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.
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.
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.
Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation
Here we showed that Sld3, which we previously identified as being one of two essential cyclin dependent kinase (CDK) substrates in replication, is a phosphopeptide binding protein which binds specifically to Mcm4 and Mcm6 when they have been phosphorylated by Dbf4 dependent kinase (DDK). Sld3 then directly recruits Cdc45 to MCM and, via CDK phosphorylation, recruits the remaining firing factors. We had previously shown that Sld3 is also one of two targets of the DNA damage checkpoint kinase involved in inhibiting origin firing in response to DNA damage. Thus, Sld3 plays key roles with all three kinases that regulate replication (CDK, DDK, Rad53).
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.
Return to quiescence of mouse neural stem cells by degradation of a proactivation protein
This paper provided the first evidence that stem cells in the adult mouse hippocampus are heterogeneous in their behaviour, with most stem cells differentiating and leaving the niche after they have become active but a small fraction returning to a shallow state of quiescence. These “resting cells” have an essential role in the long-term maintenance of an active stem cell pool.
Epithelia use butyrophilin-like molecules to shape organ-specific γδ T cell compartments
This paper established that intestinal epithelial cells use BTNL/Btnl molecules to select for and regulate tissue-specific gamma delta T cell compartments. It established a biological mechanism by which epithelial cells communicate with local T cells at steady-state (“normality sensing”). Following on from our prototypic discovery of such a mechanism in mouse skin, the work established conservation of the process across tissues as well as across species. The system is unperturbed by microbial colonisation.
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.
CDK substrate phosphorylation and ordering the cell cycle
A phosphoproteomics analysis of CDK substrates has shown that the correct cell cycle temporal order of CDK substrate phosphorylation can be established by a single CDK. It is shown that there is a 50-fold increase of in vivo CDK activity during the cell cycle. Temporal order is achieved by a combination of this rise with differential sensitivity of substrates to CDK activity. Phosphosite turnover is very rapid which helps ensure sharp cell cycle transitions.
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.
The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity
This study showed that epigenetic mechanisms play an important role in generating functional heterogeneity within tumours, and can override genetic alterations that initiate the disease by inhibiting cell proliferative potential during tumour growth. The finding that heterogeneous patterns of H1.0 are broadly observed in cancer and that H1.0 is an independent predictor of patient survival in multiple types of solid tumours makes a strong case for a general role of epigenetic regulators in cancer. Mechanistic characterisation of how H1.0 controls malignant self-renewing states also provided insights into general mechanisms through which the linker histone regulates gene expression.
Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade
We investigated how intratumour heterogeneity affects response to checkpoint blockade and how cancers might be treated based on evolutionary principles. Durable clinical benefit to checkpoint blockade in lung cancer and melanoma was associated with a high burden of clonal neoantigens; in contrast, tumours that progressed early on therapy had a higher burden of heterogeneous neoantigens. We could predict clonal neoantigens present in every tumour cell and identify immune cells that recognise them, suggesting that development of adoptive T cell or vaccination strategies targeting such clonal neoantigens might limit therapeutic escape and resistance mechanisms.
Germinal center B cells recognize antigen through a specialized immune synapse architecture
Using new high-throughput imaging designed for rare cell subsets, we revealed that germinal centre B cells form uniquely patterned immune synapses to bind antigens. The separation of antigen into small clusters, along with specific cytoskeletal organisation results in enhanced mechanical forces transferred onto the B cell receptor-antigen bonds, increasing the mechanical affinity-discrimination power of germinal centre B cells compared to other B cell subsets. The work implicated germinal centre B cell mechanics in selection of high-affinity B cell clones in antibody responses and introduced novel DNA nanosensors for measuring cellular forces.
WNK1 kinase balances T cell adhesion versus migration in vivo
In this study we identified the WNK1 kinase as a negative regulator of CD4+ T cell adhesion and a positive regulator of T cell migration. Furthermore, we showed that WNK1 controls migration through the OXSR1 and STK39 kinases and the SLC12A2 ion co-transporter. This was an unexpected finding since WNK1 had been previously shown to regulate salt homeostasis in the kidney. Our study is the first to have implicated movement of Na+, K+ and Cl- ions in the regulation of T cell migration.
DNA entry into and exit out of the cohesin ring by an interlocking gate mechanism
Building on our successful biochemical reconstitution of topological cohesin loading onto DNA, we completed the reconstitution of both dynamic loading as well as unloading. We realised that both loading and unloading follow a very similar trajectory through sequential ATPase and kleisin gates, only one of which can be open at any one time. This formed the basis for our unified DNA passage proposal both into and out of the ring.
Isoform diversity in the Arp2/3 complex determines actin filament dynamics
The Arp2/3 complex, consisting of seven evolutionarily conserved subunits, generates branched actin networks during many fundamental cellular processes. Taking advantage of actin based motility of Vaccinia virus as a model system, we demonstrate for the first time that in humans the Arp2/3 complex is actually a family of different complexes with distinct actin-nucleating properties.
Characterization of progressive HIV-associated tuberculosis using 2-deoxy-2-[18F]fluoro-ᴅ-glucose positron emission and computed tomography
This work used high-resolution PET/CT imaging to establish for the first time in humans the existence of a high-risk asymptomatic transition state between latent infection and active disease. The technique is thus a phenotypic benchmark for further experimental medicine studies of interventions to prevent progression of asymptomatic subclinical tuberculosis.