Publication highlights

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.

Human induced pluripotent stem cells (iPSCs) mimic early embryos and can become any cell type, making them a powerful tool to study development and disease. However, most existing cell lines aren't suited to study sex differences. In collaboration with AstraZeneca, Turner lab researchers Ruta Meleckyte and Wazeer Varsally addressed this by creating new iPSCs with either XX (female) or XY (male) sex chromosomes. All other chromosomes were identical, so any differences observed can be linked to sex. These openly available iPSCs will enable more accurate modelling of sex-specific biology and may help in developing better, more personalised treatments in the future.

Histone modifications are chemical marks that help regulate DNA functions. One of the most common, H4K16 acetylation (H4K16ac), is known for turning genes on in fruit flies, and it has been assumed to do so in mammalian cells too. Researchers at the Crick and the European Institute of Oncology found that in human cells, H4K16ac does not control gene activity but instead organises when and where DNA is copied during cell division. Without it, regions of the genome enriched for repetitive elements (LTRs) replicate prematurely, globally disrupting the temporal control of DNA replication. Their findings reveal an unexpected role for histone acetylation in safeguarding genome replication accuracy.

In this study, researchers at the Crick and UCL investigated how an epigenetic change called DNA methylation cooperates with genetic changes in non-small cell lung cancer (NSCLC) using 217 tumour and normal regions from 59 TRACERx patients. This is the first multiregional lung cancer cohort integrating genomic, transcriptomic, and epigenomic data to map tumour evolution in such detail. They uncovered a novel mechanism, where DNA methylation fine-tunes how oncogenes are switched on together by compacting the DNA. We also identified hypermethylated driver genes emerging early in tumour evolution and developed a new metric, Mr/Mn, to distinguish functional from passenger methylation changes. Our work highlights epigenetic drivers with therapeutic potential.

The Salmonella protein SteE forcibly reprogrammes the eukaryotic kinase GSK3 so it acts on a new set of substrates that benefit Salmonella virulence. Kinase reprogramming depends on several short linear motifs in SteE that trick GSK3 into recognising SteE as a 'normal' cellular signalling partner. Researchers at the Crick have shown how each motif contributes to manipulating GSK3, and revealed the existence of SteE-like proteins in other bacterial pathogens. This work will aid the rational design of synthetic reprogramming proteins.

When we think about cell signalling, be it developmental transitions, or be it the sequential events that make up the cell growth and division cycle, we think of regulators. Typically, a kinase is thought to exert control over downstream events, such as the cyclin-dependent kinase (CDK), which has master control over cell cycle progression. Researchers at the Crick revisit how CDK phosphorylates each of its many cell cycle targets at the right time. Not merely a decision by the kinase, they realise that the substrates themselves contribute to deciding when their phosphorylation time has come. ‘Substrate control’ likely more widely forms part of cell signalling decisions.

Organisms grow through the division of the cells that make up our bodies. As well as growth, cell division is also essential for different types of cells to decide what cell type they will become (from different neurons in our brains to the cells that line our guts). How cells divide therefore needs to be tightly controlled both in space (so that the daughter cells after division end up in the right place) and in time (so that daughter cells make the correct choice of what to become). To make this process even more complicated, each cell type is very different in terms of shape, behaviour etc…, so cell division must adapt to the needs of each tissue, an aspect of biology we know very little about. Researchers at the Crick have found a protein called Meru (called after the Bengali word for “polar”) that can tell a cell in which direction and when to divide. Meru is located at one of the poles of a cell type called the sensory organ precursor and allows this cell to orient itself in the tissue and to time its division just right to allow both daughter cells to create the right structure.

DNA in our cells must be copied only once in the life cycle of a cell to maintain gene copy number and prevent genome instability. To make sure that this happens, loading of the enzyme (MCM), which separates two strands of the double helix, is separated in time from its activation. Once activated, MCM uses the energy derived from ATP hydrolysis to move along one DNA strand and physically separate the other strand, achieving DNA unwinding. Before activation, MCM is recruited by a loader onto the double helix. Researchers knew that, to complete loading, ATP hydrolysis by MCM is required but did not know why. Here researchers at the Crick show that MCM uses ATP hydrolysis to move along duplex DNA away from its loader. Their study also provides new mechanistic information about how polymer translocases (like DNA motors or the proteasome) use ATP hydrolysis to drive movement.

Researchers at the Crick and the UCL Cancer Institute have identified a genetic change which happens early in lung cancer development, that makes cancer cells divide abnormally and become harder to treat. They studied non-small cell lung cancer samples from the Cancer Research UK-funded TRACERx study, to investigate which genetic changes make two hallmarks of cancer, chromosomal instability and whole genome doubling, more likely. They identified that a gene called FAT1 was mutated in lung cancer cells with unstable chromosomes before they doubled their genomes. Cells with a complete loss of FAT1 couldn’t divide properly to produce two new cells. When FAT1 and another gene involved in cell size regulation called YAP1 were removed, the cancer cells no longer doubled their genomes. This suggests that drugs that block YAP1 could be particularly effective against cells with high levels of chromosomal instability.

The MCM helicase enzyme separates the two strands of the double helix, enabling DNA replication, with two copies of MCM (a “double hexamer”) marking where replication can start. We have a clear understanding of how double hexamers are loaded in yeast, but not in human cells. Researchers from the Crick reconstituted double hexamer loading with purified human proteins and determined the atomic structures. They found that, unlike in yeast, loading of a human double hexamer is sufficient to start opening DNA. Two alternate loading pathways exist to load human double hexamers. Loading factors that are essential in yeast only play a dispensable, regulatory role in the human system. Thus, while the double-hexamer loaders are conserved throughout evolution, how they function is different. This work begins to unravel how human cells regulate initiation of DNA replication, ensure that their genome is duplicated only once, and prevent chromosome instability and cancer.