Tag Archives: Inflammation

Microbiology

Nasal SARS-CoV-2 vaccine outperforms existing vaccines in preclinical trial

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Bhavana KunkalikarBy Bhavana KunkalikarApr 6 2023Reviewed by Benedette Cuffari, M.Sc.

In a recent study published in the journal Nature Microbiology, researchers assess the role of the live-attenuated vaccine (LAV) sCPD9 in inducing systemic and mucosal immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

Study: Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Image Credit: TopMicrobialStock / Shutterstock.com

Study: Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Image Credit: TopMicrobialStock / Shutterstock.com

Introduction

Coronavirus disease 2019 (COVID-19) vaccines, currently administered through the intramuscular route, effectively stimulate the production of neutralizing antibodies, effector and central memory T-cells, germinal center B-cells, long-lived plasma cells, and nasal-resident CD8+ T-cells. The intramuscular route has lower efficacy in promoting long-lasting mucosal immunoglobulin A (IgA) and IgG responses, as well as pulmonary tissue-resident memory cell responses.

Notably, mucosal antibodies are important in reducing viral infectivity and transmission at the site of entry. Tissue-resident memory cells have faster recall responses and can recognize cognate antigens earlier due to their local positioning.

About the study

In the present study, researchers compare the immune responses and preclinical efficacy of the Pfizer-BioNTech BNT162b2 messenger ribonucleic acid (mRNA) COVID-19 vaccine, adenovirus-vectored spike vaccine Ad2-spike, and LAV sCPD9 in Syrian hamsters.

The efficiency and mechanism of action of the evaluated vaccines were evaluated in a heterologous SARS-CoV-2 Delta variant challenge condition. To this end, Syrian hamsters received one vaccine dose and were exposed to the SARS-CoV-2 Delta variant 21 days after vaccination to evaluate its effectiveness. Hamsters were administered two vaccine doses 21 days apart and were later infected with the virus 14 days after booster administration.

Histopathology was used to examine challenged hamsters and determine any lung damage caused by infection. Single-cell RNA sequencing (scRNA-seq) was performed on lung specimens to establish a correlation between inflammation levels and cellular responses.

The humoral responses of hamsters were assessed by analyzing their sera collected before and after vaccination and determining their neutralizing ability against SARS-CoV-2 variants at different time points.

Results

All vaccinations protected hamsters from weight loss induced by SARS-CoV-2 infection. However, the vaccines did not provide complete protection against SARS-CoV-2 Delta infection after a single dose, as viral RNA was still present in the respiratory tract. The sCPD9 vaccine was the only tested vaccine that successfully reduced replicating viral titers to undetectable levels within two days post-challenge (dpc).

The overall efficacy of the SARS-CoV-2 vaccine was enhanced through prime-boost vaccination. Despite a significant reduction after prime-boost vaccination, all groups exhibited detectable viral RNA in oropharyngeal specimens and lungs. Nevertheless, sCPD9-based vaccination was more effective in decreasing viral RNA levels.

Vaccinated animals exhibited a significant reduction in replication-competent vial levels in their lungs two days post-challenge (dpc). Only the sCPD9 booster vaccine effectively reduced replicating virus proportions below the detection threshold, irrespective of whether the entire vaccination series was heterologous or homologous.

Furthermore, sCPD9 was highly effective in preventing inflammation and pneumonia after a single vaccination. This was demonstrated by the reduced levels of consolidated lung areas, along with lower scores for bronchitis, edema, and lung inflammation.

Animals with different vaccination schedules showed more significant bronchial hyperplasia. Prime-boost regimens showed a similar trend, with the mRNA vaccine displaying better histological outcomes with a homologous boost.

Homologous sCPD9 prime-boost vaccination offered better lung protection against inflammation. Both heterologous and homologous sCDP9 vaccinated hamsters exhibited reduced inflammation- and infection-related genes in their lung transcriptome.

Sera from sCPD9 vaccine recipients showed higher neutralization capacity against the ancestral SARS-CoV-2 variant B.1 compared to other groups. The sCPD9 sera effectively neutralized the Beta and Delta variants, as well as the Omicron BA.1 sublineage.

The neutralization capacity against Omicron BA.1 was reduced in all cohorts, with sCPD9 sera associated with significant neutralization. Neutralizing antibodies increased over time in all cohorts by five dpc due to challenge infection.

Hamsters that received the sCPD9 or mRNA vaccine, along with the prime-only vaccination, produced more neutralizing antibodies than those that only received the prime-only vaccination. Booster vaccination improved the serum neutralization capacity for various variants, with Omicron BA.1 exhibiting the highest neutralization evasion capacity among the tested variants.

Hamsters vaccinated with mRNA+sCDP9 and prime-boost sCDP9 produced notable IgG antibody responses against the SARS-CoV-2 spike, nucleocapsid protein, and open reading frame (ORF)-3a. Comparatively, hamsters vaccinated with prime-boost mRNA and Ad2 only exhibited IgG reactivity against the spike protein.

Conclusions

The study findings presented a comparison of vaccines across different platforms, including a novel LAV that provided better protection against SARS-CoV-2 infection than other types of COVID-19 vaccines. Importantly, these findings on enhanced immunity through heterologous prime-boost vaccination align with other recent studies that utilize systemic priming and intranasal boosting with Ad-2 vector or mRNA vaccines.

Anti-SARS-CoV-2 IgA levels in the nasal mucosa are significantly higher among sCPD9-vaccinated animals. Animals vaccinated with sCPD9 showed significant improvement in protection against virus replication, lung inflammation, and tissue damage. Animals that received sCPD9 had a broader antigen recognition, likely due to the key features of LAV.

Journal reference:
  • Nouailles, G., Adler, J. M., Pennitz, P., et al. (2023). Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nature Microbiology 1-15. doi:10.1038/s41564-023-01352-8
Microbiology

Discovering Inflammation’s Achilles Heel: The Breakthrough That Could Change Medicine

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Researchers at Kyoto University have found that neutrophils, a type of white blood cell, can induce anti-inflammatory macrophages (M2) within granulomas, which are dense globular structures that form during chronic inflammation. This M2 macrophage polarization can help regulate inflammation and tissue health. The team believes that their findings, derived from studying tuberculosis, could also be applied to tumor development. By understanding how a bacteria-permissive microenvironment is formed, the researchers hope to contribute to more effective cancer drug development.

When our bodies become infected, various immune responses are triggered, starting with a release of granulocytes, white blood cells containing special enzymes that makeup about half or more of all human white blood cells.

Neutrophils are also granulocytes that fight off invasive bacteria and fungi, often with zero tolerance for such invaders. Sometimes, however, a balanced and less aggressive approach goes even further in providing a cure.

Now, a team of researchers at Kyoto University has determined that neutrophils induce anti-inflammatory — or M2 — macrophages deep in the core of the granulomas.

In previous studies, chronic inflammatory macrophages were found to have the potential to polarize or differentiate into two opposite versions: pro-inflammatory, or M1, and anti-inflammatory, or M2 types. These constitute an M1-M2 equilibrium that regulates the severity of inflammation and tissue health — or homeostasis.

This dual nature or polarization describes how M2 can revert to M1 or even M0 — the non-inflammatory or steady state — in the deep granuloma zone where a bacteria-permissive microenvironment is formed. The team has examined the dense globular structures of granulomas in animals, particularly in the lungs.

“Microbes and cancer cells may manipulate this permissive microenvironment to favor their survival,” says Tatsuaki Mizutani.

Human granuloma-related disorders including tuberculosis are a hallmark of chronic inflammatory diseases. Mizutani posits that the results his team obtained from tuberculosis may also be applied to tumors.

Previous studies have revealed that intercellular interactions within granulomas drive effective inflammatory responses against pathogens or contaminants, but chronic inflammation — as in tuberculosis and tumors — persists over prolonged periods of time.

To test how to predict tumor development, Mizutani’s team previously established a lung granuloma model in guinea pigs, which demonstrated the specific accumulation of Neutrophil S100A9 — or A9 — deep in the cores of granulomas. A9 is expressed in monocytes and macrophages at low levels but at high levels within neutrophils.

“What is interesting is that both the inflammatory and anti-inflammatory effects of A9 have been reported in A9-deficient mice,” notes Mizutani, whose team is now considering whether to make A9’s multifunctional nature anti-tumorigenic in the tumor microenvironment.

“Our understanding of how a permissive microenvironment in tumors is formed may be applied to effective cancer drug development,” reflects Mizutani.

Reference: “Neutrophil S100A9 supports M2 macrophage niche formation in granulomas” by Tatsuaki Mizutani, Toshiaki Ano, Yuya Yoshioka, Satoshi Mizuta, Keiko Takemoto, Yuki Ouchi, Daisuke Morita, Satsuki Kitano, Hitoshi Miyachi, Tatsuaki Tsuruyama, Nagatoshi Fujiwara and Masahiko Sugita, 29 January 2023, iScience.
DOI: 10.1016/j.isci.2023.106081

Funding: KAKENHI, Ohyama Health Foundation, Fujiwara Memorial Foundation, INFRONT Office of Directors’ Research Grants Program

Kyoto University

Microbiology

Live attenuated nasal vaccine elicits superior immunity to SARS-CoV-2 variants in hamsters

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Reviewed by Emily Henderson, B.Sc.Apr 4 2023

Since the beginning of the COVID-19 pandemic, researchers have been working on mucosal vaccines that can be administered through the nose. Now, scientists in Berlin have developed a live attenuated vaccine for the nose. In “Nature Microbiology”, they describe the special immune protection it induces.

Coronaviruses spread primarily through the air. When infected people speak, cough, sneeze or laugh, they expel droplets of saliva containing the virus. Other people then breathe in these airborne pathogens and become infected themselves. A research team in Berlin decided to try to fight the virus that causes COVID-19 where it first takes hold: the mucous membranes of the nose, mouth, throat, and lungs. To do so, the scientists developed a live attenuated SARS-CoV-2 vaccine that is administered through the nose. In the latest issue of the journal “Nature Microbiology“, the interdisciplinary team describes how this live attenuated vaccine confers better immunity than vaccines injected into muscle.

Already in the fall of last year, two nasal vaccination formulations were approved for use in India and China. These contain modified adenoviruses – which typically cause respiratory or gastrointestinal illnesses – that are self-attenuating, meaning they either replicate poorly or stop replicating altogether, and therefore never trigger disease. Other live nasal vaccines are currently undergoing development and testing around the world.

Protection at the site of infection

The benefits of a nasal vaccine go far beyond just providing an alternative for people afraid of needles. When a vaccine is injected, it infers immunity primarily in the blood and throughout the entire body. However, this means that the immune system only detects and combats coronaviruses relatively late on in an infection, as they enter the body via the mucous membranes of the upper respiratory tract. “It is here, therefore, that we need local immunity if we want to intercept a respiratory virus early on,” explains the study’s co-last author Dr. Jakob Trimpert, a veterinarian and research group leader at the Institute of Virology at Freie Universität Berlin.

“Nasal vaccines are far more effective in this regard than injected vaccines, which fail or struggle to reach the mucous membranes,” emphasizes Dr. Emanuel Wyler, another co-last author. He has been researching COVID-19 since the start of the pandemic as part of the RNA Biology and Posttranscriptional Regulation Lab, which is led by Professor Markus Landthaler at the Berlin Institute for Medical Systems Biology of the Max Delbrück Center (MDC-BIMSB).

In an ideal scenario, a live intranasal vaccine stimulates the formation of the antibody immunoglobulin A (IgA) directly on site, thus preventing infection from occurring in the first place. IgA is the most common immunoglobin in the mucous membranes of the airways. It is able to neutralize pathogens by binding to them and preventing them from infecting respiratory tract cells. At the same time, the vaccine stimulates systemic immune responses that help provide effective overall protection from infection.

Memory T cells that reside in lung tissue play a similarly useful role to antibodies in the mucosa. These white blood cells remain in affected tissue long after an infection has passed and remember pathogens they have encountered before. Thanks to their location in the lungs, they can respond quickly to viruses that enter through the airways.” The co-first author draws attention to one of the observations the team made during their study: “We were able to show that prior intranasal vaccination results in the increased reactivation of these local memory cells in the event of a subsequent SARS-CoV-2 infection. Needless to say, we were particularly pleased with this result.”

Dr. Geraldine Nouailles, immunologist and research group leader at the Department of Pneumology, Respiratory Medicine, and Intensive Care Medicine at Charité

Local immunity impedes viral infection

The scientists tested the efficacy of the newly developed intranasal COVID-19 vaccine on hamster models that had been established by Trimpert and his team at Freie Universität Berlin at the beginning of the pandemic. These rodents are currently the most important non-transgenic model organisms for research into the novel coronavirus, as they can be infected with the same virus variants as humans and develop similar symptoms. They found that after two doses of the vaccine, the virus could no longer replicate in the model organism. “We witnessed strong activation of the immunological memory, and the mucous membranes were very well protected by the high concentration of antibodies,” Trimpert explains. The vaccine could therefore also significantly reduce the transmissibility of the virus.

In addition, the scientists compared the efficacy of the live attenuated vaccine with that of vaccines injected into the muscle. To do so, they vaccinated the hamsters either twice with the live vaccine, once with the mRNA and once with the live vaccine, or twice with an mRNA or adenovirus-based vaccine. Then, after the hamsters were infected with SARS-CoV-2, they used tissue samples from the nasal mucosa and lungs to see how strongly the virus was still able to attack the mucosal cells. They also determined the extent of the inflammatory response using single-cell sequencing. “The live attenuated vaccine performed better than the other vaccines in all parameters,” Wyler summarizes. This is probably due to the fact that the nasally administered vaccine builds up immunity directly at the viral entry site. In addition, the live vaccine contains all components of the virus – not just the spike protein, as is the case with the mRNA vaccines. While spike is indeed the virus’s most important antigen, the immune system can also recognize the virus from about 20 other proteins.

Better than conventional vaccines

The best protection against the SARS-CoV-2 was provided by double nasal vaccination, followed by the combination of a muscular injection of the mRNA vaccine and the subsequent nasal administration of the live attenuated vaccine. “This means the live vaccine could be particularly interesting as a booster,” says the study’s co-first author Julia Adler, a veterinarian and doctoral student at the Institute of Virology at Freie Universität Berlin.

The principle of live attenuated vaccines is old and is already used in measles and rubella vaccinations, for example. But in the past, scientists generated the attenuation by chance – sometimes waiting years for mutations to evolve that produced an attenuated virus. The Berlin researchers, on the other hand, were able to specifically alter the genetic code of the coronaviruses. “We wanted to prevent the attenuated viruses from mutating back into a more aggressive variant,” explains Dr. Dusan Kunec, a scientist at the Institute of Virology at Freie Universität Berlin and another co-last author of the study. “This makes our live vaccine entirely safe and means it can be tailored to new virus variants,” stresses Kunec, who was instrumental in developing the vaccine.

The next step is safety testing: The researchers are collaborating with RocketVax AG, a Swiss start-up based in Basel. The biotech company is developing the live attenuated SARS-CoV-2 vaccine and preparing a phase 1 clinical trial in humans. “We are thrilled to be at the forefront of developing and manufacturing the live attenuated SARS-CoV-2 vaccine as a nasal spray at RocketVax. Our goal is to rapidly scale-up production and advance clinical development towards market access to provide protection against post-COVID symptoms for all. We see great potential in the market for seasonal nasal vaccines”, says Dr. Vladimir Cmiljanovic, CEO of RocketVax.

The future will show which nasal vaccine will ultimately provide better protection. The manufacturers of the nasal adenovirus vaccines developed in India and China have not yet applied for approval in Europe. But one thing is clear to the scientists: since they are administered as nasal sprays or drops, nasal vaccines are a good option for use in places with limited access to trained medical staff. They are also inexpensive to produce and easy to store and transport. Last but not least, live attenuated vaccines such as this one have been proven to provide cross-protection against related viral strains, and thus presumably also against future SARS-CoV-2 variants.

Source:

Max Delbrück Center for Molecular Medicine in the Helmholtz Association

Journal reference:

Nouailles, G., et al. (2023). Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nature Microbiology. doi.org/10.1038/s41564-023-01352-8

Microbiology

Lupus, Sepsis, and More: Scientists Uncover Promising New Therapeutic Target for Inflammatory Diseases

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What goes wrong in our bodies during the progression of an inflammatory disease? Scientists at the School of Biochemistry and Immunology in the Trinity Biomedical Sciences Institute at Trinity College Dublin have made a significant advancement in comprehending the underlying mechanisms of the progression of inflammatory diseases. The discovery has uncovered a promising new target for therapeutic intervention.

The researchers have discovered that the repression of an enzyme called Fumarate Hydratase occurs in macrophages, which are a type of inflammatory cell that play a role in various diseases such as Lupus, Arthritis, Sepsis, and COVID-19.

Professor Luke O’Neill, Professor of Biochemistry at Trinity is the lead author of the research article that has just been published in the leading international journal, Nature.

He said: “No one has made a link from Fumarate Hydratase to inflammatory macrophages before and we feel that this process might be targetable to treat debilitating diseases like Lupus, which is a nasty autoimmune disease that damages several parts of the body including the skin, kidneys, and joints.”

Joint first-author Christian Peace added: “We have made an important link between Fumarate Hydratase and immune proteins called cytokines that mediate inflammatory diseases. We found that when Fumarate Hydratase is repressed, RNA is released from mitochondria which can bind to key proteins ‘MDA5’ and ‘TLR7’ and trigger the release of cytokines, thereby worsening inflammation. This process could potentially be targeted therapeutically.”

Fumarate Hydratase was shown to be repressed in a model of sepsis, an often-fatal systemic inflammatory condition that can happen during bacterial and viral infections. Similarly, in blood samples from patients with Lupus, Fumarate Hydratase was dramatically decreased.

“Restoring Fumarate Hydratase in these diseases or targeting MDA5 or TLR7, therefore, presents an exciting prospect for badly needed new anti-inflammatory therapies,” said Prof O’Neill.

Excitingly, this newly published work is accompanied by another publication by a group led by Professor Christian Frezza, now at the University of Cologne, and Dr. Julien Prudent at the MRC Mitochondrial Biology Unit (MBU), who have made similar findings in the context of kidney cancer.

“Because the system can go wrong in certain types of cancer, the scope of any potential therapeutic target could be widened beyond inflammation,” added Prof O’Neill.

Reference: “Macrophage fumarate hydratase restrains mtRNA-mediated interferon production” by Alexander Hooftman, Christian G. Peace, Dylan G. Ryan, Emily A. Day, Ming Yang, Anne F. McGettrick, Maureen Yin, Erica N. Montano, Lihong Huo, Juliana E. Toller-Kawahisa, Vincent Zecchini, Tristram A. J. Ryan, Alfonso Bolado-Carrancio, Alva M. Casey, Hiran A. Prag, Ana S. H. Costa, Gabriela De Los Santos, Mariko Ishimori, Daniel J. Wallace, Swamy Venuturupalli, Efterpi Nikitopoulou, Norma Frizzell, Cecilia Johansson, Alexander Von Kriegsheim, Michael P. Murphy, Caroline Jefferies, Christian Frezza and Luke A. J. O’Neill, 8 March 2023, Nature.
DOI: 10.1038/s41586-023-05720-6

The Trinity study is a collaboration between eight universities including the MRC MBU, University of Cambridge where Dr. Dylan Ryan is co-first author along with Dr. Alex Hooftman, who is now based at the Swiss Federal Institute of Technology Lausanne. Cedars Sinai Medical Centre in Los Angeles is another key collaborator helping with the study of Lupus patients.

The study was funded by the European Research Council, Medical Research Council, and Science Foundation Ireland. Work in the Frezza lab is also supported by the ERC, further illustrating the importance of ERC funding for EU science.

Trinity College Dublin

Microbiology

NIH scientists discover an autoinflammatory disease caused by mutations in the LYN gene

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Reviewed by Emily Henderson, B.Sc.Mar 28 2023

Scientists have identified an autoinflammatory disease caused by mutations in the LYN gene, an important regulator of immune responses in health and disease. Named Lyn kinase-associated vasculopathy and liver fibrosis (LAVLI), the identification sheds light on how genes linked to certain illnesses can potentially be targets for treatment by repurposing existing drugs. The research, published in Nature Communications, was led by Adriana A. de Jesus, M.D. Ph.D., and Raphaela Goldbach-Mansky, M.D., M.H.S. of the Translational Autoinflammatory Diseases Section of the Laboratory of Clinical Immunology and Microbiology at the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health.

LAVLI was first discovered in a pediatric patient through genetic testing, which detected a mutation in LYN, the gene that encodes the Lyn kinase protein. Two additional, unrelated pediatric patients were later discovered to have two more mutations in the same gene. All three patients developed diseases linked to the LYN genetic mutation shortly after birth. Two patients developed liver fibrosis—excessive amounts of scar tissue caused by inflammation and repeated liver damage—in the first year of life. All three patients had perinatal onset of neutrophilic cutaneous small vessel vasculitis. This is an immune disorder characterized by inflammation from high numbers of neutrophils—white blood cells of the immune system—that can damage small blood vessels.

The study revealed Lyn kinase was always active and unable to shut down in the three patients with the LYN mutation, which increased neutrophil migration, altered inflammatory signals and activated scar and fibrosis-inducing liver cells. The results of this study suggest that Lyn kinase may be a potential therapeutic target for drugs that treat forms of non-syndromic small vessel vasculitis and other types of inflammation-induced liver fibrosis.

Source:

National Institutes of Health

Journal reference:

de Jesus, A. A., et al. (2023). Constitutively active Lyn kinase causes a cutaneous small vessel vasculitis and liver fibrosis syndrome. Nature Communications. doi.org/10.1038/s41467-023-36941-y.

Microbiology

Epigenome reprogramming after SARS-CoV-2 infection

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Neha MathurBy Neha MathurMar 27 2023Reviewed by Lily Ramsey, LLM

In a recent article in published in the journal Nature Microbiology, researchers in Texas, United States (US) performed a three-dimensional (3D) evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected human cells to show a direct cell-autonomous effect elicited by SARS-CoV-2 on the host chromatin.

The study aimed at improving the understanding of coronavirus disease 2019 (COVID-19)-related perturbations in the genome and epigenome of a host cell.

Study: SARS-CoV-2 restructures host chromatin architecture. Image Credit:FUNFUNPHOTO/Shutterstock.com

Study: SARS-CoV-2 restructures host chromatin architecture. Image Credit:FUNFUNPHOTO/Shutterstock.com

Background

The 3D folding of chromatin in mammals, including humans, influences deoxyribonucleic acid (DNA) replication, recombination, DNA damage repair, and transcription. It is a key determinant of how human cells act and function. Viruses, including SARS-CoV-2, antagonize host defense by rewiring their chromatin architecture, which typically has several layers, e.g., A/B compartments, chromatin loops, and topological associating domains (TADs).

The A and B compartments superimpose transcriptionally active euchromatin and relatively inactive heterochromatin, respectively. However, studies have barely investigated these effects.

In addition, epigenetic alterations impact gene expression and resulting phenotypes in the long term. Thus, a sneak peek into the interactions between the virus, host chromatin, and epigenome could help find novel methods to fight SARS-CoV-2 in the acute phase. In addition, it could unravel the molecular basis of post-acute SARS-CoV-2 sequelae or long COVID and subsequently mitigate it.

About the study

At 24 hours post-infection (24 hpi), human A549 cells expressing angiotensin-converting enzyme 2 (ACE2), infected with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.1, had high levels of infection. This was shown by ribonucleic acid-sequencing (RNA-seq). Immunofluorescence of the SARS-CoV-2 spike (S) glycoprotein also substantiated an elevated infection ratio.

So, in the present study, researchers used an improved version of in situ Hi-C high-throughput chromosome conformation capture (Hi-C) 3.0 to study host chromatin changes in these cells at 24 hpi and mock-infected cells (Mock).

In addition, the team evaluated the epigenetic features of the altered chromatin regions to understand the vulnerability to compartmental changes due to infection. To this end, they used chromatin immunoprecipitation (ChIP-seq) methods to generate data on representative histone markers and polymerase II (Pol2) in A549-ACE2 cells. This analysis covered four histone markers, viz., H3K27ac, H3K4me3, H3K9me3, and H3K27me3.

It helped them examine the epigenetic features of these six categories of bins. They ranked E1-score changes for each genomic bin to sort bins. They dubbed bins showing E1-score increase and decrease as ‘A-ing’ and ‘B-ing’ bins, respectively.

Results

The Hi-C analysis showed extensive alterations in the hosts’ 3D genome after SARS-CoV-2 infection. The researchers also plotted a Pearson correlation map of their Hi-C analysis that reaffirmed these changes alongside indicating modified chromatin compartmentalization.

A focused view of the ~0.7 Mb region showed a weakening of the rectangle-shaped chromatin domains and deregulation of chromatin loops. While SARS-CoV-2 prompted a global decline in near-diagonal short-range chromatin contacts (<560 kilobases), as seen in a P(s) curve, chromatin contacts far-separated from the diagonal (>28 megabases) were often deregulated.

Further, a P(s) curve showed that SARS-CoV-2 elicited modest and enhanced interactions in middle-to-long-distance contacts (~560 kb to 8.9 Mb) and far-positioned regions, respectively.

Fold changes in inter-chromosomal interactions or trans-vs-cis contact ratios also depicted the effect of SARS-CoV-2 infection on inter-chromosomal contacts. The enhancement of inter- and intra-chromosomal interactions indicated changes in chromatin compartmentalization. Consequently, principal component analysis (PCA) of a 100-kb bin on Hi-C background showed noticeable defects of chromatin compartmentalization in virus-infected cells.

The total PCA E1 scores quantifying E1 changes in ~30% of genomic regions showed a widespread diminishing of the A compartment, A-to-B switching, or strengthening of the B compartment post-SARS-CoV-2 infection.

Among all, A to weaker A changes were the most common and occurred in ~18% of the genome, which indicated that SARS-CoV-2 extensively weakened the host euchromatin.

Further analysis showed that the ‘B-ing’ and ‘A-ing’ genomic regions were historically enriched in active chromatin markers (e.g., H3K27ac) and repressive histone markers, especially H3K27me3. Unexpectedly, SARS-CoV-2 infection selectively modified the H3K4me3 marker of phytochrome interacting factors (PIF) gene promoters, suggesting unappreciated mechanisms at these promoters that confer deviating inflammation in COVID-19.

A flawed chromatin compartmentalization likely caused the historically well-partitioned A or B compartments to lose their identity. A saddle plot illustrating inter-compartment chromatin interactions across the genome showed these global changes.

The authors also noted weakened compartmentalization between chromosomes. For instance, in chromosomes 17 & 18, while A–B interactions were amplified, A–A/B–B homotypic interactions appeared to have become compromised.

Moreover, SARS-CoV-2 infection mechanistically depleted the cohesin complex in a pervasive but selective manner from intra-TAD regions. These changes provided a molecular explanation for the weakening of intra-TAD interactions.

It supported the notion that defective cohesin loop extrusion inside TADs releases this chromatin to engage in long-distance associations. Intriguingly, chromatin in SARS-CoV-2-infected cells exhibited a higher frequency of long-distance intra-chromosomal and inter-chromosomal interactions.

Conclusions

SARS-CoV-2 infection markedly restructured 3D host chromatin, featuring widespread compartment A weakening and A–B mixing and global reduction in intra-TAD chromatin contacts.

However, it is still unknown exactly how SARS-COV-2 infection restructures host chromatin. Likely, open reading frame 8 (ORF8) disrupts the host epigenome, suggesting that some viral factors are involved in host chromatin rewiring.

It also altered the host epigenome, including a global reduction in active chromatin mark H3K27ac and a specific increase in H3K4me3 at pro-inflammatory gene promoters. Intriguingly, all these host chromatin alterations were unique to SARS-CoV-2 infection, and other common-cold coronaviruses or immune stimuli did not elicit these changes.

Journal reference:
Microbiology

Tulane receives up to $16 million to move nasal pneumonia vaccine from the lab to clinical trials

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Reviewed by Emily Henderson, B.Sc.Mar 24 2023

The National Institute of Allergy and Infectious Diseases awarded an up to $16 million contract to Tulane University to bring to phase one clinical trial a nasal spray vaccine university researchers invented to thwart antibiotic-resistant Klebsiella pneumoniae, a leading cause of pneumonia.

Antibiotic-resistant bacteria are on the rise and are a significant cause of infections requiring hospitalization among children and the elderly. As doctors try to find new types of antibiotics to fight these so-called superbugs, Tulane University School of Medicine researchers Elizabeth Norton, PhD, and Jay Kolls, MD, inventors of the vaccine, are working to protect people before they are exposed to the pathogens in the first place.

“Multidrug-resistant bacteria are causing more severe infections and are a growing public health threat. Vaccines targeting these pathogens represent the most cost-effective option, particularly if you can use this vaccine to prevent or treat the infection in high-risk individuals,” said Norton, principal investigator and associate professor of microbiology and immunology. “Right now, there is no vaccine on the market that targets this type of pneumonia.”

Klebsiella pneumoniae is the third leading cause of hospital-acquired pneumonia and the second leading cause of bloodstream infections with the highest incidence of serious infections. It is also a major cause of childhood pneumonia in parts of Asia. The Tulane vaccine would target high-risk populations such as immunocompromised individuals, diabetics or organ transplant recipients.

Norton said that while the vaccine targets the Klebsiella bacteria, its unique design gives it the potential to be cross-reactive to other members of the Enterobacteriaceae family, the antibiotic-resistant bacterial species behind many hospital-acquired infections, including E. coli.

The vaccine, called CladeVax, is designed to efficiently target mucosa in the nose, throat and lungs to protect the area most at risk for infection.

The nasal spray vaccine uses an adjuvant -; a compound that stimulates the immune system -; named LTA1 that Norton developed at Tulane. That adjuvant, which is made using a protein derived from the E. coli bacteria, will be combined with a series of proprietary antigens identified by the Kolls lab that include outer membrane proteins from the target bacteria.

This is an entirely novel vaccine platform, from the use of the adjuvant to the needle-less route of administration. This represents an entirely new class of vaccines for bacteria that elicits protection in two ways -; both antibody and T-cell immunity. All current pneumonia vaccines only elicit antibodies against surface carbohydrates. Our platform has the potential advantage of providing a much broader protection against pneumonia.”

Jay Kolls, co-principal investigator, and the John W. Deming Endowed Chair in Internal Medicine

Tulane researchers will first test vaccine formulations in animal models and nonhuman primates for dosing and safety before advancing to clinical trials. The project will include collaborators at Tulane National Primate Research Center, the School of Public Health and Tropical Medicine, Tulane Clinical Translational Unit, and the University of North Carolina as well as contractors for GMP manufacturing.

“If this succeeds, we will have another arsenal for the growing number of antibiotic resistant sources of pneumonia or bloodstream infections,” Norton said. “And we can hopefully expand this nasal spray delivery platform to other infections, working on a single, combination vaccine that is needle-less and targets several organisms at once.”

Source:

Tulane University

Microbiology

Vaginal sex can shape the composition of urethral microbiome in healthy men

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Reviewed by Emily Henderson, B.Sc.Mar 21 2023

Contrary to common beliefs, your urine is not germ free. In fact, a new study shows that the urethra of healthy men is teeming with microbial life and that a specific activity-;vaginal sex-;can shape its composition. The research, published March 24 in the journal Cell Reports Medicine, provides a healthy baseline for clinicians and scientists to contrast between healthy and diseased states of the urethra, an entrance to the urinary and reproductive systems.

We know where bugs in the gut come from; they primarily come from our surroundings through fecal-oral transfer. But where does genital microbiology come from?”

David Nelson, co-senior author, microbiologist at Indiana University

To flush out the answer, the team of microbiologists, statisticians, and physicians sequenced the penile urethra swabs of 110 healthy adult men. These participants had no urethral symptoms or sexually transmitted infections (STIs) and no inflammation of the urethra. DNA sequencing results revealed that two types of bacterial communities call the penile urethra home-;one native to the organ, the other from a foreign source.

“It is important to set this baseline,” says co-senior author Qunfeng Dong, a bioinformatician at Loyola University Chicago. “Only by understanding what health is can we define what diseases are.”

The researchers found that most of the healthy men had a simple, sparse community of oxygen-loving bacteria in the urethra. In addition, these bacteria probably live close to the urethral opening at the tip of the penis, where there is ample oxygen. The consistent findings of these bacteria suggest that they are the core community that supports penile urethra health.

But some of the men also had a more complex secondary group of bacteria that are often found in the vagina and can disturb the healthy bacterial ecosystem of the vagina. The team speculates that these bacteria reside deeper in the penile urethra because they thrive in oxygen-scarce settings. Only men who reported having vaginal sex carry these bacteria, hinting at the microbes’ origins.

Delving into the participant’s sexual history, the team found a close link between this second bacterial community and vaginal sex but not other sexual behaviors, such as oral sex and anal sex. They also found evidence that vaginal sex has lasting effects. Vagina-associated bacteria remained detectable in the participants for at least two months after vaginal sex, indicating that sexual exposure to the vagina can reshape the male urinary-tract microbiome.

“In our study, one behavior explains 10% of the overall bacterial variation,” says Nelson, when discussing the influence of vaginal sex. “The fact that a specific behavior is such a strong determinant is just profound.”

Although current findings from the study show that vaginal bacteria can spread to the penile urethra, the team’s next plan is to test whether the reverse is true. Using the newly established baseline, the researchers also hope to offer new insights into bacteria’s role in urinary- and reproductive-tract diseases, including unexplained urethral inflammation and STIs.

“STIs really impact people who are socioeconomically disadvantaged; they disproportionately impact women and minorities,” says Nelson. “It’s a part of health care that’s overlooked because of stigma. I think our study has a potential to dramatically change how we handle STI diagnosis and management in a positive way.”

This work was supported by the National Institute of Allergy and Infectious Diseases.

Source:

Cell Press

Journal reference:

Toh, E., et al. (2023). Sexual behavior shapes male genitourinary microbiome composition. Cell Reports Medicine. doi.org/10.1016/j.xcrm.2023.100981

Microbiology

New Study Reveals How Heavy Alcohol Consumption Increases Brain Inflammation

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People with alcohol use disorder (AUD) experience a never-ending vicious cycle of changes in the brain and behavior. AUD can disrupt communication pathways in the brain, leading to an escalation of drinking behavior and further exacerbating the condition.

Scientists at Scripps Research have uncovered new insights into the role of the immune system in the cycle of alcohol use disorder (AUD). In a study published in Brain, Behavior, and Immunity, they found that the levels of the immune signaling molecule interleukin 1β (IL-1β) are elevated in the brains of mice with alcohol dependence. Furthermore, the IL-1β pathway operates differently in these mice, leading to inflammation in crucial regions of the brain that are associated with decision-making.

“These inflammatory changes to the brain could explain some of the risky decision-making and impulsivity we see in people with alcohol use disorder,” says senior author Marisa Roberto, Ph.D., the Schimmel Family Chair of Molecular Medicine and a professor of neuroscience at Scripps Research. “In addition, our findings are incredibly exciting because they suggest a potential way to treat alcohol use disorder with existing anti-inflammatory drugs targeting the IL-1β pathway.”

AUD is characterized by uncontrolled and compulsive drinking, and it encompasses a range of conditions including alcohol abuse, dependence, and binge drinking. Researchers have previously discovered numerous links between the immune system and AUD—many of them centered around IL-1β. People with certain mutations in the gene that codes for the IL-1β molecule, for instance, are more prone to developing AUD. In addition, autopsies of people who had AUD have found higher levels of IL-1β in the brain.

“We suspected that IL-1β was playing a role in AUD, but the exact mechanisms in the brain have been unclear,” says first author Florence Varodayan, Ph.D., an assistant professor at Binghamton University and former postdoctoral fellow in the Roberto lab.

In the new study, Roberto, Varodayan, and their colleagues compared alcohol-dependent mice with animals drinking moderate or no alcohol at all. They discovered that the alcohol-dependent group had about twice as much IL-1β in the medial prefrontal cortex (mPFC), a part of the brain that plays a role in regulating emotions and behaviors.

The team then went on to show that IL-1β signaling in the alcohol-dependent group was not only increased but also fundamentally different. In mice that had not been exposed to alcohol, as well as in mice that had drunk moderate amounts of alcohol, IL-1β activated an anti-inflammatory signaling pathway. In turn, this lowered levels of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA), a signaling molecule known to regulate neural activity in the brain.

However, in alcohol-dependent mice, IL-1β instead activated pro-inflammatory signaling and boosted levels of GABA, likely contributing to some of the changes in brain activity associated with AUD. Notably, these changes in IL-1β signaling in the alcohol-dependent mice persisted even during alcohol withdrawal.

Drugs that block the activity of IL-1β are already approved by the U.S. Food and Drug Administration to treat rheumatoid arthritis and other inflammatory conditions. More work is needed to determine whether these existing drugs could have utility in treating AUD.

“We plan to follow up on this study with more work on exactly how targeting specific components of the IL-1β pathway might be useful in treating alcohol use disorder,” says Roberto.

Reference: “Chronic ethanol induces a pro-inflammatory switch in interleukin-1β regulation of GABAergic signaling in the medial prefrontal cortex of male mice” by F.P. Varodayan, A.R. Pahng, T.D. Davis, P. Gandhi, M. Bajo, M.Q. Steinman, W.B. Kiosses, Y.A. Blednov, M.D. Burkart, S. Edwards, A.J. Roberts and M. Roberto, 28 February 2023, Brain, Behavior, and Immunity.
DOI: 10.1016/j.bbi.2023.02.020

The study was funded by the National Institutes of Health, The Schimmel Family Chair, The Pearson Center for Alcoholism and Addiction Research, and The Scripps Research Institute’s Animal Models Core Facility.

Scripps Research Institute

Microbiology

Top 5 Health Benefits of Cinnamon: Heart, Diabetes, Inflammation, Weight Loss, Brain

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Cinnamon is a spice that has been used for centuries in traditional medicine and cooking. It is derived from the bark of several trees in the Cinnamomum family and is known for its warm, sweet flavor. In addition to its culinary uses, cinnamon is also known for its numerous health benefits. You can even find cinnamon in supplement form as capsules, often with the active molecule cinnamaldehyde in a concentrated form. In this article, you’ll learn the major ways in which cinnamon can improve your health.

Cinnamon has been shown to have a positive effect on cardiovascular health. Studies have found that it can help to lower blood pressure, reduce cholesterol levels, and improve blood sugar control. One study found that consuming just 120 milligrams of cinnamon per day for 12 weeks resulted in a significant reduction in blood pressure.[1]

Cinnamon contains antioxidants that can help to protect the heart from oxidative stress, which is a major contributor to heart disease. By reducing oxidative stress, cinnamon can help to reduce inflammation in the arteries. In turn, this improves blood flow and reduces the risk of heart attack and stroke.

Cinnamon has even been shown to reduce blood sugar in people with type 2 diabetes. According to a meta-analysis that synthesized the results of 10 studies, cinnamon in doses of 120 mg to 6 g per day effectively reduces fasting glucose levels in people with diabetes within 4 to 18 weeks.[2]

It works by increasing insulin sensitivity. Insulin is the hormone that regulates blood sugar levels. With greater insulin sensitivity, the body can use insulin more effectively. This could potentially help prevent or manage diabetes.

Inflammation is a natural response of the body to injury or infection, but when it becomes chronic, it can lead to a host of health problems, including arthritis, heart disease, and cancer. Cinnamon contains compounds that have anti-inflammatory properties, which can help to reduce inflammation in the body. Studies have shown that cinnamon can reduce the production of inflammatory molecules and inhibit the activity of inflammatory enzymes.[3]

Cinnamon can also help to reduce inflammation in the gut, which is important for maintaining gut health. By reducing inflammation in the gut, cinnamon can help to improve digestion, reduce bloating and gas, and prevent leaky gut syndrome.

Cinnamon can also help to support weight loss. By helping to regulate blood sugar levels, cinnamon can reduce cravings for sugary foods and help to prevent overeating. It can also boost your metabolism, which can help to burn more calories and promote weight loss. A meta-analysis that pooled results from 7 studies found that cinnamon supplementation reduces body weight and body mass index (BMI). It noted the results were more drastic in people who took more than 3 grams of cinnamon per day.[4]

Cinnamon has also been shown to have a positive effect on brain function. One study found that cinnamon can improve cognitive function, including memory and attention span.[5] Another study found that cinnamon can help to protect the brain against age-related decline by increasing the production of proteins that are important for brain health.[6]

Cinnamon can also help to improve mood by increasing the production of serotonin — a neurotransmitter that is important for regulating mood and preventing depression.

Cinnamon is a delicious spice that offers numerous health benefits. Whether you sprinkle it on your oatmeal, add it to your coffee, or use it in your cooking, cinnamon is a great way to give your body a boost. From improving heart health to fighting inflammation, supporting weight loss, and boosting brain function, there are many reasons to make cinnamon a part of your daily routine. Some supplements contain concentrated forms of the active molecule in a spice or herb. If you’re taking a cinnamon supplement, be sure to take no more than the amount recommended on the product’s label.

References:

SciTechDaily.com