A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

Plaisier, Christopher L.; Pan, Min; Baliga, Nitin S.

doi:10.1101/gr.133991.111

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

Journal Article · Thu Jun 28 00:00:00 EDT 2012 · Genome Research

DOI:https://doi.org/10.1101/gr.133991.111· OSTI ID:1625617

Plaisier, Christopher L. ^[1]; Pan, Min ^[2]; Baliga, Nitin S. ^[2]

Inst. for Systems Biology, Seattle, WA (United States); DOE/OSTI
Inst. for Systems Biology, Seattle, WA (United States)

Genes regulated by the same miRNA can be discovered by virtue of their coexpression at the transcriptional level and the presence of a conserved miRNA-binding site in their 39 UTRs. Using this principle we have integrated the three best performing and complementary algorithms into a framework for inference of regulation by miRNAs (FIRM) from sets of coexpressed genes. We demonstrate the utility of FIRM by inferring a cancer–miRNA regulatory network through the analysis of 2240 gene coexpression signatures from 46 cancers. By analyzing this network for functional enrichment of known hallmarks of cancer we have discovered a subset of 13 miRNAs that regulate oncogenic processes across diverse cancers. We have performed experiments to test predictions from this miRNA-regulatory network to demonstrate that miRNAs of the miR-29 family (miR-29a, miR-29b, and miR-29c) regulate specific genes associated with tissue invasion and metastasis in lung adenocarcinoma. Further, we highlight the specificity of using FIRM inferences to identify miRNA regulated genes by experimentally validating that miR-767-5p, which partially shares the miR-29 seed sequence, regulates only a subset of miR-29 targets. By providing mechanistic linkage between miRNA dysregulation in cancer, their binding sites in the 39UTRs of specific sets of coexpressed genes, and their associations with known hallmarks of cancer, FIRM, and the inferred cancer miRNA-regulatory network will serve as a powerful public resource for discovery of potential cancer biomarkers.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Washington, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: FG02-08ER64685

OSTI ID:: 1625617

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 11 Vol. 22; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 10 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379147	image	January 2021
Additional file 11 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379150	dataset	January 2021
Additional file 12 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379153.v1	dataset	January 2021
Additional file 13 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379156	dataset	January 2021
Additional file 1 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379159.v1	image	January 2021
Additional file 2 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379162	image	January 2021
Additional file 3 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379165	dataset	January 2021
Additional file 5 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379171.v1	image	January 2021
Additional file 6 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379174	image	January 2021
Additional file 7 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379177.v1	image	January 2021
Additional file 8 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379180	dataset	January 2021
Additional file 9 of Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations Chen, Yi; Verbeek, Fons. J.; Wolstencroft, Katherine figshare https://doi.org/10.6084/m9.figshare.14379183	dataset	January 2021
Additional file 1 of Regulation of ERα-dependent breast cancer metastasis by a miR-29a signaling Lü, Jinhui; Zhao, Qian; Guo, Yuefan figshare https://doi.org/10.6084/m9.figshare.22671401.v1	dataset	January 2023
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