Publication highlights

Go inside our research

Explore a selection of research case studies from the past five years.

Read now
A Crick researcher reading a scientific paper on a screen.

Intro

Researchers at the Crick are tackling the big questions about human health and disease, and new findings are published every week.

Our faculty have picked some of the most significant papers published by Crick scientists, all of which are freely available thanks to our open science policy.

Highlights

Structure of PIK3 and RAS with drug

How to block cancer’s elusive growth switch

The RAS oncogene is mutated in around one in five cancers, and was once referred to as 'undruggable'. Scientists are now focusing on a particular enzyme RAS targets, called PI3K, hoping to stop uncontrolled cancer growth while maintaining the function of RAS in healthy cells. Researchers at the Crick and Vividion Therapeutics used chemical screening to find a series of small compounds thatmight stop the RAS-PI3K interaction without blocking PI3K's other functions. These compounds were then tested in mice with RAS-mutated lung tumours. The treatment effectively halted tumour growth, with no evidence of hyperglycaemia, which is a problem for current drugs on the market. It also slowed tumour growth in mice with HER2 mutations.

Covalent inhibitors of the PI3Kα RAS binding domain impair tumor growth driven by RAS and HER2

Published in Science

Published

Red blood cells and white blood cells

Age-related genetic changes in the blood associated with poor cancer prognosis

Researchers from the Francis Crick Institute, UCL, Gustave Roussy and Memorial Sloan Kettering Cancer Center (MSK), have discovered that expansion of mutant blood cells, a phenomenon linked to ageing, can be found in cancerous tumours, and this is associated with worse outcomes for patients. Clonal haematopoiesis of indeterminate potential (CHIP) is a condition where blood stem cells accumulate mutations over time. The researchers found that tumour-infiltrating clonal haematopoiesis, not CHIP alone, was associated with greater risk of relapse and cancer death. Patients with TI-CH had an expansion of myeloid cells which can support tumour progression and support. They also discovered that blood cells with TET2 mutations were more likely to be tumour-infiltrating, and that TET2 mutant myeloid cells remodelled the tumour microenvironment. Finally, they validated their findings in over 49,000 patients, finding that mutations were more common in harder-to-treat cancer types.

Tumor-infiltrating clonal hematopoiesis

Published in New England Journal of Medicine

Published

Tumour cells

Lung cancer test predicts survival in early stages better than current methods

Researchers at the Crick, the UCL Cancer Institute and UCLH have shown that a test called ORACLE can predict lung cancer survival at the point of diagnosis better than currently used clinical risk factors. This could help doctors make more informed treatment decisions for people with stage 1 lung cancer, potentially reducing the risk of the cancer returning or spreading. ORACLE was developed in 2019 to overcome the lack of biological markers in lung cancer, which is important for people with stage 1 lung cancer, who are normally given surgery without chemotherapy. In this study ORACLE was validated in 158 people with lung cancer in the Cancer Research UK-funded TRACERx study. The team found that ORACLE could predict which patients with stage 1 lung cancer had a lower chance of survival, and might benefit from chemotherapy as well as surgery. The researchers also found that high ORACLE risk scores were linked to regions of the tumour that were more likely to spread to another part of the body.

Prospective validation of ORACLE, a clonal expression biomarker associated with survival of patients with lung adenocarcinoma

Published in Nature Cancer

Published

Mass cytometry images of carcinogen induced lung tumours in mice.

Scaling up tests to detect interactions between proteins for drug discovery

The NanoBiT Biochemical Assay was created to investigate protein-protein interactions in live mammalian cells. Soly Ismail, Scientific Programme Manager in the Oncogene Biology Laboratory, led by Julian Downward, further developed the assay so it only needed to use parts of a extracts from cells rather than the live cells themselves, allowing it to be scaled up to undertake many tests at once. These protein-protein interactions are often difficult to visualise but could be potential new drug targets. Soly used the assay to detect and block weak interactions between a cancer-causing protein called RAS and an enzyme called PI3kK. The identified compounds that bind with PI3kK will be followed up in further tests to understand the nature of these interactions and how to optimise these compounds for drug development. Soly was awarded the Sir David Cooksey Prize in Translation for this work.

High throughput application of the NanoBiT Biochemical Assay for the discovery of selective inhibitors of the interaction of PI3K-p110α with KRAS

Published in SLAS Discovery

Published

Clusters of T cells and Tregs in colourful patches

Researchers identify shield of cells that protects lung tumours from treatment

Researchers at the Francis Crick Institute, working with the Amsterdam University Medical Centre, have found that immune cells are held back from fighting lung tumours by another type of cell in the surrounding cellular neighbourhood. The researchers saw that clusters of fighter cells called T cells were gathered near tumours in mice with cancer-causing mutations, but the cell community also contained regulatory T cells (Tregs), which were stopping immune cell coordination. When the researchers blocked the action of Tregs, the mice responded better to a KRAS inhibitor, a type of cancer drug, showing reduced tumour growth and longer survival.

Spatial multiplex analysis of lung cancer reveals that regulatory T cells attenuate KRAS-G12C inhibitor-induced immune responses

Published in Science advances

Published

Tumour in blue on the left and multicolour on the right, highlighting entry of immune cells

Combination treatment improves response to immunotherapy for lung cancer

The Oncogene Biology Laboratory at the Crick, in collaboration with Revolution Medicines, have tested a combination of treatments in mice with lung cancer and shown that these allow immunotherapies to target non-responsive tumours. They combined a newly identified KRAS G12C inhibitor, a compound that blocks a protein called SHP2 (which inhibits cancer cells and can also activate tumor immunity), and an immune checkpoint inhibitor (which blocks proteins that helps the cancer cells hide from the immune system). In mice with functional immune systems, the triplet combination shrank the tumours and, in some mice, fully eradicated them. Even in mice with ‘immune cold’ tumours that are normally unresponsive to immunotherapy, the combination allowed tumours to become sensitised to the immune checkpoint inhibitors.


Combining RAS(ON) G12C-selective inhibitor with SHP2 inhibition sensitises lung tumours to immune checkpoint blockade

Published in Nature Communications

Published

Lung cancer cell.

Why many lung cancer patients who have never smoked have worse outcomes

Researchers at the Francis Crick Institute, UCL and AstraZeneca have discovered the reason why targeted treatment for non-small cell lung cancer fails to work for some patients, particularly those who have never smoked. The study shows that lung cancer cells with two particular genetic mutations are more likely to double their genome, which helps them to withstand treatment and develop resistance to it. The researchers re-analysed data from the trials of a new EGFR inhibitor, which blocks a common genetic mutation in this type of lung cancer. They compared the impact of treatment for patients with either EGFR-only or with EGFR and p53 mutations, finding that tumours got smaller in response to treatment for patients with just EGFR mutations. But for patients with both mutations, some tumours had grown, providing evidence of rapid drug resistance. This was confirmed in mice with both mutations - resistant cells had doubled their genomes.

Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling

Published in Nature Communications

Published

Mass cytometry images of carcinogen induced lung tumours in mice.

Enzyme target identified to counteract metastasis in pancreatic cancer

This paper addresses the significance of a process called protein palmitoylation for the metastasis of pancreatic cancer cells in immunocompetent mouse models. Metastasis is the major determinant of pancreatic cancer’s extremely poor prognosis, with little known about the mediators of the process. In this paper researchers at the Crick identify a number of novel targets that promote metastasis in vivo, and examine the role of the palmitoyl transferase ZDHHC20, the most prominent of these. Despite having no effect on proliferation or migration in cells in a dish, the loss of this enzyme abolishes metastatic seeding of cancer cells in the body. Interestingly, this effect is reversed in immunodeficient mice and following depletion of immune cells called Natural Killer cells, indicating an interaction with the innate immune system. This manuscript will open avenues for further exploration of palmitoylation-regulated tumour types and provide a basis for development of ZDHHC20-targeting therapeutic strategies that may have value in counteracting metastasis in pancreatic cancer.

Palmitoyl transferase ZDHHC20 promotes pancreatic cancer metastasis

Published in Cell Reports

Published

A modified ZDHHC enzyme and lipid

Solving a lipid whodunnit creates a new class of drug target

Enzymes called ZDHHCs are responsible for directing a type of regulatory modification, palmitoylation, that adds a lipid to specific proteins, but humans have 23 different ZDHHCs, and understanding which proteins each one modifies has been very challenging. A team led by satellite group leader Ed Tate have developed a new method that identifies the set of proteins just one ZDHHC acts on, which has ramifications not just for our understanding of lipid biology, but also for therapeutic strategies targeting proteins whose activity depends on palmitoylation. To progress the research into drug discovery, the researchers have also screened a very large library of compounds to find effective ZDHHC inhibitors.

A palmitoyl transferase chemical-genetic system to map ZDHHC-specific S-acylation

Published in Nature Biotechnology

Published

APOBEC in lung cancer

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

Increasing understanding of how drivers of mutations affect lung tumour evolution is critical to prevent tumour reoccurrence and resistance. Using the TRACERx lung cancer study, a research team at the Francis Crick Institute uncovered increased expression of a mutation-driving gene called APOBEC3B (A3B) in lung tumours treated with targeted therapy.

Using multiple pre-clinical lung cancer models, they found that the role of A3B in lung tumor evolution is context dependent. When tumours first start growing, A3B restrains their growth, causes instability in their DNA, and drives tumour cell death. In contrast, with targeted lung cancer therapy, A3B actually helped cancer cells resist treatment.

These findings reinforce the concept that targeted therapies can induce adaptive changes that promote resistance.

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

Published in Nature Genetics

Published

Leaking lysosomes talk to mitochondria

Lysosomes are cellular organelles containing a potent cocktail of digestive enzymes—proteases—used to break down worn out cell parts and destroy invading viruses and bacteria. There is crosstalk between lysosomes and mitochondria, the energy generating organelles of cells, but whether this cross talk is affected by lysosomal damage is unknown. In a collaboration led by the Gutierrez lab, Bussi et al uncovered a pathway whereby protease leakage from functional lysosomes degrades mitochondrial proteins and impairs human macrophage metabolism, relevant to several diseases where compromise of the lysosomal membranes is a key intracellular event. This work uncovers an inter-organelle communication pathway, providing a general mechanism by which macrophages undergo mitochondrial metabolic reprogramming after membrane damage to the network of intercellular organelles.

Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism

Published in Nature Communications

Published

Potential combination therapy for lung cancer

Researchers in the Downward lab have studied the effects of combining immune checkpoint blockade with KRAS inhibitors, in mice. In tumours where there were already high numbers of active immune cells, so called ‘immune hot’ tumours, the treatment successfully controlled the cancer. However, in cases where the immune system was not able to mount a strong response, the combination treatment was ineffective.

Therapeutic KRASG12C inhibition drives effective interferon-mediated antitumor immunity in immunogenic lung cancers

Published in Science advances

Published

Oncogenic RAS signaling promotes tumor immunoresistance by stabilizing PD-L1 mRNA

This work establishes for the first time a link between oncogenic RAS signalling and increased immuno-suppressive expression of the immune checkpoint protein PD-L1. RAS signalling results in phosphorylation and inactivation of TTP, a factor involved in degrading PD-L1 mRNA transcripts. As TTP inactivation causes accumulation of PD-L1 mRNA, interfering with the RAS pathway increases TTP binding to AU-rich elements of the transcripts, decreases PD-L1 protein production, and leads to enhanced antitumor immunity.

View the publication

Published in Immunity

Published

RAC1P29S induces a mesenchymal phenotypic switch via serum response factor to promote melanoma development and therapy resistance

Metastatic melanoma is a lethal disease, in part because of rapid acquisition of resistance to therapy. Using genetically engineered mouse models, we demonstrate that the activating RAC1 P29S mutation, present in up to 5% of melanoma patients, cooperates with BRAF as a driver of melanoma initiation and promotes BRAF inhibitor resistance. The critical RAC1 effector pathway in melanoma is shown to be the transcription factor complex SRF/MRTF, which initiates a switch to a mesenchymal-like state characterized by therapy resistance. Therapeutic targeting of SRF/MRTF may have potential to reverse BRAF inhibitor resistance in melanoma patients bearing the oncogenic RAC1 P29S mutation

View the publication

Published in Cancer Cell

Published

Image showing a mouse lung before and after treatment, with tumours indicated by different colours. The tumours on the right are visibly smaller.

Development of combination therapies to maximize the impact of KRAS-G12C inhibitors in lung cancer

KRAS is the most commonly mutated oncogene in human lung cancer, but direct targeting of RAS proteins has proved difficult. A recently developed inhibitor of G12C mutant KRAS protein inhibits lung cancer progression in mouse models but does not provide durable regressions. By studying signalling pathways required for survival of KRAS mutant cells, we demonstrate a strong and selective potentiation of the effects of G12C KRAS inhibitors when mTOR and/or IGF1R are also inhibited. Using mutant specific G12C KRAS inhibitors rather than MEK inhibitors in these combinations is associated with greater specificity and lower toxicity. We propose that adding IGF1R and mTOR inhibitors will increase the impact of G12C KRAS inhibitors in clinical trials.

View the publication

Published in Science Translational Medicine

Published

IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche

In this work we mined this database to refine hESC culture conditions. These data will be a powerful resource for the community and will lead to changes in how hESCs are cultured in the future. Building on these data, we demonstrated that IGF1-receptor/PI3K/AKT, but not FGF receptor, signalling is required for hESC self-renewal. We built a searchable website that includes a compendium of human embryo gene expression analysis and compiled a list of all possible ligand and receptor interactions.

View the publication

Published in Nature Communications

Published