A High-throughput 3' UTR Reporter Screening Identifies MicroRNA Interactomes of Cancer Genes

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2018 Mar 10

PMID 29522551

Citations 10

Authors

Gert Van Peer

Evelien Mets

Shana Claeys

Ines De Punt

Steve Lefever

Mate Ongenaert

Pieter Rondou

Frank Speleman

Pieter Mestdagh

Jo Vandesompele

Affiliations

Soon will be listed here.

Abstract

Introduction: Despite the established contribution of deregulated microRNA (miRNA) function to carcinogenesis, relatively few miRNA-cancer gene interactions have been validated, making it difficult to appreciate the true complexity of miRNA-cancer gene regulatory networks.

Results: In this effort, we identify miRNA interactomes of 17 well-established cancer genes, involved in various cancer types, through a miRNome-wide 3' UTR reporter screening. Using a novel and performant strategy for high-throughput screening data analysis, we identify 390 interactions, quadrupling the size of the known miRNA interactome for the cancer genes under investigation. Clear enrichments of established and predicted interactions underscore the validity of the interactome data set. Interactomes appear to be primarily driven by canonical binding site interactions. Nonetheless, non-canonical binding sites, such as offset 6mer and seed-mismatched or G:U wobble sites, also have regulatory activity, albeit clearly less pronounced. Furthermore, we observe enhanced regulation in the presence of 3' supplementary pairing for both canonical and non-canonical binding sites.

Conclusions: Altogether, the cancer gene-miRNA interactome data set represents a unique resource that will aid in the unraveling of regulatory miRNA networks and the dynamic regulation of key protein-coding cancer genes. In addition, it uncovers aspects of the functional miRNA binding site's architecture and the relative contributions of different binding site types.

Citing Articles

Direct lysis of 3D cell cultures for RT-qPCR gene expression quantification.

Gysens F, Ostyn L, Goeteyn E, Blondeel E, Nuyttens J, de Wever O Sci Rep. 2023; 13(1):1520.

PMID: 36707637 PMC: 9883454. DOI: 10.1038/s41598-023-28844-1.

Druggable Biomarkers Altered in Clear Cell Renal Cell Carcinoma: Strategy for the Development of Mechanism-Based Combination Therapy.

Rustum Y, Reis R, Rustum T Int J Mol Sci. 2023; 24(2).

PMID: 36674417 PMC: 9864911. DOI: 10.3390/ijms24020902.

Elucidating miRNA Function in Cancer Biology via the Molecular Genetics' Toolbox.

Azlan A, Rajasegaran Y, Kang Zi K, Rosli A, Yik M, Mohd Yusoff N Biomedicines. 2022; 10(4).

PMID: 35453665 PMC: 9029477. DOI: 10.3390/biomedicines10040915.

The MicroRNA Landscape of MYCN-Amplified Neuroblastoma.

Misiak D, Hagemann S, Bell J, Busch B, Lederer M, Bley N Front Oncol. 2021; 11:647737.

PMID: 34026620 PMC: 8138323. DOI: 10.3389/fonc.2021.647737.

Current perspectives on the dysregulated microRNAs in gastric cancer.

Azarbarzin S, Safaralizadeh R, Khojasteh M, Baghbanzadeh A, Baradaran B Mol Biol Rep. 2020; 47(9):7253-7264.

PMID: 32776162 DOI: 10.1007/s11033-020-05720-z.

References

Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W . PubMeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Res. 2007; 36(Database issue):D842-6. PMC: 2238841. DOI: 10.1093/nar/gkm788. View

Helwak A, Kudla G, Dudnakova T, Tollervey D . Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell. 2013; 153(3):654-65. PMC: 3650559. DOI: 10.1016/j.cell.2013.03.043. View

Fabian M, Sonenberg N . The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat Struct Mol Biol. 2012; 19(6):586-93. DOI: 10.1038/nsmb.2296. View

Lewis B, Burge C, Bartel D . Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005; 120(1):15-20. DOI: 10.1016/j.cell.2004.12.035. View

Wu L, Belasco J . Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells. Mol Cell Biol. 2005; 25(21):9198-208. PMC: 1265813. DOI: 10.1128/MCB.25.21.9198-9208.2005. View

Jonas S, Izaurralde E . Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet. 2015; 16(7):421-33. DOI: 10.1038/nrg3965. View

Saetrom P, Heale B, Snove Jr O, Aagaard L, Alluin J, Rossi J . Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res. 2007; 35(7):2333-42. PMC: 1874663. DOI: 10.1093/nar/gkm133. View

Ritchie W, Flamant S, Rasko J . Predicting microRNA targets and functions: traps for the unwary. Nat Methods. 2009; 6(6):397-8. DOI: 10.1038/nmeth0609-397. View

Lefever S, Vandesompele J, Speleman F, Pattyn F . RTPrimerDB: the portal for real-time PCR primers and probes. Nucleic Acids Res. 2008; 37(Database issue):D942-5. PMC: 2686610. DOI: 10.1093/nar/gkn777. View

10.

Lim L, Lau N, Weinstein E, Abdelhakim A, Yekta S, Rhoades M . The microRNAs of Caenorhabditis elegans. Genes Dev. 2003; 17(8):991-1008. PMC: 196042. DOI: 10.1101/gad.1074403. View

11.

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A . Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002; 3(7):RESEARCH0034. PMC: 126239. DOI: 10.1186/gb-2002-3-7-research0034. View

12.

Lu L, Boldin M, Chaudhry A, Lin L, Taganov K, Hanada T . Function of miR-146a in controlling Treg cell-mediated regulation of Th1 responses. Cell. 2010; 142(6):914-29. PMC: 3049116. DOI: 10.1016/j.cell.2010.08.012. View

13.

Bustin S, Benes V, Garson J, Hellemans J, Huggett J, Kubista M . The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009; 55(4):611-22. DOI: 10.1373/clinchem.2008.112797. View

14.

Friedman R, Farh K, Burge C, Bartel D . Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2008; 19(1):92-105. PMC: 2612969. DOI: 10.1101/gr.082701.108. View

15.

Grey F, Tirabassi R, Meyers H, Wu G, McWeeney S, Hook L . A viral microRNA down-regulates multiple cell cycle genes through mRNA 5'UTRs. PLoS Pathog. 2010; 6(6):e1000967. PMC: 2891821. DOI: 10.1371/journal.ppat.1000967. View

16.

Rinck A, Preusse M, Laggerbauer B, Lickert H, Engelhardt S, Theis F . The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance. RNA Biol. 2013; 10(7):1125-35. PMC: 3849160. DOI: 10.4161/rna.24955. View

17.

Grimson A, Farh K, Johnston W, Garrett-Engele P, Lim L, Bartel D . MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007; 27(1):91-105. PMC: 3800283. DOI: 10.1016/j.molcel.2007.06.017. View

18.

Chi S, Zang J, Mele A, Darnell R . Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature. 2009; 460(7254):479-86. PMC: 2733940. DOI: 10.1038/nature08170. View

19.

Mavrakis K, Van der Meulen J, Wolfe A, Liu X, Mets E, Taghon T . A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL). Nat Genet. 2011; 43(7):673-8. PMC: 4121855. DOI: 10.1038/ng.858. View

20.

Loeb G, Khan A, Canner D, Hiatt J, Shendure J, Darnell R . Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol Cell. 2012; 48(5):760-70. PMC: 3562697. DOI: 10.1016/j.molcel.2012.10.002. View