LncRNAs–mRNAs co–expression network underlying childhood B–cell acute lymphoblastic leukaemia: A pilot study

Ornella Affinito, Katia Pane, Giovanni Smaldone, Francesca Maria Orlandella, Peppino Mirabelli, Giuliana Beneduce, Rosanna Parasole, Mimmo Ripaldi, Marco Salvatore, Monica Franzese

Research output: Contribution to journalArticlepeer-review

Abstract

Long non–coding RNAs (lncRNAs) are emerging as key gene regulators in the pathogenesis and development of various cancers including B lymphoblastic leukaemia (B–ALL). In this pilot study, we used RNA–Seq transcriptomic data for identifying novel lncRNA–mRNA cooperative pairs involved in childhood B–ALL pathogenesis. We conceived a bioinformatic pipeline based on unsupervised PCA feature extraction approach and stringent statistical criteria to extract potential childhood B–ALL lncRNA signatures. We then constructed a co–expression network of the aberrantly expressed lncRNAs (30) and protein–coding genes (754). We cross–validated our in–silico findings on an independent dataset and assessed the expression levels of the most differentially expressed lncRNAs and their co–expressed mRNAs through ex vivo experiments. Using the guilt–by–association approach, we predicted lncRNA functions based on their perfectly co–expressed mRNAs (Spearman’s correlation) that resulted closely disease–associated. We shed light on 24 key lncRNAs and their co–expressed mRNAs which may play an important role in B–ALL pathogenesis. Our results may be of clinical utility for diagnostic and/or prognostic purposes in paediatric B–ALL management.

Original languageEnglish
Article number2489
Pages (from-to)1-20
Number of pages20
JournalCancers
Volume12
Issue number9
DOIs
Publication statusPublished - Sep 2020

Keywords

  • Bioinformatics
  • Biomarker
  • Co–expression
  • Diagnostic
  • Feature extraction
  • Leukaemia
  • Long non–coding RNA
  • Network
  • NGS
  • RNA–Sequencing

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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