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MicroRNA-Target Interaction Regulatory Network in Alzheimer’s Disease

Turk, Aleksander, Kunej, Tanja, Peterlin, Borut·2021·Journal of Personalized Medicine
DOI 10.3390/jpm11121275PMC PMC8708198
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Abstract

Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia; however, early diagnosis of the disease is challenging. Research suggests that biomarkers found in blood, such as microRNAs (miRNA), may be promising for AD diagnostics. Experimental data on miRNA–target interactions (MTI) associated with AD are scattered across databases and publications, thus making the identification of promising miRNA biomarkers for AD difficult. In response to this, a list of experimentally validated AD-associated MTIs was obtained from miRTarBase. Cytoscape was used to create a visual MTI network. STRING software was used for protein–protein interaction analysis and mirPath was used for pathway enrichment analysis. Several targets regulated by multiple miRNAs were identified, including: BACE1, APP, NCSTN, SP1, SIRT1, and PTEN. The miRNA with the highest numbers of interactions in the network were: miR-9, miR-16, miR-34a, miR-106a, miR-107, miR-125b, miR-146, and miR-181c. The analysis revealed seven subnetworks, representing disease modules which have a potential for further biomarker development. The obtained MTI network is not yet complete, and additional studies are needed for the comprehensive understanding of the AD-associated miRNA targetome.

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Figure 1 Network of experimentally validated MTIs associated with AD visualized using the Cytoscape software. Orange-colored nodes represent target genes while blue-colored nodes represent miRNAs. Each edge represents an experimentally validated interaction between a miRNA and its target. (a) The largest subnetwork identified in the data set, consisting of 18 miRNAs and 15 target genes, with a total of 37 MTIs. (b) Smaller subnetworks and miRNA–target pairs identified in the data set.
Figure 1 Network of experimentally validated MTIs associated with AD visualized using the Cytoscape software. Orange-colored nodes represent target genes while blue-colored nodes represent miRNAs. Each edge represents an experimentally validated interaction between a miRNA and its target. (a) The largest subnetwork identified in the data set, consisting of 18 miRNAs and 15 target genes, with a total of 37 MTIs. (b) Smaller subnetworks and miRNA–target pairs identified in the data set.CC BY · PubMed Central
Figure 2 Protein–protein interaction network of 43 AD-associated miRNA targets using STRING software. The colors of connections between nodes represent the type interaction between the two proteins. The most reliable of these connections are “known interactions” from curated databases and experiments. Common gene neighborhoods, fusions, and co-occurrences as well as textmining, co-expression, and protein homology are considered less reliable connections and tend to require independent verification.
Figure 2 Protein–protein interaction network of 43 AD-associated miRNA targets using STRING software. The colors of connections between nodes represent the type interaction between the two proteins. The most reliable of these connections are “known interactions” from curated databases and experiments. Common gene neighborhoods, fusions, and co-occurrences as well as textmining, co-expression, and protein homology are considered less reliable connections and tend to require independent verification.CC BY · PubMed Central

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Metadata

Authors
Turk, A., Kunej, T., & Peterlin, B.
Affiliations
  • Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1230 Domžale, Slovenia
  • Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
ORCID
Kunej, Tanja
Venue
Journal of Personalized Medicine
Publisher
MDPI AG
Published
2021-12-02
Volume
11
Issue
12
Pages
1275
ISSN
2075-4426
DOI
10.3390/jpm11121275
PMC
PMC8708198
Cited by
20
References
10
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
Slovenian Research Agency (P4-0220)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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