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Type: Journal article
Title: Widespread aberrant alternative splicing despite molecular remission in chronic myeloid leukaemia patients
Author: Schmitz, U.
Shah, J.S.
Dhungel, B.P.
Monteuuis, G.
Luu, P.-L.
Petrova, V.
Metierre, C.
Nair, S.S.
Bailey, C.G.
Saunders, V.A.
Turhan, A.G.
White, D.L.
Branford, S.
Clark, S.J.
Hughes, T.P.
Wong, J.J.-L.
Rasko, J.E.J.
Citation: Cancers, 2020; 12(12):3738-1-3738-19
Publisher: MDPI AG
Issue Date: 2020
ISSN: 2072-6694
Statement of
Ulf Schmitz, Jaynish S. Shah, Bijay P. Dhungel, Geoffray Monteuuis, Phuc-Loi Luu, Veronika Petrova, Cynthia Metierre, Shalima S. Nair, Charles G. Bailey, Verity A. Saunders, Ali G. Turhan, Deborah L. White, Susan Branford, Susan J. Clark, Timothy P. Hughes, Justin J.-L. Wong, and John E.J. Rasko
Abstract: Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukaemia (CML) following tyrosine kinase inhibitor (TKI) therapy. Using RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission and compared these to healthy donors. Remarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation. Our results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease.
Keywords: Transcriptomic complexity; alternative splicing; intron retention; DNA methylation; epigenetics; BCR-ABL1; histone modifications; CML; cancer
Rights: © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (
DOI: 10.3390/cancers12123738
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