GALAXY CRUISE: Deep Insights into Interacting Galaxies in the Local Universe

We present the first results from GALAXY CRUISE, a community (or citizen) science project based on data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). The current paradigm of galaxy evolution suggests that galaxies grow hierarchically via mergers, but our observational understanding of the role of mergers is still limited. The data from HSC-SSP are ideally suited to improve our understanding with improved identifications of interacting galaxies thanks to the superb depth and image quality of HSC-SSP. We have launched a community science project, GALAXY CRUISE, in 2019 and collected over 2 million independent classifications of 20,686 galaxies at z < 0.2. We first characterize the accuracy of the participants' classifications and demonstrate that it surpasses previous studies based on shallower imaging data. We then investigate various aspects of interacting galaxies in detail. We show that there is a clear sign of enhanced activities of super massive black holes and star formation in interacting galaxies compared to those in isolated galaxies. The enhancement seems particularly strong for galaxies undergoing violent merger. We also show that the mass growth rate inferred from our results is roughly consistent with the observed evolution of the stellar mass function. The 2nd season of GALAXY CRUISE is currently under way and we conclude with future prospects. We make the morphological classification catalog used in this paper publicly available at the GALAXY CRUISE website, which will be particularly useful for machine-learning applications.Comment: 23 pages, 22 figures, PASJ in press. Data available at https://galaxycruise.mtk.nao.ac.jp/en/for_researchers.htm

Identification of prophylactic drugs for oxaliplatin-induced peripheral neuropathy using big data

Background: Drug repositioning is a cost-effective method to identify novel disease indications for approved drugs; it requires a shorter developmental period than conventional drug discovery methods. We aimed to identify prophylactic drugs for oxaliplatin-induced peripheral neuropathy by drug repositioning using data from large-scale medical information and life science information databases. Methods: Herein, we analyzed the reported data between 2007 and 2017 retrieved from the FDA’s database of spontaneous adverse event reports (FAERS) and the LINCS database provided by the National Institute of Health. The efficacy of the drug candidates for oxaliplatin-induced peripheral neuropathy obtained from the database analysis was examined using a rat model of peripheral neuropathy. Additionally, we compared the incidence of peripheral neuropathy in patients who received oxaliplatin at the Tokushima University Hospital, Japan. The effects of statins on the animal model were examined in six-week-old male Sprague–Dawley rats and seven or eight-week-old male BALB/C mice. Retrospective medical chart review included clinical data from Tokushima University Hospital from April 2009 to March 2018. Results: Simvastatin, indicated for dyslipidemia, significantly reduced the severity of peripheral neuropathy and oxaliplatin-induced hyperalgesia. In the nerve tissue of model rats, the mRNA expression of Gstm1 increased with statin administration. A retrospective medical chart review using clinical data revealed that the incidence of peripheral neuropathy decreased with statin use. Conclusion and relevance: Thus, drug repositioning using data from large-scale basic and clinical databases enables the discovery of new indications for approved drugs with a high probability of success

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

Degradation of ionic liquids by a UV/H2O2 process and CMCase from novel ionic liquid-tolerant alkaliphilic Nocardiopsis sp. SSC4

We demonstrated the degradation of two ionic liquids (1-butyl-3-methylimidazolium chloride, [BMIM]Cl, and 1-ethylpyridinium bromide, [EtPy]Br) that are useful for the solubilization of wood components. [BMIM]+ and [EtPy]+ were detected by thin-layer chromatography (TLC) and electrospray ionization–mass spectrometry (ESI-MS). [BMIM]+ was harder to degrade than [EtPy]+. Ultraviolet (UV) irradiation with 0.2% (v/v) H2O2 for 16 h degraded 1 mmol/L [BMIM]+, whereas UV irradiation alone degraded 1 mmol/L [EtPy]+. Additionally, we isolated an ionic liquid-tolerant alkaliphilic actinomycete, Nocardiopsis sp. SSC4. Strain SSC4 produced carboxymethylcellulase (CMCase) in the presence of 1.0% (v/v, 48.1 mmol/L) 1-ethyl-3-methylimidazolium trifluoromethanesulphonate ([EMIM]CF3SO3), which is useful for the extraction of cellulose-rich materials from wood. In the case of strain SSC4, CMCase was inducibly synthesized by more than 0.5% CMC. The addition of 0%–1.0% tryptone or 0%–2.0% yeast extract decreased the CMCase activity in a concentration-dependent manner. After cultivation of strain SSC4 with 1.0% (w/v) CMC medium (pH 9.0) for 48 h at 37 °C, the culture supernatant exhibited CMCase activity at 0.03 U/mg. The optimum reaction temperature of CMCase was 45 °C. CMCase was stable up to 37 °C for 20 h incubation. The degradation characteristics of [BMIM]+ and [EtPy]+ and the activity of CMCase in the presence of [EMIM]CF3SO3 may be useful for the development of a bioconversion system for biomass resources

Effect of Extracellular Signal-Regulated Protein Kinase 5 Inhibition in Clear Cell Renal Cell Carcinoma

(1) Background: Extracellular signal-regulating kinase 5 (ERK5) has been implicated in many cellular functions, including survival, proliferation, and vascularization. Our objectives were to examine the expression and effect of ERK5 in clear cell renal cell carcinoma (ccRCC). (2) Methods: The expressions of ERK5 and its regulating micro-RNA miR-143 were investigated using immunohistochemistry and quantitative reverse transcriptase PCR in surgical specimens of ccRCC patients. With invitro and in vivo studies, we used pharmacologic ERK5 inhibitor XMD8-92, RNA interference, pre-miR-143 transduction, Western blotting, MTS assay, apoptosis assay, and subcutaneous xenograft model. (3) Results: A strong ERK5 expression in surgical specimen was associated with high-grade (p = 0.01), high-recurrence free rate (p = 0.02), and high cancer-specific survival (p = 0.03). Expression levels of ERK5 and miR-143 expression level were correlated (p = 0.049). Pre-miR-143 transduction into ccRCC cell A498 suppressed ERK5 expression. ERK5 inhibition enhanced cyclin-dependent kinase inhibitor p21 expression and decreased anti-apoptotic molecules BCL2, resulting in decreased cell proliferation and survival both in ccRCC and endothelial cells. In the xenograft model, ERK5 inhibitor XMD8-92 suppressed tumor growth. (4) Conclusions: ERK5 is regulated by miR-143, and ERK5 inhibition is a promising target for ccRCC treatment