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Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures.
Sevy AM, Soto C, Bombardi RG, Meiler J, Crowe JE
(2019) BMC Bioinformatics 20: 629
MeSH Terms: Adult, Antibodies, Cohort Studies, Fetal Blood, HIV Infections, High-Throughput Nucleotide Sequencing, Humans, Influenza, Human, Middle Aged, Principal Component Analysis, Vaccination
Show Abstract · Added March 21, 2020
BACKGROUND - Advances in next-generation sequencing (NGS) of antibody repertoires have led to an explosion in B cell receptor sequence data from donors with many different disease states. These data have the potential to detect patterns of immune response across populations. However, to this point it has been difficult to interpret such patterns of immune response between disease states in the absence of functional data. There is a need for a robust method that can be used to distinguish general patterns of immune responses at the antibody repertoire level.
RESULTS - We developed a method for reducing the complexity of antibody repertoire datasets using principal component analysis (PCA) and refer to our method as "repertoire fingerprinting." We reduce the high dimensional space of an antibody repertoire to just two principal components that explain the majority of variation in those repertoires. We show that repertoires from individuals with a common experience or disease state can be clustered by their repertoire fingerprints to identify common antibody responses.
CONCLUSIONS - Our repertoire fingerprinting method for distinguishing immune repertoires has implications for characterizing an individual disease state. Methods to distinguish disease states based on pattern recognition in the adaptive immune response could be used to develop biomarkers with diagnostic or prognostic utility in patient care. Extending our analysis to larger cohorts of patients in the future should permit us to define more precisely those characteristics of the immune response that result from natural infection or autoimmunity.
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MeSH Terms
Influenza H7N9 Virus Neuraminidase-Specific Human Monoclonal Antibodies Inhibit Viral Egress and Protect from Lethal Influenza Infection in Mice.
Gilchuk IM, Bangaru S, Gilchuk P, Irving RP, Kose N, Bombardi RG, Thornburg NJ, Creech CB, Edwards KM, Li S, Turner HL, Yu W, Zhu X, Wilson IA, Ward AB, Crowe JE
(2019) Cell Host Microbe 26: 715-728.e8
MeSH Terms: Animals, Antibodies, Heterophile, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Birds, Epitopes, Humans, Influenza A Virus, H7N9 Subtype, Influenza Vaccines, Influenza in Birds, Influenza, Human, Mice, Neuraminidase, Orthomyxoviridae Infections, Pre-Exposure Prophylaxis, Vaccination, Vaccines, Inactivated, Viral Proteins, Virus Release
Show Abstract · Added March 31, 2020
H7N9 avian influenza virus causes severe infections and might have the potential to trigger a major pandemic. Molecular determinants of human humoral immune response to N9 neuraminidase (NA) proteins, which exhibit unusual features compared with seasonal influenza virus NA proteins, are ill-defined. We isolated 35 human monoclonal antibodies (mAbs) from two H7N9 survivors and two vaccinees. These mAbs react to NA in a subtype-specific manner and recognize diverse antigenic sites on the surface of N9 NA, including epitopes overlapping with, or distinct from, the enzyme active site. Despite recognizing multiple antigenic sites, the mAbs use a common mechanism of action by blocking egress of nascent virions from infected cells, thereby providing an antiviral prophylactic and therapeutic protection in vivo in mice. Studies of breadth, potency, and diversity of antigenic recognition from four subjects suggest that vaccination with inactivated adjuvanted vaccine induce NA-reactive responses comparable to that of H7N9 natural infection.
Copyright © 2019 Elsevier Inc. All rights reserved.
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20 MeSH Terms
Structural basis for influenza virus NS1 protein block of mRNA nuclear export.
Zhang K, Xie Y, Muñoz-Moreno R, Wang J, Zhang L, Esparza M, García-Sastre A, Fontoura BMA, Ren Y
(2019) Nat Microbiol 4: 1671-1679
MeSH Terms: A549 Cells, Active Transport, Cell Nucleus, Binding Sites, Cell Nucleus, Cells, Cultured, Crystallography, X-Ray, Humans, Influenza A virus, Influenza, Human, Models, Molecular, Multiprotein Complexes, Nuclear Pore Complex Proteins, Nucleocytoplasmic Transport Proteins, Protein Binding, RNA, Messenger, RNA-Binding Proteins, Viral Nonstructural Proteins
Show Abstract · Added March 3, 2020
Influenza viruses antagonize key immune defence mechanisms via the virulence factor non-structural protein 1 (NS1). A key mechanism of virulence by NS1 is blocking nuclear export of host messenger RNAs, including those encoding immune factors; however, the direct cellular target of NS1 and the mechanism of host mRNA export inhibition are not known. Here, we identify the target of NS1 as the mRNA export receptor complex, nuclear RNA export factor 1-nuclear transport factor 2-related export protein 1 (NXF1-NXT1), which is the principal receptor mediating docking and translocation of mRNAs through the nuclear pore complex via interactions with nucleoporins. We determined the crystal structure of NS1 in complex with NXF1-NXT1 at 3.8 Å resolution. The structure reveals that NS1 prevents binding of NXF1-NXT1 to nucleoporins, thereby inhibiting mRNA export through the nuclear pore complex into the cytoplasm for translation. We demonstrate that a mutant influenza virus deficient in binding NXF1-NXT1 does not block host mRNA export and is attenuated. This attenuation is marked by the release of mRNAs encoding immune factors from the nucleus. In sum, our study uncovers the molecular basis of a major nuclear function of influenza NS1 protein that causes potent blockage of host gene expression and contributes to inhibition of host immunity.
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Influenza vaccination and myocarditis among patients receiving immune checkpoint inhibitors.
Awadalla M, Golden DLA, Mahmood SS, Alvi RM, Mercaldo ND, Hassan MZO, Banerji D, Rokicki A, Mulligan C, Murphy SPT, Jones-O'Connor M, Cohen JV, Heinzerling LM, Armanious M, Sullivan RJ, Damrongwatanasuk R, Chen CL, Gupta D, Kirchberger MC, Moslehi JJ, Shah SP, Ganatra S, Thavendiranathan P, Rizvi MA, Sahni G, Lyon AR, Tocchetti CG, Mercurio V, Thuny F, Ederhy S, Mahmoudi M, Lawrence DP, Groarke JD, Nohria A, Fradley MG, Reynolds KL, Neilan TG
(2019) J Immunother Cancer 7: 53
MeSH Terms: Aged, Aged, 80 and over, Antineoplastic Agents, Immunological, Female, Humans, Influenza Vaccines, Influenza, Human, Male, Middle Aged, Myocarditis, Neoplasms, Registries, Vaccination
Show Abstract · Added February 24, 2019
BACKGROUND - Influenza vaccination (FV) is recommended for patients with cancer. Recent data suggested that the administration of the FV was associated with an increase in immune-related adverse events (irAEs) among patients on immune checkpoint inhibitors (ICIs). Myocarditis is an uncommon but serious complication of ICIs and may also result from infection with influenza. There are no data testing the relationship between FV and the development of myocarditis on ICIs.
METHODS - Patients on ICIs who developed myocarditis (n = 101) (cases) were compared to ICI-treated patients (n = 201) without myocarditis (controls). A patient was defined as having the FV if they were administered the FV from 6 months prior to start of ICI to anytime during ICI therapy. Alternate thresholds for FV status were also tested. The primary comparison of interest was the rate of FV between cases and controls. Patients with myocarditis were followed for major adverse cardiac events (MACE), defined as the composite of cardiogenic shock, cardiac arrest, hemodynamically significant complete heart block and cardiovascular death.
RESULTS - The FV was administered to 25% of the myocarditis cases compared to 40% of the non-myocarditis ICI-treated controls (p = 0.01). Similar findings of lower rates of FV administration were noted among myocarditis cases when alternate thresholds were tested. Among the myocarditis cases, those who were vaccinated had 3-fold lower troponin levels when compared to unvaccinated cases (FV vs. No FV: 0.12 [0.02, 0.47] vs. 0.40 [0.11, 1.26] ng/ml, p = 0.02). Within myocarditis cases, those administered the FV also had a lower rate of other irAEs when compared to unvaccinated cases (36 vs. 55% p = 0.10) including lower rates of pneumonitis (12 vs. 36%, p = 0.03). During follow-up (175 [IQR 89, 363] days), 47% of myocarditis cases experienced a MACE. Myocarditis cases who received the FV were at a lower risk of cumulative MACE when compared to unvaccinated cases (24 vs. 59%, p = 0.002).
CONCLUSION - The rate of FV among ICI-related myocarditis cases was lower than controls on ICIs who did not develop myocarditis. In those who developed myocarditis related to an ICI, there was less myocardial injury and a lower risk of MACE among those who were administered the FV.
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13 MeSH Terms
Antibody Determinants of Influenza Immunity.
Crowe JE
(2019) J Infect Dis 219: S21-S29
MeSH Terms: Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Antigens, Viral, B-Lymphocytes, Cross Reactions, Genetic Drift, Hemagglutinin Glycoproteins, Influenza Virus, Humans, Immunologic Memory, Influenza A virus, Influenza Vaccines, Influenza, Human, Neuraminidase, Point Mutation, Vaccination, Vaccines, Inactivated
Show Abstract · Added March 31, 2019
Understanding antigenic variation in influenza virus strains and how the human immune system recognizes strains are central challenges for vaccinologists. Antibodies directed to the 2 major viral surface membrane proteins, hemagglutinin (HA) and neuraminidase (NA), mediate protection against reinfection following natural infection or vaccination, but HA and NA protein sequences in field strains are highly variable. The central questions are how to achieve protective antibody responses in a higher proportion of individuals and how to induce responses with more breadth and durability. Studies using isolation of human monoclonal antibodies followed by structural and functional characterization revealed conserved antigenic sites recognized by broadly cross-reactive antibodies. The antigenic landscape on HA and NA proteins is coming into focus to inform studies of the correlates and mechanisms of immunity. Understanding the antibody determinants of influenza immunity points the way toward development and testing of next-generation vaccines with potential to confer broadly protective immunity.
© The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.
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17 MeSH Terms
Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses.
Sevy AM, Wu NC, Gilchuk IM, Parrish EH, Burger S, Yousif D, Nagel MBM, Schey KL, Wilson IA, Crowe JE, Meiler J
(2019) Proc Natl Acad Sci U S A 116: 1597-1602
MeSH Terms: Amino Acid Sequence, Antibodies, Neutralizing, Antibodies, Viral, Crystallography, X-Ray, Hemagglutinin Glycoproteins, Influenza Virus, Humans, Influenza A virus, Influenza, Human, Seasons
Show Abstract · Added March 31, 2019
Influenza is a yearly threat to global public health. Rapid changes in influenza surface proteins resulting from antigenic drift and shift events make it difficult to readily identify antibodies with broadly neutralizing activity against different influenza subtypes with high frequency, specifically antibodies targeting the receptor binding domain (RBD) on influenza HA protein. We developed an optimized computational design method that is able to optimize an antibody for recognition of large panels of antigens. To demonstrate the utility of this multistate design method, we used it to redesign an antiinfluenza antibody against a large panel of more than 500 seasonal HA antigens of the H1 subtype. As a proof of concept, we tested this method on a variety of known antiinfluenza antibodies and identified those that could be improved computationally. We generated redesigned variants of antibody C05 to the HA RBD and experimentally characterized variants that exhibited improved breadth and affinity against our panel. C05 mutants exhibited improved affinity for three of the subtypes used in design by stabilizing the CDRH3 loop and creating favorable electrostatic interactions with the antigen. These mutants possess increased breadth and affinity of binding while maintaining high-affinity binding to existing targets, surpassing a major limitation up to this point.
Copyright © 2019 the Author(s). Published by PNAS.
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3 Members
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MeSH Terms
Influenza Virus-Specific Human Antibody Repertoire Studies.
Crowe JE
(2019) J Immunol 202: 368-373
MeSH Terms: Antibodies, Viral, Antibody Diversity, Antigenic Variation, Antigens, Viral, B-Lymphocytes, Humans, Influenza A virus, Influenza Vaccines, Influenza, Human, Receptors, Antigen, B-Cell
Show Abstract · Added March 31, 2019
The diversity of Ag-specific adaptive receptors on the surface of B cells and in the population of secreted Abs is enormous, but increasingly, we are acquiring the technical capability to interrogate Ab repertoires in great detail. These Ab technologies have been especially pointed at understanding the complex issues of immunity to infection and disease caused by influenza virus, one of the most common and vexing medical problems in man. Influenza immunity is particularly interesting as a model system because the antigenic diversity of influenza strains and proteins is high and constantly evolving. Discovery of canonical features in the subset of the influenza repertoire response that is broadly reactive for diverse influenza strains has spurred the recent optimism for creating universal influenza vaccines. Using new technologies for sequencing Ab repertoires at great depth is helping us to understand the central features of influenza immunity.
Copyright © 2019 by The American Association of Immunologists, Inc.
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10 MeSH Terms
Incorporating Markers of Disease Severity into Near Real-Time Influenza Surveillance.
Grijalva CG, O'Donnell M, Talbot HK
(2017) Ann Am Thorac Soc 14: 1766-1767
MeSH Terms: Humans, Influenza A Virus, H1N1 Subtype, Influenza, Human, Intensive Care Units, Morbidity
Added July 27, 2018
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5 MeSH Terms
A novel real-time RT-PCR assay for influenza C tested in Peruvian children.
Howard LM, Johnson M, Gil AI, Pekosz A, Griffin MR, Edwards KM, Lanata CF, Grijalva CG, Williams JV, RESPIRA-PERU Group
(2017) J Clin Virol 96: 12-16
MeSH Terms: Child, Preschool, Female, Humans, Infant, Influenza, Human, Influenzavirus C, Male, Molecular Diagnostic Techniques, Peru, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Sensitivity and Specificity
Show Abstract · Added July 27, 2018
BACKGROUND - Influenza C virus (ICV) is associated with acute respiratory illness. Yet ICV remains under recognized, with most previous studies using only culture to identify cases.
OBJECTIVES - To develop a sensitive and specific real-time RT-PCR assay for ICV that allows for rapid and accurate detection in a clinical or research setting.
STUDY DESIGN - Multiple ICV sequences obtained from GenBank were analyzed, including 141 hemagglutinin-esterase (HE), 106 matrix (M), and 97 nucleoprotein (NP) sequences. Primers and probes were designed based on conserved regions. Multiple primer-probe sets were tested against multiple ICV strains.
RESULTS - The ICV M and NP genes offered the most conserved sequence regions. Primers and probes based on newer sequence data offered enhanced detection of ICV, especially for low titer specimens. An NP-targeted assay yielded the best performance and was capable of detecting 10-100 RNA copies per reaction. The NP assay detected multiple clinical isolates of ICV collected in a field epidemiology study conducted in Peru.
CONCLUSIONS - We report a new real-time RT-PCR assay for ICV with high sensitivity and specificity.
Copyright © 2017 Elsevier B.V. All rights reserved.
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Is It Possible to Develop a "Universal" Influenza Virus Vaccine? Potential for a Universal Influenza Vaccine.
Crowe JE
(2018) Cold Spring Harb Perspect Biol 10:
MeSH Terms: Antibodies, Neutralizing, Antibodies, Viral, Hemagglutinins, Humans, Influenza Vaccines, Influenza, Human
Show Abstract · Added March 14, 2018
Development of optimal vaccines for influenza is challenging, in part as a result of the high antigenic variability in field strains associated with genetic shift from reassortment and genetic drift from point mutations. Discovery of conserved antigenic sites on the hemagglutinin (HA) protein for neutralizing antibodies suggested the possibility that influenza vaccines could be developed that induce focused antibody responses to the conserved neutralizing determinants, especially the HA stem region. Recent studies have focused on the antigenicity and immunogenicity of such domains, using monoclonal antibodies and candidate-engineered HA stem-based vaccines. Much progress has been made, but we still do not fully understand the biology of the immune response to this unique antigenic region.
Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.
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6 MeSH Terms