Antigen-specific CD4+ T cells exhibit distinct transcriptional phenotypes in the lymph node and blood following vaccination in humans

SARS-CoV-2 infection and mRNA vaccination induce robust CD4+ T cell responses that are critical for the development of protective immunity. Here, we evaluated spike-specific CD4+ T cells in the blood and draining lymph node (dLN) of human subjects following BNT162b2 mRNA vaccination using single-cell transcriptomics. We analyze multiple spike-specific CD4+ T cell clonotypes, including novel clonotypes we define here using Trex, a new deep learning-based reverse epitope mapping method integrating single-cell T cell receptor (TCR) sequencing and transcriptomics to predict antigen-specificity. Human dLN spike-specific T follicular helper cells (TFH) exhibited distinct phenotypes, including germinal center (GC)-TFH and IL-10+ TFH, that varied over time during the GC response. Paired TCR clonotype analysis revealed tissue-specific segregation of circulating and dLN clonotypes, despite numerous spike-specific clonotypes in each compartment. Analysis of a separate SARS-CoV-2 infection cohort revealed circulating spike-specific CD4+ T cell profiles distinct from those found following BNT162b2 vaccination. Our findings provide an atlas of human antigen-specific CD4+ T cell transcriptional phenotypes in the dLN and blood following vaccination or infection.

PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis

Phosphatase and tensin homologue (PTEN) is frequently mutated in human cancer, but its roles in lymphopoiesis and tissue homeostasis remain poorly defined. Here we show that PTEN orchestrates a two-step developmental process linking antigen receptor and IL-23-Stat3 signalling to type-17 innate-like T cell generation. Loss of PTEN leads to pronounced accumulation of mature IL-17-producing innate-like T cells in the thymus. IL-23 is essential for their accumulation, and ablation of IL-23 or IL-17 signalling rectifies the reduced survival of female PTEN-haploinsufficient mice that model human patients with PTEN mutations. Single-cell transcriptome and network analyses revealed the dynamic regulation of PTEN, mTOR and metabolic activities that accompanied type-17 cell programming. Furthermore, deletion of mTORC1 or mTORC2 blocks PTEN loss-driven type-17 cell accumulation, and this is further shaped by the Foxo1 and Stat3 pathways. Collectively, our study establishes developmental and metabolic signalling networks underpinning type-17 cell fate decisions and their functional effects at coordinating PTEN-dependent tissue homeostasis.

TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs

T-cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages experimentally inferred antigen-associated TCRs to form meta-clonotypes - groups of biochemically similar TCRs - that can be used to robustly quantify functionally similar TCRs in bulk repertoires across individuals. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the SARS-CoV-2 antigen-associated TCRs that have strong evidence of restriction to patients with a specific human leukocyte antigen (HLA) genotype. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (false discovery rate [FDR]<0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package, tcrdist3, that implements this framework and facilitates flexible workflows for distance-based TCR repertoire analysis.

TCR meta-clonotypes for biomarker discovery with tcrdist3: identification of public, HLA-restricted SARS-CoV-2 associated TCR features

As the mechanistic basis of adaptive cellular antigen recognition, T cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages antigen-enriched repertoires to form meta-clonotypes - groups of biochemically similar TCRs - that can be used to robustly identify and quantify functionally similar TCRs in bulk repertoires. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the 17 SARS-CoV-2 antigen-enriched repertoires with the strongest evidence of HLA-restriction. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (FDR < 0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package, tcrdist3, that implements this framework and facilitates flexible workflows for distance-based TCR repertoire analysis.

A Fluorescent Reporter Mouse for Inflammasome Assembly Demonstrates an Important Role for Cell-Bound and Free ASC Specks during In Vivo Infection

Inflammasome activation is associated with numerous diseases. However, in vivo detection of the activated inflammasome complex has been limited by a dearth of tools. We have developed transgenic mice that ectopically express the fluorescent adaptor protein, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) and characterized the formation of assembled inflammasome complexes ("specks") in primary cells and tissues. In addition to hematopoietic cells, we have found that a stromal population in the lung tissues formed specks during the early phase of influenza infection, whereas myeloid cells showed speck formation after 2 days. In a peritonitis and group B streptococcus infection model, a higher percentage of neutrophils formed specks at early phases of infection, while dendritic cells formed specks at later time points. Furthermore, speck-forming cells underwent pyroptosis and extensive release of specks to the extracellular milieu in vivo. These data underscore the importance of free specks during inflammatory processes in vivo.

The DNA sensing inflammasome, AIM2, is critical for protection from influenza infection (P6140)

Sensing of viral-derived nucleic acids following entry into cytosol of the host cell triggers inflammasome activation leading to maturation of interleukin 1β (IL-1β) and IL-18. In addition to activating the inflammasome directly within infected cells, viral infection can cause extensive tissue damage resulting in the accumulation of endogenous danger-associated molecular patterns (DAMPs), including self-DNA, which may provide signals in triggering inflammasome activation in neighboring uninfected cells. Though several studies have shown inflammasome activation within infected cells, it is unknown whether the sensing of DAMPs by uninfected bystander cells and the subsequent inflammasome activation provides an important proinflammatory signal in establishing an effective antiviral response. Using mice deficient in the DNA-sensing inflammasome component AIM2, we demonstrate AIM2 is required for protective immunity to influenza A virus (IAV), an orthomyxovirus with an ssRNA genome and a strictly RNA replication cycle. In addition to their increase in mortality and morbidity, Aim2-deficient mice show a defect in levels caspase-1-dependent cytokines IL-1β and IL-18, both important in the activation of cellular antiviral responses, following IAV challenge. Collectively, these data findings suggest that the sensing of self-DNA by AIM2 plays a critical role in triggering innate immune responses following infection with an RNA virus.

The role of innate immune adaptor STING in suppressing lupus (P4070)

The ability of innate immune receptors such as the TLRs to sense both microbial products and self-molecules released from stressed, damaged or dying cells is well accepted. The discovery of TLR-independent DNA/RNA sensing pathways raises the possibility that additional mechanisms besides TLRs regulate self-DNA/RNA driven autoimmune diseases such as systemic lupus erythematosus (SLE). Both TLR-dependent and independent pathways lead to the induction of type I IFNs, which can promote autoimmunity. Here, we examined the role of a key inducer of type I IFNs, the cytosolic DNA-sensing stimulator of interferon genes (STING) pathway in SLE pathogenesis. We generated STING-/- mice on a lupus prone MRL/lpr background and compared disease progression to lpr/lpr littermates. Unexpectedly, STING/lpr mice display accelerated onset and progression of disease. These animals display gross increases in lymphocytic and plasma cell populations, class-switched Abs and exacerbated nephritis. Significant expansion of the myeloid compartment is concomitant with increases in serum cytokines TNF-α and IFNγ. Further analysis of STING/lpr mice shows a surprising increase in anti-SmRNPs, RNA specific Abs and an interferon stimulated gene (ISG) signature. Given the central role of type I IFNs and TLR7 in MRL/lpr pathogenesis, and the increases we see in ISGs and anti-RNA Abs, we propose an unprecedented role for STING in limiting lupus pathogenesis by regulating TLR and type I IFN signaling pathways.