Publication highlights

Members of the Chemical Glycobiology Laboratory at the Crick have developed a new method to study a type of sugar modification on proteins that is relevant for cancer. The sugar modification is initiated by an enzyme called MGAT5 that is upregulated in many types of cancer. Methods to study enzymes such as MGAT5 have been lacking, but particularly benefit from innovations in chemistry. In an international collaboration, the lab have modified the enzyme so that it can “arm” the cancer-relevant sugar with a chemical tag linked to a reporter molecule, meaning that the sugar modification and its linked proteins can be visualised, isolated and characterised.

Abnormal movement of the RNA-binding protein TDP-43 from the nucleus to the cytoplasm in vulnerable brain cells is a hallmark of motor neuron disease. Losing the function of TDP-43 in the nucleus causes genetic sequences called ‘cryptic exons’ to be erroneously included in mature RNA transcripts. While these have been detected before, most of these events were predicted to produce faulty instructions that would be discarded. Whether or not these events translate into new proteins has remained an open question.

By removing TDP-43 in human stem cells grown in the lab, the researchers at the Crick, UCL and NIH discovered 65 new small proteins called ‘cryptic peptides’ which are produced when TDP-43 is lost from the nucleus. They detected 18 of these new proteins in cerebrospinal fluid samples from people with ALS or FTD. This discovery opens the door for both an exciting new fluid biomarker of disease progression in ALS/FTD and the intriguing possibility of cryptic peptides triggering an autoimmune response in disease.

Cell-surface and secreted proteins play critical roles in human development, growth factor signalling, and cell adhesion. Proteoglycans are an important subset of these proteins and are modified with long chains of sugar molecules called Glycosaminoglycans (GAGs) such as heparan sulphate (HS) or chondroitin sulphate (CS), but they all start with the same four sugars – only after the addition of the fifth sugar is the fate of the growing chain sealed.

While protein and DNA synthesis are template-driven, from DNA or RNA, synthesis of the proteoglycan GAG chains are not. In a collaboration between the Crick and Imperial, the researchers devised a synthesis system to allow precise control of eight of the enzymes in the biosynthesis pathway. They discovered that chrondroitin sulphate is the “default” modification, and that the enzyme responsible for priming chrondroitin sulphate synthesis modifies all sites equally. They also found that the enzyme responsible for priming heparan sulphate synthesis (EXTL3) has a positively charged patch that interacts with negatively charged amino acids near the attachment site and will only modify certain substrates. This will help to predict how mutations surrounding the glycosaminoglycan attachment sites could be implicated in diseases like cancer or developmental conditions.

Thanks to continuous advances in human stem cell research, studies using embryo models are progressing quickly, including research happening at the Crick. Embryo models offer a scientific and ethical addition to the use of embryos from fertilised human eggs in research, but ethical guidelines sometimes have to play catch-up with scientific progress.

The challenge is to know how we would decide when an embryo model is ‘similar enough’ to an embryo as to fall under the same restrictions, since research keeps pushing the technology forward.

Naomi Moris, Group Leader of the Developmental Models Laboratory at the Crick, worked with an international group of biologists and ethicists to propose a refined definition of the human embryo, as a group of cells which have the potential to form a fetus, focusing on what the embryo can become rather than its origin. The group identified ‘tipping points’, where embryo models would stray into the territory of an embryo.

The cells that will eventually give rise to germ cells, sperm and egg, are originally made by the embryo early on in its development. These cells, called Primordial Germ Cells or PGCs, are an exciting group of cells to study because we still know relatively little about how they are first generated, how they move around the early embryo, and how they start to mature and eventually produce sperm or egg cells. However, current technology to make PGCs in the laboratory uses large, disorganised culture systems alongside specific chemicals to 'bias' the cells towards becoming PGCs. Instead of doing this, we have shown that mouse stem cells can be cultured in a controlled, 3D system that mirrors certain elements of the early mouse embryo.

In this work, the researchers show that these structures, called 'gastruloids', also contain PGCs, and that these cells not only appear in these structures, but that they interact with the other cells in the gastruloid in a manner that is very similar to the way they develop in the actual embryo. They also show that the gastruloid PGCs reach a more mature stage of development (at about the stage of a 13-15 days old mouse embryo) compared to traditional culture methods (that only reach day 9-10). This shows that not only can we make PGCs in a new way that might reveal new insights about these specific cells, but it also highlights the value of embryo-like models, including gastruloids, to generate rare cell types that might otherwise be difficult to access.

Prostate cancer is the most common cancer in men and it is estimated that over 350,000 men worldwide die of prostate cancer every year. There remains an unmet clinical need to improve how clinically significant prostate cancer is diagnosed and develop new treatments for advanced disease. Aberrant glycosylation is a hallmark of cancer implicated in tumour growth, metastasis, and immune evasion. One of the key drivers of aberrant glycosylation is the dysregulated expression of glycosylation enzymes within the cancer cell. Here, the researchers demonstrate using multiple independent clinical cohorts that the glycosyltransferase enzyme GALNT7 is upregulated in prostate cancer tissue. They show GALNT7 can identify men with prostate cancer, using urine and blood samples, with improved diagnostic accuracy than serum PSA alone. They also show that GALNT7 levels remain high in progression to castrate-resistant disease, and using in vitro and in vivo models, reveal that GALNT7 promotes prostate tumour growth. Mechanistically, GALNT7 can modify O-glycosylation in prostate cancer cells and correlates with cell cycle and immune signalling pathways. The study provides a new biomarker to aid the diagnosis of clinically significant disease and cements GALNT7-mediated O-glycosylation as an important driver of prostate cancer progression.

An international collaboration led by Crick Group Leader Marcus Ralser has shown that mixed communities of young and old yeast cells can co-operate and exchange resources, increasing the lifespan of all the cells. They focused on the processes used by cells to exchange metabolites, which are produced when cells create energy, and include amino acids. When young yeast cells released amino acids into the environment, these could be taken up by older cells, and the whole community of cells lived longer. One of the amino acids, methionine, was of particular importance as it is needed to kickstart the process of building proteins and is also important in many cellular processes. Uptake of methionine changed the metabolism of the older cells, affecting key anti-ageing pathways and also led to the release of metabolites with protective properties into the environment, which could then be taken up by other cells. If applicable to higher organisms, the concept underlying these results could add a new dimension to studying cells in health and disease.

Chromosomes are formed from chromatin, a complex of DNA and proteins. When cells die, chromatin is released into the surroundings and can cause inflammation and cytotoxicity. A process known as chromatin clearance is needed to remove extracellular chromatin and protect against severe disease. A collaboration led by Crick group leader Veni Papayannopoulos has found that in samples taken from people with the severest form of COVID-19 pneumonia, chromatin clearance was hindered in all cases, and when this process was affected the most, patients were less likely to survive.

Further analysis of the chromatin buildup showed that DNAses, a group of enzymes that help to break down chromatin, were being inhibited by another molecule, actin, which is released when cells die. Blood plasma samples taken from a second group of patients with microbial sepsis demonstrated a build-up of chromatin which correlated with high levels of actin in the blood. Using this information, the team developed a ‘proteomic profile’, a signature of protein levels and enzyme activity in the blood, that characterised the most severe and high-risk cases of infection. With further development, this signature could be used to help distinguish patients who might require additional treatment.