title: Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes.
abstract: The splicing factor SF3B1 is the most frequently mutated gene in myelodysplastic syndromes (MDS), and is strongly associated with the presence of ring sideroblasts (RS). We have performed a systematic analysis of cryptic splicing abnormalities from RNA sequencing data on hematopoietic stem cells (HSCs) of SF3B1-mutant MDS cases with RS. Aberrant splicing events in many downstream target genes were identified and cryptic 3' splice site usage was a frequent event in SF3B1-mutant MDS. The iron transporter ABCB7 is a well-recognized candidate gene showing marked downregulation in MDS with RS. Our analysis unveiled aberrant ABCB7 splicing, due to usage of an alternative 3' splice site in MDS patient samples, giving rise to a premature termination codon in the ABCB7 mRNA. Treatment of cultured SF3B1-mutant MDS erythroblasts and a CRISPR/Cas9-generated SF3B1-mutant cell line with the nonsense-mediated decay (NMD) inhibitor cycloheximide showed that the aberrantly spliced ABCB7 transcript is targeted by NMD. We describe cryptic splicing events in the HSCs of SF3B1-mutant MDS, and our data support a model in which NMD-induced downregulation of the iron exporter ABCB7 mRNA transcript resulting from aberrant splicing caused by mutant SF3B1 underlies the increased mitochondrial iron accumulation found in MDS patients with RS.
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: H
authors.initials: H
authors.lastname: Dolatshad
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: A
authors.initials: A
authors.lastname: Pellagatti
authors.affiliation: Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.
authors.forename: F G
authors.initials: FG
authors.lastname: Liberante
authors.affiliation: Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, UK.
authors.forename: M
authors.initials: M
authors.lastname: Llorian
authors.affiliation: The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
authors.forename: E
authors.initials: E
authors.lastname: Repapi
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: V
authors.initials: V
authors.lastname: Steeples
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: S
authors.initials: S
authors.lastname: Roy
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: L
authors.initials: L
authors.lastname: Scifo
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: R N
authors.initials: RN
authors.lastname: Armstrong
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: J
authors.initials: J
authors.lastname: Shaw
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: B H
authors.initials: BH
authors.lastname: Yip
authors.affiliation: Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK.
authors.forename: S
authors.initials: S
authors.lastname: Killick
authors.affiliation: Dubrava University hospital and Zagreb School of Medicine, University of Zagreb, Zagreb, Croatia.
authors.forename: R
authors.initials: R
authors.lastname: Kušec
authors.affiliation: The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
authors.forename: S
authors.initials: S
authors.lastname: Taylor
authors.affiliation: Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.
authors.forename: K I
authors.initials: KI
authors.lastname: Mills
authors.affiliation: Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.
authors.forename: K I
authors.initials: KI
authors.lastname: Savage
authors.affiliation: Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, UK.
authors.forename: C W J
authors.initials: CW
authors.lastname: Smith
authors.affiliation: Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.|NIHR Biomedical Research Centre, Oxford, UK.
authors.forename: J
authors.initials: J
authors.lastname: Boultwood
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics*; D001483:Base Sequence; D003513:Cycloheximide / Q000494:pharmacology; D006412:Hematopoietic Stem Cells / Q000378:metabolism; D006801:Humans; D007501:Iron / Q000378:metabolism; D008928:Mitochondria / Q000378:metabolism; D009190:Myelodysplastic Syndromes / Q000235:genetics*; D010750:Phosphoproteins / Q000235:genetics*; D012326:RNA Splicing; D000072260:RNA Splicing Factors / Q000235:genetics*; D014407:Tumor Cells, Cultured
chemical_list: C113037:ABCB7 protein, human; D018528:ATP-Binding Cassette Transporters; D010750:Phosphoproteins; D000072260:RNA Splicing Factors; C112491:SF3B1 protein, human; D003513:Cycloheximide; D007501:Iron