Publication highlights

Go inside our research

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

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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

Knitting with a thread pulled out - epigenetic changes

How epigenetics fuels genetic drivers in lung cancer

In this study, researchers at the Crick and UCL investigated how an epigenetic change called DNA methylation cooperates with genetic changes in non-small cell lung cancer (NSCLC) using 217 tumour and normal regions from 59 TRACERx patients. This is the first multiregional lung cancer cohort integrating genomic, transcriptomic, and epigenomic data to map tumour evolution in such detail. They uncovered a novel mechanism, where DNA methylation fine-tunes how oncogenes are switched on together by compacting the DNA. We also identified hypermethylated driver genes emerging early in tumour evolution and developed a new metric, Mr/Mn, to distinguish functional from passenger methylation changes. Our work highlights epigenetic drivers with therapeutic potential.

DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution

Published in Nature Genetics

Published

Lung cancer cells

Differences in immune evasion within the same tumour

In a joint effort from the Francis Crick Institute, UCL and the Netherlands Cancer Institute, researchers have demonstrated that lung cancers consist of different subclones that differ intrinsically in their capacity to evade immune attack. Cancers are genetically heterogeneous – consisting of different subclones – but to what extent this affects immune evasion remained largely unclear. Now, using samples from the TRACERx cancer evolution study, the team have established organoids – mini-tumours growing in 3D - from different regions from the same tumour, and further separated these into individual subclones. Challenging these with immune cells from the patient’s tumour showed that different subclones isolated from the same tumour differ profoundly in their ability to trigger an immune response. This provides direct functional evidence that subclonal cancer evolution has important consequences for the ability to evade immune attack.

Subclonal immune evasion in non-small cell lung cancer

Published in Cancer Cell

Published

Electrical activity in SCLC cells

Lung cancer cells can go ‘off grid’

Researchers at the Crick have found that some particularly aggressive lung cancer cells can develop their own electric network, like that seen in the body’s nervous system. They found that small cell lung cancer cells (which mainly arise from neuroendocrine cells in the lungs) had gone 'off grid' - they were able to generate their own electrical activity, becoming independent of the body's main electrical supply. They also saw important changes in gene expression as the cancer progressed, resulting in some neuroendocrine cells becoming non-neuroendocrine cancer cells. Genes enabling electrical communication were switched on in the NE cells, and genes relating to producing a supportive environment were switched on in the non-NE cells, which were shuttling lactate as an energy source for NE cells. Markers of increased electrical activity were also seen in cancer cells in people with SCLC. As their cancer progressed, non-NE cells showed markers suggesting they were increasingly pumping out lactate. These changes drive the tumour's ability to grow and spread.

Intrinsic electrical activity drives small-cell lung cancer progression

Published in Nature

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

Cancer cells in blue interacting with fibroblasts in red

Crosstalk in the tumour microenvironment

Interactions between cells in the tumour microenvironment (TME) shape cancer progression and patient prognosis. To see how the TME influences cancer outcomes, the Tumour Cell Biology Laboratory and collaborators developed a method to analyse gene expression signatures that flagged up crosstalk between supporting stroma in direct contact with cancer cells. They found that high crosstalk was predictive of worse overall survival in multiple and independent cohorts of squamous cell carcinomas. Functional analysis revealed the signalling proteins HB-EGF and EGFR as key mediators of crosstalk that ultimately favours the recruitment of macrophages into the TME. These results demonstrate a new approach to detecting biologically meaningful stromal signatures and how they can be leveraged to gain mechanistic insight.

Cancer cell – Fibroblast crosstalk via HB-EGF, EGFR, and MAPK signaling promotes the expression of macrophage chemo-attractants in squamous cell carcinoma

Published in iScience

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

Tumour tissue

Limitations of laboratory models to represent patient lung tumours

An important aspect of cancer research is the model systems that researchers use to test new therapies. Within the TRACERx lung cancer study, researchers from the CRUK Lung Cancer Centre of Excellence have performed a direct comparison of patient tumours and a commonly used laboratory model - ‘patient-derived xenograft’ or ‘PDX’ models - in which patient tumour tissue isgrown within immunocompromised mice.

The researchers found that patient tumours are often genetically complex, with many co-existing subclones (groups of cell populations with different characteristics). However, the PDX models often only represented one of these subclones. This over-simplicity of PDX models might limit their ability to predict patient responses. These findings will shape the future use of PDX models in lung cancer research and clinical studies.

Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

Published in Nature Communications

Published

Comfortably numb – how cancers survive and thrive

The evolution of established cancers is driven by selection of cells with enhanced fitness. Subclonal mutations in numerous epigenetic regulator genes are common across cancer types, but their functional impact was unclear. The Scaffidi lab has shown that disruption of the epigenetic regulatory network increases the tolerance of cancer cells to unfavourable environments by promoting the emergence of stress-resistant subpopulations via a process they term transcriptional numbness. Their findings provide a mechanistic explanation for the widespread selection of subclonal epigenetic-related mutations in cancer and uncover phenotypic inertia as a cellular trait that drives subclone expansion.

Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia

Published in Cancer Cell

Published

Scientists find that the way tumours grow impacts their genetics

Researchers from the Bates, Turajlic and Sahai labs have collaborated to develop a computer model to analyse how the way in which tumours grow affects their genetic makeup. Using this new model, they have identified links between tumour growth and shape, and how quickly a patient’s cancer might progress.

Spatial patterns of tumour growth impact clonal diversification in a computational model and the TRACERx Renal study

Published in Nature Ecology and Evolution

Published

Bone marrow backup needed to tackle respiratory infections

Researchers in the Reis e Sousa lab have found how the immune system triggers an ‘emergency’ dendritic cell response during infection. Dendritic cells have an important role in the immune system, detecting infectious bacteria, fungi or viruses that have entered the body and alerting T cells which recognise and attack the invader. However, there are few dendritic cells in healthy tissue like the lungs which means that, on infection, their numbers need to be boosted. In their study, the team monitored dendritic cells in mice infected with flu virus and found that, after infection, new dendritic cells are released from the bone marrow in response to a chemokine ‘distress’ signal which directs them to the site of infection.

Recruitment of dendritic cell progenitors to foci of influenza A virus infection sustains immunity

Published in Science Immunology

Published

Cells from the centre of tumours most likely to spread around the body

Research from a collaborative team at the Crick, Royal Marsden, UCL and Cruces University Hospital has found that cells from different parts of kidney tumours behave differently, and surprisingly, cells within the centre of a tumour are the most aggressive and have the highest chance of spreading around the body.

Selection of metastasis competent subclones in the tumour interior

Published in Nature Ecology and Evolution

Published

COVID testing

Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers

This important paper showed very high levels of infection amongst healthcare workers in a local hospital. It has influenced government policy – asymptomatic healthcare workers are to be screened as per our recommendation (announced October 12th).

View the publication

Published in The Lancet

Published

Tissue clonality of dendritic cell subsets and emergency DCpoiesis revealed by multicolor fate mapping of DC progenitors

Conventional dendritic cells (cDCs) originate from a committed precursor in bone marrow (BM) that exits via the blood as a pre-cDC to seed tissues with the cDC1 and cDC2 subsets. We used a multi-colour genetic tracing mouse model to analyse colonisation of tissues by pre-cDC. We found that cDCs in tissues comprise clones mostly composed of a single cDC subset and that ‘flu infection causes an efflux of pre-cDCs from BM and influx into the lungs. The latter finding indicates that cDCpoiesis is responsive to emergency need, which suggests previously undiscovered communication between tissues and cDC progenitors in BM.

View the publication

Published in Science Immunology

Published

NK cells stimulate recruitment of cDC1 into the tumor microenvironment promoting cancer immune control

In this paper we showed that cDC1 recruitment and infiltration in several mouse tumour models depends on the chemokines CCL5 and XCL1 produced by NK cells. In human cancers, CCL5/XCL chemokine transcripts correlate with gene signatures for NK cells and cDC1 and predict overall survival in melanoma, head and neck cancer, breast cancer and lung adenocarcinoma. Therefore, our data uncovered a mechanism for cDC1 recruitment into tumours that is translatable to humans and cancer patient survival.

View the publication

Published in Cell

Published

Cyclooxygenase-dependent tumor growth through evasion of immunity

In this paper, we uncovered a potent mechanism of cancer immune evasion, namely cyclooxygenase (COX)-dependent secretion of prostaglandin E2 (PGE2) by tumour cells. We further showed that the growth of PGE2-secreting tumours in mice can be reversed by a combination of checkpoint blockade immunotherapy and COX inhibitors, suggesting that COX inhibition might be a useful addition to both conventional and immune-based therapy of cancer. This paper led to seven clinical trials worldwide to test combinations of prostaglandin E2 inhibition with checkpoint blockade cancer therapies.

View the publication

Published in Cell

Published

A mechanically active heterotypic E-cadherin/N-cadherin adhesion enables fibroblasts to drive cancer cell invasion

Our previous work showed how stromal fibroblasts lead the collective invasion of cancer cells, and documented how remodelling of the extracellular matrix was important for this behaviour. Following our observation of direct cell-cell contacts between cancer cells and fibroblasts, we hypothesised that the two cells might be mechanically coupled; therefore, we began collaborating with Xavi Trepat (IBEC Barcelona), who is a world leader in the mechanics of multi-cellular systems. By biophysical measurements and a range of conventional cell and molecular biology manipulations, we demonstrated that fibroblasts actively ‘pull’ cancer cells into the surrounding extracellular matrix.

View the publication

Published in Nature Cell Biology

Published

Imaging showing the different types of tissue structure organised by fibroblasts.

Extracellular matrix anisotropy is determined by TFAP2C-dependent regulation of cell collisions

In this study, we used our bank of patient-dervied stromal fibroblasts to ask why some fibroblasts generate highly aligned extra-cellular matrices and other do not. We were able to show how cell migration and cell-cell collisions can dictate the patterns formed by fibroblasts, and that furthermore, the higher order organisation of fibroblasts and matrix is associated with millimetre scale contraction of reconstituted tissues and cancer invasion. The quantitative tool developed during the course of this work and a related study is now being tested for its prognostic value in simple histological stains of breast and prostate cancers.

View the publication

Published in Nature Materials

Published

Image showing mouse breast cancer cells (orange) within lung tissue (light pink) connected with protein fibres (purple).

Crosstalk with lung epithelial cells regulates Sfrp2-mediated latency in breast cancer dissemination

We set up a complex model for lung alveoli by co-culturing lung fibroblasts and alveolar epithelial type I and type II cells on a gas permeable support, with the expectation that the fibroblasts would strongly influence the behaviour of cancer cells introduced into the system. However, we discovered that the largest effect came from the alveolar epithelial cells, and we then used a range of approaches to delineate the signalling mechanisms involved. This work, together with a concomitant study from the Malanchi group, established the role of epithelial cells in the tumour microenvironment of indolent and micro-metastases.

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Published in Nature Cell Biology

Published

Cancer cells colliding with fibroblasts

STING and IRF3 in stromal fibroblasts enable sensing of genomic stress in cancer cells to undermine oncolytic viral therapy

This work shows why stromal fibroblasts are an important source of inflammatory modulators in tumours. We show fibroblasts can respond to cGAMP produced by cancer cells, but only when the two cell types are in direct contact. This in turn promotes the STING and IRF3 dependent expression of interferon beta and various chemokines. The subsequent up-regulation of interferon-stimulated gene expression undermines the efficacy of oncolytic viruses. We propose the requirement for direct contact represents a ‘tissue level’ mechanism for triggering this response specifically in the context of tissue damage, as in healthy tissue, the basement membrane precludes such interactions.

View the publication

Published in Nature Cell Biology

Published