Showing papers by "Mark M. Davis published in 2019"
TL;DR: Paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy demonstrates that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.
Abstract: Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of patients with cancer1. However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor-infiltrating lymphocytes or on recruitment of novel T cells remains unclear2-4. Here we performed paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy. Tracking T cell receptor clones and transcriptional phenotypes revealed coupling of tumor recognition, clonal expansion and T cell dysfunction marked by clonal expansion of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, the expansion of T cell clones did not derive from pre-existing tumor-infiltrating T lymphocytes; instead, the expanded clones consisted of novel clonotypes that had not previously been observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+ T cells and evident in patients with basal or squamous cell carcinoma. These results demonstrate that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.
810 citations
TL;DR: It is shown that both mouse and human iPSCs lose their immunogenicity when major histocompatibility complex (MHC) class I and II genes are inactivated and CD47 is over-expressed, which suggests that hypoimmunogenic cell grafts can be engineered for universal transplantation.
Abstract: Autologous induced pluripotent stem cells (iPSCs) constitute an unlimited cell source for patient-specific cell-based organ repair strategies. However, their generation and subsequent differentiation into specific cells or tissues entail cell line-specific manufacturing challenges and form a lengthy process that precludes acute treatment modalities. These shortcomings could be overcome by using prefabricated allogeneic cell or tissue products, but the vigorous immune response against histo-incompatible cells has prevented the successful implementation of this approach. Here we show that both mouse and human iPSCs lose their immunogenicity when major histocompatibility complex (MHC) class I and II genes are inactivated and CD47 is over-expressed. These hypoimmunogenic iPSCs retain their pluripotent stem cell potential and differentiation capacity. Endothelial cells, smooth muscle cells, and cardiomyocytes derived from hypoimmunogenic mouse or human iPSCs reliably evade immune rejection in fully MHC-mismatched allogeneic recipients and survive long-term without the use of immunosuppression. These findings suggest that hypoimmunogenic cell grafts can be engineered for universal transplantation.
392 citations
TL;DR: It is found that T cells can inhibit the proliferation of neural stem cells in co-cultures and in vivo, in part by secreting interferon-γ.
Abstract: The mammalian brain contains neurogenic niches that comprise neural stem cells and other cell types. Neurogenic niches become less functional with age, but how they change during ageing remains unclear. Here we perform single-cell RNA sequencing of young and old neurogenic niches in mice. The analysis of 14,685 single-cell transcriptomes reveals a decrease in activated neural stem cells, changes in endothelial cells and microglia, and an infiltration of T cells in old neurogenic niches. T cells in old brains are clonally expanded and are generally distinct from those in old blood, which suggests that they may experience specific antigens. T cells in old brains also express interferon-γ, and the subset of neural stem cells that has a high interferon response shows decreased proliferation in vivo. We find that T cells can inhibit the proliferation of neural stem cells in co-cultures and in vivo, in part by secreting interferon-γ. Our study reveals an interaction between T cells and neural stem cells in old brains, opening potential avenues through which to counteract age-related decline in brain function.
306 citations
TL;DR: An integrated high-dimensional measurement of immune age describes a person’s immune status better than chronological age and predicts all-cause mortality beyond well-established risk factors in the Framingham Heart Study.
Abstract: Immune responses generally decline with age. However, the dynamics of this process at the individual level have not been characterized, hindering quantification of an individual's immune age. Here, we use multiple 'omics' technologies to capture population- and individual-level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observed high inter-individual variability in the rates of change of cellular frequencies that was dictated by their baseline values, allowing identification of steady-state levels toward which a cell subset converged and the ordered convergence of multiple cell subsets toward an older adult homeostasis. These data form a high-dimensional trajectory of immune aging (IMM-AGE) that describes a person's immune status better than chronological age. We show that the IMM-AGE score predicted all-cause mortality beyond well-established risk factors in the Framingham Heart Study, establishing its potential use in clinics for identification of patients at risk.
269 citations
TL;DR: A neural network trained on diverse datasets improves prediction of HLA class II epitope presentation, and across independent cancer neoantigen studies, peptides with high MARIA scores are more likely to elicit strong CD4+ T cell responses.
Abstract: Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in vitro binding data are limited by insufficient training data and algorithmic constraints. Here we describe MARIA (major histocompatibility complex analysis with recurrent integrated architecture; https://maria.stanford.edu/
), a multimodal recurrent neural network for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. In addition to in vitro binding measurements, MARIA is trained on peptide HLA ligand sequences identified by mass spectrometry, expression levels of antigen genes and protease cleavage signatures. Because it leverages these diverse training data and our improved machine learning framework, MARIA (area under the curve = 0.89–0.92) outperformed existing methods in validation datasets. Across independent cancer neoantigen studies, peptides with high MARIA scores are more likely to elicit strong CD4+ T cell responses. MARIA allows identification of immunogenic epitopes in diverse cancers and autoimmune disease. A neural network trained on diverse datasets improves prediction of HLA class II epitope presentation.
177 citations
TL;DR: This work shows that induction generates successive waves of clonally expanded CD4+, CD8+ and γδ+ T cells in the blood and central nervous system, similar to gluten-challenge studies of patients with coeliac disease, and suggests that the induction of autoreactive CD4- T cells triggers an opposing mobilization of regulatory CD8+.
Abstract: Experimental autoimmune encephalomyelitis is a model for multiple sclerosis. Here we show that induction generates successive waves of clonally expanded CD4+, CD8+ and γδ+ T cells in the blood and central nervous system, similar to gluten-challenge studies of patients with coeliac disease. We also find major expansions of CD8+ T cells in patients with multiple sclerosis. In autoimmune encephalomyelitis, we find that most expanded CD4+ T cells are specific for the inducing myelin peptide MOG35-55. By contrast, surrogate peptides derived from a yeast peptide major histocompatibility complex library of some of the clonally expanded CD8+ T cells inhibit disease by suppressing the proliferation of MOG-specific CD4+ T cells. These results suggest that the induction of autoreactive CD4+ T cells triggers an opposing mobilization of regulatory CD8+ T cells.
120 citations
TL;DR: It is found that gluten-specific CD4+ T cells in the blood and intestines of patients with celiac disease display a surprisingly rare phenotype, suggesting a way to characterize CD4 + T cells specific for disease-driving antigens in multiple autoimmune conditions.
Abstract: Combining HLA-DQ-gluten tetramers with mass cytometry and RNA sequencing analysis, we find that gluten-specific CD4+ T cells in the blood and intestines of patients with celiac disease display a surprisingly rare phenotype. Cells with this phenotype are also elevated in patients with systemic sclerosis and systemic lupus erythematosus, suggesting a way to characterize CD4+ T cells specific for disease-driving antigens in multiple autoimmune conditions.
106 citations
Stanford University1, Seattle Children's2, University of Washington3, Baylor College of Medicine4, University of Pittsburgh5, University of Cincinnati Academic Health Center6, Cincinnati Children's Hospital Medical Center7, Boston Children's Hospital8, University of Colorado Denver9, University of Miami10, United States Public Health Service11, Michigan State University12, Washington University in St. Louis13, University of Pennsylvania14, Children's Hospital of Philadelphia15, Metro Health Hospital16, University of Michigan17, Harvard University18, University of Southern California19, Children's Hospital Los Angeles20, Children's of Alabama21, University of Alabama at Birmingham22, Columbia University Medical Center23, Yale University24, Vanderbilt University25, Hackensack University Medical Center26, The Chinese University of Hong Kong27, Children's Mercy Hospital28, University of Missouri–Kansas City29, University of Utah30, Georgia Regents University31, Northwestern University32, Albert Einstein College of Medicine33, All Children's Hospital34, Kaiser Permanente35, Cornell University36, Hospital for Special Surgery37, Hacettepe University38, Northeast Ohio Medical University39, Emory University40, University of California, San Diego41, University of Nebraska Medical Center42, University of Minnesota43, Children's Hospital of Eastern Ontario44, Hospital for Sick Children45, University of Toronto46, University of Amsterdam47, University of Wisconsin-Madison48
TL;DR: A rare, life-threatening lung disease in sJIA is defined by a constellation of unusual clinical characteristics, including acute erythematous clubbing and a high frequency of anaphylactic reactions to the interleukin (IL)-6 inhibitor, tocilizumab.
Abstract: Objective To investigate the characteristics and risk factors of a novel parenchymal lung disease (LD), increasingly detected in systemic juvenile idiopathic arthritis (sJIA). Methods In a multicentre retrospective study, 61 cases were investigated using physician-reported clinical information and centralised analyses of radiological, pathological and genetic data. Results LD was associated with distinctive features, including acute erythematous clubbing and a high frequency of anaphylactic reactions to the interleukin (IL)-6 inhibitor, tocilizumab. Serum ferritin elevation and/or significant lymphopaenia preceded LD detection. The most prevalent chest CT pattern was septal thickening, involving the periphery of multiple lobes ± ground-glass opacities. The predominant pathology (23 of 36) was pulmonary alveolar proteinosis and/or endogenous lipoid pneumonia (PAP/ELP), with atypical features including regional involvement and concomitant vascular changes. Apparent severe delayed drug hypersensitivity occurred in some cases. The 5-year survival was 42%. Whole exome sequencing (20 of 61) did not identify a novel monogenic defect or likely causal PAP-related or macrophage activation syndrome (MAS)-related mutations. Trisomy 21 and young sJIA onset increased LD risk. Exposure to IL-1 and IL-6 inhibitors (46 of 61) was associated with multiple LD features. By several indicators, severity of sJIA was comparable in drug-exposed subjects and published sJIA cohorts. MAS at sJIA onset was increased in the drug-exposed, but was not associated with LD features. Conclusions A rare, life-threatening lung disease in sJIA is defined by a constellation of unusual clinical characteristics. The pathology, a PAP/ELP variant, suggests macrophage dysfunction. Inhibitor exposure may promote LD, independent of sJIA severity, in a small subset of treated patients. Treatment/prevention strategies are needed.
96 citations
TL;DR: While there is no relationship between expression profiles and clonal expansion in iNKT or MAIT cells, highly expanded conventional CD8+ T cells down-regulate the interleukin 2 (IL-2) receptor alpha (IL2RA, or CD25) protein and show signs of senescence, which suggests inherent limits toClonal expansion that act to diversify the T cell response repertoire.
Abstract: To permit the recognition of antigens, T cells generate a vast diversity of T cell receptor (TCR) sequences. Upon binding of the TCR to an antigen-MHC complex, T cells clonally expand to establish an immune response. To study antigen-specific T cell clonality, we have developed a method that allows selection of rare cells, based on RNA expression, before in-depth scRNA-seq (named SELECT-seq). We applied SELECT-seq to collect both TCR sequences and then transcriptomes from single cells of peripheral blood lymphocytes activated by a Mycobacterium tuberculosis (Mtb) lysate. TCR sequence analysis allowed us to preferentially select expanded conventional CD8+ T cells as well as invariant natural killer T (iNKT) cells and mucosal-associated invariant T (MAIT) cells. The iNKT and MAIT cells have a highly similar transcriptional pattern, indicating that they carry out similar immunological functions and differ considerably from conventional CD8+ T cells. While there is no relationship between expression profiles and clonal expansion in iNKT or MAIT cells, highly expanded conventional CD8+ T cells down-regulate the interleukin 2 (IL-2) receptor alpha (IL2RA, or CD25) protein and show signs of senescence. This suggests inherent limits to clonal expansion that act to diversify the T cell response repertoire.
57 citations
TL;DR: It is demonstrated that pre-existing tumor-specific T cells may be limited in their capacity for re-invigoration, and that the T cell response to checkpoint blockade relies on the expansion of a distinct repertoire of T cell clones that may have just recently entered the tumor.
Abstract: Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of cancer patients. However, which tumor-specific T cells are mobilized following checkpoint blockade remains unclear. Here, we performed paired single-cell RNA- and T cell receptor (TCR)-sequencing on 79,046 cells from site-matched tumors from patients with basal cell carcinoma (BCC) or squamous cell carcinoma (SCC) pre- and post-anti-PD-1 therapy. Tracking TCR clones and transcriptional phenotypes revealed a coupling of tumor-recognition, clonal expansion, and T cell dysfunction: the T cell response to treatment was accompanied by clonal expansions of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, this expansion did not derive from pre-existing tumor infiltrating T cell clones; rather, it comprised novel clonotypes, which were not previously observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+ T cells, compared to other distinct T cell phenotypes, and was evident in BCC and SCC patients. These results, enabled by single-cell multi-omic profiling of clinical samples, demonstrate that pre-existing tumor-specific T cells may be limited in their capacity for re-invigoration, and that the T cell response to checkpoint blockade relies on the expansion of a distinct repertoire of T cell clones that may have just recently entered the tumor.
54 citations
TL;DR: In this paper, the authors sequenced antibody repertoires in longitudinal blood samples in a birth cohort from infancy through the first 3 years of life and found that whereas IgG and IgA show linear increases in mutational maturation with age, IgM and IgD mutations are more closely tied to pathogen exposure.
Abstract: Antigenic exposures at epithelial sites in infancy and early childhood are thought to influence the maturation of humoral immunity and modulate the risk of developing immunoglobulin E (IgE)-mediated allergic disease. How different kinds of environmental exposures influence B cell isotype switching to IgE, IgG, or IgA, and the somatic mutation maturation of these antibody pools, is not fully understood. We sequenced antibody repertoires in longitudinal blood samples in a birth cohort from infancy through the first 3 years of life and found that, whereas IgG and IgA show linear increases in mutational maturation with age, IgM and IgD mutations are more closely tied to pathogen exposure. IgE mutation frequencies are primarily increased in children with impaired skin barrier conditions such as eczema, suggesting that IgE affinity maturation could provide a mechanistic link between epithelial barrier failure and allergy development.
Stanford University1, Seattle Children's2, Baylor College of Medicine3, Boston Children's Hospital4, Cincinnati Children's Hospital Medical Center5, University of Colorado Denver6, University of Miami7, Michigan State University8, Washington University in St. Louis9, Children's Hospital of Philadelphia10, University of Michigan11, Children's Hospital Los Angeles12, University of Alabama at Birmingham13, Columbia University Medical Center14, Yale University15, Vanderbilt University16, Hackensack University Medical Center17, The Chinese University of Hong Kong18, University of Missouri–Kansas City19, University of Utah20, Northwestern University21, Albert Einstein College of Medicine22, All Children's Hospital23, Kaiser Permanente24, Cornell University25, Hacettepe University26, Northeast Ohio Medical University27, Emory University28, University of San Diego29, University of Nebraska Medical Center30, University of Minnesota31, Children's Hospital of Eastern Ontario32, University of Toronto33, University of Amsterdam34, University of Wisconsin-Madison35, Harvard University36
TL;DR: A rare, life-threatening LD in sJIA is defined by a constellation of unusual clinical characteristics, including regional involvement and concomitant vascular changes, and a PAP/ELP variant, suggests macrophage dysfunction.
Abstract: Objective To investigate characteristics and risk factors of a novel parenchymal lung disease, increasingly detected in systemic juvenile idiopathic arthritis (sJIA). Methods In a multi-center retrospective study, 61 cases were investigated, using physician-reported clinical information and centralized analyses of radiologic, pathologic and genetic data. Results Lung disease (LD) was associated with distinctive features, including acute erythematous clubbing and a high frequency of anaphylactic reactions to the IL-6 inhibitor, tocilizumab. Serum ferritin elevation and/or significant lymphopenia preceded LD detection. The most prevalent chest CT pattern was septal thickening, involving the periphery of multiple lobes +/- ground glass opacities. Predominant pathology (23/36) was pulmonary alveolar proteinosis and/or endogenous lipoid pneumonia (PAP/ELP), with atypical features, including regional involvement and concomitant vascular changes. Apparent severe delayed drug hypersensitivity occurred in some cases. 5-year survival was 42%. Whole-exome sequencing (20/61) did not identify a novel monogenic defect PAP-related or macrophage activation syndrome (MAS)-related mutations as likely primary cause. Trisomy 21 (T21) increased LD risk, as did young sJIA onset. Refractory sJIA was not required for LD development. Exposure to interleukin (IL)-1 and IL-6 inhibitors (46/61) was associated with multiple LD features. By several indicators, severity of sJIA was comparable in drug-exposed subjects and published sJIA cohorts. MAS at sJIA onset was increased in the drug-exposed, but it was not associated with LD features. Conclusions A rare, life-threatening LD in sJIA is defined by a constellation of unusual clinical characteristics. The pathology, a PAP/ELP variant, suggests macrophage dysfunction. Inhibitor exposure may promote LD, independent of sJIA severity, in a small subset of treated patients. Treatment/prevention strategies are needed.
TL;DR: It is demonstrated that even during exhaustion there is a subset of functional CD8+ T cells defined by surface expression of SIRPα, a protein not previously reported on lymphocytes, shown to be a phagocytosis inhibitory receptor expressed by myeloid cells.
Abstract: Prolonged exposure of CD8+ T cells to antigenic stimulation, as in chronic viral infections, leads to a state of diminished function termed exhaustion. We now demonstrate that even during exhaustion there is a subset of functional CD8+ T cells defined by surface expression of SIRPα, a protein not previously reported on lymphocytes. On SIRPα+ CD8+ T cells, expression of co-inhibitory receptors is counterbalanced by expression of co-stimulatory receptors and it is only SIRPα+ cells that actively proliferate, transcribe IFNγ and show cytolytic activity. Furthermore, target cells that express the ligand for SIRPα, CD47, are more susceptible to CD8+ T cell-killing in vivo. SIRPα+ CD8+ T cells are evident in mice infected with Friend retrovirus, LCMV Clone 13, and in patients with chronic HCV infections. Furthermore, therapeutic blockade of PD-L1 to reinvigorate CD8+ T cells during chronic infection expands the cytotoxic subset of SIRPα+ CD8+ T cells.
TL;DR: Evidence is presented of in vivo expansion of DQ6-HCRT tetramer+/TRAJ24+/CD4+ T cells in DQ 6+ individuals with and without narcolepsy, and preliminary features that may distinguish them.
Abstract: Individuals with narcolepsy suffer from abnormal sleep patterns due to loss of neurons that uniquely supply hypocretin (HCRT). Previous studies found associations of narcolepsy with the human leukocyte antigen (HLA)-DQ6 allele and T-cell receptor α (TRA) J24 gene segment and also suggested that in vitro-stimulated T cells can target HCRT. Here, we present evidence of in vivo expansion of DQ6-HCRT tetramer+/TRAJ24+/CD4+ T cells in DQ6+ individuals with and without narcolepsy. We identify related TRAJ24+ TCRαβ clonotypes encoded by identical α/β gene regions from two patients and two controls. TRAJ24-G allele+ clonotypes only expand in the two patients, whereas a TRAJ24-C allele+ clonotype expands in a control. A representative tetramer+/G-allele+ TCR shows signaling reactivity to the epitope HCRT87–97. Clonally expanded G-allele+ T cells exhibit an unconventional effector phenotype. Our analysis of in vivo expansion of HCRT-reactive TRAJ24+ cells opens an avenue for further investigation of the autoimmune contribution to narcolepsy development. T cells from narcolepsy patients were recently reported to recognize hypocretin, a wakefulness-promoting neurohormone, suggesting autoimmune origin of the disease. Here the authors show that hypocretin-specific T cells expand both in healthy controls and in narcolepsy patients, and identify preliminary features that may distinguish them.
TL;DR: It is demonstrated that functional and phenotypic shifts occur in NK cells during pregnancy that can influence the magnitude of the immune response to both infections and tumors.
Abstract: Pregnant women are particularly susceptible to complications of influenza A virus infection, which may result from pregnancy-induced changes in the function of immune cells, including natural killer (NK) cells. To better understand NK cell function during pregnancy, we assessed the ability of the two main subsets of NK cells, CD56dim, and CD56bright NK cells, to respond to influenza-virus infected cells and tumor cells. During pregnancy, CD56dim and CD56bright NK cells displayed enhanced functional responses to both infected and tumor cells, with increased expression of degranulation markers and elevated frequency of NK cells producing IFN-γ. To better understand the mechanisms driving this enhanced function, we profiled CD56dim and CD56bright NK cells from pregnant and non-pregnant women using mass cytometry. NK cells from pregnant women displayed significantly increased expression of several functional and activation markers such as CD38 on both subsets and NKp46 on CD56dim NK cells. NK cells also displayed diminished expression of the chemokine receptor CXCR3 during pregnancy. Overall, these data demonstrate that functional and phenotypic shifts occur in NK cells during pregnancy that can influence the magnitude of the immune response to both infections and tumors.
TL;DR: The finding of endogenous HLA ligands from mutated NPM1 supports future studies evaluating immunotherapeutic approaches against this shared target, for this subset of patients with AML.
Abstract: Somatic mutations in cancer are a potential source of cancer specific neoantigens Acute myeloid leukemia (AML) has common recurrent mutations shared between patients in addition to private mutations specific to individuals We hypothesized that neoantigens derived from recurrent shared mutations would be attractive targets for future immunotherapeutic approaches Here we sought to study the HLA Class I and II immunopeptidome of thirteen primary AML tumor samples and two AML cell lines (OCI-AML3 and MV4-11) using mass spectrometry to evaluate for endogenous mutation-bearing HLA ligands from common shared AML mutations We identified two endogenous, mutation-bearing HLA Class I ligands from nucleophosmin (NPM1) The ligands, AVEEVSLRK from two patient samples and C(cys)LAVEEVSL from OCI-AML3, are predicted to bind the common HLA haplotypes, HLA-A*03:01 and HLA-A*02:01 respectively Since NPM1 is mutated in approximately one-third of patients with AML, the finding of endogenous HLA ligands from mutated NPM1 supports future studies evaluating immunotherapeutic approaches against this shared target, for this subset of patients with AML
TL;DR: Simon, an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values, is applied to data from five clinical studies of seasonal influenza vaccination and reveals previously unrecognized CD4+ and T cell subsets strongly associated with a robust Ab response to influenza Ags.
Abstract: Machine learning holds considerable promise for understanding complex biological processes such as vaccine responses. Capturing interindividual variability is essential to increase the statistical power necessary for building more accurate predictive models. However, available approaches have difficulty coping with incomplete datasets which is often the case when combining studies. Additionally, there are hundreds of algorithms available and no simple way to find the optimal one. In this study, we developed Sequential Iterative Modeling "OverNight" (SIMON), an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values. We applied SIMON to data from five clinical studies of seasonal influenza vaccination. The results reveal previously unrecognized CD4+ and CD8+ T cell subsets strongly associated with a robust Ab response to influenza Ags. These results demonstrate that SIMON can greatly speed up the choice of analysis modalities. Hence, it is a highly useful approach for data-driven hypothesis generation from disparate clinical datasets. Our strategy could be used to gain biological insight from ever-expanding heterogeneous datasets that are publicly available.
TL;DR: Recent approaches and discoveries enabling advances in DNA sequencing technology and an array of complementary tools have now made their study much more tractable, filling a major gap in the ability to understand immunology as a system.
TL;DR: To the editor: Non-Hodgkin B-cell lymphomas are almost invariably derived from B lymphocytes that have undergone productive V(D)J rearrangements of their immunoglobulin genes and may additionally have experienced somatic hypermutation.
TL;DR: Three boys with DMD single nucleotide variants associated with Becker muscular dystrophy are presented with myalgia, reduced exercise capacity, neurodevelopmental symptoms and elevated creatine kinase, highlighting the diagnostic utility of muscle biopsy for mRNA studies and western blot to investigate DMD variants of uncertain pathogenicity.
TL;DR: It is shown that peanut specific CD8+ T cells are increased in peanut allergic human subjects, and IgE mediated food allergy is linked to increased T cells in these subjects.
Abstract: CD8+ T cells are seldom considered in IgE mediated food allergy; we show that peanut specific CD8+ T cells are increased in peanut allergic human subjects.
TL;DR: It is demonstrated that the cell surface protein CD38 is a key human NK cell functional receptor through a role in immune synapse formation and opens new avenues in immunotherapeutic development for cancer and infection by revealing a critical role for CD38 in NK cell function.
Abstract: Natural killer (NK) cells use a diverse array of activating and inhibitory surface receptors to detect threats and provide an early line of defense against viral infections and cancer. Here, we demonstrate that the cell surface protein CD38 is a key human NK cell functional receptor through a role in immune synapse formation. CD38 expression marks a mature subset of human NK cells with a high functional capacity. NK cells expressing high levels of CD38 display enhanced killing and IFN-γ secretion in response to influenza virus-infected and tumor cells. Inhibition of CD38 enzymatic activity does not influence NK cell function, but blockade of CD38 and its ligand CD31 abrogates killing and IFN-γ expression in response to influenza-infected cells. Blockade of CD38 on NK cells similarly inhibits killing of tumor cells. CD38 localizes and accumulates at the immune synapse between NK cells and their targets, and blocking CD38 severely abrogates the ability of NK cells to form conjugates and immune synapses with target cells. Thus, CD38 plays a critical role in NK cell immune synapse formation. These findings open new avenues in immunotherapeutic development for cancer and infection by revealing a critical role for CD38 in NK cell function.
TL;DR: The creation of a unified database, FluPRINT, is reported to enable large-scale studies exploring the cellular and molecular underpinnings of successful antibody responses to influenza vaccines, and facilitates the application of machine learning algorithms for data mining.
Abstract: Machine learning has the potential to identify novel biological factors underlying successful antibody responses to influenza vaccines. The first attempts have revealed a high level of complexity in establishing influenza immunity, and many different cellular and molecular components are involved. Of note is that the previously identified correlates of protection fail to account for the majority of individual responses across different age groups and influenza seasons. Challenges remain from the small sample sizes in most studies and from often limited data sets, such as transcriptomic data. Here we report the creation of a unified database, FluPRINT, to enable large-scale studies exploring the cellular and molecular underpinnings of successful antibody responses to influenza vaccines. Over 3,000 parameters were considered, including serological responses to influenza strains, serum cytokines, cell phenotypes, and cytokine stimulations. FluPRINT, facilitates the application of machine learning algorithms for data mining. The data are publicly available and represent a resource to uncover new markers and mechanisms that are important for influenza vaccine immunogenicity.
TL;DR: An in-depth profile of the peripheral blood mononuclear cells of children in regions at the extremes of exposure is provided and an important role for IL-8 and TGFβ is suggested in mitigating the microbial challenges faced by the Bangladeshi children.
Abstract: During the first 5 years of life, children are especially vulnerable to infection-related morbidity and mortality. Conversely, the Hygiene Hypothesis suggests that a lack of exposure to infectious agents early in life could explain the increasing incidence of allergies and autoimmunity in high-income countries. Understanding these phenomena, however, is hampered by a lack of comprehensive, direct immune monitoring in children with differing degrees of microbial exposure. Using mass cytometry, we provide an in-depth profile of the peripheral blood mononuclear cells (PBMCs) of children in regions at the extremes of exposure: the San Francisco Bay Area, USA and an economically poor district of Dhaka, Bangladesh. Despite variability in clinical health, functional characteristics of PBMCs were similar in Bangladeshi and American children at 1 year of age. However, by 2-3 years of age, Bangladeshi children's immune cells often demonstrated altered activation and cytokine production profiles upon stimulation with PMA-ionomycin, with an overall immune trajectory more in line with American adults. Conversely, immune responses in children from the US remained steady. Using principal component analysis, donor location, ethnic background, and cytomegalovirus infection status were found to account for some of the variation identified among samples. Within Bangladeshi 1-year-olds, stunting (as measured by height-for-age z-scores) was found to be associated with IL-8 and TGFβ expression in PMA-ionomycin stimulated samples. Combined, these findings provide important insights into the immune systems of children in high vs. low microbial exposure environments and suggest an important role for IL-8 and TGFβ in mitigating the microbial challenges faced by the Bangladeshi children.
TL;DR: Immunosuppression treatment downregulated microglial population activity and accelerated not only amyloid pathology but also the neuronal degeneration in this APP/PS1 model, which could promote AD pathology and cognitive decline in patients.
Abstract: over pathological progression in the hippocampus of APP/ PS1dE9 transgenic mice. Methods: Cyclosporine (15 mg/kg) and prednisone (20 mg/kg) were intraperitoneally administered to 9 month-old APP/PS1dE9 mice for 3 months. Untreated mice were used as controls. Hippocampal amyloid burden, microglial and astroglial response, cytokines production, tau phosphorylation and neurodegeneration were assessed by immunohistochemistry and molecular techniques (Western-blot and RT-qPCR). Results: The microglial marker Iba1 and some proinflammatory cytokines were found to be decreased by RT-qPCR in immunosuppressed mice compared to controls. Conversely, a significant increase in total Ab levels and the astroglial marker GFAP was detected. Moreover, the treatment exacerbated GABAergic interneuronal (Somatostatin and Neuropeptide Y-positive) degeneration. Conclusions: Immunosuppression treatment downregulated microglial population activity and accelerated not only amyloid pathology but also the neuronal degeneration in this APP/PS1 model. Deficiencies in the innate immune system with age could promote AD pathology and cognitive decline in patients. Therefore, regulating microglial activation signalling pathways might be considered as a therapeutic target for AD. Supported by PI15/00796 and PI18/01557 (to AG), PI15/00957 and PI18/1556 (to JV), and Ciberned (to AG and JV).
TL;DR: SIMON, an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values, is developed and revealed previously unrecognized CD4+ and CD8+ T cell subsets strongly associated with a robust antibody response to influenza antigens.
Abstract: Machine learning holds considerable promise for understanding complex biological processes such as vaccine responses. Capturing interindividual variability is essential to increase the statistical power necessary for building more accurate predictive models. However, available approaches have difficulty coping with incomplete datasets which is often the case when combining studies. Additionally, there are hundreds of algorithms available and no simple way to find the optimal one. Here, we developed Sequential Iterative Modelling “OverNight” or SIMON, an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values. We applied SIMON to data from five clinical studies of seasonal influenza vaccination. The results reveal previously unrecognized CD4+ and CD8+ T cell subsets strongly associated with a robust antibody response to influenza antigens. These results demonstrate that SIMON can greatly speed up the choice of analysis modalities. Hence, it is a highly useful approach for data-driven hypothesis generation from disparate clinical datasets. Our strategy could be used to gain biological insight from ever-expanding heterogeneous datasets that are publicly available.
Patent•
21 Feb 2019
TL;DR: In this paper, a method for measuring the levels of chronic inflammaging (SCI) of a subject is presented, which may comprise measuring the amount of two or more of the proteins CXCL9, TRAIL, IFNG, EOTAXIN and GROA in a sample (e.g., blood serum) from the subject calculating a score based on the weighted amounts of each of those proteins.
Abstract: Provided herein is a method for measuring the levels of chronic inflammaging (SCI) of a subject. In some embodiments, the method may comprise measuring the amount of two or more of the proteins CXCL9, TRAIL, IFNG, EOTAXIN and GROA in a sample (e.g., blood serum) from the subject calculating a score based on the weighted amounts of each of those proteins.
TL;DR: A unified database is created, entitled FluPRINT, to enable a large-scale study exploring novel cellular and molecular underpinnings of successful antibody responses to influenza vaccines, and facilitates application of machine learning algorithms for data mining.
Abstract: Recent advances in machine learning have allowed identification of molecular and cellular factors that underly successful antibody responses to influenza vaccines. Results of these studies have revealed the high level of complexity necessary to establish influenza immunity, and many different cellular and molecular components involved. However, identified correlates of protection, as measured by antibody responses fail to account for the majority of vaccinated cases across ages, cohorts, and influenza seasons. Major challenges arise from small sample sizes and from analysis of only one aspect of the biology such by using transcriptome data. The objective of the current study is to create a unified database, entitled FluPRINT, to enable a large-scale study exploring novel cellular and molecular underpinnings of successful antibody responses to influenza vaccines. Over 3,000 parameters were considered, including serological responses to influenza strains, serum cytokines, cell subset phenotypes, and cytokine stimulations. FluPRINT, thus facilitates application of machine learning algorithms for data mining. The data are publicly available and represent a resource to uncover new markers and mechanisms that are important for influenza vaccine immunogenicity.
TL;DR: MARIA-I enables accurate prediction of neoantigen presentation for MHC class I at scale and is expected to yield insights for development of therapeutic cancer vaccines as well as applications in transplantation and autoimmune pathology.
TL;DR: Analysis of the critical quality attributes of APH products to a larger cohort of patients with hematological malignancies (HM) as well as solid tumors (ST) confirmed that cryopreservation and or elutriation increases clinical MFG success.