techniques like confocal microscopy and time-lapse imaging and analysed with image analysis software like Fiji. Due to the scale of the datasets, manual analysis has become impractical, making automated approaches necessary for managing and analysing the data.
Therefore, during my PhD, I aim to :
Develop metrics to describe Notch's role in pattern formation in iPS-derived presomitic mesoderm and investigate whether these metrics can be applied to wild-type versus Notch mutant. I will employ time-lapse analysis to characterise the somitoid phenotype and establish metrics to detail somitoid morphology. Furthermore, I will refine techniques using a 2D immunofluorescence monolayer system to enhance 3D subcellular localisation and classify the presomitic mesoderm cell cycle phase.
Organisations
People |
ORCID iD |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/T00875X/1 | 30/09/2020 | 29/09/2028 | |||
| 2734158 | Studentship | BB/T00875X/1 | 18/09/2022 | 17/09/2026 |