Leveraging synthetic biology to characterise cellular neighbourhoods
Cell-cell interactions profoundly influence cellular decision-making during development, in homeostasis, and during the onset and progression of disease. However, identifying these interactions and decoding their downstream effects remains technically challenging due to a shortage of relevant analytical approaches.
In our lab, we seek to overcome these barriers by developing engineering biology tools that make it possible to fluorescently label cells that neighbour any cell of interest. This allows us, for example, to fluorescently label healthy cells interacting with mutant cells, or pluripotent cells interacting with differentiated cells. Live labelled neighbours and unlabelled non-neighbours can be isolated by flow cytometry for further downstream analysis; this includes both ‘omics studies and functional assays on these live interacting cells.
Part of the work that we do in the lab focuses on developing these engineering biology tools, and on implementing them in the experimental systems that we're interested in studying.
We have recently developed two complementary synthetic biology tools to identify neighbouring cells.
SyNPL is an adaptation of synNotch technology, optimised for use in pluripotent stem cells. This system relies on a synthetic ligand activating a synthetic receptor, and allows us to identify interacting cells in direct contact.
PUFFFIN is a novel niche-labelling tool, which functions across a range of vertebrate species. This system relies on secretion and uptake of a fluorogenic label, and allows us to identify cells in the vicinity of a label-secreting cell of interest.
It takes considerable effort to establish and screen clonal cell lines expressing individual transgenes or synthetic gene circuits, such as those required for the establishment of synthetic neighbour labelling in mammalian cells.
To streamline these process, we have developed two highly modular "landing pads" that can be targeted to "safe harbour" genomic sites in mouse and human cell lines. These allow us to rapidly and efficiently insert complex DNA fragments into these landing pads in a pre-determined genomic location, facilitating both the process of generating transgenic cell lines, and their subsequent screening.
We are interested in studying cell-cell communication in the skin.
In order to study this process in experimentally-tractable and tissue architecture-relevant settings, we are working to develop and refine a range of 3D organoid cell culture models of human skin.
We are working on establishing epidermal organoids comprising both keratinocytes and melanocytes from immortalised human skin cell lines, in collaboration with Professor Sara Brown.
Brown Lab - Skin Genetic Research
Epidermal organoids (left: keratinocyte-only organoid) are an ideal model for bottoms-up engineering approaches, allowing us tight control over cell type composition and cell ratios.
We have established self-organising human skin organoids derived entirely from human pluripotent stem cells, in collaboration with clinical dermatologist Dr Eleanor Earp.
These organoids (right) contain a range of epidermal and dermal structures, including keratinocytes, melanocytes, Merkel cells and hair follicles.
We aim to combine our tools and models to address study how cell-cell communication affects the onset and progression of melanoma skin cancer.
We are interested in understanding how melanocytes carrying early melanoma skin cancer mutations affect neighbouring healthy skin cells.
Are healthy skin cells able to sense mutant melanocytes?
Do they hinder or aid progression to melanoma skin cancer?
By combining our synthetic neighbour-labelling tools, our transgenesis platform, and our human skin organoids, we can address these questions in an unbiased manner in a tractable and relevant 3D model of human skin.
Through this work, we aim to characterise the molecular processes that accompany the onset and progression of melanoma skin cancer, to understand how molecular changes relate to cell behaviour, and to determine whether we could engineer healthy keratinocytes to sense and destroy mutant melanocyte neighbours.
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