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.
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.
Versatile humanized niche model enables study of normal and malignant human hematopoiesis
Immunodeficient mouse models have been instrumental in improving our understanding of human healthy haemopoietic stem cells and their hierarchical organisation as well as of the functional and phenotypic heterogeneity of leukaemic stem cells in acute myeloid leukaemia. However, xenotransplantation models failed at reconstituting the human bone marrow niche which remains of mouse origin. Using a bioengineered scaffold, we developed a new versatile humanised bone marrow niche which supports the engraftment of both normal and leukaemia stem cells in vivo. This 3D scaffold represents a suitable model to study and dissect the human bone marrow composition and test the effect of specific stroma cell types and niche factor functions during both normal human haemopoiesis and leukaemia.
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.
Decoding of position in the developing neural tube from antiparallel morphogen gradients
Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. Using quantitative gene expression and signalling measurements we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. This revealed a strategy that minimises patterning errors in response to the joint input of noisy opposing gradients. The study illustrates how we integrate quantitative data, developmental and microfluidic experiments with phenological and mechanistic models.
A supramolecular assembly mediates lentiviral DNA integration
Lentiviral IN proteins are notoriously poorly behaved in vitro, and the HIV 1 intasome has eluded structural biologists for over two decades. Prior research resulted in a collection of partial crystal and NMR structures that did not explain how lentiviral integrase synapses viral DNA ends. This paper described the first structure of the lentiviral intasome, solving the long-standing mystery and reconciling years of HIV-1 integrase structural biology and biochemistry.
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.
Bidirectional eukaryotic DNA replication is established by quasi-symmetrical helicase loading
This paper shows that loading of the MCM double hexamer is a quasi-symmetrical reaction: two ORC molecules bound at two opposing sites of different affinity each recruit and load a single hexamer. The distance between the ORC binding sites is not critical. Subsequent work has provided further evidence for this from cryo-EM.
Chromatin controls DNA replication origin selection, lagging-strand synthesis, and replication fork rates
In this and the accompanying paper (Yeeles et al. 2017 Mol Cel 65, 105-116) we describe the reconstitution of full chromatin replication. We first identified all of the factors required for complete and rapid replication of naked DNA. Then we identified and characterised factors required to replicate chromatinised templates. We showed FACT is essential for chromatin replication, whilst nucleosome remodellers and histone acetylases help chromatin replication. In addition, chromatin enforces origin specificity and Okazaki fragment processing. Finally, we found that histones are efficiently transferred to nascent DNA.
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.
aPKC cycles between functionally distinct PAR protein assemblies to drive cell polarity
Through the use of aPKC inhibitors and genetic mutations, we demonstrate that aPKC cycles between distinct PAR-3 and CDC-42 dependent states, which define, respectively, the ability of the aPAR network to respond to spatial cues and to displace pPAR proteins from the membrane. We further show that cue sensing depends crucially on the oligomeric nature of the PAR-3 state, that the integrity of this cycle is required for coupling of cue-sensing and effector functions of the aPAR network, and that this cycle is enforced by activity of aPKC.
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.
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.
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.
Genome editing reveals a role for OCT4 in human embryogenesis
The first demonstration of the utility of CRISPR–Cas9-mediated genome editing for investigating gene function in the context of human embryonic development. We revealed a distinct role for the developmental regulator OCT4 in human versus mouse development.
Lineage-dependent spatial and functional organization of the mammalian enteric nervous system
In this paper we use genetic lineage tracing and clonal analysis to characterise mammalian enteric nervous system progenitors, define differentiation trajectories for enteric neurons and glia during development and propose a new model for the 3-D organisation of the enteric nervous system.
Reactive oxygen species localization programs inflammation to clear microbes of different size
How inflammatory programmes are tuned to recruit sufficient numbers of neutrophils to clear microbes of different size remained unknown. Furthermore, neutrophils were not thought to serve as major regulators of inflammation in vivo. We showed that reactive oxygen species localisation allows neutrophils to regulate their own recruitment by setting the appropriate level of cytokine production.
A neuroprotective astrocyte state is induced by neuronal signal EphB1 but fails in ALS models
We addressed the hypothesis that impairment of neuroprotective astrocytic mechanisms are disrupted in ALS using in vivo models, and patient-specific iPSCs. We found that EphB1, a neuronal signal, can induce a neuroprotective astrocyte phenotype through the EphrinB1 receptor / JAK-STAT pathway and that this response fails in ALS astrocytes.
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.
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.
Feedback control of AHR signalling regulates intestinal immunity
This paper established the AHR induced feedback system of cytochrome P4501 metabolising enzymes as critical regulators of AHR signalling. Excessive ligand degradation via Cytochrome P4501 phenocopies AHR deficiency and has detrimental consequences for intestinal health which can be counterbalanced by increasing the intake of AHR ligands in the diet. The intestinal epithelium acts as gatekeeper for the supply of ligands throughout the body emphasising the importance of the gut barrier for whole body physiology.