Cytotoxic CD4+ tissue-resident memory T cells are associated with asthma severity

Patients with severe uncontrolled asthma represent a distinct endotype with persistent airway inflammation and remodeling that is refractory to corticosteroid treatment. To determine T cell subsets and effector molecules that drive pathogenesis of severe asthma, we performed single-cell transcriptome analysis of >50,000 airway CD4+ T cells isolated from bronchoalveolar lavage (BAL) samples from 30 patients with mild and severe asthma. We observed striking heterogeneity in the nature of CD4+ T cells present in asthmatics' airways with tissue-resident memory (TRM) cells making a dominant contribution. Notably, in severe asthmatics a subset of CD4+ TRM cells (CD103-expressing) was significantly increased, comprising nearly 65% of all CD4+ T cells in the airways of male patients with severe asthma when compared to mild asthma (13%). This subset was enriched for transcripts linked to T cell receptor (TCR) activation (HLA-DRB1, HLA-DPA1, CD40LG) and cytotoxicity (GZMB, GZMH), and following stimulation expressed high levels of transcripts encoding for pro-inflammatory non-TH2 cytokines (CCL3, CCL4, CCL5, TNF, LIGHT) that could fuel persistent airway inflammation and remodeling. Our findings indicate the need to look beyond the traditional T2 model of severe asthma to better understand the heterogeneity of this disease.

This work was supported by (i) NIH research grant R01HL114093 (PV) and equipment grants (S10RR027366 - BD FACSAria Fusion, and S10OD025052 - Illumina Novaseq 6000); the William K. Bowes Jr. Foundation (P.V.). The WATCH study is supported by the Southampton NIHR Biomedical Research Centre and the Southampton NIHR Clinical Research Facility which are funded by the NIHR and are a partnership between the University of Southampton and University Hospital Southampton NHS Foundation Trust.

Molecular Signatures of IL-10/IFN-γ Co-Producing CD4 T Cells During Acute Dengue Virus Infection

Dengue virus (DENV) is an emerging pathogen and a serious public health issue. It is estimated that ~390 million people are infected yearly. DENV infection is associated with a range of clinical manifestations, from asymptomatic to more severe presentations including dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). There is currently no specific therapy available for the treatment of dengue diseases other than supportive care. Thus, a better understanding of the host’s immune response against DENV, especially during the acute phase of infection, is of great public health interests. Although previous studies suggest that increased IL-10 level in the serum and plasma is associated with severe dengue disease, whether dengue-specific CD4 T cells produce IL-10 remains unknown. Here we show evidence of DENV-specific IL-10-producing CD4 T cells during acute DENV infection. Surprisingly, an IL-10+IFN-γ+ double positive (DP) CD4 T cell population is prominent in acute hospitalized DENV cases but disappear at the convalescent stage. These cells are not conventional regulatory T (Treg) cells as they lack Foxp3 expression. In contrast, RNA-sequencing and high-dimensional CyTOF analyses reveal that these cells partially exhibit previously identified signatures associated with cytotoxic CD4 T cells and type 1 regulatory T (Tr1) cells. Notably, we identified several novel signatures of DP cells including IL-19, IL-21, and IL-22, suggesting that these cells may have complex cytokine activities and functions. Overall, this study reveals unique phenotypes of DENV-specific IL-10/IFN-γ co-producing CD4 cells and provides insights into antigen-specific T cell responses during acute DENV infection.

Assessment of the global chromatin landscape and transcriptome of peripheral iNKT cell subsets

Vα14i invariant Natural Killer T (iNKT) cells are important modulators of immune responses. They differentiate into three effector cell subsets in the thymus, NKT1, NKT2, and NKT17, which resemble Th1, Th2, and Th17 CD4 T cells. After exiting the thymus, iNKT cells localize to tissues and do not recirculate, but the impact of tissue localization on the epigenetic landscape and transcriptome of each subset is not known. We assessed global chromatin accessibility and transcriptional activity using ATACseq and RNAseq in iNKT cell subsets isolated from the thymus, spleen, liver, and lung. By comparing iNKT cell subsets within each tissue, we found over 5,000 differentially accessible regions of chromatin. This is consistent with previous analyses showing great differences in the transcriptomes of the thymic iNKT cell subsets. Interestingly, relatively limited differences in the accessible chromatin or transcriptome were observed when comparing the same subset from different sites, e.g., NKT1 cells from different tissues. An exception is the unique set of accessible chromatin regions and transcripts identified in all iNKT cell subsets in the lung. Lung iNKT cells exhibited features of increased AP-1 transcription factor activity, which has been correlated with both activation and tissue residency, found in other lung lymphocyte populations. After antigen challenge, an iNKT cell subset with features similar to T follicular helper cells is abundant; these cells are highly different from the other subsets. Taken together, these data indicate that the epigenome and transcriptome of iNKT cells is highly impacted by subset decision, and much less by tissue localization, although dynamic changes occur after antigen exposure.