ArticlePloS one2014
Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- Correlation of VEGF +405C/G Polymorphism with Gastrointestinal Tract Cancers Risk: An Updated Meta-Analysis.Asian Pacific journal of cancer prevention : APJCP · 2025Pooled it
- Interaction between microRNA and KRAS in Glioblastoma.Current medicinal chemistry · 2026Review
- The role of secondary structures in the functioning of 3' untranslated regions of mRNA: A review of functions of 3' UTRs' secondary structures and hypothetical involvement of secondary structures in cytoplasmic polyadenylation in Drosophila.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Review
- An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder.Molecular psychiatry · 2019Article
- Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes.Scientific reports · 2019Article
- A splice-site variant in the lncRNA geneMolecular vision · 2019Article
- Single nucleotide polymorphisms and cancer susceptibility.Oncotarget · 2017Review
- The effects of structure on pre-mRNA processing and stability.Methods (San Diego, Calif.) · 2017Review
- The roles of RNA processing in translating genotype to phenotype.Nature reviews. Molecular cell biology · 2017Review
- Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.Briefings in bioinformatics · 2016Review
- Preliminary Application of Precision Genomic Medicine Detecting Gene Variation in Patients with Multifocal Osteosarcoma.Orthopaedic surgery · 2016Article
- RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins.Nucleic acids research · 2016Article
- Single-nucleotide polymorphism in microRNA-binding site of SULF1 target gene as a protective factor against the susceptibility to breast cancer: a case-control study.OncoTargets and therapy · 2016Article
- LncRNA-RMRP Acts as an Oncogene in Lung Cancer.PloS one · 2016Article
- miR-211 promotes non-small cell lung cancer proliferation by targeting SRCIN1.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2016Article
- Differential miRNA expressions in peripheral blood mononuclear cells for diagnosis of lung cancer.Laboratory investigation; a journal of technical methods and pathology · 2015Article
- Functional classification of 15 million SNPs detected from diverse chicken populations.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Competing endogenous RNA interplay in cancer: mechanism, methodology, and perspectives.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2015Review
- miR-599 Inhibits Vascular Smooth Muscle Cells Proliferation and Migration by Targeting TGFB2.PloS one · 2015Article
- MicroRNA-mediated regulation of KRAS in cancer.Journal of hematology & oncology · 2014Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways.
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