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

Overexpression of Rice BSR2 Confers Disease Resistance and Induces Enlarged Flowers in Torenia fournieri Lind

Plant pathogens evade basal defense systems and attack different organs and tissues of plants. Genetic engineering of plants with genes that confer resistance against pathogens is very effective in pathogen control. Conventional breeding for disease resistance in ornamental crops is difficult and lagging relative to that in non-ornamental crops due to an inadequate number of disease-resistant genes. Therefore, genetic engineering of these plants with defense-conferring genes is a practical approach. We used rice BSR2 encoding CYP78A15 for developing transgenic Torenia fournieri Lind. lines. The overexpression of BSR2 conferred resistance against two devastating fungal pathogens, Rhizoctonia solani and Botrytis cinerea. In addition, BSR2 overexpression resulted in enlarged flowers with enlarged floral organs. Histological observation of the petal cells suggested that the enlargement in the floral organs could be due to the elongation and expansion of the cells. Therefore, the overexpression of BSR2 confers broad-spectrum disease resistance and induces the production of enlarged flowers simultaneously. Therefore, this could be an effective strategy for developing ornamental crops that are disease-resistant and economically more valuable

The additional utility of apparent diffusion coefficient values of clear-cell renal cell carcinoma for predicting metastasis during clinical staging

Background The apparent diffusion coefficient (ADC) value is known to be an indicator of tumor activity. The ADC value of high-grade clear-cell renal cell carcinoma (RCC) is significantly lower than that of low-grade clear-cell RCC. Purpose To investigate the utility of ADC values of clear-cell RCC by comparing ADC values between groups with T1a RCC (tumor size ≤ 4 cm) without metastasis and the group with metastasis. Material and Methods A retrospective review was performed on 51 patients with 51 RCCs who underwent 1.5 T magnetic resonance imaging (MRI) for evaluating a renal mass confirmed pathologically to be clear-cell RCC between January 2010 and August 2014. We compared ADC values between group A (T1a RCC without metastasis, T1aN0M0) and group B (RCC with metastasis) using the Mann–Whitney U test. Results The patients were divided into group A (n = 30; tumor size: median, 24.5 mm; range, 8–40 mm; ADC value [×10−3 mm2/s]: median, 1.71; range, 1.23–2.24) and group B (n = 21; tumor size: median, 87.5 mm; range, 18–150 mm; ADC value [×10−3 mm2/s]: median, 1.35; range, 0.91–1.94). The ADC value differed significantly between the two groups. The area under the receiver operating characteristic curve was 0.869. Using the optimum cutoff value (1.552 × 10−3 mm2/s), ADC had a sensitivity of 80.0% and specificity of 81.0%. Conclusion There was a statistically significant difference in the ADC between group A (T1a clear-cell RCC without distant metastasis) and group B (advanced clear-cell RCC with lymph node metastasis or distant metastasis)

Innovative clinical pathway shortened the length of hospital stay and prevented readmission in patients with acute decompensated heart failure

Background: With the rapidly aging population in Japan, the number of patients hospitalized for acute decompensated heart failure (ADHF) is increasing. Mitoyo General Hospital created an innovative clinical pathway (CP) for promoting early discharge in patients with ADHF. Major points of the CP were as follows: using tolvaptan as a standard therapy, completing the acute therapies within three days, and starting cardiac rehabilitation from the second day after admission. Methods: We collected data for patients with ADHF who were admitted to our hospital before introduction of the CP (non-CP group) (April 2014-July 2015) and after introduction of the CP (CP group) (August 2015-July 2019). We investigated the impact of the CP on the length of hospital stay (LOHS) and readmission after discharge. Results: After screening, 593 patients were enrolled in this study. After performing propensity score matching, 129 patients in the non-CP group and 129 patients in the CP group were analyzed. LOHS of patients in the CP group was significantly shorter than that of patients in the non-CP group [20 (14-28) days vs 12 (8-21) days] (p < 0.001) without an increase in mortality during hospitalization or an increase in the rate of readmission due to ADHF within 30 days. Use of the CP was an independent negative factor contributing to LOHS for patients with ADHF, even after adjustment of other factors including the use of tolvaptan (p < 0.001). The CP significantly decreased the proportion of patients readmitted to hospitals due to ADHF within 6 months [n = 32 (27%) vs n = 18 ( 15%), p = 0.026] and 1 year [n = 40 (34%) vs n = 23 ( 19%), p = 0.009] after discharge compared to the proportion in the non-CP group. Conclusions: The CP significantly reduced the LOHS of patients without increasing the in-hospital mortality and it also reduced the risk of readmission in the mid-term and long-term. (c) 2021 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved

Innovative clinical pathway shortened the length of hospital stay and prevented readmission in patients with acute decompensated heart failure

Background: With the rapidly aging population in Japan, the number of patients hospitalized for acute decompensated heart failure (ADHF) is increasing. Mitoyo General Hospital created an innovative clinical pathway (CP) for promoting early discharge in patients with ADHF. Major points of the CP were as follows: using tolvaptan as a standard therapy, completing the acute therapies within three days, and starting cardiac rehabilitation from the second day after admission. Methods: We collected data for patients with ADHF who were admitted to our hospital before introduction of the CP (non-CP group) (April 2014-July 2015) and after introduction of the CP (CP group) (August 2015-July 2019). We investigated the impact of the CP on the length of hospital stay (LOHS) and readmission after discharge. Results: After screening, 593 patients were enrolled in this study. After performing propensity score matching, 129 patients in the non-CP group and 129 patients in the CP group were analyzed. LOHS of patients in the CP group was significantly shorter than that of patients in the non-CP group [20 (14-28) days vs 12 (8-21) days] (p Conclusions: The CP significantly reduced the LOHS of patients without increasing the in-hospital mortality and it also reduced the risk of readmission in the mid-term and long-term. (c) 2021 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved