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Trsova I, Hrustincova A, Krejcik Z, Kundrat D, Holoubek A, Staflova K, Janstova L, Vanikova S, Szikszai K, Klema J, Rysavy P, Belickova M, Kaisrlikova M, Vesela J, Cermak J, Jonasova A, Dostal J, Fric J, Musil J, Dostalova Merkerova M. Expression of circular RNAs in myelodysplastic neoplasms and their association with mutations in the splicing factor gene SF3B1. Mol Oncol 2023; 17:2565-2583. [PMID: 37408496 DOI: 10.1002/1878-0261.13486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/27/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Mutations in the splicing factor 3b subunit 1 (SF3B1) gene are frequent in myelodysplastic neoplasms (MDS). Because the splicing process is involved in the production of circular RNAs (circRNAs), we investigated the impact of SF3B1 mutations on circRNA processing. Using RNA sequencing, we measured circRNA expression in CD34+ bone marrow MDS cells. We defined circRNAs deregulated in a heterogeneous group of MDS patients and described increased circRNA formation in higher-risk MDS. We showed that the presence of SF3B1 mutations did not affect the global production of circRNAs; however, deregulation of specific circRNAs was observed. Particularly, we demonstrated that strong upregulation of circRNAs processed from the zinc finger E-box binding homeobox 1 (ZEB1) transcription factor; this upregulation was exclusive to SF3B1-mutated patients and was not observed in those with mutations in other splicing factors or other recurrently mutated genes, or with other clinical variables. Furthermore, we focused on the most upregulated ZEB1-circRNA, hsa_circ_0000228, and, by its knockdown, we demonstrated that its expression is related to mitochondrial activity. Using microRNA analyses, we proposed miR-1248 as a direct target of hsa_circ_0000228. To conclude, we demonstrated that mutated SF3B1 leads to deregulation of ZEB1-circRNAs, potentially contributing to the defects in mitochondrial metabolism observed in SF3B1-mutated MDS.
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Affiliation(s)
- Iva Trsova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Andrea Hrustincova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Zdenek Krejcik
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - David Kundrat
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Aleš Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Karolina Staflova
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucie Janstova
- Department of Modern Immunotherapy, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sarka Vanikova
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Katarina Szikszai
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Czech Technical University, Prague, Czech Republic
| | - Petr Rysavy
- Department of Computer Science, Czech Technical University, Prague, Czech Republic
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Monika Kaisrlikova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jitka Vesela
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jaroslav Cermak
- Laboratory of Anemias, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Anna Jonasova
- First Department of Medicine, General University Hospital, Prague, Czech Republic
| | - Jiri Dostal
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Fric
- Department of Modern Immunotherapy, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- International Clinical Research Center of St. Anne's University Hospital (FNUSA-ICRC), Brno, Czech Republic
| | - Jan Musil
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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