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

Delayed Development of Nervous System in Mice Homozygous for Disrupted Microtubule-associated Protein 1B (MAP1B) Gene

Microtubule-associated protein 1B (MAP1B), one of the microtubule-associated proteins (MAPs), is a major component of the neuronal cytoskeleton. It is expressed at high levels in immature neurons during growth of their axons, which indicates that it plays a crucial role in neuronal morphogenesis and neurite extension. To better define the role of MAP1B in vivo, we have used gene targeting to disrupt the murine MAP1B gene. Heterozygotes of our MAP1B disruption exhibit no overt abnormalities in their development and behavior, while homozygotes showed a slightly decreased brain weight and delayed nervous system development. Our data indicate that while MAP1B is not essential for survival, it is essential for normal time course development of the murine nervous system. These conclusions are very different from those of a previous MAP1B gene–targeting study (Edelmann, W., M. Zervas, P. Costello, L. Roback, I. Fischer, A. Hammarback, N. Cowan, P. Davis, B. Wainer, and R. Kucherlapati. 1996. Proc. Natl. Acad. Sci. USA. 93: 1270–1275). In this previous effort, homozygotes died before reaching 8-d embryos, while heterozygotes showed severely abnormal phenotypes in their nervous systems. Because the gene targeting event in these mice produced a gene encoding a 571–amino acid truncated product of MAP1B, it seems likely that the phenotypes seen arise from the truncated MAP1B product acting in a dominant-negative fashion, rather than a loss of MAP1B function

Open versus laparoscopic resection of primary tumor for incurable stage IV colorectal cancer: a large multicenter consecutive patients cohort study.

Objective: To investigate the hypothesis that laparoscopic primary tumor resection is safe and effective when compared with the open approach for colorectal cancer patients with incurable metastases. Background: There are only a few reports with small numbers of patients on laparoscopic tumor resection for stage IV colorectal cancer. Methods: Data from consecutive patients who underwent palliative primary tumor resection for stage IV colorectal cancer between January 2006 and December 2007 were collected retrospectively from 41 institutions. Short- and long-term outcomes were compared between patients who underwent laparoscopic or open resection. Results: A total of 904 patients (laparoscopic group: 226, open group: 678) with a median age of 64 years (range: 22-95) were included in the analysis. Conversion was required in 28 patients (12.4%) and the most common reasons for conversion (23/28: 82%) were bulky or invasive tumors. There was no 30-day postoperative mortality in either group. The complication rate (NCI-CTCAE grade 2-4) after laparoscopic surgery (17%) was significantly lower than that after open surgery (24%) (P = 0.02), and the difference was greater (4% vs 12%; P =grade 3) complications. The median length of postoperative hospital stay in the laparoscopic group was significantly shorter than that in the open group (14 vs 17 days; P = 0.002). In univariate analysis, overall survival for the laparoscopic group was significantly better than that for open surgery (median survival time: 25.9 vs 22.3 months, P = 0.04), although no difference was apparent in multivariate analysis. Conclusions: Compared with open surgery, laparoscopic primary tumor resection has advantages in the short term and no disadvantages in the long term. It is a reasonable treatment option for certain stage IV colorectal cancer patients with incurable disease

Relative Reactivity Measurements of Stabilized CH₂OO, Produced by Ethene Ozonolysis, Toward Acetic Acid and Water Vapor Using Chemical Ionization Mass Spectrometry

We investigated the relative reactivity of stabilized CH₂OO, produced by ethene ozonolysis, toward acetic acid and water vapor at a temperature of 298 ± 2 K and atmospheric pressure. Hydroperoxymethyl acetate produced through the reaction between stabilized CH₂OO and acetic acid was monitored using a chemical ionization mass spectrometer as a function of the acetic acid concentration at different relative humidities. The rate of the reaction between CH₂OO and water vapor depended quadratically on the water vapor concentration, suggesting that CH₂OO reacted with water dimers in preference to water monomers. We obtained the bimolecular rate constant for the reaction between CH₂OO and water dimer relative to the rate constant for the reaction between CH₂OO and acetic acid, <i>k</i>₃/<i>k</i>₁, of (6.3 ± 0.4) × 10^–2. The <i>k</i>₃ value of (8.2 ± 0.8) × 10^–12 cm³ molecule^–1 s^–1 was derived by combining with a <i>k</i>₁ value of (1.3 ± 0.1) × 10^–10 cm³ molecule^–1 s^–1, which has been previously reported by direct kinetic studies. The <i>k</i>₃ value thus obtained is consistent with the absolute rate constants measured directly, suggesting that the reactivity of CH₂OO is irrespective of the CH₂OO generation method, namely, ethene ozonolysis or diiodomethane photolysis. We indirectly determined the yield of stabilized CH₂OO from the ozonolysis of ethene of 0.59 ± 0.17 and 0.55 ± 0.16 under dry and humid (relative humidity 23–24%) conditions, respectively, suggesting that the yield is independent of the water vapor concentration. Our results suggest that hydroperoxymethyl acetate is the sole product of the reaction between stabilized CH₂OO and acetic acid. The approach presented here can likely be extended to studies of the reactivities of more complicated and atmospherically relevant stabilized Criegee intermediates

Uptake of MicroRNAs from Exosome-Like Nanovesicles of Edible Plant Juice by Rat Enterocytes

MicroRNAs (miRNAs) are small RNAs present in extracellular vesicles (EVs) that, when transferred to a target cell, affect its biological functions. Plant miRNAs regulate the expression of certain mammalian genes. Here, we characterized EVs in fruit and vegetable juice, and their miRNA cargo, and investigated whether such miRNA-containing EVs could be taken up by mammalian enterocytes in vitro. Using filtration and ultra-centrifugation methods, EVs were purified from commercially available and manually squeezed plant juice. EV morphological features and subcellular localization were analyzed using the NanoSight tracking system and electron microscopy. Plant EV miRNA levels were evaluated using quantitative reverse transcription PCR. For the in vitro EV uptake experiments, rat intestinal epithelial cells (IEC6) were used. Plant EVs shared morphological features with mammalian EVs and contained miR156a-5p, miR166a-3p, and miR168a-5p. EVs were present in the cell sap-filled central vacuoles and were taken up by IEC6 cells. Edible plant cells produce EVs that contain various miRNAs and release them into the central vacuole. The exogenous plant EVs are taken up by mammalian enterocytes in vitro. These findings suggest the possibility that exogenous plant miRNAs carried by EVs can be absorbed via the gastrointestinal tract

Study on environment conscious technologies in a super tall building: Evaluation of PV performance considering aerological climate

In recent years, buildings have tended to be taller, and their energy potential is expected be used effectively . Photovoltaics is considered one of technologies affected by air temperature, outside air velocity, and solar radiation from the aerological climate of supertall buildings with a height of 390 m. The energy potential of the “height” of photovoltaic power generation systems is affected by two factors: aerological climate and shadows cast by surrounding buildings. Taking these effects into account, the predicted annual power generation amount was calculated. At 390 m above ground, it was confirmed that the power generation amount was greater than that on the ground, when considering the effectiveness of photovoltaic systems. Then, we calculated the predicted annual power generation amount on each wall and roof surface of a tall building with a height of 390 m above the ground. By evaluating the energy-saving effect of adopting photovoltaic systems, we evaluated the photovoltaic system using the wall surface from the viewpoint of the primary energy reduction and primary energy consumption of the building

Organ-Specific MicroRNAs (MIR122, 137, and 206) Contribute to Tissue Characteristics and Carcinogenesis by Regulating Pyruvate Kinase M1/2 (PKM) Expression

Pyruvate kinase is known as the glycolytic enzyme catalyzing the final step in glycolysis. In mammals, two different forms of it exist, i.e., pyruvate kinase M1/2 (PKM) and pyruvate kinase L/R (PKLR). Also, PKM has two isoforms, i.e., PKM1 and PKM2. These genes have tissue-specific distribution. Namely, PKM1 is distributed in high-energy-demanding organs, such as brain and muscle. Also, PKM2 is distributed in various other organs, such as the colon. On the other hand, PKLR is distributed in liver and red blood cells (RBCs). Interestingly, PKM2 has been recognized as one of the essential genes for the cancer-specific energy metabolism termed the &ldquo;Warburg effect&rdquo;. However, the mechanism(s) underlying this fact have remained largely unclear. Recently, we found that some organ-specific microRNAs (miRNAs, MIR) regulate PKM isoform expression through direct targeting of polypyrimidine tract binding protein 1 (PTBP1), which is the splicer responsible for PKM2-dominant expression. In this study, we examined whether this machinery was conserved in the case of other PTBP1- and PKM-targeting miRNAs. We focused on the MIRs 122, 137, and 206, and investigated the expression profiles of each of these miRNAs in tissues from mouse and human organs. Also, we examined the regulatory mechanisms of PKM isoform expression by testing each of these miRNAs in human cancer cell lines. Presently, we found that brain-specific MIR137 and muscle-specific MIR206 predominantly induced PKM1 expression through direct targeting of PTBP1. Also, liver-specific MIR122 suppressed the expression of both PKM1 and PKM2, which action occurred through direct targeting of PKM to enable the expression of PKLR. Moreover, the expression levels of these miRNAs were downregulated in cancer cells that had originated from these tissues, resulting in PKM2 dominance. Our results suggest that the organ-specific distribution of miRNAs is one of the principal means by which miRNA establishes characteristics of a tissue and that dysregulation of these miRNAs results in cancer development through a change in the ratio of PKM isoform expression. Also, our results contribute to cancer diagnosis and will be useful for cancer-specific therapy for the Warburg effect in the near future