The 3′-Phosphoadenosine 5′-Phosphosulfate Transporters, PAPST1 and 2, Contribute to the Maintenance and Differentiation of Mouse Embryonic Stem Cells

Recently, we have identified two 3′-phosphoadenosine 5′-phosphosulfate (PAPS) transporters (PAPST1 and PAPST2), which contribute to PAPS transport into the Golgi, in both human and Drosophila. Mutation and RNA interference (RNAi) of the Drosophila PAPST have shown the importance of PAPST-dependent sulfation of carbohydrates and proteins during development. However, the functional roles of PAPST in mammals are largely unknown. Here, we investigated whether PAPST-dependent sulfation is involved in regulating signaling pathways required for the maintenance of mouse embryonic stem cells (mESCs), differentiation into the three germ layers, and neurogenesis. By using a yeast expression system, mouse PAPST1 and PAPST2 proteins were shown to have PAPS transport activity with an apparent Km value of 1.54 µM or 1.49 µM, respectively. RNAi-mediated knockdown of each PAPST induced the reduction of chondroitin sulfate (CS) chain sulfation as well as heparan sulfate (HS) chain sulfation, and inhibited mESC self-renewal due to defects in several signaling pathways. However, we suggest that these effects were due to reduced HS, not CS, chain sulfation, because knockdown of mouse N-deacetylase/N-sulfotransferase, which catalyzes the first step of HS sulfation, in mESCs gave similar results to those observed in PAPST-knockdown mESCs, but depletion of CS chains did not. On the other hand, during embryoid body formation, PAPST-knockdown mESCs exhibited abnormal differentiation, in particular neurogenesis was promoted, presumably due to the observed defects in BMP, FGF and Wnt signaling. The latter were reduced as a result of the reduction in both HS and CS chain sulfation. We propose that PAPST-dependent sulfation of HS or CS chains, which is regulated developmentally, regulates the extrinsic signaling required for the maintenance and normal differentiation of mESCs

Synthesis and Luminescence Properties of Near-Infrared N-Heterocyclic Luciferin Analogues for In Vivo Optical Imaging

As a means of achieving highly sensitive bioluminescence imaging of deep tissues utilizing the firefly luciferin-luciferase (L-L) reaction, we previously reported a luciferin analogue, AkaLumine, which exhibits high cell-permeability and emits near-infrared (NIR) light with high tissue-penetration by the L-L reaction. However, while AkaLumine enables us to observe targets in deep tissues, its poor solubility in aqueous media limits its utility for in vivo imaging. Herein, to address this issue, we have synthesized three AkaLumine derivatives with N-heterocyclic aromatic rings as new red luciferin analogues that have substantially higher solubility than that of AkaLumine in phosphate buffered saline solution. One of the derivatives (herein termed seMpai) exhibits an emission maximum at 675 nm upon L-L reaction with Photinus pyralis luciferase and presents an activity in mouse-tissue imaging similar to that of AkaLumine. It is hoped that seMpai will extend the application of high-sensitivity NIR bioluminescence imaging in a wide range of biomedical research fields

Cell-Free DNA Analysis of Epithelial Growth Factor Receptor Mutations in Lung Adenocarcinoma Patients by Droplet Digital PCR

Cell-free DNA (cfDNA) analysis may provide a non-invasive diagnostic approach for lung adenocarcinoma patients. Recently, droplet digital PCR (ddPCR) has been developed as a highly sensitive detection method for a low mutant allele percentage. The ddPCR detection limit for epithelial growth factor receptor (EGFR) mutations was evaluated using cell lines, NCI-H1975 for EGFR L858R point mutation and PC-9 for EGFR E746-A750del. Subsequently, detection of EGFR mutations by ddPCR was performed in tumor DNA (tDNA) and cfDNA samples of 19 lung adenocarcinoma patients whose tumor biopsies were already evaluated for EGFR mutations by clamp PCR (13 of L858R, 3 of E746-750del, and 3 of EGFR negative). In 12 cases, immunohistochemical analysis was performed to quantify the number of EGFR L858R-positive cells rate. EGFR point mutation or deletion were detected in 16 tumor DNA samples. In the measurable cfDNA samples, the rate of detection by ddPCR in cfDNA was 61.5% (8/13) for L858R and 100% (3/3) for E746-A750del. A relative correlation was found between the allele fraction (AF) of tDNA and the number of EGFR L858R-positive cells rate. No correlation was found between the AF of tDNA and AF of cfDNA. In our study, cfDNA mutation detection was not associated with clinicopathological features, but cases with high AF of cfDNA did have metastatic lesions. Our study shows that ddPCR enables cfDNA analysis for EGFR L858R and E746-A750del, with a high detection rate. Therefore, cfDNA analysis using ddPCR may complement to tumor biopsy and is beneficial for precision medicine in lung adenocarcinoma patients

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

Super-resolution imaging detects BP180 autoantigen in immunoglobulin M pemphigoid

Bullous pemphigoid is generally caused by immunoglobulin (Ig)G autoantibodies against hemidesmosomal BP180 and/or BP230. Recently, the concept of IgM pemphigoid has been proposed. A 23-year-old Japanese woman presented with a 4-month history of severely itchy papules showing subepidermal separations with mild neutrophil infiltration. Direct immunofluorescence (DIF) revealed IgM deposits at the dermoepidermal junction, but neither IgG nor IgA deposits. Indirect immunofluorescence on 1 M NaCl-split skin demonstrated deposits on the epidermal side. The optical density (OD) value of a modified IgM enzyme-linked immunosorbent assay for full-length BP180, but not for BP180-NC16A, was increased. The patient was diagnosed with IgM pemphigoid and was treated with diphenyl sulfone at 50 mg/day without recurrence. To confirm the precise autoantigen, we tried to obtain super-resolution imaging. The deposition pattern of IgM autoantibodies seemed to be oriented parallel to that of BP180. The detailed images detect DIF deposits apart from BP180-NC16A staining, but are close to type VII collagen-NC1 staining. This result suggests that the IgM autoantibodies in the patient might target the C-terminus of BP180. IgM pemphigoid is still not a widely accepted concept, and the clinical course remains unknown. We will carefully follow-up the patient. Super-resolution images may help to detect precise autoantigens in autoimmune blistering diseases

Theoretical and Numerical Analysis of the Single-Ring OpenPET Geometry for In-beam PET

We are developing the OpenPET, an open type PET geometry having an accessible and observable open space between detector rings which allows easy access to a patient during PET measurements. Our first generation OpenPET which we called dual-ring OpenPET consisted of two detector rings having a gap between them and it could provide an extended axial field of view (FOV). For applications such as in-beam PET to monitor dose distribution in situ during particle therapy, however, higher sensitivity is required rather than a wide FOV. As the next generation OpenPET, we proposed the single-ring OpenPET which was a geometry having an accessible and observable open space with higher sensitivity and a reduced number of detectors than the earlier geometry. In this paper, we provide a theoretical analysis of the sensitivity for the single-ring OpenPET and we compare it with the dual-ring OpenPET and a geometry in which the conventional PET is positioned at a slant angle against the patient bed to form an accessible open space, which we called slant PET. The theoretical analysis shows that the single-ring OpenPET has a sensitivity 1.2 times higher than the dual-ring OpenPET and 1.3 times higher than the slant PET when designed for about 200 detector blocks, each with a front area of 2500 mm2. In addition, numerical simulation using the Geant4 Monte Carlo toolkit is done to show the three-dimensional imaging performance that the single-ring OpenPET realized with the ellipsoidal rings of block detectors. The numerical simulation demonstrates that the depth-of-interaction detector can provide uniform resolution even when the detectors are arranged in an ellipsoidal ring.2012 Nuclear Science Symposium, Medical Imaging Conference & Workshop on Room-Temperature Semiconductor X-Ray and Gamma-Ray Detector

Related Stocks Selection with Data Collaboration Using Text Mining

We propose an extended scheme for selecting related stocks for themed mutual funds. This scheme was designed to support fund managers who are building themed mutual funds. In our preliminary experiments, building a themed mutual fund was found to be quite difficult. Our scheme is a type of natural language processing method and based on words extracted according to their similarity to a theme using word2vec and our unique similarity based on co-occurrence in company information. We used data including investor relations and official websites as company information data. We also conducted several other experiments, including hyperparameter tuning, in our scheme. The scheme achieved a 172% higher F1 score and 21% higher accuracy than a standard method. Our research also showed the possibility that official websites are not necessary for our scheme, contrary to our preliminary experiments for assessing data collaboration