Tag Archives: Lymph Nodes

Microbiology

Scientists identify a distinct role of retinoic acid during immune response of the gut

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

A team of scientists from the Renaissance School of Medicine (RSOM) at Stony Brook University have identified a distinct role of retinoic acid, a metabolite of vitamin A, during the immune response of the gut. This finding, detailed in a paper published in the Journal of Experimental Medicine, and highlighted in a broader piece in the journal, could help lead to ways to control the retinoic acid response and therefore be used as a therapy or for vaccine development against infection or even to treat GI tumors.

Led by Brian Sheridan, PhD, Associate Professor in the Department of Microbiology and Immunology and Center for Infectious Diseases, the study involves basic research that centers on unraveling the factors that control the generation of cytotoxic memory CD8 T cells, which are an important arm of the body’s anti-pathogen immune response as they kill pathogen-infected cells and produce anti-pathogen cytokines. In fact, memory CD8 T cells provide long-lived and frontline protection at barrier tissues, highlighting their importance in vaccine design.

To date scientists have known that retinoic acid in the gut-draining lymph nodes promotes effector CD8 T cell migration to the intestines, enhancing the immune response. Additionally, vitamin A deficiency is associated with increased infections and poor vaccine efficiency.

Sheridan and his co-authors, including Zhijuan Qiu, PhD, a post-doctoral fellow in the department, identified a new role for retinoic acid, which is a key part of the immune process in the gut. They demonstrated in the lab that T cell activation in gut-associated lymph nodes regulates memory CD8 T cell differentiation in the intestine. They also demonstrated in contrast that T cells activated at other sites were impaired in the ability to differentiate into memory CD8 T cells after entry into the intestine.

During this process, they demonstrated that activation within the gut-associated lymph nodes, but not in other sites, promotes intestinal memory CD8 T cell development and that retinoic acid signals provided during this window of T cell activation in the lymph nodes enhances intestinal memory CD8 T cell development to a wider degree.

Our study highlights a fundamental new role of T cell activation on the generation of the intestinal memory CD8 T cells that appears distinct from other barrier sites like the lungs and skin. Remarkably, we can alter intestinal T cell development by promoting or limiting retinoic acid signals during T cell activation, independent of the role of retinoic acid on T cell migration.”

Brian Sheridan, PhD, Associate Professor in the Department of Microbiology and Immunology and Center for Infectious Diseases

Because the research team was able to replicate this limiting or promoting of retinoic acid signals in the gut, they believe that manipulating retinoic acid signals during T cell activation may provide a strategy for clinicians to promote or limit intestinal CD8 T cells to improve vaccine outcomes or limit immunopathology.

This research is supported in part by a grant (R01AI172919) from the National Institutes of Health’s National Institute of Allergy and Infectious Diseases (NIAID) to Brian Sheridan.

Source:

Stony Brook University

Journal reference:

Qiu, Z., et al. (2023). Retinoic acid signaling during priming licenses intestinal CD103+ CD8 TRM cell differentiation. Journal of Experimental Medicine. doi.org/10.1084/jem.20210923.

Microbiology

Novel subset of memory B cells predicts long-lived antibody responses to influenza vaccination

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Reviewed by Emily Henderson, B.Sc.Mar 22 2023

Memory B cells play a critical role to provide long-term immunity after a vaccination or infection. In a study published in the journal Immunity, researchers describe a distinct and novel subset of memory B cells that predict long-lived antibody responses to influenza vaccination in humans.

These effector memory B cells appear to be poised for a rapid serum antibody response upon secondary challenge one year later, Anoma Nellore, M.D., Fran Lund, Ph.D., and colleagues at the University of Alabama at Birmingham and Emory University report. Evidence from transcriptional and epigenetic profiling shows that the cells in this subset differ from all previously described memory B cell subsets.

The UAB researchers identified the novel subset by the presence of FcRL5 receptor protein on the cell surface. In immunology, a profusion of different cell-surface markers is used to identify and separate immune-cell types. In the novel memory B cell subset, FcRL5 acts as a surrogate marker for positive expression of the T-bet transcription factor inside the cells. Various transcription factors act as master regulators to orchestrate the expression of many different gene sets as various cell types grow and differentiate.

Nellore, Lund and colleagues found that the FcRL5+ T-bet+ memory B cells can be detected seven days after immunization, and the presence of these cells correlates with vaccine antibody responses months later. Thus, these cells may represent an early, easily monitored cellular compartment that can predict the development of a long-lived antibody response to vaccines.

This could be a boon to the development of a more effective yearly influenza vaccine. “New annual influenza vaccines must be tested, and then manufactured, months in advance of the winter flu season,” Lund said. “This means we must make an educated guess as to which flu strain will be circulating the next winter.”

Why are vaccine candidates made so far in advance? Pharmaceutical companies, Lund says, need to wait many weeks after vaccinating volunteers to learn whether the new vaccine elicits a durable immune response that will last for months. “One potential outcome of the current study is we may have identified a new way to predict influenza vaccine durability that would give us an answer in days, rather than weeks or months,” Lund said. “If so, this type of early ‘biomarker’ could be used to test flu vaccines closer to flu season -; and moving that timeline might give us a better shot at predicting the right flu strain for the new annual vaccine.”

Seasonal flu kills 290,000 to 650,000 people each year, according to World Health Organization estimates. The global flu vaccine market was more than $5 billion in 2020.

To understand the Immunity study, it is useful to remember what happens when a vaccinated person subsequently encounters a flu virus.

Following exposure to previously encountered antigens, such as the hemagglutinin on inactivated influenza in flu vaccines, the immune system launches a recall response dominated by pre-existing memory B cells that can either produce new daughter cells or cells that can rapidly proliferate and differentiate into short-lived plasmablasts that produce antibodies to decrease morbidity and mortality. These latter B cells are called “effector” memory B cells.

“The best vaccines induce the formation of long-lived plasma cells and memory B cells,” said Lund, the Charles H. McCauley Professor in the UAB Department of Microbiology and director of the Immunology Institute. “Plasma cells live in your bone marrow and make protective antibodies that can be found in your blood, while memory B cells live for many years in your lymph nodes and in tissues like your lungs.

“Although plasma cells can survive for decades after vaccines like the measles vaccine, other plasma cells wane much more quickly after vaccination, as is seen with COVID-19,” Lund said. “If that happens, memory B cells become very important because these long-lived cells can rapidly respond to infection and can quickly begin making antibody.”

In the study, the UAB researchers looked at B cells isolated from blood of human volunteers who received flu vaccines over a span of three years, as well as B cells from tonsil tissue obtained after tonsillectomies.

They compared naïve B cells, FcRL5+ T-bet+ hemagglutinin-specific memory B cells, FcRL5neg T-betneg hemagglutinin-specific memory B cells and antibody secreting B cells, using standard phenotype profiling and single-cell RNA sequencing. They found that the FcRL5+ T-bet+ hemagglutinin-specific memory B cells were transcriptionally similar to effector-like memory cells, while the FcRL5neg T-betneg hemagglutinin-specific memory B cells exhibited stem-like central memory properties.

Antibody-secreting B cells need to produce a lot of energy to churn out antibody production, and they also must turn on processes that protect the cells from some of the detrimental side effects of that intense metabolism, including controlling the dangerous reactive oxygen species and boosting the unfolded protein response.

The FcRL5+ T-bet+ hemagglutinin-specific memory B cells did not express the plasma cell commitment factor, but did express transcriptional, epigenetic and metabolic functional programs that poised these cells for antibody production. These included upregulated genes for energy-intensive metabolic processes and cellular stress responses.

Accordingly, FcRL5+ T-bet+ hemagglutinin-specific memory B cells at Day 7 post-vaccination expressed intracellular immunoglobulin, a sign of early transition to antibody-secreting cells. Furthermore, human tonsil-derived FcRL5+ T-bet+ memory B differentiated more rapidly into antibody-secreting cells in vitro than did FcRL5neg T-betneg hemagglutinin-specific memory B cells.

Lund and Nellore, an associate professor in the UAB Department of Medicine Division of Infectious Diseases, are co-corresponding authors of the study, “A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans.”

Co-authors with Lund and Nellore are Esther Zumaquero, R. Glenn King, Betty Mousseau, Fen Zhou and Alexander F. Rosenberg, UAB Department of Microbiology; Christopher D. Scharer, Tian Mi, Jeremy M. Boss, Christopher M. Tipton and Ignacio Sanz, Emory University School of Medicine, Atlanta, Georgia; Christopher F. Fucile, UAB Informatics Institute; John E. Bradley and Troy D. Randall, UAB Department of Medicine, Division of Clinical Immunology and Rheumatology; and Stuti Mutneja and Paul A. Goepfert, UAB Department of Medicine Division of Infectious Diseases.

Funding for the work came from National Institutes of Health grants AI125180, AI109962 and AI142737 and from the UAB Center for Clinical and Translational Science.

Source:

University of Alabama at Birmingham

Journal reference:

Nellore, A., et al. (2023). A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans. Immunity. doi.org/10.1016/j.immuni.2023.03.001.

Microbiology

Leaving lymph nodes intact until after immunotherapy could boost efficacy against solid tumors

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Reviewed by Emily Henderson, B.Sc.Mar 20 2023

Cancer treatment routinely involves taking out lymph nodes near the tumor in case they contain metastatic cancer cells. But new findings from a clinical trial by researchers at UC San Francisco and Gladstone Institutes shows that immunotherapy can activate tumor-fighting T cells in nearby lymph nodes.

The study, published March 16, 2023 in Cell, suggests that leaving lymph nodes intact until after immunotherapy could boost efficacy against solid tumors, only a small fraction of which currently respond to these newer types of treatments.

Most immunotherapies are aimed only at reinvigorating T cells in the tumor, where they often become exhausted battling the tumor’s cancer cells. But the new research shows that allowing the treatment to activate the immune response of the lymph nodes as well can play an important role in driving positive response to immunotherapy.

This work really changes our thinking about the importance of keeping lymph nodes in the body during treatment.”

Matt Spitzer, PhD, investigator for the Parker Institute for Cancer Immunotherapy and Gladstone-UCSF Institute of Genomic Immunology and senior author of the study

Lymph nodes are often removed because they are typically the first place metastatic cancer cells appear, and without surgery, it can be difficult to determine whether the nodes contain metastases.

“Immunotherapy is designed to jump start the immune response, but when we take out nearby lymph nodes before treatment, we’re essentially removing the key locations where T cells live and can be activated,” Spitzer said, noting that the evidence supporting the removal of lymph nodes is from older studies that predate the use of today’s immunotherapies.

Aim for the lymph nodes, not the tumor

Researchers have largely been working under the assumption that cancer immunotherapy works by stimulating the immune cells within the tumor, Spitzer said. But in a 2017 study in mice, Spitzer showed that immunotherapy drugs are actually activating the lymph nodes.

“That study changed our understanding of how these therapies might be working,” said Spitzer. Rather than the immunotherapy pumping up the T cells in the tumor, he said, T cells in the lymph nodes are likely the source for T cells circulating in the blood. Such circulating cells can then go into the tumor and kill off the cancer cells.

Having shown that intact lymph nodes can temper cancer’s hold in mice, Spitzer’s team wanted to know whether the same would prove true in human patients. They chose to design a trial for patients with head and neck cancers because of the high number of lymph nodes in those areas.

The trial enrolled 12 patients whose tumors hadn’t yet metastasized past the lymph nodes. Typically, such patients would undergo surgery to remove the tumor, followed by other treatments if recommended.

Instead, patients received a single cycle of an immunotherapy drug called atezolizumab (anti-PD-L1) that is produced by Genentech, a sponsor of the trial. A week or two later, Spitzer’s team measured how much the treatment activated the patients’ immune systems.

The treatment also included surgically removing each patient’s tumor and nearby lymph nodes after immunotherapy and analyzing how the immunotherapy affected them.

The team found that, after immunotherapy, the cancer-killing T cells in the lymph nodes began springing into action. They also found higher numbers of related immune cells in the patients’ blood.

Spitzer attributes some of the trial’s success to its design, which allowed the team to get a lot of information from a small number of patients by looking at the tissue before and after surgery and running detailed analyses.

“Being able to collect the tissue from surgery shortly after the patients had been given the drug was a really unique opportunity,” he said. “We were able to see, at the cellular level, what the drug was doing to the immune response.”

That kind of insight would be challenging to get from a more traditional trial in patients with later-stage disease, who would not typically benefit from undergoing surgery after immunotherapy.

Metastases inhibit immune response

Another benefit of the study design was that it allowed researchers to compare how the treatment affected lymph nodes with and without metastases, or a second cancer growth.

“No one had looked at metastatic lymph nodes in this way before,” said Spitzer. “We could see that the metastases impaired the immune response relative to what we saw in the healthy lymph nodes.”

It could be that the T cells in these metastatic nodes were less activated by the therapy, Spitzer said. If so, that could explain, in part, the poor performance of some immunotherapy treatments.

Still, the therapy prompted enough T-cell activity in the metastatic lymph nodes to consider leaving them in for a short period of time until treatment ends. “Removing lymph nodes with metastatic cancer cells is probably still important but taking them out before immunotherapy treatment may be throwing the baby out with the bathwater,” said Spitzer.

A subsequent goal of the current trial is to determine whether giving immunotherapy before surgery protects against the recurrence of tumors in the future. Researchers won’t know the answer to that until they’ve had a chance to monitor the participants for several years.

“My hope is that if we can activate a good immune response before the tumor is taken out, all those T cells will stay in the body and recognize cancer cells if they come back,” Spitzer said.

Next, the team plans to study better treatments for patients with metastatic lymph nodes, using drugs that would be more effective at reactivating their immune responses.

Source:

University of California – San Francisco

Journal reference:

Rahim, M. K., et al. (2023). Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes. Cell. doi.org/10.1016/j.cell.2023.02.021

Microbiology

Host immune system forms small lesions in the intestines in response to bacterial infection

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Reviewed by Emily Henderson, B.Sc.Mar 14 2023

Yersinia bacteria cause a variety of human and animal diseases, the most notorious being the plague, caused by Yersinia pestis. A relative, Yersinia pseudotuberculosis, causes gastrointestinal illness and is less deadly but naturally infects both mice and humans, making it a useful model for studying its interactions with the immune system.

These two pathogens, as well as a third close cousin, Y. enterocolitica, which affects swine and can cause food-borne illness if people consume infected meat, have many traits in common, particularly their knack for interfering with the immune system’s ability to respond to infection.

The plague pathogen is blood-borne and transmitted by infected fleas. Infection with the other two depends on ingestion. Yet the focus of much of the work in the field had been on interactions of Yersinia with lymphoid tissues, rather than the intestine. A new study of Y. pseudotuberculosis led by a team from Penn’s School of Veterinary Medicine and published in Nature Microbiology demonstrates that, in response to infection, the host immune system forms small, walled-off lesions in the intestines called granulomas. It’s the first time these organized collections of immune cells have been found in the intestines in response to Yersinia infections.

The team went on to show that monocytes, a type of immune cell, sustain these granulomas. Without them, the granulomas deteriorated, allowing the mice to be overtaken by Yersinia.

“Our data reveal a previously unappreciated site where Yersinia can colonize and the immune system is engaged,” says Igor Brodsky, senior author on the work and a professor and chair of pathobiology at Penn Vet. “These granulomas form in order to control the bacterial infection in the intestines. And we show that if they don’t form or fail to be maintained, the bacteria are able to overcome the control of the immune system and cause greater systemic infection.”

The findings have implications for developing new therapies that leverage the host immune system, Brodsky says. A drug that harnessed the power of immune cells to not only keep Yersinia in check but to overcome its defenses, they say, could potentially eliminate the pathogen altogether.

A novel battlefield

Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica share a keen ability to evade immune detection.

“In all three Yersinia infections, a hallmark is that they colonize lymphoid tissues and are able to escape immune control and replicate, cause disease, and spread,” Brodsky says.

Earlier studies had shown that Yersinia prompted the formation of granulomas in the lymph nodes and spleen but had never observed them in the intestines until Daniel Sorobetea, a research fellow in Brodsky’s group, took a closer look at the intestines of mice infected with Y. pseudotuberculosis.

“Because it’s an orally acquired pathogen, we were interested in how the bacteria behaved in the intestines,” Brodsky says. “Daniel made this initial observation that, following Yersinia pseudotuberculosis infection, there were macroscopically visible lesions all along the length of the gut that had never been described before.”

The research team, including Sorobetea and later Rina Matsuda, a doctoral student in the lab, saw that these same lesions were present when mice were infected with Y. enterocolitica, forming within five days after an infection.

A biopsy of the intestinal tissues confirmed that the lesions were a type of granuloma, known as a pyogranuloma, composed of a variety of immune cells, including monocytes and neutrophils, another type of white blood cell that is part of the body’s front line in fighting bacteria and viruses.

Granulomas form in other diseases that involve chronic infection, including tuberculosis, for which Y. pseudotuberculosis is named. Somewhat paradoxically, these granulomas-;while key in controlling infection by walling off the infectious agent-;also sustain a population of the pathogen within those walls.

The team wanted to understand how these granulomas were both formed and maintained, working with mice lacking monocytes as well as animals treated with an antibody that depletes monocytes. In the animals lacking monocytes “these granulomas, with their distinct architecture, wouldn’t form,” Brodsky says.

Instead, a more disorganized and necrotic abscess developed, neutrophils failed to be activated, and the mice were less able to control the invading bacteria. These animals experienced higher levels of bacteria in their intestines and succumbed to their infections.

Groundwork for the future

The researchers believe the monocytes are responsible for recruiting neutrophils to the site of infection and thus launching the formation of the granuloma, helping to control the bacteria. This leading role for monocytes may exist beyond the intestines, the researchers believe.

We hypothesize that it’s a general role for the monocytes in other tissues as well.”

Igor Brodsky, senior author

But the discoveries also point to the intestines as a key site of engagement between the immune system and Yersinia.

“Previous to this study we knew of Peyer’s patches to be the primary site where the body interacts with the outside environment through the mucosal tissue of the intestines,” says Brodsky. Peyer’s patches are small areas of lymphoid tissue present in the intestines that serve to regulate the microbiome and fend off infection.

In future work, Brodsky and colleagues hope to continue to piece together the mechanism by which monocytes and neutrophils contain the bacteria, an effort they’re pursing in collaboration with Sunny Shin’s lab in the Perelman School of Medicine’s microbiology department.

A deeper understanding of the molecular pathways that regulate this immune response could one day offer inroads into host-directed immune therapies, by which a drug could tip the scales in favor of the host immune system, unleashing its might to fully eradicate the bacteria rather than simply corralling them in granulomas.

“These therapies have caused an explosion of excitement in the cancer field,” Brodsky says, “the idea of reinvigorating the immune system. Conceptually we can also think about how to coax the immune system to be reinvigorated to attack pathogens in these settings of chronic infection as well.”

Source:

University of Pennsylvania

Journal reference:

Sorobetea, D., et al. (2023). Inflammatory monocytes promote granuloma control of Yersinia infection. Nature Microbiology. doi.org/10.1038/s41564-023-01338-6.

Microbiology

Healthy gut bacteria can travel to other parts of the body and boost antitumor immunity

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

Researchers at UT Southwestern Medical Center have discovered how healthy bacteria can escape the intestine, travel to lymph nodes and cancerous tumors elsewhere in the body, and boost the effectiveness of certain immunotherapy drugs. The findings, published in Science Immunology, shed light on why antibiotics can weaken the effect of immunotherapies and could lead to new cancer treatments.

Scientists have been stumped as to how bacteria inside your gut can have an impact on a cancer in your lungs, breasts, or skin. Now we understand that mechanism much better and, in the future, hope to use this knowledge to better fight cancer.”

Andrew Y. Koh, M.D., Associate Professor of Pediatrics, Microbiology, and in the Harold C. Simmons Comprehensive Cancer Center at UT Southwestern

Previous studies, including one led by Dr. Koh at UT Southwestern, have shown an association between the composition of gut microbiomes – the microorganisms found inside the digestive tract – and the effectiveness of cancer treatments that target the immune system, including pembrolizumab (Keytruda) and ipilimumab (Yervoy). However, researchers have reached conflicting conclusions about the ideal balance of microorganisms to optimize therapy, with studies pointing to different beneficial bacteria.

Dr. Koh and colleagues used mice with melanoma tumors to probe how the drugs, called immune checkpoint inhibitors, affected the movement of gut microbes through the body. They found that immune checkpoint inhibitors, which boost the activity of the immune system against tumors, also cause inflammation in the digestive system that leads to remodeling of lymph nodes in the gut.

Due to these changes, bacteria can leave the intestines and travel to lymph nodes near the tumor and the tumor itself, the researchers found. Here, the microbes activate a set of immune cells that act to kill tumor cells.

“Immune checkpoint inhibitors work by releasing the brakes on the immune system to target cancer,” said Dr. Koh, who is also Director of the Cellular and ImmunoTherapeutics Program at UTSW and Children’s Health. “What we think is that these microorganisms and the immune cells they’re activating are essentially pressing on the accelerator of the immune system at the same time.”

The findings suggest that a course of antibiotics, which can eliminate most gut microbes, is detrimental to immune checkpoint inhibitors because the bacteria can no longer play this role of immune accelerant. It also helps explain why researchers have found many types of bacteria in patient microbiomes that seem to be beneficial for treatment.

“As long as a subset of beneficial bacteria can translocate from the gut to the lymph node or tumor, it may not matter exactly which bacteria it is,” said Dr. Koh.

Dr. Koh’s team is now working toward the development of bacterial-based treatments to boost the efficacy of immune checkpoint inhibitors.

Other UTSW researchers who contributed to the study include first author and UTSW graduate student Yongbin Choi, Lora Hooper, Jake Lichterman, Laura Coughlin, Nicole Poulides, Wenling Li, Priscilla Del Valle, Suzette Palmer, Shuheng Gan, Jiwoong Kim, Xiaowei Zhan, Yajing Gao, and Bret Evers.

Dr. Hooper, a Howard Hughes Medical Institute Investigator, holds the Jonathan W. Uhr, M.D. Distinguished Chair in Immunology and is a Nancy Cain and Jeffrey A. Marcus Scholar in Medical Research, in honor of Dr. Bill S. Vowell.

The research was supported by funding from the National Institutes of Health (R01 CA231303, K24 AI123163, R01 DK070855), the Crow Family Fund, the UT Southwestern Medical Center and Children’s Health Cellular and ImmunoTherapeutics Program, National Research Service Award-Integrative Immunology Training Grant (5T32AI005284-43), The Welch Foundation (I-1874), and the Howard Hughes Medical Institute.

Source:

UT Southwestern Medical Center

Journal reference:

Choi, Y., et al. (2023) Immune checkpoint blockade induces gut microbiota translocation that augments extraintestinal antitumor immunity. Science Immunology. doi.org/10.1126/sciimmunol.abo2003.

Microbiology

Multi-stage HIV vaccine regimen shows promising results in Phase 1 clinical trial

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Reviewed by Emily Henderson, B.Sc.Dec 8 2022

The George Washington University Vaccine Research Unit in partnership with Scripps Research, IAVI, Fred Hutchinson Cancer Center (FHCC) and the National Institutes of Health, National Institute of Allergy and Infectious Diseases Vaccine Research Center published the results of their Phase 1 Clinical Trial in Science. The results show critical new insights into their novel vaccine strategy, which involves a stepwise approach to producing antibodies capable of targeting a wide range of HIV variants.

The trial, known as IAVI G001, tested the first stage in a multi-stage HIV vaccine regimen the researchers are developing. The trial results show that the vaccine had a favorable safety profile and induced the targeted response in 97% of people who were vaccinated. Importantly, the study also provides a detailed immunological analysis of the vaccine responses.

HIV has continued to be a difficult virus to create a vaccine for given its ability to mutate and quickly evade the immune system. The findings from this trial bring new hope to stopping HIV and may help find vaccines for other difficult infectious diseases as well.”

David Diemert, Professor of Medicine, GWU School of Medicine and Health Sciences

The novel vaccine strategy that was tested in this trial is focused on producing broadly neutralizing antibodies (“bnAbs”), which are a rare type of antibody that can fight and protect against many different variants of a virus, including HIV.

The researchers in the study are using a procedure known as ‘germline targeting’ to eventually produce bnAbs that can protect against HIV. The first step of germline targeting involves stimulating the rare immune cells-;known as bnAb-precursor B cells-;that can evolve into the cells that produce the bnAbs needed to block the virus. To accomplish this, the researchers designed a customized molecule-;known as an immunogen-;that would “prime” the immune system and elicit responses from these rare bnAb-precursor cells.

For this clinical trial, a novel method of sampling lymph nodes was developed by the clinical and biorepository teams at GW, FHCC and IAVI, which included ultrasound-guided fine needle aspiration of lymph nodes near the injection site. “This is the first time such a technique has been used routinely in a vaccine clinical trial,” Jeffrey Bethony, professor of microbiology, immunology and tropical medicine at GW SMHS said. “It enabled us to acquire a cell population critical to germline stimulation that do not circulate but remains sequestered in lymph node tissue.”

The GW VRU has partnered with IAVI on two other HIV vaccine-related Phase I clinical trials over the past five years, serving as a lead site, central biorepository and support unit. In addition, the unit has conducted a number of other clinical vaccine trials to date, including a Phase III trial to test the now FDA-authorized COVID-19 vaccine from biotechnology company Moderna; a Phase II clinical trial for a COVID-19 vaccine booster from the biopharmaceutical company Sanofi; and a Phase I trial of a vaccine to prevent Lassa fever, an acute, animal-borne viral disease endemic to parts of West Africa.

Source:

George Washington University

Microbiology

SARS-CoV-2 detected in white-tailed deer in Canada

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Bhavana KunkalikarBy Bhavana KunkalikarNov 14 2022Reviewed by Aimee Molineux

In a recent study published in Nature Microbiology, researchers investigated the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer.

Study: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Image Credit: Holly Kuchera/Shutterstock
Study: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Image Credit: Holly Kuchera/Shutterstock

Background

Wildlife reservoirs of viruses with a broad host range can facilitate the emergence of human-infecting viral variants. There is phylogenomic evidence of the continuous transmission of SARS-CoV-2 from humans to Odocoileus virginianus or white-tailed deer in North America. However, there is no evidence of viral transmission from deer to humans.

About the study

In the present study, researchers determined the extent of SARS-CoV-2 infection in white-tailed deer and the chances of deer-to-human transmission of the virus.

During the yearly shooting season between 1 November and 31 December 2021, the team sampled 300 white-tailed deer in Eastern and Southwestern Ontario, Canada. Most white-tailed deer in the sample were adults, with equal proportions of males and females. Approximately 213 nose swabs and tissue samples were obtained from 294 retropharyngeal lymph nodes (RPLN). These were analyzed by reverse transcription polymerase chain reaction (RT–PCR) for SARS-CoV-2 ribonucleic acid (RNA).

Three high-quality SARS-CoV-2 consensus genomes were sequenced from five SARS-CoV-2 positive nasal swabs with a standard amplicon-based technique employed to estimate the viral lineage and perhaps deduce significant epidemiological relationships. For confirmation, each sample was extracted and sequenced individually using a capture-probe-based method.

The prevalence of mutations was evaluated in the Global Initiative on Sharing All Influenza Data (GISAID) and within animal-derived variants of concern (VOC) to recognize and contextualize essential mutations. This was achieved using five complete deer-derived sequences along with human-derived sequences.  Viral isolation was performed on Vero E6 cells that expressed human transmembrane protease serine 2 (TMPRSS2) to test the infectivity of the SARS-CoV-2 positive samples.

Results

Out of the 213 nose swabs collected, five tested positive based on the results of two independent RT-PCR analyses conducted at separate institutions. Additionally, 16 RPLNs were validated by PCR. SARS-CoV-2 RNA was found in 21 samples, which accounted for 6% of white-tailed deer harvested by hunters. All SARS-CoV-2 positive animals were adult white-tailed deer found in Southwestern Ontario, with the majority female.

Combining the sequence data obtained from the amplicon and capture-probe led to the recovery of five high-quality genomes with two incomplete genomes. Most of the non-SARS-CoV-2 reads matched that of the reference genome of the white-tailed deer, indicating that contamination with human-derived SARS-CoV-2 sequences was extremely unlikely. The team also noted that the viral genomes derived from the deer samples created a highly divergent clade in the B.1 Phylogenetic Assignment of Named Global Outbreak (PANGO) lineage/20C Nextstrain clade, which had a most recent common ancestor (MRCA).

The Ontario deer lineage constitutes a very lengthy branch having 76 conserved nucleotide mutations compared to those in the SARS-CoV-2 Wuhan Hu-1 strain and 49 as compared to their most recent common ancestor with other GISAID genomes. Human-derived sequences obtained from Michigan, US, were estimated to share an MRCA between May and August 2020 with the Ontario deer lineage. These sequences obtained from humans are closely connected to a mixed clade of mink and human sequences collected in September and October 2020 in Michigan. The white-tailed deer lineage in Ontario has been identified as PANGO lineage B.1.641.

Among the 76 mutations that were similar among the six B.1.641 sequences, nine were in the SARS-CoV-2 spike (S), while 51 were in the open-reading frame (ORF)-1ab. The six nonsynonymous mutations in S include five substitutions and a six-nucleotide deletion. These S mutations, except H49Y, evolved before the divergence of B.1.641 lineage from the MRCA shared by the Michigan samples. Furthermore, only a few S mutations were preserved throughout B.1.641, S:L1265I, and S:613H and were unique to the human sample. Three other nonsynonymous mutations were detected in either 4658 or 4662 white-tailed deer samples, while 4662S:L959 exhibited a frameshift.

The team observed that four days post-infection, four of the samples displayed that 50% or less of the cell monolayer was affected by the cytopathic effect. In comparison to the original swab consensus sequences, confirmatory sequencing revealed only small frequency variations corresponding to one or two single-nucleotide polymorphism (SNP) changes.

Unlike SARS-CoV-2 Omicron, which needed three vaccine doses to neutralize B.1.641S, sera from vaccinated patients who had received two or three doses and sera from convalescent persons effectively neutralized all B.1.641S proteins. Importantly, there was no change in the neutralizing ability of sera against SARS-CoV-2 D614G or other SARS-CoV-2 isolates from Ontario white-tailed deer. Collectively, these findings imply that mutations in the S-gene of the white-tailed deer do not have a significant antigenic effect on antigenicity.

Conclusion

Overall, the study findings highlighted a distinct SARS-CoV-2 lineage in white-tailed deer and provided evidence of host adaptability and transient transfer from deer to humans. White-tailed deer have numerous characteristics essential for a viral reservoir to be sustained, including social behavior, highly transitory populations with multiple human–deer encounters, high density, and sylvatic relationships with other animals.

Journal reference: