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Article ; Online: Genome-wide screening of upstream transcription factors using an expression library [version 2; peer review

Naoya Yahagi / Yoshinori Takeuchi

F1000Research, Vol

2 approved]

2021 Volume 10

Abstract: The identification of upstream transcription factors regulating the expression of a gene is generally not an easy process. To facilitate this task, we constructed an expression cDNA library named Transcription Factor Expression Library (TFEL), which is ... ...

Abstract	The identification of upstream transcription factors regulating the expression of a gene is generally not an easy process. To facilitate this task, we constructed an expression cDNA library named Transcription Factor Expression Library (TFEL), which is composed of nearly all the transcription factors in the mouse genome. Genome-wide screening using this library (TFEL scan method) enables us to easily identify transcription factors controlling any given promoter or enhancer of interest in a chromosomal context-dependent manner. Thus, TFEL scan method is a powerful approach to explore transcriptional regulatory networks.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A comparison of estimators from self-controlled case series, case-crossover design, and sequence symmetry analysis for pharmacoepidemiological studies

Yoshinori Takeuchi / Tomohiro Shinozaki / Yutaka Matsuyama

BMC Medical Research Methodology, Vol 18, Iss 1, Pp 1-

2018 Volume 15

Abstract: Abstract Background Despite the frequent use of self-controlled methods in pharmacoepidemiological studies, the factors that may bias the estimates from these methods have not been adequately compared in real-world settings. Here, we comparatively ... ...

Abstract	Abstract Background Despite the frequent use of self-controlled methods in pharmacoepidemiological studies, the factors that may bias the estimates from these methods have not been adequately compared in real-world settings. Here, we comparatively examined the impact of a time-varying confounder and its interactions with time-invariant confounders, time trends in exposures and events, restrictions, and misspecification of risk period durations on the estimators from three self-controlled methods. This study analyzed self-controlled case series (SCCS), case-crossover (CCO) design, and sequence symmetry analysis (SSA) using simulated and actual electronic medical records datasets. Methods We evaluated the performance of the three self-controlled methods in simulated cohorts for the following scenarios: 1) time-invariant confounding with interactions between the confounders, 2) time-invariant and time-varying confounding without interactions, 3) time-invariant and time-varying confounding with interactions among the confounders, 4) time trends in exposures and events, 5) restricted follow-up time based on event occurrence, and 6) patient restriction based on event history. The sensitivity of the estimators to misspecified risk period durations was also evaluated. As a case study, we applied these methods to evaluate the risk of macrolides on liver injury using electronic medical records. Results In the simulation analysis, time-varying confounding produced bias in the SCCS and CCO design estimates, which aggravated in the presence of interactions between the time-invariant and time-varying confounders. The SCCS estimates were biased by time trends in both exposures and events. Erroneously short risk periods introduced bias to the CCO design estimate, whereas erroneously long risk periods introduced bias to the estimates of all three methods. Restricting the follow-up time led to severe bias in the SSA estimates. The SCCS estimates were sensitive to patient restriction. The case study showed that although macrolide ...
Keywords	Bias ; Interaction ; Medical database ; Misspecified risk period ; Restriction ; Self-controlled methods ; Medicine (General) ; R5-920
Subject code	310
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: FoxO-KLF15 pathway switches the flow of macronutrients under the control of insulin

Yoshinori Takeuchi / Naoya Yahagi / Yuichi Aita / Zahra Mehrazad-Saber / Man Hei Ho / Yiren Huyan / Yuki Murayama / Akito Shikama / Yukari Masuda / Yoshihiko Izumida / Takafumi Miyamoto / Takashi Matsuzaka / Yasushi Kawakami / Hitoshi Shimano

iScience, Vol 24, Iss 12, Pp 103446- (2021)

2021

Abstract: Summary: KLF15 is a transcription factor that plays an important role in the activation of gluconeogenesis from amino acids as well as the suppression of lipogenesis from glucose. Here we identified the transcription start site of liver-specific KLF15 ... ...

Abstract	Summary: KLF15 is a transcription factor that plays an important role in the activation of gluconeogenesis from amino acids as well as the suppression of lipogenesis from glucose. Here we identified the transcription start site of liver-specific KLF15 transcript and showed that FoxO1/3 transcriptionally regulates Klf15 gene expression by directly binding to the liver-specific Klf15 promoter. To achieve this, we performed a precise in vivo promoter analysis combined with the genome-wide transcription-factor-screening method “TFEL scan”, using our original Transcription Factor Expression Library (TFEL), which covers nearly all the transcription factors in the mouse genome. Hepatic Klf15 expression is significantly increased via FoxOs by attenuating insulin signaling. Furthermore, FoxOs elevate the expression levels of amino acid catabolic enzymes and suppress SREBP-1c via KLF15, resulting in accelerated amino acid breakdown and suppressed lipogenesis during fasting. Thus, the FoxO-KLF15 pathway contributes to switching the macronutrient flow in the liver under the control of insulin.
Keywords	Molecular biology ; Molecular network ; Diabetology ; Science ; Q
Subject code	570
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis

Motohiro Sekiya / Kenta Kainoh / Takehito Sugasawa / Ryunosuke Yoshino / Takatsugu Hirokawa / Hiroaki Tokiwa / Shogo Nakano / Satoru Nagatoishi / Kouhei Tsumoto / Yoshinori Takeuchi / Takafumi Miyamoto / Takashi Matsuzaka / Hitoshi Shimano

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 19

Abstract: Sensing of nutrient status coordinates the regulation of liver glucose and lipid metabolism, and is important for metabolic homeostasis. Here the authors report that transcriptional the corepressor CtBP2 can sense nutrient status and coordinate ... ...

Abstract	Sensing of nutrient status coordinates the regulation of liver glucose and lipid metabolism, and is important for metabolic homeostasis. Here the authors report that transcriptional the corepressor CtBP2 can sense nutrient status and coordinate repression of liver glucose and lipid metabolism via Fox01 and SREBP1, respectively.
Keywords	Science ; Q
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Characterization of Osteoarthritis in a Medial Meniscectomy-Induced Animal Model Using Contrast-Enhanced X-ray Microtomography

Takehito Sugasawa / Tomoaki Kuji / Kai Aoki / Koki Yanazawa / Akiko Takenouchi / Makoto Watanabe / Yoshiya Tome / Yoshinori Takeuchi / Yuichi Aita / Naoya Yahagi / Yasuhiro Shishikura / Seiko Ono / Yasuko Yoshida / Yasushi Kawakami / Kazuhiro Takekoshi

Biomedicines, Vol 8, Iss 3, p

2020 Volume 56

Abstract: The aim of this study was to clarify degradation characteristics in each tissue of the knee complex of a medial meniscectomy (MMx)-induced knee osteoarthritis (KOA) animal model using classical methods and an alternative comprehensive evaluation method ... ...

Abstract	The aim of this study was to clarify degradation characteristics in each tissue of the knee complex of a medial meniscectomy (MMx)-induced knee osteoarthritis (KOA) animal model using classical methods and an alternative comprehensive evaluation method called contrast-enhanced X-ray micro-computed tomography (CEX-μCT), which was developed in the study. Surgical MMx was performed in the right knee joints of five male Wistar rats to induce KOA. At four weeks post-surgery, the synovitis was evaluated using quantitative polymerase chain reaction (qPCR). Degradations of the articular cartilage of the tibial plateau were evaluated using classical methods and CEX-μCT. Evaluation of the synovitis demonstrated significantly increased expression levels of inflammation-associated marker genes in MMx-treated knees compared with those in sham-treated knees. Evaluation of the articular cartilage using classical methods showed that MMx fully induced degradation of the cartilage. Evaluation using CEX-μCT showed that local areas of the medial cartilage of the tibial plateau were significantly reduced in MMx-treated knees compared with those in sham-treated knees. On the other hand, total cartilage volumes were significantly increased in MMx-treated knees. On the basis of the findings of this study, the method could be relevant to study new treatments in KOA research.
Keywords	osteoarthritis ; synovitis ; articular cartilage ; microfocus x-ray ct ; 3d analysis ; Biology (General) ; QH301-705.5
Subject code	616
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Influence of Intermittent Cold Stimulations on CREB and Its Targeting Genes in Muscle

Takehito Sugasawa / Yoshiya Tome / Yoshinori Takeuchi / Yasuko Yoshida / Naoya Yahagi / Rahul Sharma / Yuichi Aita / Haruna Ueda / Reina Maruyama / Kaoru Takeuchi / Shohei Morita / Yasushi Kawamai / Kazuhiro Takekoshi

International Journal of Molecular Sciences, Vol 21, Iss 4588, p

Investigations into Molecular Mechanisms of Local Cryotherapy

2020 Volume 4588

Abstract: Local cryotherapy is widely used as a treatment for sports-related skeletal muscle injuries. The molecular mechanisms are unknown. To clarify these mechanisms, we applied one to three 15-min cold stimulations at 4 °C to various cell lines (in vitro), the ...

Abstract	Local cryotherapy is widely used as a treatment for sports-related skeletal muscle injuries. The molecular mechanisms are unknown. To clarify these mechanisms, we applied one to three 15-min cold stimulations at 4 °C to various cell lines (in vitro), the tibialis anterior (TA) muscle (ex vivo), and mouse limbs (in vivo). In the in vitro assay, cyclic AMP (cAMP) response element binding protein 1 (CREB1) was markedly phosphorylated (p-CREB1), and the CREB-binding protein (CBP) was recruited to p-CREB-1 in response to two or three cold stimulations. In a reporter assay with the cAMP-responsive element, the signals significantly increased after two to three cold stimulations at 4 °C. In the ex vivo study, CREB-targeting genes were significantly upregulated following two or three cold stimulations. The in vivo experiment disclosed that cold stimulation of a mouse limb for 9 days significantly increased mitochondrial DNA copy number and upregulated genes involved in mitochondrial biogenesis. The results suggest that local cryotherapy increases CREB transcription and upregulates CREB-targeting genes, in a manner dependent on cold stimulation frequency and duration. This information will inform further investigations into local cryotherapy as a treatment for sports-related skeletal muscle trauma.
Keywords	CREB ; cryotherapy ; gene expression ; icing ; mitochondria ; Pgc-1α ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The detection of trans gene fragments of hEPO in gene doping model mice by Taqman qPCR assay

Kai Aoki / Takehito Sugasawa / Kouki Yanazawa / Koichi Watanabe / Tohru Takemasa / Yoshinori Takeuchi / Yuichi Aita / Naoya Yahagi / Yasuko Yoshida / Tomoaki Kuji / Nanami Sekine / Kaoru Takeuchi / Haruna Ueda / Yasushi Kawakami / Kazuhiro Takekoshi

PeerJ, Vol 8, p e

2020 Volume 8595

Abstract: Background With the rapid progress of genetic engineering and gene therapy methods, the World Anti-Doping Agency has raised concerns regarding gene doping, which is prohibited in sports. However, there is no standard method available for detecting ... ...

Abstract	Background With the rapid progress of genetic engineering and gene therapy methods, the World Anti-Doping Agency has raised concerns regarding gene doping, which is prohibited in sports. However, there is no standard method available for detecting transgenes delivered by injection of naked plasmids. Here, we developed a detection method for detecting transgenes delivered by injection of naked plasmids in a mouse model that mimics gene doping. Methods Whole blood from the tail tip and one piece of stool were used as pre-samples of injection. Next, a plasmid vector containing the human erythropoietin (hEPO) gene was injected into mice through intravenous (IV), intraperitoneal (IP), or local muscular (IM) injection. At 1, 2, 3, 6, 12, 24, and 48 h after injection, approximately 50 µL whole blood was collected from the tail tip. One piece of stool was collected at 6, 12, 24, and 48 h. From each sample, total DNA was extracted and transgene fragments were analyzed by Taqman quantitative PCR (qPCR) and SYBR green qPCR. Results In whole blood DNA samples evaluated by Taqman qPCR, the transgene fragments were detected at all time points in the IP sample and at 1, 2, 3, 6, and 12 h in the IV and IM samples. In the stool-DNA samples, the transgene fragments were detected at 6, 12, 24, and 48 h in the IV and IM samples by Taqman qPCR. In the analysis by SYBR green qPCR, the transgene fragments were detected at some time point in both specimens; however, many non-specific amplicons were detected. Conclusions These results indicate that transgene fragments evaluated after each injection method of naked plasmids were detected in whole-blood and stool DNA samples. These findings may facilitate the development of methods for detecting gene doping.
Keywords	Gene doping ; Erythropoietin ; Plasmid ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2020-02-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rapid manipulation of mitochondrial morphology in a living cell with iCMM

Takafumi Miyamoto / Hideki Uosaki / Yuhei Mizunoe / Song-Iee Han / Satoi Goto / Daisuke Yamanaka / Masato Masuda / Yosuke Yoneyama / Hideki Nakamura / Naoko Hattori / Yoshinori Takeuchi / Hiroshi Ohno / Motohiro Sekiya / Takashi Matsuzaka / Fumihiko Hakuno / Shin-Ichiro Takahashi / Naoya Yahagi / Koichi Ito / Hitoshi Shimano

Cell Reports: Methods, Vol 1, Iss 4, Pp 100052- (2021)

2021

Abstract: Summary: Engineered synthetic biomolecular devices that integrate elaborate information processing and precisely regulate living cell behavior have potential in various applications. Although devices that directly regulate key biomolecules constituting ... ...

Abstract	Summary: Engineered synthetic biomolecular devices that integrate elaborate information processing and precisely regulate living cell behavior have potential in various applications. Although devices that directly regulate key biomolecules constituting inherent biological systems exist, no devices have been developed to control intracellular membrane architecture, contributing to the spatiotemporal functions of these biomolecules. This study developed a synthetic biomolecular device, termed inducible counter mitochondrial morphology (iCMM), to manipulate mitochondrial morphology, an emerging informative property for understanding physiopathological cellular behaviors, on a minute timescale by using a chemically inducible dimerization system. Using iCMM, we determined cellular changes by altering mitochondrial morphology in an unprecedented manner. This approach serves as a platform for developing more sophisticated synthetic biomolecular devices to regulate biological systems by extending manipulation targets from conventional biomolecules to mitochondria. Furthermore, iCMM might serve as a tool for uncovering the biological significance of mitochondrial morphology in various physiopathological cellular processes. Motivation: Mitochondria exhibit a variety of morphologies depending on the physiopathological condition of the cell, but the significance of changes in mitochondrial morphology remains almost unresolved. Although a method to induce mitochondrial morphological changes by altering the expression of proteins involved in mitochondrial dynamics has been established, this method requires several hours or more to induce mitochondrial morphological changes. Accordingly, a method to induce mitochondrial morphological changes at any given point in time on a minute timescale is needed.
Keywords	mitochondria ; mitochondrial morphology ; synthetic biocomputing device ; synthetic biology ; Boolean logic gate ; Biotechnology ; TP248.13-248.65 ; Biochemistry ; QD415-436 ; Science ; Q
Subject code	500
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Measuring streetscape complexity based on the statistics of local contrast and spatial frequency.

André Cavalcante / Ahmed Mansouri / Lemya Kacha / Allan Kardec Barros / Yoshinori Takeuchi / Naoji Matsumoto / Noboru Ohnishi

PLoS ONE, Vol 9, Iss 2, p e

2014 Volume 87097

Abstract: Streetscapes are basic urban elements which play a major role in the livability of a city. The visual complexity of streetscapes is known to influence how people behave in such built spaces. However, how and which characteristics of a visual scene ... ...

Abstract	Streetscapes are basic urban elements which play a major role in the livability of a city. The visual complexity of streetscapes is known to influence how people behave in such built spaces. However, how and which characteristics of a visual scene influence our perception of complexity have yet to be fully understood. This study proposes a method to evaluate the complexity perceived in streetscapes based on the statistics of local contrast and spatial frequency. Here, 74 streetscape images from four cities, including daytime and nighttime scenes, were ranked for complexity by 40 participants. Image processing was then used to locally segment contrast and spatial frequency in the streetscapes. The statistics of these characteristics were extracted and later combined to form a single objective measure. The direct use of statistics revealed structural or morphological patterns in streetscapes related to the perception of complexity. Furthermore, in comparison to conventional measures of visual complexity, the proposed objective measure exhibits a higher correlation with the opinion of the participants. Also, the performance of this method is more robust regarding different time scenarios.
Keywords	Medicine ; R ; Science ; Q
Subject code	910
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Octacosanol and policosanol prevent high-fat diet-induced obesity and metabolic disorders by activating brown adipose tissue and improving liver metabolism

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 12

Abstract: Abstract Brown adipose tissue (BAT) is an attractive therapeutic target for treating obesity and metabolic diseases. Octacosanol is the main component of policosanol, a mixture of very long chain aliphatic alcohols obtained from plants. The current study ...

Abstract	Abstract Brown adipose tissue (BAT) is an attractive therapeutic target for treating obesity and metabolic diseases. Octacosanol is the main component of policosanol, a mixture of very long chain aliphatic alcohols obtained from plants. The current study aimed to investigate the effect of octacosanol and policosanol on high-fat diet (HFD)-induced obesity. Mice were fed on chow, or HFD, with or without octacosanol or policosanol treatment for four weeks. HFD-fed mice showed significantly higher body weight and body fat compared with chow-fed mice. However, mice fed on HFD treated with octacosanol or policosanol (HFDo/p) showed lower body weight gain, body fat gain, insulin resistance and hepatic lipid content. Lower body fat gain after octacosanol or policosanol was associated with increased BAT activity, reduced expression of genes involved in lipogenesis and cholesterol uptake in the liver, and amelioration of white adipose tissue (WAT) inflammation. Moreover, octacosanol and policosanol significantly increased the expression of Ffar4, a gene encoding polyunsaturated fatty acid receptor, which activates BAT thermogenesis. Together, these results suggest that octacosanol and policosanol ameliorate diet-induced obesity and metabolic disorders by increasing BAT activity and improving hepatic lipid metabolism. Thus, these lipids represent promising therapeutic targets for the prevention and treatment of obesity and obesity-related metabolic disorders.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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