Many of the largest research projects in the life sciences are underpinned by cell biology. From uncovering cancer’s weaknesses to mapping every cell type in the body, understanding cells is fundamental to understanding human health and disease. Cells are also the vehicles for understanding how the genome works – how the genetic code relates to form and function.
The Cellular Generation and Phenotyping (CGaP) department is a powerhouse for much of the large-scale science at the Sanger Institute. The team is researching, developing and employing the latest cellular techniques as part of some of the biggest biology projects in the world.
CGaP’s work starts with a person, as each sample of body tissue or cells is donated by an individual. That person is often a patient with a particular condition, for example, someone with cancer. Or, they may be healthy and having a biopsy for diagnosis or another purpose. Some tissues and cells are gifted by organ donors.
The team collaborates with hospitals and clinics across the country who arrange consent, surgery and couriers to transport the cells for the different projects underway. Each sample is a precious resource.
Dr Mya Fekry-Troll is an Advanced Research Assistant in CGaP. “When the clinical sites inform us that samples are coming our way, we have to prep the lab, make sure we have everything ready and make sure we have time set aside in our diary. The samples are a very precious biological gift for us to work with,” she said.
Mya works on an organoid derivation project, creating organoid models from donated cancer cells.
Organoids are ‘mini-organs’ - 3D clusters of cells that represent a specific organ or tumour. The aim is to closely replicate how cells work in the body, so they can be used to understand how a tumour or organ works or responds to a treatment. “The idea is to get organoids from patients that have a broad range of cancers, so we can model the whole range of cancers in a population,” said Laura Letchford, a Senior Research Assistant in CGaP.
The team is part of an international effort to create hundreds of cancer organoids1. They are constantly refining and developing their techniques to create organoids from different tissues. Success rates vary between cancer types but are usually about 30 per cent. A successful organoid can be divided, frozen, thawed and it will re-grow, meaning it can be kept alive indefinitely in a laboratory.
“We are very transparent with what we are doing – both the methods and results we are getting,” said Mya. “Open data is really important to us. Scientists can contact us, and we undertake a lot of collaborative work.”
Once created, an organoid model is sent to ATCC2 to be stored and distributed, making it available for any researcher worldwide to use.
Within the Sanger Institute, the organoid models are sent to DNA pipelines for sequencing to uncover genetic changes leading to cancer, used to test potential cancer drug treatments, and used in projects employing CRISPR-Cas9 technology to understand the role of each gene in the genome - all as part of the cancer research programme3.
Sophie and Emily working in the CGaP laboratories, 2019
Emily Souster is a Research Assistant in CGaP. She is testing 2D cell lines using CRISPR-Cas9 screens. “I work in cancer cell culture – I have cells on the go the whole time. I transduce them to express the Cas9 enzyme. Then I transduce them again with a ‘library’ that tells the Cas9 where to cut. The aim is to cut out every gene in a different cell,” Emily said. If a cell doesn’t grow after a gene is cut – the gene is considered essential for that cancer’s survival.
Working with cells involves regularly feeding them, changing the liquid they live in, dividing them as they grow, and keeping them free from infections. “Each cell line has its own different personality,” said Emily. “Cancer cell lines all look different. They behave differently too, even within the same cancer type.”
Other members of the team are also undertaking the CRISPR-Cas9 screens in the cancer organoids. Growing organoids and CRISPR-Cas9 gene editing are both relatively new techniques, and researchers are just beginning to put them together. The process, and analysing the data it produces, is challenging.
“The work we do is really fulfilling. When you think about the downstream applications of the cell lines and organoid models we are making, the amount of research we are enabling is incredible,” says Mya.
A day in the life
“The best thing about working in CGaP is no two days are the same,” said Sophie Pritchard, an Advanced Research Assistant. “If tissue from a donor comes in at short notice, they take priority. People will drop everything else to help - it’s a huge team effort,” she said.
Sophie works on the Human Cell Atlas project, using some of the latest techniques in spatial transcriptomics to look at the active genes in a cell in situ and map out every cell type in the human body4.
“I really love the imaging side of my work,” Sophie said. Part of her job involves staining tissues with coloured probes, to show where different genes are active. She uses RNAscope technology to look at specific genes, or Visium to look at all the genes active within a tissue. Researchers have only developed the techniques in the last few years. The team is currently working on scaling up their throughput, so hundreds of tissues can be processed per year.
Eye cells with H&E stain Eye cells stained with fluorescence and RNAscope probes
“Collaborating with so many researchers here is great. We meet before starting any work to discuss a project. We often see things in different ways, coming from different angles, and work together to get the best results,” Sophie said.
Research and development
The CGaP team also undertakes research and development. “It’s an important part of our work,” says Laura. “If something isn’t working, we troubleshoot. We do a lot of optimisation to improve techniques, culture methods and assays to make delivery of the projects faster, cheaper and safer.
“For the organoids project we currently work on three cancer types, but the aim is to expand to cover more. This requires research and development to work up protocols for growing these. For example, we’ve just received our first few samples of ovarian ascites fluid, and we’re currently working to create models of ovarian cancer.”
“When we’re setting up new tissue types or workflows we get everyone involved together. We get to meet clinicians, the nurses who take samples, the researchers who are using the data. It’s important to see how everything fits together.”
Staff in CGaP have taken various paths before joining the department; some straight from an undergraduate degree, others following a Masters or PhD, and others from working in the NHS.
They all enjoy working in the bustling lab surroundings, and all mentioned the friendly atmosphere. Emily said, “In CGaP there is a great team format, and a really nice family feel to working.”