Integrated Dissection of lncRNA-Perturbated Triplets Reveals Novel Prognostic Signatures Across Cancer Types

Autor: Dianjing Guo, Yunzhen Wei, Yingzhang Huang, Limeng Zhou
Jazyk: angličtina
Rok vydání: 2020
Předmět:
congenital
hereditary
and neonatal diseases and abnormalities
pan-cancer analysis
Lung Neoplasms
Datasets as Topic
macromolecular substances
Computational biology
Adenocarcinoma
Biology
Article
Catalysis
Conserved sequence
Inorganic Chemistry
lcsh:Chemistry
lncRNA
Trinucleotide Repeats
lncRNA-perturbated triplets
Neoplasms
Cancer genome
microRNA
Biomarkers
Tumor
medicine
Humans
Gene Regulatory Networks
RNA
Messenger
Physical and Theoretical Chemistry
Molecular Biology
lcsh:QH301-705.5
Spectroscopy
Messenger RNA
prognostic signatures
Gene Expression Profiling
Organic Chemistry
Cancer
Genomics
General Medicine
Prognosis
medicine.disease
Long non-coding RNA
Computer Science Applications
Gene Expression Regulation
Neoplastic
MicroRNAs
lcsh:Biology (General)
lcsh:QD1-999
A549 Cells
Potential biomarkers
RNA
Long Noncoding
Transcriptome
Zdroj: International Journal of Molecular Sciences, Vol 21, Iss 6087, p 6087 (2020)
International Journal of Molecular Sciences
Volume 21
Issue 17
ISSN: 1661-6596
1422-0067
Popis: Long noncoding RNA (lncRNA)/microRNA(miRNA)/mRNA triplets contribute to cancer biology. However, identifying significative triplets remains a major challenge for cancer research. The dynamic changes among factors of the triplets have been less understood. Here, by integrating target information and expression datasets, we proposed a novel computational framework to identify the triplets termed as &ldquo
lncRNA-perturbated triplets&rdquo
We applied the framework to five cancer datasets in The Cancer Genome Atlas (TCGA) project and identified 109 triplets. We showed that the paired miRNAs and mRNAs were widely perturbated by lncRNAs in different cancer types. LncRNA perturbators and lncRNA-perturbated mRNAs showed significantly higher evolutionary conservation than other lncRNAs and mRNAs. Importantly, the lncRNA-perturbated triplets exhibited high cancer specificity. The pan-cancer perturbator OIP5-AS1 had higher expression level than that of the cancer-specific perturbators. These lncRNA perturbators were significantly enriched in known cancer-related pathways. Furthermore, among the 25 lncRNA in the 109 triplets, lncRNA SNHG7 was identified as a stable potential biomarker in lung adenocarcinoma (LUAD) by combining the TCGA dataset and two independent GEO datasets. Results from cell transfection also indicated that overexpression of lncRNA SNHG7 and TUG1 enhanced the expression of the corresponding mRNA PNMA2 and CDC7 in LUAD. Our study provides a systematic dissection of lncRNA-perturbated triplets and facilitates our understanding of the molecular roles of lncRNAs in cancers.
Databáze: OpenAIRE
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