Health News

Scientists map structure of potent antibody against coronavirus

Scientists at Fred Hutchinson Cancer Research Center in Seattle have shown that a potent antibody from a COVID-19 survivor interferes with a key feature on the surface of the coronavirus’s distinctive spikes and induces critical pieces of those spikes to break off in the process.

The antibody — a tiny, Y-shaped protein that is one of the body’s premier weapons against pathogens including viruses — was isolated by the Fred Hutch team from a blood sample received from a Washington state patient in the early days of the pandemic.

The team led by Drs. Leo Stamatatos, Andrew McGuire and Marie Pancera previously reported that, among dozens of different antibodies generated naturally by the patient, this one — dubbed CV30 — was 530 times more potent than any of its competitors.

Using tools derived from high-energy physics, Hutch structural biologist Pancera and her postdoctoral fellow Dr. Nicholas Hurlburt have now mapped the molecular structure of CV30. They and their colleagues published their results online today in the journal Nature Communications.

The product of their research is a set of computer-generated 3D images that look to the untrained eye as an unruly mass of noodles. But to scientists they show the precise shapes of proteins comprising critical surface structures of antibodies, the coronavirus spike and the spike’s binding site on human cells. The models depict how these structures can fit together like pieces of a 3D puzzle.

“Our study shows that this antibody neutralizes the virus with two mechanisms. One is that it overlaps the virus’s target site on human cells, the other is that it induces shedding or dissociation of part of the spike from the rest,” Pancera said.

On the surface of the complex structure of the antibody is a spot on the tips of each of its floppy, Y-shaped arms. This infinitesimally small patch of molecules can neatly stretch across a spot on the coronavirus spike, a site that otherwise works like a grappling hook to grab onto a docking site on human cells.

The target for those hooks is the ACE2 receptor, a protein found on the surfaces of cells that line human lung tissues and blood vessels. But if CV30 antibodies cover those hooks, the coronavirus cannot dock easily with the ACE2 receptor. Its ability to infect cells is blunted.

This very effective antibody not only jams the business end of the coronavirus spike, it apparently causes a section of that spike, known as S1, to shear off. Hutch researcher McGuire and his laboratory team performed an experiment showing that, in the presence of this antibody, there is reduction of antibody binding over time, suggesting the S1 section was shed from the spike surface.

The S1 protein plays a crucial role in helping the coronavirus to enter cells. Research indicates that after the spike makes initial contact with the ACE2 receptor, the S1 protein swings like a gate to help the virus fuse with the captured cell surface and slip inside. Once within a cell, the virus hijacks components of its gene and protein-making machinery to make multiple copies of itself that are ultimately released to infect other target cells.

The incredibly small size of antibodies is difficult to comprehend. These proteins are so small they would appear to swarm like mosquitos around a virus whose structure can only be seen using the most powerful of microscopes. The tiny molecular features Pancera’s team focused on the tips of the antibody protein are measured in nanometers — billionths of a meter.

Yet structural biologists equipped with the right tools can now build accurate 3D images of these proteins, deduce how parts of these structures fit like puzzle pieces, and even animate their interactions.

Fred Hutch structural biologists developed 3D images of an antibody fished from the blood of an early COVID-19 survivor that efficiently neutralized the coronavirus.

Dr. Nicholas Hurlburt, who helped develop the images, narrates this short video showing how that antibody interacts with the notorious spikes of the coronavirus, blocking their ability to bind to a receptor on human cells that otherwise presents a doorway to infection.

Key to building models of these nanoscale proteins is the use of X-ray crystallography. Structural biologists determine the shapes of proteins by illuminating frozen, crystalized samples of these molecules with extremely powerful X-rays. The most powerful X-rays come from a gigantic instrument known as a synchrotron light source. Born from atom-smashing experiments dating back to the 1930s, a synchrotron is a ring of massively powerful magnets that are used to accelerate a stream of electrons around a circular track at close to the speed of light. Synchrotrons are so costly that only governments can build and operate them. There are only 40 of them in the world.

Pancera’s work used the Advanced Photon Source, a synchrotron at Argonne National Laboratory near Chicago, which is run by the University of Chicago and the U.S. Department of Energy. Argonne’s ring is 1,200 feet in diameter and sits on an 80-acre site.

As the electrons whiz around the synchrotron ring, they give off enormously powerful X-rays — far brighter than the sun but delivered in flashes of beams smaller than a pinpoint.

Structural biologists from around the world rely on these brilliant X-ray beamlines to illuminate frozen crystals of proteins. They reveal their structure in the way these bright beams are bent as they pass though the molecules. It takes powerful computers to translate the data readout from these synchrotron experiments into the images of proteins that are eventually completed by structural biologists.

The Fred Hutch team’s work on CV30 builds on that of other structural biologists who are studying a growing family of potent neutralizing antibodies against the coronavirus. The goal of most coronavirus vaccine candidates is to stimulate and train the immune system to make similar neutralizing antibodies, which can recognize the virus as an invader and stop COVID-19 infections before they can take hold.

Neutralizing antibodies from the blood of recovered COVID-19 patients may also be infused into infected patients — an experimental approach known as convalescent plasma therapy. The donated plasma contains a wide variety of different antibodies of varying potency. Although once thought promising, recent studies have cast doubt on its effectiveness.

However, pharmaceutical companies are experimenting with combinations of potent neutralizing antibodies that can be grown in a laboratory. These “monoclonal antibody cocktails” can be produced at industrial scale for delivery by infusion to infected patients or given as prophylactic drugs to prevent infection. After coming down with COVID-19, President Trump received an experimental monoclonal antibody drug being tested in clinical trials by the biotech company Regeneron, and he attributes his apparently quick recovery to the advanced medical treatment he received.

The Fred Hutch research team holds out hope that the protein they discovered, CV30, may prove to be useful in the prevention or treatment of COVID-19. To find out, this antibody, along with other candidate proteins their team is studying, need to be tested preclinically and then in human trials.

“It is too early to tell how good they might be,” Pancera said.

This work was supported by donations to the Fred Hutch COVID-19 Research Fund.


Healthcare as a climate solution

Although the link may not be obvious, healthcare and climate change — two issues that pose major challenges around the world — are in fact more connected than society may realize. So say researchers, who are increasingly proving this to be true.

Case in point: A new study by UC Santa Barbara’s Andy MacDonald found that improving healthcare in rural Indonesia reduced incentives for illegal logging in a nearby national park, averting millions of dollars’ worth of atmospheric carbon emissions.

The analysis, published in the Proceedings of the National Academy of Sciences, finds that deforestation in the national park declined 70% in the 10 years after an affordable health clinic opened in the area. This equates to more than $65 million worth of avoided carbon emissions when translated to the European carbon market, the study reports.

“The results illustrate a strong link between human health and conservation in tropical forests in the developing world,” said MacDonald, an assistant researcher at the Earth Research Institute who coauthored the study with UC Santa Barbara’s David Lopez-Carr and colleagues at Stanford University, North Carolina State University Raleigh, Oregon Health and Science University, Natural Capital Advisors, and two NGOs involved in the intervention.

The Indonesian clinic accepts barter as payment and gives discounts to villages based on community-wide reductions in logging. Given its success, it could provide a blueprint for preserving the world’s biodiverse carbon sinks while reducing poverty and illness.

“This innovative model has clear global health implications,” said coauthor Michele Barry, senior associate dean of global health at Stanford and director of the Center for Innovation in Global Health. “Health and climate can and should be addressed in unison, and done in coordination with and respect for local communities.”

Every second, more than 100 trees disappear from tropical forests around the world. These forests, some of the world’s most important carbon reservoirs, are crucial to slowing climate change and mass extinction.

The current paradigm for conserving tropical forests — establishing protected areas — often excludes and disenfranchises local communities. This failure to address people’s needs can lead communities with few economic alternatives to illegally log and convert the land. Lack of access to high-quality, affordable healthcare can compound the problem by perpetuating cycles of poor health and expanding out-of-pocket costs.

With this in mind, the nonprofit organizations Alam Sehat Lestari and Health In Harmony in 2007 established a healthcare clinic adjacent to Gunung Palung National Park in West Kalimantan, Indonesia, with the support of the local government. The clinic was able to serve thousands of patients by accepting a range of alternative payments, such as tree seedlings, handicrafts and labor — an approach that was created in collaboration with the communities themselves.

Through agreements with most of the region’s district leaders, the clinic also provided discounts to villages that could show evidence of reductions in illegal logging. Between 1985 and 2001, this region had lost 60% of its forest to this activity. In addition to affordable health care, the intervention provided training in sustainable, organic agriculture and a chainsaw buyback program.

Researchers worked with the two non-profits to analyze more than 10 years of the clinic’s patient health records, coupled with satellite observations of forest cover over that time. “Private foundations funded the interventions, but it’s innovative new programs at Stanford and the University of California that are funding the research,” MacDonald said.

The medical care led to a significant decline in a range of diseases such as malaria, tuberculosis and diabetes. At the same time, satellite images of the national park showed a 70% reduction in deforestation, compared to forest loss at control sites, an amount equivalent to more than 6,770 acres of rainforest.

“We didn’t know what to expect when we started evaluating the program’s health and conservation impacts, but we were continually amazed that the data suggested such a strong link between improvements in healthcare access and tropical forest conservation,” said lead author Isabel Jones, who recently earned her doctorate in biology at Stanford. Looking more closely at community-level logging rates, the researchers found that the greatest drop-offs in logging occurred adjacent to villages with the highest rates of clinic usage.

A global blueprint

“This is a case study of how to design, implement and evaluate a planetary health intervention that addresses human health and the health of rainforests on which our health depends,” said coauthor Susanne Sokolow, a senior research scientist at Stanford.

Globally, about 35% of protected areas are traditionally owned, managed, used or occupied by Indigenous and local communities. Yet the perspective and guidance of Indigenous peoples and local communities are rarely considered in the design of conservation and climate mitigation programs. By contrast, the Indonesian clinic’s success grew out of the early and continued input of local communities who identified the mechanisms driving health and environmental problems as well as possible solutions.

Such holistic approaches can have greater long-term effects by preserving and restoring the ecosystem services that protect human health. These include natural filtering processes that reduce the risk of waterborne diseases and shade-providing forest canopies that reduce ground temperature and heat-related illnesses.

“The data support two important conclusions: human health is integral to the conservation of nature and vice versa, and we need to listen to the guidance of rainforest communities who know best how to live in balance with their forests,” said Monica Nirmala, the executive director of the clinic from 2014 to 2018 and current board member of Health In Harmony.

The clinic in West Kalimantan is still active, and the researchers are currently working on a follow-up project to see whether it and similar interventions in Indonesia have alleviated some of the shock from COVID-19 both on human health and deforestation.

“We would expect illegal logging activity to respond to changes in timber market prices or loss of income associated with COVID-19,” MacDonald said. “We want to know whether the interventions buffered communities against these effects, as well as whether they increased the communities’ resilience in terms of health and wellbeing.

“Health in Harmony is also expanding to Madagascar and Brazil,” he added, “and we want to be able to robustly evaluate the impacts of their interventions there.”


New imaging method reveals HIV’s sugary shield in unprecedented detail

Scientists from Scripps Research and Los Alamos National Laboratory have devised a method for mapping in unprecedented detail the thickets of slippery sugar molecules that help shield HIV from the immune system.

Mapping these shields will give researchers a more complete understanding of why antibodies react to some spots on the virus but not others, and may shape the design of new vaccines that target the most vulnerable and accessible sites on HIV and other viruses.

The sugar molecules, or “glycans,” are loose and stringy, and function as shields because they are difficult for antibodies to grip and block access to the protein surface. The shields form on the outermost spike proteins of HIV and many other viruses, including SARS-CoV-2, the coronavirus that causes COVID-19, because these viruses have evolved sites on their spike proteins where glycan molecules — normally abundant in cells — will automatically attach.

“We now have a way to capture the full structures of these constantly fluctuating glycan shields, which to a great extent determine where antibodies can and can’t bind to a virus such as HIV,” says the study’s lead author Zachary Berndsen, PhD, a postdoctoral research associate in the structural biology lab of Scripps Research Professor Andrew Ward, PhD.

The same wavy flexibility that makes these sugary molecules resistant to antibodies has made them impossible for researchers to capture with traditional atomic-scale imaging. In the new study, which appears in the Proceedings of the National Academy of Sciences, the scientists developed techniques that, for the first time, allow these elusive molecules to be mapped in great detail on the surface of the HIV spike protein, known as “Env.”

The Scripps Research team collaborated with the lab of Gnana Gnanakaran, PhD, staff scientist at Los Alamos National Laboratory, which is equipped with high-performance computing resources that enabled fresh approaches for modeling the glycans.

The researchers combined an atomic-scale imaging method called cryo-electron microscopy (cryo-EM) with sophisticated computer modeling and a molecule-identifying technique called site-specific mass spectrometry. Cryo-EM relies on averaging tens or hundreds of thousands of individual snapshots to create a clear image, thus highly flexible molecules like glycans will appear only as a blur, if they show up at all.

But by integrating cryo-EM with the other technologies, the researchers were able to recover this lost glycan signal and use it to map sites of vulnerability on the surface of Env.

“This is the first time that cryo-EM has been used along with computational modeling to describe the viral shield structure in atomic detail,” says Srirupa Chakraborty, PhD, co-lead author and post-doctoral researcher in the Gnanakaran lab at Los Alamos National Laboratory.

The new combined approach revealed the glycans’ structure and dynamic nature in extreme detail and helped the team better understand how these complex dynamics affect the features observed in the cryo-EM maps. From this wealth of information, the team observed that individual glycans do not just wiggle around randomly on the spike protein’s surface, as once was thought, but instead clump together in tufts and thickets.

“There are chunks of glycans that seem to move and interact together,” Berndsen says. “In between these glycan microdomains is where antibodies apparently have the opportunity to bind.”

Experimental HIV vaccines rely on modified, lab-made Env proteins to elicit antibody responses. In principle, these vaccines’ effectiveness depends in part on the positioning and extent of the shielding glycans on these lab-made viral proteins. Therefore, Berndsen and colleagues applied their method to map the glycans on a modified HIV Env protein, BG505 SOSIP.664, which is used in an HIV vaccine currently being evaluated in clinical trials.

“We found spots on the surface of this protein that normally would be covered with glycans but weren’t — and that may explain why antibody responses to that site have been noted in vaccination trials,” Berndsen says.

That finding, and others in the study, showed that Env’s glycan shield can vary depending on what type of cell is being used to produce it. In HIV’s infections of humans, the virus uses human immune cells as factories to replicate its proteins. But viral proteins used to make vaccines normally are produced in other types of mammalian cells.

In another surprise discovery, the team observed that when they used enzymes to slowly remove glycans from HIV Env, the entire protein began to fall apart. Berndsen and colleagues suspect that Env’s glycan shield, which has been considered merely a defense against antibodies, may also have a role in managing Env’s shape and stability, keeping it poised for infection.

The team expect that their new glycan-mapping methods will be particularly useful in the design and development of vaccines — and not only for HIV. Many of the techniques can be applied directly to other glycan-shielded viruses such as influenza viruses and coronaviruses, and can be extended to certain cancers in which glycans play a key role, the researchers say.


PTSD and alcohol abuse go hand-in-hand, but males and females exhibit symptoms differently

Through intricate experiments designed to account for sex-specific differences, scientists at Scripps Research have collaborated to zero in on certain changes in the brain that may be responsible for driving alcohol abuse among people with post-traumatic stress disorder, or PTSD.

In studies with rodents, researchers found that males and females exhibit their own distinct symptoms and brain features of PTSD and alcohol use disorder. Such differences are not typically accounted for in laboratory-based studies yet could lead to more successful clinical treatments.

The findings, published in Molecular Psychiatry, also present a new model for identifying biomarkers that may indicate a person with PTSD is more likely to develop alcohol use disorder.

“Having PTSD significantly increases the risk of developing alcohol use disorder, as individuals use alcohol to cope with stress and anxiety. Yet the underlying biology of comorbid disorders is generally not well understood,” says Dean Kirson, PhD, a postdoctoral fellow in neurophysiology in the lab of professor Marisa Roberto, PhD, and a co-lead author with Michael Steinman, PhD. “We hope our new knowledge of sex-specific changes in the brain will help propel the development of more targeted treatments.”

About 7 percent to 8 percent of the country’s population will have PTSD at some point in their life, according to the U.S. Department of Veterans Affairs. Causes include combat exposure, physical abuse, an accident or other forms of trauma. Alcohol abuse disorder is also common, affecting some 15 million people in the United States. Those with stress and anxiety disorders such as PTSD are not only more likely to abuse alcohol, but also have increased alcohol withdrawal symptoms and relapse risk.

“Most people know or will know someone struggling with one or both of these disorders and may try to help them. However, there are very few effective treatments currently,” Roberto says. “Both are complex disorders that affect similar brain circuitry. My lab has been studying addiction and stress separately, so here we teamed up with the Zorrilla lab to apply a novel translationally-relevant behavioral model to examine what changes occur when these disorders are comorbid.”

The joint study between Roberto and Eric Zorrilla, PhD — who are co-senior authors — examined behavior, sleep patterns, inflammatory immune responses and levels of a neurotransmitter known as GABA (short for gamma-Aminobutyric acid), which lowers anxiety and increases feelings of relaxation and is a common feature of alcohol dependence.

For both male and female rats, traumatic stress and alcohol exacerbated other behaviors common in PTSD, such as social avoidance startle reactions and defensive behavior. Those who were identified as “drinking-vulnerable” prior to trauma most strongly showed avoidance of trauma-reminiscent places.

However, the scientists noted key differences in how males and females behave following trauma and saw markedly different patterns of GABA signaling. For example, males showed increased GABA receptor function, while females showed increased GABA release.

“This may be important because there is growing awareness that medicines could potentially have different levels of effectiveness in male and female patients and understanding the biology that explains why these differences exist could improve outcomes,” Steinman says.

The team also found that males exhibited an immune-based biomarker — small proteins known as cytokines, which are secreted by immune cells — that determined vulnerability to alcohol use disorder. The females did not.

“We identified profiles of specific cytokines, many not previously linked to stress behaviors, that strongly related to poor drinking outcomes,” says Zorilla, associate professor

In the Department of Molecular Medicine. “These may be important clinically or even mechanistically, but they were unique to males, so we have work ahead of us to find similar biomarkers for females.”

The Roberto and Zorrilla labs plan to conduct additional research into the mechanisms behind the biological changes they observed and test which brain systems can be targeted to treat both PTSD and alcohol abuse.

“We also plan to further investigate the role of the immune system in these disorders,” Roberto says. “These distinct biomarkers may aid in targeted treatment.”


COVID-19 a double blow for chronic disease patients

There has never been a more dangerous time than the COVID-19 pandemic for people with non-communicable diseases (NCDs) such as diabetes, cancer, respiratory problems or cardiovascular conditions, new UNSW Sydney research has found.

Among the adverse impacts of the pandemic for people with NCDs, the study found they are more vulnerable to catching and dying from COVID-19, while their exposure to NCD risk factors — such as substance abuse, social isolation and unhealthy diets — has increased during the pandemic.

The researchers also found COVID-19 disrupted essential public health services which people with NCDs rely on to manage their conditions.

The study, published in Frontiers in Public Health recently, reviewed the literature on the synergistic impact of COVID-19 on people with NCDs in low and middle-income countries such as Brazil, India, Bangladesh, Nepal, Pakistan and Nigeria.

The paper, which analysed almost 50 studies, was a collaboration between UNSW and public health researchers in Nepal, Bangladesh and India.

Lead author Uday Yadav, PhD candidate under Scientia Professor Mark Harris of UNSW Medicine, said the interaction between NCDs and COVID-19 was important to study because global data showed COVID-19-related deaths were disproportionally high among people with NCDs — as the UNSW researchers confirmed.

“This illustrates the negative effect of the COVID-19 ‘syndemic’ — also known as a ‘synergistic epidemic’ — a term coined by medical anthropologist Merrill Singer in the 1990s to describe the relationship between HIV/AIDS, substance abuse and violence,” Mr Yadav said.

“We applied this term to describe the interrelationship between COVID-19 and the various biological and socio-ecological factors behind NCDs.

“So, people are familiar with COVID-19 as a pandemic, but we analysed it through a syndemic lens in order to determine the impact of both COVID-19 and future pandemics on people with NCDs.”

Mr Yadav said the COVID-19 syndemic would persist, just as NCDs affected people in the long-term.

“NCDs are the result of a combination of genetic, physiological, environmental and behavioural factors and there is no quick fix, such as a vaccine or cure,” he said.

“So, it’s no surprise we found that NCD patients’ exposure to NCD risk factors has increased amid the pandemic, and they are more vulnerable to catching COVID-19 because of the syndemic interaction between biological and socio-ecological factors.

“The evidence we analysed also showed there was poor self-management of NCDs at a community level and COVID-19 has disrupted essential public health services which people with NCDs rely on.”

Tackling NCDs in the COVID-19 era

Mr Yadav said the researchers’ findings led them to recommend a series of strategies for healthcare stakeholders — such as decision-makers, policymakers and frontline health workers — to better manage people with NCDs in light of the COVID-19 syndemic.

“Healthcare systems — such as Australia’s — do have some of these strategies in place, but they need improvement,” he said.

Highlights from the recommended strategies include:

  • Develop plans for how to best provide health services to people with NCDs, from the moment they are assessed through to their treatment and palliation.
  • Develop digital campaigns to disseminate information on how to make positive behaviour changes and better self-manage NCDs and COVID-19.
  • Decentralise healthcare delivery for people with NCDs: involving local health districts and investing in community health worker programs could help to mitigate future outbreaks. In addition, tailor self-management interventions for people with NCDs.
  • Ensure effective social and economic support for people with NCDs who are vulnerable to catching COVID-19, particularly Indigenous, rural, Culturally and Linguistically Diverse (CALD) and refugee communities, as well as people with severe mental illness.
  • Evaluate technology-assisted medical interventions to improve healthcare services, because complex case management, assessment and support is increasingly being done via telehealth appointments or other technology.

Why healthcare must focus on prevention

Mr Yadav said high-income countries could also learn from the researchers’ findings.

“COVID-19 has been a major threat to people with NCDs in developed countries — for example, new statistics from Britain show that in 2020, high numbers of people in England and Wales died from NCDs at home after shunning the healthcare system because of the pandemic,” he said.

“In Australia, COVID-19 will increase inequality and poses a risk to some high and middle-income earners, but it’s a double threat to others such as Indigenous, rural, CALD and refugee communities, as well as people with severe mental illness — as reflected in our paper.”

Mr Yadav said in Australia in 2018, the most recent data available, 89 per cent of deaths were associated with 10 chronic diseases.

“The Australian healthcare system needs a bigger focus on preventive healthcare, to improve outcomes for patients with NCDs and prevent more people from developing these diseases amid the COVID-19 pandemic,” he said.

Mr Yadav said putting serious preventive healthcare investment on the backburner could lead to individual, societal and economic upheaval in the long-term.

“If this trend continues, Australia will struggle to achieve Sustainable Development Goal (SDG) target 3.4, which is to reduce premature mortality from NCDs by a third by 2030 — relative to 2015 levels and to promote mental health and wellbeing,” he said.

“Investment in prevention today will help save healthcare costs in the long-term, help reduce the incidence of NCDs and enhance our resilience against future pandemics.”