Dram1 regulates DNA damage-induced alternative autophagy

Autophagy is an evolutionarily conserved process that degrades subcellular constituents. Mammalian cells undergo two types of autophagy; Atg5-dependent conventional autophagy and Atg5-independent alternative autophagy, and the molecules required for the latter type of autophagy are largely unknown. In this study, we analyzed the molecular mechanisms of genotoxic stress-induced alternative autophagy, and identified the essential role of p53 and damage-regulated autophagy modulator (Dram1). Dram1 was sufficient to induce alternative autophagy. In the mechanism of alternative autophagy, Dram1 functions in the closure of isolation membranes downstream of p53. These findings indicate that Dram1 plays a pivotal role in genotoxic stress-induced alternative autophagy

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

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

〈論文・報告〉希土類元素一タンパク質--SDBS系の蛍光特性を利用したタンパク質の検出

[概要]希土類元素--タンパク質--ドデシルベンゼンスルホン酸ナトリウム(SDBS)系における蛍光増感効果を調べた。Tb^3+-SDBS-タンパク質系の蛍光は大変弱い。しかしながら、この系にGd^3+やエタノールを加えると、蛍光が著しく増加した。 コラーゲンの場合には、この効果が最大であった。この結果をもとに、タンパク質をナノグラム/mlレベルで感度良く検出する方法を確立した。 [Abstract] The fluorescence enhancement effect in rare earth-protein-sodium dodecyl benzenesulfonate (SDBS) system has been studied. The photoluminescence of Tb^3+-SDBS-protein system was very weak. However, when Gd^3+or ethanol was added into this system, the fluorescence was significantly enhanced. In the case of collagen, this effect was greatest. Based on this, a method was established to determine proteins sensitively at nanogram/ml level

Control of container crane by binary input using Mixed Logical Dynamical system

Abstract. This paper proposes an effective control system for a container crane that takes into account disturbances such as a wind. For efficient crane operation, it is neces-sary to realize accurate positioning of cranes, to minimize oscillation of containers and to realize the fastest possible control time while they are being carried. The crane input is assumed to be a binary with maximum and minimum values for quick control. The entire crane system including the binary input is considered as a hybrid system. A hybrid system is a generic term for a system in which continuous and discrete dynamics exist together. We control the entire crane system using the Mixed Logical Dynamical System (MLDS). An MLDS, which is a representation method for a hybrid system, is used for the crane system. It is generally known that an MLDS can be controlled by Model Pre-dictive Control (MPC). We confirm the effectiveness of the proposed technique through computer simulation of the crane

Coculture with macrophages alters ferroptosis susceptibility of triple-negative cancer cells

Abstract Various treatment options, such as molecular targeted drugs and immune checkpoint blockades, are available for patients with cancer. However, some cancer types are refractory to molecular targeted therapies or acquire drug resistance after long-term treatment. Thus, ferroptosis, a newly defined type of programmed cell death caused by the iron-dependent accumulation of lipid peroxidation, has gained attention as a novel cancer treatment strategy. Understanding cell–cell interactions in the tumor microenvironment is important for the clinical application of ferroptosis inducers. However, the effects of cell–cell interactions on ferroptosis sensitivity remain unclear. Thus, we aimed to evaluate the effects of macrophage–cancer cell interactions on ferroptosis induction. Coculture experiments showed that conditioned medium prepared from macrophages did not alter the ferroptosis sensitivity of cancer cells. By contrast, coculture via transwell, which enables cell–cell interactions through secretion, increased the sensitivity of cancer cells to ferroptosis inducers. Additionally, direct coculture increased the susceptibility of cancer cells to RSL3-induced ferroptosis. Mechanistically, coculture with macrophages upregulated the levels of intracellular ferrous ions and lipid peroxidation in cancer cells. These findings provide novel insights into the mechanisms by which cell–cell interactions influence ferroptosis induction and application of ferroptosis inducers as a cancer treatment option

A Ratiometric Fluorescent Probe for pH Measurement over a Wide Range Composed of Three Types of Fluorophores Assembled on a DNA Scaffold

The desirable properties of the sophisticated fluorescent pH probe are ratiometric detection properties and a wide detection range. In this study, three types of fluorophores with different fluorescence properties were assembled on a DNA origami nanostructure. DNA nanostructure has the advantage of being a scaffold that can assemble different types of fluorophores with control over their number and position. The defined number of three different fluorophores, i.e., pH-sensitive fluorescein (CF) and Oregon Green (OG), and pH-insensitive tetramethylrhodamine (CR), assembled on the DNA scaffold provided a ratiometric fluorescent pH probe with a wide pH detection range that could cover the variation of intracellular pH

A novel neural-specific BMP antagonist, Brorin-like, of the Chordin family

AbstractWe identified a gene encoding a novel secreted protein in mice, humans, and zebrafish. As the protein of 222 amino acids is similar to Brorin, a secreted BMP antagonist, which is a member of the Chordin family, we named it Brorin-like. Recombinant Brorin-like protein weakly but significantly inhibited the activity of BMP in mouse preosteoblastic cells and promoted neurogenesis in mouse neural precursor cells. Brorin-like was predominantly expressed in the adult brain and embryonic neural tissues. The inhibition of Brorin-like functions in zebrafish resulted in the impairment of neural development. Brorin-like potentially plays roles in neural development and functions