What is a single cell facility?
Scientists now understand that cells are not all the same. Even cells from within the same tissues show significant variations in gene expression so if cells are pooled together for analysis, researchers will be unable to understand how each cell behaves differently.
So, for researchers there is a need to isolate and analyse single cells or small biological samples to get a better understand the processes that promote health, and how these pathways can go wrong in disease,
A single cell facility provides an environment, with the technology, training, and expertise, for researchers to isolate cells and undertake genomic analysis at a single cell level. At the Kennedy Institute this includes single cell analysis of gene and protein expression, immune cell receptor diversity and chromatin landscape accessibility.
These sorts of techniques have enabled researchers to make great strides in stem cell research, cancer treatments and the immune response.
the evolution of the Kennedy's in-house single cell facility.
The Powrie and Sansom labs were the first to adopt single-cell approaches at the Kennedy for the study of regulatory T-cells and thymic epithelial cells. Then, a partnership between the Sansom group and the Bowden group at the Wellcome Centre for Human Genetics (WHG) led to the Kennedy's access to the first-generation single-cell technologies, which were trialled by the Udalova and Sansom groups.
In 2017, with funds awarded by the University's John Fell fund, the Kennedy and WHG acquired the droplet-based 10x system which opened the flood gates for high throughput studies of immune cells. In one of the first studies published using this platform, the Udalova and Sansom groups reported a new role for the transcription factor in Irf5 in controlling intestinal inflammation in the journal Science Immunology.
In parallel, to support the growing need for single cell analysis at the Kennedy, Irina and Steve secured seed funding from Kennedy Trust for Rheumatology Research to recruit a dedicated single cell genomics research associate. Moustafa Attar joined the Sansom lab and was embedded with the single-cell team at the WHG to help Kennedy researchers perform single-cell experiments. This led to many high-profile publications over the following years including a study from the Buckley and Sansom labs that demonstrated that distinct populations of fibroblasts drive inflammation and damage in arthritis (Nature, 2019).
When more and more Kennedy groups began to generate single cell data and with the advent of complementary spatial genomics technologies, Irina and Steve led a KTRR funded effort to establish an in-house single cell and spatial facility, which opened in 2021.
How does the single cell facility support and enhance the KENNEDY's research?
The mission at the Kennedy is to carry out research that drives the development of transformative therapies for chronic inflammatory and degenerative disease. To do this, researchers need to understand the underlying processes at work in maintaining health, and explain where these processes go wrong in disease. Increasingly this means exploring the fundamental units of life; the single cell.
Most of the research projects at the Kennedy now involve some kind of understanding of cell heterogeneity in the tissue of interest. The process involves cells being isolated from the tissues which can help define the function and unique characteristics of the cell, identify different cell types, and explore how different cell types interact and change throughout their life.
"So a single cell becomes a big thing," said Irina.
As an example, single cell analysis led the Udalova lab to identify a subset of immune cells that could be a new therapeutic target to treat inflamed blood vessels. They discovered an immature population of neutrophils that accumulates in the blood of patients with Giant Cell Arteritis (GCA). These can trigger changes in blood vessel cells, potentially causing the development of inflammatory lesions.
In another study recently published in the journal Immunity, the Sansom group worked with the Arnon group to investigate how resident memory B cells can control secondary viral infections. There were many different candidate mechanisms, but single-cell analysis helped to pinpoint the role of specific cell types and signalling molecules in directing the recruitment of resident memory B cells to sites of infection.
"A key advantage of bringing capabilities in house is the ability to process samples quickly and on demand," adds Steve. "This has enabled Kennedy researchers to scale up application of single-cell approaches for clinical research. Many KIR groups now perform analysis of patient biopsies samples to study different inflammatory conditions, including, for example, study of the cellular basis of anti-TNF therapy within the A-TAP program."
The new facility offers a range of technologies to enable end-to-end workflows that enable the isolation of cells alongside variations of preparation and analysis.
Steve explained: "The facility is equipped with the 10x Chromium and BD Rhapsody machines for cell capture.
A key strength of the 10X Chromium platform is the ability to perform multimodal single cell analysis, in which surface protein expression and immune receptor sequences can be profiled alongside the transcriptome.
The complementary BD Rhapsody solution can be used to perform a less expensive, targeted analysis. In addition, it uses a different cell capture approach that can improve the capture of certain cell types."
The facility also offers a cassette-based Sony fluorescence-activated cell sorter system, that helps to isolate live cells for single cell analysis.
Following up on the success of single-cell analysis of isolated cells, the facility is currently expanding into single cell analysis in tissue, using state-of-the-art spatial transcriptomic approaches. "We are eagerly awaiting the arrival of the next-generation Nanostring CosMx platform which will allow sensitive spatial of the expression of hundreds of genes at subcellular resolution in intact tissues", said Steve.