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Hart M, Kern F, Fecher-Trost C, Krammes L, Aparicio E, Engel A, Hirsch P, Wagner V, Keller V, Schmartz GP, Rheinheimer S, Diener C, Fischer U, Mayer J, Meyer MR, Flockerzi V, Keller A, Meese E. Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease. Exp Mol Med 2024; 56:935-945. [PMID: 38556547 PMCID: PMC11059366 DOI: 10.1038/s12276-024-01202-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA-target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson's disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ).
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Affiliation(s)
- Martin Hart
- Human Genetics, Saarland University, 66421, Homburg, Germany.
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Claudia Fecher-Trost
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Lena Krammes
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ernesto Aparicio
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Viktoria Wagner
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Department for Internal Medicine II, Saarland University Hospital, 66421, Homburg, Germany
| | | | | | - Caroline Diener
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ulrike Fischer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Jens Mayer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Veit Flockerzi
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
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