title: Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations.
abstract: Spliceosome mutations are frequently observed in patients with myelodysplastic syndromes (MDS). However, it is largely unknown how these mutations contribute to the disease. MicroRNAs (miRNAs) are small noncoding RNAs, which have been implicated in most human cancers due to their role in post transcriptional gene regulation. The aim of this study was to analyze the impact of spliceosome mutations on the expression of miRNAs in a cohort of 34 MDS patients. In total, the expression of 76 miRNAs, including mirtrons and splice site overlapping miRNAs, was accurately quantified using reverse transcriptase quantitative PCR. The majority of the studied miRNAs have previously been implicated in MDS. Stably expressed miRNA genes for normalization of the data were identified using GeNorm and NormFinder algorithms. High-resolution melting assays covering all mutational hotspots within SF3B1, SRSF2, and U2AF1 (U2AF35) were developed, and all detected mutations were confirmed by Sanger sequencing. Overall, canonical miRNAs were downregulated in spliceosome mutated samples compared to wild-type (P = 0.002), and samples from spliceosome mutated patients clustered together in hierarchical cluster analyses. Among the most downregulated miRNAs were several tumor-suppressor miRNAs, including several let-7 family members, miR-423, and miR-103a. Finally, we observed that the predicted targets of the most downregulated miRNAs were involved in apoptosis, hematopoiesis, and acute myeloid leukemia among other cancer- and metabolic pathways. Our data indicate that spliceosome mutations may play an important role in MDS pathophysiology by affecting the expression of tumor suppressor miRNA genes involved in the development and progression of MDS.
authors: Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
authors: Derya
authors: D
authors: Aslan
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors: Christian
authors: C
authors: Garde
authors: Department of Hematology, Aalborg University Hospital, Aalborg, Denmark.
authors: Mette Katrine
authors: MK
authors: Nygaard
authors: Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
authors: Alexandra Søgaard
authors: AS
authors: Helbo
authors: Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
authors: Konstantinos
authors: K
authors: Dimopoulos
authors: Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
authors: Jakob Werner
authors: JW
authors: Hansen
authors: Department of Hematology, Aalborg University Hospital, Aalborg, Denmark.
authors: Marianne Tang
authors: MT
authors: Severinsen
authors: Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
authors: Marianne Bach
authors: MB
authors: Treppendahl
authors: Department of Pathology, Rigshospitalet, Copenhagen, Denmark.
authors: Lene Dissing
authors: LD
authors: Sjø
authors: Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
authors: Kirsten
authors: K
authors: Grønbæk
authors: Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
authors: Lasse Sommer
authors: LS
authors: Kristensen
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D017398:Alternative Splicing / Q000235:genetics; D016000:Cluster Analysis; D015331:Cohort Studies; D004252:DNA Mutational Analysis / Q000379:methods; D015536:Down-Regulation; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D016147:Genes, Tumor Suppressor; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000145:classification / Q000235:genetics*; D008875:Middle Aged; D009154:Mutation; D009190:Myelodysplastic Syndromes / Q000235:genetics* / Q000473:pathology; D010750:Phosphoproteins / Q000235:genetics; D000072260:RNA Splicing Factors / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D000068103:Serine-Arginine Splicing Factors / Q000235:genetics; D017381:Spliceosomes / Q000235:genetics*; D000072668:Splicing Factor U2AF / Q000235:genetics
chemical_list: D035683:MicroRNAs; D010750:Phosphoproteins; D000072260:RNA Splicing Factors; C112491:SF3B1 protein, human; D000072668:Splicing Factor U2AF; C076753:U2AF1 protein, human; C073288:SRSF2 protein, human; D000068103:Serine-Arginine Splicing Factors
keywords: RT-qPCR; high-resolution melting; microRNAs; myelodysplastic syndrome; spliceosome mutations