Cholesterol May Be Key to New Therapies for Alzheimer’s Disease, Diabetes (Medicine)

University of Arizona Health Sciences researcher examined the role of cholesterol in both Alzheimer’s disease and Type 2 diabetes to identify a small molecule that may help regulate cholesterol levels in the brain, making it a potential new therapeutic target for Alzheimer’s disease.

There is no known cure for Alzheimer’s disease, which affects more than 5.5 million people in the United States. In the last decade, scientists have found increasing evidence linking the underlying causes of Type 2 diabetes and Alzheimer’s disease.

Type 2 diabetes occurs when insulin becomes less efficient at removing glucose from the bloodstream, resulting in high blood sugar that can cause abnormal cholesterol levels. A similar situation occurs in Alzheimer’s disease, but rather than affecting the body as a whole, the effects are localized in the brain.

“Alzheimer’s and diabetes share many common causes,” said Gregory Thatcher, PhD, professor of pharmacology and toxicology in the UArizona College of Pharmacy and the newly named R. Ken and Donna Coit Endowed Chair in Drug Discovery. “Our goal was to develop a way of identifying compounds that would counteract many detrimental changes that contribute to both Alzheimer’s and Type 2 diabetes.”

The paper, “Discovery of Nonlipogenic ABCA1 Inducing Compounds with Potential in Alzheimer’s Disease and Type 2 Diabetes,” was published in the journal ACS Pharmacology and Translational Science.

When cholesterol rises, due to insulin resistence or other factors, the body starts a process known as reverse cholestrol transport, during which specific molecules carry excess cholesterol to the liver to be excreted. Apolipoprotein E (APOE) is one of the proteins involved in reverse cholesterol transport.

APOE is also the strongest risk factor gene for Alzheimer’s disease and related dementia, and an independent risk factor for Type 2 diabetes and cardiovascular disease. Similarly, reduced activity of another cholesterol transporter, ATP-binding cassette transporter A1 (ABCA1), correlates with increased risk of cardiovascular disease, Type 2 diabetes and Alzheimer’s disease.

“While most people are aware of so-called ‘good cholesterol,’ and ‘bad cholesterol,’ associated with risk of heart attack and stroke, these broad concepts are also applicable to a healthy brain,” said Dr. Thatcher, who has been working to develop advanced therapeutics for Alzheimer’s for more than 20 years. “Moving cholesterol to where it is needed in the body has positive effects on many physiological processes and can help clear misfolded proteins that accumulate in the brain.” 

Increasing the activity of ABCA1 is expected to positively influence insulin signaling and reduce inflammation in the brain, making it a potential therapy for both Type 2 diabetes and Alzheimer’s disease. In this study, Dr. Thatcher and the research team designed a way to identify small molecules that improve the function of ABCA1 in the body while avoiding unwanted effects to the liver.

In a March 20 paper in the journal EBioMedicine, “Metabolomic analysis of a selective ABCA1 inducer in obesogenic challenge provides a rationale for therapeutic development,” Dr. Thatcher’s team honed in on a specific small molecule, CL2-57, due to its ability to stimulate ABCA1 activity with positive effects on liver and plasma triglycerides. The use of this compound showed improved glucose tolerance and insulin sensitivity, as well as reduced weight gain, among other beneficial effects.

Their future research will seek to improve the properties of the small molecules to increase the levels in the brain. Their long-term goal is to understand which patients suffering from the cognitive and neuropsychiatric symptoms of Alzheimer’s and dementia will benefit from the treatment.

“During the Covid-19 pandemic we hear about the mounting deaths in nursing homes and it’s important to remember that Alzheimer’s and related dementia is a major cause of the elderly moving to nursing homes,” Dr. Thatcher said. “It would be good to think of a future in which healthspan was extended, especially a healthy brain; maybe that’s more important than lifespan.”   

Featured image: Gregory Thatcher, PhD © University of Arizona Health Sciences

Provided by University of Arizona Health Sciences

Therapeutic Bed Can Help Keep Preterm Newborns’ Brain Oxygen Levels Stable (Medicine)

A medical device that has been shown to manage pain among babies born preterm can also help keep their brain oxygen levels steady during medical procedures, finds new analysis by researchers at UBC.

The device, called Calmer, is a pillow-sized therapeutic bed covered in soft fabric and inserted into the incubator. It can be programmed to mimic a parent’s heartbeat and breathing rate— providing a soothing presence by moving up and down gently to simulate a breathing motion and heartbeat sound for the baby when their parent cannot be present.

Dr. Manon Ranger © UBC

“For newborns and particularly for preterm babies, it’s critical to keep overall blood oxygen levels steady, especially in the brain. The more stable their brain oxygenation is, the better for their brain development,” says researcher Dr. Manon Ranger, a UBC nursing professor who studies the health of vulnerable infants.

The team conducted a randomized clinical trial with 29 premature babies admitted to the neonatal intensive care unit, or NICU, at BC Women’s Hospital + Health Centre. Half the participants received the usual care—facilitated tucking, where a caregiver holds the infant in a flexed position, plus a soother—during a painful procedure (a blood draw). The other half were placed on Calmer.

When their brain oxygen levels were measured, both groups showed similar results: their brain oxygen levels stayed largely steady during the procedure.

“A parent’s touch, generally speaking, is ultimately the most soothing presence for an infant. It relieves pain, helps them gain weight and promotes brain growth while reducing stress,” said Ranger, who is also an investigator at BC Children’s Hospital and Women’s Health Research Institute.

“However, this option is not always available in NICUs. Our research shows that when a parent or caregiver cannot be physically present, Calmer is an effective alternative. This is especially relevant in the current COVID-19 pandemic context, where many hospital settings must restrict contact with visitors.”

Dr. Liisa Holsti © UBC

Calmer was developed by Dr. Liisa Holsti, a professor in the department of occupational science and occupational therapy at UBC, and an investigator at BC Children’s Hospital and Women’s Health Research Institute; and Dr. Karon Maclean, a UBC professor of computer science. Other researchers from BC Children’s Hospital, the British Columbia Institute of Technology and the BC Women’s Hospital and Health Centre also contributed to its development.

“We were very pleased that our preliminary trial results showed that Calmer has the potential to benefit these infants whose brains are particularly vulnerable to pain and stress,” said Holsti. “We are expanding our evaluation of this device in more rigorous real-world conditions, and we’re in the process of redesigning it to be used in low- and middle-income countries, so that infants worldwide who need it can have the benefit of Calmer treatment.”

For their next step, the team is planning to test longer-term use of Calmer on preterm infants’ physical growth and brain development in the NICU. This project recently received funding from UBC’s Health Innovation Funding Investment (HIFI) awards.

Featured image: Premature baby resting on Calmer in the NICU at BC Children’s Hospital. Photo credit: Liisa Holsti

Provided by University of British Columbia

Scientists Uncover a Process That Stands in The Way of Making Quantum Dots Brighter (Physics)

The results have important implications for today’s TV and display screens and for future technologies where light takes the place of electrons and fluids.

Bright semiconductor nanocrystals known as quantum dots give QLED TV screens their vibrant colors. But attempts to increase the intensity of that light generate heat instead, reducing the dots’ light-producing efficiency.

A new study explains why, and the results have broad implications for developing future quantum and photonics technologies where light replaces electrons in computers and fluids in refrigerators, for example.

In a QLED TV screen, dots absorb blue light and turn it into green or red. At the low energies where TV screens operate, this conversion of light from one color to another is virtually 100% efficient. But at the higher excitation energies required for brighter screens and other technologies, the efficiency drops off sharply. Researchers had theories about why this happens, but no one had ever observed it at the atomic scale until now.

To find out more, scientists at the Department of Energy’s SLAC National Accelerator Laboratory used a high-speed “electron camera” to watch dots turn incoming high-energy laser light into their own glowing light emissions.  

The experiments revealed that the incoming high-energy laser light ejects electrons from the dot’s atoms, and their corresponding holes – empty spots with positive charges that are free to move around – become trapped at the surface of the dot, producing unwanted waste heat.

In addition, electrons and holes recombine in a way that gives off additional heat energy. This increases the jiggling of the dot’s atoms, deforms its crystal structure and wastes even more energy that could have gone into making the dots brighter.

SLAC and Stanford researchers have made the first atomic-scale observations of how nanocrystals known as quantum dots lose their light-producing efficiency when excited with intense light. Dots were excited with green light (top) or higher-energy purple light (bottom), and scientists watched them respond with an “electron camera,” MeV-UED. When hit with green light, the dots relaxed, and excited pairs of electrons and holes converted virtually all of the incoming energy to light. But when hit with purple light, some of the energy was trapped on the surface of the dot; this distorted the arrangement of surrounding atoms and wasted energy as heat. The results have broad implications for developing future quantum and photonics technologies where light replaces electrons in computers and fluids in refrigerators. (B. Guzelturk et al., Nature Communications, 25 March 2021)

“This represents a key way that energy is sucked out of the system without giving rise to light,” said Aaron Lindenberg, a Stanford University associate professor and investigator with the Stanford Institute for Materials and Energy Sciences at SLAC who led the study with postdoctoral researcher Burak Guzelturk.

“Trying to figure out what underlies this process has been the subject of study for decades,” he said. “This is the first time we could see what the atoms are actually doing while excited state energy is being lost as heat.”

The research team, which included scientists from SLAC, Stanford, the University of California, Berkeley and DOE’s Lawrence Berkeley National Laboratory, described the results in Nature Communications today.

Emitting a pure, brilliant glow

Despite their tiny size – they have about the same diameter as four strands of DNA – quantum dot nanocrystals are surprisingly complex and highly engineered. They emit extremely pure light whose color can be tuned by adjusting their size, shape, composition and surface chemistry. The quantum dots used in this study were invented more than two decades ago, and today they’re widely used in bright, energy-efficient displays and in imaging tools for biology and medicine.

Understanding and fixing problems that stand in the way of making dots more efficient at higher energies is a very hot field of research right now, said Guzelturk, who carried out experiments at SLAC with postdoctoral researcher Ben Cotts.

Previous studies had focused on how the dots’ electrons behaved. But in this study, the team was able to see the movements of whole atoms, too, with an electron camera known as MeV-UED. It hits samples with short pulses of electrons with very high energies, measured in millions of electronvolts (MeV). In a process called ultrafast electron diffraction (UED), the electrons scatter off the sample and into detectors, creating patterns that reveal what both electrons and atoms are doing.

As the SLAC/Stanford team measured the behavior of quantum dots that had been hit with various wavelengths and intensities of laser light, UC Berkeley graduate students Dipti Jasrasaria and John Philbin worked with Berkeley theoretical chemist Eran Rabani to calculate and understand the resulting interplay of electronic and atomic motions from a theoretical standpoint.

“We met with the experimenters quite often,” Rabani said. “They came with a problem and we started to work together to understand it. Thoughts were going back and forth, but it was all seeded from the experiments, which were a big breakthrough in being able to measure what happens to the quantum dots’ atomic lattice when it’s intensely excited.”

A future of light-based technology

The study was carried out by researchers in a DOE Energy Frontier Research Center, Photonics at Thermodynamic Limits, led by Jennifer Dionne, a Stanford associate professor of materials science and engineering and senior associate vice provost of research platforms/shared facilities. Her research group worked with Lindenberg’s group to help develop the experimental technique for probing the nanocrystals.

The center’s ultimate goal, Dionne said, is to demonstrate photonic processes, such as light absorption and emission, at the limits of what thermodynamics allows. This could bring about technologies like refrigeration, heating, cooling and energy storage – as well as quantum computers and new engines for space exploration – powered entirely by light.

“To create photonic thermodynamic cycles, you need to precisely control how light, heat, atoms, and electrons interact in materials,” Dionne said. “This work is exciting because it provides an unprecedented lens on the electronic and thermal processes that limit the light emission efficiency. The particles studied already have record quantum yields, but now there is a path toward designing almost-perfect optical materials.” Such high light emission efficiencies could open a host of big futuristic applications, all driven by tiny dots probed with ultrafast electrons.

This work is part of the Photonics at Thermodynamic Limits Energy Frontier Research Center, funded by the DOE Office of Science. MeV-UED is operated as part of SLAC’s Linac Coherent Light Source, a DOE Office of Science user facility. Parts of the work were performed at the Center for Nanoscale Materials, a DOE Office of Science user facility at Argonne National Laboratory, and at the Stanford Nano Shared Facilities.

Citation: Burak Guzelturk et al., “Dynamic lattice distortions driven by surface trapping in semiconductor nanocrystals”, Nature Communications, 25 March 2020 (10.1038/s41467-021-22116-0)

Provided by SLAC

Protein Fingerprinting in Minutes (Medicine)

New technology enables ultrafast identification of COVID-19 biomarkers

Researchers from Charité – Universitätsmedizin Berlin and the Francis Crick Institute have developed a mass spectrometry-based technique capable of measuring samples containing thousands of proteins within just a few minutes. It is faster and cheaper than a conventional blood count. To demonstrate the technique’s potential, the researchers used blood plasma collected from COVID-19 patients. Using the new technology, they identified eleven previously unknown proteins which are markers of disease severity. The work has been published in Nature Biotechnology*.

Thousands of proteins are active inside the human body at any given time, providing its structure and enabling reactions which are essential to life. The body raises and lowers the activity levels of specific proteins as required, including when responding to external factors such as pathogens and drugs. The detailed patterns of the proteins found inside cells, tissues and blood samples can therefore help researchers to better understand diseases or make diagnoses and prognoses. In order to obtain this ‘protein fingerprint’, researchers use mass spectrometry, a technology known to be both time-consuming and cost-intensive. ‘Scanning SWATH’, a new mass-spectrometry-based technology, promises to change this. Developed under the leadership of Prof. Dr. Markus Ralser, Director of Charité’s Institute of Biochemistry, this technology, which is much faster and cost-effective than previous methods, enables researchers to measure several hundred samples per day.

“In order to speed up this technology, we changed the mass spectrometer’s electric fields. The data produced are of such extreme complexity that humans can no longer analyze them,” explains Einstein Professor Prof. Ralser, who is also a Group Leader at the Francis Crick Institute in London. He adds: “We therefore developed computer algorithms that are based on neural networks and which use these data to extract the relevant biological information. This enables us to identify thousands of proteins in parallel and greatly reduces measuring timescales. Fortunately, this method is also more precise.” 

This high-throughput technology has a broad range of potential applications, ranging from basic research and large-scale drug development to the identification of biological markers (biomarkers), which can be used to estimate an individual patient’s risk. The technology’s suitability for the latter was demonstrated by the researchers’ study on COVID-19. As part of this research, the team analyzed blood plasma samples from 30 Charité inpatients with COVID-19 of varying degrees of disease severity, comparing the protein patterns obtained with those of 15 healthy individuals. The actual measurements conducted on individual samples only took a few minutes.

The researchers were able to identify a total of 54 proteins whose serum levels varied according to the severity of COVID-19. While 43 of these proteins had already been linked to disease severity during earlier studies, no such relationship had been established for 11 of the proteins identified. Several of the previously unknown proteins associated with COVID-19 are involved in the body’s immune response to pathogens which increases clotting tendency. “In the shortest of timeframes, we discovered protein fingerprints in blood samples which we are now able to use to categorize COVID-19 patients according to severity of disease,” says one of the study’s lead authors, Dr. Christoph Messner, who is a researcher at Charité’s Institute of Biochemistry and the Francis Crick Institute. He continues: “This type of objective assessment can be extremely valuable, as patients will occasionally underestimate the severity of their disease. However, in order to be able to use mass spectrometry analysis for the routine categorization of COVID-19 patients, this technology will need to be refined further and turned into a diagnostic test. It may also become possible to use rapid protein pattern analysis to predict the likely course of a case of COVID-19. While the initial findings we have collected are promising, further studies will be needed before this can be used in routine practice.”

Prof. Ralser is convinced that mass spectrometry-based investigations of the blood could one day complement conventional blood count profiles. “Proteome analysis is now cheaper than a complete blood count. By identifying many thousands of proteins at the same time, proteomic analysis also produces far more information. I therefore see enormous potential for widespread use, for instance in the early detection of diseases. We will therefore continue to use our studies to develop proteome technology for this type of application.”

*Messner CB et al. Ultra-fast proteomics with Scanning SWATH. Nat Biotech 2021. doi: 10.1038/s41587-021-00860-4

About the study
The study is the result of a collaboration with the University of Cambridge, United Kingdom, the Chalmers University of Technology, Sweden, the Bernhardt Nocht Institute for Tropical Medicine in Hamburg, Germany, and SCIEX, a Canadian manufacturer of mass spectrometers.

Mass spectrometry

Mass spectrometry is an analytical technique used to measure the mass of molecules and atoms. The substance to be analyzed is first converted into gas-phase molecules which are subsequently converted into ions. Once accelerated to high velocity by an electrical field, these ions are then sorted by the mass spectrometer system’s analyzer and separated according to their mass/charge ratios. The resulting mass spectrum provides information on a substance’s molecular composition. Mass spectrometry is suitable for the identification, characterization and quantification of a myriad of biomolecules such as proteins, metabolites, sugars and fats, all of which behave differently depending on the precise clinical picture which manifests in a particular patient.

Proteomics platform to study covid-19 at Charité 

The data underpinning the published article were generated using the Pa-COVID-19 platform. Pa-COVID-19 is a prospective registry study for patients with COVID-19 at Charité. The aim of the registry is to collate comprehensive clinical and molecular data on patients with COVID-19 in order to identify individual risk factors for severe disease, as well as prognostic biomarkers and treatment targets. The protocol for the study is available here.

Featured image: The new Scanning SWATH technology renders mass spectrometry significantly more time- and cost-effective than before. Photo: Arne Sattler/Charité

Reference: Messner, C.B., Demichev, V., Bloomfield, N. et al. Ultra-fast proteomics with Scanning SWATH. Nat Biotechnol (2021).

Provided by Charité Universität Berlin

DNA Damage ‘Hot Spots’ Discovered Within Neurons (Neuroscience)

NIH labs collaborate to develop new methods for studying genome-wide DNA damage and repair

Researchers at the National Institutes of Health (NIH) have discovered specific regions within the DNA of neurons that accumulate a certain type of damage (called single-strand breaks or SSBs). This accumulation of SSBs appears to be unique to neurons, and it challenges what is generally understood about the cause of DNA damage and its potential implications in neurodegenerative diseases.

Because neurons require considerable amounts of oxygen to function properly, they are exposed to high levels of free radicals–toxic compounds that can damage DNA within cells. Normally, this damage occurs randomly. However, in this study, damage within neurons was often found within specific regions of DNA called “enhancers” that control the activity of nearby genes.

Fully mature cells like neurons do not need all of their genes to be active at any one time. One way that cells can control gene activity involves the presence or absence of a chemical tag called a methyl group on a specific building block of DNA. Closer inspection of the neurons revealed that a significant number of SSBs occurred when methyl groups were removed, which typically makes that gene available to be activated.

An explanation proposed by the researchers is that the removal of the methyl group from DNA itself creates an SSB, and neurons have multiple repair mechanisms at the ready to repair that damage as soon as it occurs. This challenges the common wisdom that DNA damage is inherently a process to be prevented. Instead, at least in neurons, it is part of the normal process of switching genes on and off. Furthermore, it implies that defects in the repair process, not the DNA damage itself, can potentially lead to developmental or neurodegenerative diseases.

This study was made possible through the collaboration between two labs at the NIH: one run by Michael E. Ward, M.D., Ph.D. at the National Institute of Neurological Disorders and Stroke (NINDS) and the other by Andre Nussenzweig, Ph.D. at the National Cancer Institute (NCI). Dr. Nussenzweig developed a method for mapping DNA errors within the genome. This highly sensitive technique requires a considerable number of cells in order to work effectively, and Dr. Ward’s lab provided the expertise in generating a large population of neurons using induced pluripotent stem cells (iPSCs) derived from one human donor. Keith Caldecott, Ph.D. at the University of Sussex also provided his expertise in single strand break repair pathways.

The two labs are now looking more closely at the repair mechanisms involved in reversing neuronal SSBs and the potential connection to neuronal dysfunction and degeneration.

Featured image: Neurons (labeled in purple) show signs of an active DNA repair process (labeled in yellow). The cells’ DNA itself is labeled in cyan (in this image, overlap between cyan and yellow appears green). Image courtesy of Ward lab, NINDS

Reference: Wu, W., Hill, S.E., Nathan, W.J. et al. Neuronal enhancers are hotspots for DNA single-strand break repair. Nature (2021).

Provided by NIH/NINDS

Study Reveals How Long-term Infection and Inflammation Impairs Immune Response As We Age (Medicine)

Humans are born with tens of thousands of hematopoietic stem cells (HSCs) that collectively ensure lifelong production of blood and immune cells that protect us from infections. HSCs can either duplicate to produce more stem cell progeny or differentiate to produce distinct immune cell lineages, an extremely critical decision that ensures that the body achieves the fine balance between having enough immune cells to fight invaders while still retaining enough HSCs to maintain future blood production. As we age, HSCs accumulate mutations that lead to the emergence of genetically distinct subpopulations. This common phenomenon known as clonal hematopoiesis (CH) is known to start in early fifties and is frequently associated with loss of function mutations in the DNMT3A gene. CH is associated with a significantly higher risk of blood cancers, cardiovascular disease, stroke and all-cause mortality.

A study led by Dr. Katherine King, associate professor at Baylor College of Medicine and Texas Children’s Hospital, shows for the first time that long-term infection and chronic inflammation drive CH mediated by the loss of Dnmt3a function. In addition, the study offers key insights into the mechanism by which chronic inflammation leads to CH and demonstrates the critical role of DNMT3a in regulating normal HSC responses to infections. The study was published in the journal Cell Stem Cell.

“Previously, we showed that chronic infection significantly impairs the ability of wild-type HSCs to remain in a quiescent stem cell state. Prolonged (lasting several months) exposure to a systemic bacterial infection promoted extensive differentiation of HSCs. While this produced sufficient immune cells to fight the infection, it also reduced the number of bone marrow HSCs by 90%,” King said. “In contrast, HSCs in mice lacking Dnmt3a gene did not differentiate much. In fact, they underwent self-renewal to produce more HSCs. We undertook the current study to test our prediction that defective differentiation and increased duplication of Dnmt3a HSCs allows them to overtake and outcompete normal HSCs when fighting chronic infections or facing long-term inflammatory conditions.”

To test their hypothesis, researchers used a combination of experimental and mathematical modeling experiments to test how HSCs from Dnmt3a mutant mice respond to long-term infection and chronic inflammation. For experimental validation, they generated mosaic mice that were generated by transplanting a mixture of whole bone marrow from Dnmt3a-mutant mice and normal mice into irradiated mice, which allowed them to track how each subpopulation of HSC contracts or grows relative to one another over time when infected for several months with Mycobacterium avium bacteria.

Using this model that mimics chronic infection in humans, they found long-term infection caused specific expansion of Dnmt3a-loss of function HSCs along with a concomitant reduction in their ability to differentiate into immune cells, which is contrary to the behavior exhibited by normal HSCs to chronic infection. Moreover, compared to the normal HSCs, Dnmt3a HSCs were more resistant to exhaustion and were less sensitive to stress-induced apoptosis (‘cell death’) upon chronic infection. Collectively, this indicates how a minor population of Dnmt3a HSCs could eventually overtake a major population of normal HSCs in the presence of chronic infection.

A number of viral or bacterial infections and chronic inflammatory stress conditions including tuberculosis, hepatitis, herpetic infections, and inflammatory bowel disease trigger the release of interferon gamma (IFNγ) by the immune system, which in turn, initiates a cascade of protective immune responses. The team found that compared to wild-type HSCs, Dnmt3a-loss of function HSCs exhibited an entirely opposite set of cellular responses and global changes in gene expression patterns in response to IFNγ, which tended towards preserving or even increasing the numbers of stem cells at the expense of mounting an effective response against imminent invaders or stress.

“We are excited by the findings of this study which opens several areas of future investigations. We have shown for the first time how chronic inflammation due to long-term infections or autoimmune conditions such as rheumatoid arthritis, ulcerative colitis or Crohn’s disease dampen the body’s immune response as we age. Moreover, it sheds light on the critically important role of DNMT3a in modulating immune responses during chronic infection or stress and also explains how aging and inflammation are linked to blood cancers,” King concluded.

Other authors involved in the study are Daniel Hormaechea-Agulla, Katie Matatall, Duy Le, Grant Challen, and Marek Kimmel. They are affiliated with one or more institutions: Baylor College of Medicine, Rice University, Silesian University of Technology, and Washington University School of Medicine. Grants from the National Institutes of Health, Dan L. Duncan Cancer Center, and Polish National Science Center supported this work.

Featured image: Chronic infection and inflammation promotes promotes differentiation in normal HSCs while it promotes self-renewal in Dnmt3a-mutant HSCs leading to aberrant immune responses to infections and inflammatory stress. © Hormaechea-Agulla et al., Cell Stem Cell, 2021.

Reference: Daniel Hormaechea-Agulla, Katie A. Matatall et al., “Chronic infection drives Dnmt3a-loss-of-function clonal hematopoiesis via IFNγ signaling”, 2021. DOI:

Provided by Texas Children’s Hospital

Researchers Reveal How Lipids and Water Molecules Regulate 5-HT Receptors (Biology)

Serotonin, or 5-hydroxytryptamine (5-HT), is a kind of neurotransmitter. 5-HT can regulate multifaceted physiological functions such as mood, cognition, learning, memory, and emotions through 5-HT receptors. 5-HT receptors are a type of G protein-coupled receptor and can be divided into 12 subtypes in humans. As drug targets, they play a vital role in the treatment of schizophrenia, depression, and migraine. 

However, the structural and functional mechanisms of 5-HT receptors have been largely unknown. 

In a study published in Nature on March 24, Prof. H. Eric XU and Prof. JIANG Yi from the Shanghai Institute of Materia Medica (SIMM) of the Chinese Academy of Sciences, together with Prof. ZHANG Yan from Zhejiang University, and their collaborators, have clarified the critical role of PtdIns4P and cholesterol in G-protein coupling and ligand recognition as well as the molecular basis of basal activity and the drug recognition mode of 5-HT receptors, by resolving the cryo-electron microscopy (cryo-EM) structures of five 5-HT receptor–Gi complexes. 

These five 5-HT receptor–Gi complexes include three with 5-HT1A structures (one in the apo state, one bound to 5-HT, and one bound to aripiprazole, an antipsychotic drug), one with 5-HT1D bound to 5-HT, and one with 5-HT1E bound to the 5-HT1E- and 5-HT1F-selective agonist BRL-54443. 

PtdIns4P is one of the major classes of phosphoinositides. In this study, the researchers first identified PtdIns4P as a major phospholipid at the 5-HT1A–G protein interface, which stabilizes the 5-HT1A-G protein complex. 

They found that PtdIns4P is sandwiched between two cholesterol molecules surrounding the 5-HT1A receptor, therefore providing a structural basis for the modulation of 5-HT1A signaling by cholesterol and phospholipids. 

Researchers also found several structured water molecules that form hydrogen bonds with the apo receptor within the orthosteric binding pocket. Water molecules mimic the polar functionalities of 5-HT in the active apo-5-HT1A–Gi complex, thus revealing the key role of water molecules in sustaining the basal activity of 5-HT receptors. 

In addition, the researchers revealed the basis of ligand selectivity and drug recognition in 5-HT receptors. They identified residue at position 6×55 as a key determinant for the BRL-54443 and 5-CT selectivity of 5-HT receptors. 

An outward shift of the extracellular end of TM7 in 5-HT1A stabilizes the quinolinone group of aripiprazole, resulting in 5-HT1A’s high selectivity for aripiprazole.  

A cholesterol molecule was further found to be involved in the stabilization of the aripiprazole pocket and causes aripiprazole to have a higher binding affinity for 5-HT1A. 

The observations in this study have wide implications for a mechanistic understanding of 5-HT signaling and for drug discovery targeting the 5-HT receptor family. 

Featured image: Cryo-EM structures of the 5-HT1A-Gi, 5-HT1D-Gi, and 5-HT1E-Gi complexes (Image by H. Eric Xu’s group) 

Reference: Xu, P., Huang, S., Zhang, H. et al. Structural insights into the lipid and ligand regulation of serotonin receptors. Nature (2021).

Provided by Chinese Academy of Sciences

Plant Gene Found in Insect, Shields it From Leaf Toxins (Biology)

Millions of years ago, aphid-like insects called whiteflies incorporated a portion of DNA from plants into their genome. A Chinese research team, publishing March 25th in the journal Cell, reveals that whiteflies use this stolen gene to degrade common toxins plants use to defend themselves against insects, allowing the whitefly to feed on the plants safely.

“This seems to be the first recorded example of the horizontal gene transfer of a functional gene from a plant into an insect,” says co-author Ted Turlings (@FARCE_lab), a chemical ecologist and entomologist at the University of Neuchâtel, in Switzerland. “You cannot find this gene, BtPMaT1, which neutralizes toxic compounds produced by the plant, in any other insect species.”

Scientists believe that plants probably use BtPMaT1 within their own cells to store their noxious compounds in a harmless form, so the plant doesn’t poison itself. The team, led by Youjun Zhang from the Institute of Vegetables and Flowers at the Chinese Academy of Agricultural Sciences, used a combination of genetic and phylogenetic analyses, to reveal that roughly 35 million years ago, whiteflies stole this defense gene, granting the insect the ability to detoxify these compounds for themselves.

“We think a virus within the plant may have taken up this BtPMaT1 gene and, after ingestion by a whitefly, the virus then must have done something inside the insect whereby that gene was integrated into the whiteflies genome,” says Turlings. “Of course, this is an extremely unlikely event, but if you think about millions of years and billions of individual insects, viruses, and plants across time, once in a while this could happen, and if the acquired gene is a benefit to the insects, then it will be evolutionarily favored and may spread.”

Whiteflies have become a major agricultural pest worldwide, able to attack at least 600 different species of plants worldwide. “One of the questions we’ve been asking ourselves is how these insects acquired these incredible adaptations to circumvent plant defenses, and with this discovery we have revealed at least one reason as to why,” Turlings says.

Using this knowledge, Turlings’ Chinese colleagues created a strategy to undo the whiteflies’ stolen superpower. They developed a small RNA molecule that interferes with the whiteflies’ BtPMaT1 gene, making the whiteflies susceptible to the plant’s toxic compounds.

“The most exciting step of this design was when our colleagues genetically manipulated tomato plants to start producing this RNA molecule” says Turlings. “Once the whiteflies fed on the tomatoes and ingested the plant-produced RNA, their BtPMaT1 gene was silenced, causing 100% mortality of the insect, but the genetic manipulation had no impact on the survival of other insects that were tested.”

With focused efforts to produce genetically modified crops that are able to silence the whitefly gene, this could function as a targeted strategy for pest control to combat agricultural devastation caused by whitefly populations.

“There are definitely still some hurdles this method needs to get over, most notably the skepticism about using transgenic plants,” he says “But in the future, I do see this as a very clear way of controlling whiteflies because now we know exactly the mechanism behind it, and we are equipped to deal with possible changes in the whitefly gene that may arise.

This research was supported by the National Key R & D Program of China, the National Natural Science Foundation of China, the China Agriculture Research System, the Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables, and the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences.

Featured image: This image shows a whitefly on a leaf © Jixing Xia and Zhaojiang Guo

Reference: Cell, Xia et al.: “Whitefly hijacks a plant detoxification gene that neutralizes plant toxins”

Provided by Cell Press

Combination Therapy Protects Against Advanced Marburg Virus Disease (Medicine)

New paper published in Nature Communications shows effectiveness of combining monoclonal antibodies and remdesivir in defense of lethal MARV.

A new study conducted at the Galveston National Laboratory at the The University of Texas Medical Branch at Galveston (UTMB) has shown substantial benefit to combining monoclonal antibodies and the antiviral remdesivir against advanced Marburg virus. The study was published today in Nature Communications.

“Marburg is a highly virulent disease in the same family as the virus that causes Ebola. In Africa, patients often arrive to a physician very ill. It was important to test whether a combination of therapies would work better with really sick people, said Tom Geisbert, a professor in the Department of Microbiology & Immunology at UTMB and the principal investigator for the study. “Our data suggests that this particular combination allowed for recovery when given at a very late stage of disease.”

Dr. Zachary A. Bornholdt, Senior Director of Antibody Discovery and Research for Mapp Biopharmaceutical and a co-author on the study, said, “Often small molecules and antibodies are positioned to compete with each other for a single therapeutic indication. Here we see the benefit of pursuing both treatment strategies in tandem and ultimately finding synergy upon combining both approaches together.”

Geisbert, Bornholdt and a large team at UTMB, Mapp Biopharmaceuticals and Gilead have been developing monoclonal antibody (mAbs) therapies to treat extremely dangerous viruses like Marburg and Ebola for several years. The treatments have proven to be highly effective in laboratory studies and emergency use, particularly when delivered early in the disease course.

In this study, using a rhesus model, treatment with monoclonal antibodies began six days post infection, a critical point in disease progression. The combination therapy with the antiviral remdesivir showed an 80 percent protection rate, indicating promise for treatment of advanced Marburg infections.

The study was supported by the Department of Health and Human Services, National Institutes of Health grant U19AI142785 and UC7AI094660 for BSL-4 operations support of the Galveston National Laboratory.

Featured image: Histologic changes in rhesus macaques infected with MARV with and without treatment. © Cross et al.

Reference: Cross, R.W., Bornholdt, Z.A., Prasad, A.N. et al. Combination therapy protects macaques against advanced Marburg virus disease. Nat Commun 12, 1891 (2021).

Provided by University of Texas Medical Branch at Galveston