Tag Archives: T Cell

Microbiology

First-in-human nanoparticle HIV vaccine induces broad and publicly targeted helper T cell responses

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Reviewed by Lily Ramsey, LLMMay 25 2023

Researchers from Fred Hutchinson Cancer Center in Seattle, Scripps Research in La Jolla, California, IAVI and other collaborating institutions have characterized robust T-cell responses in volunteers participating in the IAVI G001 Phase 1 clinical trial to test the safety and immune response of a self-assembling nanoparticle HIV vaccine.

Their work, published in Science Translational Medicine, signals a major step toward development of a vaccine approach to end the HIV/AIDS epidemic worldwide. The antigen used in this study was jointly developed by IAVI and Scripps Research and has been shown in previous analyses to stimulate VRC01-class B cells, an immune response considered promising enough for boosting in further studies.

We were quite impressed that this vaccine candidate produced such a vigorous T-cell response in almost all trial participants who received the vaccine. These results highlight the potential of this HIV-1 nanoparticle vaccine approach to induce the critical T-cell help needed for maturing antibodies toward the pathway of broadly neutralizing against HIV.”

Julie McElrath, MD, PhD, senior vice president and director of Fred Hutch’s Vaccine and Infectious Disease Division and co-senior author of the study

However, she added, this is the first step, and heterologous booster vaccines will still be needed to eventually produce VRC01-class broadly neutralizing antibodies, which in previous studies have demonstrated the ability to neutralize approximately 90% of HIV strains.

“We showed previously that this vaccine induced the desired B-cell responses from HIV broadly neutralizing antibody precursors. Here we demonstrated strong CD4 T-cell responses, and we went beyond what is normally done by drilling down to identify the T cell epitopes and found several broadly immunogenic epitopes that might be useful for developing boosters and for other vaccines,” William Schief, PhD, executive director of vaccine design for IAVI’s Neutralizing Antibody Center at Scripps Research and professor, Department of Immunology and Microbiology, at Scripps Research, who is co-senior author of the study.

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The trial is a phase 1, randomized, double-blind and placebo-controlled study to evaluate the safety and effectiveness of a nanoparticle HIV vaccine in healthy adult volunteers without HIV. It was comprised of two groups with 18 vaccine and six placebo recipients per group, with 48 total enrollees. Participants were given two doses of the vaccine or placebo eight weeks apart.

McElrath acknowledged the groundbreaking work of her lab team, the biostatistical team and Fred Hutch’s Vaccine Trials Unit for their invaluable contributions to the study. The Vaccine Trials Unit conducts multiple vaccine trials and was one of only two sites for this study.

Findings from the study include:

  • Vaccine-specific CD4 T cells were induced in almost all vaccine recipients.
  • Lymph node GC T follicular helper cells increased after vaccination compared to placebo.
  • Lumazine synthase protein, needed for self-assembly of the particle, also induced T-cell responses that can provide additional help to ultimately enhance efficacy in a sequential vaccine strategy.
  • Vaccine-specific CD4 T cells were polyfunctional and had diverse phenotypes.
  • LumSyn-specific CD8 T cells were highly polyfunctional and had a predominantly effector memory phenotype.
  • CD4 T-cell responses were driven by immunodominant epitopes with diverse and promiscuous HLA restriction.
  • CD8 T-cell responses to LumSyn were driven by HLA-A*02-restricted immunodominant epitopes B- and T-cell responses correlated within but not between LN and peripheral blood compartments.

This study was funded by the Bill & Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery; IAVI Neutralizing Antibody Center; National Institute of Allergy and Infectious Diseases; and Ragon Institute of MGH, MIT and Harvard.

Study authors WRS and SM are inventors on a patent filed by Scripps and IAVI on the eOD-GT8 monomer and 60-mer immunogens (patent number 11248027, “Engineered outer domain (eOD) of HIV gp 120 and mutants thereof”). WRS, KWC and MJM are inventors on patents filed by Scripps, IAVI and Fred Hutch on immunodominant peptides from LumSyn (Title: Immunogenic compositions; filing no. 63127975).

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Source:

Fred Hutchinson Cancer Center

Journal reference:

Cohen, K. W., et al. (2023) A first-in-human germline-targeting HIV nanoparticle vaccine induced broad and publicly targeted helper T cell responses. Science Translational Medicine. doi.org/10.1126/scitranslmed.adf3309.

Microbiology

Previous smallpox vaccine provides immunity to mpox

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Vaccines against smallpox given until the mid-1970s offer continuing cross-reactive immunity to mpox (previously known as monkeypox), researchers from Karolinska Institutet in Sweden report in a study published in the scientific journal Cell Host & Microbe.

During last year’s mpox outbreak, the virus spread for the first time outside Africa, causing over 85,000 cases of the disease to date. Men who have sex with men account for the most infections, with a marked skew towards the young.

The virus that causes mpox is what is known as an orthopoxvirus and is very similar to the virus that caused smallpox until the mid-1970s when it was finally eradicated.

Since there were data indicating that the old smallpox vaccine could protect against mpox, the researchers at Karolinska Institutet wondered if the individuals who were vaccinated decades ago against the former would have some protection against the latter owing to a remaining memory response.

“Our study shows that this is the case, which implies that the memory cells are very long-lived and that they can recognise closely related viruses such as the mpox virus and provide overlapping, or cross-reactive immunity,” says the study’s corresponding author Marcus Buggert, docent and researcher at the Center for Infectious Medicine, Karolinska Institutet.

By analysing the T-cell immune response in 105 healthy blood donors, the researchers were able to show that individuals born before 1976 had a significantly stronger immune response against both viral types. The researchers also analysed the immune response in 22 men with a recent mpox infection and showed that they also exhibited a strong immune response to the virus, which may provide future immunity.

The current study was too small to judge how much protection previous smallpox vaccination provides, but Dr. Buggert refers to a recently published British observational study examining the effect of a smallpox vaccine given to risk-group males in 2022.

“This study shows that smallpox vaccine can provide about 80 percent protection against mpox,” he says.

The study was financed by the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the ERC, Karolinska Institutet, the Swedish Society for Medical Research (SSMF), the Swedish Cancer Society, the Åke Wiberg Foundation, the Magnus Bergvall Foundation and the Jonas Söderquist Foundation.

Marcus Buggert is a consultant for Oxford Immunotec, Mabtech, BMS and MSD.

Facts about mpox

Mpox (formerly monkeypox) is a viral infection spread mainly through close physical contact with an infected person. Physical sexual contact poses a particularly high risk. Common symptoms are blistering, sores and rashes, fever, and swollen glands. It can also cause pain and discomfort but typically clears up on its own after two to four weeks.

In Sweden, the smallpox vaccination programme started in the early 19th century and was discontinued in 1976 when the disease was eradicated. The vaccine was mandatory for the entire population.

The vaccine currently given for mpox is essentially a smallpox vaccine.

  • Sarah Adamo, Yu Gao, Takuya Sekine, Akhirunnesa Mily, Jinghua Wu, Elisabet Storgärd, Victor Westergren, Finn Filén, Carl-Johan Treutiger, Johan K. Sandberg, Matti Sällberg, Peter Bergman, Sian Llewellyn-Lacey, Hans-Gustaf Ljunggren, David A. Price, Anna-Mia Ekström, Alessandro Sette, Alba Grifoni, Marcus Buggert. Memory profiles distinguish cross-reactive and virus-specific T cell immunity to mpox. Cell Host & Microbe, 2023; DOI: 10.1016/j.chom.2023.04.015

    • Karolinska Institutet
    Microbiology

    Novel computational platform can expand the pool of cancer immunotherapy targets

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    Reviewed by Megan Craig, M.Sc.May 17 2023

    Researchers at Children’s Hospital of Philadelphia (CHOP) and the University of California, Los Angeles (UCLA) have developed a computational platform capable of discovering tumor antigens derived from alternative RNA splicing, expanding the pool of cancer immunotherapy targets. The tool, called “Isoform peptides from RNA splicing for Immunotherapy target Screening” (IRIS), was described in a paper published today in the Proceedings of the National Academy of Sciences.

    Immunotherapy has revolutionized cancer treatment, but for many cancers including pediatric cancers, the repertoire of antigens is incomplete, underscoring a need to expand the inventory of actionable immunotherapy targets. We know that aberrant alternative RNA splicing is widespread in cancer and generates a range of potential immunotherapy targets. In our study, we were able to show that our computational platform was able to identify immunotherapy targets that arise from alternative splicing, introducing a broadly applicable framework for discovering novel cancer immunotherapy targets that arise from this process.”

    Yi Xing, PhD, co-senior author, director of the Center for Computational and Genomic Medicine at CHOP

    Cancer immunotherapy has ushered in a sea change in the treatment of many hematologic cancers, harnessing the power of a patient’s own immune system to fight the disease. Chimeric antigen receptor T-cell (CAR-T) and T cell receptor-engineered T cell (TCR-T) therapies modify a patient’s own T cells to attack known antigens on the surface of cancer cells and have often led to durable responses for cancers that were once considered incurable. However, the field has encountered challenges in the solid tumor space, in large part due to a lack of known and suitable targets for these cancers, highlighting the need for novel approaches to expand the pool of immunotherapy targets.

    Alternative splicing is an essential process that allows for one gene to code for many gene products, based on where the RNA is cut and joined, or spliced, before being translated into proteins. However, the splicing process is dysregulated in cancer cells, which often take advantage of this process to produce proteins that promote growth and survival, allowing them to replicate uncontrollably and metastasize. This happens in many adult and pediatric cancers. Scientists have suggested splicing dysregulation could be a source of novel tumor antigens for immunotherapy, but identifying such antigens has been a challenge.

    To address this difficulty, the researchers created IRIS to leverage large-scale tumor and normal RNA sequencing data and incorporate multiple screening approaches to discover tumor antigens that arise due to alternative splicing. Integrating RNA sequencing-based transcriptomics data and mass spectrometry-based proteomics data, the researchers showed that hundreds of IRIS-predicted TCR targets are presented by human leukocyte antigen (HLA) molecules, the part of the human immune system that presents antigens to T cells.

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    The researchers then applied IRIS to RNA sequencing data from neuroendocrine prostate cancer (NEPC), a metastatic and highly lethal disease known to involve shifts in RNA splicing, as discovered in a prior study by CHOP and UCLA researchers. From 2,939 alternative splicing events enriched in NEPC, IRIS predicted 1,651 peptides as potential TCR targets. The researchers then applied a more stringent screening test, which prioritized 48 potential targets. Interestingly, the researchers found that these targets were highly enriched for peptides encoded by short sequences of less than 30 nucleotides in length – also known as “microexons” – which may arise from a unique program of splicing dysregulation in this type of cancer.

    To validate the immunogenicity of these targets, the researchers isolated T cells reactive to IRIS-predicted targets, and then used single-cell sequencing to identify the TCR sequences. The researchers modified human peripheral blood mononuclear cells with seven TCRs and found they were highly reactive against targets predicted by IRIS to be good immunotherapy candidates. One TCR was particularly efficient at killing tumor cells expressing the target peptide of interest.

    “Immunotherapy is a powerful tool that has had a significant impact on the treatment of some cancers, but the benefits have not been fully realized in many lethal cancers that could benefit from this approach,” said Owen N. Witte, MD, University Professor of Microbiology, Immunology, and Molecular Genetics and member of the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA. “The discovery of new antigenic targets that may be shared among different patients – and even different tumor types – could be instrumental in expanding the value of cell-based therapies. Analyzing massive amounts of data on tumor and normal tissues, which requires sophisticated computational tools like those developed by the Xing Lab, provides actionable insights on targets that one day could be tested in the clinic.”

    “This proof-of-concept study demonstrates that alternatively spliced RNA transcripts are viable targets for cancer immunotherapy and provides a big data and multiomics-powered computational platform for finding these targets,” Dr. Xing added. “We are applying IRIS for target discovery across a wide range of pediatric and adult cancers. We are also developing a next-generation IRIS platform that harnesses newer transcriptomics technologies, such as long read and single cell analysis.”

    This research was supported in part by the Immuno-Oncology Translational Network (IOTN) of the National Cancer Institute’s Cancer Moonshot Initiative, other National Institutes of Health funding, the Parker Institute for Cancer Immunotherapy, the Cancer Research Institute, and the Ressler Family Fund.

    Source:

    Children’s Hospital of Philadelphia

    Journal reference:

    Pan, Y., et al. (2023) IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing. PNAS. doi.org/10.1073/pnas.2221116120.

    Microbiology

    Luring the virus into a trap

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    Viruses like influenza A and Ebola invade human cells in a number of steps. In an interdisciplinary approach, research teams from Heidelberg University and Heidelberg University Hospital investigated the final stages of viral penetration using electron tomography and computer simulations. In the case of influenza A, they were able to determine how the immune system fights off the virus using a small protein. For Ebola viruses, they discovered that a specific protein structure must be disassembled in order for an infection to take hold. So-called fusion pores, through which the viral genome is released into the host cell, play a central role in these processes. If they can be prevented from forming, the virus is also blocked. The Heidelberg scientists describe previously unknown mechanisms, which might lead to new approaches to prevent infections.

    Many viruses that infect humans are covered with a lipid membrane that has glycoproteins that can dock with human cells. In viruses like influenza A, which enter through the respiratory tract, these are the spike proteins that mainly bind to epithelial cells in the nose and lungs. In contrast, the highly infectious Ebola virus spreads through direct contact with infected bodily fluids and can penetrate a broad spectrum of cell types. After invading human cells, these viruses must open a fusion pore between the virus membrane and the host membrane to release their genome into the host cell and propagate.

    To fight off the virus, the human immune system attempts to block the formation of the fusion pore in a multi-stage process. Infected cells sense the presence of the foreign genome and send a signal, in the form of an interferon molecule, to as yet uninfected cells. This signal triggers the uninfected cells to produce a small cellular protein called interferon-induced transmembrane protein 3 (IFITM3). “This specialised protein can effectively prevent viruses such as influenza A, SARS-CoV-2, and Ebola from penetrating, but the underlying mechanisms were unknown,” states virologist Dr Petr Chlanda, whose working group belongs to the BioQuant Center of Heidelberg University and the Center for Integrative Infectious Disease Research of Heidelberg University Hospital. The researchers were now able to demonstrate that for influenza A viruses, IFITM3 selectively sorts the lipids in the membrane locally. This prevents the fusion pores from forming. “The viruses are literally captured in a lipid trap. Our research indicates that they are ultimately destroyed,” explains Dr Chlanda.

    To analyse the structural details of viruses, Dr Chlanda and his team took advantage of equipment from the Cryo-Electron Microscopy Network at Ruperto Carola. In an interdisciplinary approach, the research groups led by Prof. Dr Ulrich Schwarz of the BioQuant-Center and the Institute for Theoretical Physics along with Prof. Dr Walter Nickel of the Heidelberg University Biochemistry Center predicted this process with the aid of computer simulations. In the context of antiviral therapy, the researchers believe it is possible to develop lipid-sorting peptides that insert themselves into the virus membrane, rendering the viruses incapable of membrane fusion. “Such peptides could be used in a nasal spray, for example,” states Petr Chlanda.

    In a second study, the Heidelberg researchers investigated the penetration and fusion of the Ebola virus. The filamentous morphology of the virus is determined by a flexible protein envelope known as the VP40 matrix protein layer. “It has always puzzled us how this long virus could penetrate the cell, fuse with the membrane, and release its genome,” states Dr Chlanda. Using their structural analysis of infected but inactive cells provided by collaborators from the Friedrich Loeffler Institute in Greifswald, the researchers discovered that this virus protein envelope disassembles at a low pH, i.e. in an acidic environment. This step is not least decisive for the formation of fusion pores, as further computer simulations by Prof. Schwarz and Prof. Nickel showed. During this process, the electrostatic interactions of the VP40 matrix with the membrane are weakened, thereby reducing the energy barrier of pore formation. The results of the Heidelberg basic research suggest that a blockade of the disassembly of this layer would be one way to maintain Ebola viruses in a state that does not permit fusion pore formation. Similar to the influenza A virus, the Ebola virus would then be lured into a trap from which it could not escape.

    The studies were part of the Collaborative Research Centre “Integrative Analysis of Pathogen Replication and Spread” (CRC 1129) funded by the German Research Foundation. The research results were published in both “Cell Host & Microbe” as well as the EMBO Journal.

  • Sophie L Winter, Gonen Golani, Fabio Lolicato, Melina Vallbracht, Keerthihan Thiyagarajah, Samy Sid Ahmed, Christian Lüchtenborg, Oliver T Fackler, Britta Brügger, Thomas Hoenen, Walter Nickel, Ulrich S Schwarz, Petr Chlanda. The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion. The EMBO Journal, 2023; DOI: 10.15252/embj.2023113578

    • Heidelberg University
    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

    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

    Memory B cell marker predicts long-lived antibody response to flu vaccine

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    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.

  • Anoma Nellore, Esther Zumaquero, Christopher D. Scharer, Christopher F. Fucile, Christopher M. Tipton, R. Glenn King, Tian Mi, Betty Mousseau, John E. Bradley, Fen Zhou, Stuti Mutneja, Paul A. Goepfert, Jeremy M. Boss, Troy D. Randall, Ignacio Sanz, Alexander F. Rosenberg, Frances E. Lund. A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans. Immunity, 2023; DOI: 10.1016/j.immuni.2023.03.001

    • University of Alabama at Birmingham
    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

    SARS-CoV-2 infection damages the CD8+ T cell response to vaccination

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

    The magnitude and quality of a key immune cell’s response to vaccination with two doses of the Pfizer-BioNTech COVID-19 vaccine were considerably lower in people with prior SARS-CoV-2 infection compared to people without prior infection, a study has found. In addition, the level of this key immune cell that targets the SARS-CoV-2 spike protein was substantially lower in unvaccinated people with COVID-19 than in vaccinated people who had never been infected. Importantly, people who recover from SARS-CoV-2 infection and then get vaccinated are more protected than people who are unvaccinated. These findings, which suggest that the virus damages an important immune-cell response, were published today in the journal Immunity.

    The study was co-funded by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, and led by Mark M. Davis, Ph.D. Dr. Davis is the director of the Stanford Institute for Immunity, Transplantation and Infection and a professor of microbiology and immunology at Stanford University School of Medicine in Palo Alto, California. He is also a Howard Hughes Medical Institute Investigator.

    Dr. Davis and colleagues designed a very sensitive tool to analyze how immune cells called CD4+ T cells and CD8+ T cells respond to SARS-CoV-2 infection and vaccination. These cells coordinate the immune system’s response to the virus and kill other cells that have been infected, helping prevent COVID-19. The tool was designed to identify T cells that target any of dozens of specific regions on the virus’s spike protein as well as some other viral regions. The Pfizer-BioNTech vaccine uses parts of the SARS-CoV-2 spike protein to elicit an immune response without causing infection.

    The investigators studied CD4+ and CD8+ T-cell responses in blood samples from three groups of volunteers. One group had never been infected with SARS-CoV-2 and received two doses of the Pfizer-BioNTech COVID-19 vaccine. The second group had previously been infected with SARS-CoV-2 and received two doses of the vaccine. The third group had COVID-19 and was unvaccinated.

    The researchers found that vaccination of people who had never been infected with SARS-CoV-2 induced robust CD4+ and CD8+ T-cell responses to the virus’ spike protein. In addition, these T cells produced multiple types of cell-signaling molecules called cytokines, which recruit other immune cells—including antibody-producing B cells—to fight pathogens. However, people who had been infected with SARS-CoV-2 prior to vaccination produced spike-specific CD8+ T cells at considerably lower levels—and with less functionality—than vaccinated people who had never been infected. Moreover, the researchers observed substantially lower levels of spike-specific CD8+ T cells in unvaccinated people with COVID-19 than in vaccinated people who had never been infected.

    Taken together, the investigators write, these findings suggest that SARS-CoV-2 infection damages the CD8+ T cell response, an effect akin to that observed in earlier studies showing long-term damage to the immune system after infection with viruses such as hepatitis C or HIV. The new findings highlight the need to develop vaccination strategies to specifically boost antiviral CD8+ T cell responses in people previously infected with SARS-CoV-2, the researchers conclude.  

    Source:

    National Institutes of Health

    Journal reference:

    Gao, F., et al. (2023). Robust T cell responses to Pfizer/BioNTech vaccine compared to infection and evidence of attenuated peripheral CD8+ T cell responses due to COVID-19. Immunity. doi.org/10.1016/j.immuni.2023.03.005.

    Microbiology

    Antibiotics can destroy many types of bacteria, but increasingly, bacterial pathogens are gaining resistance to many commonly used …

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    Antibiotics can destroy many types of bacteria, but increasingly, bacterial pathogens are gaining resistance to many commonly used types. As the threat of antibiotic resistance looms large, researchers have sought to find new antibiotics and other ways to destroy dangerous bacteria. But new antibiotics can be extremely difficult to identify and test. Bacteriophages, which are viruses that only infect bacterial cells, might offer an alternative. Bacteriophages (phages) were studied many years ago, before the development of antibiotic drugs, and they could help us once again.

    Image credit: Pixabay

    If we are going to use bacteriophages in the clinic to treat humans, we should understand how they work, and how bacteria can also become resistant to them. Microbes are in an arms race with each other, so while phages can infect bacteria, some bacterial cells have found ways to thwart the effects of those phages. New research reported in Nature Microbiology has shown that when certain bacteria carry a specific genetic mutation, phages don’t work against them anymore.

    In this study, the researchers used a new technique so they could actually see a phage attacking bacteria. Mycobacteriophages infect Mycobacterial species, including the pathogens Mycobacterium tuberculosis and Mycobacterium abscessus, as well as the harmless Mycobacterium smegmatis, which was used in this research.

    The scientists determined that Mycobacterial gene called lsr2 is essential for many mycobacteriophages to successfully infect Mycobacteria. Mycobacteria that carry a mutation that renders the Lsr2 protein non-functional are resistant to these phages.

    Normally, Lsr2 aids in DNA replication in bacterial cells. Bacteriophages can harness this protein, however, and use it to reproduce the phage’s DNA. Thus, when Lsr2 stops working, the phage cannot replicate and it cannot manipulate bacterial cells.

    In the video above, by first study author Charles Dulberger, a genetically engineered mutant phage infects Mycobacterium smegmatis. First, one phage particle (red dot at 0.42 seconds) binds to a bacterium. The phage DNA (green fluorescence) is injected into the bacterial cell (2-second mark). The bright green dots at the cells’ ends are not relevant. For a few seconds, the DNA forms a zone of phage replication, and fills the cell. Finally, the cell explodes at 6:25 seconds. (About three hours have been compressed to make this video.)

    The approach used in this study can also be used to investigate other links between bacteriophages and the bacteria they infect.

    “This paper focuses on just one bacterial protein,” noted co-corresponding study author Graham Hatfull, a Professor at the University of Pittsburgh. But there are many more opportunities to use this technique. “There are lots of different phages and lots of other proteins.”

    Sources: University of Pittsburgh, Nature Microbiology


    Carmen Leitch