T o date, hundreds of thousands of deaths have been attributed to coronavirus disease 2019 (COVID-19) 1. Millions of infections by SARS-CoV-2, the virus responsible for COVID-19, have been reported, although its full extent has yet to be determined owing to limited testing 2. Government interventions to slow viral spread have disrupted daily life and economic activity for billions of people. Strategies to ease restraints on human mobility and interaction without provoking a major resurgence of transmission and mortality will depend on accurate estimates of population levels of infection and immunity 3. Current testing for the virus largely depends on labor-intensive molecular techniques 4. Individuals with positive molecular tests represent only a small fraction of all infections, given limited deployment and the brief time window when real-time (RT)-PCR testing has the highest sensitivity 5-7. The proportion of undocumented cases in the original epidemic focus was estimated to be as high as 86% 8 , and asymptomatic infections are suspected to play a substantial role in transmission 9-14. Widely available, reliable antibody detection assays would enable more accurate estimates of SARS-CoV-2 prevalence and incidence. On February 4, 2020, the Secretary of the US Department of Health and Human Services issued an emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 15 , allowing nucleic acid detection and immunoassay tests to be offered based on manufacturer-reported data without formal US Food and Drug Administration (FDA) clearance 16. In response, dozens of companies began to market laboratory-based immunoassays and point-of-care (POC) tests. Rigorous, comparative performance data are crucial to inform clinical care and public health responses.

Naturally occurring cases of monogenic type 1 diabetes (T1D) help establish direct mechanisms driving this complex autoimmune disease. A recently identified de novo germline gain-of-function (GOF) mutation in the transcriptional regulator STAT3 was found to cause neonatal T1D. We engineered a novel knock-in mouse incorporating this highly diabetogenic human STAT3 mutation (K392R) and found that these mice recapitulated the human autoimmune diabetes phenotype. Paired single-cell TCR and RNA sequencing revealed that STAT3-GOF drives proliferation and clonal expansion of effector CD8+ cells that resist terminal exhaustion. Single-cell ATAC-seq showed that these effector T cells are epigenetically distinct and have differential chromatin architecture induced by STAT3-GOF. Analysis of islet TCR clonotypes revealed a CD8+ cell reacting against known antigen IGRP, and STAT3-GOF in an IGRP-reactive TCR transgenic model demonstrated that STAT3-GOF intrinsic to CD8+ cells is sufficient to accelerate diabetes onset. Altogether, these findings reveal a diabetogenic CD8+ T cell response that is restrained in the presence of normal STAT3 activity and drives diabetes pathogenesis.

CD8+ T cells are critical for the immune response to pathogens and tumors, and CD8+ T cell memory protects against repeat infections. In this study, we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of CD8+ T cell immune responses. Mice with a T cell–specific deletion of ATF7ip have a CD8+ T cell–intrinsic enhancement of Il7r expression and Il2 expression leading to enhanced effector and memory responses. Chromatin immunoprecipitation sequencing studies identified ATF7ip as a repressor of Il7r and Il2 gene expression through the deposition of the repressive histone mark H3K9me3 at the Il7r gene and Il2–Il21 intergenic region. Interestingly, ATF7ip targeted transposable elements for H3K9me3 deposition at both the IL7r locus and the Il2–Il21 intergenic region, indicating that ATF7ip silencing of transposable elements is important for regulating CD8+ T cell function. These results demonstrate a new epigenetic pathway by which IL-7R and IL-2 production are constrained in CD8+ T cells, and this may open up new avenues for modulating their production.

Naturally occurring cases of monogenic type 1 diabetes (T1D) provide rare opportunities to establish direct mechanisms that cause this complex autoimmune disease. A recently identified de novo germline gain-of-function (GOF) mutation in the transcriptional regulator signal transducer and activator of transcription 3 (STAT3) was shown to cause neonatal T1D at birth. To investigate the role of STAT3 hyperactivity in T1D, we engineered a novel knock-in (KI) mouse incorporating this highly diabetogenic human mutation (K392R) in the STAT3 gene. These mice developed accelerated diabetes with severe insulitis and insulin autoantibodies, thereby recapitulating the human autoimmune diabetes phenotype. Paired T cell receptor (TCR) and transcriptome (RNA) sequencing in single cells revealed that STAT3-GOF drives the proliferation and clonal expansion of highly cytotoxic effector CD8+ T cells that are resistant to terminal exhaustion. Single-cell ATAC-seq showed that these effector T cells are epigenetically distinct and revealed differential chromatin architecture induced by STAT3-GOF. Analysis of islet TCR clonotypes revealed an effector CD8+ T cell reacting against the known antigen IGRP, and STAT3-GOF in an IGRP-reactive TCR transgenic model demonstrated that STAT3-GOF intrinsic to CD8+ T cells is sufficient to accelerate diabetes onset. Taken together, these findings reveal a diabetogenic CD8+ T cell response that is restrained in the presence of normal STAT3 activity and drives diabetes pathogenesis.