Publication highlights

Go inside our research

Explore a selection of research case studies from the past five years.

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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

Cell death programmes

Unravelling a cell death programme evaded by half of all cancers

When normal cells become cancer cells, they undergo a series of genetic changes that allow them to divide indefinitely. One such change involves the loss of a protein called Schlafen 11 (SLFN11), which occurs in half of all cancers. SLFN11 activity results in programmed cell death in response to damaged DNA, which naturally occurs during cancer cell transformation. Thus, loss of SLFN11 renders cancer cells immune to DNA damage and resistant to wide range of chemotherapies currently used in the clinic. However, how damaged DNA activates SLFN11 to cause programmed cell death is not known. Here, researchers at the Crick have uncovered what cellular processes lead to a specific type of DNA damage that activates SLFN11 and programmed cell death. This work provides insight as to why half of all cancers lose SLFN11 in response to naturally occurring DNA damage.

RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

Published in Nature Cell Biology

Published

Astrocytes

Uncovering early hypoxic stress in ALS astrocytes

Researchers at the Crick and UCL have shown that reported that astrocytes show signs of hypoxic stress long before neurons begin to die in ALS. Using stem cells from patients to generate astrocytes carrying ALS-linked mutations in a gene called VCP, which is linked to inherited forms of ALS, the team showed that astrocytes exhibited clear signs of 'pseudo-hypoxia'. This meant they had switched on a low-oxygen response despite being in normal oxygen conditions. This was driven by HIF-1a, a master regulator of how cells respond to oxygen. Instead of being degraded under normal conditions, it had accumulated in the nucleus and activated genes involved in metabolism, energy production and stress responses. As a result ALS astrocytes showed mitochondrial dysfunction and a reduced ability to support motor neurons. This is particularly exhibited as an inability to correct the mislocalisation of RNA-binding proteins, a well-known molecular hallmark of ALS, compromising neuron survival.

Hypoxic stress is an early pathogenic event in human VCP-mutant ALS astrocytes

Published in Stem Cell Reports

Published

RAD51 complex

Capping RAD51 filaments to protect genome stability

Our cells rely on DNA repair systems to prevent genome instability and cancer. One of the most accurate is homologous recombination, driven by RAD51 and assisted by five RAD51-like proteins whose roles were unclear. Using cryo-electron microscopy, biochemistry and single molecule analyses, Crick researchers show that these proteins assemble into two distinct complexes. The RAD51B complex helps initiate repair by assembling RAD51 filaments, while the XRCC3 complex plays the more ancient and conserved role: capping and stabilising RAD51 filament ends and promoting DNA strand pairing. This work uncovers a fundamental mechanism for genome protection and clarifies how mutations in RAD51-like genes contribute to cancer.

Cryo-electron microscopy visualization of RAD51 filament assembly and end-capping by XRCC3-RAD51C-RAD51D-XRCC2

Published in Science

Published

Two different representations of tetra-ubiquitin - a molecular 'tag' used to mark proteins inside cells.

Platform developed to profile reactive fragments

Small molecule probes offer powerful tools for the study of biological systems and can serve as starting points for the development of therapeutics. The vast majority of human proteins lack such chemical tools, which hinders our ability to explore their function in the context of health and disease. Screening libraries of “reactive fragments”, small molecules that form covalent bonds with their protein targets, by mass spectrometry enables the discovery of new ligands in the native cellular environment. Together with GSK as part of the Crick-GSK Biomedical LinkLabs Prosperity Partnership, researchers at the Crick have developed a robust and versatile proteomics platform for profiling of cysteine-reactive fragments against the native proteome and have identified hundreds of new protein-ligand interactions for probe development.

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics

Published in Nature Communications

Published

DNA damage in mouse embryonic stem cells.

Radiation or genotoxic drugs do not activate cGAS-STING signalling

Researchers at the Crick investigated cGAS-STING, a pathway that evolved to sense cytoplasmic DNA following bacterial or viral infection, triggering an immune response. They used ionising radiation or genotoxic compounds to damage nuclear DNA, which then formed micronuclei - small compartments that encapsulate the damaged DNA in the cytoplasm. The researchers found that micronuclei induced by radiation failed to activate cGAS-STING signalling, as did genotoxic compounds such as reversine and hydroxyurea. This was due to the presence of histones in the micronuclei that package DNA into chromatin, which inhibits activation of the cGAS-STING pathway. This research challenges the notion that all cytosolic DNA in micronuclei activates cGAS-STING and suggests potential limitations for using genotoxic drugs to stimulate the immune system in cancer therapy.

Micronuclei induced by radiation, replication stress, or chromosome segregation errors do not activate cGAS-STING

Published in Molecular Cell

Published

DNA damage in mouse embryonic stem cells.

Observing human BRCA2 tumour suppressor directly in action

BRCA2 is a tumour suppressor frequently mutated in breast and ovarian cancer. BRCA2 is a large, 3418 amino acid-long protein that plays a central role in homologous recombination, a pathway to repair broken DNA. How exactly BRCA2 acts during the repair process was unclear. To address this, researchers from the Crick and Imperial College London isolated BRCA2 and its partner, Rad51 recombinase, from cells and labelled them with fluorescent chemicals. They then used optical tweezers, powerful lasers capable of holding and moving small objects, to stretch individual single DNA molecules bearing a gap in one of the strands – mimicking DNA damage that BRCA2 and Rad51 repair in cells.

Finally, after adding labelled BRCA2 and Rad51, the researchers used fluorescence microscopy to make a movie of BRCA2 recognising and delivering Rad51 to gapped DNA in real time. The researchers analysed these movies and observed BRCA2 can recognise the DNA damage directly, bind to a border of damaged and undamaged DNA and surprisingly, also slide along DNA to reach the damaged site. When researchers engineered mutations in BRCA2, it was less able to search for DNA damage. This work shows in unprecedented detail how BRCA2 delivers Rad51 to repair DNA damage to prevent tumour formation.

Visualization of direct and diffusion-assisted RAD51 nucleation by full-length human BRCA2 protein

Published in Molecular Cell

Published

Human stem cell derived spinal motor neurons.

Excessive DNA damage found in Motor Neuron Disease

Amyotrophic lateral sclerosis (ALS), also known as Motor Neuron Disease, is a devastating neurological disease that causes motor neurons to die, leading to muscle weakness and ultimately death. It has been challenging to access motor neurons to identify the underlying causes of the disease, due to high risk of complications that come with a biopsy of the fragile spinal cord. Researchers have turned to studying motor neurons derived from induced pluripotent stem cells (iPSC) to better understand ALS. However, previous iPSC studies were limited to small numbers of patients, and there is no consensus on how ALS develops.

In this study, researchers combined iPSC-derived motor neurons and post-mortem spinal cord tissue data into a large resource, to identify changes that cause motor neuron death in ALS. They found that ALS leads to an accumulation of somatic mutations and a heightened DNA damage response. Although these changes were observed in various types of ALS, they were most notable in cases where the nuclear protein, TDP-43, was relocated to the cytoplasm. This study highlights genome instability as a hallmark of ALS and could help in the development of new therapies.

Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology

Published in Nature Communications

Published

New DNA repair mechanism holds promise for precision cancer therapies

DNA double-strand breaks (DSBs) are one of the most serious forms of DNA damage. A collaboration between the Boulton lab and researchers at the University of Birmingham has identified two new proteins (BOD1L and SETD1A) that are vital for repairing DSBs. Changes catalysed by SETD1A regulate DSB repair at an entirely new level by controlling the repair protein RIF1, and loss of SETD1A confers resistance to targeted anti-cancer therapies in cells deficient for the tumour suppressor BRCA1.This research has the potential to change how cancer patients are identified for treatment and to predict resistance to different drugs, which will improve treatment efficiency as well as patient outcomes.

H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ

Published in Molecular Cell

Published

HELQ enzyme facilitates DNA repair

Researchers from the Boulton Lab, in collaboration with the MRC London Institute of Medical Sciences and the Memorial Sloan Kettering Cancer Center, have uncovered the mechanism by which an enzyme called HELQ assists in repairing DNA. Through the use of biochemical analysis and single-molecule imaging, the team have shown HELQ can mend DNA double-stranded breaks by virtue of two distinct activities that are enhanced through its interaction with two other proteins, RAD51 and RPA. Loss of HELQ causes defects in DNA repair, which can lead to cancer and cause infertility, and these results explain the reason for its importance.

HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51

Published in Nature

Published

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.

View the publication

Published in Cell

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.

View the publication

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

TRF2-independent chromosome end protection during pluripotency

This work revealed that telomere protection is solved by distinct mechanisms in pluripotent and somatic tissues. In somatic cells, TRF2 sequesters the telomere within a t-loop, preventing telomere end-to-end fusions and inviability. In contrast, TRF2 is dispensable for telomere protection in pluripotent cells; ESCs lacking TRF2 grow normally, do not fuse their telomeres and form functional t-loops. Upon differentiation this unique attribute of stem cells is lost and TRF2 assumes its full role in end protection. The retention of end protection in the presence of t-loops, but absence of TRF2, confirmed that t-loops are a key mediator of telomere end protection irrespectively of how they form.

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Published in Nature

Published

Accumulation of DNA breaks (red dots) in human cancer cells treated with the PARP inhibitor Olaparib and hmdU and where the DNPH1 protein has been blocked.

Targeting the nucleotide salvage factor DNPH1 sensitizes BRCA-deficient cells to PARP inhibitors

A study led by the West lab has found that blocking a specific protein could increase tumour sensitivity to treatment with PARP inhibitors. Their work suggests that combining treatments could lead to improved therapy for cancer patients.

View the publication

Published in Science

Published