miRNA expression atlas in male rat

Minami, Kenji; Uehara, Takeki; Morikawa, Yuji; Omura, Ko; Kanki, Masayuki; Horinouchi, Akira; Ono, Atsushi; Yamada, Hiroshi; Ohno, Yasuo; Urushidani, Tetsuro

doi:10.1038/sdata.2014.5

Cited by 51 publications

(46 citation statements)

References 32 publications

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“…Indeed, a relatively small and focused 13-panel miRNA profile clustered colon and small intestine separately from skin, Zymbal’s gland, spleen, and lung. Similar groupings were reported following genome-wide miRNA profiling of 55 different organs and tissues in the rat (Minami et al 2014). …”

Section: Discussionsupporting

confidence: 74%

A miRNA signature for an environmental heterocyclic amine defined by a multi-organ carcinogenicity bioassay in the rat

et al. 2017

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Heterocyclic amines (HCAs) produced during high-temperature cooking have been studied extensively in terms of their genotoxic/genetic effects, but recent work has implicated epigenetic mechanisms involving non-coding RNAs. Colon tumors induced in the rat by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) have altered microRNA (miRNA) signatures linked to dysregulated pluripotency factors, such as c-Myc and Krüppel-like factor 4 (KLF4). We tested the hypothesis that dysregulated miRNAs from PhIP-induced colon tumors would provide a “PhIP signature” for use in other target organs obtained from a 1-year carcinogenicity bioassay in the rat. Downstream targets that were corroborated in the rat were then investigated in human cancer datasets. The results confirmed that multiple let-7 family members were downregulated in PhIP-induced skin, colon, lung, small intestine, and Zymbal’s gland tumors, and were associated with c-myc and Hmga2 upregulation. PhIP signature miRNAs with the profile mir-21high/mir-126low/mir-29clow/mir-215low/mir-145low were linked to reduced Klf4 levels in rat tumors, and in human pan-cancer and colorectal cancer. It remains to be determined whether this PhIP signature has predictive value, given that more than 20 different genotoxic HCAs are present in the human diet, plus other agents that likely induce or repress many of the same miRNAs. Future studies should define more precisely the miRNA signatures of other HCAs, and their possible value for human risk assessment.

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Section: Discussionsupporting

confidence: 74%

A miRNA signature for an environmental heterocyclic amine defined by a multi-organ carcinogenicity bioassay in the rat

et al. 2017

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“…Because there is a high degree of miRNA sequence conservation across mammals and especially between rodents (Bak et al, 2008; Minami et al, 2014), we hypothesized that mouse-derived GABA mAGNETs might achieve some interneuron selectivity in the rat brain. We injected GABA mAGNET and control viruses in adult, WT rats (n = 3 per virus) at two cortical sites equivalent to the coordinates in the mice (see Supplemental Experimental Procedures).…”

Section: Resultsmentioning

confidence: 99%

A MicroRNA-Based Gene-Targeting Tool for Virally Labeling Interneurons in the Rodent Cortex

Keaveney

Tseng

et al. 2018

Cell Reports

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In Brief Viral targeting of neuron subtypes is desirable for neuroscience research. Keaveney et al. developed a microRNA-based viral tool for labeling cortical interneurons. They demonstrate its utility via neuron subtype labeling in a murine disease model and in rats and through dual-color optogenetic control of two neuron types. SUMMARY More specific and broadly applicable viral gene-targeting tools for labeling neuron subtypes are needed to advance neuroscience research, especially in rodent transgenic disease models and genetically intractable species. Here, we develop a viral vector that restricts transgene expression to GABAergic interneurons in the rodent neocortex by exploiting endogenous microRNA regulation. Our interneurontargeting, microRNA-guided neuron tag, ‘‘GABA mAGNET,’’ achieves >95% interneuron selective labeling in the mouse cortex, including in a murine model of autism and also some preferential labeling of interneurons in the rat brain. We demonstrate an application of our GABA mAGNET by performing simultaneous, in vivo optogenetic control of two distinct neuron subtypes. This interneuron labeling tool highlights the potential of microRNA-based viral gene targeting to specific neuron subtypes.

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“…MiRNA expression profiles in 55 organs and tissues of normal rats were downloaded from the published data. The expression profiles were obtained using 8 × 15k customized Agilent Rat miRNA microarray containing both miRBase 15.0 and 16.0 probes, and all signal intensities were scaled to the 75th percentile of the median of the dynamic target value for each array using the central tendency normalization method (Minami et al ., , Gene Expression Omnibus GSE52754, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE52754). Profiles comparing two different sampling conditions, with or without perfusion, were provided for a subset of four organs (heart, kidney, liver and lung); the data from the perfused organs were used for the present analysis.…”

Section: Methodsmentioning

confidence: 99%

“…To be used as a plasma biomarker for tissue injury, the ideal miRNA should be abundantly and exclusively produced in the target organ, as large amounts of such a miRNA would then leak into circulating blood from the cytoplasm of the injured cells of the target organ. Recently, a miRNA dataset derived from as many as 55 different organs and tissues in normal rats has been reported (Minami et al, 2014). The dataset encompasses multiple relevant organs and tissues, and therefore is expected to be of great use for the selection of candidate miRNA biomarkers for toxicity of a specific organ.…”

Section: Introductionmentioning

confidence: 99%

Plasma miR‐208 as a useful biomarker for drug‐induced cardiotoxicity in rats

Nishimura

Kondo

Morikawa

et al. 2014

J of Applied Toxicology

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Cardiotoxicity is one of the major safety concerns in drug development. Therefore, detecting and monitoring cardiotoxicity throughout preclinical and clinical studies is important for pharmaceutical companies. The present study was conducted in order to explore a plasma miRNA biomarker for cardiotoxicity in rats. As organ specificity is an important factor for a biomarker, we analyzed the miRNA microarray dataset in 55 organs/tissues in normal male rats. Based on this analysis, 5 miRNAs consisting of miR-208 (heart-specific), miR-1, miR-133a, miR-133b (heart and skeletal muscle-specific) and miR-206 (skeletal muscle-specific) were selected. Next, we evaluated the usefulness of those 5 miRNAs as circulating biomarkers in rats administered with single-dose isoproterenol or doxorubicin. Plasma miR-208 was consistently increased through 24 h after dosing in rats administered with isoproterenol, whereas plasma concentrations of cardiac troponin (cTn) showed transient elevation. In contrast, the plasma levels of miR-1, miR-133a, miR-133a and miR-206 were elevated after treatment with doxorubicin, probably as a result of skeletal muscle toxicity. Additionally, the plasma miR-208 level was elevated even after repeat-dose administration (once daily for 7 days) of isoproterenol under which the pathological condition proceeded to the sub-chronic phase such as fibrosis. Thus, our data suggest that miR-208 is a promising plasma biomarker for cardiotoxicity in rats. Monitoring of plasma miR-208 levels in rats may lead to more accurate evaluation of cardiotoxicity in preclinical studies.

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miRNA expression atlas in male rat

Cited by 51 publications

References 32 publications

A miRNA signature for an environmental heterocyclic amine defined by a multi-organ carcinogenicity bioassay in the rat

A miRNA signature for an environmental heterocyclic amine defined by a multi-organ carcinogenicity bioassay in the rat

A MicroRNA-Based Gene-Targeting Tool for Virally Labeling Interneurons in the Rodent Cortex

Plasma miR‐208 as a useful biomarker for drug‐induced cardiotoxicity in rats

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