Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection

Abstract Human intestinal epithelial cells form a primary barrier protecting us from pathogens, yet only limited knowledge is available about individual contribution of each cell type to mounting an immune response against infection. Here, we developed a framework combining single‐cell RNA‐Seq and highly multiplex RNA FISH and applied it to human intestinal organoids infected with human astrovirus, a model human enteric virus. We found that interferon controls the infection and that astrovirus infects all major cell types and lineages and induces expression of the cell proliferation marker MKI67. Intriguingly, each intestinal epithelial cell lineage exhibits a unique basal expression of interferon‐stimulated genes and, upon astrovirus infection, undergoes an antiviral transcriptional reprogramming by upregulating distinct sets of interferon‐stimulated genes. These findings suggest that in the human intestinal epithelium, each cell lineage plays a unique role in resolving virus infection. Our framework is applicable to other organoids and viruses, opening new avenues to unravel roles of individual cell types in viral pathogenesis

Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut

Abstract Exacerbated pro‐inflammatory immune response contributes to COVID‐19 pathology. However, despite the mounting evidence about SARS‐CoV‐2 infecting the human gut, little is known about the antiviral programs triggered in this organ. To address this gap, we performed single‐cell transcriptomics of SARS‐CoV‐2‐infected intestinal organoids. We identified a subpopulation of enterocytes as the prime target of SARS‐CoV‐2 and, interestingly, found the lack of positive correlation between susceptibility to infection and the expression of ACE2. Infected cells activated strong pro‐inflammatory programs and produced interferon, while expression of interferon‐stimulated genes was limited to bystander cells due to SARS‐CoV‐2 suppressing the autocrine action of interferon. These findings reveal that SARS‐CoV‐2 curtails the immune response and highlights the gut as a pro‐inflammatory reservoir that should be considered to fully understand SARS‐CoV‐2 pathogenesis

Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2

https://kent-islandora.s3.us-east-2.amazonaws.com/node/10691/83863-thumbnail.jpgSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, utilizes angiotensin-converting enzyme 2 (ACE2) for entry into target cells. ACE2 has been proposed as an interferon-stimulated gene (ISG). Thus, interferon-induced variability in ACE2 expression levels could be important for susceptibility to COVID-19 or its outcomes. Here, we report the discovery of a novel, transcriptionally independent truncated isoform of ACE2, which we designate as deltaACE2 (dACE2). We demonstrate that dACE2, but not ACE2, is an ISG. In The Cancer Genome Atlas, the expression of dACE2 was enriched in squamous tumors of the respiratory, gastrointestinal and urogenital tracts. In vitro, dACE2, which lacks 356 amino-terminal amino acids, was non-functional in binding the SARS-CoV-2 spike protein and as a carboxypeptidase. Our results suggest that the ISG-type induction of dACE2 in IFN-high conditions created by treatments, an inflammatory tumor microenvironment or viral co-infections is unlikely to increase the cellular entry of SARS-CoV-2 and promote infection. &nbsp; Preprint available here on biorxiv:&nbsp;https://doi.org/10.1101/2020.07.19.210955</p

Taxonomic composition and seasonal dynamics of the air microbiome in West Siberia

Here, we describe taxonomical composition, as well as seasonal and diel dynamics of airborne microbial communities in West Siberia. A total of 78 airborne biomass samples from 39 time intervals were analysed, within a temperature range of 48 °C (26 °C to - 22 °C). We observed a 5-170-fold decrease in DNA yield extracted from the airborne biomass in winter compared to summer, nevertheless, yielding sufficient material for metagenomic analysis. The airborne microbial communities included Actinobacteria and Proteobacteria, Ascomycota and Basidiomycota fungi as major components, as well as some Streptophyta plants. In summer, bacterial and fungal plant pathogens, and wood-rotting saprophytes were predominant. In winter, Ascomycota moulds and cold-related or stress environment bacterial species were enriched, while the fraction of wood-rotting and mushroom-forming Basidiomycota fungi was largely reduced. As recently reported for the tropical climate, the airborne microbial communities performed a diel cycle in summer, however, in winter diel dynamics were not observed.Ministry of Education (MOE)Published versionThis study was supported by Academic Research Fund (AcRF) Tier 3, Singapore Ministry of Education (grant number: MOE2013-T3-1-013). V.N.K and V.A.S were supported by the Russian Foundation of Basic Research (Project #18-29-13045). We thank Dr. Sharon Longford, Senior Assistant Director, Science Communications, Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University for critical reading of this manuscript

SARS‐CoV‐2 infection remodels the host protein thermal stability landscape

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a global threat to human health and has compromised economic stability. In addition to the development of an effective vaccine, it is imperative to understand how SARS‐CoV‐2 hijacks host cellular machineries on a system‐wide scale so that potential host‐directed therapies can be developed. In situ proteome‐wide abundance and thermal stability measurements using thermal proteome profiling (TPP) can inform on global changes in protein activity. Here we adapted TPP to high biosafety conditions amenable to SARS‐CoV‐2 handling. We discovered pronounced temporal alterations in host protein thermostability during infection, which converged on cellular processes including cell cycle, microtubule and RNA splicing regulation. Pharmacological inhibition of host proteins displaying altered thermal stability or abundance during infection suppressed SARS‐CoV‐2 replication. Overall, this work serves as a framework for expanding TPP workflows to globally important human pathogens that require high biosafety containment and provides deeper resolution into the molecular changes induced by SARS‐CoV‐2 infection

Complete genome sequence of Curtobacterium sp. strain SGAir0471, isolated from Singapore air samples

Curtobacterium sp. strain SGAir0471 was isolated from tropical air samples collected in Singapore. The genome was assembled using PacBio RS II long reads and Illumina MiSeq short paired-end reads. The complete genome measures 3.53 Mb and consists of 3,151 protein-coding genes, 49 tRNAs, and 12 rRNAs.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of Acinetobacter schindleri SGAir0122 isolated from Singapore air

Acinetobacter schindleri strain SGAir0122 was isolated from tropical air samples collected in Singapore. The prevalence of nosocomial infection caused by this Gram-negative bacterium indicates its clinical significance as an opportunistic human pathogen. Its complete genome consists of one chromosome of 3.105 Mb and a plasmid of 181 kb.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of Pseudomonas stutzeri type strain SGAir0442, isolated from Singapore air samples

Pseudomonas stutzeri strain SGAir0442 was isolated from tropical air samples collected in Singapore. It is a Gram-negative denitrifying bacterium and an opportunistic human pathogen. Its complete genome consists of one chromosome of 4.52 Mb, containing 4,129 protein-coding genes, 12 rRNA subunits, and 62 tRNAs.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of the bacterium Serratia marcescens SGAir0764, isolated from Singapore air

Serratia marcescens strain SGAir0764 was isolated from a tropical air sample collected in Singapore. The complete genome, sequenced on the PacBio RS II platform, consists of one chromosome with 5.1 Mb and one plasmid with 76.4 kb. Genome annotation predicts 4,723 protein-coding genes, 89 tRNAs, and 22 rRNAs.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of Nissabacter sp. strain SGAir0207, isolated from an air sample collected in Singapore

Nissabacter sp. strain SGAir0207 was isolated from a tropical air sample collected in Singapore. Its genome was assembled using a hybrid approach with long and short reads, resulting in one chromosome of 3.9 Mb and 7 plasmids. The complete genome consists of 4,403 protein-coding, 84 tRNA, and 22 rRNA genes.MOE (Min. of Education, S’pore)Published versio