The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination.

Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.

A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy.

The increased incidence of whooping cough worldwide suggests that current vaccination against Bordetella pertussis infection has limitations in quality and duration of protection. The resurgence of infection has been linked to the introduction of acellular vaccines (aP), which have an improved safety profile compared with the previously used whole-cell (wP) vaccines. To determine immunological differences between aP and wP priming in infancy, we performed a systems approach of the immune response to booster vaccination. Transcriptomic, proteomic, cytometric, and serologic profiling revealed multiple shared immune responses with different kinetics across cohorts, including an increase of blood monocyte frequencies and strong antigen-specific IgG responses. Additionally, we found a prominent subset of aP-primed individuals (30%) with a strong differential signature, including higher levels of expression for CCL3, NFKBIA, and ICAM1. Contrary to the wP individuals, this subset displayed increased PT-specific IgE responses after boost and higher antigen-specific IgG4 and IgG3 antibodies against FHA and FIM2/3 at baseline and after boost. Overall, the results show that, while broad immune response patterns to Tdap boost overlap between aP- and wP-primed individuals, a subset of aP-primed individuals present a divergent response. These findings provide candidate targets to study the causes and correlates of waning immunity after aP vaccination.

Modeling human adaptive immune responses with tonsil organoids.

Most of what we know about adaptive immunity has come from inbred mouse studies, using methods that are often difficult or impossible to confirm in humans. In addition, vaccine responses in mice are often poorly predictive of responses to those same vaccines in humans. Here we use human tonsils, readily available lymphoid organs, to develop a functional organotypic system that recapitulates key germinal center features in vitro, including the production of antigen-specific antibodies, somatic hypermutation and affinity maturation, plasmablast differentiation and class-switch recombination. We use this system to define the essential cellular components necessary to produce an influenza vaccine response. We also show that it can be used to evaluate humoral immune responses to two priming antigens, rabies vaccine and an adenovirus-based severe acute respiratory syndrome coronavirus 2 vaccine, and to assess the effects of different adjuvants. This system should prove useful for studying critical mechanisms underlying adaptive immunity in much greater depth than previously possible and to rapidly test vaccine candidates and adjuvants in an entirely human system.

Systems Biological Analysis of Immune Response to Influenza Vaccination.

The last decade has witnessed tremendous progress in immunology and vaccinology, owing to several scientific and technological breakthroughs. Systems vaccinology is a field that has emerged at the forefront of vaccine research and development and provides a unique way to probe immune responses to vaccination in humans. The goals of systems vaccinology are to use systems-based approaches to define signatures that can be used to predict vaccine immunogenicity and efficacy and to delineate the molecular mechanisms driving protective immunity. The application of systems biological approaches in influenza vaccination studies has enabled the discovery of early signatures that predict immunogenicity to vaccination and yielded novel mechanistic insights about vaccine-induced immunity. Here we review the contributions of systems vaccinology to influenza vaccine development and critically examine the potential of systems vaccinology toward enabling the development of a universal influenza vaccine that provides robust and durable immunity against diverse influenza viruses.

Adjuvanted H5N1 influenza vaccine enhances both cross-reactive memory B cell and strain-specific naive B cell responses in humans.

There is a need for improved influenza vaccines. In this study we compared the antibody responses in humans after vaccination with an AS03-adjuvanted versus nonadjuvanted H5N1 avian influenza virus inactivated vaccine. Healthy young adults received two doses of either formulation 3 wk apart. We found that AS03 significantly enhanced H5 hemagglutinin (HA)-specific plasmablast and antibody responses compared to the nonadjuvanted vaccine. Plasmablast response after the first immunization was exclusively directed to the conserved HA stem region and came from memory B cells. Monoclonal antibodies (mAbs) derived from these plasmablasts had high levels of somatic hypermutation (SHM) and recognized the HA stem region of multiple influenza virus subtypes. Second immunization induced a plasmablast response to the highly variable HA head region. mAbs derived from these plasmablasts exhibited minimal SHM (naive B cell origin) and largely recognized the HA head region of the immunizing H5N1 strain. Interestingly, the antibody response to H5 HA stem region was much lower after the second immunization, and this suppression was most likely due to blocking of these epitopes by stem-specific antibodies induced by the first immunization. Taken together, these findings show that an adjuvanted influenza vaccine can substantially increase antibody responses in humans by effectively recruiting preexisting memory B cells as well as naive B cells into the response. In addition, we show that high levels of preexisting antibody can have a negative effect on boosting. These findings have implications toward the development of a universal influenza vaccine.

Squalene emulsion-based vaccine adjuvants stimulate CD8 T cell, but not antibody responses, through a RIPK3-dependent pathway.

The squalene-based oil-in-water emulsion (SE) vaccine adjuvant MF59 has been administered to more than 100 million people in more than 30 countries, in both seasonal and pandemic influenza vaccines. Despite its wide use and efficacy, its mechanisms of action remain unclear. In this study we demonstrate that immunization of mice with MF59 or its mimetic AddaVax (AV) plus soluble antigen results in robust antigen-specific antibody and CD8 T cell responses in lymph nodes and non-lymphoid tissues. Immunization triggered rapid RIPK3-kinase dependent necroptosis in the lymph node which peaked at 6 hr, followed by a sequential wave of apoptosis. Immunization with alum plus antigen did not induce RIPK3-dependent signaling. RIPK3-dependent signaling induced by MF59 or AV was essential for cross-presentation of antigen to CD8 T cells by Batf3-dependent CD8+ DCs. Consistent with this, RIPK3 deficient or Batf3 deficient mice were impaired in their ability to mount adjuvant-enhanced CD8 T cell responses. However, CD8 T cell responses were unaffected in mice deficient in MLKL, a downstream mediator of necroptosis. Surprisingly, antibody responses were unaffected in RIPK3-kinase or Batf3 deficient mice. In contrast, antibody responses were impaired by in vivo administration of the pan-caspase inhibitor Z-VAD-FMK, but normal in caspase-1 deficient mice, suggesting a contribution from apoptotic caspases, in the induction of antibody responses. These results demonstrate that squalene emulsion-based vaccine adjuvants induce antigen-specific CD8 T cell and antibody responses, through RIPK3-dependent and-independent pathways, respectively.

Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans.

Emerging evidence indicates a central role for the microbiome in immunity. However, causal evidence in humans is sparse. Here, we administered broad-spectrum antibiotics to healthy adults prior and subsequent to seasonal influenza vaccination. Despite a 10,000-fold reduction in gut bacterial load and long-lasting diminution in bacterial diversity, antibody responses were not significantly affected. However, in a second trial of subjects with low pre-existing antibody titers, there was significant impairment in H1N1-specific neutralization and binding IgG1 and IgA responses. In addition, in both studies antibiotics treatment resulted in (1) enhanced inflammatory signatures (including AP-1/NR4A expression), observed previously in the elderly, and increased dendritic cell activation; (2) divergent metabolic trajectories, with a 1,000-fold reduction in serum secondary bile acids, which was highly correlated with AP-1/NR4A signaling and inflammasome activation. Multi-omics integration revealed significant associations between bacterial species and metabolic phenotypes, highlighting a key role for the microbiome in modulating human immunity.

Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination.

Vaccines are among the most effective public health tools for combating certain infectious diseases such as influenza. The role of the humoral immune system in vaccine-induced protection is widely appreciated; however, our understanding of how antibody specificities relate to B cell function remains limited due to the complexity of polyclonal antibody responses. To address this, we developed the Spec-seq framework, which allows for simultaneous monoclonal antibody (mAb) characterization and transcriptional profiling from the same single cell. Here, we present the first application of the Spec-seq framework, which we applied to human plasmablasts after influenza vaccination in order to characterize transcriptional differences governed by B cell receptor (BCR) isotype and vaccine reactivity. Our analysis did not find evidence of long-term transcriptional specialization between plasmablasts of different isotypes. However, we did find enhanced transcriptional similarity between clonally related B cells, as well as distinct transcriptional signatures ascribed by BCR vaccine recognition. These data suggest IgG and IgA vaccine-positive plasmablasts are largely similar, whereas IgA vaccine-negative cells appear to be transcriptionally distinct from conventional, terminally differentiated, antigen-induced peripheral blood plasmablasts.

Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters.

In the mid-1990s, whole-cell pertussis (wP) vaccines were associated with local and systemic adverse events that prompted their replacement with acellular pertussis (aP) vaccines in many high-income countries. In the past decade, rates of pertussis disease have increased in children receiving only aP vaccines. We compared the immune responses to aP boosters in individuals who received their initial doses with either wP or aP vaccines using activation-induced marker (AIM) assays. Specifically, we examined pertussis-specific memory CD4+ T cell responses ex vivo, highlighting a type 2/Th2 versus type 1/Th1 and Th17 differential polarization as a function of childhood vaccination. Remarkably, after a contemporary aP booster, cells from donors originally primed with aP were (a) associated with increased IL-4, IL-5, IL-13, IL-9, and TGF-ß and decreased IFN-γ and IL-17 production, (b) defective in their ex vivo capacity to expand memory cells, and (c) less capable of proliferating in vitro. These differences appeared to be T cell specific, since equivalent increases of antibody titers and plasmablasts after aP boost were seen in both groups. In conclusion, our data suggest that there are long-lasting effects and differences in polarization and proliferation of T cell responses in adults originally vaccinated with aP compared with those that initially received wP, despite repeated acellular boosters.

Usability test of a hand exoskeleton for activities of daily living: an example of user-centered design.

PURPOSE: (1) To assess a robotic device (Handexos) during the design process with regard to usability, end user satisfaction and safety, (2) to determine whether Handexos can improve the activities of daily living (ADLs) of spinal cord injury (SCI) patients and stroke patients with upper-limb dysfunction. METHODS: During a 2-year development stage of the device, a total of 37 participants (aged 22-68), 28 clinicians (experts) and nine patients with SCI or stroke (end users) were included in a user-centered design process featuring usability tests. They performed five grasps wearing the device. The assessments were obtained at the end of the session by filling out a questionnaire and making suggestions. RESULTS: The experts' opinion was that the modified device was an improvement over the preliminary version, although this was not reflected in the scores. Whereas end user scores for comfort, grasp, performance and safety were above the sufficiency threshold, the scores for year 2 were lower than those for year 1. CONCLUSIONS: The findings demonstrate that although Handexos meets the initial functional requirements and underlines the potential for assisting SCI and post-stroke subjects in ADLs, several aspects such as mechanical complexity and low adaptability to different hand sizes need to be further addressed. Implications for Rehabilitation Wearable robotics devices could improve the activities of daily living in patients with spinal cord injury or stroke. They could be a tool for rehabilitation of the upper limb. Further usability tests to improve this type of tools are recommended.

Refined protocol for generating monoclonal antibodies from single human and murine B cells.

Generating monoclonal antibodies from single B cells is a valuable tool for characterizing the specificity and functional properties of humoral responses. We and others developed protocols that have facilitated major advances in our understanding of B cell development, tolerance, and effector responses to HIV and influenza. Here, we demonstrate various refinements and dramatically reduce the time required to produce recombinant antibodies. Further, we present new methods for cloning and isolating antibodies from cells with lower immunoglobulin mRNA levels that may be resistant to traditional techniques. Together, these refinements significantly increase single-cell antibody expression efficiency and are easily integrated into established and novel pipelines.

Vision-Based Pose Estimation for Robot-Mediated Hand Telerehabilitation.

Vision-based Pose Estimation (VPE) represents a non-invasive solution to allow a smooth and natural interaction between a human user and a robotic system, without requiring complex calibration procedures. Moreover, VPE interfaces are gaining momentum as they are highly intuitive, such that they can be used from untrained personnel (e.g., a generic caregiver) even in delicate tasks as rehabilitation exercises. In this paper, we present a novel master-slave setup for hand telerehabilitation with an intuitive and simple interface for remote control of a wearable hand exoskeleton, named HX. While performing rehabilitative exercises, the master unit evaluates the 3D position of a human operator's hand joints in real-time using only a RGB-D camera, and commands remotely the slave exoskeleton. Within the slave unit, the exoskeleton replicates hand movements and an external grip sensor records interaction forces, that are fed back to the operator-therapist, allowing a direct real-time assessment of the rehabilitative task. Experimental data collected with an operator and six volunteers are provided to show the feasibility of the proposed system and its performances. The results demonstrate that, leveraging on our system, the operator was able to directly control volunteers' hands movements.

Systems biology of immunity to MF59-adjuvanted versus nonadjuvanted trivalent seasonal influenza vaccines in early childhood.

The dynamics and molecular mechanisms underlying vaccine immunity in early childhood remain poorly understood. Here we applied systems approaches to investigate the innate and adaptive responses to trivalent inactivated influenza vaccine (TIV) and MF59-adjuvanted TIV (ATIV) in 90 14- to 24-mo-old healthy children. MF59 enhanced the magnitude and kinetics of serum antibody titers following vaccination, and induced a greater frequency of vaccine specific, multicytokine-producing CD4(+) T cells. Compared with transcriptional responses to TIV vaccination previously reported in adults, responses to TIV in infants were markedly attenuated, limited to genes regulating antiviral and antigen presentation pathways, and observed only in a subset of vaccinees. In contrast, transcriptional responses to ATIV boost were more homogenous and robust. Interestingly, a day 1 gene signature characteristic of the innate response (antiviral IFN genes, dendritic cell, and monocyte responses) correlated with hemagglutination at day 28. These findings demonstrate that MF59 enhances the magnitude, kinetics, and consistency of the innate and adaptive response to vaccination with the seasonal influenza vaccine during early childhood, and identify potential molecular correlates of antibody responses.

Gastrocnemius myoelectric control of a robotic hip exoskeleton.

In this paper we present a novel EMG-based assistive control strategy for lower-limb exoskeletons. An active pelvis orthosis (APO) generates torque profiles for the hip flexion motion assistance, according to the Gastrocnemius Medialis EMG signal. The strategy has been tested on one healthy subject: experimental results show that the user is able to reduce his muscular activation when the assistance is switched on with respect to the free walking condition.

Enhancing brain-machine interface (BMI) control of a hand exoskeleton using electrooculography (EOG).

BACKGROUND: Brain-machine interfaces (BMIs) allow direct translation of electric, magnetic or metabolic brain signals into control commands of external devices such as robots, prostheses or exoskeletons. However, non-stationarity of brain signals and susceptibility to biological or environmental artifacts impede reliable control and safety of BMIs, particularly in daily life environments. Here we introduce and tested a novel hybrid brain-neural computer interaction (BNCI) system fusing electroencephalography (EEG) and electrooculography (EOG) to enhance reliability and safety of continuous hand exoskeleton-driven grasping motions. FINDINGS: 12 healthy volunteers (8 male, mean age 28.1 ± 3.63y) used EEG (condition #1) and hybrid EEG/EOG (condition #2) signals to control a hand exoskeleton. Motor imagery-related brain activity was translated into exoskeleton-driven hand closing motions. Unintended motions could be interrupted by eye movement-related EOG signals. In order to evaluate BNCI control and safety, participants were instructed to follow a visual cue indicating either to move or not to move the hand exoskeleton in a random order. Movements exceeding 25% of a full grasping motion when the device was not supposed to be moved were defined as safety violation. While participants reached comparable control under both conditions, safety was frequently violated under condition #1 (EEG), but not under condition #2 (EEG/EOG). CONCLUSION: EEG/EOG biosignal fusion can substantially enhance safety of assistive BNCI systems improving their applicability in daily life environments.

Analysis of relative displacement between the HX wearable robotic exoskeleton and the user's hand.

BACKGROUND: Advances in technology are allowing for the production of several viable wearable robotic devices to assist with activities of daily living and with rehabilitation. One of the most pressing limitations to user satisfaction is the lack of consistency in motion between the user and the robotic device. The displacement between the robot and the body segment may not correspond because of differences in skin and tissue compliance, mechanical backlash, and/or incorrect fit. FINDINGS: This report presents the results of an analysis of relative displacement between the user's hand and a wearable exoskeleton, the HX. HX has been designed to maximize comfort, wearability and user safety, exploiting chains with multiple degrees-of-freedom with a modular architecture. These appealing features may introduce several uncertainties in the kinematic performances, especially when considering the anthropometry, morphology and degree of mobility of the human hand. The small relative displacements between the hand and the exoskeleton were measured with a video-based motion capture system, while the user executed several different grips in different exoskeleton modes. CONCLUSIONS: The analysis furnished quantitative results about the device performance, differentiated among device modules and test conditions. In general, the global relative displacement for the distal part of the device was in the range 0.5-1.5 mm, while within 3 mm (worse but still acceptable) for displacements nearest to the hand dorsum. Conclusions over the HX design principles have been drawn, as well as guidelines for future developments.

Translating glycolytic metabolism to innate immunity in dendritic cells.

Growing evidence supports a role for glycolysis in immune activation. Everts et al. (2014) now show that TLR-mediated stimulation of dendritic cells rapidly induces glycolysis, which regenerates NADPH and TCA intermediates to support fatty acid production. This enhances ER and Golgi membrane synthesis and innate activation of dendritic cells.

Kinematics and design of a portable and wearable exoskeleton for hand rehabilitation.

We present the kinematic design and actuation mechanics of a wearable exoskeleton for hand rehabilitation of post-stroke. Our design method is focused on achieving maximum safety, comfort and reliability in the interaction, and allowing different users to wear the device with no manual regulations. In particular, we propose a kinematic and actuation solution for the index finger flexion/extension, which leaves full movement freedom on the abduction-adduction plane. This paper presents a detailed kineto-static analysis of the system and a first prototype of the device.

NEUROExos: A powered elbow orthosis for post-stroke early neurorehabilitation.

This paper presents the development of a portable version of the robotic elbow exoskeleton NEUROExos, designed for the treatment of stroke survivors in acute/sub-acute phases. The design was improved by a novel Series Elastic Actuation (SEA) system. The system implements two control modalities: a near-zero output impedance torque control and a passive-compliance position control.

MF59 and Pam3CSK4 boost adaptive responses to influenza subunit vaccine through an IFN type I-independent mechanism of action.

The innate immune pathways induced by adjuvants required to increase adaptive responses to influenza subunit vaccines are not well characterized. We profiled different TLR-independent (MF59 and alum) and TLR-dependent (CpG, resiquimod, and Pam3CSK4) adjuvants for the ability to increase the immunogenicity to a trivalent influenza seasonal subunit vaccine and to tetanus toxoid (TT) in mouse. Although all adjuvants boosted the Ab responses to TT, only MF59 and Pam3CSK4 were able to enhance hemagglutinin Ab responses. To identify innate immune correlates of adjuvanticity to influenza subunit vaccine, we investigated the gene signatures induced by each adjuvant in vitro in splenocytes and in vivo in muscle and lymph nodes using DNA microarrays. We found that flu adjuvanticity correlates with the upregulation of proinflammatory genes and other genes involved in leukocyte transendothelial migration at the vaccine injection site. Confocal and FACS analysis confirmed that MF59 and Pam3CSK4 were the strongest inducers of blood cell recruitment in the muscle compared with the other adjuvants tested. Even though it has been proposed that IFN type I is required for adjuvanticity to influenza vaccines, we found that MF59 and Pam3CSK4 were not good inducers of IFN-related innate immunity pathways. By contrast, resiquimod failed to enhance the adaptive response to flu despite a strong activation of the IFN pathway in muscle and lymph nodes. By blocking IFN type I receptor through a mAb, we confirmed that the adjuvanticity of MF59 and Pam3CSK4 to a trivalent influenza vaccine and to TT is IFN independent.