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Finding the causes of cancer has been a long-standing goal for many researchers at the Wellcome Sanger Institute. Armed with the latest DNA sequencing technologies, there are a variety of approaches to pinpointing the genetic mutations that are relevant for ageing, disease, or those that could be drug targets. Whichever route is taken, or whichever question is looked at, the data are noisy and complex. Analysis may involve sifting and processing terabytes of genomic data, encompassing millions of genetic variations across thousands of samples. In this photo essay, we explore some of the work of staff aiming to understand the molecular underpinnings of cancer and the genetic architectures of our cells.

Dr Jo Fowler is a Senior Staff Scientist at the Sanger Institute. She works on normal skin and normal epithelia from the lining of the oesophagus. She is part of Phil Jones’ team, which has developed a new way to grow these tissues in the laboratory that recapitulates their 3D structure. They are combining this with deep genome sequencing techniques to study the DNA changes that alter cell behaviour.

In real life, cells in our skin and oesophagus accumulate thousands of genetic changes as we age. By middle-age, cells are riddled with mutations. In some cases these DNA changes give some cells an advantage over others, driving the game of clones. Yet most cells, including ones with changes in ‘cancer’ genes do not go on to become cancer.

In the 3D tissue models, the team uses gene editing to see the effects of different DNA mutations on a cell’s growth and behaviour. “We can knock out or mutate genes, or put in genetic mutations that we commonly see in cancer, or combinations of different edits, to see what happens,” says Jo. They can also stress the cells to mimic environmental conditions, like adding ultraviolet light or causing oxidative stress. Analysing the genomes, gene activity and regulation in single cells is giving them detailed information on cellular functions. Live imaging gives them real-time data on the rivalries.

“Our ultimate aim is to understand how these cells are competing in this microscopic landscape. And then, how that relates to cancer, or cancer risk. If we can understand that, there might be places to intervene and prevent disease,” says Jo. “It’s a real privilege that we are allowed to work with donated tissue to understand these fundamental questions.”

Yvette Hooks is a Senior Technical Specialist in the Cancer, Ageing and Somatic Mutations (CASM) programme. She has worked as a histologist at the Sanger Institute for 18 years. Histology has changed over her time, nearly disappearing completely from the Institute, before making a comeback due to work using laser-capture microdissection in cancer research.

Samples arrive in the department from all over the UK and world. Mostly they are human samples, but Yvette has worked on tissues from tiger, giraffe, naked mole rats and others, too. Yvette works with researchers to understand the experiments they want to do, and how the tissue needs to be processed to achieve their goals. The first step is usually fixing a tissue, often in PAXgene to protect the DNA in the cells. The tissues then have to be cut, trimmed according to size and orientated before being set in wax. The blocks are then sectioned, producing sections of 5 – 16 microns, less than the thickness of a human hair, before being attached to slides and stained.

Many of the sample slides are next sent to Paul Scott, who manages the laser-capture microdissection facility.

Laser-capture microdissection (LCM) brings the precision of a surgeon’s scalpel to dissection, but on a microscopic scale. The technique enables researchers to see and then accurately cut out tiny subpopulations of cells from a piece of tissue. The process uses a laser beam to remove the target cells, usually groups of 10s to 100s, for further analysis. The advantage of pinpointing such a small group means researchers can study the clones – those groups of cells with the same genome that have formed a small population. The handful of cells is then enough to accurately sequence their entire genome, as well as which genes are active.

After DNA is extracted, it is sent to sequencing, where biological data are converted into digital. The digital data are processed, tracked and handled by the Cancer, Ageing and Somatic Mutations Informatics Team (CASM IT), comprising of a crucial mix of software developers and bioinformaticians.

The team, led by Victoria Offord, works closely with faculty researchers. They build and maintain high-throughput data pipelines as well as develop and publish new software and analysis tools. While there are existing tools out there, researchers need specific, bespoke analysis to track their genome editing. At the moment, CASM IT are working with Faculty on developing a tool for quantifying single guide and combinatorial CRISPR screens.

In thousands of experiments running in parallel, CRISPR is used to disrupt the DNA sequence of cells. Each cell will have a different disruption in just one if it’s 20,000 genes, or other, regulatory areas of the genome. One readout – to check the cells have the expected DNA sequence change – is sequencing. CRISPR is used in several large cancer research projects at the Sanger Institute. For example, researchers are using the technique to disrupt every gene in the genome of cancer cells, and then monitor the effects on the cells. This work aims to uncover which genes are ‘essential’ to a cancer cells survival, and therefore are potential drug targets.

David Adam’s group has a long-held interest in understanding the chain of events that take place within a cell that cause it to become cancerous. One of their projects is ‘combinatorial CRISPR screening’. To probe the inner workings of a cell, the team uses CRISPR DNA editing to target, and disrupt, pairs of genes at the same time. The aim is to identify when targeting two genes at once is lethal to the cell. They are systematically screening cancer cells – testing tens of thousands of combinations of genes. They are focussed on melanoma and lung cancer, as these are cancers of unmet clinical need. If the disruption of a pair of genes causes a cancer cell to die, the team investigates those genes further, in ‘deep-dive’ experiments that aim to understand their biology and roles within a cell.

They are also using saturation genome editing (SGE), a relatively new genome editing technique that uses CRISPR-Cas9 to introduce each and every possible mutation to a gene, or another stretch of DNA. They use the technique to search for harmful variants in cancer genes – including those that have never been seen in people before. They recently published their findings on RAD51C, a gene linked to breast and ovarian cancer. Their work could help in the clinical management of patients and advance targeted therapies.

Grace Ping, Head of Operations, and her team underpin everything in the programme. They support the scientists with end-to-end processes for thousands of samples as they arrive at the Institute, move between different laboratories, as DNA is prepared and sequenced, and data are ready for analysis. She oversees the core laboratory teams, core IT teams, and research management teams. The idea is to have this comprehensive support in place so the researchers can really focus on the things they need to do, from designing experiments to writing manuscripts. She relishes the challenges of her role – from balancing competing priorities to ensuring staff in the core teams get the recognition they deserve.

There are 43 nationalities represented in the Programme, and several people in Grace’s teams have been at the Institute for over 20 years, since the very first human genome was sequenced. For Grace, it’s a reflection of the pride that people feel. “We’re all part of a mission that we’ve committed to deliver. Not everyone’s name is out there, but we feel a sense of contributing.”

Find out more about the Cancer Ageing and Somatic Mutations Programme at the Sanger Institute on our website, or browse our current vacancies.