Invariant natural killer T cells are found in low numbers in the airways of subjects with asthma, subjects with COPD, and controls.

-Severe acute respiratory syndrome (SARS) is a newly emerged disease that rapidly spread around the world. The disease originated in southern China and a novel coronavirus (SARS CoV) has been implicated as the causative organism. The path this virus took to set up human infection remains a mystery, though preliminary data point to origins in an animal reservoir. Nosocomial transmission of SARS CoV has been a striking feature in this epidemic. The clinical illness is similar to many acute respiratory infections, although a large proportion of patients show a rapid deterioration with respiratory distress towards the end of the second week of illness. The management principles are broadly similar to treating any community acquired pneumonia but the infection control measures take a pivotal role. There is no proven antiviral agent against SARS CoV. The most remarkable feature about the SARS epidemic was the speed with which the global community acted in a coordinated way to control it. HistoryPlagues are as certain as death and taxes. 3 Over the last century several important human microbes causing severe acute respiratory disease have emerged (Table 1). SARS CoV is not the first, and nor will it be the last of its kind. All these infections, with the exception of Legionnaires' disease, have one thing in common: the origin of the infective agent is in animals, either domestic or wild. Chlamydia pneumoniae and human metapneumovirus are examples of other new pathogens causing severe acute respiratory illness in which humans have always been the likely host. The source of SARS CoV remains to be determined.When reports of a mysterious respiratory illness began to emerge from southern China in late 2002, no one knew what caused it. Would history be repeated with a strain as deadly as the 1918 pandemic strain which killed up to 40 million people? Was this caused by a supervirulent strain of flu, as seemed to be suggested by the coincidence of two deaths due to H5N1 influenza? Even in mid-March, when outbreaks elsewhere in Asia caused the WHO to release its first ever global alert that shot SARS on to the world's news agenda, the pathogen remained unknown. 1 The infectiousness of the disease, its mode of transmission and death rate were also unclear. Health officials were not sure whether they were dealing with a troubling, but ultimately limited, threat or a global mass killer. 4 The earliest cases are now known to have occurred in mid-November 2002 in Guangdong Province, China. SARS was carried out into the world at large on 21 February 2003 when an infected medical doctor from Guangdong checked into a ninth floor room of a Hong Kong hotel. That single hotel floor n REVIEWS 152

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Chronic damage and repair of the bronchial epithelium are features of asthma. We have previously reported that ex vivo stimulation of normal bronchial epithelial cells with epidermal growth factor (EGF), a key factor of epithelial repair, enhances the mechanisms of neutrophil accumulation, thereby promoting neutrophil defences during acute injury but potentially enhancing inflammation in chronic airway diseases. We have now sought to (i) determine whether this EGF-dependent pro-neutrophil activity is increased in asthma, where EGF and its epithelial receptor are over-expressed, and (ii) elucidate some of the mechanisms underlying this asthmatic epithelial-neutrophil interaction. Primary bronchial epithelial cells (PBEC) from healthy subjects, mild asthmatics and moderate-to-severe asthmatics (Mod/Sev) were stimulated with EGF, a model that mimics a repairing epithelium. Conditioned culture media (EGF-CM) were assessed for neutrophil chemotactic and anti-apoptotic activities and inflammatory mediator production. EGF induced the epithelium to produce soluble mediators with neutrophil chemotactic (p<0.001) and pro-survival (p = 0.021) activities which were related to the clinical severity of asthma (trend p = 0.010 and p = 0.009, respectively). This was associated with enhanced IL-6, IL-8, GM-CSF and TNF-α release, and cytokine-neutralising experiments using EGF-CM from Mod/Sev asthmatics demonstrated a role for GM-CSF in neutrophil survival (p<0.001). Pre-treatment of neutrophils with specific inhibitors of the myeloid-restricted class I phosphatidylinositol-3-OH kinase (PI(3)K) isoforms showed that the EGF-CM from Mod/Sev asthmatics depended on the γ (p<0.021) but not δ isoforms, while neutrophil survival required multiple class I PI(3)Ks. The EGF-induced chemotactic, but not pro-survival activity, involved RhoA signaling in neutrophils (p = 0.012). EGF whose activity is upregulated in asthma induces ex vivo the epithelium from asthmatic patients to produce pro-neutrophil activities; these are related to asthma severity and, in moderate-to-severe asthmatics, involves class IB PI(3)Kγ signaling, providing a potential therapeutic target for neutrophilic forms of asthma.

While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (database of immune cell expression, expression quantitative trait loci (eQTLs), and epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis (https://dice-database.org).

BackgroundCancer is characterized by an accumulation of somatic mutations, of which a significant subset can generate cancer-specific neoepitopes that are recognized by autologous T cells. Such neoepitopes are emerging as important targets for cancer immunotherapy, including personalized cancer vaccination strategies.MethodsWe used whole-exome and RNA sequencing analysis to identify potential neoantigens for a patient with non-small cell lung cancer. Thereafter, we assessed the autologous T-cell reactivity to the candidate neoantigens using a long peptide approach in a cultured interferon gamma ELISpot and tracked the neoantigen-specific T-cells in the tumor by T-cell receptor (TCR) sequencing. In parallel, identified gene variants were incorporated into a Modified Vaccinia Ankara-based vaccine, which was evaluated in the human leucocyte antigen A*0201 transgenic mouse model (HHD).ResultsSequencing revealed a tumor with a low mutational burden: 2219 sequence variants were identified from the primary tumor, of which 23 were expressed in the transcriptome, involving 18 gene products. We could demonstrate spontaneous T-cell responses to 5/18 (28%) mutated gene variants, and further analysis of the TCR repertoire of neoantigen-specific CD4+ and CD8+ T cells revealed TCR clonotypes that were expanded in both blood and tumor tissue. Following vaccination of HHD mice, de novo T-cell responses were generated to 4/18 (22%) mutated gene variants; T cells reactive against two variants were also evident in the autologous setting. Subsequently, we determined the major histocompatibility complex restriction of the T-cell responses and used in silico prediction tools to determine the likely neoepitopes.ConclusionsOur study demonstrates the feasibility of efficiently identifying tumor-specific neoantigens that can be targeted by vaccination in tumors with a low mutational burden, promising successful clinical exploitation, with trials currently underway.

To determine the nature of CD4 + T cells that provide 'help' for generating robust anti-tumor CD8 + cytotoxic T cell (CTL) responses, we profiled the transcriptomes of patient-matched CD4 + and CD8 + T cells present in the tumor micro-environment (TME) and analyzed them jointly using integrated weighted gene correlation network analysis. We found the follicular helper T cell (T FH ) program in CD4 + T cells was strongly associated with proliferation and tissue-residency in CD8 + CTLs. Single-cell analysis demonstrated the presence of T FHlike cells and features linked to cytotoxic function and their provision of CD8 + T cell 'help'. Tumor-infiltrating T FH -like cells expressed PD-1 and were enriched in tumors following checkpoint blockade, suggesting that they may respond to anti-PD-1 therapy. Adoptive transfer or induction of T FH cells in mouse models resulted in augmented CD8 + CTL responses and impairment of tumor growth, indicating an important role of T FH -like CD4 + T cells in anti-tumor immunity. RESULTS Follicular program in CD4 + T cells is associated with CD8 + CTL proliferation, cytotoxicity and tissue residency in the TMETo characterize the molecular interplay between cells in the TME and to define the properties in CD4 + T cells that are strongly associated with robust anti-tumor CD8 + CTL effector and T RM responses across our cohort of patients with lung cancer, we developed a novel method, iWGCNA, for joint transcriptome analysis of co-expression patterns across different cell types (Figure 1A). Standard coexpression analysis (WGCNA (28)), is designed for studying one cell type at a time, and genes with similar expression patterns across a set of samples are grouped together into discrete clusters or modules. These modules can then be correlated with specific molecular traits to determine the group of genes whose expression is strongly associated with that trait(28). However, for a complex system, as found in the TME, where multiple cell types interact and co-regulate the trait of interest, it is important to analyze the cell transcriptomes in an integrated fashion. The goal of iWGCNA is to group transcript expression from different cell types in the TME of matched patients to form integrated gene modules that can reveal the molecular cross-talk between cell types and their relationship to specific traits.Here, we performed iWGCNA by merging the transcriptomes from patient-matched CD4 + and CD8 + T cells present in the TME (n = 36) (3) and generated 29 gene network modules, each of which was composed of varying proportions of CD4 + T cell-and CD8 + T cell-transcripts ( Figure 1A and B; Supplementary Tables 1 and 2).To determine what properties in CD4 + T cells were associated with robust CD8 + T cell responses in the TME, we correlated these gene modules with CD8 + T cell proliferation signature as a trait (Methods), as it represented a feature of robust anti-tumor T cell responses in the TME.Module 7 (407 CD8 + T cell-and 178 CD4 + T cell-transcripts) exhibited the highest correlation with the...

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