Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here, we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, MERS-CoV, bat coronavirus HKU5 expressing the SARS-CoV-1 spike, and VSV expressing the SARS-CoV-2 spike. We identify known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways including HMGB1 and the SWI/SNF chromatin remodeling complex that are SARS-lineage and pan-coronavirus specific, respectively. We show HMGB1 regulates ACE2 expression and is critical for viral entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. Together this identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS-lineage specific and pan-coronavirus host factors that regulate susceptibility to highly pathogenic coronaviruses.

Accumulating evidence suggests that neurodegeneration induced by pathogenic proteins depends on contributions from surrounding glia. Here we demonstrate that NF-B signaling in microglia is critically involved in neuronal death induced by amyloid-␤ (A␤) peptides, which are widely presumed to cause Alzheimer disease. Constitutive inhibition of NF-B signaling in microglia by expression of the nondegradable IB␣ superrepressor blocked neurotoxicity, indicating a pivotal role for microglial NF-B signaling in mediating A␤ toxicity. Stimulation of microglia with A␤ increased acetylation of RelA/p65 at lysine 310, which regulates the NF-B pathway. Overexpression of SIRT1 deacetylase and the addition of the SIRT1 agonist resveratrol markedly reduced NF-B signaling stimulated by A␤ and had strong neuroprotective effects. Our results support a glial loop hypothesis by demonstrating a critical role for microglial NF-B signaling in A␤-dependent neurodegeneration. They also implicate SIRT1 in this pathway and highlight the therapeutic potential of resveratrol and other sirtuin-activating compounds in Alzheimer disease.Neurodegenerative diseases appear to be caused by pathogenic proteins that affect neurons directly or contribute to neuronal death by engaging neurotoxic pathways in surrounding glia (1-3). In Alzheimer disease (AD), 3 neurodegeneration may be exacerbated by chronic inflammatory reactions of cells surrounding neuritic plaques, including microglia and astrocytes (4, 5). High concentrations of fibrillar A␤ can activate microglia, resulting in tumor necrosis factor-␣-dependent expression of inducible nitric-oxide synthase (iNOS) and neuronal apoptosis (6). Nonfibrillar A␤, which may be the major pathogenic form of A␤ in the early stages of AD, also stimulates microglia to induce neurodegeneration. Dimeric and trimeric assemblies of A␤-(1-42) isolated from amyloid deposits elicited profound neurotoxicity in hippocampal neurons but only in the presence of microglia (7). Stimulation with soluble A␤ caused microglia to secrete toxic factors, including cathepsin B, and mediated neurodegeneration (8). Inhibiting the induction of long term potentiation with soluble A␤ involves activation of microglia and stimulation of iNOS and superoxide (9).We hypothesized that the pathogenic engagement of microglia by A␤ involves activation of NF-B, a transcription factor that mediates immune and inflammatory responses (10) and controls the expression of both iNOS and cathepsin B (11, 12). In AD brains, RelA/p65 immunoreactivity is greater in neurons and astrocytes surrounding amyloid plaques, raising the possibility of a role for NF-B in AD pathogenesis (13). In cultured neurons and glia, A␤ stimulation led to NF-B activation (12-15). However, it remains unclear whether NF-B signaling actually contributes to AD-related neurodegeneration.To test our hypothesis, we took advantage of the fact that NF-B activation is tightly regulated by inhibitory proteins, such as IB␣ (16). In response to stimuli, IB␣ is degraded to release the NF-B p50/...

Alzheimer's disease (AD) may result from the accumulation of amyloid-beta (Abeta) peptides in the brain. The cysteine protease cathepsin B (CatB) is associated with amyloid plaques in AD brains and has been suspected to increase Abeta production. Here, we demonstrate that CatB actually reduces levels of Abeta peptides, especially the aggregation-prone species Abeta1-42, through proteolytic cleavage. Genetic inactivation of CatB in mice with neuronal expression of familial AD-mutant human amyloid precursor protein (hAPP) increased the relative abundance of Abeta1-42, worsening plaque deposition and other AD-related pathologies. Lentivirus-mediated expression of CatB in aged hAPP mice reduced preexisting amyloid deposits, even thioflavin S-positive plaques. Under cell-free conditions, CatB effectively cleaved Abeta1-42, generating C-terminally truncated Abeta peptides that are less amyloidogenic. Thus, CatB likely fulfills antiamyloidogenic and neuroprotective functions. Insufficient CatB activity might promote AD; increasing CatB activity could counteract the neuropathology of this disease.

Cross-linking of high-affinity immunoglobulin E (IgE) results in the life-threatening allergic reaction anaphylaxis. Yet the cellular mechanisms that induce B cells to produce IgE in response to allergens remain poorly understood. T follicular helper (TFH) cells direct the affinity and isotype of antibodies produced by B cells. Although TFH cell–derived interleukin-4 (IL-4) is necessary for IgE production, it is not sufficient. We report a rare population of IL-13–producing TFH cells present in mice and humans with IgE to allergens, but not when allergen-specific IgE was absent or only low-affinity. These “TFH13” cells have an unusual cytokine profile (IL-13hiIL-4hiIL-5hiIL-21lo) and coexpress the transcription factors BCL6 and GATA3. TFH13 cells are required for production of high- but not low-affinity IgE and subsequent allergen-induced anaphylaxis. Blocking TFH13 cells may represent an alternative therapeutic target to ameliorate anaphylaxis.

Our data suggest that in women, up to one drink per day does not impair cognitive function and may actually decrease the risk of cognitive decline.

There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host–viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air–liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.

Transcription factors (TFs) direct developmental transitions by binding to target DNA sequences, influencing gene expression and establishing complex gene-regultory networks. To systematically determine the molecular components that enable or constrain TF activity, we investigated the genomic occupancy of FOXA2, GATA4 and OCT4 in several cell types. Despite their classification as pioneer factors, all three TFs exhibit cell-type-specific binding, even when supraphysiologically and ectopically expressed. However, FOXA2 and GATA4 can be distinguished by low enrichment at loci that are highly occupied by these factors in alternative cell types. We find that expression of additional cofactors increases enrichment at a subset of these sites. Finally, FOXA2 occupancy and changes to DNA accessibility can occur in G 1 -arrested cells, but subsequent loss of DNA methylation requires DNA replication.NATuRE GENETiCS | www.nature.com/naturegenetics © 2018 Nature America Inc., part of Springer Nature. All rights reserved. Articles NATure GeNeTiCsBecause primary TF engagement cannot be adequately dissected by using endogenous systems that already express FOXA2 as part of their regulatory circuitry, we engineered a doxycycline (DOX)-inducible system in immortalized foreskin fibroblasts (BJ), which do not normally express FOXA2 or other FOXA family members ( Supplementary Fig. 1d). We derived several clonal cell lines ) cell lines. Cropped western blots of FOXA2 and H3 protein levels in two distinct BJ FOXA2 clones. d, Browser tracks displaying differential binding across ectopic BJ FOXA2 and dEN (chr 18: 19745852-19782939). FOXA2 FPKM values are shown at right. Below the scatter plot, output of DiffBind 42 differential peak-set analysis between dEN and BJ FOXA2 is shown. Red dots, peaks with statistically significant differential enrichment between the two datasets. Axes are reads per kilobase of transcript per million mapped reads (RPKM). e, Read-density heat map (normalized read count) of ectopic FOXA2 enrichment in BJ FOXA2 cells at dEN FOXA2 regions. Vertical side bar, peaks shared between BJ FOXA2 and dEN. Dashed lines mark the start and end of peaks, extended by 2 kb on either side. Most dEN sites still showed low-level enrichment in BJ FOXA2 yet were not called as significantly enriched. f, Read-density heat maps of ectopic OCT4 signal in BJ OCT4 at human ESC occupied regions (n = 22,477) and ectopic GATA4 signal in BJ GATA4 at dEN occupied regions (n = 42,477). Vertical side bar, peaks shared between the ectopic and endogenous context for either factor, as shown in e for FOXA2. In contrast to FOXA2 and GATA4, fewer ESC OCT4 sites showed any notable enrichment in BJ OCT4. g, Density plot displaying FOXA2, OCT4 and GATA4 ectopic enrichment in BJs at union sets of ectopic and endogenous sites (FOXA2, orange; OCT4, navy; GATA4, purple). Dashed lines demarcate regions within the background distribution, sampled sites (shaded) and peaks.NATuRE GENETiCS | www.nature.com/naturegenetics © 2018 Nature America Inc., part of Sprin...

Soluble forms of ACE2 have recently been shown to inhibit SARS-CoV-2 infection. We report on an improved soluble ACE2, termed a “microbody” in which the ACE2 ectodomain is fused to Fc domain 3 of the immunoglobulin heavy chain. The protein is smaller than previously described ACE2-Ig Fc fusion proteins and contains an H345A mutation in the ACE2 catalytic active site that inactivates the enzyme without reducing its affinity for the SARS-CoV-2 spike. The disulfide-bonded ACE2 microbody protein inhibits entry of SARS-CoV-2 spike protein pseudotyped virus and replication of live SARS-CoV-2 in vitro and in a mouse model. Its potency is 10-fold higher than soluble ACE2 and it can act after virus bound to the cell. The microbody inhibits the entry of β coronaviruses and virus with the variant D614G spike. The ACE2 microbody may be a valuable therapeutic for COVID-19 that is active against viral variants and future coronaviruses.