A comprehensive catalog of LncRNAs expressed in T-cell acute lymphoblastic leukemia

Abstract

Several studies have demonstrated that LncRNAs can play major roles in cancer development. The creation of a catalog of LncRNAs expressed in T cell acute lymphoblastic leukemia (T-ALL) is thus of particular importance. However, this task is challenging as LncRNA expression is highly restricted in time and space manner and thus may greatly differ between samples. We performed a systematic transcript discovery in RNA-Seq data obtained from T-ALL primary cells and cell lines. This led to the identification of 2560 novel LncRNAs. After the integration of these transcripts into a large compendium of LncRNAs (n = 30478) containing both known LncRNAs and those previously described in T-ALLs, we then performed a systematic genomic and epigenetic characterization of these transcript models demonstrating that these novel LncRNAs share properties with known LncRNAs. Finally, we provide evidence that these novel transcripts could be enriched in LncRNAs with potential oncogenic effects and identified a subset of LncRNAs coregulated with T-ALL oncogenes. Overall, our study represents a comprehensive resource of LncRNAs expressed in T-ALL and might provide new cues on the role of lncRNAs in this type of leukemia.

Keywords:

• Large non-coding RNA
• LncRNA
• T-cell acute leukemia
• T-ALL
• oncogenes

Acknowledgments

We thank the Transcriptomics and Genomics Marseille-Luminy (TGML) platform for sequencing of ChIP samples and the Marseille-Luminy cell biology platform for management of cell culture.

Potential conflict of interest

Disclosure forms provided by the authors are available with the full text of this article online at http:\\<10.1080/10428194.2018.1551534>

Additional information

Funding

Work in the TAGC laboratory was supported by recurrent funding from INSERM and Aix-Marseille University and by the Foundation for Cancer Research ARC (ARC PJA 20151203149) and A*MIDEX (ANR-11-IDEX-0001-02), the Cancéropôle PACA, Plan Cancer 2015 (C15076AS) and Ligue Nationale contre le Cancer, of which the TAGC lab is an ‘Equipe Labellisée’. Y.K. and W.S. were supported, by the Franco-Algerian partnership Hubert Curien (PHC) Tassili (15MDU935).