Development of an atmospheric Cherenkov imaging camera for the CANGAROO-III experiment

A Cherenkov imaging camera for the CANGAROO-III experiment has been developed for observations of gamma-ray induced air-showers at energies from 10$^{11}$ to 10$^{14}$ eV. The camera consists of 427 pixels, arranged in a hexagonal shape at 0.17$^\circ$ intervals, each of which is a 3/4-inch diameter photomultiplier module with a Winston-cone--shaped light guide. The camera was designed to have a large dynamic range of signal linearity, a wider field of view, and an improvement in photon collection efficiency compared with the CANGAROO-II camera. The camera, and a number of the calibration experiments made to test its performance, are described in detail in this paper.Comment: 25 pages, 29 figures, elsart.cls, to appear in NIM-

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

STUDY ON AUTOIMMUNE PHENOMENON IN LIVER DISEASES -Blastoid Cell Transformation of Lymphocytes Cultured With Autologous Liver Homogenate-

Correlation between self-perpetuation of hepatitis and autoimmune phenomenon still remains obscure. Recently, attention has been drawn to the fact that blastoid cell transformation occurs with the addition of phytohemagglutinin when culturing human lymphocytes. Using lymphocytes taken from 55 patients with chronic liver diseases, which were cultured with a medium containing autologous liver homogenate obtained by needle biopsy, the occurrence of blastoid cell transformation was studied. Blastoid cell transformation was demonstrated in about one-third of the patients. The transformation rate, ranging from 0.2% to 7.4%, was lower than that of lymphocyte cultures to which phytohemagglutinin was added. But no evidence of blastoid cells was found in the patients without liver diseases. As compared to those with a negative response, the values of GOT, GPT and BSP were significantly elevated in the patients with a positive response and, histologically, marked infiltration of small lymphocytes and necrosis of liver cells were observed. Furthermore, a tendency toward poor prognosis was shown by many patients with a positive response. In patients with a positive blastoid cell response, positive rheumatoid serologic findings were also present significantly, indicating a close correlation between the two. The above observations suggest that the lymphocytes, sensitized by the patient’s own liver, play a certain part in the mechanism of self-perpetuation of hepatitis

Expression analysis of genes associated with the radioprotective effect of p53 modulator 5CHQ on acute intestinal radiation injury

In radiation therapy, the presence of highly radiosensitive organs around the target tumor limits the prescription dose. To develop radioprotectors that are specific for normal tissues is a solution to increase the tolerance dose of these organs. We have previously reported that an 8-hydroxyquinoline derivative, 5-chloro-8-quinolinol (5CHQ), exerts a significant radioprotective effect in a p53-dependent manner. The characteristic action of 5CHQ is to upregulate a radioprotective p53 target gene, Cdkn1a, and to downregulate a proapoptotic p53 target gene, Bbc3. The purpose of this study is to discover new genes involved in the radioresistance by 5CHQ treatment other than Cdkn1a and Bbc3. In a comprehensive analysis of mRNA expression of the jejunal epithelium using female ICR mice, the gene expression changes of irradiated mice with or without 5CHQ were examined by mRNA-seq analysis using a next-generation sequencer. Based on the obtained results, absolute qPCR quantification was performed to confirm the reproducibility of mRNA expression changes. Expression of the well-known p53 target genes was not largely changed, but humoral factors involved in intestinal stem cell protection were increased by 5CHQ. Furthermore, by comparing Trp53-knockout mice with wild-type mice, the expression of some cytokines was found to be p53-dependent. We consider that some of these genes will be the candidate genes that are responsible for the radioprotection by 5CHQ. We plan to examine the radioprotective effects of these humoral candidate factors in the intestine to identify new protective factors in 5CHQ action.放射線災害・医科学拠点第５回国際シンポジウ

Degeneration of retinal on bipolar cells induced by serum including autoantibody against TRPM1 in mouse model of paraneoplastic retinopathy.

The paraneoplastic retinopathies (PRs) are a group of eye diseases characterized by a sudden and progressive dysfunction of the retina caused by an antibody against a protein in a neoplasm. Evidence has been obtained that the transient receptor potential melastatin 1 (TRPM1) protein was one of the antigens for the autoantibody against the ON bipolar cells in PR patients. However, it has not been determined how the autoantibody causes the dysfunction of the ON bipolar cells. We hypothesized that the antibody against TRPM1 in the serum of patients with PR causes a degeneration of retinal ON bipolar cells. To test this hypothesis, we injected the serum from the PR patient, previously shown to contain anti-TRPM1 antibodies by westerblot, intravitreally into mice and examined the effects on the retina. We found that the electroretinograms (ERGs) of the mice were altered acutely after the injection, and the shape of the ERGs resembled that of the patient with PR. Immunohistochemical analysis of the eyes injected with the serum showed immunoreactivity against bipolar cells only in wild-type animals and not in TRPM1 knockout mice,consistent with the serum containing anti-TRPM1 antibodies. Histology also showed that some of the bipolar cells were apoptotic by 5 hours after the injection in wild type mice, but no bipolar cell death was found in TRPM1 knockout mice, . At 3 months, the inner nuclear layer was thinner and the amplitudes of the ERGs were still reduced. These results indicate that the serum of a patient with PR contained an antibody against TRPM1 caused an acute death of retinal ON bipolar cells of mice