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

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

A novel Xenopus laevis larval keratin gene, xlk2 : its gene structure and expression during regeneration and metamorphosis of limb and tail

A novel cytokeratin (CK) gene, xlk2, was cloned from a cDNA library prepared from regenerating limbs of Xenopus larvae. The deduced amino acid sequence indicated that its product, XLK2, is a 48 kDa type I (acidic) CK and has a high similarity to CK13, 15, and 19 with the highest homology (58%) to mouse CK15. The gene of xlk2 exclusively expressed in basal cells of the bi-layered larval epidermis, but not in other cells in larvae and not in other periods of life. Its expression was down-regulated during spontaneous and thyroid hormone-induced metamorphosis. The basal cells of the apical epidermal cap (AEC) formed on the regenerate of larval limbs terminated the expression of xlk2, whereas those of the adjacent normal epidermis continued to express it. The AEC-basal cells did not re-express the gene in the regenerate. In contrast, the basal cells of the tail regenerate also once terminated the expression of xlk2, but was able to re-express xlk2 later, supporting a notion that the "de-differentiated" basal cells of the tail epidermal regenerate re-differentiate into larval normal epidermal cells

Phase Behavior of a Piperidinium-Based Room-Temperature Ionic Liquid Exhibiting Scanning Rate Dependence

The structural flexibility and conformational variety of the ions in room-temperature ionic liquids (RTILs) have significant effects on their physicochemical properties. To begin a systematic study of the thermodynamic properties of nonaromatic RTILs, 1-methyl-1-butylpiperidinium bis­(fluorosulfonyl)­amide ([Pip_1,4]­[FSA]) was selected as the first sample. In addition to the rotational flexibility of the alkyl group, the [Pip_1,4]⁺ cation has characteristic ring-flipping flexibility, which is very different from the behavior of the well-studied imidazolium-based cations. Calorimetry investigations using laboratory-made high-sensitivity calorimeters and Raman spectroscopy revealed that [Pip_1,4]­[FSA] has two crystalline phases, Cryst-α and Cryst-β, and that every phase change is linked to conformational changes of both the cation and anion. Each phase change is also governed by very slow dynamics. The phase changes from supercooled liquid to Cryst-α and from Cryst-α to Cryst-β, which were observed only during heating, are not in fact phase transitions but structural relaxations. Notably, the temperatures of these structural relaxations exhibited heating rate dependences, from which the activation energy of the ring-flipping was estimated to be 38.8 kJ/mol. It is thought that this phenomenon is due to the associated conformational changes of the constituent ions in viscous surroundings

Comprehensive Conformational and Rotational Analyses of the Butyl Group in Cyclic Cations: DFT Calculations for Imidazolium, Pyridinium, Pyrrolidinium, and Piperidinium

The flexibility and conformational variety of the butyl group in cations of ionic liquids (ILs) play an important role in dictating the macroscopic and microscopic properties of ILs. Here we calculate potential energy surfaces for the dihedral angles of the butyl group in four different types of cyclic cations, imidazolium, pyridinium, pyrrolidinium, and piperidinium, using the density functional theory method. The calculation results highlight the role of the butyl group in these cations by comparison of five-membered and six-membered rings, and of aromatic and alicyclic rings, in terms of stable conformations and rotational barriers. A striking result is that the butyl group rotation in pyrrolidinium induces pseudorotation of the ring whereas such a phenomenon does not occur in piperidinium. This difference is thought to be because of the relationship in rotational activation energy between the butyl group (10–40 kJ mol^–1) and the ring (<6 kJ mol^–1 for pyrrolidinium and 40–50 kJ mol^–1 for piperidinium). The calculated stable conformers are compared with the ones observed in crystals recorded in the Cambridge Structural Database. Although conformers with lower calculated energy generally have higher chances to be experimentally observed, roughly independent of the cation structure, some calculated conformers deviate from this trend and show very low population. It is found that not only low energy but also high rotational activation energy (i.e., long lifetime) is required to observe conformers in crystalline states. In the last part of this article, to identify conformers in real systems, the applicability of the calculated Raman bands of cations with different butyl group conformations is discussed

RESPONSE OF A TRUE SLIME MOLD, Physarum polycephalum, TO SALT STRESS II : The Effects of The Inhibitors for RNA and Protein Syntheses on Stress-induced Microcyst Formation

As reported before, under high salt conditions, haploid myxoamoebae of a true slime mold, Physarum polycephalum retract their pseudopodia and change their cell shape into disk-like form, after which they construct the cell wall to form their dormant type, microcysts. We found the change of the intracellular distribution of actin filaments associated with the cellular morphological changes from myxoamoebae to microcysts, and the induction of syntheses of some species of stress proteins, among which 66kD protein, p66 was most prominently induced (1,2). But we did not know whether the induction of these proteins are completely necessary for the process of cyst formation. In this report, we examined the effects of the inhibition of RNA and protein syntheses using some inhibitors for their syntheses on stress-induced microcyst formation to know whether the expression of new RNA and proteins are necessary for the induction of morphological changes. And we showed that newly synthesized RNA and protein (s) were necessary for the stress-induced microcyst formation