Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations

TY - JOUR

T1 - Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations

AU - Aslan, Derya

AU - Garde, Christian

AU - Nygaard, Mette Katrine

AU - Helbo, Alexandra Søgaard

AU - Dimopoulos, Konstantinos

AU - Hansen, Jakob Werner

AU - Severinsen, Marianne Tang

AU - Treppendahl, Marianne Bach

AU - Sjø, Lene Dissing

AU - Grønbæk, Kirsten

AU - Sommer Kristensen, Lasse

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - Aged

KW - Aged, 80 and over

KW - Alternative Splicing

KW - Cluster Analysis

KW - Cohort Studies

KW - DNA Mutational Analysis

KW - Down-Regulation

KW - Female

KW - Gene Expression Profiling

KW - Genes, Tumor Suppressor

KW - Humans

KW - Male

KW - MicroRNAs

KW - Middle Aged

KW - Mutation

KW - Myelodysplastic Syndromes

KW - Phosphoproteins

KW - RNA Splicing Factors

KW - Reverse Transcriptase Polymerase Chain Reaction

KW - Serine-Arginine Splicing Factors

KW - Spliceosomes

KW - Splicing Factor U2AF

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.18632/oncotarget.7127

DO - 10.18632/oncotarget.7127

M3 - Journal article

C2 - 26848861

SN - 1949-2553

VL - 7

SP - 9951

EP - 9963

JO - Oncotarget

JF - Oncotarget

IS - 9

ER -