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

Simple Trapezoidal Recursive Convolution Technique for the Frequency-Dependent FDTD Analysis of a Drude-Lorentz Model

A concise formulation of the frequency-dependent finite-difference time-domain (FDTD) method is presented using the trapezoidal recursive convolution (TRC) technique for the analysis of a Drude?Lorentz model. The TRC technique requires single convolution integral in the formulation as in the recursive convolution (RC) technique, while maintaining the accuracy comparable to the piecewise linear RC (PLRC) technique with two convolution integrals. The TRC technique is introduced not only to the traditional explicit FDTD, but also to the unconditionally stable implicit FDTD based on the locally one-dimensional (LOD)scheme. Through the analysis of a surface plasmon waveguide, the effectiveness of the TRC technique is investigated for both explicit FDTD and LOD-FDTD, along with the existing RC and PLRC LOD-FDTD, along with the existing RC and PLRC techniques

A Frequency-Dependent LOD-FDTD Method and Its Application to the Analyses of Plasmonic Waveguide Devices

Detailed frequency-dependent formulations are presented for several efficient locally one-dimensional finite-difference time-domain methods (LOD-FDTDs) based on the recursive convolution (RC), piecewise linear RC (PLRC), trapezoidal RC (TRC), auxiliary differential equation, and Z　transform techniques. The performance of each technique is investigated through the analyses of surface plasmon waveguides, the dispersions of which are expressed by the Drude and Drude-Lorentz models. The simple TRC technique requiring a single convolution integral is found to offer the comparable accuracy to the PLRC technique with two convolution integrals. As an application, a plasmonic grating filter is studied using the TRC-LOD-FDTD. The use of an apodized and a chirped grating is found quite effective in reducing sidelobes in the transmission spectrum, maintaining a large bandgap. Furthermore, a plasmonic microcavity is analyzed, in which a defect section is introduced into a grating filter. Varying the air core width is shown to exhibit tunable properties of the resonance wavelength

Two Aberrant Splicings Caused by Mutations in the Insulin Receptor Gene in Cultured Lymphocytes from a Patient With Rabson-Mendenhall’s Syndrome

Rabson-Mendenhall’s syndrome is one of the most severe forms of insulin resistance syndrome. We analyzed an English patient described elsewhere and found novel mutations in both alleles of the insulin receptor gene. One is a substitution of G for A at the 3 � splice acceptor site of intron 4, and the other is an eight–base pair deletion in exon 12. Both decrease mRNA expression in a cis-dominant manner, and are predicted to produce severely truncated proteins. Surprisingly, nearly normal insulin receptor levels were expressed in the patient’s lymphocytes, although the level of expression assessed by immunoblot was � 10 % of the control cells. Insulin binding affinity was markedly reduced, but insulin-dependent tyrosine kinase activity was present. Analyzing the insulin receptor mRNA of the patient’s lymphocytes by reverse transcription PCR, we discovered aberrant splicing caused by activation of a cryptic splice site in exon 5, resulting in a four–amino acid deletion and one amino acid substitution, but restoring an open reading frame. Skipped exon 5, another aberrant splicing, was found in both the patient and the mother who had the heterozygotic mutation, whereas activation of the cryptic splice site occurred almost exclusively in the patient. Transfectional analysis in COS cells revealed that the mutant receptor produced by cryptic site activation has the same characteristics as those expressed in patient’s lymphocytes. We speculate that this mutant receptor may be involved in the relatively long survival of the patient by rescuing otherwise more severe phenotypes resulting from the complete lack of functional insulin receptors. (J. Clin. Invest. 1998. 101:588–594.) Key words: cryptic splice site • exon skipping • insulin binding • insulin resistance syndrome • polymerase chain reactio

Experimental PET/CT study of imaging the small amount of positron emitters generated by carbon ion beam irradiation

[Purpose] Detecting the distribution of positron emitter generated by nuclear fragmentation reaction in carbon ion beam therapy (auto-activation) applied at Heavy Ion Medical Accelerator in Chiba (HIMAC) by means of positron emission tomography (PET) is novel method for therapy quality assurance especially assessing irradiated area. Since a new 3D irradiation system with pencil-beam scanning (fast- scanning system) has been developed at NIRS, and we are planning to assess the accuracy of the delivered dose distribution by clinical auto-activation PET study. In preparation for this purpose, we performed some phantom experiments for determine optimal scan duration and compare PET image quality of auto-activation PET study between conventional irradiation system and fast scanning system. \n[Materials and Methods] A SET-3000GCT/X (PET/CT; Shimadzu Corp.) dedicated to the 3D-acquisition mode is used for auto-activation PET imaging. It uses gadolinium oxyorthosilicate (GSO) detectors and provides 99 sections with a center-to-center distance of 2.6mm. To determine the optical scan duration, the phantom irradiated with carbon-ion beam is scanned for 60min in list-mode, then a 5min transmission scan with a 137Cs point source is performed. Before reconstruction, list-mode events are histogrammed as PET raw data obtained at each acquisition time (10, 20, 30, 40, 50 and 60min). The emission images are reconstructed with the manufacturer software using Fourier rebinning followed by 2D-dynamic-RAMLA. Reconstructed images are evaluated visually and normal mean square error (NMSE) is assessed. In addition, image noise is derived from region-of-interest (ROI) analysis. Image noise was defined as the coefficient of variation (COV, 100 x SD/mean [%]) of the pixel values within a homogeneous ROI. \n[Results] There is no obvious difference of image quality between 40min acquisition and 60min acquisition by visually evaluation. Based on statistical analysis, NMSE value and COV are 0.0017 and 12% at 40min acquisition, respectively, while NMSE value and COV are 0.0023 and 14% at 30 min acquisition, respectively. According to these results, we conclude the 40min acquisition as optimal scan duration for clinical auto-activation PET study. The distribution of positron emitters generated by carbon ion beam for a clinical target volume (CTV) is slightly larger in fast-scanning system compared with conventional irradiation system. The difference is all explained by presence of penumbra in fast-scanning system. These results show that auto-activation PET method can visualize precisely the absorbed radiation area. \n[Conclusions] According to our analysis, it is clarified that auto-activation PET method can detect precisely absorbed radiation area and it plays an important role in quality assurance of heavy ion beam therapy.EANM Annual Congress 201