MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data.
Biomark Insights. 2015; 10:21-31.BI

Abstract

BACKGROUND

Alzheimer's disease (AD) is the most common cause of dementia with no curative therapy currently available. Establishment of sensitive and non-invasive biomarkers that promote an early diagnosis of AD is crucial for the effective administration of disease-modifying drugs. MicroRNAs (miRNAs) mediate posttranscriptional repression of numerous target genes. Aberrant regulation of miRNA expression is implicated in AD pathogenesis, and circulating miRNAs serve as potential biomarkers for AD. However, data analysis of numerous AD-specific miRNAs derived from small RNA-sequencing (RNA-Seq) is most often laborious.

METHODS

To identify circulating miRNA biomarkers for AD, we reanalyzed a publicly available small RNA-Seq dataset, composed of blood samples derived from 48 AD patients and 22 normal control (NC) subjects, by a simple web-based miRNA data analysis pipeline that combines omiRas and DIANA miRPath.

RESULTS

By using omiRas, we identified 27 miRNAs expressed differentially between both groups, including upregulation in AD of miR-26b-3p, miR-28-3p, miR-30c-5p, miR-30d-5p, miR-148b-5p, miR-151a-3p, miR-186-5p, miR-425-5p, miR-550a-5p, miR-1468, miR-4781-3p, miR-5001-3p, and miR-6513-3p and downregulation in AD of let-7a-5p, let-7e-5p, let-7f-5p, let-7g-5p, miR-15a-5p, miR-17-3p, miR-29b-3p, miR-98-5p, miR-144-5p, miR-148a-3p, miR-502-3p, miR-660-5p, miR-1294, and miR-3200-3p. DIANA miRPath indicated that miRNA-regulated pathways potentially downregulated in AD are linked with neuronal synaptic functions, while those upregulated in AD are implicated in cell survival and cellular communication.

CONCLUSIONS

The simple web-based miRNA data analysis pipeline helps us to effortlessly identify candidates for miRNA biomarkers and pathways of AD from the complex small RNA-Seq data.

Links

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Authors+Show Affiliations

Satoh J

Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan.

Kino Y

Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan.

Niida S

BioBank Omics Unit, National Center for Geriatrics and Gerontology (NCGG), bu, Aichi, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

25922570

Citation

Satoh, Jun-Ichi, et al. "MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease From Public Data." Biomarker Insights, vol. 10, 2015, pp. 21-31.

Satoh J, Kino Y, Niida S. MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data. Biomark Insights. 2015;10:21-31.

Satoh, J., Kino, Y., & Niida, S. (2015). MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data. Biomarker Insights, 10, 21-31. https://doi.org/10.4137/BMI.S25132

Satoh J, Kino Y, Niida S. MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease From Public Data. Biomark Insights. 2015;10:21-31. PubMed PMID: 25922570.

* Article titles in AMA citation format should be in sentence-case

TY - JOUR T1 - MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data. AU - Satoh,Jun-Ichi, AU - Kino,Yoshihiro, AU - Niida,Shumpei, Y1 - 2015/04/15/ PY - 2015/02/19/received PY - 2015/03/22/revised PY - 2015/03/23/accepted PY - 2015/4/30/entrez PY - 2015/4/30/pubmed PY - 2015/4/30/medline KW - Alzheimer’s disease KW - DIANA miRPath KW - biomarkers KW - data analysis pipeline KW - microRNA KW - omiRas KW - small RNA-Seq SP - 21 EP - 31 JF - Biomarker insights JO - Biomark Insights VL - 10 N2 - BACKGROUND: Alzheimer's disease (AD) is the most common cause of dementia with no curative therapy currently available. Establishment of sensitive and non-invasive biomarkers that promote an early diagnosis of AD is crucial for the effective administration of disease-modifying drugs. MicroRNAs (miRNAs) mediate posttranscriptional repression of numerous target genes. Aberrant regulation of miRNA expression is implicated in AD pathogenesis, and circulating miRNAs serve as potential biomarkers for AD. However, data analysis of numerous AD-specific miRNAs derived from small RNA-sequencing (RNA-Seq) is most often laborious. METHODS: To identify circulating miRNA biomarkers for AD, we reanalyzed a publicly available small RNA-Seq dataset, composed of blood samples derived from 48 AD patients and 22 normal control (NC) subjects, by a simple web-based miRNA data analysis pipeline that combines omiRas and DIANA miRPath. RESULTS: By using omiRas, we identified 27 miRNAs expressed differentially between both groups, including upregulation in AD of miR-26b-3p, miR-28-3p, miR-30c-5p, miR-30d-5p, miR-148b-5p, miR-151a-3p, miR-186-5p, miR-425-5p, miR-550a-5p, miR-1468, miR-4781-3p, miR-5001-3p, and miR-6513-3p and downregulation in AD of let-7a-5p, let-7e-5p, let-7f-5p, let-7g-5p, miR-15a-5p, miR-17-3p, miR-29b-3p, miR-98-5p, miR-144-5p, miR-148a-3p, miR-502-3p, miR-660-5p, miR-1294, and miR-3200-3p. DIANA miRPath indicated that miRNA-regulated pathways potentially downregulated in AD are linked with neuronal synaptic functions, while those upregulated in AD are implicated in cell survival and cellular communication. CONCLUSIONS: The simple web-based miRNA data analysis pipeline helps us to effortlessly identify candidates for miRNA biomarkers and pathways of AD from the complex small RNA-Seq data. SN - 1177-2719 UR - https://www.unboundmedicine.com/medline/citation/25922570/MicroRNA_Seq_Data_Analysis_Pipeline_to_Identify_Blood_Biomarkers_for_Alzheimer's_Disease_from_Public_Data_ DB - PRIME DP - Unbound Medicine ER -

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MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data.Biomark Insights. 2015; 10:21-31.BI