Living Systems Institute

Smith Group

Pluripotent stem cell biology

Pluripotency is the flexibility of single cells to generate all cell types of the animal. This cellular plasticity is the foundation of mammalian development. In the embryo pluripotency is dynamic and short-lived, but in vitro pluripotent stem cells can be established and multiplied without limit. The most pristine type of pluripotent stem cell exists in a naive  state, as found in the pre-implantation embryo. To execute their potential for differentiation, naive cells must gain lineage competence, a process termed formative transition. Knowledge of this process can be applied to optimise preparation of pluripotent stem cells for biomedical applications such as disease modelling or cell therapy.

We seek to understand:

  1. how potency and competence are encoded in a dynamic regulatory network of signals, transcription factors and chromatin
  2. how cells transition between states of competence and how fate decisions are made
  3. how the trajectory and regulatory machinery of pluripotency are adapted in different mammals

Recent papers:

Further information on the Smith Group: Profile | Living Systems Institute | University of Exeter

PhD Opportunities

Decoding signal computation in pluripotent stem cells

Understanding how cells change identities in response to signalling cues is one of the fundamental challenges in modern biosciences. This question is most prescient for pluripotent cells that can form all the cell lineages in the mammalian embryo. Pluripotency is transient in the embryo,  but it is possible to maintain pluripotent stem cells (PSCs) long term in the laboratory (PMID:39180242). PSCs decide compute biochemical and biophysical signals from other cells in the embryo or provided in the culture environment to decide between self-renewal or differentiation. Our laboratory has established signalling environments for culturing three different types of human PSC. They correspond to sequential stages that pluripotent cells pass through in the early embryo:  the pre-lineage inner cell mass (ICM); the naïve epiblast; and the primed epiblast. The three PSC states have distinct cell biological and molecular properties and exhibit different capabilities for differentiation into extraembryonic or embryonic cell lineages. Each type of PSC requires  different signalling inputs to maintain self-renewal or switch to differentiation.

This project will focus on a signalling module known as YAP/TEAD that is instrumental for cell fate decisions in the early embryo (PMID:19289085). YAP shuttles between cytoplasm and nucleus in response to changes in the microenvironment. When in the nucleus YAP can interact with TEAD transcription factors to activate expression of target genes. We have found that increased YAP/TEAD signalling is required for differentiation (PMID:36398796). In addition, however, low level YAP/TEAD appears to be necessary for PSC maintenance. How does a single pathway regulate such different responses?

The aim of this project is to investigate the hypothesis that dynamic nucleocytoplasmic shutting of YAP conveys information that is richer than concentration alone and is computed into specific transcriptional outcomes (and thence cell decisions). Testing this hypothesis requires quantitative analysis of YAP localisation dynamics together with transcriptomic assays of gene expression. You will create YAP fusions with fluorescent reporters to visualise nucleocytoplasmic shuttling in live cells (PMID:32917893). Applying advanced image analysis techniques you will measure parameters such as amplitude, frequency and residency time. In parallel you will generate single cell RNA-seq and chromatin accessibility profiles. These analyses will be performed during self-renewal, transitions between PSC states, and  differentiation induction. Chemical and genetic perturbations will probe robustness and causation. The overall goal is to produce an explanatory and predictive mathematical network model for how YAP/TEAD gates transcription to guide alternative fate decisions in pluripotent cells.

Supervisory team:
Main supervisor: Prof Austin Smith
Second supervisor: Dr Marc Goodfellow
Day to day supervisor: Dr Zhili Ren

Funding scheme and application details: SWBiosciences Doctoral Training Partnership; Deadline 11 December 2024

Postdoc Opportunities

Postdoc opportunities are also available for stem cell and molecular developmental biologists motivated by fundamental curiosity with a particular interest in early development and/or cell fate decision-making:

Post 1: Naïve pluripotent stem cells have to date been established only from rodents and primates. Our goal is to design signalling environments for capturing naïve pluripotent stem cells from livestock and other mammals, including marsupials. Approaches will include pluripotency network resetting and somatic cell reprogramming, as well as direct derivations from livestock embryos. This post requires cell culture aptitude, experience with genetic manipulations, and knowledge of developmental signalling.

Post 2: Mouse and human naïve pluripotent stem cells have overlapping but distinct gene regulatory networks and exhibit different direct lineage potencies. Our goal is to uncover the core gene regulatory network shared across mammalian species. Approaches will include genetic perturbations, transcriptome and chromatin analyses, and network inference. This post requires advanced skills in molecular cell genetics, ability to use basic sequencing analysis pipelines, and an interest in molecular networks.

Informal enquiries to: austin.smith@exeter.ac.uk