title: Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression.
abstract: Cancer is a multifactorial disease driven by a combination of genetic and environmental factors. Many cancer driver mutations have been characterised in protein-coding regions of the genome. However, mutations in noncoding regions associated with cancer have been less investigated. G-quadruplex (G4) nucleic acids are four-stranded secondary structures formed in guanine-rich sequences and prevalent in the regulatory regions. In this study, we used published whole cancer genome sequence data to find mutations in cancer patients that overlap potential RNA G4-forming sequences in 5' UTRs. Using RNAfold, we assessed the effect of these mutations on the thermodynamic stability of predicted RNA G4s in the context of full-length 5' UTRs. Of the 217 identified mutations, we found that 33 are predicted to destabilise and 21 predicted to stabilise potential RNA G4s. We experimentally validated the effect of destabilising mutations in the 5' UTRs of BCL2 and CXCL14 and one stabilising mutation in the 5' UTR of TAOK2. These mutations resulted in an increase or a decrease in translation of these mRNAs, respectively. These findings suggest that mutations that modulate the G4 stability in the noncoding regions could act as cancer driver mutations, which present an opportunity for early cancer diagnosis using individual sequencing information.
authors.affiliation: Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.|St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: Mahdi
authors.initials: M
authors.lastname: Zeraati
authors.affiliation: Children's Medical Research Institute, University of Sydney, Sydney, NSW, 2145, Australia.
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Moye
authors.affiliation: Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: Jason W H
authors.identifier: http://orcid.org/0000-0003-2953-7728
authors.initials: JWH
authors.lastname: Wong
authors.affiliation: Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: Dilmi
authors.initials: D
authors.lastname: Perera
authors.affiliation: Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.|St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Cowley
authors.affiliation: Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.|St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: Daniel U
authors.initials: DU
authors.lastname: Christ
authors.affiliation: Children's Medical Research Institute, University of Sydney, Sydney, NSW, 2145, Australia.
authors.forename: Tracy M
authors.identifier: http://orcid.org/0000-0002-7990-5501
authors.initials: TM
authors.lastname: Bryan
authors.affiliation: Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia. m.dinger@garvan.org.au.|St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia. m.dinger@garvan.org.au.
authors.forename: Marcel E
authors.identifier: http://orcid.org/0000-0003-4423-934X
authors.initials: ME
authors.lastname: Dinger
mesh_terms: D020121:5' Untranslated Regions; D045744:Cell Line, Tumor; D019743:Chemokines, CXC / Q000235:genetics; D054856:G-Quadruplexes; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D019254:Genes, bcl-2; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D017354:Point Mutation; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D020871:RNA Stability; D013816:Thermodynamics; D020506:Untranslated Regions
chemical_list: D020121:5' Untranslated Regions; C118056:CXCL14 protein, human; D019743:Chemokines, CXC; D020506:Untranslated Regions; D012313:RNA