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Hater N, Iwaniuk KM, Leifeld C, Grüten P, Wiek C, Raba K, Zhang F, Fischer JC, Andreassen PR, Hanenberg H, Trompeter HI. Identification of new RAD51D-regulating microRNAs that also emerge as potent inhibitors of the Fanconi anemia/homologous recombination pathways. Hum Mol Genet 2022; 31:4241-4254. [PMID: 35904444 PMCID: PMC9759333 DOI: 10.1093/hmg/ddac177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Accepted: 07/27/2022] [Indexed: 01/21/2023] Open
Abstract
The Fanconi anemia (FA) and homologous recombination (HR) pathways, which partially overlap and include RAD51 and its paralogs, are key for the repair of different types of DNA damage, such as DNA interstrand crosslinks. First, to broadly assess the impact of microRNA-mediated regulation, we examined microRNA expression profiles in five isogenic fibroblast cell pairs, either deficient in DNA repair due to germline mutations in FANCA, FANCB, FANCC, FANCI or BRIP1/FANCJ or proficient due to correction with retroviral vectors. In each pair, we observed lower abundance of specific microRNAs in the FA-deficient cells. From the list of microRNAs, we experimentally confirmed the effects of miR-141-3p and miR-369-3p targeting RAD51B and miR-15a-5p, miR-494-3p as well as miR-544a targeting RAD51D. However, by western blotting, only RAD51D protein was reduced by a mixture of its regulating microRNAs. Gene ontology analyses and identification of additional FA/HR factors as targets of miR-15a-5p, miR-494-3p and miR-544a strongly suggested the widespread influence of these microRNAs on HR. Interestingly, only miR-494-3p directly reduced RAD51 foci formation, while a mixture of miR-15a-5p, miR-494-3p and miR-544a strongly reduced HR activity in green fluorescent protein (GFP) repair assays. In summary, by successfully employing this novel loss- and gain-of-function strategy, we have identified new microRNAs strongly inhibiting HR in mammalian cells. Understanding and modulating such miRNA regulation of DNA repair genes/pathways might help to overcome the reduced repair capacity of FA patients with biallelic hypomorphic mutations or help to engineer synthetic lethality strategies for patients with mutations in cancer-associated FA/HR genes.
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Affiliation(s)
- Nina Hater
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Katharina M Iwaniuk
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Carina Leifeld
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Pia Grüten
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology & Head/Neck Surgery, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Katharina Raba
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Johannes C Fischer
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Hans-Ingo Trompeter
- To whom correspondence should be addressed. Tel: +49 211 8118751; Fax: +49 211 8119109;
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Ferragut Cardoso AP, Banerjee M, Nail AN, Lykoudi A, States JC. miRNA dysregulation is an emerging modulator of genomic instability. Semin Cancer Biol 2021; 76:120-131. [PMID: 33979676 PMCID: PMC8576067 DOI: 10.1016/j.semcancer.2021.05.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Genomic instability consists of a range of genetic alterations within the genome that contributes to tumor heterogeneity and drug resistance. It is a well-established characteristic of most cancer cells. Genome instability induction results from defects in DNA damage surveillance mechanisms, mitotic checkpoints and DNA repair machinery. Accumulation of genetic alterations ultimately sets cells towards malignant transformation. Recent studies suggest that miRNAs are key players in mediating genome instability. miRNAs are a class of small RNAs expressed in most somatic tissues and are part of the epigenome. Importantly, in many cancers, miRNA expression is dysregulated. Consequently, this review examines the role of miRNA dysregulation as a causal step for induction of genome instability and subsequent carcinogenesis. We focus specifically on mechanistic studies assessing miRNA(s) and specific subtypes of genome instability or known modes of genome instability. In addition, we provide insight on the existing knowledge gaps within the field and possible ways to address them.
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Affiliation(s)
- Ana P Ferragut Cardoso
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Mayukh Banerjee
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Alexandra N Nail
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Angeliki Lykoudi
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - J Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA.
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Ketley RF, Gullerova M. Jack of all trades? The versatility of RNA in DNA double-strand break repair. Essays Biochem 2020; 64:721-735. [PMID: 32618336 PMCID: PMC7592198 DOI: 10.1042/ebc20200008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022]
Abstract
The mechanisms by which RNA acts in the DNA damage response (DDR), specifically in the repair of DNA double-strand breaks (DSBs), are emerging as multifaceted and complex. Different RNA species, including but not limited to; microRNA (miRNA), long non-coding RNA (lncRNA), RNA:DNA hybrid structures, the recently identified damage-induced lncRNA (dilncRNA), damage-responsive transcripts (DARTs), and DNA damage-dependent small RNAs (DDRNAs), have been shown to play integral roles in the DSB response. The diverse properties of these RNAs, such as sequence, structure, and binding partners, enable them to fulfil a variety of functions in different cellular contexts. Additionally, RNA can be modified post-transcriptionally, a process which is regulated in response to cellular stressors such as DNA damage. Many of these mechanisms are not yet understood and the literature contradictory, reflecting the complexity and expansive nature of the roles of RNA in the DDR. However, it is clear that RNA is pivotal in ensuring the maintenance of genome integrity. In this review, we will discuss and summarise recent evidence which highlights the roles of these various RNAs in preserving genomic integrity, with a particular focus on the emerging role of RNA in the DSB repair response.
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Affiliation(s)
- Ruth F Ketley
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, United Kingdom
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