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

Interaction of BMI and respiratory status in obstructive sleep apnea, a cross-sectional COPD study

Abstract This cross-sectional study of 136 patients with chronic obstructive pulmonary disease (COPD) investigated the mechanism underlying overlap syndrome, defined as coexisting COPD and obstructive sleep apnea (OSA). OSA was defined as a respiratory event index (REI) ≥ 5 events/h, determined using type-3 portable monitors. The mean REI was 12.8 events/h. Most participants (60.1%) had mild OSA (REI: 5–15 events/h). The REI was positively correlated with forced expiratory volume in one second (%FEV1) (r = 0.33, p < 0.001), body mass index (BMI) (r = 0.24, p = 0.005), and fat-free mass index (r = 0.31, p = 0.005), and negatively correlated with residual volume divided by total lung capacity (r = −0.27, p = 0.003). Receiver-operating characteristic curve analysis revealed an optimal BMI cutoff of 21.96 kg/m2 for predicting moderate/severe OSA. A BMI ≥ 21.96 kg/m2 was associated with OSA among participants with %FEV1 ≥ 50%, but not those with %FEV1 < 50%. This study revealed an interaction between airflow limitation and hyperinflation, nutritional status, and OSA

Cluster analysis of long COVID in Japan and association of its trajectory of symptoms and quality of life

Background Multiple prolonged symptoms observed in patients who recovered from COVID-19 are defined as long COVID. Although diverse phenotypic combinations are possible, they remain unclear. This study aimed to perform a cluster analysis of long COVID in Japan and clarify the association between its characteristics and background factors and quality of life (QOL).Methods This multicentre prospective cohort study collected various symptoms and QOL after COVID-19 from January 2020 to February 2021. This study included 935 patients aged ≥18 years with COVID-19 at 26 participating medical facilities. Hierarchical cluster analysis was performed using 24 long COVID symptom at 3 months after diagnosis.Results Participants were divided into the following five clusters: numerous symptoms across multiple organs (cluster 1, n=54); no or minor symptoms (cluster 2, n=546); taste and olfactory disorders (cluster 3, n=76); fatigue, psychoneurotic symptoms and dyspnoea (low prevalence of cough and sputum) (cluster 4, n=207) and fatigue and dyspnoea (high prevalence of cough and sputum) (cluster 5, n=52). Cluster 1 included elderly patients with severe symptoms, while cluster 3 included young female with mild symptoms. No significant differences were observed in the comorbidities. Cluster 1 showed the most impaired QOL, followed by clusters 4 and 5; these changes as well as the composition of symptoms were observed over 1 year.Conclusions We identified patients with long COVID with diverse characteristics into five clusters. Future analysis of these different pathologies could result in individualised treatment of long COVID.Trial registration number The study protocol is registered at UMIN clinical trials registry (UMIN000042299)

Chemical composition of carbonaceous asteroid Ryugu from synchrotron spectroscopy in the mid- to far-infrared of Hayabusa2-returned samples

International audienceContext. The current period is conducive to exploring our Solar System's origins with recent and future space sample return missions, which provide invaluable information from known Solar System asteroids and comets The Hayabusa2 mission of the Japan Aerospace Exploration Agency (JAXA) recently brought back samples from the surface of the Ryugu carbonaceous asteroid. Aims. We aim to identify the different forms of chemical composition of organic matter and minerals that constitute these Solar System primitive objects, to shed light on the Solar System's origins. Methods. In this work, we recorded infrared (IR) hyper-spectral maps of whole-rock Ryugu asteroid samples at the highest achievable spatial resolution with a synchrotron in the mid-IR (MIR). Additional global far-IR (FIR) spectra of each sample were also acquired. Results. The hyper-spectral maps reveal the variability of the functional groups at small scales and the intimate association of phyllosilicates with the aliphatic components of the organic matter present in Ryugu. The relative proportion of column densities of the identified IR functional groups (aliphatics, hydroxyl + interlayer and/or physisorbed water, carbonyl, carbonates, and silicates) giving access to the composition of the Ryugu samples is estimated from these IR hyper-spectral maps. Phyllosilicate spectra reveal the presence of mixtures of serpentine and saponite. We do not detect anhydrous silicates in the samples analysed, at the scales probed. The carbonates are dominated by dolomite. Aliphatics organics are distributed over the whole samples at the micron scale probed with the synchrotron, and intimately mixed with the phyllosilicates. The aromatic C=C contribution could not be safely deconvolved from OH in most spectra, due to the ubiquitous presence of hydrated minerals. The peak intensity ratios of the organics methylene to methyl (CH 2 /CH 3) of the Ryugu samples vary between about 1.5 and 2.5, and are compared to the ratios in chondrites from types 1 to 3. Overall, the mineralogical and organic characteristics of the Ryugu samples show similarities with those of CI chondrites, although with a noticeably higher CH 2 /CH 3 in Ryugu than generally measured in C1 chondrites collected on Earth, and possibly a higher carbonate content

AFM-IR nanospectroscopy of nanoglobule-like particles in Ryugu samples returned by the Hayabusa2 mission

International audienceContext. The JAXA Hayabusa2 mission returned well-preserved samples collected from the carbonaceous asteroid Ryugu, providing unique non-terrestrially weathered samples from a known parent body.Aims. This work aims to provide a better understanding of the formation and evolution of primitive asteroidal matter by studying the fine scale association of organic matter and minerals in Ryugu samples. We characterized the samples by IR nanospectroscopy using infrared photothermal nanospectroscopy (AFM-IR) technique. This technique overcomes the diffraction limit (of several microns) of conventional infrared microspectroscopy (µ-FTIR). The samples were mapped in the mid-IR range at a lateral spatial resolution about a hundred times better than with µ-FTIR. This provided us with unique in situ access to the distribution of the different infrared signatures of organic components at the sub-micron scale present in the Ryugu whole-rock samples as well as to the characterization of the compositional variability of Ryugu in the insoluble organic matter (IOM) chemically extracted from the Ryugu samples.Methods. The AFM-IR maps of whole-rock particles and IOM residues from Ryugu samples were recorded with a lateral resolution of tens of nanometers. Spectra were recorded in the 1900–900 cm−1 spectral range by AFM-IR (Icon-IR) for all samples, and additional spectra were recorded from 2700 to 4000 cm−1 for one IOM sample by an optical photothermal IR (O-PTIR) technique using a mIRage® IR microscope.Results. Organic matter is present in two forms in the whole-rock samples: as a diffuse phase intermixed with the phyllosilicate matrix and as individual organic nanoparticles. We identify the Ryugu organic nanoparticles as nanoglobule-like inclusions texturally resembling nanoglobules present in primitive meteorites. Using AFM-IR, we record for the first time the infrared spectra of Ryugu organic nanoparticles that clearly show enhanced carbonyl (C=O) and CH contributions with respect to the diffuse organic matter in Ryugu whole-rock and IOM residue