Publications by authors named "Kei Iida"

70 Publications

CDC2-like (CLK) protein kinase inhibition as a novel targeted therapeutic strategy in prostate cancer.

Sci Rep 2021 Apr 12;11(1):7963. Epub 2021 Apr 12.

Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.

Dysregulation of alternative splicing is a feature of cancer, both in aetiology and progression. It occurs because of mutations in splice sites or sites that regulate splicing, or because of the altered expression and activity of splice factors and of splice factor kinases that regulate splice factor activity. Recently the CDC2-like kinases (CLKs) have attracted attention due to their increasing involvement in cancer. We measured the effect of the CLK inhibitor, the benzothiazole TG003, on two prostate cancer cell lines. TG003 reduced cell proliferation and increased apoptosis in PC3 and DU145 cells. Conversely, the overexpression of CLK1 in PC3 cells prevented TG003 from reducing cell proliferation. TG003 slowed scratch closure and reduced cell migration and invasion in a transwell assay. TG003 decisively inhibited the growth of a PC3 cell line xenograft in nude mice. We performed a transcriptomic analysis of cells treated with TG003. We report widespread and consistent changes in alternative splicing of cancer-associated genes including CENPE, ESCO2, CKAP2, MELK, ASPH and CD164 in both HeLa and PC3 cells. Together these findings suggest that targeting CLKs will provide novel therapeutic opportunities in prostate cancer.
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http://dx.doi.org/10.1038/s41598-021-86908-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041776PMC
April 2021

Improvement of Moloney murine leukemia virus reverse transcriptase thermostability by introducing a disulfide bridge in the ribonuclease H region.

Protein Eng Des Sel 2021 Feb;34

Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.

Moloney murine leukemia virus (MMLV) reverse transcriptase (RT) is widely used in research and clinical diagnosis. Improvement of MMLV RT thermostability has been an important topic of research for increasing the efficiency of cDNA synthesis. In this study, we attempted to increase MMLV RT thermostability by introducing a disulfide bridge in its RNase H region using site-directed mutagenesis. Five variants were designed, focusing on the distance between the two residues to be mutated into cysteine. The variants were expressed in Escherichia coli and purified. A551C/T662C was determined to be the most thermostable variant.
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http://dx.doi.org/10.1093/protein/gzab006DOI Listing
February 2021

S1PR3-G-biased agonist ALESIA targets cancer metabolism and promotes glucose starvation.

Cell Chem Biol 2021 Feb 2. Epub 2021 Feb 2.

Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan. Electronic address:

Metabolic activities are altered in cancer cells compared with those in normal cells, and the cancer-specific pathway becomes a potential therapeutic target. Higher cellular glucose consumption, which leads to lower glucose levels, is a hallmark of cancer cells. In an objective screening for chemicals that induce cell death under low-glucose conditions, we discovered a compound, denoted as ALESIA (Anticancer Ligand Enhancing Starvation-induced Apoptosis). By our shedding assay of transforming growth factor α in HEK293A cells, ALESIA was determined to act as a sphingosine-1-phosphate receptor 3-G-biased agonist that promotes nitric oxide production and oxidative stress. The oxidative stress triggered by ALESIA resulted in the exhaustion of glucose, cellular NADPH deficiency, and then cancer cell death. Intraperitoneal administration of ALESIA improved the survival of mice with peritoneally disseminated rhabdomyosarcoma, indicating its potential as a new type of anticancer drug for glucose starvation therapy.
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http://dx.doi.org/10.1016/j.chembiol.2021.01.004DOI Listing
February 2021

Examining the Beneficial Aspects of Nutritional Guidance Using Estimated Daily Salt Intake in Cancer Patients with Ischemic Heart Disease.

Med Sci Monit Basic Res 2021 Jan 19;27:e927719. Epub 2021 Jan 19.

Division of Cardiology, Shizuoka Cancer Center, Nagaizumi, Shizuoka, Japan.

BACKGROUND The outcomes associated with nutritional guidance for patients with ischemic heart disease undergoing cancer treatment have not been explored. We examined the effects of nutritional guidance using estimated daily salt intake in cancer patients with ischemic heart disease. MATERIAL AND METHODS We examined the data from physical examinations and laboratory assessments of 27 patients with suspected excessive salt intake who underwent coronary angiography for the first time and received nutritional guidance on their next visit to the Department of Cardiology of Shizuoka Cancer Center between May 2018 and March 2020. Salinity measurement was not used in the nutritional guidance method, but the patients were instructed to reduce consumption of salt-containing foods. We compared the frequency of the estimated daily salt intake with the frequency of categories requiring salt control (food, cooking, and table salts). RESULTS The median age of the participants was 74 (range, 63-86) years. The estimated daily salt intake and the rate of change in the triglyceride level were negatively correlated (r=-0.61, P<0.01). The estimated daily salt intake was reduced in 16 cases; there was a relative decrease in the frequency of food intake among categories requiring salt control compared with that in the nonimproved cases (P<0.01). No difference was found between the cancer stage and the affected site of the digestive system in either group (P=0.64, P=0.39). CONCLUSIONS Nutritional guidance on dietary habits without using salinity measurement was beneficial in preventing ischemic heart disease and food intake reduction in cancer patients.
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http://dx.doi.org/10.12659/MSMBR.927719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7834217PMC
January 2021

Comparison of Measured Data between Pre- and Post-Radiotherapy in a Patient with Cardiac Resynchronization Therapy Defibrillator.

Int Heart J 2020 Nov 13;61(6):1311-1314. Epub 2020 Nov 13.

Division of Anesthesiology, Shizuoka Cancer Center Hospital.

Although some researches proved the influence of radiation therapy (RT) on pacemakers and implantable cardioverter defibrillators, little has been reported on cardiac resynchronization therapy defibrillators (CRTDs). We experienced a case of RT on CRTD and had a new finding.A patient with CRTD implanted for dilated cardiomyopathy was diagnosed with lung squamous cell carcinoma and started receiving RT. All the implanted devices, including the main body of CRTD, left ventricular lead (LV), right ventricular lead with high-voltage conductor, and right atrial lead, were from the same manufacturer. The radiation targeted the tumor of 67 mm in diameter in the right superior lobe for 5 min per session. The CRTD was outside the radiation field, which is 65 mm, but the leads were inside. Plan 1 used 2 Gy/fr with 8 megavolt photons, and Plan 1 was irradiated at 0° and 180° for 16 RT sessions. The dosage was increased to 3 Gy for Plan 2 for 4 sessions. Plan 3 used 2 Gy with 6 and 8 megavolt photons, and Plan 3 was irradiated at 27.7° and 200.7° for 11 RT sessions. Changes in measured parameters were assessed before and after RT.Changes in impedance of LV and high-voltage lead exceeded prespecified threshold. However, no significant errors were detected in the CRTD on the dosages and energy we used.We hypothesize that the lead insulator could have been affected by radiation.
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http://dx.doi.org/10.1536/ihj.20-047DOI Listing
November 2020

Identification of Qk as a Glial Precursor Cell Marker that Governs the Fate Specification of Neural Stem Cells to a Glial Cell Lineage.

Stem Cell Reports 2020 10 24;15(4):883-897. Epub 2020 Sep 24.

Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.

During brain development, neural stem cells (NSCs) initially produce neurons and change their fate to generate glias. While the regulation of neurogenesis is well characterized, specific markers for glial precursor cells (GPCs) and the master regulators for gliogenesis remain unidentified. Accumulating evidence suggests that RNA-binding proteins (RBPs) have significant roles in neuronal development and function, as they comprehensively regulate the expression of target genes in a cell-type-specific manner. We systematically investigated the expression profiles of 1,436 murine RBPs in the developing mouse brain and identified quaking (Qk) as a marker of the putative GPC population. Functional analysis of the NSC-specific Qk-null mutant mouse revealed the key role of Qk in astrocyte and oligodendrocyte generation and differentiation from NSCs. Mechanistically, Qk upregulates gliogenic genes via quaking response elements in their 3' untranslated regions. These results provide crucial directions for identifying GPCs and deciphering the regulatory mechanisms of gliogenesis from NSCs.
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http://dx.doi.org/10.1016/j.stemcr.2020.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7562946PMC
October 2020

Multilateral Bioinformatics Analyses Reveal the Function-Oriented Target Specificities and Recognition of the RNA-Binding Protein SFPQ.

iScience 2020 Jul 28;23(7):101325. Epub 2020 Jun 28.

Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Konoecho Yoshida Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

RNA-binding proteins (RBPs) recognize consensus sequences and regulate specific target mRNAs. However, large-scale CLIP-seq revealed loose and broad binding of RBPs to larger proportion of expressed mRNAs: e.g. SFPQ binds to >10,000 pre-mRNAs but distinctly regulates <200 target genes during neuronal development. Identification of crucial binding for regulation and rules of target recognition is highly anticipated for systemic understanding of RBP regulations. For a breakthrough solution, we developed a bioinformatical method for CLIP-seq and transcriptome data by adopting iterative hypothesis testing. Essential binding was successfully identified in C-rich sequences close to the 5' splice sites of long introns, which further proposed target recognition mechanism via association between SFPQ and splicing factors during spliceosome assembly. The identified features of functional binding enabled us to predict regulons and also target genes in different species. This multilateral bioinformatics approach facilitates the elucidation of functionality, regulatory mechanism, and regulatory networks of RBPs.
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http://dx.doi.org/10.1016/j.isci.2020.101325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358709PMC
July 2020

Effect of VCP modulators on gene expression profiles of retinal ganglion cells in an acute injury mouse model.

Sci Rep 2020 03 6;10(1):4251. Epub 2020 Mar 6.

Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan.

In glaucoma, retinal ganglion cells are damaged, leading to the progressive constriction of the visual field. We have previously shown that the valosin-containing protein (VCP) modulators, Kyoto University Substance (KUS)121 and KUS187, prevent the death of retinal ganglion cells in animal models of glaucoma, including the one generated by N-methyl-D-aspartate (NMDA)-induced neurotoxicity. KUSs appeared to avert endoplasmic reticulum (ER) stress by maintaining ATP levels, resulting in the protection of ganglion cells from cell death. To further elucidate the protective mechanisms of KUSs, we examined gene expression profiles in affected ganglion cells. We first injected KUS-treated mice with NMDA and then isolated the affected retinal ganglion cells using fluorescence-activated cell sorting. Gene expression in the cells was quantified using a next-generation sequencer. Resultantly, we found that KUS121 upregulated several genes involved in energy metabolism. In addition, we observed the upregulation of Zfp667, which has been reported to suppress apoptosis-related genes and prevent cell death. These results further support the suitability of KUS121 as a therapeutic drug in protecting retinal ganglion cells in ophthalmic disorders, such as glaucoma.
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http://dx.doi.org/10.1038/s41598-020-61160-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060332PMC
March 2020

Cancer-associated cerebral infarction during direct oral anticoagulant treatment in cancer patients: a case series.

Int Cancer Conf J 2019 Jul 19;8(3):130-135. Epub 2019 Mar 19.

3Research Institute, Shizuoka Cancer Center, Shizuoka, Japan.

The effect of direct oral anticoagulants (DOACs) on cancer-associated cerebral infarction (CI) is unclear. We present the clinical course of 20 consecutive patients with cancer-associated CI that developed during treatment with DOACs. The incidence rate of cancer-associated CI during the treatment with DOACs was 3.4%. The median modified Rankin scale (mRS) and Karnofsky performance status (KPS) after CI were 5 and 30, respectively. The median survival time after CI was 1 month. In the group in which the thrombus due to venous thromboembolism (VTE) was reduced before CI, the median mRS, KPS, and prognosis after CI were significantly better than in those of the group with unchanged thrombus. Cancer-associated CI also developed in patients taking DOACs and those who did not show VTE recurrence. When the VTE thrombus decreased or disappeared with DOAC treatment, the clinical course after cancer-associated CI was improved.
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http://dx.doi.org/10.1007/s13691-019-00370-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545186PMC
July 2019

Loss of RNA-Binding Protein Sfpq Causes Long-Gene Transcriptopathy in Skeletal Muscle and Severe Muscle Mass Reduction with Metabolic Myopathy.

iScience 2019 Mar 27;13:229-242. Epub 2019 Feb 27.

Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

Growing evidences are suggesting that extra-long genes in mammals are vulnerable for full-gene length transcription and dysregulation of long genes is a mechanism underlying human genetic disorders. How long-distance transcription is achieved is a fundamental question to be elucidated. In previous study, we had discovered that RNA-binding protein SFPQ preferentially binds to long pre-mRNAs and specifically regulates the cluster of neuronal genes >100 kbp. Here we investigated the roles of SFPQ for long gene expression, target specificities, and also physiological functions in skeletal muscle. Loss of Sfpq selectively downregulated genes >100 kbp including Dystrophin, which is 2.26 Mbp in length. Sfpq knockout (KO) mice showed progressive muscle mass reduction and metabolic myopathy characterized by glycogen accumulation and decreased abundance of mitochondrial oxidative phosphorylation complexes. Functional clustering analysis identified energy metabolism pathway genes as SFPQ's targets. These findings indicate target gene specificities and tissue-specific physiological functions of SFPQ in skeletal muscle.
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http://dx.doi.org/10.1016/j.isci.2019.02.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416966PMC
March 2019

A Cavity Communicating with the Right Atrium.

Intern Med 2019 08 25;58(16):2407-2408. Epub 2019 Feb 25.

Division of Cardiology, Shizuoka Cancer Center, Japan.

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http://dx.doi.org/10.2169/internalmedicine.2363-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6746641PMC
August 2019

Use of direct oral anti-coagulants for the treatment of venous thromboembolism in patients with advanced cancer: a prospective observational study.

Int J Clin Oncol 2019 Jul 12;24(7):876-881. Epub 2019 Feb 12.

Clinical Research Promotion Unit, Clinical Research Support Center, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.

Background: The efficacy of direct oral anti-coagulants (DOACs) for the treatment of venous thromboembolism (VTE) in Japanese patients with advanced cancer is largely unknown.

Methods: This prospective single-center observational study enrolled Japanese patients with unresectable advanced cancer who started DOAC treatment for new-onset VTE between December 2015 and May 2018. Patients were followed for 3 months to evaluate bleeding and VTE recurrences. The primary study endpoint was major and non-major bleeding.

Results: One hundred and forty-five of 147 enrolled patients were analyzed. Of these, 8 [5.5%, 95% confidence interval (CI) 2.8-10.5] and 29 patients (20%, 95% CI 14.3-27.2) experienced major and non-major bleeding, respectively. Patients with bleeding were more likely to have a poor performance status (PS) [hazard rate (HR) 2.04, 95% CI 1.15-3.63] and more frequent use of non-steroidal anti-inflammatory drugs (NSAIDs) (HR 2.75, 95% CI 1.62-4.67) relative to those without bleeding. In a multivariate analysis, combined DOAC and NSAID use correlated significantly with bleeding (odds ratio 4.63, 95% CI 1.70-12.9, p = 0.003). Among 105 of 145 patients included in the VTE recurrence assessment, 9 experienced a VTE recurrence (8.6%, 95% CI 4.6-15.5).

Conclusions: Our findings confirm the risk of bleeding during DOAC treatment for VTE in Japanese patients with advanced cancer, particularly those with poor PS and those using NSAIDs. The risk of bleeding in these patients may be reduced by avoiding the combined use of DOACs and NSAIDs.
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http://dx.doi.org/10.1007/s10147-019-01415-zDOI Listing
July 2019

Effect of Switching from the Initial Direct Oral Anticoagulant to Another One on Exacerbation of Venous Thromboembolism in Patients with Cancer: A Retrospective Study.

Ann Vasc Dis 2018 Dec;11(4):531-534

Research Institute, Shizuoka Cancer Center, Shizuoka, Japan.

: To determine the effect of switching from the initial direct oral anticoagulant (DOAC) to another DOAC on exacerbation of deep vein thrombosis (DVT). : We retrospectively reviewed the data of patients with advanced cancer who experienced exacerbated DVT during initial treatment with DOAC due to new venous thromboembolism (VTE). After switching to another DOAC for VTE recurrence, changes in the thrombus and bleeding were evaluated for 3 months. Eighteen patients met these criteria. We compared the effect of anticoagulant switching on the switched-drug group in those 18 patients with the effect of no anticoagulant switching on the single-drug group of patients (n=78) with a similar background. : The recurrence rate of VTE in the switched-drug group was 6%. Non-major bleeding occurred in 11% of patients. Recurrent VTE occurred in 6% of patients in both the switched-drug and single-drug groups, respectively [risk ratio (RR): 0.9, 95% confidence interval (CI): 0.11-7.6]. Non-major bleeding occurred in 11% and 14% of patients in the switched-drug and single-drug groups, respectively (RR: 0.79, 95%CI: 0.19-3.2). : Switching DOAC may be a treatment option for exacerbation of DVT in patients with advanced cancer.
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http://dx.doi.org/10.3400/avd.oa.18-00072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326063PMC
December 2018

Integrative network analysis reveals biological pathways associated with Williams syndrome.

J Child Psychol Psychiatry 2019 05 25;60(5):585-598. Epub 2018 Oct 25.

Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

Background: Williams syndrome (WS) is a neurodevelopmental disorder that has been attributed to heterozygous deletions in chromosome 7q11.23 and exhibits a variety of physical, cognitive, and behavioral features. However, the genetic basis of this phenotypic variability is unclear. In this study, we identified genetic clues underlying these complex phenotypes.

Methods: Neurobehavioral function was assessed in WS patients and healthy controls. Total RNA was extracted from peripheral blood and subjected to microarray analysis, RNA-sequencing, and qRT-PCR. Weighted gene co-expression network analysis was performed to identify specific alterations related to intermediate disease phenotypes. To functionally interpret each WS-related module, gene ontology and disease-related gene enrichment were examined. We also investigated the micro (mi)RNA expression profiles and miRNA co-expression networks to better explain the regulation of the transcriptome in WS.

Results: Our analysis identified four significant co-expression modules related to intermediate WS phenotypes. Notably, the three upregulated WS-related modules were composed exclusively of genes located outside the 7q11.23 region. They were significantly enriched in genes related to B-cell activation, RNA processing, and RNA transport. BCL11A, which is known for its association with speech disorders and intellectual disabilities, was identified as one of the hub genes in the top WS-related module. Finally, these key upregulated mRNA co-expression modules appear to be inversely correlated with a specific downregulated WS-related miRNA co-expression module.

Conclusions: Dysregulation of the mRNA/miRNA network involving genes outside of the 7q11.23 region is likely related to the complex phenotypes observed in WS patients.
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http://dx.doi.org/10.1111/jcpp.12999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7379192PMC
May 2019

Author Correction: Synaptic N-methyladenosine (mA) epitranscriptome reveals functional partitioning of localized transcripts.

Nat Neurosci 2018 Oct;21(10):1493

Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.

In the version of this article initially published, a Supplementary Fig. 6f was cited in the last paragraph of the Results. No such panel exists; the citation has been deleted. The error has been corrected in the HTML and PDF versions of the article.
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http://dx.doi.org/10.1038/s41593-018-0219-9DOI Listing
October 2018

Synaptic N-methyladenosine (mA) epitranscriptome reveals functional partitioning of localized transcripts.

Nat Neurosci 2018 07 27;21(7):1004-1014. Epub 2018 Jun 27.

Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.

A localized transcriptome at the synapse facilitates synapse-, stimulus- and transcript-specific local protein synthesis in response to neuronal activity. While enzyme-mediated mRNA modifications are known to regulate cellular mRNA turnover, the role of these modifications in regulating synaptic RNA has not been studied. We established low-input mA-sequencing of synaptosomal RNA to determine the chemically modified local transcriptome in healthy adult mouse forebrains and identified 4,469 selectively enriched mA sites in 2,921 genes as the synaptic mA epitranscriptome (SME). The SME is functionally enriched in synthesis and modulation of tripartite synapses and in pathways implicated in neurodevelopmental and neuropsychiatric diseases. Interrupting mA-mediated regulation via knockdown of readers in hippocampal neurons altered expression of SME member Apc, resulting in synaptic dysfunction including immature spine morphology and dampened excitatory synaptic transmission concomitant with decreased clusters of postsynaptic density-95 (PSD-95) and decreased surface expression of AMPA receptor subunit GluA1. Our findings indicate that chemical modifications of synaptic mRNAs critically contribute to synaptic function.
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http://dx.doi.org/10.1038/s41593-018-0173-6DOI Listing
July 2018

SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology.

Genome Biol 2018 06 6;19(1):66. Epub 2018 Jun 6.

Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.

We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.
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http://dx.doi.org/10.1186/s13059-018-1446-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989370PMC
June 2018

Accurate fidelity analysis of the reverse transcriptase by a modified next-generation sequencing.

Enzyme Microb Technol 2018 Aug 3;115:81-85. Epub 2018 May 3.

Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan. Electronic address:

We evaluated fidelity of various reverse transcriptases (RTs) by a novel method with modified next-generation sequencing (NGS). In the optimized condition, one NGS run could handle cDNA products from multiple cDNA synthesis reactions performed at different conditions. This was achieved using a primer containing not only the tag of 14 randomized bases to label each cDNA molecule but also a tag of five bases to label each reaction condition. With this method, we quantitated the error rates of 44 cDNA synthesis reactions by retroviral RTs or genetically engineered DNA polymerases with RT activity under different conditions. The results indicated that high concentrations of MgCl, Mn(OCOCH), and dNTP decrease the fidelity and that these effects are more pronounced in reactions using RT from human immunodeficiency virus type 1. This is the first report about a precise fidelity monitoring of various RTs by a direct sequence determination.
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http://dx.doi.org/10.1016/j.enzmictec.2018.05.001DOI Listing
August 2018

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain.

Cell Rep 2018 05;23(5):1326-1341

Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

Genes specifically expressed in neurons contain members with extended long introns. Longer genes present a problem with respect to fulfilment of gene length transcription, and evidence suggests that dysregulation of long genes is a mechanism underlying neurodegenerative and psychiatric disorders. Here, we report the discovery that RNA-binding protein Sfpq is a critical factor for maintaining transcriptional elongation of long genes. We demonstrate that Sfpq co-transcriptionally binds to long introns and is required for sustaining long-gene transcription by RNA polymerase II through mediating the interaction of cyclin-dependent kinase 9 with the elongation complex. Phenotypically, Sfpq disruption caused neuronal apoptosis in developing mouse brains. Expression analysis of Sfpq-regulated genes revealed specific downregulation of developmentally essential neuronal genes longer than 100 kb in Sfpq-disrupted brains; those genes are enriched in associations with neurodegenerative and psychiatric diseases. The identified molecular machinery yields directions for targeted investigations of the association between long-gene transcriptopathy and neuronal diseases.
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http://dx.doi.org/10.1016/j.celrep.2018.03.141DOI Listing
May 2018

Crizotinib-induced simultaneous multiple cardiac toxicities.

Invest New Drugs 2018 10 2;36(5):949-951. Epub 2018 May 2.

Division of Thoracic Oncology, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.

Crizotinib is a receptor tyrosine kinase inhibitor that has several targets, including c-ros oncogene 1 and the MET proto-oncogene. Considering its known cardiac toxicity, bradycardia is often investigated following treatment with crizotinib. Our patients had bradycardia, QT prolongation, ventricular rhythm, ventricular fibrillation, and pericarditis simultaneously. The cardiotoxicity of crizotinib can sometimes be simultaneous; thus, intensive observation is needed.
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http://dx.doi.org/10.1007/s10637-018-0605-xDOI Listing
October 2018

Myocardial Infarction Caused by Asymptomatic Spontaneous Coronary Dissection.

Intern Med 2018 09 27;57(18):2763-2764. Epub 2018 Apr 27.

Research Institute, Shizuoka Cancer Center, Japan.

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http://dx.doi.org/10.2169/internalmedicine.0719-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191582PMC
September 2018

Monitoring Transcriptomic Changes in Soil-Grown Roots and Shoots of Arabidopsis thaliana Subjected to a Progressive Drought Stress.

Methods Mol Biol 2018 ;1761:223-230

Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Sciences, Yokohama, Kanagawa, Japan.

Numerous experiments have been performed in Arabidopsis to monitor changes in gene expression that occur in response to a variety of abiotic and biotic stresses, different growth conditions, and at various developmental stages. In addition, gene expression patterns have also been characterized among wild-type and mutant genotypes. Despite these numerous reports, transcriptional changes occurring in roots of soil-grown plants subjected to a progressive drought stress have remained undocumented. To fill this gap, we established a system that allows one to establish water-deficit conditions and to collect root and shoot samples with minimal damage to the root system. Arabidopsis plants are grown in a ceramic-based granular soil and subjected to progressive drought stress by withholding water. Root and shoot samples were collected separately, RNA was purified, and a microarray analysis of drought-stressed roots and shoots was performed at 0, 1, 3, 5, 7, and 9 days after the onset of drought stress treatment. Here, we describe the detailed protocol used to analyze the transcriptomic changes occurring in roots and shoots of soil-grown Arabidopsis subjected to a progressive drought stress.
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http://dx.doi.org/10.1007/978-1-4939-7747-5_17DOI Listing
January 2019

A Patient with a Massive Single Cardiac Metastasis of Lung Adenocarcinoma, Diagnosed via a Biopsy.

Intern Med 2018 Jun 11;57(11):1637-1640. Epub 2018 Jan 11.

Division of Thoracic Oncology, Shizuoka Cancer Center, Japan.

A patient with a history of lung adenocarcinoma was admitted because of palpitation. Transthoracic echocardiogram revealed a mass (74×42 mm) in the right ventricle. Computed tomography showed a tumor lesion in the right ventricular cavity but no other distant metastasis. Coronary angiography revealed well-developed small branches to the tumor. After right heart catheterization, a pathological analysis of a tumor biopsy demonstrated adenocarcinoma. We diagnosed the patient with right ventricular metastasis of lung cancer. With large cardiac metastasis, a tumor biopsy with a right heart catheter may help obtain a pathological diagnosis and also serve as a re-biopsy to confirm the gene mutation status.
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http://dx.doi.org/10.2169/internalmedicine.9893-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028669PMC
June 2018

Characteristics of cellular composition in malignant pericardial effusion and its association with the clinical course of carcinomatous pericarditis.

Jpn J Clin Oncol 2018 Mar;48(3):291-294

Clinical Research Promotion Unit, Clinical Research Center, Shizuoka Cancer Center, Shizuoka, Japan.

To date, the cellular composition of malignant pericardial effusion (MPE) and its association with the clinical course of carcinomatous pericarditis remain unclear. We aimed to determine the MPE cellular composition and its association with carcinomatous pericarditis. Forty-four cases indicated for pericardial drainage due to symptomatic carcinomatous pericarditis were retrospectively reviewed; the blood cell count and composition of MPE were examined. The most dominant cells in MPE were neutrophils. The appearance ratio of an atypical cell in cytologically positive MPE was 95.5%. Low neutrophil and high lymphocyte counts were significantly associated with good effusion failure-free survival at 1 month. The survival after pericardial drainage was significantly shorter when the neutrophil/lymphocyte ratio was 3.5 or more (P = 0.041). Patients whose performance status improved due to drainage had significantly high leukocyte counts in MPE (P = 0.02). Prediction of the course of drainage through basic examination of MPE cellular composition might be beneficial in clinical practice.
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http://dx.doi.org/10.1093/jjco/hyx187DOI Listing
March 2018

DNA hypermethyation and silencing of correlated with advanced stage and poor postoperative prognosis of esophageal squamous cell carcinoma.

Oncotarget 2017 Oct 28;8(48):84434-84448. Epub 2017 Sep 28.

Department of Gastroenterology, The Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba, Japan.

Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed. We found 159 genes with significantly decreased expression in ESCC compared to that in noncancerous esophageal mucosa. MeDIP-seq analysis identified hypermethylation in the promoter region of 56 of these genes. Using surgically resected tissues of 40 cases, we confirmed that the paired-like homeodomain 1 gene was hypermethylated in ESCC compared to that in normal tissues ( < 0.0001) by pyrosequencing. PITX1 overexpression in ESCC cell lines inhibited cell growth and colony formation, whereas PITX1 knockdown accelerated cell growth. A PITX1-transfected ESCC cell line, KYSE30, formed smaller tumors in nude mice than in mock-transfected cells. Hypermethylation of was associated with tumor depth ( = 0.0011) and advanced tumor stage ( = 0.0052) and predicted poor survival in ESCC (hazard ratio, 0.1538; 95% confidence interval, 0.03159-0.7488; = 0.0169). In this study, we found a novel tumor suppressor gene of ESCC, PITX1, which is silenced by DNA hypermethylation. Downregulation of PITX1 contributes to the growth and progression of ESCC. Hypermethylation of the in ESCC correlated with tumor progression and advanced stage cancer, and may predict a poor prognosis.
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http://dx.doi.org/10.18632/oncotarget.21375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663609PMC
October 2017

Next-generation sequencing-based analysis of reverse transcriptase fidelity.

Biochem Biophys Res Commun 2017 10 1;492(2):147-153. Epub 2017 Aug 1.

Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan.

In this study, we devised a simple and rapid method to analyze fidelity of reverse transcriptase (RT) using next-generation sequencing (NGS). The method comprises a cDNA synthesis reaction from standard RNA with a primer containing a tag of 14 randomized bases and the RT to be tested, PCR using high-fidelity DNA polymerase, and NGS. By comparing the sequence of each read with the reference sequence, mutations were identified. The mutation can be identified to be due to an error introduced by either cDNA synthesis, PCR, or NGS based on whether the sequence reads with the same tag contain the same mutation or not. The error rates in cDNA synthesis with Moloney murine leukemia virus (MMLV) RT thermostable variant MM4 or the recently developed 16-tuple variant of family B DNA polymerase with RT activity, RTX, from Thermococcus kodakarensis, were 0.75-1.0 × 10 errors/base, while that in the reaction with the wild-type human immunodeficiency virus type 1 (HIV-1) RT was 2.6 × 10 errors/base. Overall, our method could precisely evaluate the fidelity of various RTs with different reaction conditions in a high-throughput manner without the use of expensive optics and troublesome adaptor ligation.
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http://dx.doi.org/10.1016/j.bbrc.2017.07.169DOI Listing
October 2017

Takotsubo Cardiomyopathy after Head and Neck Reconstructive Surgery.

Plast Reconstr Surg Glob Open 2017 Jun 28;5(6):e1366. Epub 2017 Jun 28.

Division of Plastic and Reconstructive Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan; Division of Cardiology, Shizuoka Cancer Center Hospital, Shizuoka, Japan; and Department of Plastic Surgery, Jichi Medical University, Tochigi, Japan.

Takotsubo cardiomyopathy (TCM) is a form of transient heart failure that clinically mimics acute coronary syndrome and is characterized by left ventricular wall motion abnormalities. The pathophysiology of TCM is not well established. TCM is often preceded by emotional or physical stress and may occur after surgery. We present 3 cases of TCM occurring after head and neck reconstructive surgery. Echocardiography plays a central role in the diagnosis of TCM. Left ventricular wall motion abnormalities extend beyond the territory of a single coronary artery. Coronary angiography and cardiac computed tomography can demonstrate the absence of coronary atherosclerosis and are useful for confirming the diagnosis of TCM. Particularly after reconstructive surgery, it is necessary to carefully monitor fluid replacement to avoid dehydration, which may compromise flap blood flow, although congestive heart failure is the most common complication of TCM. It is important to encourage ambulation as soon as possible, while considering the degree of cardiac impairment.
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http://dx.doi.org/10.1097/GOX.0000000000001366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505839PMC
June 2017

Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase.

Plant Physiol 2017 Sep 14;175(1):457-472. Epub 2017 Jul 14.

Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

Our previous study identified approximately 6,000 abiotic stress-responsive noncoding transcripts existing on the antisense strand of protein-coding genes and implied that a type of antisense RNA was synthesized from a sense RNA template by (). Expression analyses revealed that the expression of novel abiotic stress-induced antisense RNA on 1,136 gene loci was reduced in the mutants. RNase protection indicated that the antisense RNA and other RDR1/2/6-dependent antisense RNAs are involved in the formation of dsRNA. The accumulation of stress-inducible antisense RNA was decreased and increased in and , respectively, but not changed in , and RNA-seq analyses revealed that the majority of the RDR1/2/6-dependent antisense RNA loci did not overlap with RDR1/2/6-dependent 20-30 nt RNA loci. Additionally, mutants decreased the degradation rate of the sense RNA and exhibited arrested root growth during the recovery stage following a drought stress, whereas mutants did not. Collectively, these results indicate that RDRs have stress-inducible antisense RNA synthesis activity and a novel biological function that is different from the known endogenous small RNA pathways from protein-coding genes. These data reveal a novel mechanism of RNA regulation during abiotic stress response that involves complex RNA degradation pathways.
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http://dx.doi.org/10.1104/pp.17.00787DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580770PMC
September 2017

Chemotherapy-induced cardiomyopathy caused by Pemetrexed.

Invest New Drugs 2018 02 28;36(1):147-150. Epub 2017 Jun 28.

Division of Pathology, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.

Chemotherapy-related cardiac toxicity is a rare but serious adverse event in patients with cancer. Thus far, no case of serious cardiac toxicity of pemetrexed has been reported. We describe the case of a patient with advanced lung cancer and cardiomyopathy due to pemetrexed. A 59-year-old woman visited our hospital, and we found abnormal findings on a chest radiograph. She was diagnosed as having stage IV lung adenocarcinoma. Chemotherapy with cisplatin and pemetrexed every 3 weeks was initiated. After four cycles of chemotherapy, maintenance chemotherapy with pemetrexed was administered every 3 weeks. During the seventeenth cycle of pemetrexed, she had shortness of breath in her daily life. A chest radiograph showed an enlarged cardiothoracic ratio (66%), and the transthoracic echocardiogram demonstrated expansion of the left ventricle (diastolic diameter, 67 mm), severe global hypokinesis, and reduced left ventricular ejection fraction (28%). The coronary angiogram showed no coronary constriction. There was no delayed accumulation on the contrast-enhanced cardiac magnetic resonance imaging scan. After right heart catheterization, pathological results of a myocardial biopsy from the ventricular septum indicated no cardiac muscle hypertrophy, cardiac fibrosis, inflammatory cell infiltration, or myocyte disarray. Eventually, she was diagnosed as having pemetrexed-induced cardiomyopathy. Pemetrexed was discontinued, and furosemide, enalapril, and carvedilol were started. Then her symptoms and cardiac function improved. Early detection and discontinuation of causative agents are the most important treatment strategies in similar patients. Diuretics, angiotensin-conversion enzyme inhibitors, and beta-blockers may be effective for treating heart failure.
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http://dx.doi.org/10.1007/s10637-017-0485-5DOI Listing
February 2018

Synthetic ligand promotes gene expression by affecting GC sequence in promoter.

Bioorg Med Chem Lett 2017 08 3;27(15):3391-3394. Epub 2017 Jun 3.

Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan. Electronic address:

A naphthyridine carbamate tetramer (NCT8) is a synthetic compound, which selectively binds to nucleic acids containing CGG/CGG sequence. Although NCT8 is a promising compound for a wide range of DNA and RNA based biotechnology such as modulation of specific gene expression, little is known about its behavior in human cells. In the present study, we investigated the changes induced in gene expression by NCT8. Genes differentially expressed in the presence of NCT8 in HeLa cells were identified by whole-transcriptome analysis. The whole-transcriptome analysis showed that NCT8 significantly induced up-regulation of specific genes, whose promoter region has GC-rich sequence.
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http://dx.doi.org/10.1016/j.bmcl.2017.06.006DOI Listing
August 2017