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| Status |
Public on Nov 22, 2014 |
| Title |
RNA sequencing of bone marrow CD34+ cells from myelodysplastic syndrome patients with and without SF3B1 mutation and from healthy controls |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The splicing factor SF3B1 is the most commonly mutated gene in the myelodysplastic syndromes (MDS), particularly in patients with refractory anemia with ring sideroblasts (RARS). MDS is a disorder of the hematopoietic stem cell and we thus studied the transcriptome of CD34+ cells from MDS patients with SF3B1 mutations using RNA-sequencing. Genes significantly differentially expressed at the transcript and/or exon level in SF3B1 mutant compared to wildtype cases include genes involved in MDS pathogenesis (ASXL1, CBL), iron homeostasis and mitochondrial metabolism (ALAS2, ABCB7, SLC25A37) and RNA splicing/processing (PRPF8, HNRNPD). Many genes regulated by a DNA damage-induced BRCA1-BCLAF1-SF3B1 protein complex showed differential expression/splicing in SF3B1 mutant cases. Our data indicate that SF3B1 plays a critical role in MDS by affecting the expression and splicing of genes involved in specific cellular processes/pathways, many of which are relevant to the known RARS pathophysiology, suggesting a causal link.
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| Overall design |
RNA-Seq was performed to compare the transcriptome of bone marrow CD34+ cells from eight MDS patients with SF3B1 mutation, four MDS patients with no known splicing mutation and five healthy controls.
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| |
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| Contributor(s) |
Dolatshad H, Pellagatti A |
| Citation(s) |
25428262 |
| |
| Submission date |
Nov 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Hamid Dolatshad |
| E-mail(s) |
hamid.dolatshad@ndcls.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
RDM-NDCLS
|
| Street address |
John Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DU |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA268220 |
| SRA |
SRP050146 |
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