Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients.

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Item Type: Article
Status: Published
Official URL: https://doi.org/10.3390/cancers12123738
Journal or Publication Title: Cancers
Volume: 12
Number: 12
Page Range: p. 3738
Date: 2020
Divisions: Gene and Stem Cell Therapy
Epigenetics and RNA Biology
Depositing User: General Admin
Identification Number: 10.3390/cancers12123738
ISSN: 2072-6694
Date Deposited: 29 Mar 2021 05:55
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.

Creators:
Creators
Email
Schmitz, Ulf
UNSPECIFIED
Shah, Jaynish S.
UNSPECIFIED
Dhungel, Bijay P.
UNSPECIFIED
Monteuuis, Geoffray
UNSPECIFIED
Luu, Phuc-Loi
UNSPECIFIED
Petrova, Veronika
UNSPECIFIED
Metierre, Cynthia
UNSPECIFIED
Nair, Shalima S.
UNSPECIFIED
Bailey, Charles G.
UNSPECIFIED
Saunders, Verity A.
UNSPECIFIED
Turhan, Ali G.
UNSPECIFIED
White, Deborah L.
UNSPECIFIED
Branford, Susan
UNSPECIFIED
Clark, Susan J.
UNSPECIFIED
Hughes, Timothy P.
UNSPECIFIED
Wong, Justin J.-L.
UNSPECIFIED
Rasko, John E.J.
UNSPECIFIED
Last Modified: 29 Mar 2021 05:55
URI: https://eprints.centenary.org.au/id/eprint/953

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