Limits...
MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data.

Satoh J, Kino Y, Niida S - Biomark Insights (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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

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.

No MeSH data available.


Related in: MedlinePlus

DIANA miRPath analysis of target genes for miRNAs upregulated in AD blood. The set of 13 miRNAs upregulated in AD, except for hsa-miR-6513–3p whose information is absent in DIANA-microT, was imported into DIANA miRPath. It identified the second-rank significant KEGG pathway potentially downregulated in AD, termed long-term potentiation (hsa04720), relevant to target gene network for imported miRNAs. The genes targeted by more than one miRNA are colored by orange, while the genes targeted by a single miRNA are colored by yellow.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4401249&req=5

f4-bmi-10-2015-021: DIANA miRPath analysis of target genes for miRNAs upregulated in AD blood. The set of 13 miRNAs upregulated in AD, except for hsa-miR-6513–3p whose information is absent in DIANA-microT, was imported into DIANA miRPath. It identified the second-rank significant KEGG pathway potentially downregulated in AD, termed long-term potentiation (hsa04720), relevant to target gene network for imported miRNAs. The genes targeted by more than one miRNA are colored by orange, while the genes targeted by a single miRNA are colored by yellow.

Mentions: By DIANA miRPath, we identified KEGG biological pathways constructed by predicted targets for differentially expressed miRNAs based on the DIANA-microT-CDS algorithm. For the set of 13 miRNAs upregulated in AD, without the inclusion of miR-6513–3p whose information is absent in DIANA-microT, it identified top three most significant pathways potentially downregulated in AD, such as dopaminergic synapse (hsa04728) (P = 2.100E−16), long-term potentiation (hsa04720) (P = 7.706E−15) (Fig. 4), and ubiquitin-mediated proteolysis (hsa04120) (P = 6.233E−12) (Table 2). For the set of 14 miRNAs downregulated in AD, it identified top three most significant pathways potentially upregulated in AD, such as PI3K-Akt signaling pathway (hsa04151) (P = 4.359E−33) (Fig. 5), ECM–receptor interaction (hsa04512) (P = 1.404E−21), and focal adhesion (hsa04510) (P = 1.404E−21).


MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data.

Satoh J, Kino Y, Niida S - Biomark Insights (2015)

DIANA miRPath analysis of target genes for miRNAs upregulated in AD blood. The set of 13 miRNAs upregulated in AD, except for hsa-miR-6513–3p whose information is absent in DIANA-microT, was imported into DIANA miRPath. It identified the second-rank significant KEGG pathway potentially downregulated in AD, termed long-term potentiation (hsa04720), relevant to target gene network for imported miRNAs. The genes targeted by more than one miRNA are colored by orange, while the genes targeted by a single miRNA are colored by yellow.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4401249&req=5

f4-bmi-10-2015-021: DIANA miRPath analysis of target genes for miRNAs upregulated in AD blood. The set of 13 miRNAs upregulated in AD, except for hsa-miR-6513–3p whose information is absent in DIANA-microT, was imported into DIANA miRPath. It identified the second-rank significant KEGG pathway potentially downregulated in AD, termed long-term potentiation (hsa04720), relevant to target gene network for imported miRNAs. The genes targeted by more than one miRNA are colored by orange, while the genes targeted by a single miRNA are colored by yellow.
Mentions: By DIANA miRPath, we identified KEGG biological pathways constructed by predicted targets for differentially expressed miRNAs based on the DIANA-microT-CDS algorithm. For the set of 13 miRNAs upregulated in AD, without the inclusion of miR-6513–3p whose information is absent in DIANA-microT, it identified top three most significant pathways potentially downregulated in AD, such as dopaminergic synapse (hsa04728) (P = 2.100E−16), long-term potentiation (hsa04720) (P = 7.706E−15) (Fig. 4), and ubiquitin-mediated proteolysis (hsa04120) (P = 6.233E−12) (Table 2). For the set of 14 miRNAs downregulated in AD, it identified top three most significant pathways potentially upregulated in AD, such as PI3K-Akt signaling pathway (hsa04151) (P = 4.359E−33) (Fig. 5), ECM–receptor interaction (hsa04512) (P = 1.404E−21), and focal adhesion (hsa04510) (P = 1.404E−21).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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

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.

No MeSH data available.


Related in: MedlinePlus