南極昭和基地及び北極ニーオルスンにおける雲の変動

第6回極域科学シンポジウム[OM] 極域気水圏11月16日（月）　統計数理研究所 セミナー室2（D304

Defining Hypo-Methylated Regions of Stem Cell-Specific Promoters in Human iPS Cells Derived from Extra-Embryonic Amnions and Lung Fibroblasts

BACKGROUND: Human induced pluripotent stem (iPS) cells are currently used as powerful resources in regenerative medicine. During very early developmental stages, DNA methylation decreases to an overall low level at the blastocyst stage, from which embryonic stem cells are derived. Therefore, pluripotent stem cells, such as ES and iPS cells, are considered to have hypo-methylated status compared to differentiated cells. However, epigenetic mechanisms of "stemness" remain unknown in iPS cells derived from extra-embryonic and embryonic cells. METHODOLOGY/PRINCIPAL FINDINGS: We examined genome-wide DNA methylation (24,949 CpG sites covering 1,3862 genes, mostly selected from promoter regions) with six human iPS cell lines derived from human amniotic cells and fetal lung fibroblasts as well as two human ES cell lines, and eight human differentiated cell lines using Illumina's Infinium HumanMethylation27. A considerable fraction (807 sites) exhibited a distinct difference in the methylation level between the iPS/ES cells and differentiated cells, with 87.6% hyper-methylation seen in iPS/ES cells. However, a limited fraction of CpG sites with hypo-methylation was found in promoters of genes encoding transcription factors. Thus, a group of genes becomes active through a decrease of methylation in their promoters. Twenty-three genes including SOX15, SALL4, TDGF1, PPP1R16B and SOX10 as well as POU5F1 were defined as genes with hypo-methylated SS-DMR (Stem cell-Specific Differentially Methylated Region) and highly expression in iPS/ES cells. CONCLUSIONS/SIGNIFICANCE: We show that DNA methylation profile of human amniotic iPS cells as well as fibroblast iPS cells, and defined the SS-DMRs. Knowledge of epigenetic information across iPS cells derived from different cell types can be used as a signature for "stemness" and may allow us to screen for optimum iPS/ES cells and to validate and monitor iPS/ES cell derivatives for human therapeutic applications

船舶搭載型全天カメラと雲底高度計観測データ解析による雲の特徴

第6回極域科学シンポジウム[OM] 極域気水圏11月16日（月）　国立極地研究所１階交流アトリウ

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

Peripheral VA-ECMO and pericardial drainage connected to the ECMO circuit for cardiac tamponade from blowout rupture: a case report

Abstract Background Left ventricular free wall rupture, particularly the blowout type, is still one of the most lethal complications of myocardial infarction and can cause catastrophic cardiac tamponade. Extracorporeal membrane oxygenation (ECMO) is often used to treat haemodynamic instability due to cardiac tamponade. However, elevated pericardial pressure can cause collapse of the right atrium, resulting in inadequate ECMO inflow and preventing the stabilisation of the circulation. Further, it can interfere with the venous return from the superior vena cava (SVC), increasing the intracranial pressure and reducing cerebral perfusion levels. Case presentation A 65-year-old man was hospitalised for out-of-hospital cardiac arrest. We used ECMO for cardiopulmonary resuscitation. After the establishment of ECMO, transthoracic echocardiography and left ventriculography revealed massive pericardial effusion. The treatment was supplemented with pericardial drainage since ECMO flow was frequently hampered by suction events. However, the blowout rupture led to the requirement of constant drainage from the pericardial catheter. To tend to this leak, we connected the venous cannula of ECMO and the pericardial drainage catheter. The surgery was performed with stable circulation without suction failure of ECMO. During the course of the intensive care management, the neurological prognosis of the patient was revealed to be poor, and the patient was shifted to palliative care. Unfortunately, the patient died on day 10 of hospitalisation. Conclusion We present a case wherein the combination of pericardial drainage and ECMO was used to maintain circulation in a patient with massive pericardial effusion due to cardiac rupture

Glycosylceramides Purified from the Japanese Traditional Non-Pathogenic Fungus <i>Aspergillus</i> and <i>Koji</i> Increase the Expression of Genes Involved in Tight Junctions and Ceramide Delivery in Normal Human Epidermal Keratinocytes

Koji, which is used for manufacturing Japanese traditional fermented foods, has long been safely used as a cosmetic product. Although its cosmetic effect has been empirically established, the underlying mechanism has not been reported. We and other groups have previously elucidated that koji contains glycosylceramides, including N-2&#8242;-hydroxyoctadecanoyl-1-O-&#946;-d-glucosyl-9-methyl-4,8-sphingadienine and N-2&#8242;-hydroxyoctadecanoyl-1-O-&#946;-d-galactosyl-9-methyl-4,8-sphingadienine. This led us to hypothesise that koji exerts its cosmetic effect by acting on the keratinocytes through glycosylceramides on the gene level. Therefore, in this study, we investigated the effects of glycosylceramides from various sources on gene expression in normal human epidermal keratinocytes. The results revealed that glycosylceramides purified from white koji and the white koji-producing non-pathogenic fungus Aspergillus luchuensis and A. oryzae increased the expression of occludin (OCLN, an epidermal tight junction protein) and ATP-binding cassette sub-family A member 12 (ABCA12, a cellular membrane transporter), albeit the effect was modest relative to that of ceramides. Indeed, ceramide was increased in the keratinocytes upon koji lipid extract addition. These results indicate that glycosylceramides, which are the major sphingolipids of most natural materials, have an effect of increasing ABCA12 and OCLN expression, and suggest that koji exerts its cosmetic effect by increasing ceramide and tight junctions via glycosylceramides

DNA double-strand break repair pathway regulates PD-L1 expression in cancer cells

Accumulating evidence suggests that exogenous cellular stress induces PD-L1 upregulation in cancer. A DNA double-strand break (DSB) is the most critical type of genotoxic stress, but the involvement of DSB repair in PD-L1 expression has not been investigated. Here we show that PD-L1 expression in cancer cells is upregulated in response to DSBs. This upregulation requires ATM/ATR/Chk1 kinases. Using an siRNA library targeting DSB repair genes, we discover that BRCA2 depletion enhances Chk1-dependent PD-L1 upregulation after X-rays or PARP inhibition. In addition, we show that Ku70/80 depletion substantially enhances PD-L1 upregulation after X-rays. The upregulation by Ku80 depletion requires Chk1 activation following DNA end-resection by Exonuclease 1. DSBs activate STAT1 and STAT3 signalling, and IRF1 is required for DSB-dependent PD-L1 upregulation. Thus, our findings reveal the involvement of DSB repair in PD-L1 expression and provide mechanistic insight into how PD-L1 expression is regulated after DSBs