Boris Julg

Staphylococcus aureus remains a major global pathogen with no licensed vaccine and high recurrent infection burden, yet correlates of protection remain undefined. In a prospective pediatric cohort, we profiled 319 children spanning non-carriers, asymptomatic carriers, those with skin and soft tissue infection (SSTI), or invasive disease. We interrogated 182,149 antibody features, generating the most comprehensive S. aureus immune profiling dataset to date. Antibody responses increased with age, marked by expansion of IgG subclasses and Fc-receptor engagement. Asymptomatic carriage was associated with functional antibody profiles targeting conserved surface antigens and select toxins. Multivariate modeling robustly distinguished clinical phenotypes and identified high-value antigens associated with disease resilience. Protection from recurrent disease converged on enhanced FcγR binding and antibody effector function. These findings nominate key antigen targets, and highlight anti-Hla neutralizing antibodies and functional antibodies to additional surface antigens that can be recapitulated through Fc engineering, informing next-generation vaccine and monoclonal antibody strategies.

Background Despite high vaccination coverage, pertussis has resurged globally. Whole-cell (wP) and acellular (aP) pertussis vaccines induce distinct immune profiles, yet immune correlates of protection against infection and symptomatic disease remain incompletely defined. We leveraged a controlled human infection model (CHIM) to identify systemic and mucosal humoral signatures associated with resistance to Bordetella pertussis. Methods Adults with documented history of vaccination had previously been enrolled in a CHIM study and challenged intranasally with B. pertussis D420. For the present work, longitudinal serum and nasal wash samples were analyzed using systems serology to comprehensively profile antibody features. Multivariate modeling and network analyses were performed to define discriminatory immune features. Findings Baseline aP vaccine antigen-specific antibodies did not distinguish infection outcomes. In wP-primed individuals, protection from B. pertussis infection was associated with broad, high-magnitude, polyfunctional antibody responses targeting non-canonical antigens, including BrkA, TcfA, OmpP, OmlA, FauA, and Pal. Protective signatures associated with resistance to symptomatic disease in both vaccine groups were characterized by enhanced Fc-receptor-engaging antibody profiles with distinct antigenic patterns shaped by vaccine history. Importantly, while conventional aP vaccine antigens failed to reliably distinguish individuals susceptible to infection or symptom development, correlates generated by integrated serum and mucosal models based on select non-canonical antigens achieved near-perfect discrimination of infection and symptom outcomes, outperforming models restricted to aP-vaccine. antigens only. Interpretation Resistance to infection was largely restricted to wP-primed individuals and was associated with integrated systemic and mucosal antibody responses directed against antigens beyond those included in acellular vaccines. Protection from symptomatic disease in both vaccine groups was linked to distinct antibody response signatures, shaped by prior vaccination history. These findings indicate that immune mechanisms preventing infection differ from those limiting clinical disease and provide a framework for redesign of next-generation pertussis vaccines aimed at blocking infection and symptomatic disease.

Broadly neutralizing antibodies (bnAbs) against HIV-1 are promising components of long-acting antiretroviral treatment (ART) due to their prolonged activity and potential for recruiting additional immune effector functions. Their use is most advanced in virologically suppressed people living with HIV-1 switching from a standard daily ART regimen to a long-acting regimen comprising one or two bnAbs combined with one of the currently approved long-acting small-molecule inhibitors: cabotegravir or lenacapavir. Implementation of bnAb-based therapies, however, requires accurate assessment of viral susceptibility. Although phenotypic assays provide the most direct and reliable measures of bnAb activity, their limited scalability has prompted interest in genotypic approaches. Here we summarize evidence linking HIV-1 Env sequence characteristics to reduced bnAb susceptibility, including in vivo selection data in animal models and human studies, and in vitro selection and susceptibility data. Although genotypic analysis of HIV-1 Env may reliably identify resistance in some viruses, more research is required before genotypic methods can reliably predict susceptibility in clinical settings.

In-depth analyses of clinical samples have the potential to provide unparalleled insights into the cellular mechanisms that underlie both health and disease, as well as therapeutic and prophylactic responses. However, these specimens are often paucicellular, necessitating the use of workflows that maximize the amount of information that can be learned. Here we provide a detailed protocol for generating and analyzing single-cell multiomic data from low-input samples with the Seq-Well S³ platform. We further describe a matched pipeline for sample hashing that reduces costs and sources of technical variation in the resulting data while also enhancing throughput. In brief, our streamlined and efficient methodology involves: (1) optionally staining single-cell suspensions with antibody–oligonucleotide conjugates for cell surface protein quantification and/or sample multiplexing; (2) generating Seq-Well S³ sequencing libraries; (3) optionally producing bulk-RNA sequencing libraries via SMART-seq2 to support genetic demultiplexing; and (4) computationally analyzing the resulting data. Each step herein has been designed to leverage readily available reagents and standard laboratory equipment, substantially lowering barriers to entry for researchers. The overall Protocol can yield high-quality multiomic insights from samples in under a week.

Systemic administration of influenza virus–specific monoclonal antibodies achieves low concentrations in the nasal mucosa, the portal of infection. Intranasal administration may be more relevant for preventing infection, but the pharmacokinetics of intranasal influenza antibodies is unknown. We present results of preclinical studies and first-in-human phase 1 trials of the intranasally administered CR9114, an anti–hemagglutinin stem antibody that protects against influenza A and B viruses. We tested safety and tolerability of different schedules and doses; pharmacokinetics in nasal mucosal lining fluid of the nose and nasopharynx, saliva, and serum; and ex vivo functionality. We evaluated in vivo efficacy of CR9114 in mice and nonhuman primates. Intranasal CR9114 was safe and well tolerated across all doses and schedules. The half-life of CR9114 in the nose was ~3 hours. Steady-state concentrations were rapidly attained and sustained with multidosing. Trough concentrations were up to 92-fold higher with twice-daily administration compared with once-daily administration. Pharmacokinetics of intranasal CR9114 in nonhuman primates mirrored that of humans better than mice. Postdose nasal samples potently bound hemagglutinin from diverse strains of influenza A and B viruses and, particularly at the 10-milligram dose, neutralized A/H1N1, A/H5N1, and A/H3N2 more potently than baseline samples. Twice-daily administration of CR9114 protected nonhuman primates against influenza virus challenge with the same intranasal formulation and device as used in humans, providing evidence for the efficacy of intranasal multidosing. Together, these study findings characterize the pharmacokinetics of CR9114 after intranasal administration and provide proof of concept that intranasal antibodies can elicit efficacious passive immunity against influenza viruses.

Reducing the latent HIV-1 reservoir is essential to achieving a functional cure, and therapeutic vaccination is a promising strategy. While most approaches emphasize cytotoxic CD8⁺ T-cell responses, the role of antibodies—particularly Fc-mediated effector functions—remains incompletely defined. We evaluated the immunogenicity and functional antibody responses induced by Ad26- and MVA-based HIV-1 mosaic vaccines in SHIV-infected rhesus macaques and ART-suppressed people with HIV. In nonhuman primates, vaccination significantly increased Env-specific antibody titers, Fcγ receptor binding, and Fc-dependent functions, including cellular phagocytosis, complement deposition, and NK cell activation. Responses peaked following MVA boosting and, although they declined over time, remained elevated compared with unvaccinated controls. Humoral responses did not predict viral rebound during analytic treatment interruption but correlated inversely with post-ART viral setpoints, suggesting a role in viral control. In a parallel human study, therapeutic vaccination similarly elicited functional antibody responses, with the strongest effects observed following Ad26 mosaic vaccination combined with a gp140 protein boost, whereas Ad26 and MVA alone induced more modest responses. Ad26-based HIV vaccines, especially with protein boosting, elicit robust, multifunctional antibody responses; although human virologic outcomes remain untested, these findings support exploring Fc-mediated humoral immunity for viral control and cure strategies.

HIV-1 establishes a latent reservoir early in infection that persists during antiretroviral therapy (ART), typically leading to rapid viral rebound upon treatment interruption in most people living with HIV-1. However, a rare group known as post-treatment controllers (PTCs) can maintain low or undetectable viral loads for extended periods after ART cessation, offering critical insights into durable HIV remission. While immune responses are thought to play a key role in this control, the contribution of humoral immunity—particularly Fc-mediated antibody functions—remains insufficiently defined. In this study, we explored the influence of humoral responses on viral rebound in PTCs using a comprehensive systems serology approach. We profiled Env-specific antibody characteristics and Fc-effector functions—including antibody-dependent cellular phagocytosis, antibody-dependent neutrophil phagocytosis, antibody-dependent complement deposition, and antibody-dependent NK cell activation—in PTCs and matched non-controllers (NCs). Baseline antibody features prior to ART interruption did not clearly distinguish PTCs from NCs, and antibody responses evolved dynamically and in a highly individualized manner during viral rebound. Notably, distinct and individual-specific shifts in Fc-functional antibody signatures occurred during rebound, indicating that the humoral immune system actively adapts during this critical period. These findings highlight the complexity and adaptability of antibody-mediated responses, shaped by dynamic processes during rebound rather than static baseline features. This work underscores the value of longitudinal immune profiling to delineate how humoral immunity evolves in relation to, but not necessarily driving, post-treatment control. IMPORTANCE: Most people living with HIV experience a quick return of the virus after stopping antiretroviral therapy (ART). However, a small group—post-treatment controllers (PTCs)—can keep the virus suppressed without ongoing treatment. This study examined whether antibody responses, especially those involving Fc-mediated functions, play a role in this control. This study compared antibody features and immune functions in PTCs and matched individuals who did not control the virus after stopping ART. They found that antibody profiles before treatment interruption did not predict who would control the virus. Instead, antibody responses changed over time in unique ways during viral rebound. These shifts suggest that the immune system adapts dynamically rather than relying on fixed traits. The findings highlight the importance of tracking immune changes over time to better understand how long-term HIV control may occur, even if antibodies alone may not be the driving force behind post-treatment remission.

Broadly neutralizing antibodies (bNAbs) against HIV have demonstrated robust protective efficacy against sensitive viruses in humans and nonhuman primates. However, the potential of rare resistant viral variants to abrogate bNAb-based protection remains to be determined. Here we show that simian-human immunodeficiency virus (SHIV) challenge containing minor resistant variants can compromise protective efficacy of the V2-specific bNAb PGDM1400 in rhesus macaques. Macaques were infused with PGDM1400 and challenged intrarectally with either 500 monkey infectious dose 50 (MID50) of the PGDM1400-sensitive virus SHIV-325C or with 500 MID50 of SHIV-325C mixed with a sub-infectious 0.5 or 0.05 MID50 dose of the PGDM1400-resistant virus SHIV-SF162P3. All PGDM1400-treated animals challenged with SHIV-325C were protected as expected, but animals that received the mixed SHIV challenge were productively infected either with the resistant virus SHIV-SF162P3 or with rare resistant clones in the SHIV-325C challenge stock. These data demonstrate that minor resistant viral variants comprising just 0.01-0.1% of the challenge stock, at sub-infectious doses when administered alone, effectively abrogated bNAb protection against SHIV challenge in rhesus macaques. These findings suggest rare resistant variants may be more important than previously appreciated as a mechanism of virologic failure, emphasizing the importance of utilizing bNAb cocktails for HIV prevention.