251
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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252
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Targeting Splicing in the Treatment of Myelodysplastic Syndromes and Other Myeloid Neoplasms. Curr Hematol Malig Rep 2017; 11:408-415. [PMID: 27492253 DOI: 10.1007/s11899-016-0344-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Genome sequencing of primary cells from patients with myelodysplastic syndromes (MDS) led to the identification of recurrent heterozygous mutations in gene encoding components of the spliceosome, the cellular machinery which processes pre-messenger RNA (mRNA) to mature mRNA during gene transcription. Splicing mutations are mutually exclusive with one another and collectively represent the most common mutation class in MDS, occurring in approximately 60 % of patients overall and more than 80 % of those with ring sideroblasts. Evidence from animal models suggests that homozygous splicing mutations are lethal, and that in heterozygously mutated models, any further disruption of splicing triggers apoptosis and cell death. MDS cells with spliceosome mutations are thus uniquely vulnerable to therapies targeting splicing, which may be tolerated by healthy cells. The spliceosome is emerging as a novel therapeutic target in MDS and related myeloid neoplasms, with the first clinical trial of a splicing modulator opening in 2016.
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253
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Sallman DA, Tanaka TN, List A, Bejar R. SOHO State of the Art Update and Next Questions: Biology and Treatment of Myelodysplastic Syndromes. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2017; 17:613-620. [PMID: 29025689 DOI: 10.1016/j.clml.2017.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/19/2017] [Indexed: 11/17/2022]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms characterized by clonal hematopoiesis leading to bone marrow dysplasia and cytopenias. Recently, significant advancements have been made in understanding the pathogenic mechanisms of this disease. In particular, how a wide array of somatic mutations can induce a common clinical phenotype has been investigated. Specifically, activation of innate immune signaling (i.e. myeloid derived suppressor cells) and the NLRP3 inflammasome in hematopoietic stem/progenitor cells play a central role in the biology of MDS, leading to pyroptotic cell death and clonal expansion. Additionally, deciphering the molecular drivers of MDS using next-generation sequencing has rapidly expanded our understanding of MDS with profound implications for prognosis, treatment decisions, and future clinical investigations. Together, unraveling of the role of innate immunity/pyroptosis in the clinical phenotype of MDS patients and comprehensive molecular characterization has identified novel therapeutic strategies that offer significant promise.
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Affiliation(s)
- David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Tiffany N Tanaka
- Moores Cancer Center, University of California, San Diego, La Jolla, CA
| | - Alan List
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL.
| | - Rafael Bejar
- Moores Cancer Center, University of California, San Diego, La Jolla, CA
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254
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Armstrong RN, Steeples V, Singh S, Sanchi A, Boultwood J, Pellagatti A. Splicing factor mutations in the myelodysplastic syndromes: target genes and therapeutic approaches. Adv Biol Regul 2017; 67:13-29. [PMID: 28986033 DOI: 10.1016/j.jbior.2017.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 10/25/2022]
Abstract
Mutations in splicing factor genes (SF3B1, SRSF2, U2AF1 and ZRSR2) are frequently found in patients with myelodysplastic syndromes (MDS), suggesting that aberrant spliceosome function plays a key role in the pathogenesis of MDS. Splicing factor mutations have been shown to result in aberrant splicing of many downstream target genes. Recent functional studies have begun to characterize the splicing dysfunction in MDS, identifying some key aberrantly spliced genes that are implicated in disease pathophysiology. These findings have led to the development of therapeutic strategies using splicing-modulating agents and rapid progress is being made in this field. Splicing inhibitors are promising agents that exploit the preferential sensitivity of splicing factor-mutant cells to these compounds. Here, we review the known target genes associated with splicing factor mutations in MDS, and discuss the potential of splicing-modulating therapies for these disorders.
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Affiliation(s)
- Richard N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Violetta Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Shalini Singh
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Andrea Sanchi
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
| | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
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255
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Song X, Zeng Z, Wei H, Wang Z. Alternative splicing in cancers: From aberrant regulation to new therapeutics. Semin Cell Dev Biol 2017; 75:13-22. [PMID: 28919308 DOI: 10.1016/j.semcdb.2017.09.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022]
Abstract
Alternative splicing is one of the most common mechanisms for gene regulation in humans, and plays a vital role to increase the complexity of functional proteins. In this article, we seek to provide a general review on the relationships between alternative splicing and tumorigenesis. We briefly introduce the basic rules for regulation of alternative splicing, and discuss recent advances on dynamic regulation of alternative splicing in cancers by highlighting the roles of a variety of RNA splicing factors in tumorigenesis. We further discuss several important questions regarding the splicing of long noncoding RNAs and back-splicing of circular RNAs in cancers. Finally, we discuss the current technologies that can be used to manipulate alternative splicing and serve as potential cancer treatment.
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Affiliation(s)
- Xiaowei Song
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China.
| | - Zhenyu Zeng
- Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China
| | - Huanhuan Wei
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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256
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Mutations of RNA splicing factors in hematological malignancies. Cancer Lett 2017; 409:1-8. [PMID: 28888996 DOI: 10.1016/j.canlet.2017.08.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/22/2017] [Accepted: 08/28/2017] [Indexed: 01/01/2023]
Abstract
Systematic large-scale cancer genomic studies have produced numerous significant findings. These studies have not only revealed new cancer-promoting genes, but they also have identified cancer-promoting functions of previously known "housekeeping" genes. These studies have identified numerous mutations in genes which play a fundamental role in nuclear precursor mRNA splicing. Somatic mutations and copy number variation in many of the splicing factors which participate in the formation of multiple spliceosomal complexes appear to play a role in many cancers and in particular in myelodysplastic syndromes (MDS). Mutated proteins seem to interfere with the recognition of the authentic splice sites (SS) leading to utilization of suboptimal alternative splicing sites generating aberrantly spliced mRNA isoforms. This short review is focusing on the function of the splice factors involved in the formation of splicing complexes and potential mechanisms which affect usage of the authentic splice site recognition.
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257
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Nguyen HD, Yadav T, Giri S, Saez B, Graubert TA, Zou L. Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1. Mol Cell 2017; 65:832-847.e4. [PMID: 28257700 DOI: 10.1016/j.molcel.2017.01.029] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here we show that replication protein A (RPA), an ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops. An RPA binding-defective RNaseH1 mutant is not efficiently stimulated by RPA in vitro, fails to accumulate at R loops in cells, and loses the ability to suppress R loops and associated genomic instability. Thus, in addition to sensing DNA damage and replication stress, RPA is a sensor of R loops and a regulator of RNaseH1, extending the versatile role of RPA in suppression of genomic instability.
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Affiliation(s)
- Hai Dang Nguyen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sumanprava Giri
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Borja Saez
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Timothy A Graubert
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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258
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Glasser E, Agrawal AA, Jenkins JL, Kielkopf CL. Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry 2017; 56:4757-4761. [PMID: 28850223 DOI: 10.1021/acs.biochem.7b00551] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acquired point mutations of pre-mRNA splicing factors recur among cancers, leukemias, and related neoplasms. Several studies have established that somatic mutations of a U2AF1 subunit, which normally recognizes 3' splice site junctions, recur among myelodysplastic syndromes. The U2AF2 splicing factor recognizes polypyrimidine signals that precede most 3' splice sites as a heterodimer with U2AF1. In contrast with those of the well-studied U2AF1 subunit, descriptions of cancer-relevant U2AF2 mutations and their structural relationships are lacking. Here, we survey databases of cancer-associated mutations and identify recurring missense mutations in the U2AF2 gene. We determine ultra-high-resolution structures of the U2AF2 RNA recognition motifs (RRM1 and RRM2) at 1.1 Å resolution and map the structural locations of the mutated U2AF2 residues. Comparison with prior, lower-resolution structures of the tandem U2AF2 RRMs in the RNA-bound and apo states reveals clusters of cancer-associated mutations at the U2AF2 RRM-RNA or apo-RRM1-RRM2 interfaces. Although the role of U2AF2 mutations in malignant transformation remains uncertain, our results show that cancer-associated mutations correlate with functionally important surfaces of the U2AF2 splicing factor.
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Affiliation(s)
- Eliezra Glasser
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Anant A Agrawal
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jermaine L Jenkins
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
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259
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Manukjan G, Bösing H, Schmugge M, Strauß G, Schulze H. Impact of genetic variants on haematopoiesis in patients with thrombocytopenia absent radii (TAR) syndrome. Br J Haematol 2017; 179:606-617. [DOI: 10.1111/bjh.14913] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/23/2017] [Indexed: 01/31/2023]
Affiliation(s)
- Georgi Manukjan
- Institute of Experimental Biomedicine, Chair I; University Hospital Würzburg; Würzburg Germany
| | - Hendrik Bösing
- Institute of Experimental Biomedicine, Chair I; University Hospital Würzburg; Würzburg Germany
- Laboratory of Paediatric Molecular Biology; Charité - University Hospital Berlin; Berlin Germany
| | | | - Gabriele Strauß
- Department of Paediatric Haematology and Oncology; Helios-Klinikum Buch; Berlin Germany
| | - Harald Schulze
- Institute of Experimental Biomedicine, Chair I; University Hospital Würzburg; Würzburg Germany
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260
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Cargo C, Bowen D. Individual risk assessment in MDS in the era of genomic medicine. Semin Hematol 2017; 54:133-140. [PMID: 28958286 DOI: 10.1053/j.seminhematol.2017.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 02/06/2023]
Abstract
Assessment of risk for patients with myelodysplastic syndromes has evolved from pure morphological bone marrow assessment to a series of validated prognostic scoring systems whose 'risk' assessment is of death (overall survival) or disease progression (AML transformation). The revised International Prognostic Scoring System (2012) improved the precision for prognosis but did not consider patient-specific factors such as comorbidity and performance status, which have a clear impact on outcome, particularly in lower-risk MDS. The improved understanding of MDS biology predominantly through genomic mutational analysis, flow cytometry and gene expression profiling poses a question regarding incorporation of these parameters into the existing scoring systems. Although some gene mutations have clear prognostic significance (e.g. SF3B1, TP53), there is no definitive and reproducible evidence that this additional knowledge will change management. Although incorporation of some of these novel data into risk assessment may be imminent, the IPSS-R remains the gold standard tool for everyday practice.
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Affiliation(s)
- Catherine Cargo
- Haematological Malignancies Diagnostic Service and Department of Haematology, Leeds Teaching Hospitals, St. James's Institute of Oncology, Beckett Street, Leeds UK
| | - David Bowen
- Department of Haematology, Leeds Teaching Hospitals, St. James's Institute of Oncology, Beckett Street, Leeds UK
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261
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Lee SCW, Abdel-Wahab O. Therapeutic targeting of splicing in cancer. Nat Med 2017; 22:976-86. [PMID: 27603132 DOI: 10.1038/nm.4165] [Citation(s) in RCA: 385] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023]
Abstract
Recent studies have highlighted that splicing patterns are frequently altered in cancer and that mutations in genes encoding spliceosomal proteins, as well as mutations affecting the splicing of key cancer-associated genes, are enriched in cancer. In parallel, there is also accumulating evidence that several molecular subtypes of cancer are highly dependent on splicing function for cell survival. These findings have resulted in a growing interest in targeting splicing catalysis, splicing regulatory proteins, and/or specific key altered splicing events in the treatment of cancer. Here we present strategies that exist and that are in development to target altered dependency on the spliceosome, as well as aberrant splicing, in cancer. These include drugs to target global splicing in cancer subtypes that are preferentially dependent on wild-type splicing for survival, methods to alter post-translational modifications of splicing-regulating proteins, and strategies to modulate pathologic splicing events and protein-RNA interactions in cancer.
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Affiliation(s)
- Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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262
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Xu Y, Li Y, Xu Q, Chen Y, Lv N, Jing Y, Dou L, Bo J, Hou G, Guo J, Wang X, Wang L, Li Y, Chen C, Yu L. Implications of mutational spectrum in myelodysplastic syndromes based on targeted next-generation sequencing. Oncotarget 2017; 8:82475-82490. [PMID: 29137279 PMCID: PMC5669905 DOI: 10.18632/oncotarget.19628] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of myeloid hematological malignancies, with a high risk of progression to acute myeloid leukemia (AML). To explore the role of acquired mutations in MDS, 111 MDS-associated genes were screened using next-generation sequencing (NGS), in 125 patients. One or more mutations were detected in 84% of the patients. Some gene mutations are specific for MDS and were associated with disease subtypes, and the patterns of mutational pathways could be associated with progressive MDS. The patterns, frequencies and functional pathways of gene mutations are different, but somehow related, between MDS and AML. Multivariate analysis suggested that patients with ≥ 2 mutations had poor progression-free survival, while GATA1/GATA2, DNMT3A and KRAS/NRAS mutations were associated with poor overall survival. Based on a novel system combining IPSS-R and molecular markers, these MDS patients were further divided into 3 more accurate prognostic subgroups. A panel of 11 target genes was proposed for genetic profiling of MDS. The study offers new insights into the molecular signatures of MDS and the genetic consistency between MDS and AML. Furthermore, results indicate that MDS could be classified by mutation combinations to guide the administration of individualized therapeutic interventions.
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Affiliation(s)
- Yuanyuan Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Yan Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Qingyu Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Medical school of Nankai University, Tianjin 300071, China
| | - Yuelong Chen
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Na Lv
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yu Jing
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Liping Dou
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian Bo
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guangyuan Hou
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Xiuli Wang
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Lili Wang
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yonghui Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | | | - Li Yu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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263
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Tan Q, Yalamanchili HK, Park J, De Maio A, Lu HC, Wan YW, White JJ, Bondar VV, Sayegh LS, Liu X, Gao Y, Sillitoe RV, Orr HT, Liu Z, Zoghbi HY. Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models. Hum Mol Genet 2017; 25:5083-5093. [PMID: 28007900 DOI: 10.1093/hmg/ddw337] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/29/2016] [Indexed: 12/12/2022] Open
Abstract
Splicing regulation is an important step of post-transcriptional gene regulation. It is a highly dynamic process orchestrated by RNA-binding proteins (RBPs). RBP dysfunction and global splicing dysregulation have been implicated in many human diseases, but the in vivo functions of most RBPs and the splicing outcome upon their loss remain largely unexplored. Here we report that constitutive deletion of Rbm17, which encodes an RBP with a putative role in splicing, causes early embryonic lethality in mice and that its loss in Purkinje neurons leads to rapid degeneration. Transcriptome profiling of Rbm17-deficient and control neurons and subsequent splicing analyses using CrypSplice, a new computational method that we developed, revealed that more than half of RBM17-dependent splicing changes are cryptic. Importantly, RBM17 represses cryptic splicing of genes that likely contribute to motor coordination and cell survival. This finding prompted us to re-analyze published datasets from a recent report on TDP-43, an RBP implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), as it was demonstrated that TDP-43 represses cryptic exon splicing to promote cell survival. We uncovered a large number of TDP-43-dependent splicing defects that were not previously discovered, revealing that TDP-43 extensively regulates cryptic splicing. Moreover, we found a significant overlap in genes that undergo both RBM17- and TDP-43-dependent cryptic splicing repression, many of which are associated with survival. We propose that repression of cryptic splicing by RBPs is critical for neuronal health and survival. CrypSplice is available at www.liuzlab.org/CrypSplice.
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Affiliation(s)
- Qiumin Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Hari Krishna Yalamanchili
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Jeehye Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Antonia De Maio
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology
| | - Hsiang-Chih Lu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology
| | - Ying-Wooi Wan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Joshua J White
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Neuroscience.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vitaliy V Bondar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Layal S Sayegh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Xiuyun Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Yan Gao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Roy V Sillitoe
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology.,Department of Neuroscience.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harry T Orr
- Institute for Translational Neuroscience.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Pediatrics
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology.,Department of Neuroscience.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
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264
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Malcovati L, Gallì A, Travaglino E, Ambaglio I, Rizzo E, Molteni E, Elena C, Ferretti VV, Catricalà S, Bono E, Todisco G, Bianchessi A, Rumi E, Zibellini S, Pietra D, Boveri E, Camaschella C, Toniolo D, Papaemmanuil E, Ogawa S, Cazzola M. Clinical significance of somatic mutation in unexplained blood cytopenia. Blood 2017; 129:3371-3378. [PMID: 28424163 PMCID: PMC5542849 DOI: 10.1182/blood-2017-01-763425] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/14/2017] [Indexed: 11/20/2022] Open
Abstract
Unexplained blood cytopenias, in particular anemia, are often found in older persons. The relationship between these cytopenias and myeloid neoplasms like myelodysplastic syndromes is currently poorly defined. We studied a prospective cohort of patients with unexplained cytopenia with the aim to estimate the predictive value of somatic mutations for identifying subjects with, or at risk of, developing a myeloid neoplasm. The study included a learning cohort of 683 consecutive patients investigated for unexplained cytopenia, and a validation cohort of 190 patients referred for suspected myeloid neoplasm. Using granulocyte DNA, we looked for somatic mutations in 40 genes that are recurrently mutated in myeloid malignancies. Overall, 435/683 patients carried a somatic mutation in at least 1 of these genes. Carrying a somatic mutation with a variant allele frequency ≥0.10, or carrying 2 or more mutations, had a positive predictive value for diagnosis of myeloid neoplasm equal to 0.86 and 0.88, respectively. Spliceosome gene mutations and comutation patterns involving TET2, DNMT3A, or ASXL1 had positive predictive values for myeloid neoplasm ranging from 0.86 to 1.0. Within subjects with inconclusive diagnostic findings, carrying 1 or more somatic mutations was associated with a high probability of developing a myeloid neoplasm during follow-up (hazard ratio = 13.9, P < .001). The predictive values of mutation analysis were confirmed in the independent validation cohort. The findings of this study indicate that mutation analysis on peripheral blood granulocytes may significantly improve the current diagnostic approach to unexplained cytopenia and more generally the diagnostic accuracy of myeloid neoplasms.
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Affiliation(s)
- Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Anna Gallì
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Erica Travaglino
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Ilaria Ambaglio
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | | | | | - Chiara Elena
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | | | - Silvia Catricalà
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Elisa Bono
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Gabriele Todisco
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Antonio Bianchessi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Elisa Rumi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Silvia Zibellini
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Daniela Pietra
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
| | - Emanuela Boveri
- Department of Pathology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Clara Camaschella
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- Vita Salute University, Milan, Italy
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Elli Papaemmanuil
- Center for Molecular Oncology and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo Foundation, Pavia, Italy
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265
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Chatrikhi R, Wang W, Gupta A, Loerch S, Maucuer A, Kielkopf CL. SF1 Phosphorylation Enhances Specific Binding to U2AF 65 and Reduces Binding to 3'-Splice-Site RNA. Biophys J 2017; 111:2570-2586. [PMID: 28002734 DOI: 10.1016/j.bpj.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 12/25/2022] Open
Abstract
Splicing factor 1 (SF1) recognizes 3' splice sites of the major class of introns as a ternary complex with U2AF65 and U2AF35 splicing factors. A conserved SPSP motif in a coiled-coil domain of SF1 is highly phosphorylated in proliferating human cells and is required for cell proliferation. The UHM kinase 1 (UHMK1), also called KIS, double-phosphorylates both serines of this SF1 motif. Here, we use isothermal titration calorimetry to demonstrate that UHMK1 phosphorylation of the SF1 SPSP motif slightly enhances specific binding of phospho-SF1 to its cognate U2AF65 protein partner. Conversely, quantitative fluorescence anisotropy RNA binding assays and isothermal titration calorimetry experiments establish that double-SPSP phosphorylation reduces phospho-SF1 and phospho-SF1-U2AF65 binding affinities for either optimal or suboptimal splice-site RNAs. Domain-substitution and mutagenesis experiments further demonstrate that arginines surrounding the phosphorylated SF1 loop are required for cooperative 3' splice site recognition by the SF1-U2AF65 complex (where cooperativity is defined as a nonadditive increase in RNA binding by the protein complex relative to the individual proteins). In the context of local, intracellular concentrations, the subtle effects of SF1 phosphorylation on its associations with U2AF65 and splice-site RNAs are likely to influence pre-mRNA splicing. However, considering roles for SF1 in pre-mRNA retention and transcriptional repression, as well as in splicing, future comprehensive investigations are needed to fully explain the requirement for SF1 SPSP phosphorylation in proliferating human cells.
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Affiliation(s)
- Rakesh Chatrikhi
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Wenhua Wang
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Ankit Gupta
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Sarah Loerch
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | | | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York.
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266
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Joshi P, Halene S, Abdel-Wahab O. How do messenger RNA splicing alterations drive myelodysplasia? Blood 2017; 129:2465-2470. [PMID: 28348147 PMCID: PMC5418633 DOI: 10.1182/blood-2017-02-692715] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/23/2017] [Indexed: 12/21/2022] Open
Abstract
Mutations in RNA splicing factors are the single most common class of genetic alterations in myelodysplastic syndrome (MDS) patients. Although much has been learned about how these mutations affect splicing at a global- and transcript-specific level, critical questions about the role of these mutations in MDS development and maintenance remain. Here we present the questions to be addressed in order to understand the unique enrichment of these mutations in MDS.
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Affiliation(s)
- Poorval Joshi
- Section of Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT; and
| | - Stephanie Halene
- Section of Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT; and
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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267
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Janusz K, del Rey M, Abáigar M, Collado R, Ivars D, Hernández-Sánchez M, Valiente A, Robledo C, Benito R, Díez-Campelo M, Ramos F, Kohlmann A, Cañizo CD, Hernández-Rivas JM. A two-step approach for sequencing spliceosome-related genes as a complementary diagnostic assay in MDS patients with ringed sideroblasts. Leuk Res 2017; 56:82-87. [DOI: 10.1016/j.leukres.2017.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/22/2017] [Accepted: 01/25/2017] [Indexed: 12/28/2022]
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268
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Jenkins JL, Kielkopf CL. Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures. Trends Genet 2017; 33:336-348. [PMID: 28372848 PMCID: PMC5447463 DOI: 10.1016/j.tig.2017.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 01/08/2023]
Abstract
Somatic mutations of pre-mRNA splicing factors recur among patients with myelodysplastic syndrome (MDS) and related malignancies. Although these MDS-relevant mutations alter the splicing of a subset of transcripts, the mechanisms by which these single amino acid substitutions change gene expression remain controversial. New structures of spliceosome intermediates and associated protein complexes shed light on the molecular interactions mediated by 'hotspots' of the SF3B1 and U2AF1 pre-mRNA splicing factors. The frequently mutated SF3B1 residues contact the pre-mRNA splice site. Based on structural homology with other spliceosome subunits, and recent findings of altered RNA binding by mutant U2AF1 proteins, we suggest that affected U2AF1 residues also contact pre-mRNA. Altered pre-mRNA recognition emerges as a molecular theme among MDS-relevant mutations of pre-mRNA splicing factors.
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Affiliation(s)
- Jermaine L Jenkins
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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269
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Yip BH, Steeples V, Repapi E, Armstrong RN, Llorian M, Roy S, Shaw J, Dolatshad H, Taylor S, Verma A, Bartenstein M, Vyas P, Cross NC, Malcovati L, Cazzola M, Hellström-Lindberg E, Ogawa S, Smith CW, Pellagatti A, Boultwood J. The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes. J Clin Invest 2017; 127:2206-2221. [PMID: 28436936 PMCID: PMC5451246 DOI: 10.1172/jci91363] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022] Open
Abstract
Mutations of the splicing factor–encoding gene U2AF1 are frequent in the myelodysplastic syndromes (MDS), a myeloid malignancy, and other cancers. Patients with MDS suffer from peripheral blood cytopenias, including anemia, and an increasing percentage of bone marrow myeloblasts. We studied the impact of the common U2AF1S34F mutation on cellular function and mRNA splicing in the main cell lineages affected in MDS. We demonstrated that U2AF1S34F expression in human hematopoietic progenitors impairs erythroid differentiation and skews granulomonocytic differentiation toward granulocytes. RNA sequencing of erythroid and granulomonocytic colonies revealed that U2AF1S34F induced a higher number of cassette exon splicing events in granulomonocytic cells than in erythroid cells. U2AF1S34F altered mRNA splicing of many transcripts that were expressed in both cell types in a lineage-specific manner. In hematopoietic progenitors, the introduction of isoform changes identified in the U2AF1S34F target genes H2AFY, encoding an H2A histone variant, and STRAP, encoding serine/threonine kinase receptor–associated protein, recapitulated phenotypes associated with U2AF1S34F expression in erythroid and granulomonocytic cells, suggesting a causal link. Furthermore, we showed that isoform modulation of H2AFY and STRAP rescues the erythroid differentiation defect in U2AF1S34F MDS cells, suggesting that splicing modulators could be used therapeutically. These data have critical implications for understanding MDS phenotypic heterogeneity and support the development of therapies targeting splicing abnormalities.
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Affiliation(s)
- Bon Ham Yip
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Violetta Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Emmanouela Repapi
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Miriam Llorian
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Swagata Roy
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Jacqueline Shaw
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Hamid Dolatshad
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Stephen Taylor
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Amit Verma
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Paresh Vyas
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, and Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford, United Kingdom
| | - Nicholas Cp Cross
- Faculty of Medicine, University of Southampton, Southampton, and National Genetics Reference Laboratory (Wessex), Salisbury, United Kingdom
| | - Luca Malcovati
- Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Mario Cazzola
- Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Christopher Wj Smith
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
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270
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Kozlovski I, Siegfried Z, Amar-Schwartz A, Karni R. The role of RNA alternative splicing in regulating cancer metabolism. Hum Genet 2017; 136:1113-1127. [PMID: 28429085 DOI: 10.1007/s00439-017-1803-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
Abstract
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene. In recent years, a growing body of evidence suggests that unbalanced AS, the formation of certain pro-tumorigenic isoforms and the reduction of anti-tumorigenic isoforms, is implicated in a variety of cancers. It is becoming increasingly clear that cancer-associated AS contributes to increased growth and proliferation, partially due to effects on metabolic reprogramming. Here, we summarize the known roles of AS in regulating cancer metabolism. We present evidence supporting the idea that AS, in many types of cancer, acts as a molecular switch that alters metabolism to drive tumorigenesis. We propose that the elucidation of misregulated AS and its downstream effects on cancer metabolism emphasizes the need for new therapeutic approaches aiming to modulate the splicing machinery to selectively target cancer cells.
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Affiliation(s)
- Itamar Kozlovski
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel.
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271
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Wang JY, Ma J, Lin YN, Wang J, Shen H, Gui FM, Han C, Li QH, Song Z, Wang XJ. [Mutational analysis of RNA splicing machinery genes SF3B1, U2AF1 and SRSF2 in 118 patients with myelodysplastic syndromes and related diseases]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2017; 38:192-197. [PMID: 28395441 PMCID: PMC7348387 DOI: 10.3760/cma.j.issn.0253-2727.2017.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 11/30/2022]
Abstract
Objective: To investigate the incidence, molecular features and clinical significance of RNA splicing machinery genes mutation in myelodysplastic syndromes (MDS) and related diseases. Methods: Mutational analysis of splicing factor 3B subunit 1 (SF3B1) (K700E) , U2 small nuclear RNA auxiliary factor 1 (U2AF1) (S34, Q157P) and serine/arginine-rich splicing factor 2 (SRSF2) (P95) in 118, de novo MDS and related diseases were separately performed by using polymerase chain reaction (PCR) followed by sequence analysis. Results: Of 118 MDS patients, 76 males and 42 females, the median age was 53.5 (13-84) years old. 19.49% (23/118) had SF3B1 (K700E) mutation. As compared with those with wild type SF3B1, patients with SF3B1 K700E were of older[58 (32-78) years vs 51 (13-84) years, z=-1.981, P=0.048], lower HGB level[63 (40-95) g/L vs 77 (34-144) g/L, z=-3.192, P=0.001], higher platelet counts[121 (22-888) ×10(9)/L vs 59 (6-1 561) ×10(9)/L, z=-3.305, P=0.001], lower bone marrow blast cell counts[0.007 (0-0.122) vs 0.017 (0-0.268) , z=-2.885, P=0.004], higher ring sideroblasts percent [0 (0-64%) vs 0 (0-58%) , z=-4.664, P<0.001]. Of 105 MDS patients, 21.9% had U2AF1 (S34, Q157P) mutations. Of 107 MDS patients, 8 patients (7.48%) had SRSF2 (P95) mutations. Patients with SRSF2 mutations were older at diagnosis, the median age was 63 (50-84) years old, including 4 cases RAEB-1. The ratio of mutation was 14.29% (4/28) , and three patients transformed to AML. SF3B1 K700E and SRSF2 P95H mutations coexisted in 1 patient, and SF3B1 K700E and U2AF1 S34Y mutations were found concomitantly in 2 patients. Conclusion: Only SF3B1 gene mutation was closely related to ring sideroblasts, it was the key to pathogenesis of MDS.
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Affiliation(s)
- J Y Wang
- Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences, Tianjin 300020, China
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272
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Exploration of the role of gene mutations in myelodysplastic syndromes through a sequencing design involving a small number of target genes. Sci Rep 2017; 7:43113. [PMID: 28220884 PMCID: PMC5318910 DOI: 10.1038/srep43113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/19/2017] [Indexed: 01/19/2023] Open
Abstract
Novel sequencing designs are necessary to supplement the recognized knowledge of myelodysplastic syndrome (MDS)-related genomic alterations. In this study, we sequenced 28 target genes in 320 Chinese MDS patients but obtained 77.2% of recall factors and 82.8% of genetic abnormalities (including karyotype abnormalities). In addition to known relationships among mutations, some specific chromosomal abnormalities were found to link to specific gene mutations. Trisomy 8 tended to be linked to U2AF1 and ZRSR2 mutations, and 20q- exhibited higher SRSF2/WT1 and U2AF1 mutation frequency. Chromosome 7 involvement accounted for up to 50% of RUNX1 mutations and 37.5% of SETBP1 mutations. Patients carrying a complex karyotype were prone to present TP53 mutations (36.1%). However, individuals with normal karyotypes rarely possessed mutations in the TP53, RUNX1 and U2AF1. Moreover, DNMT3A, TP53, SRSF2, STAG2, ROBO1/2 and WT1 predicted poor survival and high AML transformation. By integrating these predictors into international prognostic scoring system (IPSS) or revised IPSS, we built a set of mutation-based prognostic risk models. These models could layer different degrees of risk in patients more satisfactorily. In summary, this sequencing design was able to detect a number of gene mutations and could be used to stratify patients with varied prognostic risk.
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273
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Kennedy JA, Ebert BL. Clinical Implications of Genetic Mutations in Myelodysplastic Syndrome. J Clin Oncol 2017; 35:968-974. [PMID: 28297619 DOI: 10.1200/jco.2016.71.0806] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Myelodysplastic syndrome (MDS) is clonal disorder characterized by ineffective hematopoiesis and a tendency to evolve into acute myeloid leukemia (AML). Genetic studies have enabled the identification of a set of recurrently mutated genes central to the pathogenesis of MDS, which can be organized into a limited number of cellular processes, including RNA splicing, epigenetic and traditional transcriptional regulation, and signal transduction. The sequential accumulation of mutations drives disease evolution from asymptomatic clonal hematopoiesis to frank MDS, and, ultimately, to secondary AML. This detailed understanding of the molecular landscape of MDS, coupled with the emergence of cost- and time-effective methodologies for DNA sequencing has led to the introduction of genetic studies into the clinical realm. Here, we review recent advances in our genetic understanding of MDS, with a particular focus on the emerging role for mutational data in clinical management as a potential tool to assist in diagnosis, risk stratification, and therapeutic decision-making.
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Affiliation(s)
- James A Kennedy
- James A. Kennedy, University Health Network, Toronto, Ontario, Canada; James A. Kennedy and Benjamin L. Ebert, Brigham and Women's Hospital; and Benjamin L. Ebert, Dana-Farber Cancer Institute, Boston, MA
| | - Benjamin L Ebert
- James A. Kennedy, University Health Network, Toronto, Ontario, Canada; James A. Kennedy and Benjamin L. Ebert, Brigham and Women's Hospital; and Benjamin L. Ebert, Dana-Farber Cancer Institute, Boston, MA
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274
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Zhou J, Chng WJ. Aberrant RNA splicing and mutations in spliceosome complex in acute myeloid leukemia. Stem Cell Investig 2017; 4:6. [PMID: 28217708 DOI: 10.21037/sci.2017.01.06] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/29/2016] [Indexed: 12/19/2022]
Abstract
The spliceosome, the cellular splicing machinery, regulates RNA splicing of messenger RNA precursors (pre-mRNAs) into maturation of protein coding RNAs. Recurrent mutations and copy number changes in genes encoding spliceosomal proteins and splicing regulatory factors have tumor promoting or suppressive functions in hematological malignancies, as well as some other cancers. Leukemia stem cell (LSC) populations, although rare, are essential contributors of treatment failure and relapse. Recent researches have provided the compelling evidence that link the erratic spicing activity to the LSC phenotype in acute myeloid leukemia (AML). In this article, we describe the diverse roles of aberrant splicing in hematological malignancies, particularly in AML and their contributions to the characteristics of LSC. We review these promising strategies to exploit the addiction of aberrant spliceosomal machinery for anti-leukemic therapy with aim to eradicate LSC. However, given the complexity and plasticity of spliceosome and not fully known functions of splicing in cancer, the challenges facing the development of the therapeutic strategies targeting RAN splicing are highlighted and future directions are discussed too.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore 117599, Singapore;; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore 117599, Singapore;; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore;; Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), Singapore 119228, Singapore
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275
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Stanley N, Olson TS, Babushok DV. Recent advances in understanding clonal haematopoiesis in aplastic anaemia. Br J Haematol 2017; 177:509-525. [PMID: 28107566 DOI: 10.1111/bjh.14510] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acquired aplastic anaemia (AA) is an immune-mediated bone marrow failure disorder inextricably linked to clonal haematopoiesis. The majority of AA patients have somatic mutations and/or structural chromosomal abnormalities detected as early as at diagnosis. In contrast to other conditions linked to clonal haematopoiesis, the clonal signature of AA reflects its immune pathophysiology. The most common alterations are clonal expansions of cells lacking glycophosphotidylinositol-anchored proteins, loss of human leucocyte antigen alleles, and mutations in BCOR/BCORL1, ASXL1 and DNMT3A. Here, we present the current knowledge of clonal haematopoiesis in AA as it relates to aging, inherited bone marrow failure, and the grey-zone overlap of AA and myelodysplastic syndrome (MDS). We conclude by discussing the significance of clonal haematopoiesis both for improved diagnosis of AA, as well as for a more precise, personalized approach to prognostication of outcomes and therapy choices.
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Affiliation(s)
- Natasha Stanley
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy S Olson
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Blood and Marrow Transplant Program, Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA, USA
| | - Daria V Babushok
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Hematology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
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276
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Decitabine priming prior to low-dose chemotherapy improves patient outcomes in myelodysplastic syndromes-RAEB: a retrospective analysis vs. chemotherapy alone. J Cancer Res Clin Oncol 2017; 143:873-882. [PMID: 28108816 PMCID: PMC5384967 DOI: 10.1007/s00432-016-2331-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 12/23/2016] [Indexed: 12/27/2022]
Abstract
Purpose The aim of this study was to examine whether decitabine priming prior to low-dose chemotherapeutic regimens could improve outcomes in patients with myelodysplastic syndromes—refractory anemia with excess of blasts (MDS-RAEB). Methods The current retrospective analysis included all MDS-RAEB patients receiving idarubicin/cytarabine (IA) or aclacinomycin/cytarabine (AA), with or without decitabine priming during a period from February 2010 to May 2015. Treatment response and toxicity were compared between patients receiving decitabine priming and those who did not. A panel of 6 MDS-related genes was examined using bone marrow specimens. Results A total of 81 patients were included in the analysis: 40 received decitabine priming prior to chemotherapy (decitabine priming group). The median follow-up was 10.9 months (IQR: 6.2–21.9). The rate of overall response (OR) and complete remission (CR) was significantly higher in the decitabine priming group than in the chemotherapy group (OR: 75.0 vs. 51.2%, p = 0.027; CR: 55.0 vs. 29.3%, p = 0.019). Overall survival (OS) did not differ significantly between the two groups (19.5 vs. 14.7 months, p = 0.082). In a subgroup analysis that included only patients at < 60 years of age, the CR rate in the decitabine priming group was significantly higher than in the chemotherapy group (65.5 vs. 31.0%, p = 0.009). Survival benefit of decitabine priming was apparent in patients at < 60 years of age (22.4 months with 95% CI of 6.7–38.1 vs. 14.7 months with 95% CI of 11.4–18.0 months in the chemotherapy group, p = 0.028), patients with intermediate and unfavorable karyotypes (22.4 months with 95% CI of 15.1–29.7 vs. 11.9 months with 95% CI of 4.0–19.8 months in the chemotherapy group, p = 0.042), and patients with mutated splicing factor genes (35.3 months with 95% CI of 21.4–49.2 vs. 17.8 months with 95% CI of 13.8–21.8 months in the chemotherapy group, p = 0.039). Grade 3–4 hematological and non-hematological toxicities were not significantly different between the two groups. Conclusions Decitabine priming prior to low-dose chemotherapy could improve treatment responses in patients with MDS-RAEB.
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277
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Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome. Nat Commun 2017; 8:14060. [PMID: 28067246 PMCID: PMC5227701 DOI: 10.1038/ncomms14060] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 11/24/2016] [Indexed: 01/05/2023] Open
Abstract
Somatic mutations in spliceosome genes are detectable in ∼50% of patients with myelodysplastic syndromes (MDS). We hypothesize that cells harbouring spliceosome gene mutations have increased sensitivity to pharmacological perturbation of the spliceosome. We focus on mutant U2AF1 and utilize sudemycin compounds that modulate pre-mRNA splicing. We find that haematopoietic cells expressing mutant U2AF1(S34F), including primary patient cells, have an increased sensitivity to in vitro sudemycin treatment relative to controls. In vivo sudemycin treatment of U2AF1(S34F) transgenic mice alters splicing and reverts haematopoietic progenitor cell expansion induced by mutant U2AF1 expression. The splicing effects of sudemycin and U2AF1(S34F) can be cumulative in cells exposed to both perturbations—drug and mutation—compared with cells exposed to either alone. These cumulative effects may result in downstream phenotypic consequences in sudemycin-treated mutant cells. Taken together, these data suggest a potential for treating haematological cancers harbouring U2AF1 mutations with pre-mRNA splicing modulators like sudemycins. Spliceosome mutations occur in approximately 50% of patients with myelodysplastic syndromes. Here, the authors show that tumour cells harbouring the S34F mutation in the U2AF spliceosome gene is sensitive to compounds that further perturb the spliceosome.
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278
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Sperling AS, Gibson CJ, Ebert BL. The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia. Nat Rev Cancer 2017; 17:5-19. [PMID: 27834397 PMCID: PMC5470392 DOI: 10.1038/nrc.2016.112] [Citation(s) in RCA: 401] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Myelodysplastic syndrome (MDS) is a clonal disease that arises from the expansion of mutated haematopoietic stem cells. In a spectrum of myeloid disorders ranging from clonal haematopoiesis of indeterminate potential (CHIP) to secondary acute myeloid leukaemia (sAML), MDS is distinguished by the presence of peripheral blood cytopenias, dysplastic haematopoietic differentiation and the absence of features that define acute leukaemia. More than 50 recurrently mutated genes are involved in the pathogenesis of MDS, including genes that encode proteins involved in pre-mRNA splicing, epigenetic regulation and transcription. In this Review we discuss the molecular processes that lead to CHIP and further clonal evolution to MDS and sAML. We also highlight the ways in which these insights are shaping the clinical management of MDS, including classification schemata, prognostic scoring systems and therapeutic approaches.
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Affiliation(s)
- Adam S Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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279
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Abstract
Cytogenetic analysis has an essential role in diagnosis, classification, and prognosis of myelodysplastic syndromes (MDS). Some cytogenetic abnormalities are sufficiently characteristic of MDS to be considered MDS defining in the appropriate clinical context. MDS with isolated del(5q) is the only molecularly defined MDS subtype. The genes responsible for many aspects of 5q- syndrome, the distinct clinical phenotype associated with this condition, have now been identified. Cytogenetics forms the cornerstone of the most widely adopted prognostic scoring systems in MDS, the international prognostic scoring system (IPSS) and the revised international prognostic scoring system (IPPS-R). Cytogenetic parameters also have utility in chronic myelomonocytic leukemia (CMML) and have been incorporated into specific prognostic scoring systems for this condition. More recently, it has been appreciated that submicroscopic copy number changes and gene mutations play a significant part in MDS pathogenesis. Integration of molecular genetics and cytogenetics holds much promise for improving clinical care and outcomes for patients with MDS.
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Affiliation(s)
- Meaghan Wall
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, 41 Victoria Parade, Fitzroy, Melbourne, VIC, 3065, Australia.
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, Melbourne, Australia.
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280
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Abstract
Cytogenetic analysis of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) is essential for disease diagnosis, classification, prognostic stratification, and treatment guidance. Molecular genetic analysis of CEBPA, NPM1, and FLT3 is already standard of care in patients with AML, and mutations in several additional genes are assuming increasing importance. Mutational analysis of certain genes, such as SF3B1, is also becoming an important tool to distinguish subsets of MDS that have different biologic behaviors. It is still uncertain how to optimally combine karyotype with mutation data in diagnosis and risk-stratification of AML and MDS, particularly in cases with multiple mutations and/or several mutationally distinct subclones.
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281
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Splicing factor gene mutations in hematologic malignancies. Blood 2016; 129:1260-1269. [PMID: 27940478 DOI: 10.1182/blood-2016-10-692400] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/25/2016] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing generates a diversity of messenger RNA (mRNA) transcripts from a single mRNA precursor and contributes to the complexity of our proteome. Splicing is perturbed by a variety of mechanisms in cancer. Recurrent mutations in splicing factors have emerged as a hallmark of several hematologic malignancies. Splicing factor mutations tend to occur in the founding clone of myeloid cancers, and these mutations have recently been identified in blood cells from normal, healthy elderly individuals with clonal hematopoiesis who are at increased risk of subsequently developing a hematopoietic malignancy, suggesting that these mutations contribute to disease initiation. Splicing factor mutations change the pattern of splicing in primary patient and mouse hematopoietic cells and alter hematopoietic differentiation and maturation in animal models. Recent developments in this field are reviewed here, with an emphasis on the clinical consequences of splicing factor mutations, mechanistic insights from animal models, and implications for development of novel therapies targeting the precursor mRNA splicing pathway.
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282
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Obenauer JC, Kavelaars FG, Sanders MA, Hoogenboezem RM, de Vries ACH, van Strien PMH, de Haas V, Locatelli F, Hasle H, Valk PJM, Touw IP, van den Heuvel-Eibrink MM. Lack of splice factor and cohesin complex mutations in pediatric myelodysplastic syndrome. Haematologica 2016; 101:e479-e481. [PMID: 27587384 PMCID: PMC5479614 DOI: 10.3324/haematol.2016.151753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Julia C Obenauer
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Pediatric Hemato-Oncology, Erasmus University Medical Center / Sophia Children's Hospital, Rotterdam, the Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mathijs A Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Remco M Hoogenboezem
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Andrica C H de Vries
- Department of Pediatric Hemato-Oncology, Erasmus University Medical Center / Sophia Children's Hospital, Rotterdam, the Netherlands
| | | | - Valerie de Haas
- Dutch Childhood Oncology Group (DCOG/SKION), The Hague, the Netherlands
| | - Franco Locatelli
- Department of Pediatric Hematology-Oncology, IRCCS Bambino Gesù Children's Hospital, University of Pavia, Rome, Italy
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital Skejby, Aarhus, Denmark
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ivo P Touw
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marry M van den Heuvel-Eibrink
- Department of Pediatric Hemato-Oncology, Erasmus University Medical Center / Sophia Children's Hospital, Rotterdam, the Netherlands
- Princess Màxima Center for Pediatric Oncology (PMC), Utrecht, the Netherlands
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283
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Koeffler HP, Leong G. Preleukemia: one name, many meanings. Leukemia 2016; 31:534-542. [PMID: 27899806 PMCID: PMC5339433 DOI: 10.1038/leu.2016.364] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 12/15/2022]
Abstract
Definition of preleukemia has evolved. It was first used to describe the myelodysplastic syndrome (MDS) with a propensity to progress to acute myeloid leukemia (AML). Individuals with germline mutations of either RUNX1, CEBPA, or GATA2 can also be called as preleukemic because they have a markedly increased incidence of evolution into AML. Also, alkylating chemotherapy or radiation can cause MDS/preleukemia, which nearly always progress to AML. More recently, investigators noted that AML patients who achieved complete morphological remission after chemotherapy often have clonal hematopoiesis predominantly marked by either DNMT3A, TET2 or IDH1/2 mutations, which were also present at diagnosis of AML. This preleukemic clone represents involvement of an early hematopoietic stem cells, which is resistant to standard therapy. The same clonal hematopoietic mutations have been identified in older ‘normal' individuals who have a modest increased risk of developing frank AML. These individuals have occasionally been said, probably inappropriately, to have a preleukemia clone. Our evolving understanding of the term preleukemia has occurred by advancing technology including studies of X chromosome inactivation, cytogenetics and more recently deep nucleotide sequencing.
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Affiliation(s)
- H P Koeffler
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,National University Cancer Institute of Singapore, National University Hospital, Singapore
| | - G Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
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284
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Cheng G, Liu F, Asai T, Lai F, Man N, Xu H, Chen S, Greenblatt S, Hamard PJ, Ando K, Chen X, Wang L, Martinez C, Tadi M, Wang L, Xu M, Yang FC, Shiekhattar R, Nimer SD. Loss of p300 accelerates MDS-associated leukemogenesis. Leukemia 2016; 31:1382-1390. [PMID: 27881875 DOI: 10.1038/leu.2016.347] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/14/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022]
Abstract
The role that changes in DNA methylation and histone modifications have in human malignancies is poorly understood. p300 and CREB-binding protein (CBP), two distinct but highly homologous lysine acetyltransferases, are mutated in several cancers, suggesting their role as tumor suppressors. In the current study, we found that deletion of p300, but not CBP, markedly accelerated the leukemogenesis ofNup98-HoxD13 (NHD13) transgenic mice, an animal model that phenotypically copies human myelodysplastic syndrome (MDS). p300 deletion restored the ability of NHD13 expressing hematopoietic stem and progenitor cells (HSPCs) to self-renew in vitro, and to expand in vivo, with an increase in stem cell symmetric self-renewal divisions and a decrease in apoptosis. Furthermore, loss of p300, but not CBP, promoted cytokine signaling, including enhanced activation of the MAPK and JAK/STAT pathways in the HSPC compartment. Altogether, our data indicate that p300 has a pivotal role in blocking the transformation of MDS to acute myeloid leukemia, a role distinct from that of CBP.
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Affiliation(s)
- G Cheng
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - F Liu
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - T Asai
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - F Lai
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - N Man
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - H Xu
- Department of Medicine, Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York,NY,USA
| | - S Chen
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - S Greenblatt
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - P-J Hamard
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - K Ando
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - X Chen
- Department of Public Health Sciences, Division of Biostatistics, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - L Wang
- Department of Public Health Sciences, Division of Biostatistics, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - C Martinez
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - M Tadi
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - L Wang
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - M Xu
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - F-C Yang
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
| | - R Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - S D Nimer
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA.,Department of Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL,USA
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285
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Fei DL, Motowski H, Chatrikhi R, Prasad S, Yu J, Gao S, Kielkopf CL, Bradley RK, Varmus H. Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival. PLoS Genet 2016; 12:e1006384. [PMID: 27776121 PMCID: PMC5077151 DOI: 10.1371/journal.pgen.1006384] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022] Open
Abstract
We have asked how the common S34F mutation in the splicing factor U2AF1 regulates alternative splicing in lung cancer, and why wild-type U2AF1 is retained in cancers with this mutation. A human lung epithelial cell line was genetically modified so that U2AF1S34F is expressed from one of the two endogenous U2AF1 loci. By altering levels of mutant or wild-type U2AF1 in this cell line and by analyzing published data on human lung adenocarcinomas, we show that S34F-associated changes in alternative splicing are proportional to the ratio of S34F:wild-type gene products and not to absolute levels of either the mutant or wild-type factor. Preferential recognition of specific 3' splice sites in S34F-expressing cells is largely explained by differential in vitro RNA-binding affinities of mutant versus wild-type U2AF1 for those same 3' splice sites. Finally, we show that lung adenocarcinoma cell lines bearing U2AF1 mutations do not require the mutant protein for growth in vitro or in vivo. In contrast, wild-type U2AF1 is required for survival, regardless of whether cells carry the U2AF1S34F allele. Our results provide mechanistic explanations of the magnitude of splicing changes observed in U2AF1-mutant cells and why tumors harboring U2AF1 mutations always retain an expressed copy of the wild-type allele.
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Affiliation(s)
- Dennis Liang Fei
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Hayley Motowski
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Rakesh Chatrikhi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, United States Of America
| | - Sameer Prasad
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Jovian Yu
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Shaojian Gao
- Genetics Branch, National Cancer Institute, Bethesda, United States Of America
| | - Clara L. Kielkopf
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States Of America
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Harold Varmus
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
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286
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The NLRP3 inflammasome functions as a driver of the myelodysplastic syndrome phenotype. Blood 2016; 128:2960-2975. [PMID: 27737891 DOI: 10.1182/blood-2016-07-730556] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/03/2016] [Indexed: 02/07/2023] Open
Abstract
Despite genetic heterogeneity, myelodysplastic syndromes (MDSs) share features of cytological dysplasia and ineffective hematopoiesis. We report that a hallmark of MDSs is activation of the NLRP3 inflammasome, which drives clonal expansion and pyroptotic cell death. Independent of genotype, MDS hematopoietic stem and progenitor cells (HSPCs) overexpress inflammasome proteins and manifest activated NLRP3 complexes that direct activation of caspase-1, generation of interleukin-1β (IL-1β) and IL-18, and pyroptotic cell death. Mechanistically, pyroptosis is triggered by the alarmin S100A9 that is found in excess in MDS HSPCs and bone marrow plasma. Further, like somatic gene mutations, S100A9-induced signaling activates NADPH oxidase (NOX), increasing levels of reactive oxygen species (ROS) that initiate cation influx, cell swelling, and β-catenin activation. Notably, knockdown of NLRP3 or caspase-1, neutralization of S100A9, and pharmacologic inhibition of NLRP3 or NOX suppress pyroptosis, ROS generation, and nuclear β-catenin in MDSs and are sufficient to restore effective hematopoiesis. Thus, alarmins and founder gene mutations in MDSs license a common redox-sensitive inflammasome circuit, which suggests new avenues for therapeutic intervention.
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287
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Spinella JF, Cassart P, Richer C, Saillour V, Ouimet M, Langlois S, St-Onge P, Sontag T, Healy J, Minden MD, Sinnett D. Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations. Oncotarget 2016; 7:65485-65503. [PMID: 27602765 PMCID: PMC5323170 DOI: 10.18632/oncotarget.11796] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with variable prognosis. It represents 15% of diagnosed pediatric ALL cases and has a threefold higher incidence among males. Many recurrent alterations have been identified and help define molecular subgroups of T-ALL, however the full range of events involved in driving transformation remain to be defined. Using an integrative approach combining genomic and transcriptomic data, we molecularly characterized 30 pediatric T-ALLs and identified common recurrent T-ALL targets such as FBXW7, JAK1, JAK3, PHF6, KDM6A and NOTCH1 as well as novel candidate T-ALL driver mutations including the p.R35L missense mutation in splicesome factor U2AF1 found in 3 patients and loss of function mutations in the X-linked tumor suppressor genes MED12 (frameshit mutation p.V167fs, splice site mutation g.chrX:70339329T>C, missense mutation p.R1989H) and USP9X (nonsense mutation p.Q117*). In vitro functional studies further supported the putative role of these novel T-ALL genes in driving transformation. U2AF1 p.R35L was shown to induce aberrant splicing of downstream target genes, and shRNA knockdown of MED12 and USP9X was shown to confer resistance to apoptosis following T-ALL relevant chemotherapy drug treatment in Jurkat leukemia cells. Interestingly, nearly 60% of novel candidate driver events were identified among immature T-ALL cases, highlighting the underlying genomic complexity of pediatric T-ALL, and the need for larger integrative studies to decipher the mechanisms that contribute to its various subtypes and provide opportunities to refine patient stratification and treatment.
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Affiliation(s)
| | - Pauline Cassart
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Chantal Richer
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Virginie Saillour
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Manon Ouimet
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Sylvie Langlois
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Pascal St-Onge
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Thomas Sontag
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Jasmine Healy
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
- Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
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288
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Qiu J, Zhou B, Thol F, Zhou Y, Chen L, Shao C, DeBoever C, Hou J, Li H, Chaturvedi A, Ganser A, Bejar R, Zhang DE, Fu XD, Heuser M. Distinct splicing signatures affect converged pathways in myelodysplastic syndrome patients carrying mutations in different splicing regulators. RNA (NEW YORK, N.Y.) 2016; 22:1535-1549. [PMID: 27492256 PMCID: PMC5029452 DOI: 10.1261/rna.056101.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Myelodysplastic syndromes (MDS) are heterogeneous myeloid disorders with prevalent mutations in several splicing factors, but the splicing programs linked to specific mutations or MDS in general remain to be systematically defined. We applied RASL-seq, a sensitive and cost-effective platform, to interrogate 5502 annotated splicing events in 169 samples from MDS patients or healthy individuals. We found that splicing signatures associated with normal hematopoietic lineages are largely related to cell signaling and differentiation programs, whereas MDS-linked signatures are primarily involved in cell cycle control and DNA damage responses. Despite the shared roles of affected splicing factors in the 3' splice site definition, mutations in U2AF1, SRSF2, and SF3B1 affect divergent splicing programs, and interestingly, the affected genes fall into converging cancer-related pathways. A risk score derived from 11 splicing events appears to be independently associated with an MDS prognosis and AML transformation, suggesting potential clinical relevance of altered splicing patterns in MDS.
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Affiliation(s)
- Jinsong Qiu
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Liang Chen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Christopher DeBoever
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Jiayi Hou
- Clinical and Translational Research Institute, University of California, San Diego, La Jolla, California 92093, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Anuhar Chaturvedi
- Department of Hematology, Hemostasis, Oncology and Stem cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Rafael Bejar
- Division of Hematology-Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Dong-Er Zhang
- Department of Pathology, Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA Institute for Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
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289
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Abstract
Tumor-associated alterations in RNA splicing result either from mutations in splicing-regulatory elements or changes in components of the splicing machinery. This review summarizes our current understanding of the role of splicing-factor alterations in human cancers. We describe splicing-factor alterations detected in human tumors and the resulting changes in splicing, highlighting cell-type-specific similarities and differences. We review the mechanisms of splicing-factor regulation in normal and cancer cells. Finally, we summarize recent efforts to develop novel cancer therapies, based on targeting either the oncogenic splicing events or their upstream splicing regulators.
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Affiliation(s)
- Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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290
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Abstract
Application of next-generation sequencing (NGS) on myeloid neoplasms has expanded our knowledge of genomic alterations in this group of diseases. Genomic alterations in myeloid neoplasms are complex, heterogeneous, and not specific to a disease entity. NGS-based panel testing of myeloid neoplasms can complement existing diagnostic modalities and is gaining acceptance in the clinics and diagnostic laboratories. Prospective, randomized trials to evaluate the prognostic significance of genomic markers in myeloid neoplasms are under way in academic medical centers.
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Affiliation(s)
- Frank C Kuo
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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291
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Ntziachristos P, Abdel-Wahab O, Aifantis I. Emerging concepts of epigenetic dysregulation in hematological malignancies. Nat Immunol 2016; 17:1016-24. [PMID: 27478938 PMCID: PMC5134743 DOI: 10.1038/ni.3517] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
The past decade brought a revolution in understanding of the structure, topology and disease-inducing lesions of RNA and DNA, fueled by unprecedented progress in next-generation sequencing. This technological revolution has also affected understanding of the epigenome and has provided unique opportunities for the analysis of DNA and histone modifications, as well as the first map of the non-protein-coding genome and three-dimensional (3D) chromosomal interactions. Overall, these advances have facilitated studies that combine genetic, transcriptomics and epigenomics data to address a wide range of issues ranging from understanding the role of the epigenome in development to targeting the transcription of noncoding genes in human cancer. Here we describe recent insights into epigenetic dysregulation characteristic of the malignant differentiation of blood stem cells based on studies of alterations that affect epigenetic complexes, enhancers, chromatin, long noncoding RNAs (lncRNAs), RNA splicing, nuclear topology and the 3D conformation of chromatin.
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Affiliation(s)
- Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Iannis Aifantis
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, New York, USA
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292
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Fernandez-Pol S, Ma L, Ohgami RS, Arber DA. Significance of myelodysplastic syndrome-associated somatic variants in the evaluation of patients with pancytopenia and idiopathic cytopenias of undetermined significance. Mod Pathol 2016; 29:996-1003. [PMID: 27255165 DOI: 10.1038/modpathol.2016.100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 12/16/2022]
Abstract
In this study, we set out to evaluate the frequency of mutations in 20 myelodysplastic syndrome-associated genes in 53 individuals with pancytopenia in which bone marrow evaluation failed to meet standard criteria for a diagnosis of myelodysplastic syndrome. These idiopathic pancytopenia cases were associated with no specific cause for their pancytopenia (n=28), aplastic anemia (n=13), pancytopenia attributable to liver disease (n=4), pancytopenia associated with autoimmune disease (n=4), and pancytopenia attributed to drug effect (n=4). We also selected 38 bone marrow aspirates from patients presenting with pancytopenia and meeting criteria for a diagnosis of myelodysplastic syndrome (n=21) or acute myeloid leukemia (n=17) as malignant comparison cases. Targeted sequencing of the 20 genes was performed on all cases. The idiopathic pancytopenia group had a lower average age (46 vs 66 years, P<0.0001) and a lower number of mutations per case that were statistically significant (0.81 vs 1.18, P=0.045). The frequency of cases with at least one mutation was higher for cases with a diagnosable myeloid neoplasm (68 vs 38%, P=0.012). Except for mutations in U2AF1, which was mutated in 5 of the 38 malignant cases (13.2%) and in none of the idiopathic pancytopenia cases (P=0.011), the frequency of mutations in the genes evaluated was not significantly different between idiopathic pancytopenia and malignant cases. Median and mean clinical follow-up for the idiopathic pancytopenia group was available for 444 and 739 days, respectively. Over this time frame, none of the idiopathic pancytopenia patients was diagnosed with a myelodysplastic syndrome or an acute myeloid leukemia. These findings provide further evidence that identification of mutations in several genes associated with myelodysplastic syndromes should not be used alone to support a diagnosis of a myelodysplastic syndrome.
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Affiliation(s)
| | - Lisa Ma
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Robert S Ohgami
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Daniel A Arber
- Department of Pathology, Stanford University, Stanford, CA, USA
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293
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Pellagatti A, Boultwood J. Splicing factor gene mutations in the myelodysplastic syndromes: impact on disease phenotype and therapeutic applications. Adv Biol Regul 2016; 63:59-70. [PMID: 27639445 DOI: 10.1016/j.jbior.2016.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 01/05/2023]
Abstract
Splicing factor gene mutations are the most frequent mutations found in patients with the myeloid malignancy myelodysplastic syndrome (MDS), suggesting that spliceosomal dysfunction plays a major role in disease pathogenesis. The aberrantly spliced target genes and deregulated cellular pathways associated with the commonly mutated splicing factor genes in MDS (SF3B1, SRSF2 and U2AF1) are being identified, illuminating the molecular mechanisms underlying MDS. Emerging data from mouse modeling studies indicate that the presence of splicing factor gene mutations can lead to bone marrow hematopoietic stem/myeloid progenitor cell expansion, impaired hematopoiesis and dysplastic differentiation that are hallmarks of MDS. Importantly, recent evidence suggests that spliceosome inhibitors and splicing modulators may have therapeutic value in the treatment of splicing factor mutant myeloid malignancies.
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Affiliation(s)
- Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford; NIHR Biomedical Research Centre, Oxford, UK.
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford; NIHR Biomedical Research Centre, Oxford, UK.
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294
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Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3' splice sites within RNA secondary structures. Oncogene 2016; 36:1123-1133. [PMID: 27524419 PMCID: PMC5311031 DOI: 10.1038/onc.2016.279] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/14/2016] [Accepted: 07/01/2016] [Indexed: 02/08/2023]
Abstract
Recurrent mutations in core splicing factors have been reported in several clonal disorders, including cancers. Mutations in SF3B1, a component of the U2 splicing complex, are the most common. SF3B1 mutations are associated with aberrant pre-mRNA splicing using cryptic 3’ splice sites (3’SS) but the mechanism of their selection is not clear. To understand how cryptic 3’SS are selected, we performed comprehensive analysis of transcriptome-wide changes to splicing and gene expression associated with SF3B1 mutations in patient samples as well as an experimental model of inducible expression. Hundreds of cryptic 3’SS were detectable across the genome in cells expressing mutant SF3B1. These 3’SS are typically sequestered within RNA secondary structures and poorly accessible compared to their corresponding canonical 3’SS. We hypothesized that these cryptic 3’SS are inaccessible during normal splicing catalysis and that this constraint is overcome in spliceosomes containing mutant SF3B1. This model of secondary structure-dependent selection of cryptic 3’SS was found across multiple clonal processes associated with SF3B1 mutations (myelodysplastic syndrome and chronic lymphocytic leukemia). We validated our model predictions in mini-gene splicing assays. Additionally, we found deregulated expression of proteins with relevant functions in splicing factor-related diseases both in association with aberrant splicing and without corresponding splicing changes. Our results show that SF3B1 mutations are associated with a distinct splicing program shared across multiple clonal processes and define a biochemical mechanism for altered 3’SS choice.
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295
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Hwang SM, Kim SY, Kim JA, Park HS, Park SN, Im K, Kim K, Kim SM, Lee DS. Short telomere length and its correlation with gene mutations in myelodysplastic syndrome. J Hematol Oncol 2016; 9:62. [PMID: 27465399 PMCID: PMC4964031 DOI: 10.1186/s13045-016-0287-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/11/2016] [Indexed: 12/16/2022] Open
Abstract
Background Telomere erosion can lead to genomic instability and cancer progression. It has been suggested that the shortest telomere, not the average telomere length (TL), is critical for cell viability. Some studies have shown shorter TL in myelodysplastic syndrome (MDS) patients but the critically short telomeres, the variability of TL within individual patient has not been evaluated. Thus, we aimed to investigate the TL of MDS patients and assessed the association of TL with recurrent genetic mutations in MDS. Methods We measured the TL of bone marrow nucleated cells for diagnostic samples at a single-cell level by quantitative fluorescence in situ hybridization (Q-FISH) for 58 MDS patients and analyzed the minimum, median, average, standard deviation, average of the 0th to 10th percentile TL within a patient, and the proportion of cells with TL that is shorter than the lowest 10th percentile of the normal control (NC). The correlations of TL to clinical parameters, cytogenetic results, and genetic mutations were assessed. Results MDS patients showed eroded telomeres and narrow distribution compared to the NC (P < 0.001, P = 0.018, respectively). Patients with mutation showed significantly lesser cells with short TL, below the lowest 10th percentile of the NC (P = 0.017), but no differences in TL were found according to mutations/cytogenetic abnormalities except for CSF3R mutation. However, those patients with a high percentage (≥80 %) of cells with short TL showed poorer overall survival (P = 0.021), and this was an independent prognostic factor, along with TP53, U2AF1 mutation, and high BM blast count (P = 0.044, 0.001, 0.004, 0.012, respectively). Conclusions The shortest TL, which determines the fate of the cell, was significantly shorter, and higher burden of cells with short TL were found in MDS, which correlated with poor survival, suggesting the need to measure TL in single cells by Q-FISH. Electronic supplementary material The online version of this article (doi:10.1186/s13045-016-0287-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Jung Ah Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee-Sue Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Si Nae Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyongok Im
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kwantae Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Min Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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296
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Knockdown of USP39 induces cell cycle arrest and apoptosis in melanoma. Tumour Biol 2016; 37:13167-13176. [PMID: 27456357 DOI: 10.1007/s13277-016-5212-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/13/2016] [Indexed: 01/13/2023] Open
Abstract
The spliceosome machinery composed of multimeric protein complexes guides precursor messenger RNAs (mRNAs) (pre-mRNAs) splicing in eukaryotic cells. Spliceosome components have been shown to be downregulated in cancer and could be a promising molecular target for anticancer therapy. The ubiquitin-specific protease 39 (USP39) is essential for pre-mRNA splicing, and upregulated USP39 expression is noted in a variety of cancers. However, the role of USP39 in the development and progression of melanoma remains unclear. In the present study, USP39 expression was found to be increased in melanoma tissues compared with that in nevus tissues. USP39 silencing via lentivirus-mediated short hairpin RNA (shRNA) significantly suppressed melanoma cell proliferation, induced G0/G1 cell cycle phase arrest, and increased apoptosis in vitro. Moreover, USP39 knockdown suppressed melanoma tumor growth in a xenograft model. In addition, USP39 silencing was associated with the increased expressions of p21, p27, and Bax. Furthermore, the inhibition of USP39 expression decreased the phosphorylation of extracellular signal-regulated kinase (ERK)1/2, indicating that ERK signaling pathways might be involved in the regulation of melanoma cell proliferation by USP39. Our findings suggest that USP39 may play crucial roles in the development and pathogenesis of melanoma, and it may serve as a potential therapeutic target for melanoma.
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297
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Eisfeld AK, Kohlschmidt J, Mrózek K, Blachly JS, Nicolet D, Kroll K, Orwick S, Carroll AJ, Stone RM, de la Chapelle A, Byrd JC, Bloomfield CD. Adult acute myeloid leukemia with trisomy 11 as the sole abnormality is characterized by the presence of five distinct gene mutations: MLL-PTD, DNMT3A, U2AF1, FLT3-ITD and IDH2. Leukemia 2016; 30:2254-2258. [PMID: 27435003 DOI: 10.1038/leu.2016.196] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- A-K Eisfeld
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - J Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - K Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - J S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - D Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - K Kroll
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - S Orwick
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - A J Carroll
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - R M Stone
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - A de la Chapelle
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - J C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - C D Bloomfield
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
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298
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The genomic landscape of myeloid neoplasms with myelodysplasia and its clinical implications. Curr Opin Oncol 2016; 27:551-9. [PMID: 26352542 DOI: 10.1097/cco.0000000000000229] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW This article will review the most recent advances in the understanding of the genetic basis of myeloid neoplasms with myelodysplasia and will discuss its clinical implications. RECENT FINDINGS Recurrent somatic mutations have been identified in about 90% of patients with myeloid neoplasms with myelodysplasia, involving genes of RNA splicing, DNA methylation, histone modification, transcription regulation, DNA repair, signal transduction, and cohesin complex. Somatic mutations are acquired in a linear manner in a multipotent hematopoietic stem cell, resulting in a growth advantage at the stem cell level and in defective differentiation and maturation of hematopoietic precursors. Recently, evidence has been provided of age-related hematopoietic clones, driven by mutations of genes recurrently mutated in myeloid neoplasms. These hematopoietic clones may represent either premalignant clones with the potential to progress to myeloid neoplasm or small malignant clones at a preclinical stage. SUMMARY The available evidence clearly indicates that greater understanding of the molecular basis of myeloid neoplasms with myelodysplasia has relevant implications in the classification of these disorders, as well as in predicting disease risk and response to specific treatment modalities, and may open avenues of research leading to novel therapeutic options and personalized treatment in the individual patient.
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299
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Abstract
The recent genomic characterization of cancers has revealed recurrent somatic point mutations and copy number changes affecting genes encoding RNA splicing factors. Initial studies of these 'spliceosomal mutations' suggest that the proteins bearing these mutations exhibit altered splice site and/or exon recognition preferences relative to their wild-type counterparts, resulting in cancer-specific mis-splicing. Such changes in the splicing machinery may create novel vulnerabilities in cancer cells that can be therapeutically exploited using compounds that can influence the splicing process. Further studies to dissect the biochemical, genomic and biological effects of spliceosomal mutations are crucial for the development of cancer therapies targeted at these mutations.
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Affiliation(s)
- Heidi Dvinge
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eunhee Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Leukemia Service, Dept. of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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300
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Ordering of mutations in acute myeloid leukemia with partial tandem duplication of MLL (MLL-PTD). Leukemia 2016; 31:1-10. [PMID: 27389053 PMCID: PMC5214979 DOI: 10.1038/leu.2016.160] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/21/2016] [Accepted: 05/25/2016] [Indexed: 12/22/2022]
Abstract
Partial tandem duplication of MLL (MLL-PTD) characterizes acute myeloid leukemia (AML) patients often with a poor prognosis. To understand the order of occurrence of MLL-PTD in relation to other major AML mutations and to identify novel mutations that may be present in this unique AML molecular subtype, exome and targeted sequencing was performed on 85 MLL-PTD AML samples using HiSeq-2000. Genes involved in the cohesin complex (STAG2), a splicing factor (U2AF1) and a poorly studied gene, MGA were recurrently mutated, whereas NPM1, one of the most frequently mutated AML gene, was not mutated in MLL-PTD patients. Interestingly, clonality analysis suggests that IDH2/1, DNMT3A, U2AF1 and TET2 mutations are clonal and occur early, and MLL-PTD likely arises after these initial mutations. Conversely, proliferative mutations (FLT3, RAS), typically appear later, are largely subclonal and tend to be unstable. This study provides important insights for understanding the relative importance of different mutations for defining a targeted therapeutic strategy for MLL-PTD AML patients.
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