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Tag: Cell

  • Study reveals age-specific differences in nasal cells’ response to SARS-CoV-2

    Study reveals age-specific differences in nasal cells’ response to SARS-CoV-2

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    Important differences in how the nasal cells of young and elderly people respond to the SARS-CoV-2 virus, could explain why children typically experience milder COVID-19 symptoms, finds a new study led by researchers at UCL and the Wellcome Sanger Institute.

    The study, published in Nature Microbiology, focused on the early effects of SARS-CoV-2 infection on the cells first targeted by the viruses, the human nasal epithelial cells (NECs).

    These cells were donated from healthy participants from Great Ormond Street Hospital (GOSH), University College London Hospital (UCLH) and the Royal Free Hospital, including children (0-11 years), adults (30 – 50 years) and, for the first time, the elderly (over 70 years).

    The cells were then cultured using specialized techniques, allowing them to regrow into the different types of cells you originally find in the nose. Using single-cell RNA sequencing techniques that enable scientists to identify the unique genetic networks and functions of thousands of individual cells, the team identified 24 distinct epithelial cell types. Cultures from each age group were then either mock infected or infected with SARS-CoV-2.

    The researchers found that, after three days, the NECs of children responded quickly to SARS-CoV-2 by increasing interferon (the body’s first line of anti-viral defense) – restricting viral replication. However, this early anti-viral effect became less pronounced with age.

    The researchers also found that NECs from elderly individuals not only produced more infectious virus particles, but also experienced increased cell shedding and damage.

    The strong antiviral response in the NECs of children could explain why younger people typically experience milder symptoms. In contrast, the increased damage and higher viral replication found in NECs from elderly individuals could be linked to the greater severity of disease observed in older adults.

    Project lead, Dr Claire Smith (Associate Professor at UCL Great Ormond Street Institute of Child Health), said: “Our research reveals how the type of cells we have in our nose changes with age, and how this affects our ability to combat SARS-CoV-2 infection. This could be crucial in developing effective anti-viral treatments tailored to different age groups, especially for the elderly who are at higher risk of severe COVID-19.”

    By carrying out SARS-CoV-2 infections of epithelial cells in vitro and studying the responses with single cell sequencing, we get a much more detailed understanding of the viral infection kinetics and see big differences in the innate immune response between cell types.”


    Dr Kerstin Meyer, Co-Senior Author, Wellcome Sanger Institute

    Children infected with SARS-CoV-2 rarely progress to respiratory failure, but the risk of mortality in infected people over the age of 85 remains high, despite vaccination and improving treatment options.

    The research underscores the importance of considering age as a critical factor in both research and treatment of infectious diseases.

    Co-senior author, Dr Marko Nikolic (UCL Division of Medicine), said: “It is fascinating that when we take away immune cells from nasal samples, and are only left with nasal epithelial cells grown in a dish, we are still able to identify age-specific differences in our body’s response to the SARS-CoV-2 between the young and elderly to explain why children are generally protected from severe COVID-19.”

    Dr Smith added: “Understanding the cellular differences at the initiation of infection is just the beginning. We now hope to investigate the long-term implications of these cellular changes and test therapeutic interventions using our unique cell culture model. This ‘gold-standard’ system is only possible with the support of our funders and the willingness of participants to provide their samples.”

    The team suggest that future research should consider how aging impacts the body’s response to other viral infections.

    This study was funded by UK Research and Innovation (UKRI), and the National Institute for Health and Care Research (NIHR) Great Ormond Street Hospital Biomedical Research Centre, Wellcome and the Chan Zuckerberg Foundation.

    Source:

    University College London

    Journal reference:

    Woodall, M. N. J., et al. (2024). Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nature Microbiology. doi.org/10.1038/s41564-024-01658-1.

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  • Tiny DNA circles are key drivers of cancer formation, study suggests

    Tiny DNA circles are key drivers of cancer formation, study suggests

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    Tiny circles of DNA that defy the accepted laws of genetics are key drivers of cancer formation, according to an international study led by researchers at Stanford Medicine.

    The circles, known as extrachromosomal DNA or ecDNA, often harbor cancer-associated genes called oncogenes. Because they can exist in large numbers in a cell, they deliver a super-charged growth signal that can override a cell’s natural programming. They also contain genes likely to dampen the immune system’s response to a nascent cancer, the researchers found.

    Previous research had suggested that the circles, which are widespread in human cancers but rarely found in healthy cells, primarily arise in advanced tumors as the abnormal cells increasingly botch the intricate steps required to copy their DNA before each cell division. But the new study shows that the roly-poly circles can be found even in precancerous cells — and their presence jump-starts a cancerous transformation. Blocking their formation, or their effect on the cells that carry them, might stop cancers from developing, the researchers believe.

    This study has profound implications for our understanding of ecDNA in tumor development. It shows the power and diversity of ecDNA as a fundamental process in cancer. It has implications for early diagnosis of precancers that put patients at risk, and it highlights the potential for earlier intervention as treatments are developed.” 


    Paul Mischel, MD, professor of pathology

    Mischel is one of six senior authors of the research, which was published April 12 in Nature. Howard Chang, MD, PhD, professor of genetics and the Virginia and D.K. Ludwig Professor in Cancer Research, is also a senior author. Other senior authors include senior staff scientist Thomas Paulson, PhD, from Seattle’s Fred Hutchison Cancer Center; assistant professor of pediatrics Sihan Wu, PhD, assistant professor at Children’s Medical Center Research Institute at the University of Texas Southwestern Medical Center; professor of computer science and engineering Vineet Bafna, PhD, from UC San Diego; and professor of cancer prevention and director of the Early Cancer Institute Rebecca Fitzgerald, MD, from the University of Cambridge.  

    “People with ecDNA in their precancerous cells are 20 to 30 times more likely than others to develop cancer,” Chang said. “This is a huge increase, and it means we really need to pay attention to this. Because we also found that some ecDNAs carry genes that affect the immune system, it suggests that they may also promote early immune escape.”

    A grand challenge

    Deciphering ecDNA’s role in cancer was one of four Cancer Grand Challenges awarded by the National Cancer Institute and Cancer Research UK in 2022. The grand challenges program was launched to bring together researchers from around the world to tackle complex research topics too daunting for any one group. Mischel was awarded $25 million to lead a team of international researchers to learn more about the circles. But first they had to jettison some key genetic principles that have guided the field for nearly 200 years.

    Source:

    Journal reference:

    Luebeck, J., et al. (2023). Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus. Nature. doi.org/10.1038/s41586-023-05937-5.

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  • Moderate vitamin E, C, and β-carotene intake reduces type 2 diabetes risk

    Moderate vitamin E, C, and β-carotene intake reduces type 2 diabetes risk

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    In a recent study published in Advances in Nutrition, researchers review the effect of vitamins C and E, as well as β-carotene, on the risk of type 2 diabetes (T2D).

    Study: Vitamins C, E, and β-Carotene and Risk of Type 2 Diabetes: A Systematic Review and Meta-Analysis. Image Credit: Suriyawut Suriya / Shutterstock.com

    About the study

    Previously published meta-analyses have discussed the protective effect of β-carotene and vitamin E, not vitamin C, against T2D incidence. Furthermore, these analyses did not focus on randomized controlled trials (RCTs) or dose-response relationships.

    In the current review, all relevant information was obtained from Embase, MEDLINE, and the Cochrane Library databases. To investigate the relationships between dietary intake, circulating levels of vitamin C, vitamin E, and β-carotene, and T2D incidence, case-cohort, cohort, nested case-control, and RCT studies were considered. Any study written in languages other than English was not included in the review.

    A total of 6,190 articles were obtained in the initial search, 40 of which fulfilled the eligibility criteria and were considered. Both observational and RCT studies indicated low, moderate, or serious risk of bias. 

    Diet and T2D

    T2Dis associated with β-cell dysfunction and insulin resistance and is one of the most common and globally prevalent metabolic diseases. Several strategies associated with weight loss, diet, and physical activities have been designed to alleviate the risks of T2D.

    Adherence to specific dietary patterns, such as the Mediterranean diet, positively reduces the risk of T2D. The Mediterranean diet emphasizes increased consumption of fruits, vegetables, olive oil, and fish, as well as minimal intake of highly processed food and meat-based products. Fruits and vegetables are high in antioxidants, such as vitamin E, vitamin C, and β-carotene, which has many positive biological effects. 

    Vitamin C is a water soluble vitamin found in vegetables and fruits and regenerates vitamin E from its oxidized form. Vitamin E is a fat-soluble vitamin found in seeds, nuts, and vegetable oils, which protects cell membranes from lipid peroxidation. Moreover, β-carotene is a provitamin A carotenoid that is often found in fruits and vegetables. 

    Antioxidants protect cells from oxidative stress that arises due to the release of free radicals. Oxidative stress increases insulin resistance by inducing inflammatory processes and suppressing insulin signaling.

    Several studies have indicated that a high level of dietary antioxidants could alleviate insulin resistance and T2D. Thus, it is important to understand the mechanisms that contribute to the antioxidant properties of each vitamin. 

    How do β-carotene, and vitamins C and E affect T2D risk?

    Dietary intake of vitamin C, vitamin E, and β-carotene has been found to reduce the risk of T2D; however, this association is non-linear and plateaus at moderate intakes.

    Vitamin C is inversely associated with insulin resistance. To date, few studies have determined the effect of vitamin C on β-cell function.

    Among the reviewed RCT studies, there was not sufficient data indicating that supplementation of these vitamins reduces the risk of T2D. In contrast to vitamin C and β-carotene, vitamin E supplementation exhibited insulin resistance. 

    Nevertheless, a nonlinear dose-response gradient, which indicated that the lowest risk of diabetes was associated with moderate intake of dietary vitamins, was observed. According to Nordic guidelines, the dietary allowance of vitamin C for men and women is 75 mg/day and 90 mg/day, respectively. The recommendation for vitamin E intake is 8-15 mg/day for both men and women. 

    These recommendations can be reached through the consumption of half of a red pepper and half of a cup of almonds for vitamins C and E, respectively. Although no reference value has been established for β-carotene, an intake of 3-6 mg/day could reduce the risk of chronic disease.

    Mendelian randomization (MR) analyses did not indicate the causal relationship between genetically predicted circulating vitamin E, vitamin C, or β-carotene and T2D manifestation. This finding was also supported by RCT data revealing that supplementation of the these antioxidants did not confer additional benefits in reducing the risks of T2D in healthy adults. 

    It is possible that vitamin C, vitamin E, and β-carotene function synergistically to inhibit oxidative stress and, therefore, do not exhibit beneficial effects when consumed individually. Individuals who adhere to the Mediterranean diet consume an adequate amount of antioxidants, which act synergistically to reduce the risk of T2D. 

    Conclusions

    Sufficient, rather than high, intake of vitamin C, vitamin E, and β-carotene prevents the risk of T2D in healthy adults. Therefore, these vitamin supplements should not be used as a preventive strategy to reduce T2D in healthy individuals.

    However, future studies are needed to identify threshold antioxidant levels for smokers and those with genetic susceptibility to diabetes to obtain optimal benefits.

    Journal reference:

    • Lampousi, A., Lundberg, T., Löfvenborg, J. E., and Carlsson, S. (2024) Vitamins C, E, and β-Carotene and Risk of Type 2 Diabetes: A Systematic Review and Meta-Analysis. Advances in Nutrition 15(5); 100211. doi:10.1016/j.advnut.2024.100211

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  • Bio-Rad announces collaboration agreement with oncocyte to commercialize transplant monitoring with droplet digital PCR

    Bio-Rad announces collaboration agreement with oncocyte to commercialize transplant monitoring with droplet digital PCR

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    Bio-Rad Laboratories, Inc. (NYSE: BIO and BIO.B) a global leader in life science research and clinical diagnostics products, today announced a collaboration agreement with Oncocyte Corporation (Nasdaq: OCX), a precision diagnostics company, to develop and commercialize transplant monitoring products using Bio-Rad’s Droplet Digital™ PCR (ddPCR™) instruments and reagents.

    Under the terms of the agreement, Bio-Rad has committed to participate in a private placement of Oncocyte’s equity and has secured exclusive commercial rights in certain markets to commercialize Oncocyte’s assay for transplant monitoring research using Bio-Rad’s QX600™ ddPCR System. 

    Transplanted organs release cell-free DNA into the bloodstream of the recipient. This donor-derived cell-free DNA (dd-cfDNA1) is a sensitive biomarker for organ health that requires only a simple blood draw. The novel approach developed by the team at Oncocyte allows the assay to be applied to clinical research of both recent and non-recent transplants.

    The utility of the ddPCR-based approach has been well demonstrated, including in a prospective, observational, multicenter cohort trial published in 2017, which showed earlier and more sensitive discrimination of liver transplant patients with acute rejection, compared to conventional liver functional test methods2. 

    Oncocyte’s transplant monitoring assays and the Bio-Rad QX600 ddPCR System provide a highly sensitive and decentralized solution that could provide a more attractive alternative for laboratories that currently rely on centralized next-generation sequencing (NGS) test providers.

    “This collaboration advances Bio-Rad’s strategy to establish Droplet Digital PCR as a foundational technology by providing researchers and laboratories with high-value assays across a variety of life science applications. We believe that Oncocyte’s transplant monitoring assays and the Bio-Rad QX600 ddPCR System solution for the noninvasive measurement and quantification of key biomarkers used in solid tissue transplant monitoring research has the potential to advance science and save lives.”

    Simon May, EVP and President of Life Sciences at Bio-Rad Laboratories

    To learn more about Bio-Rad’s ddPCR technology visit bio-rad.com/qx600system.

    Sources:

    1. Donor-derived cell-free DNA (dd-cfDNA) is also known as graft-derived cell-free DNA (GcfDNA)
    2. Schütz E et al. (2017). Graft-derived cell-free DNA, a noninvasive early rejection and graft damage marker in liver transplantation: A prospective, observational, multicenter cohort study. PLoS Med 14, e1002286.

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  • Study reveals how SARS-CoV-2 hijacks lung cells to drive COVID-19 severity

    Study reveals how SARS-CoV-2 hijacks lung cells to drive COVID-19 severity

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    In a recent study published in the Journal of Experimental Medicine, researchers identified the cellular tropism and transcriptome consequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by infecting human lung tissue and using single-cell ribonucleic acid sequencing (scRNA-seq) to rebuild the transcriptional program in “infection pseudotime” for distinct lung cell types.

    Lower respiratory infections, such as coronavirus disease 2019 (COVID-19), are a leading cause of death worldwide, producing pneumonia and acute respiratory distress syndrome. Understanding their early phases is difficult. Researchers used classical histopathological approaches and single-cell multi-omic profiling to infer early phases in human pathogenesis from lung lavage, biopsy, or autopsy materials. These approaches reveal a thorough picture of COVID-19 pneumonia at unparalleled cellular and molecular resolution, implying infection models including alveolar epithelium, capillaries, macrophages, and myeloid cells.

    Study: Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. Image Credit: Dotted Yeti / ShutterstockStudy: Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. Image Credit: Dotted Yeti / Shutterstock

    About the study

    In the present study, researchers developed an experimental COVID-19 model to investigate early molecular processes and pathogenic mechanisms of SARS-CoV-2 infection at the cellular level in native tissues of the human lung.

    The researchers established SARS-CoV-2’s cellular tropism and its unique and dynamic impacts on host cellular gene expression in specific types of lung cells. Prominent targets were lung-resident macrophages, of which one SARS-CoV-2 takes over transcriptomes, inducing a targeted host interferon (IFN) antiviral program, and several chemokines and pro-fibrotic and pro-inflammatory and cytokines signaling to various structural and immunological cells of the lung.

    To determine the early stages of COVID-19 in human lungs, the researchers sliced lung tissue obtained from surgical specimens or organ donor individuals into thick sections and used them for tissue culture analysis. Subsequently, they exposed the tissues to the SARS-CoV-2 USA-WA1 2020 strain at 1.0 multiplicity of infection (MOI) for two hours before allowing the SARS-CoV-2 infection to continue for two to three days. They performed a plaque test on culture supernatants.

    The researchers separated the slices and examined them by scRNA-seq to evaluate host and viral genetic expression during the SARS-CoV-2 infection. They also examined the viral RNA molecules’ junctional structure and processing by analyzing the scRNA-seq dataset with the SICILIAN framework. They used molecular atlas markers to distinguish lung cell types in healthy lung slices and measure viral RNA levels in infected cells.

    The team performed multiplexed single-molecule fluorescence in situ hybridization (smFISH) to confirm lung cell tropism findings and show infected cells. They used single-cell gene expression patterns to identify cellular targets for inflammatory and pro-fibrotic signals elicited by the SARS-CoV-2 infection of a-IMs. They devised a technique for purifying macrophage populations from human lungs with a SARS-CoV-2 spike (S) protein-pseudotyped lentivirus (lenti-S-NLuc-tdT) to investigate lung macrophage entrance routes.

    The researchers productively infected human lung slices cultivated ex vivo with SARS-CoV-2, with production rising between 24 and 72 hours of culture. They heat-inactivated, ultraviolet (UV)-treated, or administered 10.0 µM remdesivir, an RNA-dependent RNA polymerase inhibitor used as a COVID-19 therapeutic, to prevent viral stock infection.

    Results

    The analysis showed that SARS-CoV-2 preferentially infects active interstitial macrophages (IMs), which can amass hundreds of SARS-CoV-2 RNA molecules, comprising >60% of the cell transcriptome and producing dense viral RNA bodies. Infected alveolar macrophages (AMs) exhibit no severe reactions, with spike (S) protein-dependent viral entrance into AMs utilizing angiotensin-converting enzyme 2 (ACE2) and the cluster of differentiation 169 (CD169) and IM entry via CD209.

    They found canonical sub-genomic junctions between the unusual sequence reads beyond their 39 terminal regions, indicating canonical-type SARS-CoV-2 messenger RNA (mRNA) production in the pulmonary cultures. They also found hundreds of new subgenomic junctions, showing a wide range of non-canonical and canonical sub-genomic SARS-CoV-2 RNAs produced during pulmonary infection.

    Model of initiation, transition, and pathogenesis of COVID-19 and the viral lifecycle in AMs and IMs. (a–d) Model of COVID-19 initiation in the human lung and transition from viral pneumonia to lethal COVID-19 ARDS. (a) SARS-CoV-2 virion dissemination and arrival in the alveoli. Luminal AM encounter virions shed from the upper respiratory tract that enter the lung. AMs can express low to moderate numbers of viral RNA molecules and can propagate the infection but “contain” the viral RNA from taking over the total transcriptome and show only a very limited host cell inflammatory response to viral infection. (b) Replication and epithelial injury. SARS-CoV-2 virions enter AT2 cells through ACE2, its canonical receptor, and “replicate” to high viral RNA levels, producing infectious virions and initiating viral pneumonia. (c) a-IM takeover and inflammation signaling. SARS-CoV-2 virions spread to the interstitial space through either transepithelial release of virions by AT2 cells or injury of the epithelial barrier, and enter a-IMs. Infected a-IMs can express very high levels of viral RNA that dominate (“take over”) the host transcriptome and can propagate the infection. Viral takeover triggers induction of the chemokines and cytokines shown, forming a focus of inflammatory and fibrotic signaling. (d) Endothelial breach and immune infiltration. The a-IM inflammatory cytokine IL6 targets structural cells of the alveolus causing epithelial and endothelial breakdown, and the inflammatory cytokines recruit the indicated immune cells from the interstitium or bloodstream, which flood and infiltrate the alveolus causing COVID-19 ARDS. Local inflammatory molecules are amplified by circulating immune cells, and reciprocally can spread through the bloodstream to cause systemic symptoms of cytokine storm. (e) Comparison of the SARS-CoV-2 viral lifecycle in AMs and IMs. Although both can produce infectious virions, note differences in viral entry receptors (AMs can use ACE2 and CD169/SIGLEC1, whereas IMs use CD209); viral RNA transcription of dsRNA intermediates (greater in AMs); replication of full-length genomic RNA (greater in IMs); viral takeover, formation of RNA bodies, and induction of a robust host cell inflammatory response (only in IMs), and cell destruction/death (only in IMs).Model of initiation, transition, and pathogenesis of COVID-19 and the viral lifecycle in AMs and IMs. (a–d) Model of COVID-19 initiation in the human lung and transition from viral pneumonia to lethal COVID-19 ARDS. (a) SARS-CoV-2 virion dissemination and arrival in the alveoli. Luminal AM encounter virions shed from the upper respiratory tract that enter the lung. AMs can express low to moderate numbers of viral RNA molecules and can propagate the infection but “contain” the viral RNA from taking over the total transcriptome and show only a very limited host cell inflammatory response to viral infection. (b) Replication and epithelial injury. SARS-CoV-2 virions enter AT2 cells through ACE2, its canonical receptor, and “replicate” to high viral RNA levels, producing infectious virions and initiating viral pneumonia. (c) a-IM takeover and inflammation signaling. SARS-CoV-2 virions spread to the interstitial space through either transepithelial release of virions by AT2 cells or injury of the epithelial barrier, and enter a-IMs. Infected a-IMs can express very high levels of viral RNA that dominate (“take over”) the host transcriptome and can propagate the infection. Viral takeover triggers induction of the chemokines and cytokines shown, forming a focus of inflammatory and fibrotic signaling. (d) Endothelial breach and immune infiltration. The a-IM inflammatory cytokine IL6 targets structural cells of the alveolus causing epithelial and endothelial breakdown, and the inflammatory cytokines recruit the indicated immune cells from the interstitium or bloodstream, which flood and infiltrate the alveolus causing COVID-19 ARDS. Local inflammatory molecules are amplified by circulating immune cells, and reciprocally can spread through the bloodstream to cause systemic symptoms of cytokine storm. (e) Comparison of the SARS-CoV-2 viral lifecycle in AMs and IMs. Although both can produce infectious virions, note differences in viral entry receptors (AMs can use ACE2 and CD169/SIGLEC1, whereas IMs use CD209); viral RNA transcription of dsRNA intermediates (greater in AMs); replication of full-length genomic RNA (greater in IMs); viral takeover, formation of RNA bodies, and induction of a robust host cell inflammatory response (only in IMs), and cell destruction/death (only in IMs).

    Heat, UV-C inactivation, or remdesivir therapy prevented the development of canonical and non-canonical connections. The team observed SARS-CoV-2 takeover of an activated IM subtype in 176,382 cells with high-quality transcriptomes obtained from infected lung slices of four donor lungs and in 112,359 cells from mock-infected slices (cultured without viral addition) and 95,389 uncultured control cells (directly from freshly cut lung slices). A differential gene expression study of a-IMs over infection pseudotime revealed host gene expression alterations corresponding to SARS-CoV-2 RNA levels.

    The study found that COVID-19 pneumonia infection and takeover cause an early antiviral cell response specific to activated interstitial macrophages, resulting in a powerful immunological and fibrotic signaling center. Inflammasome activation is uncommon and only detectable late in a-IM infection. Blocking antibodies against CD169 and CD209 prevented entrance into IMs and AMs. The study also highlighted IMs as the most vulnerable lung target, with initial emphasis on inflammation and fibrosis. Two unique molecular lineages of macrophage targets react differently to SARS-CoV-2, influencing etiology and treatments.

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  • Expanding roles beyond cellular waste management

    Expanding roles beyond cellular waste management

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    The typical job of the proteasome, the garbage disposal of the cell, is to grind down proteins into smaller bits and recycle some of those bits and parts. That’s still the case, for the most part, but, Johns Hopkins Medicine researchers, studying nerve cells grown in the lab and mice, say that the proteasome’s role may go well beyond that.

    Its additional role, say the researchers, may shift from trash sorter to signal messenger in dorsal root ganglion neurons -; cells that convey sensory signals from nerve cells close to the skin to the central nervous system.

    Results of their experiments, published April 12 in Cell Reports, show that proteasomes may help those specialized neurons sense the surrounding environment, send signals to each other and potentially differentiate between sensing pain and itch, a finding that could help scientists better understand these sensory processes and new targets for treating pain and other sensory problems.

    Neurons live next to each other for a long time, and they need ways to communicate with each other about what they’re doing and who they are. Proteasomes in the membrane of neurons may help the cells fine tune this messaging process.”


    Seth S. Margolis, Ph.D., associate professor of biological chemistry, Johns Hopkins University School of Medicine

    “Proteasomes are more complicated than they appear,” says Margolis. He and his colleagues first found proteasomes in the plasma membranes of central nervous system neurons in mice in 2017, which they dubbed neuronal membrane proteasomes, and have continued studying how these special proteasomes promote messaging, or crosstalk, among neurons.

    At the time, Margolis’ focus was on the central nervous system, encompassing the brain and spinal cord. But later, he collaborated with neurobiologist Eric Villalón Landeros, Ph.D., postdoctoral fellow in Margolis’ laboratory at Johns Hopkins, whose work focuses on the peripheral nervous system, the network of neurons running through the rest of the body, closer to the skin, capturing sensory information from the environment.

    Margolis and Villalón Landeros wondered whether proteasomes could be found in peripheral neurons, and if so, what they might do.

    Using mouse antibodies that glom on to proteasomes, and other methods, the investigators found the proteasomes on the surface of neurons in the spinal cord, dorsal root ganglia, sciatic nerve and peripheral nerves innervating skin.

    The researchers were also able to find proteasomes in the same type of peripheral neurons grown in laboratory culture dishes.

    To understand the proteasome’s function in peripheral sensory neurons, the researchers gave mice biotin-epoxomicin, a cell membrane-impermeable proteasome inhibitor that blocks the function of neuronal membrane proteasomes. Then, they performed classic sensory tests.

    The researchers found that the mice that got injections of the proteasome-blocking drug biotin-epoxomicin on one side of the body were between 25% to 50% slower than the other side to respond to sensory tests.

    “This suggests that membrane proteasomes are important for sensation, and they must be facilitating this at the signaling level,” says Margolis.

    The researchers used single cell sequencing technology to determine that membrane proteasomes were expressed in a subpopulation of neurons involved in itch sensation and known to be sensitive to histamine, an immune system compound that launches an animal’s (including human’s) response to allergens.

    In laboratory culture dishes, the researchers stimulated both itch-related and non-itch related neurons and blocked their membrane proteasomes with biotin-epoxomicin. This resulted in changes to activity in all of the cells. “Blocking proteasomes seems to have an activity-modulatory effect across all the cells, despite being expressed in a subpopulation, suggesting that proteasomes facilitate a kind of cross talk between these cells,” says Margolis.

    Proteasome blockers, including one called Velcade, are currently used to treat certain types of cancer.

    Villalón Landeros and Margolis plan to continue working together to determine how neuronal membrane proteasomes function in sensory neurons and in sensing pain versus itch. “We want to see if we can manipulate neuronal membrane proteasomes to have a different outcome on pain and itch sensation,” says Villalón Landeros.

    Additional scientists who contributed to the research are Samuel Kho, Taylor Church, Anna Brennan, Fulya Türker, Michael Delannoy and Michael Caterina from Johns Hopkins.

    Funding for the research was provided by the National Institutes of Health (F32NS119202, R01 NS110754) and a Merkin Peripheral Neuropathy and Nerve Regeneration Center grant.

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  • Breakthrough study reveals melanoma’s resistance tactics to targeted therapy

    Breakthrough study reveals melanoma’s resistance tactics to targeted therapy

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    Melanoma is the deadliest form of skin cancer. With global incidence rates rising, new, more effective treatments are necessary to alleviate the health burden of the disease. Important advances in recent years include doctors using genetic tests to look for specific mutations they can target for more personalised, effective treatment.

    Around 1 in 2 melanoma patients will have mutations in the BRAF gene. This gene normally makes a protein which helps control cell growth, but mutations can cause the cells to grow and divide uncontrollably instead, happening in many different types of cancer including melanoma.

    The discovery of BRAF mutations has led to development of targeted therapies to inhibit its function. One of the standard treatment options for melanoma over the last ten years has been to simultaneously target both BRAF mutations and MEK. These two genes are part of the MAPK signalling pathway, which, in cancer, is rewired for uncontrolled growth. Targeting two different critical points in the same domino chain helps slow or stop cancer growth.

    Despite great initial responses to the combined use of the first-generation inhibitors, around 50% of melanoma patients with BRAF mutations will relapse within one year. The cancer acquires resistance to the drugs, finding other ways to reactive the MAPK pathway through mechanisms which remain poorly understood.

    Melanoma drug resistance is a huge clinical problem because it occurs in almost all BRAF-mutated patients under BRAF/MEK inhibitor therapy and there are few or no therapeutic alternatives. There is an urgent need to understand the many different underlying mechanisms and find new strategies to deal with this constantly evolving arms race.”


    Dr. Francisco Aya Moreno, medically-trained oncologist and recent PhD graduate at the Centre for Genomic Regulation (CRG) in Barcelona

    A study published today in the journal Cell Reports has disentangled the mechanisms behind one of the ways cancer cells develop resistance to targeted therapy. The study found that, in response to treatment, melanomas can ‘break’ parts of their BRAF gene, also known as genomic deletions. This helps the tumour create alternative versions of the protein (altBRAFs) which lack regions targeted by BRAF inhibitors, reactivating the MAPK pathway and making the drugs less effective. The finding was consistent across various lab models and patient tumour samples.

    The findings are important because altBRAFs were thought to be made through alternative splicing, which is when cells use the same gene to synthesise different proteins. The discovery that genomic deletions, and not splicing, are the cause means a shift away from previous proposals for using drugs that target splicing as a therapeutic strategy.

    “For years, we’ve known that some patients produce altBRAFs and these help the cancer resist treatment, but we misunderstood the mechanism behind their creation. Knowing that genomic deletions are the cause opens new avenues for developing therapies that could more effectively help patients with BRAF mutations,” explains ICREA Research Professor Juan Valcarcel, co-author of the study and researcher at the Centre for Genomic Regulation.

    Surprisingly, the researchers found evidence of the same genomic deletions in melanomas which hadn’t been treated yet. In other words, melanomas can naturally develop mechanisms that mimic drug resistance, even without exposure to drugs. Identifying and targeting these early resistance mechanisms through profound genetic testing in a clinical setting before treatment begins could improve the efficacy of first-line therapies.

    Even more surprisingly, further analyses revealed that genomic deletions might be a more widespread mechanism of oncogenesis and resistance than previously thought. Though uncommon, researchers found evidence of altBRAFs in melanomas with a normal-functioning BRAF gene, as well as in other types of cancer including non-small cell lung cancer, breast cancer, kidney cancer and prostate cancer. The findings could increase the patient population benefiting from targeted treatments which are currently under clinical development.

    “There is an emerging class of drugs known as second generation RAF inibitors. Unlike BRAF inhibitors, these drugs have a broad spectrum, and so could potentially inhibit the function of altBRAFs. Clinical trials which are assessing their effectiveness should also expand to include melanoma patients with a normal functioning BRAF gene as well, and possibly to other cancer types which express altBRAFs,” explains Dr. Aya Moreno.

    Dr. Aya Moreno is part of the second cohort of the PhD4MD programme, a joint effort by Centre for Genomic Regulation (CRG), the Institute for Research in Biomedicine (IRB Barcelona), the August Pi i Sunyer Biomedical Research Institute (IDIBAPS) and the Vall d’Hebron Research Institute (VHIR) designed to leverage the medical insight of a doctor to drive research that benefits patients.

    “Having the opportunity to approach this research with both a clinician’s perspective and a scientist’s curiosity has been invaluable. It allowed us to uncover not just how melanomas resist treatment but also how this knowledge could lead to more effective therapies for patients. This fusion of clinical insight and scientific investigation is crucial for making real progress in our fight against cancer,” concludes Dr. Aya Moreno.

    The study was led by Dr. Aya Moreno and co-supervised by Professor Juan Valcarcel at the Centre for Genomic Regulation and Dr. Ana Arance at IDIBAPS. It was also carried out in collaboration with Nuria López Bigas’ research group at IRB Barcelona. Since completing his PhD at the CRG, Dr. Aya Moreno has returned to the Medical Oncology department in the Hospital Clinic in Barcelona.

    Source:

    Center for Genomic Regulation

    Journal reference:

    Aya, F., et al. (2024). Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma. Cell Reports. doi.org/10.1016/j.celrep.2024.114048.

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  • KAIST researchers propose microbial food production from sustainable raw materials

    KAIST researchers propose microbial food production from sustainable raw materials

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    The global food crisis is increasing due to rapid population growth and declining food productivity to climate change. Moreover, today’s food production and supply system emit a huge amount of carbon dioxide, reaching 30% of the total amount emitted by humanity, aggravating climate change. Sustainable and nutritious microbial food is attracting attention as a key to overcoming this impasse.

    KAIST (President Kwang Hyung Lee) announced on April 12th that Research Professor Kyeong Rok Choi of the BioProcess Engineering Research Center and Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering published a paper that proposes a direction of research on ‘microbial food production from sustainable raw materials.’

    Microbial food refers to various foods and food ingredients produced using microorganisms. Microbial biomass contains a large amount of protein per unit in dry mass, comparable to that of meat, and emits the smallest amount of carbon dioxide and is required to produce a unit mass compared to various livestock, fish, shellfish, and crops. Since the amount of water and space requirement is small, it can be an eco-friendly, sustainable and highly nutritious food resource.

    Fermented foods are the most readily available microbial foods around us. Although the proportion of microbial biomass in fermented foods is small, compounds with relatively low nutritional value, such as carbohydrates, are consumed during the fermentation process, and as microorganisms proliferate, the content of nutrients with higher nutritional value, such as proteins and vitamins, increases.

    Various food compounds isolated and purified from biomass or culture media obtained through microbial culture are also a branch of microbial food. Examples that can be found around us include various amino acids, including monosodium glutamate, food proteins, enzymes, flavoring compounds, food colorings, and bioactive substances.

    Lastly, the most ultimate and fundamental form of microbial food can be said to be microbial biomass or extracts produced through microbial culture and foods cooked using them. A representative example is single-cell protein, which collectively refers to microbial biomass or microbial proteins extracted from it.

    In this paper, the researchers comprehensively covered various non-edible raw materials and strategies for using them that can be used to produce microbial food in a more sustainable way. Furthermore, it covers various microbial foods that are actually produced in the industry using the relevant raw materials and their characteristics, as well as prospects for the production and generalization of sustainable microbial foods.

    Microbial foods produced from various sustainable raw materials will soon be commonly encountered at our tables.”


    Research Professor Kyeong Rok Choi, first author of the paper

    Second author Seok Yeong Jung, a doctoral student, also said, “Microbial foods of the future will not be limited foods consumed only out of a sense of obligation to the environment, but will be complete foods that are consumed by choice because of their nutritional value and taste.” In addition, Distinguished Professor Sang Yup Lee said, “It is time for the industry and academia, as well as the public and private sectors, to cooperate more closely so that more diverse microbial foods can be developed and supplied in order to create a sustainable society for ourselves and our descendants.”

    This paper was published online on April 9 in ‘Nature Microbiology’ published by Nature.

    This research was conducted under the development of platform technologies of microbial cell factories for the next-generation biorefineries project (project leader KAIST Distinguished Professor Sang Yup Lee) supported by the Ministry of Science and ICT and the Cooperative Research Program for Agriculture Science and Technology Development (Project leader KAIST Research Professor Kyeong Rok Choi) of the Agricultural Microbiology Project Group (Director, Professor Pahn-Shick Chang) supported by the Rural Development Administration.

     

    Source:

    KAIST (Korea Advanced Institute of Science and Technology)

    Journal reference:

    Choi, K. R., et al. (2024). From sustainable feedstocks to microbial foods. Nature Microbiology. doi.org/10.1038/s41564-024-01671-4.

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  • Soft tumor environments prime cancer cells for survival during metastasis

    Soft tumor environments prime cancer cells for survival during metastasis

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    Researchers have discovered how the mechanical properties of tumors can prime cancer cells to better survive their spread to other organs.

    A metabolic ‘survival switch’ controlled by the stiffness of triple-negative breast tumors can significantly influence how successfully their cancerous cells spread to other organs, according to new findings from the Garvan Institute of Medical Research.

    The study in cell and mouse models showed that softer tumor environments, typical of early-stage cancer, can prime triple-negative breast cancer cells to use an extra energy source for survival during metastasis. The research suggests that drugs targeting this altered cancer cell metabolism could boost treatments for metastatic triple-negative breast cancer.

    “Our research suggests triple-negative breast cancer cells in soft tissue environments are ‘primed’ to better survive the spread to other organs and that they switch on an alternative form of metabolism to do so,” says Associate Professor Cox, Head of the Matrix & Metastasis Lab at Garvan and senior author of the study published in Advanced Science.

    “This suggests that triple-negative breast cancer cells spreading from softer tumors are more aggressive, and drugs that target cancer cell metabolism may benefit patients with metastatic triple-negative breast cancer treatment.”

    A metabolic survival advantage

    Triple-negative breast cancers are highly aggressive and difficult to treat as they lack three receptors (for estrogen, progesterone and the HER2 protein) that can be targeted in other breast cancers. New treatment options are urgently needed for the 2,500 women diagnosed every year in Australia alone.

    Using biomaterials that mimic the properties of tumors, the team investigated how triple-negative breast cancer cells respond to the physical stiffness of their environment. The researchers found the cancer cells were primed to be more resilient when grown in soft environments and, when injected into mouse models, up to 11.8 times more likely to metastasize to new sites compared to those from rigid tumor environments.

    The team also discovered that soft environments altered the cancer cells’ preference for ‘fuel’ in a way that enhanced their durability while traveling through the body. These primed cells metabolized glucose – the preferred energy source for cancer cells – but they also stockpiled lipids as internal fuel reserves and in turn ramp up lipid metabolism – a more resilient energy pathway for their journey from a primary tumor site.

    “This switch to using both glucose and fats as an energy source equips cells to better survive the mechanical stresses of travelling through the blood stream and seeding new tumor sites throughout the body,” says first author Dr Elysse Filipe, who completed the study as a postdoctoral researcher at Garvan. “By blocking lipid metabolism in triple-negative breast cancer cells, we were able to ‘starve’ their high energy demand and reduce metastasis in a cell model.”

    A new approach for triple-negative breast cancer

    Our findings highlight that the physical properties of triple-negative breast cancers, which vary dynamically as the cancer progresses, profoundly impact the cancer’s ability to spread. These findings reveal a vulnerability of triple-negative breast cancers – the metastasizing cells’ reliance on diverse fuel sources to meet their high energy demands.”


    Dr. Elysse Filipe, first author 

    Associate Professor Cox adds: “The study underscores the importance of considering the mechanical diversity within and between tumors when designing new treatments for aggressive cancers. We now plan to explore whether pairing targeted metabolic inhibitors with existing therapies could limit metastasis and improve outcomes for triple-negative breast cancer patients.”

    Source:

    Garvan Institute of Medical Research

    Journal reference:

    Filipe, E. C., et al. (2024) Tumor Biomechanics Alters Metastatic Dissemination of Triple Negative Breast Cancer via Rewiring Fatty Acid Metabolism. Advanced Science. doi.org/10.1002/advs.202307963.

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  • Research sheds light on post-sepsis immune suppression mechanism

    Research sheds light on post-sepsis immune suppression mechanism

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    Severe sepsis from bacterial or viral infections can be life-threatening and even people recovering from severe sepsis may experience long-lasting effects on the immune system, making them more susceptible to recurrent infections. The causes for this sepsis-induced immune suppression are not well understood and lack an effective treatment. To better understand the cause, Katherine MacNamara and colleagues from Albany Medical College, USA, analyzed the blood stem cells of mice with prior sepsis and their results were recently published in the journal Stem Cell Reports.

    During acute infection, blood stem cells in the bone marrow are activated by signaling molecules called inflammatory cytokines, which make them divide and migrate to the blood stream to generate large quantities of immune cells outside the bone marrow. Once infection is eliminated, cytokine levels return to baseline and blood stem cell activation and immune cell production stops.

    To understand how this process gets dysregulated after severe sepsis resolves, the researchers analyzed the blood stem cells of mice and found them to be fully recovered and functional in the bone marrow of mice 20 days after sepsis. However, upon a second round of inflammatory stimulation, using the stem cell mobilizing agent G-CSF, the blood stem cells of sepsis survivors did not undergo a new round of activation and mobilization as did those in mice without prior sepsis.

    Consequently, immune cells were not efficiently produced in those mice with prior sepsis. These observations could explain why following sepsis, patients are unable to efficiently combat new infections and why giving inflammatory cytokines and G-CSF specifically to sepsis patients had no effect against secondary infections in previous clinical trials. This knowledge may help to identify new treatments for patients with post-sepsis immune suppression.

    Source:

    International Society for Stem Cell Research

    Journal reference:

    Biswas, N., et al. (2024) Survivors of polymicrobial sepsis are refractory to G-CSF-induced emergency myelopoiesis and hematopoietic stem and progenitor cell mobilization. Stem Cell Reports. doi.org/10.1016/j.stemcr.2024.03.007.

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