Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.

T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 infection. Here, we combined two high-throughput immune profiling methods to create a quantitative picture of the T-cell response to SARS-CoV-2. First, at the individual level, we deeply characterized 3 acutely infected and 58 recovered COVID-19 subjects by experimentally mapping their CD8 T-cell response through antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I presented viral peptides (class II data in a forthcoming study). Then, at the population level, we performed T-cell repertoire sequencing on 1,015 samples (from 827 COVID-19 subjects) as well as 3,500 controls to identify shared "public" T-cell receptors (TCRs) associated with SARS-CoV-2 infection from both CD8 and CD4 T cells. Collectively, our data reveal that CD8 T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the T-cell response to SARS-CoV-2 peaks about one to two weeks after infection and is detectable for several months after recovery. As an application of these data, we trained a classifier to diagnose SARS-CoV-2 infection based solely on TCR sequencing from blood samples, and observed, at 99.8% specificity, high early sensitivity soon after diagnosis (Day 3-7 = 83.8% [95% CI = 77.6-89.4]; Day 8-14 = 92.4% [87.6-96.6]) as well as lasting sensitivity after recovery (Day 29+/convalescent = 96.7% [93.0-99.2]). These results demonstrate an approach to reliably assess the adaptive immune response both soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points. This blood-based molecular approach to characterizing the cellular immune response has applications in vaccine development as well as clinical diagnostics and monitoring.

Continuous hydroxylation of the HIF-1 transcription factor ␣ subunit by oxygen and 2-oxoglutarate-dependent dioxygenases promotes decay of this protein and thus prevents the transcriptional activation of many genes involved in energy metabolism, angiogenesis, cell survival, and matrix modification. Hypoxia blocks HIF-1␣ hydroxylation and thus activates HIF-1␣-mediated gene expression. Several nonhypoxic stimuli can also activate HIF-1, although the mechanisms involved are not well known. Here we show that the glucose metabolites pyruvate and oxaloacetate inactivate HIF-1␣ decay in a manner selectively reversible by ascorbate, cysteine, histidine, and ferrous iron but not by 2-oxoglutarate or oxygen. Pyruvate and oxaloacetate bind to the 2-oxoglutarate site of HIF-1␣ prolyl hydroxylases, but their effects on HIF-1 are not mimicked by other Krebs cycle intermediates, including succinate and fumarate. We show that inactivation of HIF-1 hydroxylation by glucose-derived 2-oxoacids underlies the prominent basal HIF-1 activity commonly seen in many highly glycolytic cancer cells. Since HIF-1 itself promotes glycolytic metabolism, enhancement of HIF-1 by glucose metabolites may constitute a novel feed-forward signaling mechanism involved in malignant progression.Mammalian cells adapt to hypoxia through the action of the heterodimeric transcription factor HIF-1. Such adaptations can also promote carcinogenesis by inducing angiogenesis, treatment resistance, and invasiveness in hypoxic cancer cells within tumors (1). In the presence of oxygen, the HIF-1␣ subunit undergoes rapid decay via a ubiquitin-proteasome degradation pathway involving the von HippelLindau tumor suppressor gene product pVHL (2-4). The binding of pVHL to HIF-1␣ requires the post-translational hydroxylation of proline residues (Pro 402 and Pro 564 ) within the HIF-1␣ oxygen-dependent degradation (ODD) 4 domain (5, 6). This modification is prevented during hypoxia, thus allowing HIF-1␣ to escape proteolysis, dimerize with HIF-1␤, and translocate to the nucleus. A separately controlled, O 2 -dependent hydroxylation of asparagine 803 in the HIF-1␣ C-terminal transactivation domain inhibits HIF-1 interaction with the p300/CBP coactivator, thereby blocking HIF-1 transcriptional activity in the presence of oxygen (7,8). Three HIF-1␣ prolyl hydroxylases (HPH1 to -3; also referred to as PHD3 to -1, respectively) and one O 2 -dependent HIF-1␣ asparaginyl hydroxylase (factor inhibiting HIF, or FIH) have been clearly identified so far (9 -11). These enzymes are all members of the 2-oxoglutarate-dependent family of dioxygenases and have an absolute requirement for oxygen, ferrous iron, and 2-oxoglutarate (2-OG). This explains how hypoxia, iron chelators such as desferrioxamine (DFO), and artificial 2-OG analogs such as N-oxalylglycine or its cellpermeable precursor dimethyloxalylglycine (DMOG) can all prevent HIF-1␣ proteolysis and activate HIF-mediated gene expression. Ascorbate is also required for the sustained activity of many 2-OG-dependent dioxygenases (12, 1...

The genetic basis of Lewy body dementia (LBD) is not well understood. Here, we performed whole-genome sequencing in large cohorts of LBD cases and neurologically healthy controls to study the genetic architecture of this understudied form of dementia and to generate a resource for the scientific community. Genome-wide association analysis identified five independent risk loci, whereas genome-wide gene-aggregation tests implicated mutations in the gene GBA . Genetic risk scores demonstrate that LBD shares risk profiles and pathways with Alzheimer’s disease and Parkinson’s disease, providing a deeper molecular understanding of the complex genetic architecture of this age-related neurodegenerative condition.