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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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.

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Published in Journal of Clinical Investigation

Published

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.

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Published in Science

Published

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.

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Published in Science

Published

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.

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Published in Science

Published

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.

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Published in Molecular Cell

Published

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.

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Published in Immunity

Published

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.

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Published in Developmental Cell

Published

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.

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Published in Nature

Published

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.

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Published in Science

Published

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.

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Published in Immunity

Published

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.

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Published in Nature Communications

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.

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Published in Nature Cell Biology

Published

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.

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Published in Nature

Published

UV irradiation induces a non-coding RNA that functionally opposes the protein encoded by the same gene

A detailed, genome-wide study of the transcriptional response to DNA damage, including the identification of genes that start expressing short, alternative splice isoforms after genomic insult. One of these genes, ASCC3, normally expresses a protein-coding mRNA, but after UV-irradiation shifts expression to a short non-coding RNA isoform, which is important for survival after DNA damage. The protein-coding ASCC3 isoform counteracts the function of the non-coding isoform, indicating crosstalk between them.

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Published in Cell

Published

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

This TRACERx work shows that bespoke patient-specific panels to analyse ctDNA can be used to monitor MRD recurrence and tumour branched evolution in the adjuvant setting in the absence of macroscopic disease, and that tumour Ki67 index, necrosis, squamous histology and FDG-PET avidity are closely associated with ctDNA release. We further demonstrate the limitations of ctDNA approaches for early detection as a function of tumour volume and cancer cell number, and show that the subclone identified in ctDNA prior to disease recurrence is identical to the tumour subclone identified at metastatic sites, permitting adjuvant MRD studies to prevent recurrence.

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Published in Nature

Published

Tracking the evolution of non-small-cell lung cancer

This work evaluates the relationship between intratumour heterogeneity of single nucleotide variants and somatic copy number aberrations and recurrence free survival in non-small cell lung cancer. Diversity of chromosome number or structure rather than single nucleotide variants is associated with poorer recurrence free survival, independent of tumour stage in multivariable analyses. Through subclonal copy number analyses, mirrored subclonal allelic imbalance is found, driving parallel evolution of chromosome copy number gains or losses on either the maternal or paternal chromosome in different regions of the same tumour.

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Published in New England Journal of Medicine

Published

Allele-specific HLA loss and immune escape in lung cancer evolution

Through an analysis of TRACERx, extended from our haplotyping analysis, we developed an algorithm called LOHHLA which infers allele specific copy number aberrations in HLA. We find HLA loss occurs in 40% of early stage lung cancers, usually as a subclonal event, and is permissive for branched evolution associated with expansion of mutations predicted to bind the lost HLA allele.

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Published in Cell

Published

B cell antigen extraction is regulated by physical properties of antigen-presenting cells

We demonstrated that mechanical forces and not enzymatic liberation are the physiological mechanism for acquisition of antigens by B cells from live presenting cells. Using DNA-based nanosensors we showed that B cell affinity discrimination is regulated by physical properties of the antigen-presenting cells and identified follicular dendritic cells as a stiff antigen presenting subset that promotes B cell affinity discrimination in germinal centres.

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Published in Journal of Cell Biology

Published

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

The first pan-tumour study to evaluate the contribution of fremashift mutations to generation of immunogenic peptides and anti-tumour immunity. Patent arising.

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Published in Lancet Oncology

Published

Fertile offspring from sterile sex chromosome trisomic mice

Here, we described a technique for reversing infertility in XXY (Klinefelter) and XYY (Jacob) syndrome mice. We showed that reprogramming of fibroblasts from these mice resulted in elimination of the extra sex chromosome, and that resulting XY cells could be converted by in vitro gametogenesis into functional sperm. Reprogramming could also chromosomally correct cells from Down syndrome mice and patients. The work revealed an unexpected role for reprogramming as a form of chromosome therapy.

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Published in Science

Published