Edit

Dorrity Group

Environmental response at the single-cell level

At EMBL from January 2022

The Dorrity group investigates how variability propagates from the level of molecules to developing cells and tissues, and ultimately to organismal phenotype.

Previous and current research

Effects of environmental stress are variable, with some individuals more sensitive than others. This variability obscures the influence of the environment during development, limits our understanding of genotype–phenotype relationships, and leaves us unable to predict how a changing climate will shape populations and ecologies globally.

To better understand how environmentally induced variability propagates across scales, the lab uses single-cell genomics as a phenotyping tool to capture cell- and tissue-level processes, along with molecular phenotypes. We conduct this multiscale phenotyping in individual zebrafish embryos, a model for aquatic vertebrate development. Using computational and statistical approaches to partition variability at each level (molecular, cellular, and organismal), we can define sources of environmental responsiveness and uncover potential mechanisms of environmental adaptation. We validate and explore these mechanisms experimentally by targeting key factors using dominant negative protein fragments, gene editing, and pharmacological inhibitors.

Our previous work has shown that raising zebrafish embryos in elevated water temperatures has profound effects on the programme of development: abundances of cell types are altered in the embryo, specific cell types show increased variability across individual embryos, and temperature-dependent changes to developmental rate are introduced non-uniformly across cell types. These findings reveal how a broad stressor like temperature nevertheless induces cell type-specific effects, which underlie variable whole-animal phenotypes.

At the molecular level, cell type-specific stress sensitivity can be linked to components of proteostasis, or the maintenance of proper folding, synthesis, and degradation of proteins in cells. To investigate the role of proteostasis in environmentally induced variability at the molecular level, we have also developed multiplex assays of protein function. Leveraging high-throughput sequencing to characterise protein variants in yeast, we can identify dominant negative protein fragments that inhibit a target of interest, and we can determine functional consequences of hundreds of thousands of missense mutations for a given protein. We can use these high-throughput screens to identify variants that disrupt or alter function of proteins or pathways involved in environmental sensing.

Future projects and goals

We will build on these experimental and computational tools to predict how a changing climate will influence animal development across scales. Activities will include:

  • Profiling embryos raised in a wide range of environments to identify environmentally sensitive cell types and tissues.
  • Defining molecular processes imparting cell type-specific environmental sensitivity and dissecting misregulation of gene expression under stress.
  • Engineering stress resilience in the molecular processes that control development.
  • Mapping adaptive genetic variation in cell type-specific responses to the environment.
Figure 1: Integrating the effects of the environment at multiple scales to identify mechanisms of developmental robustness.
Figure 1: Integrating the effects of the environment at multiple scales to identify mechanisms of developmental robustness. Members of the Dorrity group focus on understanding the role of the environment at the level of molecules, cells, and tissues in zebrafish (Danio rerio), and ask how environmental sensing mechanisms determined in the lab may manifest in natural populations adapting to changing environments.
Figure 2: Multiscale phenotyping with single-cell genomics to identify environmentally sensitive developmental processes.
Figure 2: Multiscale phenotyping with single-cell genomics to identify environmentally sensitive developmental processes. Using single-cell genomics data from individually barcoded animals (A), we can use molecular features to measure variation in their (B) anatomical composition and developmental rate in response to environmental perturbations.
Edit