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

Diagnostic evaluation of optical coherence tomography angiography and fundus autofluorescence in bilateral diffuse uveal melanocytic proliferation

Purpose: To demonstrate the utility of optical coherence tomography angiography (OCTA) in visualizing the choroidal vasculature in bilateral diffuse uveal melanocytic proliferation (BDUMP), so as to elucidate pathophysiology and also aid in diagnosis. Additionally, to recommend autofluorescence (AF) over traditional angiography for purposes of noninvasive diagnosis. Observations: Three BDUMP cases are examined using AF, and two are examined using OCTA. Additionally, the cases vary in etiology and include a case with iris cysts, which we believe to have only been recorded once before in scientific literature, steroids were successfully used to treat two cases and anti-tumor drugs were used to treat the third case. OCTA revealed altered choroidal vasculature in the two cases tested, and AF was successfully used to diagnose all three cases regardless of etiology. Conclusions and importance: We believe the OCTA findings are potentially elucidative regarding the pathophysiology at the choroidal layer, where BDUMP lesions primarily exist. Given the limited number of recorded BDUMP cases and relatively unknown pathophysiology, OCTA may prove to be invaluable in visualizing disease progression. Also we were able to use AF to diagnose all three cases ranging from extremely rare iris cysts to a more conventional presentation, indicating its utility regardless of etiology. Keywords: Bilateral diffuse uveal melanocytic proliferation, Iris cysts, Optical coherence tomography angiography, Autofluorescenc

Benign prostatic hyperplasia: clinical treatment can complicate cataract surgery

PURPOSE: To investigate the effects of alpha-1 adrenergic receptor antagonists for the treatment of benign prostatic hyperplasia (BPH) regarding potential risks of complications in the setting of cataract surgery. AIM: To address recommendations, optimal control therapy, voiding symptoms and safety within the setting of cataract surgery. MATERIALS AND METHODS: A comprehensive literature review was performed using MEDLINE with MeSH terms and keywords "benign prostatic hyperplasia", "intraoperative floppy iris syndrome", "adrenergic alpha-antagonist" and "cataract surgery". In addition, reference lists from identified publications were reviewed to identify reports and studies of interest from 2001 to 2009. RESULTS: The first report of intraoperative floppy iris syndrome (IFIS) was observed during cataract surgery in patients taking systemic alpha-1 AR antagonists in 2005. It has been most commonly seen related to use of tamsulosin. Changes of medication and washout periods of up to 2 weeks have been attempted to reduce the risk of complications in the setting of cataract surgery. CONCLUSION: Patients under clinical treatment for BPH should be informed about potential risks of this drug class so that it can be discuss with their healthcare providers, in particular urologist and ophthalmologist, prior to cataract surgery

Generation and Utilization of a Monoclonal Antibody against Hepatitis B Virus Core Protein for a Comprehensive Interactome Analysis

Hepatitis B virus (HBV) core antigen (HBc) is a structural protein that forms the viral nucleocapsid and is involved in various steps of the viral replication cycle, but its role in the pathogenesis of HBV infection is still elusive. In this study, we generated a mouse monoclonal antibody (mAb) against HBc and used it in antibody-based in situ biotinylation analysis in order to identify host proteins that interact with HBc. HBc antigen was produced with a wheat germ cell-free protein synthesis system and used to immunize mice. Among the established hybridoma clones, a single clone (mAb #7) was selected and further characterized for its ability in the antibody-based in situ biotinylation analysis to collect host proteins that are in the vicinity of HBc. Using mass spectrometry, we identified 215 HBc-interacting host proteins, three of which bind HBc most significantly under hypoxic conditions. Our results indicate that mAb #7 can be used to systematically identify host proteins that interact with HBc under pathophysiological conditions, and thus may be useful to explore the molecular pathways involved in HBV-induced cytopathogenesis

Controlling Shape Anisotropy of ZnS–AgInS₂ Solid Solution Nanoparticles for Improving Photocatalytic Activity

Independently controlling the shape anisotropy and chemical composition of multinary semiconductor particles is important for preparing highly efficient photocatalysts. In this study, we prepared ZnS–AgInS₂ solid solution ((AgIn)_<i>x</i>Zn_{2(1–<i>x</i>)}S₂, ZAIS) nanoparticles with well-controlled anisotropic shapes, rod and rice shapes, by reacting corresponding metal acetates with a mixture of sulfur compounds with different reactivities, elemental sulfur, and 1,3-dibutylthiourea, via a two-step heating-up process. The chemical composition predominantly determined the energy gap of ZAIS particles: the fraction of Zn²⁺ in rod-shaped particles was tuned by the ratio of metal precursors used in the nanocrystal formation, while postpreparative Zn²⁺ doping was necessary to increase the Zn²⁺ fraction in the rice-shaped particles. The photocatalytic H₂ evolution rate with irradiation to ZAIS particles dispersed in an aqueous solution was significantly dependent on the chemical composition in the case of using photocatalyst particles with a constant morphology. In contrast, photocatalytic activity at the optimum ZAIS composition, <i>x</i> of 0.35–0.45, increased with particle morphology in the order of rice (size: ca. 9 × ca. 16 nm) < sphere (diameter: ca. 5.5 nm) < rod (size: 4.6 × 27 nm). The highest apparent quantum yield for photocatalytic H₂ evolution was 5.9% for rod-shaped ZAIS particles, being about two times larger than that obtained with spherical particles