EGR1

A new study suggests that cognitive loss in patients with brain metastases may be due to the interference that cancer produces in neuronal circuits. When cancer spreads in the brain, it changes the brain's chemistry, interfering with the communication between neurons. This is a very different hypothesis from the one previously accepted, with implications for the diagnosis and treatment of brain metastases. The authors have used artificial intelligence to show that metastasis alters brain activity. Nearly half of all patients with brain metastasis experience cognitive impairment. Until now, it was thought that this was due to the physical presence of the tumour pressing on neural tissue. But this 'mass effect' hypothesis is flawed because there is often no relationship between the size of the tumour and its cognitive impact. Small tumours can cause significant changes, and large tumours can produce mild effects. Why is this? The explanation may lie in the fact that brain metastasis hacks the brain's activity, a study featured on Cancer Cell's cover shows for the first time. The authors, from the Spanish National Research Council (CSIC) and the Spanish National Cancer Research Centre (CNIO), have discovered that when cancer spreads (metastasises) in the brain, it changes the brain's chemistry and disrupts neuronal communication -- neurons communicate through electrical impulses generated and transmitted by biochemical changes in the cells and their surroundings. In this study, the laboratories of Manuel Valiente (CNIO) and Liset Menéndez de La Prida (Cajal Institute CSIC) have collaborated within the EU-funded NanoBRIGHT project, aimed at developing new technologies for the study of the brain, and with the participation of other funding agencies such as MICINN, AECC, ERC, NIH and EMBO. Demonstration with artificial intelligence The researchers measured the electrical activity of the brains of mice with and without metastases and observed that the electrophysiological recordings of the two groups of animals with cancer were different from each other. To be sure that this difference was attributable to metastases, they turned to artificial intelligence. They trained an automatic algorithm with numerous electrophysiological recordings, and the model was indeed able to identify the presence of metastases. The system was even able to distinguish metastases from different primary tumours -- skin, lung and breast cancer. These results show that metastasis does indeed affect the brain's electrical activity in a specific way, leaving clear and recognizable signatures. For the authors, the study represents a "paradigm shift" in the basic understanding of the development of brain metastases and has implications for the prevention, early diagnosis and treatment of this pathology. On the trail of a drug against neurocognitive effects In addition to recording changes in brain electrical activity in the presence of metastasis, the researchers have begun to explore the biochemical changes that might explain this alteration. By analysing the genes expressed in the affected tissues, they have identified a molecule, EGR1, that may play an important role in this process. This finding opens up the possibility of designing a drug to prevent or alleviate the neurocognitive effects of brain metastasis. As Manuel Valiente, head of the CNIO's Brain Metastasis Group explains, "our multidisciplinary study challenges the hitherto accepted assumption that neurological dysfunction, which is very common in patients with brain metastasis, is due solely to the mass effect of the tumour. We suggest that these symptoms are a consequence of changes in brain activity resulting from tumour-induced biochemical and molecular alterations. This is a paradigm shift that could have important implications for diagnosis and therapeutic strategies." Liset Menéndez de la Prida, director of the Laboratory of Neural Circuits the Cajal Institute (CSIC), says: "Using machine learning, we have been able to integrate all the data to create a model that allows us to know whether there is or not metastasis in a brain, just by looking at its electrical activity. This computational approach may even be able to predict subtypes of brain metastases at an early stage. It is a completely pioneering work that opens up an unexplored path." Both authors emphasise the multidisciplinary nature of this complex study that combines neuroscience, oncology and computational analysis, each using a wide range of different techniques. Cognitive study of patients and development of non-invasive techniques The change in focus brought about by this result means that researchers now want to analyse the cognitive status of patients with brain metastasis much more systematically. For Valiente, this is one of the most important next steps. The key to this will be the National Brain Metastasis Network (RENACER) initiated and coordinated by CNIO, which has already served to generate the largest collection of living brain metastasis samples in the world (with prior consent from patients, tissue samples collected during surgical interventions are made available to the international scientific community in the CNIO Biobank), and in which they will now introduce protocols for the neurocognitive assessment of the participating patients. For her part, Liset Menéndez de La Prida will work on integrating the recording of brain activity with the analysis of the molecules involved, "in order to develop new diagnostic probes for brain tumours," she says. This task is in line with the European NanoBRIGHTproject, which aims to develop non-invasive techniques for studying the brain and treating its pathologies, and in which CSIC and CNIO are participating. Another goal is to find drugs that protect the brain from cancer-induced disruptions in neuronal circuits, using the strategies described above. "We will look for molecules involved in metastasis-induced changes in neuronal communication, and evaluate them as possible therapeutic targets," explains Valiente. In addition to the artificial intelligence developed by the CSIC team, they will use the METPlatform technology designed by CNIO to evaluate the potential therapeutic activity of hundreds of compounds simultaneously on brain tissue samples affected by metastasis.

Short-lived proteins control gene expression in cells to carry out a number of vital tasks, from helping the brain form connections to helping the body mount an immune defense. These proteins are made in the nucleus and are quickly destroyed once they've done their job. The mechanism degrades short-lived proteins that support brain and immune functions. Short-lived proteins control gene expression in cells to carry out a number of vital tasks, from helping the brain form connections to helping the body mount an immune defense. These proteins are made in the nucleus and are quickly destroyed once they've done their job. Despite their importance, the process by which these proteins get broken down and removed from cells once they are no longer needed has eluded scientists for decades -- until now. In a cross-departmental collaboration, researchers from Harvard Medical School identified a protein called midnolin that plays a key role in degrading many short-lived nuclear proteins. The study shows that midnolin does so by directly grabbing the proteins and pulling them into the cellular waste-disposal system, called the proteasome, where they are destroyed. The findings are published Aug. 24 in Science. "These particular short-lived proteins have been known for over 40 years, but no one had established how they are actually degraded," said co-lead author Xin Gu, a research fellow in neurobiology at HMS. Because the proteins broken down by this process modulate genes with important functions related to the brain, the immune system, and development, scientists may eventually be able to target the process as a way of controlling protein levels to alter these functions and correct any dysfunction. "The mechanism we found is very simple and quite elegant," added co-lead author Christopher Nardone, a PhD candidate in genetics at HMS. "It is a basic science discovery, but there are many implications for the future." A molecular mystery It is well established that cells can break down proteins by tagging them with a small molecule called ubiquitin. The tag tells the proteasome that the proteins are no longer needed, and it destroys them. Much of the pioneering research on this process was done by the late Fred Goldberg at HMS. However, sometimes the proteasome breaks down proteins without the help of ubiquitin tags, leading researchers to suspect that there was another, ubiquitin-independent mechanism of protein degradation. "There has been sporadic evidence in the literature that somehow the proteasome can directly degrade unmarked proteins, but no one understood how that can happen," Nardone said. One group of proteins that seemed to be degraded by an alternative mechanism are stimuli-induced transcription factors: Proteins rapidly made in response to cellular stimuli that travel to the nucleus of a cell to turn on genes, after which they are rapidly destroyed. "What struck me in the beginning is that these proteins are extremely unstable and they have a very short half-life -- once they are produced, they carry out their function, and they are quickly degraded afterwards," Gu said. These transcription factors support a range of important biological processes in the body, yet even after decades of research, "the mechanism of their turnover was largely unknown," said Michael Greenberg, the Nathan Marsh Pusey Professor of Neurobiology in the Blavatnik Institute at HMS and a co-senior author on the paper with Stephen Elledge, the Gregor Mendel Professor of Genetics and of Medicine at HMS and Brigham and Women's Hospital. From a handful to hundreds To investigate this mechanism, the team began with two familiar transcription factors: Fos, studied extensively by the Greenberg lab for its role in learning and memory, and EGR1, which is involved in cell division and survival. Using sophisticated protein and genetic analyses developed in the Elledge lab, the researchers homed in on midnolin as a protein that helps break down both transcription factors. Follow-up experiments revealed that in addition to Fos and EGR1, midnolin may also be involved in breaking down hundreds of other transcription factors in the nucleus. Gu and Nardone recall being shocked and skeptical about their results. To confirm their findings, they decided they needed to figure out exactly how midnolin targets and degrades so many different proteins. "Once we identified all these proteins, there were many puzzling questions about how the midnolin mechanism actually works," Nardone said. With the aid of a machine learning tool called AlphaFold that predicts protein structures, plus results from a series of lab experiments, the team was able to flesh out the details of the mechanism. They established that midnolin has a "Catch domain" -- a region of the protein that grabs other proteins and feeds them directly into the proteasome, where they are broken down. This Catch domain is composed of two separate regions linked by amino acids (think mittens on a string) that grab a relatively unstructured region of a protein, thus allowing midnolin to capture many different types of proteins. Of note are proteins like Fos that are responsible for turning on genes that prompt neurons in the brain to wire and rewire themselves in response to stimuli. Other proteins like IRF4 activate genes that support the immune system by ensuring that cells can make functional B and T cells. "The most exciting aspect of this study is that we now understand a new general, ubiquitination-independent mechanism that degrades proteins," Elledge said. Tantalizing translational potential In the short term, the researchers want to delve deeper into the mechanism they discovered. They are planning structural studies to better understand the fine-scale details of how midnolin captures and degrades proteins. They are also making mice that lack midnolin to understand the protein's role in different cells and stages of development. The scientists say their finding has tantalizing translational potential. It may offer a pathway that researchers can harness to control levels of transcription factors, thus modulating gene expression, and in turn, associated processes in the body. "Protein degradation is a critical process and its deregulation underlies many disorders and diseases," including certain neurological and psychiatric conditions, as well as some cancers, Greenberg said. For example, when cells have too much or too little of transcription factors such as Fos, problems with learning and memory may arise. In multiple myeloma, cancer cells become addicted to the immune protein IRF4, so its presence can fuel the disease. The researchers are especially interested in identifying diseases that may be good candidates for the development of therapies that work through the midnolin-proteasome pathway. "One of the areas we are actively exploring is how to tune the specificity of the mechanism so it can specifically degrade proteins of interest," Gu said. Funding was provided by a National Mah Jongg League Fellowship from the Damon Runyon Cancer Research Foundation, a National Science Foundation Graduate Research Fellowship, and the National Institutes of Health (T32 HG002295; R01 NS115965; AG11085). Elledge is a founder of TScan Therapeutics, Maze Therapeutics, ImmuneID, and Mirimus, serves on the scientific advisory boards of Homology Medicines, ImmuneID, Maze Therapeutics, X-Chem, and TScan Therapeutics, and is an advisor for MPM Capital.