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

UTERINE ESTROGEN RECEPTOR ASSAYED BY THE CONTROLLED PORE GLASS (CPG) METHOD IN ADULT RAT AFTER STEROID ADMINISTRATION

The interaction of estrogen and androgen was studied at the estrogen receptor level of adult rat uterus by the in vivo experiment. Both the free and total estrogen receptor in the cytosol and nucleus were assayed by the controlled pore glass beads method [2]. Testosterone was given by daily injection for 5 days to the rats treated with estradiol dipropionate (long-acting estradiol) 3 or 5 days before. In the estradiol dipropionate-treated rats the plasma estradiol concentration remained at an extremely high level for 7 days and then decreased to 5-fold of that of proestrus control by the 14th day. There was no significant change in the uterine estrogen receptor of the adult rat with a high estradiol concentration induced by testosterone

Improving Deep Neural Network in Predicting Electron Ionization Mass Spectra by Molecular Similarity-wise Sampling

Mass spectrometry is a widely used technique for identifying molecules in a variety of applications, including organic synthesis and metabolomics. Recently,a deep neural network model for mass spectrometry has been developed and numerically assessed. However, we confirmed that the model performs poorly for a specific target such as highly-fluorinated compound, this study introduces a simple dataset undersampling scheme using a molecular similarity. The model trained on the undersampled dataset shows that the predictive performance was improved for fluorinated compounds and was relatively maintained even for non-fluorinated compounds. This performance is probably ascribed to the reduction of bit collisions of ECFPs. The undersampling approach is general and applicable to any specific target

Evaluation of the proper dosage of lapatinib and its safety in dogs

Lapatinib is a low-molecular-weight agent targeting the epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2). It is one of the antitumor agents used against advanced breast cancer in human. We intended to apply it against canine mammary gland tumors (cMGTs). To this end, we evaluated the tolerated dosage and the side effects of lapatinib in healthy dogs. In this study, we conducted a dose-escalation toxicity test starting from 30 mg/kg to determine the maximum tolerated dose. Grade 3 toxicity, which was apparent as weight loss, was observed at the dose of 40 mg/kg/day. We then performed a long-term administration test and found that the dose of 35 mg/kg/day was well-tolerated within 7 weeks but caused grade 3 hepatic toxicity by the eighth week. In conclusion, our findings reveal that the dose of 35 mg/kg/day administered for no more than 8 weeks is fairly safe for use in healthy dogs. This dose is higher than the recommended dose for humans; thus, further studies evaluating the effective dose against canine tumors are needed

Combination of restriction endonuclease digestion with the Delta Delta Ct method in real-time PCR to monitor etoxazole resistance allele frequency in the two-spotted spider mite

Monitoring resistance allele frequency at the early stage of resistance development is important for the successful acaricide resistance management. Etoxazole is a mite growth inhibitor to which resistance is conferred by an amino acid substitution in the chitin synthase 1 (CHS1; I1017F) in T. urticae. If the susceptible allele can be specifically digested by restriction endonuclease, the ΔΔCt method using real-time PCR for genomic DNA (RED-ΔΔCt method) may be available for monitoring the resistance allele frequency. We tested whether the etoxazole resistance allele frequency in a pooled sample was accurately measured by the RED-ΔΔCt method and validated whether the resistance variant frequency was correlated with etoxazole resistance phenotype in a bioassay. Finally, we performed a pilot test using field populations. Strong linearity of the measures by the RED-ΔΔCt method with practical resistance allele frequencies; resistance allele frequency in the range between 0.5% to at least 0.75% was strictly represented. The strong linear relationship between hatchability of haploid male eggs after the etoxazole treatments (phenotype) and resistance allele frequencies in their mothers provided direct evidence that I1017F is a primary resistance factor to etoxazole in the strains used for experiments. The pilot test revealed a significant correlation between egg hatchability (including both diploid female eggs and haploid male eggs) and estimators in field populations. Consequently, we concluded that the RED-ΔΔCt method is a powerful tool for monitoring a resistance allele in a pooled sample

New proposal to revise the classification for squamous cell carcinoma of the external auditory canal and middle ear

Background The prognosis of patients with advanced squamous cell carcinoma of the external auditory canal and middle ear has been improved by advances in skull base surgery and multidrug chemoradiotherapy during the last two decades. Methods Ninety-five patients with squamous cell carcinoma of the external auditory canal and middle ear who were treated between 1998 and 2017 were enrolled. The number of patients with tumour stages T1, T2, T3 and T4 was 15, 22, 24 and 34, respectively. Oncological outcomes and prognostic factors were retrospectively investigated. Results Among patients with T4 disease, invasion of the brain (p = 0.024), carotid artery (p = 0.049) and/or jugular vein (p = 0.040) were significant predictors of poor prognosis. The five-year overall survival rate of patients with at least one of these factors (T4b) was significantly lower than that of patients without these factors (T4a) (25.5 vs 65.5 per cent, p = 0.049). Conclusion It is proposed that stage T4 be subclassified into T4a and T4b according to the prognostic factors

Comparison of the effects of open and laparoscopic approach on body composition in gastrectomy for gastric cancer: A propensity score‐matched study

Abstract Aim To compare the effects of open (OG) and laparoscopic gastrectomy (LG) on body composition and muscle strength. Methods This study performed a propensity score matching analysis using cases from a large‐scale, multicenter, phase III randomized controlled trial concerning oral nutritional supplements after gastrectomy and analyzed both the whole and matched cohorts. Measurements of body composition and hand grip strength (HGS) were performed at baseline (preoperatively) and at 1, 2, 3, 6, and 12 months after gastrectomy. Results Of 835 patients, 275 and 560 underwent OG and LG, respectively. Skeletal muscle mass (SMM) and HGS loss were significantly lesser in the LG group than in the OG group. The propensity score‐matched analysis, including 120 pairs of patients, confirmed that the % SMM loss values at 1, 2, 3, 6, and 12 POM were −4.5%, −4.0%, −4.7%, −4.6%, and −5.8% in the OG group and −3.0%, −1.9%, −2.4%, −2.2%, and −2.7% in the LG group, respectively. The % SMM loss was significantly lesser in the LG group than in the OG group (repeated measures ANOVA p < 0.001). The HGS loss was non‐significantly smaller in the LG group than in the OG group. Conclusion Skeletal muscle mass loss was significantly lesser in the LG group than in the OG group in both cohorts, indicating that LG may be more effective than OG for maintaining muscle mass