Péter Attila Szabó - Academia.edu (original) (raw)

Papers by Péter Attila Szabó

Nature Immunology

Genomics 5′ scRNA-seq, along with V region sequencing of TCRA and TCRB genes of T cells isolated ... more Genomics 5′ scRNA-seq, along with V region sequencing of TCRA and TCRB genes of T cells isolated from multiple tissue sites of individual donors. Barrier sites contain tissue-adapted T cell populations To examine subset composition and phenotypic heterogeneity of T cells maintained across the body, we used a high-dimensional CyTOF panel incorporating multiple markers of T cell differentiation, function, and migration to analyze CD3 + T cells obtained from blood and tissues of three donors, aged 22, 40 and 70 years (Fig. 1 and Supplementary Tables 1 and 2). Unsupervised clustering based on marker expression identified 31 clusters, representing heterogeneous populations of CD4 + and CD8 + T cell subsets (Fig. 1a and Extended Data Fig. 1a). Subsets included naive T cells (CCR7 + CD45RA + CD95 −), central memory T cells (T CM ; CCR7 + CD45RA − CD28 +), T EM (CCR7 − CD45RA −), T EMRA (CCR7 − CD45RA +) and T RM (CCR7 − CD45RA − CD69 +). Functional subsets included follicular helper T cells (T FH ; CD4 + CXCR5 + PD-1 + ICOS +) 22 , regulatory T cells (T reg ; CD4 + CD25 + CD127 −) 23 , type 1 helper T cells (T H 1), defined by the transcription factor T-bet 24 , and type 2 helper T cells (T H 2) with enhanced expression of CRTH2 (ref. 25). Innate-like T cells were mostly represented by γδ T cells (gdTCR + ; Fig. 1a,b). The composition of CD4 + and CD8 + T cell subsets was similar between individuals, despite their broad age range (Fig. 1c and Extended Data Fig. 1b). CD4 + T cells comprised subsets of naive, T CM , T FH , T reg and T RM subsets expressing CD69 and to a lesser extent CD103, T H 1-like cells expressing T-bet and the senescent marker CD57 (cluster 13), and T H 2-like CRTH2 + cells (cluster 20; Fig. 1a-c). CD8 + T cells comprised naive and memory subsets, along with higher frequencies of T EMRA cells and γδ T cells than in CD4 + T cells (Fig. 1a-c). CD8 + T EM and T EMRA cells were further subdivided on the basis of the differential expression of CD57, inhibitory molecules (PD-1, TIGIT) and cytotoxic mediators (granzyme B, perforin) (Fig. 1a,b). Between donors, the oldest donor had the lowest frequency of naive CD8 + T cells and a distinct population of T EM and T EMRA cells expressing CD57, TIGIT and PD-1 (cluster 14; Extended Data Figs. 1b and 2). For all donors, the composition and distribution of T cell subsets were site-specific, consistent with previous findings for naive and memory T cells assessed by flow cytometry 7-9,11. However, this high-dimensional profiling revealed which subpopulations were similar between sites and which had site-specific adaptations. Blood contained CD4 + naive, T CM , T EM and T reg , as well as CD8 + naive and T EM /T EMRA , populations (Fig. 1c,d and Extended Data Fig. 2), while all three lymph node sites contained a distinct composition from blood consisting of mostly CD4 + subsets (naive T CM , T FH , T RM and T reg) and lower frequencies of CD8 + naive and T RM cells (Fig. 1c,d and Extended Data Fig. 2). The spleen contained subsets found in both blood and lymph nodes, along with additional CD8 + T EM /T EMRA and T RM populations (Fig. 1c,d and Extended Data Fig. 2). Each barrier site, however, contained a unique composition of T cells compared with all the other sites (Fig. 1c,d and Extended Data Fig. 2). Lungs contained CD4 + and CD8 + T RM , distinct CD57 + T EM (clusters 13 and 19), T EMRA and γδ T (cluster 25) cells. Jejunum contained predominantly CD69 + CD103 + T RM cells and a Tbet + CCR5 + T FH population (cluster 18); skin contained CD4 + and CD8 + T RM cells expressing CXCR4 (clusters 10 and 12), implicated in skin T cell homing 26 , and T EM (cluster 8)

The Journal of Immunology

Natural killer (NK) cells are innate immune cells with the inherent ability to directly kill tumo... more Natural killer (NK) cells are innate immune cells with the inherent ability to directly kill tumor and virus infected cells. Due to their ability to kill cancer cells without any prior priming, and their role in preventing metastasis NK cells have since long been the choice for autologous adoptive cell transfer therapy in cancer. However, poor expansion potential of PBMC derived NK cells in vitro is a major roadblock preventing the widespread use of NK cells in immunotherapy. We found that human NK cells isolated from lymph nodes (LNs) express higher levels of genes encoding for stem-like transcription factors (TCF7, LEF1, MYC) compared to NK cells from blood, spleen, bone marrow (BM) and lung. Therefore, we hypothesized that NK cells isolated from LNs will show superior expansion potential in vitro. Flow cytometric analysis shows that LN derived NK cells express high levels of TCF1 protein ex vivo, and show greater proliferation compared to NK cells isolated from blood, spleen and ...

The Journal of Immunology

T cells persist as heterogeneous subsets throughout the body and are essential in mounting protec... more T cells persist as heterogeneous subsets throughout the body and are essential in mounting protective immune responses. In healthy humans, most of our knowledge of T cell activation derives from sampling the peripheral blood and therefore the transcriptional states of tissue T cells, their functional responses to stimulation, and how they relate to T cells in blood have been poorly defined. Here, we profile the activation dynamics of T cells isolated from human lungs (LG), lymph nodes (LN), bone marrow (BM) and blood following TCR-stimulation by single cell RNA-sequencing (scRNA-seq). Analysis of >50,000 individual resting and activated T cells using clustering and new factorization methods reveals lineage-specific gene expression signatures and discrete activation trajectories in all tissues. Between sites, T cells from LG and LN are most distinct, while blood T cells are most similar to those in BM but persist in a more activated basal state. We identify a common transcriptiona...

Nature Medicine

Older people are particularly susceptible to infectious and neoplastic diseases of the lung and i... more Older people are particularly susceptible to infectious and neoplastic diseases of the lung and it is unclear how lifelong exposure to environmental pollutants affects respiratory immune function. In an analysis of human lymph nodes (LNs) from 84 organ donors aged 11-93 years, we found a specific age-related decline in lung-associated, but not gut-associated, LN immune function linked to the accumulation of inhaled atmospheric particulate matter. Increasing densities of particulates were found in lung-associated LNs with age, but not in the corresponding gut-associated LNs. Particulates were specifically contained within CD68 + CD169 − macrophages, which exhibited decreased activation, phagocytic capacity, and altered cytokine production compared with non-particulate-containing macrophages. The structures of B cell follicles and lymphatic drainage were also disrupted in lung-associated LNs with particulates. Our results reveal that the cumulative effects of environmental exposure and age may compromise immune surveillance of the lung via direct effects on immune cell function and lymphoid architecture.

Science Immunology, 2021

SARS-CoV-2–specific memory cells persist in multiple sites months after infection, particularly i... more SARS-CoV-2–specific memory cells persist in multiple sites months after infection, particularly in lungs and associated lymph nodes.

Immunity, 2021

Immune response dynamics in COVID-19 and its severe manifestations have largely been studied in c... more Immune response dynamics in COVID-19 and its severe manifestations have largely been studied in circulation. Here, we examined the relationship between immune processes in the respiratory tract and circulation through longitudinal phenotypic, transcriptomic and cytokine profiling of paired airway and blood samples from patients with severe COVID-19 relative to heathy controls. In COVID-19 airways, T cells exhibited activated, tissue-resident, and protective profiles; higher T cell frequencies correlated with survival and younger age. Myeloid cells in COVID-19 airways featured hyper-inflammatory signatures and higher frequencies of these cells correlated with mortality and older age. In COVID-19 blood, aberrant CD163+ monocytes predominated over conventional monocytes, and were found in corresponding airway samples and in damaged alveoli. High levels of myeloid chemoattractants in airways suggest recruitment of these cells through a CCL2-CCR2 chemokine axis. Our findings provide insights into immune processes driving COVID-19 lung pathology with therapeutic implications for targeting inflammation in the respiratory tract.

ABSTRACTClinical manifestations of COVID-19 caused by the novel coronavirus SARS-CoV-2 are associ... more ABSTRACTClinical manifestations of COVID-19 caused by the novel coronavirus SARS-CoV-2 are associated with age. While children are largely spared from severe respiratory disease, they can present with a SARS-CoV-2-associated multisystem inflammatory syndrome (MIS-C) similar to Kawasaki’s disease. Here, we show distinct antibody (Ab) responses in children with MIS-C compared to adults with severe COVID-19 causing acute respiratory distress syndrome (ARDS), and those who recovered from mild disease. There was a reduced breadth and specificity of anti-SARS-CoV-2-specific antibodies in MIS-C patients compared to the COVID patient groups; MIS-C predominantly generated IgG Abs specific for the Spike (S) protein but not for the nucleocapsid (N) protein, while the COVID-19 cohorts had anti-S IgG, IgM and IgA Abs, as well as anti-N IgG Abs. Moreover, MIS-C patients had reduced neutralizing activity compared to both COVID-19 cohorts, indicating a reduced protective serological response. These...

Cell, 2020

Highlights d High-resolution map of human NK cells shows tissue-driven distribution across ages d... more Highlights d High-resolution map of human NK cells shows tissue-driven distribution across ages d Differentiated NK cells predominate in blood, bone marrow, spleen, and lungs d Tissue-resident NK cells exhibit specific adaptations in mucosal and lymphoid sites d Lymph nodes and intestines are reservoirs for precursor and immature NK cells

Nature Communications, 2019

Human T cells coordinate adaptive immunity in diverse anatomic compartments through production of... more Human T cells coordinate adaptive immunity in diverse anatomic compartments through production of cytokines and effector molecules, but it is unclear how tissue site influences T cell persistence and function. Here, we use single cell RNA-sequencing (scRNA-seq) to define the heterogeneity of human T cells isolated from lungs, lymph nodes, bone marrow and blood, and their functional responses following stimulation. Through analysis of >50,000 resting and activated T cells, we reveal tissue T cell signatures in mucosal and lymphoid sites, and lineage-specific activation states across all sites including distinct effector states for CD8+ T cells and an interferon-response state for CD4+ T cells. Comparing scRNA-seq profiles of tumor-associated T cells to our dataset reveals predominant activated CD8+ compared to CD4+ T cell states within multiple tumor types. Our results therefore establish a high dimensional reference map of human T cell activation in health for analyzing T cells i...

A93. ASTHMA BREAKTHROUGHS: THE ROLE OF THE IMMUNE SYSTEM IN HUMAN ASTHMA, 2019

ABSTRACTHuman T cells coordinate adaptive immunity by localization in diverse tissue sites, thoug... more ABSTRACTHuman T cells coordinate adaptive immunity by localization in diverse tissue sites, though blood T cells are the most readily studied. Here, we used single-cell RNA-seq to define the functional responses of T cells isolated from human lungs, lymph nodes, bone marrow, and blood to TCR-stimulation. We reveal how human T cells in tissues relate to those in blood, and define activation states for CD4+ and CD8+T cells across all sites, including an interferon-response state for CD4+T cells and distinct effector states for CD8+T cells. We further show how profiles of individual tumor-associated T cells can be projected onto this healthy reference map, revealing their functional state.

Cancer Immunology Research, 2019

Natural killer (NK) cells are innate immune cells with the ability to kill tumor cells without pr... more Natural killer (NK) cells are innate immune cells with the ability to kill tumor cells without prior exposure. NK cells express multiple activating and inhibitory receptors in addition to the low-affinity immunoglobulin G binding receptor CD16. Accumulating evidence implicates a role of NK cells in not only direct killing of tumor cells, but also in cancer immunosurveillance and preventing metastasis to tissues sites. However, at present the distribution, diversity and tissue driven differences in NK cell function are not well characterized which may have an implication on the anti-cancer potential of tissue NK cells. Through collaboration with LiveOnNY our local organ procurement organization, we receive blood, bone marrow (BM), lung, intestines, tonsil and associated lymph nodes (LN) from research consented organ donors. Here we used this unique tissue resource to investigate the distribution, phenotypic, functional and transcriptional diversity of NK cell subsets in human tissues...

Mucosal Immunology, 2018

Defining adaptive immunity with the complex structures of the human gastrointestinal (GI) tract o... more Defining adaptive immunity with the complex structures of the human gastrointestinal (GI) tract over life is essential for understanding immune responses to ingested antigens, commensal and pathogenic microorganisms, and dysfunctions in disease. We present here an analysis of lymphocyte localization and T cell subset composition across the human GI tract including mucosal sites (jejunum, ileum, colon), gut-associated lymphoid tissues (isolated lymphoid follicles (ILFs), Peyer's patches (PPs), appendix), and mesenteric lymph nodes (MLNs) from a total of 68 donors spanning eight decades of life. In pediatric donors, ILFs and PP containing naïve T cells and regulatory T cells (Tregs) are prevalent in the jejunum and ileum, respectively; these decline in frequency with age, contrasting stable frequencies of ILFs and T cell subsets in the colon. In the mucosa, tissue resident memory T cells develop during childhood, and persist in high frequencies into advanced ages, while T cell composition changes with age in GALT and MLN. These spatial and temporal features of human intestinal T cell immunity define signatures that can be used to train predictive machine learning algorithms. Our findings demonstrate an anatomic basis for age-associated alterations in immune responses, and establish a quantitative baseline for intestinal immunity to define disease pathologies.

PLoS biology, 2017

Superantigens (SAgs) are potent exotoxins secreted by Staphylococcus aureus and Streptococcus pyo... more Superantigens (SAgs) are potent exotoxins secreted by Staphylococcus aureus and Streptococcus pyogenes. They target a large fraction of T cell pools to set in motion a "cytokine storm" with severe and sometimes life-threatening consequences typically encountered in toxic shock syndrome (TSS). Given the rapidity with which TSS develops, designing timely and truly targeted therapies for this syndrome requires identification of key mediators of the cytokine storm's initial wave. Equally important, early host responses to SAgs can be accompanied or followed by a state of immunosuppression, which in turn jeopardizes the host's ability to combat and clear infections. Unlike in mouse models, the mechanisms underlying SAg-associated immunosuppression in humans are ill-defined. In this work, we have identified a population of innate-like T cells, called mucosa-associated invariant T (MAIT) cells, as the most powerful source of pro-inflammatory cytokines after exposure to SA...

Journal of immunology (Baltimore, Md. : 1950), Apr 20, 2017

Toxic shock syndrome (TSS) is caused by staphylococcal and streptococcal superantigens (SAgs) tha... more Toxic shock syndrome (TSS) is caused by staphylococcal and streptococcal superantigens (SAgs) that provoke a swift hyperinflammatory response typified by a cytokine storm. The precipitous decline in the host's clinical status and the lack of targeted therapies for TSS emphasize the need to identify key players of the storm's initial wave. Using a humanized mouse model of TSS and human cells, we herein demonstrate that SAgs elicit in vitro and in vivo IL-17A responses within hours. SAg-triggered human IL-17A production was characterized by remarkably high mRNA stability for this cytokine. A distinct subpopulation of CD4(+) effector memory T (TEM) cells that secrete IL-17A, but not IFN-γ, was responsible for early IL-17A production. We found mouse "TEM-17" cells to be enriched within the intestinal epithelium and among lamina propria lymphocytes. Furthermore, interfering with IL-17A receptor signaling in human PBMCs attenuated the expression of numerous inflammatory ...

The Journal of infectious diseases, Mar 29, 2016

During toxic shock syndrome (TSS), bacterial superantigens trigger a polyclonal T cell response l... more During toxic shock syndrome (TSS), bacterial superantigens trigger a polyclonal T cell response leading to a potentially catastrophic 'cytokine storm'. Whether innate-like invariant natural killer T(iNKT) cells, with remarkable immunomodulatory properties, participate in TSS is unclear. Using genetic and cell depletion approaches, we generated iNKT cell-deficient, superantigen-sensitive HLA-DR4-transgenic (DR4tg) mice, which were compared with their iNKT-sufficient counterparts for responsiveness to staphylococcal enterotoxin B(SEB). Both approaches indicate that iNKT cells are pathogenic in TSS. Importantly, treating DR4tg mice with a TH2-polarizing glycolipid agonist of iNKT cells reduced SEB-inflicted morbidity/mortality. Therefore, iNKT cells may constitute an attractive therapeutic target in superantigen-mediated illnesses.

The Journal of infectious diseases, Jun 9, 2016

Toxic shock syndrome (TSS) and other superantigen-mediated illnesses are associated with 'sys... more Toxic shock syndrome (TSS) and other superantigen-mediated illnesses are associated with 'systemic' immunosuppression that jeopardizes the host's ability to fight pathogens. Here, we define a novel mechanism of 'local' immunosuppression that may benefit the host. Systemic exposure to staphylococcal enterotoxin B (SEB) rapidly and selectively recruited CD11b(+)Gr-1(high)Ly-6C(+) granulocytic myeloid-derived suppressor cells (MDSCs) to the liver of HLA-DR4 transgenic mice. Hepatic MDSCs inhibited SEB-triggered T cell proliferation in a reactive oxygen species-dependent manner, and ex vivo-generated human MDSCs also similarly attenuated the proliferative response of autologous T cells to SEB. We propose a role for MDSCs in mitigating excessive tissue injury during TSS.

Nature Immunology

Genomics 5′ scRNA-seq, along with V region sequencing of TCRA and TCRB genes of T cells isolated ... more Genomics 5′ scRNA-seq, along with V region sequencing of TCRA and TCRB genes of T cells isolated from multiple tissue sites of individual donors. Barrier sites contain tissue-adapted T cell populations To examine subset composition and phenotypic heterogeneity of T cells maintained across the body, we used a high-dimensional CyTOF panel incorporating multiple markers of T cell differentiation, function, and migration to analyze CD3 + T cells obtained from blood and tissues of three donors, aged 22, 40 and 70 years (Fig. 1 and Supplementary Tables 1 and 2). Unsupervised clustering based on marker expression identified 31 clusters, representing heterogeneous populations of CD4 + and CD8 + T cell subsets (Fig. 1a and Extended Data Fig. 1a). Subsets included naive T cells (CCR7 + CD45RA + CD95 −), central memory T cells (T CM ; CCR7 + CD45RA − CD28 +), T EM (CCR7 − CD45RA −), T EMRA (CCR7 − CD45RA +) and T RM (CCR7 − CD45RA − CD69 +). Functional subsets included follicular helper T cells (T FH ; CD4 + CXCR5 + PD-1 + ICOS +) 22 , regulatory T cells (T reg ; CD4 + CD25 + CD127 −) 23 , type 1 helper T cells (T H 1), defined by the transcription factor T-bet 24 , and type 2 helper T cells (T H 2) with enhanced expression of CRTH2 (ref. 25). Innate-like T cells were mostly represented by γδ T cells (gdTCR + ; Fig. 1a,b). The composition of CD4 + and CD8 + T cell subsets was similar between individuals, despite their broad age range (Fig. 1c and Extended Data Fig. 1b). CD4 + T cells comprised subsets of naive, T CM , T FH , T reg and T RM subsets expressing CD69 and to a lesser extent CD103, T H 1-like cells expressing T-bet and the senescent marker CD57 (cluster 13), and T H 2-like CRTH2 + cells (cluster 20; Fig. 1a-c). CD8 + T cells comprised naive and memory subsets, along with higher frequencies of T EMRA cells and γδ T cells than in CD4 + T cells (Fig. 1a-c). CD8 + T EM and T EMRA cells were further subdivided on the basis of the differential expression of CD57, inhibitory molecules (PD-1, TIGIT) and cytotoxic mediators (granzyme B, perforin) (Fig. 1a,b). Between donors, the oldest donor had the lowest frequency of naive CD8 + T cells and a distinct population of T EM and T EMRA cells expressing CD57, TIGIT and PD-1 (cluster 14; Extended Data Figs. 1b and 2). For all donors, the composition and distribution of T cell subsets were site-specific, consistent with previous findings for naive and memory T cells assessed by flow cytometry 7-9,11. However, this high-dimensional profiling revealed which subpopulations were similar between sites and which had site-specific adaptations. Blood contained CD4 + naive, T CM , T EM and T reg , as well as CD8 + naive and T EM /T EMRA , populations (Fig. 1c,d and Extended Data Fig. 2), while all three lymph node sites contained a distinct composition from blood consisting of mostly CD4 + subsets (naive T CM , T FH , T RM and T reg) and lower frequencies of CD8 + naive and T RM cells (Fig. 1c,d and Extended Data Fig. 2). The spleen contained subsets found in both blood and lymph nodes, along with additional CD8 + T EM /T EMRA and T RM populations (Fig. 1c,d and Extended Data Fig. 2). Each barrier site, however, contained a unique composition of T cells compared with all the other sites (Fig. 1c,d and Extended Data Fig. 2). Lungs contained CD4 + and CD8 + T RM , distinct CD57 + T EM (clusters 13 and 19), T EMRA and γδ T (cluster 25) cells. Jejunum contained predominantly CD69 + CD103 + T RM cells and a Tbet + CCR5 + T FH population (cluster 18); skin contained CD4 + and CD8 + T RM cells expressing CXCR4 (clusters 10 and 12), implicated in skin T cell homing 26 , and T EM (cluster 8)

The Journal of Immunology

Natural killer (NK) cells are innate immune cells with the inherent ability to directly kill tumo... more Natural killer (NK) cells are innate immune cells with the inherent ability to directly kill tumor and virus infected cells. Due to their ability to kill cancer cells without any prior priming, and their role in preventing metastasis NK cells have since long been the choice for autologous adoptive cell transfer therapy in cancer. However, poor expansion potential of PBMC derived NK cells in vitro is a major roadblock preventing the widespread use of NK cells in immunotherapy. We found that human NK cells isolated from lymph nodes (LNs) express higher levels of genes encoding for stem-like transcription factors (TCF7, LEF1, MYC) compared to NK cells from blood, spleen, bone marrow (BM) and lung. Therefore, we hypothesized that NK cells isolated from LNs will show superior expansion potential in vitro. Flow cytometric analysis shows that LN derived NK cells express high levels of TCF1 protein ex vivo, and show greater proliferation compared to NK cells isolated from blood, spleen and ...

The Journal of Immunology

T cells persist as heterogeneous subsets throughout the body and are essential in mounting protec... more T cells persist as heterogeneous subsets throughout the body and are essential in mounting protective immune responses. In healthy humans, most of our knowledge of T cell activation derives from sampling the peripheral blood and therefore the transcriptional states of tissue T cells, their functional responses to stimulation, and how they relate to T cells in blood have been poorly defined. Here, we profile the activation dynamics of T cells isolated from human lungs (LG), lymph nodes (LN), bone marrow (BM) and blood following TCR-stimulation by single cell RNA-sequencing (scRNA-seq). Analysis of >50,000 individual resting and activated T cells using clustering and new factorization methods reveals lineage-specific gene expression signatures and discrete activation trajectories in all tissues. Between sites, T cells from LG and LN are most distinct, while blood T cells are most similar to those in BM but persist in a more activated basal state. We identify a common transcriptiona...

Nature Medicine

Older people are particularly susceptible to infectious and neoplastic diseases of the lung and i... more Older people are particularly susceptible to infectious and neoplastic diseases of the lung and it is unclear how lifelong exposure to environmental pollutants affects respiratory immune function. In an analysis of human lymph nodes (LNs) from 84 organ donors aged 11-93 years, we found a specific age-related decline in lung-associated, but not gut-associated, LN immune function linked to the accumulation of inhaled atmospheric particulate matter. Increasing densities of particulates were found in lung-associated LNs with age, but not in the corresponding gut-associated LNs. Particulates were specifically contained within CD68 + CD169 − macrophages, which exhibited decreased activation, phagocytic capacity, and altered cytokine production compared with non-particulate-containing macrophages. The structures of B cell follicles and lymphatic drainage were also disrupted in lung-associated LNs with particulates. Our results reveal that the cumulative effects of environmental exposure and age may compromise immune surveillance of the lung via direct effects on immune cell function and lymphoid architecture.

Science Immunology, 2021

SARS-CoV-2–specific memory cells persist in multiple sites months after infection, particularly i... more SARS-CoV-2–specific memory cells persist in multiple sites months after infection, particularly in lungs and associated lymph nodes.

Immunity, 2021

Immune response dynamics in COVID-19 and its severe manifestations have largely been studied in c... more Immune response dynamics in COVID-19 and its severe manifestations have largely been studied in circulation. Here, we examined the relationship between immune processes in the respiratory tract and circulation through longitudinal phenotypic, transcriptomic and cytokine profiling of paired airway and blood samples from patients with severe COVID-19 relative to heathy controls. In COVID-19 airways, T cells exhibited activated, tissue-resident, and protective profiles; higher T cell frequencies correlated with survival and younger age. Myeloid cells in COVID-19 airways featured hyper-inflammatory signatures and higher frequencies of these cells correlated with mortality and older age. In COVID-19 blood, aberrant CD163+ monocytes predominated over conventional monocytes, and were found in corresponding airway samples and in damaged alveoli. High levels of myeloid chemoattractants in airways suggest recruitment of these cells through a CCL2-CCR2 chemokine axis. Our findings provide insights into immune processes driving COVID-19 lung pathology with therapeutic implications for targeting inflammation in the respiratory tract.

ABSTRACTClinical manifestations of COVID-19 caused by the novel coronavirus SARS-CoV-2 are associ... more ABSTRACTClinical manifestations of COVID-19 caused by the novel coronavirus SARS-CoV-2 are associated with age. While children are largely spared from severe respiratory disease, they can present with a SARS-CoV-2-associated multisystem inflammatory syndrome (MIS-C) similar to Kawasaki’s disease. Here, we show distinct antibody (Ab) responses in children with MIS-C compared to adults with severe COVID-19 causing acute respiratory distress syndrome (ARDS), and those who recovered from mild disease. There was a reduced breadth and specificity of anti-SARS-CoV-2-specific antibodies in MIS-C patients compared to the COVID patient groups; MIS-C predominantly generated IgG Abs specific for the Spike (S) protein but not for the nucleocapsid (N) protein, while the COVID-19 cohorts had anti-S IgG, IgM and IgA Abs, as well as anti-N IgG Abs. Moreover, MIS-C patients had reduced neutralizing activity compared to both COVID-19 cohorts, indicating a reduced protective serological response. These...

Cell, 2020

Highlights d High-resolution map of human NK cells shows tissue-driven distribution across ages d... more Highlights d High-resolution map of human NK cells shows tissue-driven distribution across ages d Differentiated NK cells predominate in blood, bone marrow, spleen, and lungs d Tissue-resident NK cells exhibit specific adaptations in mucosal and lymphoid sites d Lymph nodes and intestines are reservoirs for precursor and immature NK cells

Nature Communications, 2019

Human T cells coordinate adaptive immunity in diverse anatomic compartments through production of... more Human T cells coordinate adaptive immunity in diverse anatomic compartments through production of cytokines and effector molecules, but it is unclear how tissue site influences T cell persistence and function. Here, we use single cell RNA-sequencing (scRNA-seq) to define the heterogeneity of human T cells isolated from lungs, lymph nodes, bone marrow and blood, and their functional responses following stimulation. Through analysis of >50,000 resting and activated T cells, we reveal tissue T cell signatures in mucosal and lymphoid sites, and lineage-specific activation states across all sites including distinct effector states for CD8+ T cells and an interferon-response state for CD4+ T cells. Comparing scRNA-seq profiles of tumor-associated T cells to our dataset reveals predominant activated CD8+ compared to CD4+ T cell states within multiple tumor types. Our results therefore establish a high dimensional reference map of human T cell activation in health for analyzing T cells i...

A93. ASTHMA BREAKTHROUGHS: THE ROLE OF THE IMMUNE SYSTEM IN HUMAN ASTHMA, 2019

ABSTRACTHuman T cells coordinate adaptive immunity by localization in diverse tissue sites, thoug... more ABSTRACTHuman T cells coordinate adaptive immunity by localization in diverse tissue sites, though blood T cells are the most readily studied. Here, we used single-cell RNA-seq to define the functional responses of T cells isolated from human lungs, lymph nodes, bone marrow, and blood to TCR-stimulation. We reveal how human T cells in tissues relate to those in blood, and define activation states for CD4+ and CD8+T cells across all sites, including an interferon-response state for CD4+T cells and distinct effector states for CD8+T cells. We further show how profiles of individual tumor-associated T cells can be projected onto this healthy reference map, revealing their functional state.

Cancer Immunology Research, 2019

Natural killer (NK) cells are innate immune cells with the ability to kill tumor cells without pr... more Natural killer (NK) cells are innate immune cells with the ability to kill tumor cells without prior exposure. NK cells express multiple activating and inhibitory receptors in addition to the low-affinity immunoglobulin G binding receptor CD16. Accumulating evidence implicates a role of NK cells in not only direct killing of tumor cells, but also in cancer immunosurveillance and preventing metastasis to tissues sites. However, at present the distribution, diversity and tissue driven differences in NK cell function are not well characterized which may have an implication on the anti-cancer potential of tissue NK cells. Through collaboration with LiveOnNY our local organ procurement organization, we receive blood, bone marrow (BM), lung, intestines, tonsil and associated lymph nodes (LN) from research consented organ donors. Here we used this unique tissue resource to investigate the distribution, phenotypic, functional and transcriptional diversity of NK cell subsets in human tissues...

Mucosal Immunology, 2018

Defining adaptive immunity with the complex structures of the human gastrointestinal (GI) tract o... more Defining adaptive immunity with the complex structures of the human gastrointestinal (GI) tract over life is essential for understanding immune responses to ingested antigens, commensal and pathogenic microorganisms, and dysfunctions in disease. We present here an analysis of lymphocyte localization and T cell subset composition across the human GI tract including mucosal sites (jejunum, ileum, colon), gut-associated lymphoid tissues (isolated lymphoid follicles (ILFs), Peyer's patches (PPs), appendix), and mesenteric lymph nodes (MLNs) from a total of 68 donors spanning eight decades of life. In pediatric donors, ILFs and PP containing naïve T cells and regulatory T cells (Tregs) are prevalent in the jejunum and ileum, respectively; these decline in frequency with age, contrasting stable frequencies of ILFs and T cell subsets in the colon. In the mucosa, tissue resident memory T cells develop during childhood, and persist in high frequencies into advanced ages, while T cell composition changes with age in GALT and MLN. These spatial and temporal features of human intestinal T cell immunity define signatures that can be used to train predictive machine learning algorithms. Our findings demonstrate an anatomic basis for age-associated alterations in immune responses, and establish a quantitative baseline for intestinal immunity to define disease pathologies.

PLoS biology, 2017

Superantigens (SAgs) are potent exotoxins secreted by Staphylococcus aureus and Streptococcus pyo... more Superantigens (SAgs) are potent exotoxins secreted by Staphylococcus aureus and Streptococcus pyogenes. They target a large fraction of T cell pools to set in motion a "cytokine storm" with severe and sometimes life-threatening consequences typically encountered in toxic shock syndrome (TSS). Given the rapidity with which TSS develops, designing timely and truly targeted therapies for this syndrome requires identification of key mediators of the cytokine storm's initial wave. Equally important, early host responses to SAgs can be accompanied or followed by a state of immunosuppression, which in turn jeopardizes the host's ability to combat and clear infections. Unlike in mouse models, the mechanisms underlying SAg-associated immunosuppression in humans are ill-defined. In this work, we have identified a population of innate-like T cells, called mucosa-associated invariant T (MAIT) cells, as the most powerful source of pro-inflammatory cytokines after exposure to SA...

Journal of immunology (Baltimore, Md. : 1950), Apr 20, 2017

Toxic shock syndrome (TSS) is caused by staphylococcal and streptococcal superantigens (SAgs) tha... more Toxic shock syndrome (TSS) is caused by staphylococcal and streptococcal superantigens (SAgs) that provoke a swift hyperinflammatory response typified by a cytokine storm. The precipitous decline in the host's clinical status and the lack of targeted therapies for TSS emphasize the need to identify key players of the storm's initial wave. Using a humanized mouse model of TSS and human cells, we herein demonstrate that SAgs elicit in vitro and in vivo IL-17A responses within hours. SAg-triggered human IL-17A production was characterized by remarkably high mRNA stability for this cytokine. A distinct subpopulation of CD4(+) effector memory T (TEM) cells that secrete IL-17A, but not IFN-γ, was responsible for early IL-17A production. We found mouse "TEM-17" cells to be enriched within the intestinal epithelium and among lamina propria lymphocytes. Furthermore, interfering with IL-17A receptor signaling in human PBMCs attenuated the expression of numerous inflammatory ...

The Journal of infectious diseases, Mar 29, 2016

During toxic shock syndrome (TSS), bacterial superantigens trigger a polyclonal T cell response l... more During toxic shock syndrome (TSS), bacterial superantigens trigger a polyclonal T cell response leading to a potentially catastrophic 'cytokine storm'. Whether innate-like invariant natural killer T(iNKT) cells, with remarkable immunomodulatory properties, participate in TSS is unclear. Using genetic and cell depletion approaches, we generated iNKT cell-deficient, superantigen-sensitive HLA-DR4-transgenic (DR4tg) mice, which were compared with their iNKT-sufficient counterparts for responsiveness to staphylococcal enterotoxin B(SEB). Both approaches indicate that iNKT cells are pathogenic in TSS. Importantly, treating DR4tg mice with a TH2-polarizing glycolipid agonist of iNKT cells reduced SEB-inflicted morbidity/mortality. Therefore, iNKT cells may constitute an attractive therapeutic target in superantigen-mediated illnesses.

The Journal of infectious diseases, Jun 9, 2016

Toxic shock syndrome (TSS) and other superantigen-mediated illnesses are associated with 'sys... more Toxic shock syndrome (TSS) and other superantigen-mediated illnesses are associated with 'systemic' immunosuppression that jeopardizes the host's ability to fight pathogens. Here, we define a novel mechanism of 'local' immunosuppression that may benefit the host. Systemic exposure to staphylococcal enterotoxin B (SEB) rapidly and selectively recruited CD11b(+)Gr-1(high)Ly-6C(+) granulocytic myeloid-derived suppressor cells (MDSCs) to the liver of HLA-DR4 transgenic mice. Hepatic MDSCs inhibited SEB-triggered T cell proliferation in a reactive oxygen species-dependent manner, and ex vivo-generated human MDSCs also similarly attenuated the proliferative response of autologous T cells to SEB. We propose a role for MDSCs in mitigating excessive tissue injury during TSS.