Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth.

The dynamics of immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infants and young children by analyzing blood samples and weekly nasal swabs collected before, during, and after infection with Omicron and non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, showed no sign of decay for up to 300 days. Infants mounted a robust mucosal immune response characterized by inflammatory cytokines, interferon (IFN) α, and T helper (Th) 17 and neutrophil markers (interleukin [IL]-17, IL-8, and CXCL1). The immune response in blood was characterized by upregulation of activation markers on innate cells, no inflammatory cytokines, but several chemokines and IFNα. The latter correlated with viral load and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell multi-omics. Together, these data provide a snapshot of immunity to infection during the initial weeks and months of life.

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.

SREBP signaling is essential for effective B cell responses.

Our previous study using systems vaccinology identified an association between the sterol regulatory binding protein (SREBP) pathway and humoral immune response to vaccination in humans. To investigate the role of SREBP signaling in modulating immune responses, we generated mice with B cell- or CD11c+ antigen-presenting cell (APC)-specific deletion of SCAP, an essential regulator of SREBP signaling. Ablation of SCAP in CD11c+ APCs had no effect on immune responses. In contrast, SREBP signaling in B cells was critical for antibody responses, as well as the generation of germinal centers,memory B cells and bone marrow plasma cells. SREBP signaling was required for metabolic reprogramming in activated B cells. Upon mitogen stimulation, SCAP-deficient B cells could not proliferate and had decreased lipid rafts. Deletion of SCAP in germinal center B cells using AID-Cre decreased lipid raft content and cell cycle progression. These studies provide mechanistic insights coupling sterol metabolism with the quality and longevity of humoral immunity.

Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination.

Several studies have shown that the pre-vaccination immune state is associated with the antibody response to vaccination. However, the generalizability and mechanisms that underlie this association remain poorly defined. Here, we sought to identify a common pre-vaccination signature and mechanisms that could predict the immune response across 13 different vaccines. Analysis of blood transcriptional profiles across studies revealed three distinct pre-vaccination endotypes, characterized by the differential expression of genes associated with a pro-inflammatory response, cell proliferation, and metabolism alterations. Importantly, individuals whose pre-vaccination endotype was enriched in pro-inflammatory response genes known to be downstream of nuclear factor-kappa B showed significantly higher serum antibody responses 1 month after vaccination. This pro-inflammatory pre-vaccination endotype showed gene expression characteristic of the innate activation state triggered by Toll-like receptor ligands or adjuvants. These results demonstrate that wide variations in the transcriptional state of the immune system in humans can be a key determinant of responsiveness to vaccination.

Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses.

Systems vaccinology has defined molecular signatures and mechanisms of immunity to vaccination. However, comparative analysis of immunity to different vaccines is lacking. We integrated transcriptional data of over 3,000 samples, from 820 adults across 28 studies of 13 vaccines and analyzed vaccination-induced signatures of antibody responses. Most vaccines induced signatures of innate immunity and plasmablasts at days 1 and 7, respectively, after vaccination. However, the yellow fever vaccine induced an early transient signature of T and B cell activation at day 1, followed by delayed antiviral/interferon and plasmablast signatures that peaked at days 7 and 14-21, respectively. Thus, there was no evidence for a 'universal signature' that predicted antibody response to all vaccines. However, accounting for the asynchronous nature of responses, we defined a time-adjusted signature that predicted antibody responses across vaccines. These results provide a transcriptional atlas of immunity to vaccination and define a common, time-adjusted signature of antibody responses.

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.

Metabolic Phenotypes of Response to Vaccination in Humans.

Herpes zoster (shingles) causes significant morbidity in immune compromised hosts and older adults. Whereas a vaccine is available for prevention of shingles, its efficacy declines with age. To help to understand the mechanisms driving vaccinal responses, we constructed a multiscale, multifactorial response network (MMRN) of immunity in healthy young and older adults immunized with the live attenuated shingles vaccine Zostavax. Vaccination induces robust antigen-specific antibody, plasmablasts, and CD4+ T cells yet limited CD8+ T cell and antiviral responses. The MMRN reveals striking associations between orthogonal datasets, such as transcriptomic and metabolomics signatures, cell populations, and cytokine levels, and identifies immune and metabolic correlates of vaccine immunity. Networks associated with inositol phosphate, glycerophospholipids, and sterol metabolism are tightly coupled with immunity. Critically, the sterol regulatory binding protein 1 and its targets are key integrators of antibody and T follicular cell responses. Our approach is broadly applicable to study human immunity and can help to identify predictors of efficacy as well as mechanisms controlling immunity to vaccination.

Systems vaccinology of the BNT162b2 mRNA vaccine in humans.

The emergency use authorization of two mRNA vaccines in less than a year from the emergence of SARS-CoV-2 represents a landmark in vaccinology1,2. Yet, how mRNA vaccines stimulate the immune system to elicit protective immune responses is unknown. Here we used a systems vaccinology approach to comprehensively profile the innate and adaptive immune responses of 56 healthy volunteers who were vaccinated with the Pfizer-BioNTech mRNA vaccine (BNT162b2). Vaccination resulted in the robust production of neutralizing antibodies against the wild-type SARS-CoV-2 (derived from 2019-nCOV/USA_WA1/2020) and, to a lesser extent, the B.1.351 strain, as well as significant increases in antigen-specific polyfunctional CD4 and CD8 T cells after the second dose. Booster vaccination stimulated a notably enhanced innate immune response as compared to primary vaccination, evidenced by (1) a greater frequency of CD14+CD16+ inflammatory monocytes; (2) a higher concentration of plasma IFNγ; and (3) a transcriptional signature of innate antiviral immunity. Consistent with these observations, our single-cell transcriptomics analysis demonstrated an approximately 100-fold increase in the frequency of a myeloid cell cluster enriched in interferon-response transcription factors and reduced in AP-1 transcription factors, after secondary immunization. Finally, we identified distinct innate pathways associated with CD8 T cell and neutralizing antibody responses, and show that a monocyte-related signature correlates with the neutralizing antibody response against the B.1.351 variant. Collectively, these data provide insights into the immune responses induced by mRNA vaccination and demonstrate its capacity to prime the innate immune system to mount a more potent response after booster immunization.

Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures.

Systems approaches have been used to describe molecular signatures driving immunity to influenza vaccination in humans. Whether such signatures are similar across multiple seasons and in diverse populations is unknown. We applied systems approaches to study immune responses in young, elderly, and diabetic subjects vaccinated with the seasonal influenza vaccine across five consecutive seasons. Signatures of innate immunity and plasmablasts correlated with and predicted influenza antibody titers at 1 month after vaccination with >80% accuracy across multiple seasons but were not associated with the longevity of the response. Baseline signatures of lymphocyte and monocyte inflammation were positively and negatively correlated, respectively, with antibody responses at 1 month. Finally, integrative analysis of microRNAs and transcriptomic profiling revealed potential regulators of vaccine immunity. These results identify shared vaccine-induced signatures across multiple seasons and in diverse populations and might help guide the development of next-generation vaccines that provide persistent immunity against influenza.

Persistent SARS-CoV-2 PCR Positivity Despite Anti-viral Treatment in Immunodeficient Patients.

PURPOSE: COVID-19 infection in immunodeficient individuals can result in chronically poor health, persistent or relapsing SARS-CoV-2 PCR positivity, and long-term infectious potential. While clinical trials have demonstrated promising outcomes using anti-SARS-CoV-2 medicines in immunocompetent hosts, their ability to achieve sustained viral clearance in immunodeficient patients remains unknown. We therefore aimed to study long-term virological outcomes in patients treated at our centre. METHODS: We followed up immunocompromised inpatients treated with casirivimab-imdevimab (Ronapreve) between September and December 2021, and immunocompromised patients who received sotrovimab, molnupiravir, nirmatrelvir/ritonavir (Paxlovid), or no treatment from December 2021 to March 2022. Nasopharyngeal swab and sputum samples were obtained either in hospital or in the community until sustained viral clearance, defined as 3 consecutive negative PCR samples, was achieved. Positive samples were sequenced and analysed for mutations of interest. RESULTS: We observed sustained viral clearance in 71 of 103 patients, none of whom died. Of the 32/103 patients where sustained clearance was not confirmed, 6 died (between 2 and 34 days from treatment). Notably, we observed 25 cases of sputum positivity despite negative nasopharyngeal swab samples, as well as recurrence of SARS-CoV-2 positivity following a negative sample in 12 cases. Patients were then divided into those who cleared within 28 days and those with PCR positivity beyond 28 days. We noted lower B cell counts in the group with persistent PCR positivity (mean (SD) 0.06 (0.10) ×109/L vs 0.22 (0.28) ×109/L, p = 0.015) as well as lower IgA (median (IQR) 0.00 (0.00-0.15) g/L vs 0.40 (0.00-0.95) g/L, p = 0.001) and IgM (median (IQR) 0.05 (0.00-0.28) g/L vs 0.35 (0.10-1.10) g/L, p = 0.005). No differences were seen in CD4+ or CD8+ T cell counts. Antiviral treatment did not impact risk of persistent PCR positivity. CONCLUSION: Persistent SARS-CoV-2 PCR positivity is common among immunodeficient individuals, especially those with antibody deficiencies, regardless of anti-viral treatment. Peripheral B cell count and serum IgA and IgM levels are predictors of viral persistence.

Social Media Use in Psychiatric Graduate Medical Education: Where We Are and the Places We Could Go.

This commentary discusses the use of social media in psychiatric graduate medical education (GME) based on a systematic search of the literature. The authors conclude that research on social media use in psychiatric GME is in its infancy. For the most part, the few articles that have been published on this topic caution against the use of social media in psychiatric training. However, reports from other specialties, in which social media use in medical education has been more extensively studied, suggest that there may be significant benefits to incorporating social media into medical education. Although additional challenges may exist in implementing these tools in psychiatric education, the authors suggest that this is an emerging field of scholarship that merits further investigation.

Outcomes for ulnar collateral ligament reconstruction: a retrospective review using the KJOC assessment score with two-year follow-up in an overhead throwing population.

BACKGROUND: Injury to the ulnar collateral ligament (UCL) often results in valgus elbow instability requiring reconstruction. No standardized and validated outcome measure has compared outcomes between surgical techniques and institutions in the overhead throwing athlete. The aim of this study was to use the Kerlan-Jobe Orthopaedic Clinic shoulder and elbow score (KJOC score) to report functional outcomes in overhead throwing athletes undergoing UCL reconstruction. We predict that the KJOC score in our general throwing population will provide an accurate assessment of postoperative outcomes consistent with previously published reports. METHODS: A retrospective review of 33 patients undergoing UCL reconstruction was carried out during a 5-year period between 2004 and 2009. Minimum follow-up was 2.2 years with an average of 3.7 years. All surgeries were performed by fellowship-trained surgeons using either the docking (n = 12) or modified Jobe technique (n = 21). Age, sport, position, and return to play status were obtained. The KJOC score was administered to assess final functional outcome. RESULTS: A total of 33 athletes underwent UCL reconstruction-30 baseball players and 3 javelin throwers. Of these, 27 (82%) returned to their sport at their previous level in an average of 12.25 months. The overall average KJOC score was 76. Athletes who returned to their previous level of play had a mean KJOC score of 77. Those who were unable to return to play had a mean score of 69. CONCLUSION: Our study demonstrates consistent outcomes for UCL reconstruction using the KJOC shoulder and elbow score compared with previously reported data.

Serial founder effects slow range expansion in an invasive social insect.

Invasive populations often experience founder effects: a loss of genetic diversity relative to the source population, due to a small number of founders. Even where these founder effects do not impact colonization success, theory predicts they might affect the rate at which invasive populations expand. This is because secondary founder effects are generated at advancing population edges, further reducing local genetic diversity and elevating genetic load. We show that in an expanding invasive population of the Asian honey bee (Apis cerana), genetic diversity is indeed lowest at range edges, including at the complementary sex determiner, csd, a locus that is homozygous-lethal. Consistent with lower local csd diversity, range edge colonies had lower brood viability than colonies in the range centre. Further, simulations of a newly-founded and expanding honey bee population corroborate the spatial patterns in mean colony fitness observed in our empirical data and show that such genetic load at range edges will slow the rate of population expansion.

A Qualitative Exploration of Self-Advocacy Experiences of Black Women in the Perinatal Period: Who Is Listening?

INTRODUCTION: Black women face poor maternal health outcomes including being over 3 times more likely to die from pregnancy complications than White women. Yet the lived experience of how these women self-advocate has not been clearly explored. The goal of this cross-sectional qualitative study was to describe the lived experiences of Black women advocating for their needs and priorities during the perinatal period. METHODS: Between January and October of 2022, we recruited Black women from obstetric clinics, research registries, and community advocacy groups who were either in their third trimester of pregnancy or within a year postpartum. Participants completed one-on-one interviews describing their experiences of self-advocacy. These data were analyzed using descriptive content analysis approaches that summarized women's experiences by iteratively creating major themes and subthemes that encapsulate their self-advocacy descriptions. RESULTS: Fifteen Black women completed interviews. Major themes and subthemes describing women's experience of self-advocacy were the following: (1) carrying a burden with subthemes of having to be good and easy, not trusting health care information and providers, and being dismissed; (2) building comfort with health care providers with subthemes of trusting I have a good provider, comfort in knowing they understand, and wanting low-touch, high-concern care; and (3) advocating for my child and myself when I need to with subthemes of going with the flow, becoming informed, pushing to ask questions, and balancing being proactive and pushy. DISCUSSION: Women reported self-advocating mainly due to experiences related to the burdens associated with not trusting providers and health care information. These findings provide clarity to how women carefully balance between ensuring their health is taken seriously while not jeopardizing their health or that of their newborn. This study offers promising directions to support Black women in advocating for their perinatal health care needs and values.

Drones Do Not Drift between Nests in a Wild Population of Apis cerana.

The modes through which individuals disperse prior to reproduction has important consequences for gene flow in populations. In honey bees (Apis sp.), drones (males) reproduce within a short flight range of their natal nest, leaving and returning each afternoon within a narrow mating window. Drones are assumed to return to their natal nests as they depend on workers to feed them. However, in apiaries, drones are reported to regularly make navigation errors and return to a non-natal nest, where they are accepted and fed by unrelated workers. If such a "drone drift" occurred in wild populations, it could facilitate some further degree of dispersal for males, particularly if drones drift into host nests some distance away from their natal nest. Here, we investigated whether drone drift occurs in an invasive population of the Asian honey bee (Apis cerana). Based on the genotypes of 1462 drones from 19 colonies, we found only a single drone that could be considered a candidate drifter (~0.07%). In three other colonies, drones whose genotypes differed from the inferred queen were best explained by recent queen turnover or worker-laying. We concluded that drone drift in this population is low at best, and A. cerana drones either rarely make navigation errors in wild populations or are not accepted into foreign nests when they do so. We therefore confirm that drone dispersal distance is limited to the distance of daily drone flights from natal nests, a key assumption of both colony density estimates based on sampling of drone congregation areas and population genetic models of gene flow in honey bees.

What are We Asking Patients to Do? A Critical Ethical Review of the Limits of Patient Self-Advocacy in the Oncology Setting.

Increasing emphasis on patient self-management, including having patients advocate for their needs and priorities, is generally a good thing, but it is not always wanted or attainable by patients. The aim of this critical ethical review is to deepen the current discourse in patient self-advocacy by exposing various situations in which patients struggle to self-advocate. Using examples from oncology patient populations, we disambiguate different notions of self-advocacy and then present limits to the more demanding varieties (i.e., health-related, trust-based, and psychological); we argue that these limits create ethical dilemmas with respect to whether it is always desirable to encourage patients to self-advocate. We conclude that self-advocacy can be both under and overrated with respect to how much it benefits the patient with cancer, with many instances being indeterminate. Ultimately, providers must understand the patient's perspective relative to the challenges they are experiencing and work with them to meet their needs.

Describing Self-Advocacy in Underrepresented Women With Advanced Cancer.

PURPOSE: To describe the self-advocacy experiences of women from underrepresented groups who have advanced breast or gynecologic cancer. PARTICIPANTS & SETTING: To be eligible for the study, participants had to self-identify as vulnerable, which was defined as a member of a group considered at risk for poor cancer outcomes and underrepresented in clinical research. METHODOLOGIC APPROACH: This descriptive, longitudinal, qualitative study consisted of one-on-one interviews of women within three months of an advanced breast or gynecologic cancer diagnosis. FINDINGS: 10 participants completed 25 interviews. The average age of participants was 60.2 years (range = 38-75 years). Three major themes emerged: (a) speaking up and speaking out, (b) interacting with the healthcare team, and (c) relying on support from others. IMPLICATIONS FOR NURSING: Women with advanced cancer who are from underrepresented groups self-advocated in unique ways, learning over time the importance of how to communicate their needs and manage their healthcare team. Future research should incorporate these findings into tailored self-advocacy interventions.

A Scoping Review on Work Experiences of Nurses After Being Diagnosed With Cancer.

PROBLEM IDENTIFICATION: To map key concepts underpinning work-related studies about nurses with cancer and identify knowledge gaps. LITERATURE REVIEW: A search was conducted in the PubMed®, CINAHL®, and PsycINFO® databases for articles about nurses with cancer and work-related topics published through March 2023. DATA EVALUATION: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews Checklist was used to report results, and the JBI critical appraisal tools were used to assess the quality of studies. Eleven articles were included. SYNTHESIS: The following four critical concepts were identified: role adjustments at work, cancer impacts on work, organizational support, and translating insights gained from cancer experience into work. Research gaps identified by the scoping review were a lack of theoretical or conceptual frameworks, lack of syntheses of main ideas, and lack of clear data about participants' socioeconomic status across studies. IMPLICATIONS FOR RESEARCH: Minimal research exists to map predictors, outcomes, or intervention targets to guide organizational strategies to support nurses' retention in the nursing workforce. A guiding framework, recruitment of diverse nurses, and focus on the four critical concepts identified in this scoping review are suggested for future research.