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Identification of translational microRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing

ABSTRACT: Identification of translational microRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing

PROVIDER: PRJNA670714 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12879947.fastq.gz	Fastqsanger.gz
	SRR12879948.fastq.gz	Fastqsanger.gz
	SRR12879949.fastq.gz	Fastqsanger.gz
	SRR12879950.fastq.gz	Fastqsanger.gz
	SRR12879951.fastq.gz	Fastqsanger.gz

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Identification of translational ncRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing

Project description:Identification of translational ncRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing

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Identification of translational microRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing

Project description:The exposure to nano-plastics affects mammalian neurotoxic hazard characterization remains to be determined. Our aim was to investigate the neurotoxicity of nano-plastics in rodents. Animals were randomly divided into two groups: a control group and 50 mg/kg body weight PS NPs treatment groups. Before treatment, animals were fasted overnight. PS NPs were suspended into waters, vigorously stirred. The PS NPs via oral gavage once per day and for 6 months. The mice were treated with water in control group. We found that exposure to PS NPs caused cognitive decline. PS NPs exposure influenced the prefrontal cortex cells with more pathological alteration with increasing dosage. High-throughput RNA sequencing was conducted to explore miRNA expression in prefrontal cortex. Twenty-nine differentially expressed miRNAs were detected, including 12 upregulated and 17 downregulated miRNAs. This finding provided a reference for further studies on the development mechanisms of ncRNA during cognitive dysfunction.

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Identification of translational ncRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing

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Identification of translational microRNA biomarker candidates for ketoconazole-induced liver injury using next-generation sequencing

Project description:Identification of translational microRNA biomarker candidates for ketoconazole-induced liver injury using next-generation sequencing

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Identification of translational microRNA biomarker candidates for ketoconazole-induced liver injury using next-generation sequencing

Project description:Drug induced liver injury (DILI) is a leading cause of acute liver failure. Reliable and translational biomarkers are needed for early detection of DILI. microRNAs (miRNAs) have received wide attention as a novel class of potential DILI biomarkers. However, it is unclear how DILI drugs other than acetaminophen may influence miRNA expression or which miRNAs could serve as useful biomarkers in humans. We selected ketoconazole (KCZ), a classic hepatotoxin, to study miRNA biomarkers for DILI as a proof-of-concept for a workflow that integrated in vivo, in vitro, and bioinformatics analyses. We examined hepatic miRNA expression in KCZ-treated rats at multiple doses and durations using miRNA-sequencing and correlated our results with conventional DILI biomarkers such as liver histology. Significant dysregulation of rno-miR-34a-5p, rno-miR-331-3p, rno-miR-15b-3p, and rno-miR-676 was associated with cytoplasmic vacuolization, a phenotype in rat livers with KCZ-induced injury, which preceded the elevation of serum liver transaminases (ALT and AST). Between rats and humans, miR-34a-5p, miR-331-3p, and miR-15b-3p were evolutionarily conserved with identical sequences, whereas miR-676 showed 73% sequence similarity. Using quantitative PCR, we found that the levels of hsa-miR-34a-5p, hsa-miR-331-3p, and hsa-miR-15b-3p were significantly elevated in the culture media of HepaRG cells treated with 100 mM KCZ (a concentration that could induce cytotoxicity). Additionally, we computationally characterized the miRNA candidates for their gene targeting, target functions, and miRNA/target evolutionary conservation. In conclusion, we identified miR-34a-5p, miR-331-3p, and miR-15b-3p as translational biomarker candidates for early detection of KCZ-induced liver injury with a workflow applicable to computational toxicology studies.

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Label-free Proteomics for Discovering Biomarker Candidates for Controlling Krypton Misuse in Castrated Horses (Geldings)

Project description:Recent advances in label-free quantitative proteomics may support its application in identifying and monitoring biomarkers for the purpose of doping control in equine sports. In this study, we developed a workflow of label-free quantitative proteomics to propose plasma protein biomarkers in horses after administration with krypton (Kr), a potential erythropoiesis-stimulating agent. Plasma proteomes were profiled by using nano-liquid chromatography-high resolution mass spectrometry. An in-house mass spectral library consisting of 1,121 proteins was compiled using samples collected from geldings (castrated horses) in the administration trial and geldings in training. A data-independent acquisition (DIA) method was used to quantify an array of plasma proteins across plasma samples from the administration trial. Statistical analyses proposed a profile of 83 biomarker candidates that successfully differentiated Kr-administered samples from control samples, with the ability to detect Kr exposure for up to 13 days (the last sample collected in the administration trial). The model also correctly classified 32 in-training geldings as untreated controls. This is significantly longer than the one hour detection time of plasma Kr using headspace gas chromatography-tandem mass spectrometry. Bioinformatic analyses enriched biomarker candidates relevant to complement activation and iron metabolism. The upregulation of transferrin receptor protein 1 (TFRC), one of the candidates related to iron metabolism, in plasma after Kr administration was validated by selected reaction monitoring (SRM) of corresponding peptides. These results have demonstrated label-free quantitative proteomics as a promising approach to propose plasma protein biomarkers to enhance doping control.

2020-02-20 | PXD017262 | Pride

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