Publication highlights

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

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Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation

This work reveals that amino acids, rather than fructose 1,6-bisphosphate, are the relevant cellular regulators of pyruvate kinase M2 (PKM2), a critical node in cancer metabolism. It further elucidates the molecular mechanism of PKM2 regulation by amino acids with a new algorithm that predicts allosteric pathways in proteins, a major and difficult problem in structural biology.

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Published in eLife

Published

CD9 identifies pancreatic cancer stem cells and modulates glutamine metabolism to fuel tumour growth

This work identifies a cancer stem cell (CSC) population in pancreatic ductal adenocarcinoma (PDAC) marked by the tetraspanin CD9. We showed that CD9Hi CSCs are required for the epithelial and mesenchymal cellular heterogeneity seen in PDAC. We found that CD9 assembles a protein complex involved in regulating PDAC metabolism on the cell surface. CD9 depletion dramatically inhibited PDAC growth, identifying CD9 as a therapeutic PDAC target.
These findings suggest that the cellular composition of pancreatic cancer is controlled by a CSC population.

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Published in Nature Cell Biology

Published

3D image of a pancreas

Tissue curvature and apicobasal mechanical tension imbalance instruct cancer morphogenesis

This study introduces a new technique, FLASH, which enables immunostaining of whole organs for imaging and opens up the possibility of analysing a plethora of antigens and tissues that were previously impossible to study in 3D. By achieving this feat, we were able to study epithelial deformation from the moment of transformation within the intact pancreas, to show that early tumours adopt different shapes depending on tissue curvature, due to the distribution of intracellular forces. The work connects cell mechanics with the biology of tumour development in an unprecedented manner.

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Published in Nature

Published

Phospho-dependent regulation of SAMHD1 oligomerisation couples catalysis and restriction

This study explained the mechanism of SAMHD1 regulation by phosphorylation/tetramerisation and correlated restriction activity with the capacity of SAMHD1 to form long lived, stable tetramers. These data form the basis of the prevailing model for SAMHD1 restriction of HIV-1 where dNTP-stabilised SAMHD1 tetramers deplete and maintain low levels of dNTPs in the non-permissive cells resistant to HIV-1 infection.

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Published in PLOS Pathogens

Published

Rad51 paralogs remodel pre-synaptic Rad51 filaments to stimulate homologous recombination

This study was the first to demonstrate that RAD51 paralogues bind to and structurally remodel the pre-synaptic RAD-51-ssDNA filament to a stabilised, “open”, and flexible conformation, which facilitates strand exchange with the template duplex. We showed that RAD51 paralogues act by binding the end of the presynaptic filament, which induces a conformational change that stabilises RAD-51 bound to ssDNA and primes the filament for strand exchange. These observations established for the first time the underlying mechanism of HR stimulation by Rad51 paralogues and revealed a new paradigm for the action of HR mediator proteins.

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Published in Cell

Published

Chromosomes showing telomeres at their ends.

CDK phosphorylation of TRF2 controls t-loop dynamics during the cell cycle

Evidence suggested that the telomere adopts a lasso-like t-loop configuration, which safeguards chromosome ends from being recognised as DNA double strand breaks. However, the regulation and physiological importance of t-loops in end-protection was uncertain. This study uncovered a phospho-switch in TRF2 that coordinates the timely assembly and disassembly of t-loops during the cell cycle, which protects telomeres from replication stress and an unscheduled DNA damage response. These results were the first to definitively establish the t-loop as a physiologically important structure required to suppress checkpoint activation at telomere ends.

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Published in Nature

Published

Structural basis for retroviral integration into nucleosomes

Here, we described a cryo-EM structure of a retroviral intasome in a functional complex with a nucleosome. The structure revealed a multivalent interface of the viral integration machinery and chromatin, involving both gyres of nucleosomal DNA and histones. Whilst the histone octamer remains intact, the DNA is lifted from its surface to allow for strand transfer at highly preferred integration sites. These data provided a unique snapshot of an enzyme recognizing and acting upon nucleosomal DNA. The structure was the first to illustrate nucleosome flexibility facilitating a biological process and, as such, had far-reaching implications for chromosome biology.

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Published in Nature

Published

Stochastic neighbour embedding plot.

Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma

Oesophageal adenocarcinoma shows high genetic heterogeneity making the identification of cancer drivers challenging. We developed a machine learning algorithm to identify cancer drivers in 261 oesophageal adenocarcinomas. Although most predicted drivers were rare or patient-specific, they all perturbed well-known cancer pathways. Using the recurrence of the same pathway perturbations rather than individual genes, we stratified patients into six groups different for their clinical features. We validated experimentally the contribution of these genes to disease progression and revealed acquired dependencies exploitable in therapy. This study described a new way to identify cancer drivers that we have recently further developed for application in precision oncology.

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Published in Nature Communications

Published

Mechanism of head-to-head MCM double-hexamer formation revealed by cryo-EM

The MCM replicative helicase is loaded onto duplex DNA as a double hexamer. Here we use time-resolved cryo-EM to show that ORC binds to its high affinity binding site to load the first MCM hexamer. ORC then releases this site and it, or another ORC molecule then binds the B2 element, which contains a degenerate ORC binding site. This binding is stabilised by a novel interaction between the Orc6 subunit of ORC and the N-terminus of the MCM hexamer. ORC then recruits and loads the second hexamer by the same mechanism as the first hexamer. We employed newly developed in silico reconstitution approaches to describe the full context of the helicase loading reaction, studied on a near-native, chromatinised origin of replication. This study radically changes our approach to investigating chromosome replication with cryo-EM.

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Published in Nature

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

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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.

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Published in Science Translational Medicine

Published

A cell-size threshold limits cell polarity and asymmetric division potential

A key requirement for patterning networks is that the scale of pattern be appropriately matched to the size of the system to be patterned. Through a combination of theory and experiment, we show that failure of the PAR network to scale with cell size restricts stable cell polarity to a specific size range and imposes a minimum cell size threshold for polarity. Experimental alteration of cell size indicates that embryos are sensitive to this size threshold. We thus propose a general strategy by which cells can use intrinsic length scales of patterning networks to enable size-dependent decision making.

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Published in Nature Physics

Published

Antioxidant role for lipid droplets in a stem cell niche of Drosophila

This paper is a continuation of our major research theme on how dividing stem cells in the CNS are able to resist environmental stresses that shut down proliferation in most other developing tissues. It reports the first identification, in any species, of lipid droplets as protectors of stem cells. We discovered that hypoxia induces lipid droplets in the neural stem cell niche and that these protect the neural stem cells themselves from damaging polyunsaturated fatty acid (PUFA) peroxidation reactions. This study laid the foundation for our current mechanistic studies into the antioxidant functions of lipid droplets during development and tumorigenesis.

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Published in Cell

Published

Scientists visualise the TB antibiotic bedaquiline in lipid droplets (circular structures) and Mycobacterium tuberculosis (rod-shaped structures) inside human host cells. 

Subcellular antibiotic visualization reveals a dynamic drug reservoir in infected macrophages

Improving chemotherapies against intracellular pathogens requires an understanding of how antibiotic distribution within infected cells affects efficacy. In this work, we developed an approach to visualise antibiotics in human macrophages infected with the tubercle bacillus. We showed that the antitubercular (anti-TB) drug bedaquiline accumulated in host lipid droplets, which seemed to act as an antibiotic reservoir that could be transferred to bacteria during host lipid consumption. Indeed, alterations in host lipid droplet content affected the anti-TB activity of bedaquiline against intracellular bacilli.

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Published in Science

Published

A temporal window for signal activation dictates the dimensions of a nodal signaling domain

This paper shows how temporal information in the zebrafish embryo is transformed into a spatial pattern. We demonstrate how the Nodal signalling gradient is formed in the early zebrafish embryo and show that its size and shape are determined by a temporal signal activation window created by a microRNA-mediated delay in the translation of Lefty, a Nodal antagonist. This paper was important as it not only challenged the long-held view in the field that the Nodal gradient was formed by a reaction–diffusion mechanism, but highlighted the importance of signalling duration in gradient formation.

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Published in Developmental Cell

Published

Heatmap showing expression of melanoma-specific transcripts across a range of cancer types. The three columns with high expression are from melanoma samples.

LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly

We assembled and disseminated the most complete, to date, transcriptome with a focus on transcripts initiated by or overlapping with endogenous retroelements. This assembly doubles the number of known transcripts and forms the basis for in-depth analysis of retroelement studies in health and disease, particularly in cancer. It also provided unconventional targets for novel cancer vaccines that are being developed by Enara Bio.

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Published in Genome Research

Published

Neutrophils support lung colonization of metastasis-initiating breast cancer cells

In this study we found that via the release of leukotrienes, neutrophils selectively support the more metastatic subset of cancer cells infiltrating the distant tissue and that this activity can be blocked by an inhibitor of leukotriene production. This is one of the most important publications from my laboratory, as it has contributed to the understanding of the crucial responses of neutrophils during metastatic progression.

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Published in Nature

Published

Transcriptional profiling unveils type I and II interferon networks in blood and tissues across diseases

Using advanced bioinformatics approaches, we deciphered the global transcriptional response in the lungs of mice infected or challenged with a broad spectrum of infectious pathogens, including parasites, bacteria, viruses, fungi, or allergens; we also determined to what extent each of these responses is preserved in the blood. We demonstrated a unique global transcriptional signature for each of the different diseases in both lung and blood. The lung transcriptional signatures showed a gradation, ranging from IFN-inducible gene clusters, to those associated with granulocyte/neutrophil/IL-17 dominated genes, to responses dominated by expression of genes encoding TH2 cytokines, mast cells and B cells.

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Published in Nature Communications

Published

Cellular geometry scaling ensures robust division site positioning

Here we describe our discovery that preservation of specific cellular geometry across a range of cell sizes is essential for correct division site positioning and survival, demonstrating the organismal-level function for scaling.

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Published in Nature Communications

Published

Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism

We report a new and powerful metabolic anti-stress mechanism, ‘Lysine harvesting’, that protects microbial cells in stress situations. We noticed that extracellular lysine is taken up to reach concentrations up to 100x higher than those required for growth. Uptake is dependent on the polyamine pathway, connected via promiscuous metabolic reactions, and triggers a reprogramming of redox metabolism: NADPH is channelled into glutathione metabolism, leading to a large increase in glutathione, lower levels of reactive oxygen species and increased oxidant tolerance. Therefore, nutrient uptake occurs not only to enable cell growth, but allows cells to reconfigure their metabolism to preventatively mount stress protection.

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Published in Nature

Published