The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Successful treatment of pulmonary injury after nitrogen oxide exposure with corticosteroid therapy: A case report and review of the literature

Nitrogen oxides are representative chemicals of occupational and environmental exposure, which can lead to fatal pulmonary injury. These oxides are also known to cause delayed occurrence of bronchiolitis obliterans (BO). Herein, we report a case of nitrogen oxide-induced lung injury. A 50-year-old man developed pulmonary edema after nitric acid exposure. Hypoxemia and respiratory failure were immediately improved after introduction of corticosteroid pulse therapy with supplemental oxygen. This was followed by administration of oral prednisolone, and delayed BO did not develop. This case supports the therapeutic efficacy of corticosteroids against pulmonary injury and late-onset BO after nitrogen oxide exposure. Key clinical message: Prolonged oral prednisolone might be a potential therapy to prevent delayed onset of bronchiolitis obliterans after nitric acid exposure

Lymphotoxin β receptor signaling induces IL-8 production in human bronchial epithelial cells.

Asthma-related mortality has been decreasing due to inhaled corticosteroid use, but severe asthma remains a major clinical problem. One characteristic of severe asthma is resistance to steroid therapy, which is related to neutrophilic inflammation. Recently, the tumor necrosis factor superfamily member (TNFSF) 14/LIGHT has been recognized as a key mediator in severe asthmatic airway inflammation. However, the profiles and intracellular mechanisms of cytokine/chemokine production induced in cells by LIGHT are poorly understood. We aimed to elucidate the molecular mechanism of LIGHT-induced cytokine/chemokine production by bronchial epithelial cells. Human bronchial epithelial cells express lymphotoxin β receptor (LTβR), but not herpesvirus entry mediator, which are receptors for LIGHT. LIGHT induced various cytokines/chemokines, such as interleukin (IL)-6, oncostatin M, monocyte chemotactic protein-1, growth-regulated protein α and IL-8. Specific siRNA for LTβR attenuated IL-6 and IL-8 production by BEAS-2B and normal human bronchial epithelial cells. LIGHT activated intracellular signaling, such as mitogen-activated protein kinase and nuclear factor-κB (NF-κB) signaling. LIGHT also induced luciferase activity of NF-κB response element, but not of activator protein-1 or serum response element. Specific inhibitors of phosphorylation of extracellular signal-regulated kinase (Erk) and that of inhibitor κB attenuated IL-8 production, suggesting that LIGHT-LTβR signaling induces IL-8 production via the Erk and NF-κB pathways. LIGHT, via LTβR signaling, may contribute to exacerbation of airway neutrophilic inflammation through cytokine and chemokine production by bronchial epithelial cells

Interleukin-17A and Toll-Like Receptor 3 Ligand Poly(I:C) Synergistically Induced Neutrophil Chemoattractant Production by Bronchial Epithelial Cells.

Chronic inflammatory airway diseases, such as bronchial asthma and chronic obstructive pulmonary disease, are common respiratory disorders worldwide. Exacerbations of these diseases are frequent and worsen patients' respiratory condition and overall health. However, the mechanisms of exacerbation have not been fully elucidated. Recently, it was reported that interleukin (IL)-17A might play an important role in neutrophilic inflammation, which is characteristic of such exacerbations, through increased production of neutrophil chemoattractants. Therefore, we hypothesized that IL-17A was involved in the pathogenesis of acute exacerbation, due to viral infection in chronic inflammatory airway diseases. In this study, we assessed chemokine production by bronchial epithelial cells and investigated the underlying mechanisms. Comprehensive chemokine analysis showed that, compared with poly(I:C) alone, co-stimulation of BEAS-2B cells with IL-17A and poly(I:C) strongly induced production of such neutrophil chemoattractants as CXC chemokine ligand (CXCL)8, growth-related oncogene (GRO), and CXCL1. Co-stimulation synergistically induced CXCL8 and CXCL1 mRNA and protein production by BEAS-2B cells and normal human bronchial epithelial cells. Poly(I:C) induced chemokine expression by BEAS-2B cells mainly via Toll-like receptor 3/TIR-domain-containing adapter-inducing interferon-β-mediated signals. The co-stimulation with IL-17A and poly(I:C) markedly activated the p38 and extracellular-signal-regulated kinase 1/2 pathway, compared with poly(I:C), although there was little change in nuclear factor-κB translocation into the nucleus or the transcriptional activities of nuclear factor-κB and activator protein 1. IL-17A promoted stabilization of CXCL8 mRNA in BEAS-2B cells treated with poly(I:C). In conclusion, IL-17A appears to be involved in the pathogenesis of chronic inflammatory airway disease exacerbation, due to viral infection by promoting release of neutrophil chemoattractants from bronchial epithelial cells

Comprehensive analysis of LIGHT-induced cytokine and chemokine production.

<p>BEAS-2B cells were stimulated with LIGHT (100 ng/ml) for 24 h, followed by determination of the protein levels of cytokines and chemokines by densitometry using a cytokine array. (A) The left image shows the unstimulated samples, while the right image shows the samples at 24 h after stimulation with LIGHT. (B) This table shows array mapping. The red color indicates cytokines that were upregulated more than twofold compared to the unstimulated sample. LIGHT induced inflammatory cytokines, such as GRO, GRO-α, oncostatin M, MCP-1, IL-6 and IL-8. (C) We investigated whether BEAS-2B cells produced LIGHT. THP-1 cells, which were used as a positive control, produced LIGHT when stimulated with PMA 50 ng/ml, but BEAS-2B cells did not.</p

Comprehensive analysis of LIGHT-induced cytokine and chemokine production.

<p>BEAS-2B cells were stimulated with LIGHT (100 ng/ml) for 24 h, followed by determination of the protein levels of cytokines and chemokines by densitometry using a cytokine array. (A) The left image shows the unstimulated samples, while the right image shows the samples at 24 h after stimulation with LIGHT. (B) This table shows array mapping. The red color indicates cytokines that were upregulated more than twofold compared to the unstimulated sample. LIGHT induced inflammatory cytokines, such as GRO, GRO-α, oncostatin M, MCP-1, IL-6 and IL-8. (C) We investigated whether BEAS-2B cells produced LIGHT. THP-1 cells, which were used as a positive control, produced LIGHT when stimulated with PMA 50 ng/ml, but BEAS-2B cells did not.</p

Erk1/2 signaling and NF-κB release.

<p>(A) To evaluate the relationship between Erk1/2 signaling and NF-κB release, BEAS-2B cells were pretreated with U0126 (10 µM) 1 h before stimulation with LIGHT. U0126 did not inhibit IκBα phosphorylation or NF-κB translocation from the cytoplasm to the nucleus. (B) We evaluated the effect of LTβR knockdown on Erk1/2 signaling and NF-κB release. BEAS-2B cells were transfected with negative control siRNA (NC siRNA) or LTβR siRNA#2, stimulated with LIGHT (50 ng/ml) and analyzed by western blotting. The cells that were transfected with LTβR siRNA showed attenuation of Erk1/2 phosphorylation and NF-κB translocation induced by LIGHT.</p

Primer sequences.

<p>Primer sequences.</p