Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations

Alicja Pacholewska; Matthias Lienhard; Mirko Brüggemann; Heike Hänel; Lorina Bilalli; Anja Königs; Felix Heß; Kerstin Becker; Karl Köhrer; Jesko Kaiser; Holger Gohlke; Norbert Gattermann; Michael Hallek; Carmen D. Herling; Julian König; Christina Grimm; Ralf Herwig; Kathi Zarnack; Michal R. Schweiger

doi:10.1101/gr.279327.124

Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations

¹Institute for Translational Epigenetics, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany;
²Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, 50931 Cologne, Germany;
³Department of Computational Molecular Biology, Max Planck Institute (MPI) for Molecular Genetics, 14195 Berlin, Germany;
⁴Buchmann Institute for Molecular Life Sciences and Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany;
⁵Institute of Molecular Biology, 55128 Mainz, Germany;
⁶Genomics and Transcriptomics Laboratory, Biological and Medical Research Center, Heinrich Heine University and West German Genome Center, 40225 Düsseldorf, Germany;
⁷Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, 50931 Cologne, Germany;
⁸Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
⁹Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, 52428 Jülich, Germany;
¹⁰Department of Hematology, Oncology, and Clinical Immunology, University Hospital Düsseldorf, 40225 Düsseldorf, Germany;
¹¹Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf, University Hospital Cologne, 50937 Cologne, Germany;
¹²Department for Hematology, Cellular Therapy, Hemostaseology and Infectious Diseases, University Hospital Leipzig, 04103 Leipzig, Germany

↵13 These authors contributed equally as first authors to this work.
↵14 These authors contributed equally as last authors to this work.

Corresponding author: mschweig{at}uni-koeln.de

Abstract

Mutations in splicing factor 3B subunit 1 (SF3B1) frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDSs). These mutations have different effects on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge on SF3B1 mutation effects on RNA splicing and its contribution to patient survival and treatment options. We applied long-read transcriptome sequencing (LRTS) to 44 MDS and CLL patients, as well as two pairs of isogenic cell lines with and without SF3B1 mutations, and found >60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected the usage of introns and 3′ splice sites. Our data highlighted a constrained window at canonical 3′ splice sites in which dynamic splice-site switches occurred in SF3B1-mutated patients. Using transcriptome-wide RNA-binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3′ splice sites and predicted reduced RNA binding at the second binding pocket of SF3B1^K700E. Our work presents the hitherto most-complete LRTS study of the SF3B1 mutation in CLL and MDS and provides a resource to study aberrant splicing in cancer. Moreover, we showed that different disease prognosises result most likely from the different cell types expanded during carcinogenesis rather than different mechanisms of action of the mutated SF3B1. These results have important implications for understanding the role of SF3B1 mutations in hematological malignancies and other related diseases.

Footnotes

[Supplemental material is available for this article.]
Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279327.124.
Freely available online through the Genome Research Open Access option.

Received March 15, 2024.
Accepted August 27, 2024.

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.