Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood

Infancy and childhood are critical life stages for generating immune memory to protect against pathogens; however, the timing, location, and pathways for memory development in humans remain elusive. Here, we investigated T cells in mucosal sites, lymphoid tissues, and blood from 96 pediatric donors aged 0-10 years using phenotypic, functional, and transcriptomic profiling. Our results revealed that memory T cells preferentially localized in the intestines and lungs during infancy and accumulated more rapidly in mucosal sites compared with blood and lymphoid organs, consistent with site-specific antigen exposure. Early life mucosal memory T cells exhibit distinct functional capacities and stem-like transcriptional profiles. In later childhood, they progressively adopt proinflammatory functions and tissue-resident signatures, coincident with increased T cell receptor (TCR) clonal expansion in mucosal and lymphoid sites. Together, our findings identify staged development of memory T cells targeted to tissues during the formative years, informing how we might promote and monitor immunity in children.

SARS-CoV-2 infection and recovery in children: Distinct T cell responses in MIS-C compared to COVID-19

SARS-CoV-2 infection for most children results in mild or minimal symptoms, though in rare cases severe disease can develop, including a multisystem inflammatory syndrome (MIS-C) with myocarditis. Here, we present longitudinal profiling of immune responses during acute disease and following recovery in children who developed MIS-C, relative to children who experienced more typical symptoms of COVID-19. T cells in acute MIS-C exhibited transient signatures of activation, inflammation, and tissue residency which correlated with cardiac disease severity, while T cells in acute COVID-19 upregulated markers of follicular helper T cells for promoting antibody production. The resultant memory immune response in recovery showed increased frequencies of virus-specific memory T cells with pro-inflammatory functions in children with prior MIS-C compared to COVID-19 while both cohorts generated comparable antibody responses. Together our results reveal distinct effector and memory T cell responses in pediatric SARS-CoV-2 infection delineated by clinical syndrome, and a potential role for tissue-derived T cells in the immune pathology of systemic disease.

Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity

Infants and young children are more susceptible to common respiratory pathogens than adults but can fare better against novel pathogens like severe acute respiratory syndrome coronavirus 2. The mechanisms by which infants and young children mount effective immune responses to respiratory pathogens are unknown. Through investigation of lungs and lung-associated lymph nodes from infant and pediatric organ donors aged 0-13 years, we show that bronchus-associated lymphoid tissue (BALT), containing B cell follicles, CD4+ T cells and functionally active germinal centers, develop during infancy. BALT structures are prevalent around lung airways during the first 3 years of life, and their numbers decline through childhood coincident with the accumulation of memory T cells. Single-cell profiling and repertoire analysis reveals that early life lung B cells undergo differentiation, somatic hypermutation and immunoglobulin class switching and exhibit a more activated profile than lymph node B cells. Moreover, B cells in the lung and lung-associated lymph nodes generate biased antibody responses to multiple respiratory pathogens compared to circulating antibodies, which are mostly specific for vaccine antigens in the early years of life. Together, our findings provide evidence for BALT as an early life adaptation for mobilizing localized immune protection to the diverse respiratory challenges during this formative life stage.

Tissue immunity to SARS-CoV-2: Role in protection and immunopathology

The SARS-CoV-2 pandemic has demonstrated the importance of studying antiviral immunity within sites of infection to gain insights into mechanisms for immune protection and disease pathology. As SARS-CoV-2 is tropic to the respiratory tract, many studies of airway washes, lymph node aspirates, and postmortem lung tissue have revealed site-specific immune dynamics that are associated with the protection or immunopathology but are not readily observed in circulation. This review summarizes the growing body of work identifying immune processes in tissues and their interplay with immune responses in circulation during acute SARS-CoV-2 infection, severe disease, and memory persistence. Establishment of tissue resident immunity also may have implications for vaccination and the durability of immune memory and protection.

Children with Multi-System Inflammatory Syndrome (MIS-C) develop functionally competent T cell memory against SARS-CoV-2 following recovery

While pediatric SARS-CoV-2 infection is largely spared from severe COVID-19, a small fraction of children develop a life-threatening condition known as MIS-C, which is associated with an aberrant peripheral blood immunophenotype; namely within adaptive immune cell populations. Little is known about how MIS-C impacts memory generation that would be imperative for future SARS-CoV-2 responses. Here, we used high dimensional flow cytometry and TCR sequencing to assess the peripheral blood T cell profile during acute MIS-C (n=17), following recovery (MIS-C-R) up to 9 months post-MIS-C (n=9), and relative to age-matched convalescent, mild pediatric COVID-19 (non-MIS-C; n=5) and uninfected controls (n=3). We also applied antigen-specific analyses to determine the magnitude and functional capacity of SARS-CoV-2-specific T cells in MIS-C-R (n=10) and non-MIS-C children (n=16). Flow cytometry showed unique T cell composition in MIS-C which resolved in recovery: lacking persistence of exhausted CD8+ T cells observed during MIS-C, and reestablishment of the naïve T cell pool. TCR sequencing showed decreased clonal diversity and distinct TCR Vβ usage in acute MIS-C compared to MIS-C-R. Results from antigen-specific analyses show that while T cell memory is similar phenotypically, MIS-C-R children have greater frequencies of SARS-CoV-2-specific CD4+ T cells than non-MIS-C up to 9 months since diagnosis. Meanwhile, SARS-CoV-2-specific CD8+ T cells in MIS-C children were more cytokine-producing, while more cytotoxic in non-MIS-C children. Together, these results reveal a restoration in global T cell phenotype in MIS-C-R children, as well as the robust production of functionally competent SARS-CoV-2 specific T cell memory.

This work is supported by grants from NIH (K23 AI141686, 3U01 AI100119-10S1)

Tissue- and age-specific adaptations of human γδT cells in early life

γδT cells are unconventional T lymphocytes which seed peripheral tissues in early life. They provide frontline anti-pathogen, anti-cancer and homeostatic responses, rapidly initiated in response to signals of cellular stress independent of MHC-recognition. However, the role of γδT cells in humans has been difficult to assess given their purported tissue residency. Using tissues obtained from organ donors, we conducted flow cytometry, TCR-sequencing, and stimulation assays on γδT cells isolated from blood, spleen, lung, intestines and lymph nodes (LN) to create an ‘atlas’ across the human body throughout life. γδT cells were enriched in the blood, spleen, lung, and jejunum in early life, whereas LN proportions were maintained at low levels. Vδ1 and Vδ2 γδT cell subsets also exhibited tissue- and age-specific phenotypes: Vδ1 cells predominated in all organs in infancy except the lung. They were ‘naïve-like’, acquiring a mature phenotype with age, whereas Vδ2 possessed an effector memory signature, even in donors a few days old. Functionally, Vδ2 cells produced IFNγ, TNFα, GzmB and perforin at high levels in childhood. By contrast, Vδ1 cells favored Areg production during infancy but acquired a cytotoxic profile into adulthood. TCR analysis revealed clonal expansion in mucosal organs, whereas lymphoid sites had increased diversity in early life. Despite this site-specific clonal expansion, V-chain usage was stably distributed across organs and did not show the tissue-specific biases seen in mice. Our analyses reveal that γδT cells may play an outsized role in pediatric tissue immune responses and identify potentially divergent roles of specific subsets that contribute to tissue immunity during the most vulnerable years of life.

Persistence of immune memory to SARS-CoV-2 vaccine in lymphoid tissue

Immunization with novel mRNA vaccines against SARS-CoV-2 administered worldwide protects against COVID-19 through the generation of neutralizing antibodies directed against the viral spike protein. While immune responses generated from vaccines have been evaluated in blood, the cellular stores of memory T and B cells are maintained in tissues. Using tissues from vaccinated, but previously uninfected organ donors, we surveyed lymphoid and barrier sites for the presence of SARS-CoV-2 vaccine specific memory B and T cells. Fluorescently labeled, full length Spike and RBD probes were used to identify vaccine specific memory B cells, while vaccine specific T cells were identified by expression of activation induced markers following stimulation with peptide pools spanning the entire spike protein. All donors were confirmed negative for anti-nucleocapsid antibodies and positive for anti-spike and anti-RBD antibodies via ELISA. Spike specific T cells were identified in the blood, spleen, lung, and lung associated lymph nodes (LLN), but not bone marrow (BM). In all tissues, these vaccine specific T cells were primarily CD4 and exhibited a mixed central- and effector-memory phenotype; in the LLN the majority (up to 55%) were T-follicular helper cells (CXCR5+/PD-1+). Spike and RBD specific memory B cells were detected in blood, lung, spleen, BM, and LLN. These vaccine specific B cells in the LLN specifically expressed the tissue residency marker CD69, but only a minority had features of germinal center B cells. These results indicate that memory B and T cells generated from mRNA vaccination localize primarily to lymphoid organs, including those draining the lung, which is important for understanding their longevity and protective capacity.

Supported by grants from NIH (U19 AI128949, PO1  AI106697, T32 GM007367)

Early Life Development of Bronchial Associated Lymphoid Tissue Containing Germinal Center in the Human Lung

Early life susceptibility to respiratory pathogens is well established in infants and young children, however the specific adaptations of the infant immune system for responding to multiple respiratory challenges are not known. Here, we examined lung and lung-associated lymph nodes derived from infant and pediatric organ donors (0–13 years) by confocal immunofluorescence and high dimensional flow cytometry. We identified early formation of bronchial associated lymphoid tissue (BALT) where active immune responses are initiated. At 8 days of life, few immune cells were present around the airways. By 5 months old, we start to observe BALT formation. However, BALT lose their structure with aging and are mostly absent by 10 years of age with CD4 memory T cells dominating the population around the central airways. Germinal centers are seen in 50–60% of BALT during the first two years of life. The percentage of BALT with germinal centers decreases over age, while germinal center formation in lung lymph nodes is maintained throughout infancy and childhood. Flow cytometry data shows seeding of transitional and immature B cells in the lung during infancy, which decreases over age. However, proportion of IgG and IgA memory B cells increases significantly over age both in the lung and lung lymph nodes. The frequency of naïve B cells is stable throughout childhood in both sites. Our results suggest that localized tertiary lymphoid structures in pediatric lungs may be an important mechanism for mobilizing rapid in situ protection during the first few years of life when memory T cells and B cells are not fully established.

Supported by grants listed below: “Human Atlas of Neonatal Development and Early Life-Immunity (HANDEL-I)”(award Number 2018PG-T1D071 The Leona M. and Harry B. Helmsley Charitable Trust) “Immunobiology and alveolar physiology of the aging lung” (U01 HL145547, NIH/NHLBI )  

Dietary iron deficiency impairs the functionality but not generation or establishment of memory T cells following influenza infection

Protection from viral respiratory tract infections (VRTIs) is dependent on the activation, differentiation, and maintenance of antigen specific memory T cells. Iron is essential for fundamental metabolic processes in the human body, with iron deficiency, the most prevalent micronutrient deficiency worldwide, resulting in increased morbidity and mortality to VRTIs. The role of iron in the establishment and maintenance of memory T cells is not fully defined. Using a murine model of dietary iron modulation, we define the impact of iron deficiency on anti-viral T cell memory formation, functionality, and resultant protection during primary and heterosubtypic influenza infections. Multi-parameter flow cytometry and stimulation assays were performed on T cells isolated from lung and spleen at effector and memory time points following primary (X31) infection, as well as 5 days post heterosubtypic (PR8) challenge. Strikingly, there was no significant difference in the numbers or proportions of CD4+ and CD8+ influenza specific memory T-cells at any time point when comparing iron deficient to iron replete mice. However, memory T cells generated by iron deficient mice displayed impaired production of key effector cytokines, most notably IFN-γ and IL-17a. Importantly, following heterosubtypic challenge, iron deficient mice exhibited increased morbidity, as defined by increased weight loss, and significantly diminished IFN-γ production by T cells across all sites. This work reveals that distinct iron profiles did not interfere with the generation or maintenance of influenza specific T cells but iron deficiency significantly impacts memory T cell anti-viral functionality resulting in impaired protective responses.

Supported by -K23 AI141686 -UL1 TR001873

Inactivated and live-attenuated seasonal influenza vaccines boost broadly neutralizing antibodies in children

The induction of broadly neutralizing antibodies (bNAbs) that target the hemagglutinin stalk domain is a promising strategy for the development of “universal” influenza virus vaccines. bNAbs can be boosted in adults by sequential exposure to heterosubtypic viruses through natural infection or vaccination. However, little is known about if or how bNAbs are induced by vaccination in more immunologically naive children. Here, we describe the impact of repeated seasonal influenza vaccination and vaccine type on induction of bNAbs against group 1 influenza viruses in a pediatric cohort enrolled in randomized controlled trials of seasonal influenza vaccination. Repeated seasonal vaccination results in significant boosting of a durable bNAb response. Boosting of serological bNAb titers is comparable within inactivated and live attenuated (LAIV) vaccinees and declines with age. These data provide insights into vaccine-elicited bNAb induction in children, which have important implications for the design of universal influenza vaccine modalities in this critical population.

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Repeated inactivated influenza vaccination boosts bNAbs

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Inactivated and live attenuated vaccines are similarly efficient at boosting bNAbs

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The magnitude of IIV and LAIV vaccine-elicited bNAb boosting declines with age

SARS-CoV-2 infection generates tissue-localized immunological memory in humans

[Figure: see text].

Human parainfluenza virus evolution during lung infection of immunocompromised humans promotes viral persistence

The capacity of respiratory viruses to undergo evolution within the respiratory tract raises the possibility of evolution under the selective pressure of the host environment or drug treatment. Long-term infections in immunocompromised hosts are potential drivers of viral evolution and development of infectious variants. We show that intra-host evolution in chronic human parainfluenza virus 3 (HPIV3) infection in immunocompromised individuals elicited mutations that favor viral entry and persistence, suggesting that similar processes may operate across enveloped respiratory viruses. We profiled longitudinal HPIV3 infections from two immunocompromised individuals that persisted for 278 and 98 days. Mutations accrued in the HPIV3 attachment protein hemagglutinin-neuraminidase (HN), including the first in vivo mutation in HN's receptor binding site responsible for activating the viral fusion process. Fixation of this mutation was associated with exposure to a drug that cleaves host cell sialic acid moieties. Longitudinal adaptation of HN was associated with features that promote viral entry and persistence in cells, including greater avidity for sialic acid and more active fusion activity in vitro, but not with antibody escape. Long term infection thus led to mutations promoting viral persistence, suggesting that host-directed therapeutics may support the evolution of viruses that alter their biophysical characteristics to persist in the face of these agents in vivo.

Inhibition of Measles Viral Fusion Is Enhanced by Targeting Multiple Domains of the Fusion Protein

Measles virus (MeV) infection remains a significant public health threat despite ongoing global efforts to increase vaccine coverage. As eradication of MeV stalls, and vulnerable populations expand, effective antivirals against MeV are in high demand. Here, we describe the development of an antiviral peptide that targets the MeV fusion (F) protein. This antiviral peptide construct is composed of a carbobenzoxy-d-Phe-l-Phe-Gly (fusion inhibitor peptide; FIP) conjugated to a lipidated MeV F C-terminal heptad repeat (HRC) domain derivative. Initial in vitro testing showed high antiviral potency and specific targeting of MeV F-associated cell plasma membranes, with minimal cytotoxicity. The FIP and HRC-derived peptide conjugates showed synergistic antiviral activities when administered individually. However, their chemical conjugation resulted in markedly increased antiviral potency. In vitro mechanistic experiments revealed that the FIP-HRC lipid conjugate exerted its antiviral activity predominantly through stabilization of the prefusion F, while HRC-derived peptides alone act predominantly on the F protein after its activation. Coupled with in vivo experiments showing effective prevention of MeV infection in cotton rats, FIP-HRC lipid conjugates show promise as potential MeV antivirals via specific targeting and stabilization of the prefusion MeV F structure.

Genetic diversity and molecular epidemiology of respiratory syncytial virus circulated in Antananarivo, Madagascar, from 2011 to 2017: Predominance of ON1 and BA9 genotypes

BACKGROUND

Respiratory syncytial virus is the main cause of acute respiratory infections leading to a considerable morbidity and mortality among under-5 years children. A comprehensive scheme of RSV virus evolution is of great value in implementing effective universal RSV vaccine.

OBJECTIVE

We investigated the clinical spectrum and molecular characteristics of detected RSV over a period of seven years (January 2011 to June 2017) in Antananarivo, the capital city of Madagascar.

STUDY DESIGN

671 nasopharyngeal samples taken from children aged less than 5 years suffered from ARI were screened for RSV by real-time PCR. Clinical data were retrieved from case report forms. Genotype identification was performed by reverse-transcription PCR and sequencing of the second hyper variable region (HVR2) of the G glycoprotein.

RESULTS

Amongst samples tested, 292 (43.5 %) were found positive for RSV. RSV A predominated during the study period which accounted for 62.3 % (182/292) of positive samples while RSV B represented 37.0 % (108/292). Phylogenetic analyses identified NA1 and ON1 genotypes among RSV A. Though NA1 widespread from 2011 to 2013, ON1 became prevalent during the following years. Among RSV B, THB, CB1 and BA9 genotypes were detected. A co-circulation of THB and CB1 strains occurred during the 2011 season that was substituted by the BA9 from 2012. Malagasy ON1 strains carried some characteristic amino acid substitutions that distinguish them from the worldwide ON1 strains. By analyzing clinical spectrum, ON1 and BA genotypes seemed to prevail in mild infections compared to NA1.

CONCLUSION

Results obtained here will have its implication in predicting temporal evolution of RSV at the local level. Considering the insularity of the country, information obtained should help in comparative analysis with global RSV strains to optimize vaccine efficacy.

Effective in Vivo Targeting of Influenza Virus through a Cell-Penetrating/Fusion Inhibitor Tandem Peptide Anchored to the Plasma Membrane

The impact of influenza virus infection is felt each year on a global scale when approximately 5-10% of adults and 20-30% of children globally are infected. While vaccination is the primary strategy for influenza prevention, there are a number of likely scenarios for which vaccination is inadequate, making the development of effective antiviral agents of utmost importance. Anti-influenza treatments with innovative mechanisms of action are critical in the face of emerging viral resistance to the existing drugs. These new antiviral agents are urgently needed to address future epidemic (or pandemic) influenza and are critical for the immune-compromised cohort who cannot be vaccinated. We have previously shown that lipid tagged peptides derived from the C-terminal region of influenza hemagglutinin (HA) were effective influenza fusion inhibitors. In this study, we modified the influenza fusion inhibitors by adding a cell penetrating peptide sequence to promote intracellular targeting. These fusion-inhibiting peptides self-assemble into ∼15-30 nm nanoparticles (NPs), target relevant infectious tissues in vivo, and reduce viral infectivity upon interaction with the cell membrane. Overall, our data show that the CPP and the lipid moiety are both required for efficient biodistribution, fusion inhibition, and efficacy in vivo.