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Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia

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Item Type:Article
Title:Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia
Creators Name:James, A.R., Schroeder, M.P., Neumann, M., Bastian, L., Eckert, C., Gökbuget, N., Tanchez, J.O., Schlee, C., Isaakidis, K., Schwartz, S., Burmeister, T., von Stackelberg, A., Rieger, M.A., Göllner, S., Horstman, M., Schrappe, M., Kirschner-Schwabe, R., Brüggemann, M., Müller-Tidow, C., Serve, H., Akalin, A. and Baldus, C.D.
Abstract:BACKGROUND: Long non-coding RNAs (lncRNAs) have emerged as a novel class of RNA due to its diverse mechanism in cancer development and progression. However, the role and expression pattern of lncRNAs in molecular subtypes of B cell acute lymphoblastic leukemia (BCP-ALL) have not yet been investigated. Here, we assess to what extent lncRNA expression and DNA methylation is driving the progression of relapsed BCP-ALL subtypes and we determine if the expression and DNA methylation profile of lncRNAs correlates with established BCP-ALL subtypes. METHODS: We performed RNA sequencing and DNA methylation (Illumina Infinium microarray) of 40 diagnosis and 42 relapse samples from 45 BCP-ALL patients in a German cohort and quantified lncRNA expression. Unsupervised clustering was applied to ascertain and confirm that the lncRNA-based classification of the BCP-ALL molecular subtypes is present in both our cohort and an independent validation cohort of 47 patients. A differential expression and differential methylation analysis was applied to determine the subtype-specific, relapse-specific, and differentially methylated lncRNAs. Potential functions of subtype-specific lncRNAs were determined by using co-expression-based analysis on nearby (cis) and distally (trans) located protein-coding genes. RESULTS: Using an integrative Bioinformatics analysis, we developed a comprehensive catalog of 1235 aberrantly dysregulated BCP-ALL subtype-specific and 942 relapse-specific lncRNAs and the methylation profile of three subtypes of BCP-ALL. The 1235 subtype-specific lncRNA signature represented a similar classification of the molecular subtypes of BCP-ALL in the independent validation cohort. We identified a strong correlation between the DUX4-specific lncRNAs and genes involved in the activation of TGF-β and Hippo signaling pathways. Similarly, Ph-like-specific lncRNAs were correlated with genes involved in the activation of PI3K-AKT, mTOR, and JAK-STAT signaling pathways. Interestingly, the relapse-specific lncRNAs correlated with the activation of metabolic and signaling pathways. Finally, we found 23 promoter methylated lncRNAs epigenetically facilitating their expression levels. CONCLUSION: Here, we describe a set of subtype-specific and relapse-specific lncRNAs from three major BCP-ALL subtypes and define their potential functions and epigenetic regulation. The subtype-specific lncRNAs are reproducible and can effectively stratify BCP-ALL subtypes. Our data uncover the diverse mechanism of action of lncRNAs in BCP-ALL subtypes defining which lncRNAs are involved in the pathogenesis of disease and are relevant for the stratification of BCP-ALL subtypes.
Keywords:BCP-ALL Subtypes, DUX4, Ph-Like, NH-HeH, Subtype-Specific lncRNAs, Key Signaling Pathways, Relapse-Specific lncRNAs, Epigenetically Altered lncRNAs
Source:Journal of Hematology & Oncology
ISSN:1756-8722
Publisher:BioMed Central
Volume:12
Number:1
Page Range:8
Date:14 January 2019
Official Publication:https://doi.org/10.1186/s13045-018-0692-3
PubMed:View item in PubMed

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