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.
CD1d-mediated lipid presentation by CD11c+ cells regulates intestinal homeostasis
Intestinal homeostasis requires a continuous dialogue between commensal bacteria and intestinal immune cells. Natural Killer T (NKT) cells are a population of CD1d-restricted lipid-reactive lymphocytes contributing to the regulation of mucosal immunity, but the mechanisms underlying this are poorly understood. Here we show that lipid presentation by CD1d+ intestinal dendritic cells and macrophages controls NKT cell function and activation which in turn regulates commensal bacteria and immune cell populations in the gut. These results reveal an NKT cell-dendritic cell crosstalk as a key mechanism for the regulation of intestinal homeostasis.
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.
A protease cascade regulates release of the human malaria parasite Plasmodium falciparum from host red blood cells
This study showed that egress involves an enzyme cascade in which the serine protease SUB1 activates a second, cysteine protease called SERA6, enabling SERA6 to rapidly and precisely cleave the major red cell cytoskeletal protein β-spectrin and dismantle the cytoskeleton. It provides the first plausible model to explain how the parasite accomplishes timely rupture of its host cell membrane.
Stabilization of reversed replication forks by telomerase drives telomere catastrophe
This study defined the mechanism leading to critically short telomeres in the absence of RTEL1 and showed that telomerase, which extends telomeres in normal cells, is pathological when forks encounter an obstacle within the telomere. We showed that replication forks stall and reverse at persistent t-loops, which creates a pseudo-telomere substrate that is inappropriately stabilised by telomerase. Removing telomerase or blocking replication fork reversal rescued telomere dysfunction in Rtel1 deficient cells. We proposed that when persistent t-loops stall the replisome, telomerase inhibits fork restart, triggering the excision of the t-loop by SLX1/4 and loss of a substantial part of the telomere.
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.
Nervous system regionalization entails axial allocation before neural differentiation
The prevailing view of neural induction in vertebrate embryos had been that cells are initially induced with anterior (forebrain) identity and then caudalising signals convert a proportion to posterior fates (spinal cord). Using chromatin accessibility, to define how cells adopt region-specific neural fates, combined with genetic and biochemical perturbations, we found that contrary to the established model, cells commit to a regional identity before acquiring neural identity. These findings prompt a revision to textbook models of neural induction. The study illustrates our adoption of new genomic methods (ATACseq) to address long-standing questions, and our capacity to productively collaborate with computational biologists.
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).
The mechanism of eukaryotic CMG helicase activation
This paper provided the first view of how the inactive MCM double hexamer is converted to two active CMG helicases. We showed MCM remains bound to ADP after loading; firing factors trigger ADP-ATP exchange; ATP rebinding causes double hexamer splitting, initial DNA melting and CMG formation. Active helicases then translocate N-terminus first.
α-synuclein oligomers interact with ATP synthase and open the permeability transition pore in Parkinson’s disease
Protein aggregation drives neuronal death in Parkinson’s disease, although how transition of monomeric protein structures to aggregated forms causes toxicity is unknown. We demonstrate that aggregation of the protein α-synuclein generates beta sheet-rich oligomers, which localise to the mitochondrial inner membrane, where they impair complex I-dependent respiration, induce oxidation of ATP synthase and cause mitochondrial lipid peroxidation. These oxidation events result in opening of the permeability transition pore, triggering mitochondrial swelling, and ultimately cell death. This work highlights how structural conversion of a protein changes its physiological interaction with proteins and lipids, and induces pathology in human cell models of disease.
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.
Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila
This reports the first identification, in any species, of the microbiome as a key mediator of developmental stress-induced longevity. We found that mild oxidative stress during development robustly increases lifespan via the selective elimination of Acetobacter from the microbiome. This study also highlights that targeted remodelling of the early-life microbiome can provide an efficient strategy for extending healthspan and lifespan.
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.
Long-range signaling activation and local inhibition separate the mesoderm and endoderm lineages
The induction of endoderm and mesoderm by the signalling molecule Nodal has long been a textbook example of how a morphogen patterns vertebrate tissues. This study overturned the view that tissues are patterned through a single long-range morphogen gradient. Instead we demonstrated that Nodal functions in an incoherent feedforward loop with Fgf, to determine endoderm and mesoderm specification. Nodal induces long-range Fgf signaling, which is required for mesoderm induction, while simultaneously inducing a cell-autonomous Fgf signaling inhibitor within cells destined to become endoderm. This work represents a major step forward in deciphering the organising principles underlying early embryonic patterning.
Plasmodium-specific atypical memory B cells are short-lived activated B cells
This paper provides strong evidence that “atypical” B cells are short-lived activated B cells, and are probably the result of chronic stimulation and not the cause of chronic malaria. This questions the commonly held view that atypical B cells are evidence of an aberrant or defective response in malaria.
Sex reversal following deletion of a single distal enhancer of Sox9
This systematic study revealed the complexity of the Sox9 regulatory region, but just one enhancer, “Enh13”, was shown by mutation studies to be essential for testis and subsequent male development. Sox9 expression is at the same very low level in XY Enh13 mutant embryos as in control XX gonads. Enh13 is efficiently bound by Sry in vivo and functions to initiate Sertoli cell fate during a short time window. This is in contrast to other redundant enhancers (e.g. TES) that bind Sry, but act later. This study helped explain Disorders of Sex Differentiation (DSDs), due to deletions and duplications mapping far upstream of Sox9, where the human Enh13 equivalent is located, as well as showing that some enhancers can be pioneering rather than redundant.
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.