Publication highlights

About half of glioblastomas have rogue rings of DNA floating outside of chromosomes called extrachromosomal DNA (ecDNA). The Cancer Grand Challenges eDyNAmiC team, including researchers from Stanford University, Queen Mary University of London and the Crick, integrated genomic and imaging data from people with glioblastomas with advanced computational modelling of the evolution of ecDNAs in space and time. Their analysis revealed that most ecDNA rings contained EGFR, a potent cancer-driving gene. EGFR DNA appeared early in the cancer's evolution and also frequently gained extra changes that made the cancer more aggressive. The time between the first appearance of EGFR ecDNA and the emergence of more aggressive variants may represent a window of opportunity to detect and treat the disease.

Lymph nodes are small organs distributed throughout the body that orchestrate immune processes. In response to infection, vaccination, or cancer, a germinal centre (GC) forms within them, driving the maturation of memory B cells and plasma cells. Because of their 3D structure and diverse cell types, GCs are ideal for 3D imaging. This protocol describes rapid, high-resolution multicolour imaging of whole immunised lymph nodes, covering harvesting, fixation, permeabilisation, staining, and clearing. Imaging is performed with a fluorescence lightsheet microscope, and analysis with Imaris. It quantifies GC B cells, plasma cells, and follicular T cells, and includes optimised stainings for visualising other lymph node structures.

As ALS involves disruption to RNA-binding proteins, which coordinate the movement and metabolism of genetic messages called RNAs, researchers at the Crick and UCL investigated how changes to an RNA-binding protein called SFPQ could underpin some of the disease pathology. They identified an alternative version of the SFPQ protein, which is found in a different cellular location compared to the regular SFPQ protein. The team then found that ALS-affected cells are more likely to produce and use the alternative SFPQ protein rather than the regular one, which mirrors findings in ALS patient tissues that SFPQ is often found in abnormal places in the cell. Finally, they showed that the alternative SFPQ has different behaviour and function, which may underlie hallmarks of the disease in ALS-affected cells. This work suggests that correcting levels of alternative SFPQ might alleviate some of the negative downstream consequences for RNA molecules and ultimately damage to nerve cells in ALS.

Researchers at the Crick have discovered that the heart's own contractions trigger biological signals that guide the formation of a functional beating heart. Their study in zebrafish highlights the heart's ability to remodel and adapt to physiological demands and could also reveal what goes wrong during congenital heart conditions. They followed the early development of the heart's muscular structures, called trabeculae, in zebrafish using live 4D imaging. The team observed that trabeculae don't grow and develop by cell division, as previously thought. Instead, neighbouring cells are recruited to build trabecular complexity, thus increasing the heart's muscle mass and contractile efficiency. Finally, they uncovered a feedback mechanisms between heart contraction and its own development, dictating a healthy pace of growth.

Researchers have mapped the human metabolic pathways that Cryptosporidium, an intestinal parasite, requires to survive. They conducted a genome-scale screening experiment that involves systematically disabling nearly every protein-coding gene, individually, from human intestinal cells, before infecting the cells with Cryptosporidium. The team found that genes involved in making cholesterol appeared to have opposing effects - some boosting infection and others blocking it. This balance hinged on a molecule midway through the cholesterol production line, squalene. This molecule protects against oxidative stress by stimulating the production of glutathione, which Cryptosporidium needs but cannot make. This leaves the parasite dependent on glutathione from the host cell, a dependency which can be targeted with a high cholesterol drug called lapaquistat. This drug reduced infection in a mouse model of disease and completely blocked intestinal damage, suggesting it could be repurposed to fight Cryptosporidium.

Researchers from the Crick and Liverpool John Moores University (LJMU) have extracted and sequenced the oldest Egyptian DNA to date from an individual who lived around 4,500 to 4,800 years ago, the age of the first pyramids. The individual was buried in Nuwayrat, a village 265km south of Cairo, and had been buried in a ceramic pot in a tomb cut into the hillside. Most of his ancestry mapped to ancient individuals who lived in North Africa and the remaining 20% of his ancestry could be traced to ancient individuals who lived in the Fertile Crescent. This is genetic evidence that people moved into Egypt and mixed with local populations at this time, which was previously only visible in archaeological artefacts. Finally, the team used evidence from his skeleton to suggest he could have worked as a potter or in a trade requiring comparable movements.

The DNA replication checkpoint is essential for maintaining genome stability. Without it, when DNA copying restarts after a stall, too many replication origins—the starting points for copying—are mistakenly activated, ultimately leading to cell death. Researchers at the Crick showed, in human cells lacking this checkpoint, that excessive DNA synthesis from surplus origins consumes the vital replication proteins PCNA and RFC, preventing normal restart of stalled copying at replication forks. Without the protection of PCNA and RFC, the ends of the forks are attacked by a protein called HLTF, causing irreversible damage. Removing HLTF helps cells survive even in the absence of the checkpoint, which has implications for how resistance to anti-checkpoint cancer therapies may arise.

Researchers have uncovered that topoisomerase 2, which maintains the integrity of our genome, also plays critical roles in vaccinia virus replication. Upon infection, viral protein synthesis triggers the relocation of both topoisomerase 2 isoforms, TOP2A/B, from the nucleus to the cytoplasm, where they carry out opposing functions. TOP2A promotes replication by interacting with viral DNA replication machinery, whereas TOP2B suppresses infection by enhancing the formation of double-stranded RNA and antiviral granules. This study provides new insights into host-poxvirus interactions and highlights important roles for topoisomerase 2 outside the nucleus. It also suggests that topoisomerase inhibitors used in the clinic would make excellent antiviral drugs.