Comprehensive Transcriptomic Analysis of COVID-19 Blood, Lung, and Airway

Abstract

SARS-CoV2 is a previously uncharacterized coronavirus and causative agent of the COVID-19 pandemic. The host response to SARS-CoV2 has not yet been fully delineated, hampering a precise approach to therapy. To address this, we carried out a comprehensive analysis of gene expression data from the blood, lung, and airway of COVID-19 patients. Our results indicate that COVID-19 pathogenesis is driven by populations of myeloid-lineage cells with highly inflammatory but distinct transcriptional signatures in each compartment. The relative absence of cytotoxic cells in the lung suggests a model in which delayed clearance of the virus may permit exaggerated myeloid cell activation that contributes to disease pathogenesis by the production of inflammatory mediators. The gene expression profiles also identify potential therapeutic targets that could be modified with available drugs. The data suggest that transcriptomic profiling can provide an understanding of the pathogenesis of COVID-19 in individual patients.3 1 Methods Read quality, trimming, mapping and summarizationPublicly available data sets used in this study are listed in Table S1. RNA-seq data were processed using a consistent workflow using FASTQC, Trimmomatic, STAR, Sambamba, and featureCounts. As described below SRA files were downloaded and converted into FASTQ format using SRA toolkit. Read ends and adapters were trimmed with Trimmomatic (v0.38) using a sliding window, ilmnclip, and headcrop filters. Both datasets were head cropped at 6bp and adapters were removed before read alignment.Reads were mapped to the human reference genome hg38 using STAR, and the .sam files were converted to sorted .bam files using Sambamba. Read counts were summarized using the featureCounts function of the Subread package (v1.61.)The RNA-seq tools are all free, open source programs available at the following web addresses SRA toolkit -https

Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution

“…Notably, we did not identify IL6 as a potential pan-ligand as its differential expression between mild and severe patients in our study was not statistically significant in any cell type. All of the pan-ligands we report have been previously implicated in SARSr-CoV infection, with IL-18, CCL8, and IFN-γ having been detected in serum from COVID-19 patients [9,13,14], SPP1 upregulation measured in microarrays from SARS-CoV-infected nonhuman primates, and CCL3, CCL8, IL18, and IFNG upregulation detected in single-cell or bulk RNA-seq from the lungs of COVID-19 patients [21,22,27,28]. Importantly, our data supports accumulating evidence for a nuanced interferon response in severe disease depending on cell type and local versus systemic immune environment, as discussed above [25,26,28,33,34,36,55].…”

“…Cell type-specific immunopathological responses in severe COVID-19 have been investigated at both local and systemic levels in recent studies comparing severe patients to healthy controls [21,22,23,24,25,26,32,53,54,55]. We sought to build on this knowledge by determining the cell-type specific biological responses that differentiate mild and severe disease courses in the lung and systemic circulation.…”

“…While months of clinical observations in hospitals across the world have led to consistent descriptions of COVID-19 severity at a clinical level [18,19,20], the biological underpinnings of immune hyperactivation in severe COVID-19 are only beginning to be defined. Bulk RNA sequencing (bulk RNAseq) and single-cell RNA sequencing (scRNA-seq) studies have identified stark transcriptional differences between bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cell (PBMC) samples in hospitalized COVID-19 patients, indicating that immunological responses may be highly compartmentspecific [21,22]. A number of recent studies have compared severe patients to healthy control subjects in an effort to define immunological hallmarks of disease severity in both the lung and peripheral circulation using scRNA-seq.…”

Monocyte activation in systemic Covid-19 infection: Assay and rationale

“…Tissue resident macrophage populations in the adult derive from embryonic progenitors and differ markedly in phenotype from bone marrow-derived monocytes, which are recruited to tissues in response to increased demand, for instance infection and tissue damage [19] . Monocyte- derived macrophages are the main generators of inflammation in COVID-19 [ 2 , 17 , 18 , 20 , [22] , [23] , [24] ]. These mononuclear phagocytes express a broad repertoire of plasma membrane and intracellular receptors, serving as sensors of micro-organisms, dying cells and soluble products, to mediate recognition, signaling, migration and activation [19] .…”

“…While epithelial and endothelial cells are the major targets of viral infection through expression of the ACE2 receptor [ 13 , 14 ] innate and adaptive immune responses of the host contribute critical resistance and pathogenic responses at all stages of disease. Effector cells of the Mononuclear Phagocyte System (MPS), whether they become infected [15] or not, depend mostly on recruitment of bone marrow-derived monocytes to tissues [16] , [17] , [18] rather than resident macrophages of embryonic origin [ 16 , 19 ]. Mononuclear phagocytes collaborate with other immune and non-immune pathways to mediate local and systemic anti-viral resistance and recovery, while also promoting morbidity and mortality.…”