Tag Archives: Therapeutics

Microbiology

University of Louisville researchers receive $5.8 million to prevent immune system dysregulation

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Reviewed by Megan Craig, M.Sc.Jun 2 2023

Researchers at the University of Louisville have received $5.8 million in two grants from the National Institutes of Health to expand their work to better understand and prevent immune system dysregulation responsible for acute respiratory distress, the condition responsible for serious illness and death in some COVID-19 patients. A separate $306,000 NIH Small Business Innovation Research grant supports early testing of a compound developed at UofL as a potential treatment.

The three grants combined total $6.1 million.

During the pandemic, health care providers worked tirelessly to treat patients who became seriously ill with COVID-19. Some of those patients developed severe lung disease known as acute respiratory distress syndrome (ARDS) due to an excessive response of the immune system often called cytokine storm.

As they treated these critically ill patients, physicians and other providers at UofL Health shared their clinical insights and patient samples with researchers at UofL to discover the cause of the immune system overresponse.

At one time we had over 100 patients with COVID in the hospital. Once they were on a ventilator, mortality was about 50%. We were looking at this issue to see why some people would do well while some developed bad lung disease and did not do well or died.”

Jiapeng Huang, an anesthesiologist with UofL Health and professor and vice chair of the Department of Anesthesiology and Perioperative Medicine in the UofL School of Medicine

The UofL researchers, led by immunologist Jun Yan, discovered that a specific type of immune cells, low-density inflammatory neutrophils, became highly elevated in some COVID-19 patients whose condition became very severe. This elevation signaled a clinical crisis point and increased likelihood of death within a few days due to lung inflammation, blood clotting and stroke. Their findings were published in 2021 in JCI Insight.

With the new NIH funding, Yan is leading research to build on this discovery with deeper understanding of what causes a patient’s immune system to respond to an infection in this way and develop methods to predict, prevent or control the response.

“Through this fruitful collaboration, we now have acquired NIH funding for basic and translational studies and even progress toward commercialization of a potential therapy,” Yan said. “That’s why we do this research – eventually we want to benefit the patients.”

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Yan, chief of the UofL Division of Immunotherapy in the Department of Surgery, a professor of microbiology and immunology and a senior member of the Brown Cancer Center, will lead the new research, along with Huang and Silvia M. Uriarte, university scholar and professor in the Department of Oral Immunology and Infectious Diseases in the UofL School of Dentistry.

“COVID-19 continues to spotlight the impactful synergy between the clinical and research teams at the University of Louisville,” said Jason Smith, UofL Health chief medical officer. “Innovation is in the DNA of academic medicine. We collaborate to provide each patient the best options for prevention and treatment today, while developing the even better options for tomorrow.”

In addition to two research grants of $2.9 million each awarded directly to UofL, a $306,000 grant to a startup company will support early testing of a compound developed in the lab of UofL Professor of Medicine Kenneth McLeish that shows promise in preventing the dangerous cytokine storm while allowing the neutrophils to retain their ability to kill harmful bacteria and viruses. The compound, DGN-23, will be tested by UofL and Degranin Therapeutics, a startup operated by McLeish, Yan, Huang, Uriarte and Madhavi Rane, associate professor in the Department of Medicine.

“This is one more example of how UofL has led the charge in finding new and innovative ways to detect, contain and fight COVID-19 and other potential public health threats,” said Kevin Gardner, UofL’s executive vice president for research and innovation. “This team’s new research and technology could help keep people healthy and safe here and beyond.”

The knowledge gained through these studies may benefit not only COVID-19 patients, but those with other conditions in which immune dysregulation can occur, such as other types of viral and bacterial pneumonia and autoimmune diseases, and patients undergoing cancer immunotherapy and organ transplantation.

The grants

Grant 1 – $2.9 million, four-year grant to UofL. Investigators will study the new subset of neutrophils Yan identified to better understand how they contribute to acute respiratory distress and clotting. They also will determine whether a novel compound will prevent these complications. They will use lab techniques and studies with animal models that allow for manipulation of certain conditions that cannot be done in human subjects.

Grant 2 – $2.9 million, five-year grant to UofL. This work examines a more comprehensive landscape to characterize different subsets of neutrophils and measure their changes over the course of COVID-19 disease progression and how neutrophils contribute to immune dysfunction.

Grant 3 – $306,000, one-year grant to Degranin Therapeutics and UofL for early testing of DGN-23, a compound developed at UofL, to determine its effectiveness in preventing or reducing immune dysregulation.

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Source:

University of Louisville

Microbiology

Novel antibodies target human receptors to neutralize SARS-CoV-2 variants and future sarbecoviruses

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Neha MathurBy Neha MathurMay 17 2023Reviewed by Lily Ramsey, LLM

In a recent study published in the Nature Microbiology Journal, researchers generated six human monoclonal antibodies (mAbs) that prevented infection by all human angiotensin-converting enzyme 2 (ACE2) binding sarbecoviruses tested, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, Delta and Omicron.

They targeted the hACE2 epitope that binds to the SARS-CoV-2 spike (S) glycoprotein rather than targeting the S protein, which all previous therapeutic mAbs for SARS-CoV-2 targeted.

Study: Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies. Image Credit: paulista/Shutterstock.comStudy: Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies. Image Credit: paulista/Shutterstock.com

Background

The emergence of new variants of SARS-CoV-2, especially Omicron sublineages, made all therapeutic mAbs targeting SARS-CoV-2 S obsolete.

Any new S-targeting mAb therapy will also probably have limited utility because SARS-CoV-2 will continue to adapt to human antibodies. Ideally, mAbs developed in anticipation of future pandemics caused by sarbecoviruses should be resilient to mutations that arise in them.

About the study

In the present study, researchers developed hACE2-binding mAbs that blocked infection by pseudotypes of all tested sarbecoviruses at potencies matching SARS-CoV-2 S targeting therapeutic mAbs. The binding affinity of these mAbs to hACE2 was in the nanomolar to picomolar range.

To develop these mAbs, researchers used the KP and Av AlivaMab mouse strains that generate a human Kappa (κ) light chain and Kappa (κ) and Lambda (λ) light chains carrying antibodies, respectively.

They immunized these mice with monomeric and dimeric recombinant hACE2 extracellular domains. Fusion to the fraction, crystallizable (Fc) portion of human immunoglobulin G1 (IgG1) rendered them dimeric.

Further, the team generated hybridomas from mice using sera that inhibited SARS-CoV-2 pseudotyped viruses. They used enzyme-linked immunosorbent assay (ELISA) to screen hybridoma supernatants for hACE2-binding mAbs.

Furthermore, the researchers tested the ability of the six most potent mAbs to inhibit Wuhan-hu-1 S pseudotyped infection in Huh-7.5 target cells.

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The team purified chimeric mAbs from the hybridoma culture supernatants and used a SARS-CoV-2 pseudotype assay to reconfirm their antiviral activity. They also sequenced the human Fab variable regions, VH and VL.

The team cloned VH and VL domains from the six most potent chimeric human-mouse mAbs into a human IgG1 expression vector to generate fully human anti-hACE2 mAbs.

They used single-particle cryo-electron microscopy (cryo-EM) to delineate the structural basis for broad neutralization of anti-hACE2 mAbs.

Specifically, they determined the structure of soluble hACE2 bound to the antigen-binding fragment (Fab) of 05B04, one of the most potent mAbs unaffected by naturally occurring human ACE2 variations.

Finally, the researchers tested these hACE2 mAbs in an animal model and determined their pharmacokinetic behavior.

Results

The researchers identified 82 hybridomas expressing hACE2-binding mAbs, of which they selected ten based on their potency in inhibiting pseudotyped virus infection of Huh-7.5 cells.

These ten mAbs were 1C9H1, 4A12A4, 05B04, 2C12H3, 2F6A6, 2G7A1, 05D06, 05E10, 05G01 and 05H02. Four of the five mAbs from the KP AlivaMab mice, viz., 05B04, 05E10, 05G01, and 05D06, shared identical complementarity-determining regions (CDRs). Conversely, AV AlivaMab mice-derived mAbs were diverse.

While allosteric inhibition of hACE2 activity by the mAbs was theoretically feasible, such inhibition did not occur.

Also, the anti-hACE2 mAbs did not affect hACE2 internalization or recycling, suggesting that the anti-hACE2 mAbs would unlikely undergo accelerated target-dependent clearance from the circulation during in vivo use.

These two findings confirmed that these mAbs would not have harmful side effects based on their target specificity.

In addition, the anti-hACE2 mAbs showed favorable pharmacokinetics and no ill effects on the hACE2 knock-in mice. When used prophylactically in hACE2 knock-in mice, these mAbs conferred near-sterilizing protection against lung SARS-CoV-2 infection.

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Moreover, they presented a high genetic barrier to the acquisition of resistance by SARS-CoV-2.

The six anti-hACE2 mAbs also inhibited infection by pseudotyped SARS-CoV-2 variants, Delta, and Omicron, with similar potency, i.e., half maximal inhibitory concentration (IC50) values ranging between 8.2 ng ml−1 and 197 ng ml−1.

A cryo-EM structure of the 05B04-hACE2 complex at 3.3 Å resolution revealed a 05B04 Fab bound to the N-terminal helices of hACE2.

05B04-mediated inhibition of ACE2-binding sarbecoviruses through molecular mimicry of SARS-CoV-2 receptor-binding domain (RBD) interactions, providing high binding affinity to hACE2 despite the smaller binding footprint on hACE2.

None of the four most potent mAbs affected hACE2 enzymatic activity or induced the internalization of hACE2 localized on the host cell surface. Thus, based on their target specificity, these mAbs shall not have deleterious side effects.

Though these anti-ACE2 antibodies could effectively inhibit sarbecovirus infection in humans, the fact that the antibodies target a host receptor molecule rather than the SARS-CoV-2 S protein will necessitate their testing in terms of safety, efficacy, and pharmacological behavior in primate models before human clinical trials.

Conclusions

SARS-CoV-2 might evolve and start using receptors other than ACE2, creating another genetic hurdle to overcome for researchers working on the development of SARS-CoV-2 therapeutics.

However, the human anti-hACE2 mAbs engineered in this study showed exceptional breadth and potency in inhibiting infection by hACE2-utilizing sarbecoviruses.

Thus, they represent a long-term, ‘resistance-proof’ prophylaxis and treatment for SARS-CoV-2, even for future outbreaks of SARS-like coronaviruses.

In addition, these mAbs might prove particularly useful for susceptible patients like those with immunodeficiency and in which vaccine-induced protective immunity is unattainable or difficult to attain.

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Journal reference:
Microbiology

Study may provide new avenues for addressing somatosensory symptoms of long COVID

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Reviewed by Emily Henderson, B.Sc.May 9 2023

COVID-19, the disease resulting from SARS-CoV-2 infection, is associated with highly variable clinical outcomes that range from asymptomatic disease to death. For those with milder infections, COVID-19 can produce respiratory infection symptoms (cough, congestion, fever) and sensory phenotypes such as headache and loss of sense of smell. In more severe cases, SARS-CoV-2 infection can affect nearly every organ and result in strokes from vascular occlusion, cardiovascular damage and acute renal failure. A substantial number of actively infected patients suffering from both mild and severe infections experience sensory-related symptoms, such as headache, visceral pain, Guillain-Barre syndrome, nerve pain and inflammation. In most patients these symptoms subside after the infection ends, but, for other patients, they can persist.

In a new study, researchers from Boston University Chobanian & Avedisian School of Medicine, Icahn School of Medicine at Mount Sinai (Icahn Mount Sinai) and New York University (NYU), have found that thousands of genes were affected by SARS-CoV-2-mediated disease even after the viral infection had been cleared. These genes were associated with neurodegeneration and pain-related pathways, suggesting lasting damage to dorsal root ganglia (spinal nerves that carry sensory messages from various receptors) that may underlie symptoms of Post-Covid Conditions also known as Long Covid.

Several studies have found that a high proportion of Long Covid patients suffer from abnormal perception of touch, pressure, temperature, pain or tingling throughout the body. Our work suggests that SARS-CoV-2 might induce lasting pain in a rather unique way, emphasizing the need for therapeutics that target molecular pathways specific to this virus.”

Venetia Zachariou, PhD, corresponding author, chair of pharmacology, physiology & biophysics at BU Chobanian & Avedisian School of Medicine

This work was performed in collaboration with Benjamin tenOever, PhD, professor of microbiology and medicine at NYU, formerly at Icahn Mount Sinai.

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Using an experimental model infected with SARS-CoV-2, the researchers studied the effects of infection on sensitivity to touch, both during active infection and well after the infection had cleared. They then compared the effects of SARS-CoV-2 to those triggered by influenza A virus infection. In the experimental model, they observed a slow but progressive increase in sensory sensitivity over time – one that differed substantially from viral control, influenza A virus, which caused quick hypersensitivity during active infection but returned to normal by the time infection was over.

According to the researchers, this model can be used to gain information on genes and pathways affected by SARS-CoV-2, providing novel information to the scientific community on gene expression changes in sensory ganglia several weeks after infection.

“We hope this study will provide new avenues for addressing somatosensory symptoms of long COVID and ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome), which are only just now beginning to be addressed by mainstream medicine. While we have begun using this information by validating one promising target in this study, we believe our now publicly available data can yield insights into many new therapeutic strategies,” adds Zachariou.

These findings appear online in the journal Science Signaling.

This study was supported by National Institute of Neurological Disorders and Stroke NS086444S1 (R.A.S), the Zegar Family Foundation (B.T.) and the Friedman Brain Institute Research Scholars Program (V.Z., B.T., R.A.S., J.J.F.).

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Source:

Boston University School of Medicine

Journal reference:

Serafini, R. A., et al. (2023) SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model. Science Signaling. doi.org/10.1126/scisignal.ade4984.

Microbiology

Anticoronavirals: the development of COVID-19 therapies and the challenges that remain

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Neha MathurBy Neha MathurMay 8 2023Reviewed by Danielle Ellis, B.Sc.

In a recent article published in Nature Microbiology, researchers highlighted the pace of development of coronavirus disease 2019 (COVID-19) therapies during the pandemic and the challenges that hinder the widespread availability of anticoronavirals.

Study: Therapeutics for COVID-19. Image Credit: Viacheslav Lopatin/Shutterstock.com
Study: Therapeutics for COVID-19. Image Credit: Viacheslav Lopatin/Shutterstock.com

Background

COVID-19 is the third coronavirus disease in the past 20 years after severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). While the two predecessors caused severe mortality, they did not cause a pandemic. On the contrary, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggered a pandemic, and by 21 February 2023, it had caused more than 757 million confirmed cases, including >6.8 million deaths worldwide.

Vaccines and monoclonal antibody (mAb) treatments for COVID-19 became available within a year of the pandemic. Yet, there is a substantial need for more effective therapeutics to treat unvaccinated and immunocompromised patients and those whose vaccine immunity waned over time.

About the study

In this study, the authors highlighted four stages of SARS-CoV-2 infection that require different therapeutic interventions as critical for identifying COVID-19 therapeutic targets. At stage 1, when viral replication begins inside the host, oral or intravenous administration of monoclonal antibodies and antiviral therapies are effective. However, an ideal time for prophylactic administration of vaccines is Stage 0 preceding the infection.

Clinical trials have established that mAbs and antivirals effectively combat COVID-19 when administered up to 10 days after symptom onset and within three to five days following the onset of symptoms, respectively. COVID-19 patients in stage 2 develop viral pneumonia, cough and fever, lung inflammation causing shortness of breath, and lung aberrations, such as ground glass opacities.

The most serious is stage 3 characterized by a hyperinflammatory state or acute respiratory distress syndrome (ARDS). Some patients might also develop coagulation disorders or shock or systemic inflammatory response syndrome (SIRS). Thus, at stage 3, a patient needs antiviral drugs and immunomodulatory therapy.

Stage 4 represents post-COVID-19 conditions when patients experience hyperinflammatory illnesses, e.g., multi-system inflammatory syndrome in children (MISC), following acute SARS-CoV-2 infection. Unfortunately, possible preventative measures and treatment for post-acute sequelae of SARS-CoV-2 (PASC) are not fully understood. It is a growing area of unmet medical need; thus, extensive research efforts are ongoing to classify PASC, which might be a conglomeration of several syndromes, and determine its cause(s).

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The National Institutes of Health (NIH) Treatment Guidelines Panel makes recommendations for the treatment and prevention of COVID-19. Early in the pandemic, clinicians used azithromycin and hydroxychloroquine as a possible COVID-19 treatment for hospitalized patients based on in vitro evidence of their synergistic effect on SARS-CoV-2 infection. Later, clinical trials found this combination ineffective. Similarly, the NIH panel did not specify recommendations for empirical antimicrobials.

The NIH rejected giving vitamin/mineral supplements, e.g., zinc, for hospitalized COVID-19 patients. On the contrary, they recommended prompt use of supplemental oxygenation and high-flow nasal cannula in patients with ARDS. In the absence of effective treatments, clinical recommendations by NIH continue to change and evolve.

Early drug repurposing efforts targeted nucleotide prodrugs, e.g., remdesivir (or GS-5734), AT-527, favipiravir, and molnupiravir (or MK-4482). However, only three antivirals received full Emergency Use Authorization (EUA) approval from the United States Food and Drug Administration (US-FDA), remdesivir, molnupiravir, and nirmatrelvir.

Pre-clinical characterization of remdesivir for other coronaviruses, pharmacokinetic and safety evaluation in humans in a failed clinical trial for Ebola virus, all acquired before the beginning of the COVID-19 pandemic, enabled rapid progression of remdesivir.

A phase 3 study conducted among patients in outpatient facilities and nursing facilities showed that remdesevir administration within seven days of symptom onset decreased hospitalization risk by 87%. Thus, its approval extended to high-risk non-hospitalized patients as well. Currently, phase 1b/2a study for inhaled remdesivir, and pre-clinical evaluation of an oral prodrug based on remdesivir is ongoing.

Another randomized phase III trial evaluated ivermectin, metformin, and fluvoxamine, all repurposed drug candidates, for early COVID-19 treatment of overweight or obese adults. Earlier pivotal efficacy and clinical studies found that molnupiravir provided no clinical benefit in hospitalized COVID-19 patients.

Conversely, the MOVe-OUT outpatient study demonstrated that treatment initiated within five days of symptom onset reduced the hospitalization risk or death. Accordingly, molnupiravir attained an EUA in the US on in late 2021 for treatment of mild-to-moderately ill COVID-19 patients at high risk of progression to severe disease. However, an outpatient study suggested that molnupiravir might augment SARS-CoV-2 evolution in immunocompromised individuals.

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In the USA, multiple initiatives have been undertaken to identify candidate agents that may be repurposed as COVID-19 drugs. For instance, the Bill and Melinda Gates Foundation launched the Therapeutics Accelerator in March 2020, wherein they adopted a three-way approach to test approved drugs, screen drug repositories, and evaluate novel small molecules, including mAbs against SARS-CoV-2.

Encouragingly, apilimod, a PIKfyve kinase inhibitor developed for treating autoimmune diseases, is being tested for COVID-19 in clinical studies. Likewise, multiple clinical trials are ongoing for camostat mesilate, an inhibitor of transmembrane protease serine 2 (TMPRSS2), an approved chronic pancreatitis treatment in Japan.

Among anti-inflammatory and immunomodulating drugs, dexamethasone, a corticosteroid, baricitinib, a Janus kinase (JAK) inhibitor, and tocilizumab have received FDA approval. Among mAb therapies, casirivimab with imdevimab and bamlanivimab with etesevimab, Sotrovimab, Bebtelovimab, Tixagevimab–cilgavimab have received FDA approval. However, as SARS-CoV-2 continues to evolve, changes in the spike protein led to EUAs being withdrawn for all mAb therapies due to loss of efficacy.

Conclusions

There is a vast knowledge gap regarding COVID-19 pathogenesis. Despite the absence of a viral reservoir, severe disease persists for weeks or even months after COVID-19 recovery. Another intriguing area of investigation is why autoantibodies increase over time during COVID-19. In February 2022, the government of the United States of America (USA) started a flagship program, RECOVER, to understand, prevent and treat COVID-19-related long-term health effects.

Amid decreasing vaccine uptake and waning efficacy of mAbs as SARS-CoV-2 mutates, there is a need for new, safe, and effective COVID-19 therapies for population-level deployment and the potential to reduce resistance development. Researchers need to accelerate research targeting small molecule candidates that would mechanistically target the conserved region of SARS-CoV-2 and not become ineffective across mutant strains.

To be prepared for another pandemic, a large repository of small molecules that have already progressed through early pre-clinical and clinical evaluation is needed to develop drugs, like remdesivir, developed in a short span of two years.

More importantly, research efforts should continue to advance the development of antivirals for other pathogens, including coronaviruses, in preparation for the next pandemic.

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Journal reference:
Microbiology

Discovery of Helicobacter’s Achilles heel offers great potential for the development of new drugs

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Reviewed by Emily Henderson, B.Sc.Apr 26 2023

LMU researchers have discovered a weakness in the bacterium Helicobacter pylori, which could be exploited to develop new drugs.

The pathogen Helicobacter pylori, which is responsible for widespread illnesses such as gastric ulcers and stomach cancer, has a weak point, which could be exploited to create new drugs. This was discovered by a research group led by LMU biologists Professor Rainer Haas and Dr. Wolfgang Fischer from the Max von Pettenkofer Institute of Hygiene and Medical Microbiology. Their results have now been published in the journal Cell Chemical Biology.

More than four billion people worldwide are infected with the stomach bacterium, leading to over 800,000 cases of stomach cancer every year. Because the bacterium is becoming increasingly resistant to current drugs, the World Health Organization (WHO) has classified it as a pathogen with high priority for the research and development of new antibiotics. New approaches and therapeutics are urgently required to replace or complement established treatment methods.

The new study has taken an important step in this direction. “We were able to demonstrate that the bacteria are very sensitive to certain substances that inhibit cellular respiration,” says Haas.

Fighting helicobacter and protecting the gut microbiome

The researchers were able to identify several compounds from various substance groups that incapacitate the respiratory chain of H. pylori even in small concentrations. For other useful bacteria, including representatives of the normal gut microbiome, these substances are unproblematic. These bacteria tolerate larger amounts of the substances.

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The authors of the study used a broad spectrum of biochemical and microbiological methods as well as molecular modeling techniques to discover why H. pylori reacts so sensitively to these substance groups. They identified the cause in a slightly modified structure of the so-called quinone binding pocket in respiratory complex I.

This Achilles heel offers great potential for the development of specifically tailored new active agents that could be used as pathogen blockers against H. pylori. “Our results reveal a surprising weakness in the metabolism of these bacteria, which are well adapted otherwise to their unusual environment,” says Fischer.

The research team at LMU was also able to identify possible mutations that would make the bacteria less sensitive to the inhibitors. However, these mutations also weaken the metabolism of the pathogens. This means that less resistance is formed to the complex I inhibitors.

“Overall, our results are very promising,” adds Haas. “We managed to identify a whole group of inhibitors that do not exhibit any cross-resistance with current therapeutics. They are less susceptible to the development of resistance and have a small impact on the gut microbiome.”

In addition to scientists at LMU, the German Center for Infection Research and researchers from Ghent University, the Max Planck Institute of Biophysics in Frankfurt, the Technical University of Munich, Helmholtz Munich and Helmholtz Braunschweig, Goethe University Frankfurt, and BASF Ludwigshafen all made significant contributions to the study.

Source:

Ludwig-Maximilians-Universitaet Muenchen (LMU)

Microbiology

Updated booster shots vital for keeping COVID-19 in check

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Reviewed by Emily Henderson, B.Sc.Apr 3 2023

Between natural infection and a global vaccination campaign, most people now have some immunity against the virus that causes COVID-19. This widespread immunity hasn’t stopped people from getting infected, but it has dampened the massive waves of illness and death that roiled the globe in the early years of the pandemic. Keeping the virus in check requires maintaining this level of immunity, a difficult task because the virus is constantly spinning off new variants that can partially evade antibodies elicited by vaccines and prior infections.

New research from scientists at Washington University School of Medicine in St. Louis suggests that updated booster shots will be important for shoring up population immunity as new variants emerge – but there’s a caveat.

Their research, published April 3 in Nature, shows that vaccinating people against the original strain of the virus and then boosting with a shot that targets a new variant can elicit a broad antibody response capable of neutralizing a wide array of variants, including ones that have not yet emerged. The trick is to target a variant for the booster that is so different from the original strain of the virus that it triggers the maturation of new and diverse antibody-producing cells.

The challenge with COVID-19 is that the virus keeps mutating. It’s not that the vaccines don’t elicit a lasting antibody response. They do. The problem is that the virus changes and the existing antibodies become irrelevant. Here we showed that it’s possible to design a variant-specific booster that doesn’t just strengthen the antibodies people already have but elicits new antibodies. This means that periodically giving boosters targeting new variants would allow population-level protection to be maintained even as the virus evolves.”

Ali Ellebedy, PhD, senior author, associate professor of pathology & immunology, of medicine, and of molecular microbiology

The first COVID-19 vaccines reduced the risk of severe illness and death by more than 90%. But then the virus changed. The antibodies that had worked so well against the original strain proved less effective at recognizing and neutralizing emerging variants, leading to breakthrough infections. The obvious solution was to update the vaccines to target new variants, but the success of the first vaccines against the original strain made designing an effective variant booster shot tricky, Ellebedy said.

“The whole point of making boosters against new variants is to teach the immune system to recognize features in the new variants that are different from the original strain,” Ellebedy said. “But the new variants still share a lot of features with the original strain, and it’s possible that the response to these shared features could dominate the response to new features. The boosters could end up just engaging immune memory cells that are already present rather than creating new memory cells, which is what we need for protection against new variants.”

To gauge the effectiveness of boosters at eliciting new antibodies, Ellebedy and colleagues studied people who received a COVID-19 vaccine targeted against the original strain, followed by a combined booster targeting two of the early variants -; beta and delta -; or a booster targeting the newer omicron variant. Along with Ellebedy, the research team included co-corresponding author Jackson Turner, PhD, an instructor in pathology & immunology, and co-first authors Wafaa B. Alsoussi, a graduate student, and Sameer Kumar Malladi, PhD, a postdoctoral researcher, both in Ellebedy’s lab.

The first studies were discouraging, Ellebedy noted. The researchers looked at 39 people who had received the two-shot primary sequence of the Pfizer/BioNTech or Moderna COVID-19 vaccines, followed by an experimental booster shot targeting the beta and delta variants. All participants produced antibodies that neutralized the original virus strain and the beta and delta variants. But none of the antibodies studied were unique to beta or delta. The absence of such antibodies indicates that the variant booster had failed to trigger the development of detectable new antibody-producing cells, Ellebedy said.

“This was disappointing but not surprising,” said Ellebedy, who is also an expert on influenza vaccines. “If you look at the sequences for the beta and delta spike proteins, they are not really very different from the original strain. If we saw this degree of difference among influenza strains, we would say there’s no reason to update the annual vaccine. But the omicron variant is a different matter.”

The omicron variant, dominant worldwide since late 2021, carries dozens of new mutations relative to the original strain of the virus. Ellebedy and colleagues recruited eight people who had received the Pfizer/BioNTech or Moderna COVID-19 vaccine and gave them a booster targeted against the omicron variant alone. The CDC later recommended the use of updated boosters that target both the omicron variant and the original strain. Such bivalent boosters became available to the public in fall 2022, manufactured by both Pfizer/BioNTech and Moderna.

Studying blood samples provided by participants four months after their boosters, the researchers identified more than 300 distinct antibodies capable of neutralizing the original strain, or one or more of the variants. Of those, six neutralized omicron but not the original strain, an indication that the booster successfully triggered the creation of new antibodies optimized for omicron. One such new antibody even neutralized BA.5, a subvariant of omicron that is circulating widely now but had not yet emerged at the time the booster was made.

“This booster engaged naive B cells and created new memory cells, which means it expanded people’s immune repertoire and equipped them to respond to a greater diversity of variants,” Ellebedy said. “Designing boosters to maintain immunity to the evolving virus is not going to be easy. The extent of the difference between the old and the new variants is clearly important. But if we are careful about how we choose which variants to include in boosters, I think we can stay ahead of this virus.”

Source:

Washington University School of Medicine

Journal reference:

Alsoussi, W. B., et al. (2023). SARS-CoV-2 Omicron boosting induces de novo B cell response in humans. Nature. doi.org/10.1038/s41586-023-06025-4.

Microbiology

Monocytes may be a stable reservoir of HIV in patients taking antiretroviral therapy

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Reviewed by Emily Henderson, B.Sc.Mar 27 2023

To develop treatments that may one day entirely rid the body of HIV infection, scientists have long sought to identify all of the places that the virus can hide its genetic code. Now, in a study using blood samples from men and women with HIV on long-term suppressive therapy, a team led by Johns Hopkins Medicine scientists reports new evidence that one such stable reservoir of HIV genomes can be found in circulating white blood cells called monocytes.

Monocytes are short-lived circulating immune cells that are a precursor to macrophages, immune cells able to engulf and destroy viruses, bacteria and other cells foreign to the host.

In the current research, published March 27 in Nature Microbiology, the scientists found evidence that blood samples from people with HIV undergoing long term, standard antiretroviral therapy contained monocytes that harbor stable HIV DNA capable of infecting neighboring cells.

The scientists say the findings may provide a new direction for efforts to improve therapies and eventually cure HIV, which affects more than 34 million people worldwide, according to the World Health Organization. Current antiretroviral drugs can successfully suppress HIV to nearly undetectable levels, but have not resulted in total eradication of the virus.

We don’t know how critical these monocytes and macrophages are to eradication of HIV, but our results suggest we should continue research efforts to understand their role in this disease.”

Janice Clements, Ph.D., professor of molecular and comparative pathobiology, Johns Hopkins University School of Medicine

Scientists have long known that HIV stashes its genome most often in a type of immune cell called a CD4+ T-cell. These hiding places are known as reservoirs.

“To eradicate HIV, the goal is to find biomarkers for cells that harbor the HIV genome and eliminate those cells,” says Rebecca Veenhuis, Ph.D., assistant professor of molecular and comparative pathobiology at the Johns Hopkins University School of Medicine.

To further study the role of monocytes and macrophages in circulating blood as HIV reservoirs, the Johns Hopkins-led team of scientists obtained blood samples between 2018 and 2022 from 10 men with HIV, all of them taking long-term, standard antiretroviral medications.

The researchers extracted blood cells from the samples and grew the cells in the laboratory. Typically, monocytes transform very quickly -; within about three days -; into macrophages, producing monocyte-derived macrophages.

All 10 men had detectable HIV DNA in their monocytes-turned-macrophages, but at levels 10 times lower than those found in the men’s CD4+ T cells, the well-established HIV reservoir.

For the next phase of the research, to determine if HIV genomes were present in monocytes prior to macrophage differentiation, the team used an experimental assay to detect intact HIV genomes in monocytes. The assay was based on one that fellow Johns Hopkins scientist Robert Siliciano, M.D., Ph.D., developed in 2019 to detect the HIV genome in CD4+ T cells.

The scientists, including research associate Celina Abreu, Ph.D., used the assay on blood samples taken from another group of 30 people (eight men from the first group and 22 female participants) with HIV, also treated with standard antiretroviral therapy. The researchers found HIV DNA in the CD4+ T cells and in monocytes of all 30 participants.

The scientists were also able to isolate HIV produced by infected monocytes from half of the research participants. The virus extracted from these cells was able to infect CD4+ T cells.

Three of the participants had their blood examined several times over the four-year study period, and each time, the scientists found HIV DNA and infectious virus produced by their monocyte-derived macrophages. “These results suggest that monocytes may be a stable reservoir of HIV,” says Clements.

In further research, the Johns Hopkins research team plans to pinpoint the subset of monocytes found to harbor HIV DNA and the source of these infected cells.

Source:

Johns Hopkins Medicine

Journal reference:

Veenhuis, R. T., et al. (2023). Monocyte-derived macrophages contain persistent latent HIV reservoirs. Nature Microbiology. doi.org/10.1038/s41564-023-01349-3.

Microbiology

The right combination of bile salt hydrolases may offer a new approach to treat C. diff

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Reviewed by Emily Henderson, B.Sc.Mar 13 2023

Not all probiotics are created equal. In a new study, researchers found that certain enzymes within a class known as bile salt hydrolases (BSHs) can restrict Clostridioides difficile (C. diff.) colonization by both altering existing bile acids and by creating a new class of bile acids within the gut’s microbial environment. The work could lead to “designer” probiotics that protect against disease by introducing specific BSHs to the gut after antibiotic treatment.

Selecting the right suite of BSH-producing bacteria is critical, because the study found that interactions between BSHs and bile acids differ depending upon the type of bacteria the BSHs come from.

Certain bacteria within the gut microbiota contain BSH enzymes, which chemically modify bile acids. Bile acids are made in the liver and play an important role in modulating cholesterol levels, regulating fat absorption, shaping the immune system, and affecting which bacteria can colonize the gut.

Although researchers had long suspected a connection between BSHs from beneficial bacteria, the bile acid pool, gut microbial composition and host health, until now relatively little was known about how BSHs function and their potential impacts on host health.

The old dogma – that BSHs are needed for gut colonization because they render toxic bile acids non-toxic – oversimplified what’s actually happening.”

Casey Theriot, associate professor of infectious disease at North Carolina State University and co-corresponding author of the study

“The reality is that BSHs’ interactions are context-dependent, meaning they’re affected by the type of bacteria they come from,” Theriot says. “And they don’t just interact with bile acids produced by the host. BSHs in the microbiota can create and interact with a new class of bile acids called microbial conjugated bile acids (MCBAs) – bile acids that we didn’t even know existed until recently.”

In the new study, Theriot led a collaborative research team that included microbiologists, chemists, biochemists, and clinicians from NC State, the University of North Carolina at Chapel Hill, and the University of California, San Diego on a deep dive into BSHs.

Specifically, they looked at hundreds of BSHs from different Lactobacillaceae bacteria (which houses most probiotic strains) and then included BSHs from the gut microbiota (nearly 1,000 unique BSHs in total).

Matthew Redinbo, Kenan Distinguished Professor of Chemistry in UNC-Chapel Hill’s College of Arts and Sciences, and his departmental colleagues (led by then graduate student Morgan Walker) were instrumental in determining the structure of BSHs and how they “choose” to interact with bile acids, by either adding or taking away certain amino acids.

“We found the tiny molecular fingerprint that defined whether a BSH would ‘turn left’ or ‘turn right’ in terms of what they processed,” Redinbo says. “Knowing that allowed Casey’s team to steer the bile acid pool in whatever direction they wanted.”

The researchers used a cocktail of Lactobacillus BSHs to figure out if they could change the bile acid pool enough to alter C. diff colonization in both human stool samples collected from patients susceptible to C. diff infection (CDI) and in a mouse model of CDI. In both human stool samples and mice, the researchers saw that pre-treatment with BSH cocktails impacted C. diff colonization. Interestingly, the researchers noted elevated levels of MCBAs in the gut microbiota of the BSH-treated mice.

To determine whether the MCBAs were also involved in inhibiting C. diff germination and growth, they tested the MCBAs against C. diff in vitro. In most cases, the presence of MCBAs inhibited multiple steps of the C. diff life cycle.

“This is more evidence that BSHs are driving changes in the bile acid pool – including making MCBAs – that could serve to inhibit C. diff,” Theriot says. “We’ve uncovered a new function for BSH enzymes.”

“This work highlights the importance of BSHs as key intestinal enzymes and promising new therapeutics,” says Matt Foley, research scholar at NC State and co-first author of the study. “Using BSHs in combination with other strategies may offer a new approach to treat C. diff.“

The researchers see the work as the first step toward potential probiotics that could be customized to protect against a variety of bacterial infections and intestinal diseases. But first, more work must be done to determine how and why the BSHs decide which MCBAs to produce and/or target.

“This is an important illustration of how deciphering the biochemical and genetic basis for probiotic functionality both leads to a better understanding of how we can combat gut disease with novel modalities, and also practically design and formulate next-generation commercial probiotics,” says Rodolphe Barrangou, the Todd R. Klaenhammer Distinguished Professor in Probiotics Research at NC State and co-corresponding author of the study.

The work appears in Nature Microbiology and was supported by the National Institutes of Health, the National Science Foundation, IFF Corporation and the U.S. Environmental Protection Agency. The MCBA detection work was done by Erin Baker, formerly of NC State and currently at UNC-Chapel Hill, Allison Stewart of NC State, and Emily Gentry and Pieter Dorrestein from UCSD.

Source:

North Carolina State University

Journal reference:

Foley, M. H., et al. (2023). Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. Nature Microbiology. doi.org/10.1038/s41564-023-01337-7.

Microbiology

Review on factors related to variations in human microbiota

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Pooja Toshniwal PahariaBy Pooja Toshniwal PahariaMar 8 2023Reviewed by Aimee Molineux

In a recent review published in Current Opinion in Microbiology, researchers reviewed existing data on variations in human microbiota, emphasizing on ageing- and ethnicity-associated changes in the microbiota.

Study: Human microbiome variance is underestimated. Image Credit: Troyan/Shutterstock
Study: Human microbiome variance is underestimated. Image Credit: Troyan/Shutterstock

Background

Human microbial heterogeneity lays the foundation for precision therapeutics, and thus, the potential of personalized microbiota-based diagnostic and therapeutic strategies can be tapped fully by understanding human microbial variations. However, the factors associated with alterations in the human microbiome have yet to be well-characterized.

Further, most of the human microbiota data has been obtained from residents of westernized and socioeconomically developed nations, with the probable skewing of microbiota variations and their associations with health. Moreover, the under-sampling of ethnic minorities in microbiota analyses must be addressed for assessing the history, context, and evolving dynamics of the human microbiota in the context of disease risks.

About the review

In the present review, researchers highlighted recent advances in characterizing human microbiota variations associated with ageing and various ethnicities globally.

Age-related changes in the microbiota of humans

Factors that shape the human microbiota include birth type, family sizes, cohabitation, housing, domestic animals, age, sex, physical fitness, diet, antibiotics, non-antibiotic drugs, and alcohol intake. At the societal level, complex associations of health inequalities, socioeconomic status, and social networks with the human microbiome balance have been reported.

Studies have demonstrated an inverse association between the microbiota and an individual’s age, and conversely, microbial compositional variations contribute to the process of ageing and age-associated diseases. All individuals do not age uniformly, and the differential ageing rates reflect in the human microbiota. Therefore, the human microbiota abundance is evolving as a biomarker to evaluate differences in the biological age and chronological age and between health and disease. Human microbiomes lacking Bacteroides species have been strongly associated with a healthy type of ageing.

Other factors related to variations in the human microbiota composition

Mediterranean diets, involving reduced intake of saturated-type fats, red meat, and milk products, with high consumption of fruits, vegetables, fish, legumes, nuts, and olive oil, have been reported to reverse age-associated microbiota alterations and delay cognitive decline. Studies have reported the co-evolution of human beings and intestinal microbes, with notable variations in Helicobacter pylori diversity associated with human migration.

Microbiome compositions vary among individuals residing in industrialized or non-industrialized regions. Non-industrialized region-associated microbiomes or ancestral microbes have adapted to metabolizing complex-type carbohydrates from diets with high fibre content. The microbial compositions vary by season, climatic fluctuations, and accessibility to unprocessed-type foods. The microbiome of individuals living in non-industrialized regions reportedly has lower Bacteroides/Prevotella spp. ratio, elevated counts of Treponema species, and varying abundance of parasites that affect the immunity of the host.

Naturally maintained palaeofaeces microbiome genomes resemble the genomes of non-industrialized human intestinal microbiota. Socioeconomic developments and industrialization have been associated with microbiome diversity losses, lowered parasitism, reduced counts of ancestral microbes like Helicobacter pylori species and elevated counts of microbes associated with non-communicable and chronic metabolic and inflammatory diseases.

Immigration has been related to an increased abundance of microbes associated with obesity. A study on Irish travellers reported three key factors influencing the human microbiota composition, i.e., living conditions, closeness to domestic pets during childhood and family sizes, with the average number of siblings among traveller families and other families being 10, and one, respectively).

Conclusions

Based on the review findings, the human microbiome is influenced by age, diet, ethnicity and immigration. Further research is required to improve understanding of age-related microbiome changes to identify targets and develop tailored microbiota-based therapeutic interventions. The increase or decrease in microbial abundance associated with changes in dietary patterns and modernization needs to be assessed further to develop highly specific precision medicine catered to the residential locations and food consumed.

The co-diversification of microbes with humans globally warrants in-depth analysis of microbial compositions by ethnicity, region, diet, and industrialization status to maximize the benefit of microbiota-based interventions to one and all. Microbial analyses were performed to evaluate the risk of disease in relation to microbiome dysbiosis and abrupt changes following immigration could inform policy-makers and decision-making and aid in developing personalized therapeutics to improve the standard of care for all individuals across the globe.

Journal reference:
Microbiology

Infections with many different types of bacteria including Streptococcus pneumonia, Listeria monocytogens, and Neisseria mengitidis can cause bacterial …

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Infections with many different types of bacteria including Streptococcus pneumonia, Listeria monocytogens, and Neisseria mengitidis can cause bacterial meningitis. It’s estimated that every year over 1.2 million cases of bacterial meningitis happen around the world, and without treatment, this deadly disease is fatal to seven of ten people who are sickened by it. Even with antibiotic treatments, three of ten patients die. Survivors are left with issues like chronic headaches, seizures, loss of vision or hearing, and other neurological consequences. New research reported in Nature has revealed how bacteria are able to penetrate the meninges that surround and protect the brain to cause bacterial meningitis. The findings have shown that bacteria use neurons to evade immunity and infect the brain, and the work may aid in the creation of new therapeutics.

A digitally-colorized SEM image depicts of Streptococcus pneumoniae bacteria (lavender), as they were being attacked by a white blood cell (pink). / Credit: CDC/ Dr. Richard Facklam

Right now, antibiotics can help eliminate the bacterial pathogens that cause this illness. But steroids are also needed to control the dangerous inflammation that can occur along with the infection. However, reducing inflammation also weakens the immune response, making it harder to get rid of the infection.

In this research, the scientists used Streptococcus pneumoniae and Streptococcus agalactiae bacteria, which can both cause bacterial meningitis in humans. They determined that when these bacteria get to the meninges, they release a toxin, which activates neurons in the meninges that sense pain. This pain neuron activation could explain why bacterial meningitis patients get horrible headaches, noted the researchers.

The activated pain neurons then release a signaling molecule called CGRP, which binds to a receptor called RAMP1 on the surface of immune cells called macrophages. Once CGRP binds to RAMP1 on macrophages, the immune cells are basically disabled, and they stop responding to bacterial infections like they normally would.

The link between CGRP and RAMP1 on macrophages also stops them from signaling to other immune cells, which allows the bacterial infection to not only penetrate the meninges but to spread infection.

This work was confirmed with the use of a mouse model that lacked the pain neurons that are activated by bacteria. Compared to mice with those neurons, the engineered mice had less severe brain infections when they were exposed to bacteria that cause meningitis. There were also lower levels of CGRP in the engineered mice compared to normal mice. The normal mice, however, had higher levels of bacteria in the meninges.

Additional experiments also showed that when mice were treated with drugs that block RAMP1, the severity of the bacterial infection was reduced. Mice treated with RAMP1 blockers were able to clear their infections faster too.

It may be possible to help the immune system clear cases of bacterial meningitis with medications that block either CGRP or RAMP1, potentially in conjunction with antibiotics. There are already drugs that can do this, and they are generally used to treat migraine.

Sources: Harvard Medical School, Nature


Carmen Leitch