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Fan J, Li Z, Pei L, Hou Y. Post-transcriptional regulation of DEAD-box RNA helicases in hematopoietic malignancies. Genes Dis 2024; 11:101252. [PMID: 38993792 PMCID: PMC11237855 DOI: 10.1016/j.gendis.2024.101252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 07/13/2024] Open
Abstract
Hematopoiesis represents a meticulously regulated and dynamic biological process. Genetic aberrations affecting blood cells, induced by various factors, frequently give rise to hematological tumors. These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events, including RNA alternative splicing, RNA localization, RNA degradation, and storage. Notably, post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis. The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors, intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing, RNA modification, and ribosome assembly. This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEAD-Box RNA helicases in malignant hematopoiesis. Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system.
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Affiliation(s)
- Jiankun Fan
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhigang Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Li Pei
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yu Hou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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2
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Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, Verma A, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol Cell 2024; 84:1475-1495.e18. [PMID: 38521065 PMCID: PMC11061666 DOI: 10.1016/j.molcel.2024.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
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Affiliation(s)
- Prajwal C Boddu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Rahul Roy
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Bárbara De La Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Anne Olazabal-Herrero
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Namrata S Chandhok
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Darren King
- Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Gary M Kupfer
- Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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3
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Strauss G, Mott K, Klopocki E, Schulze H. Thrombocytopenia Absent Radius (TAR)-Syndrome: From Current Genetics to Patient Self-Empowerment. Hamostaseologie 2023; 43:252-260. [PMID: 37611607 DOI: 10.1055/a-2088-1801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
Thrombocytopenia absent radius (TAR) syndrome is a rare form of hereditary thrombocytopenia associated with a bilateral radial aplasia. TAR syndrome is genetically defined by the combination of a microdeletion on chromosome 1 which includes the gene RBM8A, and a single nucleotide polymorphism (SNP) in the second RBM8A allele. While most patients with TAR syndrome harbor a SNP in either the 5' UTR region or in intron 1 of RBM8A, further SNPs associated with TAR syndrome are still being identified. Here, we report on the current understanding of the genetic basis, diagnosis, and therapy of TAR syndrome and discuss patient self-empowerment by enabling networking and exchange between affected individuals and families.
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Affiliation(s)
- Gabriele Strauss
- Department of Paediatric Haematology and Oncology, Helios-Klinikum Buch, Berlin, Germany
| | - Kristina Mott
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - Eva Klopocki
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Harald Schulze
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
- Center for Rare Blood Cell Disorders, Center for Rare Diseases, University Hospital Würzburg, Würzburg, Germany
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4
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Oder B, Chatzidimitriou A, Langerak AW, Rosenquist R, Österholm C. Recent revelations and future directions using single-cell technologies in chronic lymphocytic leukemia. Front Oncol 2023; 13:1143811. [PMID: 37091144 PMCID: PMC10117666 DOI: 10.3389/fonc.2023.1143811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically and biologically heterogeneous disease with varying outcomes. In the last decade, the application of next-generation sequencing technologies has allowed extensive mapping of disease-specific genomic, epigenomic, immunogenetic, and transcriptomic signatures linked to CLL pathogenesis. These technologies have improved our understanding of the impact of tumor heterogeneity and evolution on disease outcome, although they have mostly been performed on bulk preparations of nucleic acids. As a further development, new technologies have emerged in recent years that allow high-resolution mapping at the single-cell level. These include single-cell RNA sequencing for assessment of the transcriptome, both of leukemic and non-malignant cells in the tumor microenvironment; immunogenetic profiling of B and T cell receptor rearrangements; single-cell sequencing methods for investigation of methylation and chromatin accessibility across the genome; and targeted single-cell DNA sequencing for analysis of copy-number alterations and single nucleotide variants. In addition, concomitant profiling of cellular subpopulations, based on protein expression, can also be obtained by various antibody-based approaches. In this review, we discuss different single-cell sequencing technologies and how they have been applied so far to study CLL onset and progression, also in response to treatment. This latter aspect is particularly relevant considering that we are moving away from chemoimmunotherapy to targeted therapies, with a potentially distinct impact on clonal dynamics. We also discuss new possibilities, such as integrative multi-omics analysis, as well as inherent limitations of the different single-cell technologies, from sample preparation to data interpretation using available bioinformatic pipelines. Finally, we discuss future directions in this rapidly evolving field.
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Affiliation(s)
- Blaž Oder
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anastasia Chatzidimitriou
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Anton W. Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Österholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Cecilia Österholm,
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Boddu PC, Gupta A, Roy R, De La Pena Avalos B, Herrero AO, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma AK, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530019. [PMID: 36891287 PMCID: PMC9994134 DOI: 10.1101/2023.02.25.530019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two commonly mutated splicing factors in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired association of HTATSF1 with mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy. GRAPHICAL ABSTRACT HIGHLIGHTS Oncogenic mutations of SF3B1 and U2AF1 cause a gene-body RNAPII elongation defectRNAPII transcription elongation defect leads to transcription replication conflicts, DNA damage response, and changes to chromatin organization and H3K4me3 marksThe transcription elongation defect is linked to disruption of the early spliceosome formation through impaired interaction of HTATSF1 with mutant SF3B1.Changes to chromatin organization reveal potential therapeutic strategies by targeting the Sin3/HDAC pathway.
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Holland DO, Gotea V, Fedkenheuer K, Jaiswal SK, Baugher C, Tan H, Fedkenheuer M, Elnitski L. Characterization and clustering of kinase isoform expression in metastatic melanoma. PLoS Comput Biol 2022; 18:e1010065. [PMID: 35560144 PMCID: PMC9132324 DOI: 10.1371/journal.pcbi.1010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/25/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations to the human kinome are known to play causal roles in cancer. The kinome regulates numerous cell processes including growth, proliferation, differentiation, and apoptosis. In addition to aberrant expression, aberrant alternative splicing of cancer-driver genes is receiving increased attention as it could lead to loss or gain of functional domains, altering a kinase's downstream impact. The present study quantifies changes in gene expression and isoform ratios in the kinome of metastatic melanoma cells relative to primary tumors. We contrast 538 total kinases and 3,040 known kinase isoforms between 103 primary tumor and 367 metastatic samples from The Cancer Genome Atlas (TCGA). We find strong evidence of differential expression (DE) at the gene level in 123 kinases (23%). Additionally, of the 468 kinases with alternative isoforms, 60 (13%) had significant difference in isoform ratios (DIR). Notably, DE and DIR have little correlation; for instance, although DE highlights enrichment in receptor tyrosine kinases (RTKs), DIR identifies altered splicing in non-receptor tyrosine kinases (nRTKs). Using exon junction mapping, we identify five examples of splicing events favored in metastatic samples. We demonstrate differential apoptosis and protein localization between SLK isoforms in metastatic melanoma. We cluster isoform expression data and identify subgroups that correlate with genomic subtypes and anatomic tumor locations. Notably, distinct DE and DIR patterns separate samples with BRAF hotspot mutations and (N/K/H)RAS hotspot mutations, the latter of which lacks effective kinase inhibitor treatments. DE in RAS mutants concentrates in CMGC kinases (a group including cell cycle and splicing regulators) rather than RTKs as in BRAF mutants. Furthermore, isoforms in the RAS kinase subgroup show enrichment for cancer-related processes such as angiogenesis and cell migration. Our results reveal a new approach to therapeutic target identification and demonstrate how different mutational subtypes may respond differently to treatments highlighting possible new driver events in cancer.
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Affiliation(s)
- David O. Holland
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Fedkenheuer
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sushil K. Jaiswal
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Catherine Baugher
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Fedkenheuer
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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7
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Kataoka N, Matsumoto E, Masaki S. Mechanistic Insights of Aberrant Splicing with Splicing Factor Mutations Found in Myelodysplastic Syndromes. Int J Mol Sci 2021; 22:ijms22157789. [PMID: 34360561 PMCID: PMC8346168 DOI: 10.3390/ijms22157789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
Pre-mRNA splicing is an essential process for gene expression in higher eukaryotes, which requires a high order of accuracy. Mutations in splicing factors or regulatory elements in pre-mRNAs often result in many human diseases. Myelodysplastic syndrome (MDS) is a heterogeneous group of chronic myeloid neoplasms characterized by many symptoms and a high risk of progression to acute myeloid leukemia. Recent findings indicate that mutations in splicing factors represent a novel class of driver mutations in human cancers and affect about 50% of Myelodysplastic syndrome (MDS) patients. Somatic mutations in MDS patients are frequently found in genes SF3B1, SRSF2, U2AF1, and ZRSR2. Interestingly, they are involved in the recognition of 3' splice sites and exons. It has been reported that mutations in these splicing regulators result in aberrant splicing of many genes. In this review article, we first describe molecular mechanism of pre-mRNA splicing as an introduction and mainly focus on those four splicing factors to describe their mutations and their associated aberrant splicing patterns.
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Affiliation(s)
- Naoyuki Kataoka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
- Correspondence: ; Tel.: +81-3-5841-5372; Fax: +81-3-5841-8014
| | - Eri Matsumoto
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
| | - So Masaki
- Laboratory of Molecular Medicinal Science, Department of Pharmaceutical Sciences, Ritsumeikan University, Shiga 525-8577, Japan;
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8
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Matutes E. Diagnostic and therapeutic challenges in hairy cell leukemia-variant: where are we in 2021? Expert Rev Hematol 2021; 14:355-363. [PMID: 33759673 DOI: 10.1080/17474086.2021.1908121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Hairy cell leukemia-variant (HCL-V) is a rare B-cell neoplasm arising or homing primarily in the spleen. It has been considered in the WHO classification of Hemopoietic and Lymphoid Tumors as a provisional entity since 2008 and included under the umbrella of unclassifiable splenomegalic B-cell leukemia/lymphomas. The diagnosis is a challenge to hematopathologists and management of these patients by the clinicians is difficult due to the lack of diagnostic and therapeutic guidelines and prospective studies. AREAS COVERED This manuscript is a comprehensive review of the clinical features, pathology, immunophenotypic profile, genomic alterations and therapeutic options of HCL-V. Diagnostic and therapeutic dilemmas are extensively outlined considering the information derived from a literature search covering from 1980 to 2019. Integration of all the data is needed and recommended for establishing the diagnosis of this leukemia. EXPERT OPINION More extensive information of genomic aberrations underlying the pathogenesis of the disease would be a solid stone for the diagnosis. To this end, a collaborative work among scientists and pathologists from different centers is required and expected. In turn, this might have a relevant clinical translation by allowing to identify putative targets for therapy and to improve the outlook of these patients.
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Zhou D, Xie T, Chen S, Ling Y, Xu Y, Chen B, Ouyang J, Yang Y. An unusual hematopoietic stem cell transplantation for donor acute lymphoblastic leukemia: a case report. BMC Cancer 2020; 20:195. [PMID: 32143579 PMCID: PMC7060641 DOI: 10.1186/s12885-020-6681-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/26/2020] [Indexed: 11/14/2022] Open
Abstract
Background Donor acute lymphoblastic leukemia with recipient intact is a rare condition. We report a case of donor developing acute lymphoblastic leukemia 8 yrs after donating both bone marrow and peripheral blood hematopoietic stem cells. Case presentation This case report describes a 51-year old female diagnosed with acute lymphoblastic leukemia who donated both bone marrow and peripheral blood stem cells 8 yrs ago for her brother with severe aplastic anemia. Whole exome sequencing revealed leukemic genetic lesions (SF3B1 and BRAF mutation) only appeared in the donor sister, not the recipient, and an unusual type of hematopoietic stem cell transplantation with the recipient’s peripheral blood stem cells was done. The patient remained in remission for 3 months before disease relapsed. CD19 CAR-T therapy followed by HLA-identical unrelated hematopoietic stem cell transplantation was applied and the patient remains in remission for 7 months till now. Conclusions This donor leukemia report supports the hypothesis that genetic lesions happen randomly in leukemogenesis. SF3B1 combined with BRAF mutation might contribute to the development of acute lymphoblastic leukemia.
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Affiliation(s)
| | | | - Suning Chen
- Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Yipeng Ling
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, People's Republic of China
| | - Yueyi Xu
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, People's Republic of China
| | - Bing Chen
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, People's Republic of China
| | - Jian Ouyang
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, People's Republic of China
| | - Yonggong Yang
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, People's Republic of China.
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10
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Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N, Kildebeck E, Newman AM, Bratman SV, Porteus MH, Chang HY, Alizadeh AA, Diehn M. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nat Commun 2019; 10:5712. [PMID: 31836708 PMCID: PMC6911043 DOI: 10.1038/s41467-019-13392-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/07/2019] [Indexed: 12/23/2022] Open
Abstract
The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To characterize this interaction, we profiled effects of S34F on the transcriptome-wide distribution of RNA binding and alternative splicing in cells harboring the ROS1 translocation. Compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3' splice junctions. The presence of S34F caused a shift in cross-linking at 3' splice sites, which was significantly associated with alternative splicing of skipped exons. U2AF1 S34F induced expression of genes involved in the epithelial-mesenchymal transition (EMT) and increased tumor cell invasion. Finally, S34F increased splicing of the long over the short SLC34A2-ROS1 isoform, which was also associated with enhanced invasiveness. Taken together, our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUAD.
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Affiliation(s)
- Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Luke J Lee
- Stanford Cancer Institute, Stanford University, Stanford, USA
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Noriko Ishisoko
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Eric Kildebeck
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Scott V Bratman
- Department of Radiation Oncology, Stanford University, Stanford, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, University of Toronto, Toronto, CA, USA
| | | | - Howard Y Chang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Department of Radiation Oncology, Stanford University, Stanford, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA.
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11
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Affiliation(s)
- Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
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12
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BCAS2 is essential for hematopoietic stem and progenitor cell maintenance during zebrafish embryogenesis. Blood 2018; 133:805-815. [PMID: 30482793 DOI: 10.1182/blood-2018-09-876599] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) originate from the hemogenic endothelium via the endothelial-to-hematopoietic transition, are self-renewing, and replenish all lineages of blood cells throughout life. BCAS2 (breast carcinoma amplified sequence 2) is a component of the spliceosome and is involved in multiple biological processes. However, its role in hematopoiesis remains unknown. We established a bcas2 knockout zebrafish model by using transcription activator-like effector nucleases. The bcas2 -/- zebrafish showed severe impairment of HSPCs and their derivatives during definitive hematopoiesis. We also observed significant signs of HSPC apoptosis in the caudal hematopoietic tissue of bcas2 -/- zebrafish, which may be rescued by suppression of p53. Furthermore, we show that the bcas2 deletion induces an abnormal alternative splicing of Mdm4 that predisposes cells to undergo p53-mediated apoptosis, which provides a mechanistic explanation of the deficiency observed in HSPCs. Our findings revealed a novel and vital role for BCAS2 during HSPC maintenance in zebrafish.
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13
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The Development and Use of Scalable Systems for Studying Aberrant Splicing in SF3B1-Mutant CLL. Methods Mol Biol 2018. [PMID: 30350199 DOI: 10.1007/978-1-4939-8876-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Mutational landscape of CLL is now known to include recurrent non-synonymous mutations in SF3B1, a core splicing factor. About 5-10% of newly diagnosed CLL harbor these mutations which are typically limited to HEAT domains in the carboxyl-terminus of the protein. Importantly, the mutations are not specific to CLL but also present in several unrelated clonal disorders. Analysis of patient samples and cell lines has shown the primary splicing aberration in SF3B1-mutant cells to the use of novel or "cryptic" 3' splice sites (3SS). Advances in genome-editing and next-generation sequencing (NGS) have allowed development of isogenic models and detailed analysis of changes to the transcriptome with relative ease. In this manuscript, we focus on two relevant methods to study splicing factor mutations in CLL: development of isogenic scalable cell lines and informatics analysis of RNA-Seq datasets.
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14
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Huang Y, Hale J, Wang Y, Li W, Zhang S, Zhang J, Zhao H, Guo X, Liu J, Yan H, Yazdanbakhsh K, Huang G, Hillyer CD, Mohandas N, Chen L, Sun L, An X. SF3B1 deficiency impairs human erythropoiesis via activation of p53 pathway: implications for understanding of ineffective erythropoiesis in MDS. J Hematol Oncol 2018; 11:19. [PMID: 29433555 PMCID: PMC5810112 DOI: 10.1186/s13045-018-0558-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 01/23/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND SF3B1 is a core component of splicing machinery. Mutations in SF3B1 are frequently found in myelodysplastic syndromes (MDS), particularly in patients with refractory anemia with ringed sideroblasts (RARS), characterized by isolated anemia. SF3B1 mutations have been implicated in the pathophysiology of RARS; however, the physiological function of SF3B1 in erythropoiesis remains unknown. METHODS shRNA-mediated approach was used to knockdown SF3B1 in human CD34+ cells. The effects of SF3B1 knockdown on human erythroid cell differentiation, cell cycle, and apoptosis were assessed by flow cytometry. RNA-seq, qRT-PCR, and western blot analyses were used to define the mechanisms of phenotypes following knockdown of SF3B1. RESULTS We document that SF3B1 knockdown in human CD34+ cells leads to increased apoptosis and cell cycle arrest of early-stage erythroid cells and generation of abnormally nucleated late-stage erythroblasts. RNA-seq analysis of SF3B1-knockdown erythroid progenitor CFU-E cells revealed altered splicing of an E3 ligase Makorin Ring Finger Protein 1 (MKRN1) and subsequent activation of p53 pathway. Importantly, ectopic expression of MKRN1 rescued SF3B1-knockdown-induced alterations. Decreased expression of genes involved in mitosis/cytokinesis pathway including polo-like kinase 1 (PLK1) was noted in SF3B1-knockdown polychromatic and orthochromatic erythroblasts comparing to control cells. Pharmacologic inhibition of PLK1 also led to generation of abnormally nucleated erythroblasts. CONCLUSIONS These findings enabled us to identify novel roles for SF3B1 in human erythropoiesis and provided new insights into its role in regulating normal erythropoiesis. Furthermore, these findings have implications for improved understanding of ineffective erythropoiesis in MDS patients with SF3B1 mutations.
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Affiliation(s)
- Yumin Huang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 Henan People’s Republic of China
- Laboratory of Membrane Biology, New York Blood Center, New York, NY 10065 USA
| | - John Hale
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY 10065 USA
| | - Yaomei Wang
- Laboratory of Membrane Biology, New York Blood Center, New York, NY 10065 USA
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People’s Republic of China
| | - Wei Li
- Laboratory of Membrane Biology, New York Blood Center, New York, NY 10065 USA
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People’s Republic of China
- Department of Immunology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450008 People’s Republic of China
| | - Shijie Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People’s Republic of China
| | - Jieying Zhang
- Laboratory of Membrane Biology, New York Blood Center, New York, NY 10065 USA
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, Changsha, 410078 People’s Republic of China
| | - Huizhi Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People’s Republic of China
| | - Xinhua Guo
- Laboratory of Membrane Biology, New York Blood Center, New York, NY 10065 USA
| | - Jing Liu
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, Changsha, 410078 People’s Republic of China
| | - Hongxia Yan
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY 10065 USA
| | - Karina Yazdanbakhsh
- Laboratory of Complement Biology, New York Blood Center, New York, NY 10065 USA
| | - Gang Huang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | | | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY 10065 USA
| | - Lixiang Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People’s Republic of China
| | - Ling Sun
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 Henan People’s Republic of China
| | - Xiuli An
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 Henan People’s Republic of China
- Laboratory of Membrane Biology, New York Blood Center, New York, NY 10065 USA
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People’s Republic of China
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15
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Potts KS, Bowman TV. Modeling Myeloid Malignancies Using Zebrafish. Front Oncol 2017; 7:297. [PMID: 29255698 PMCID: PMC5722844 DOI: 10.3389/fonc.2017.00297] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/20/2017] [Indexed: 02/04/2023] Open
Abstract
Human myeloid malignancies represent a substantial disease burden to individuals, with significant morbidity and death. The genetic underpinnings of disease formation and progression remain incompletely understood. Large-scale human population studies have identified a high frequency of potential driver mutations in spliceosomal and epigenetic regulators that contribute to malignancies, such as myelodysplastic syndromes (MDS) and leukemias. The high conservation of cell types and genes between humans and model organisms permits the investigation of the underlying mechanisms of leukemic development and potential therapeutic testing in genetically pliable pre-clinical systems. Due to the many technical advantages, such as large-scale screening, lineage-tracing studies, tumor transplantation, and high-throughput drug screening approaches, zebrafish is emerging as a model system for myeloid malignancies. In this review, we discuss recent advances in MDS and leukemia using the zebrafish model.
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Affiliation(s)
- Kathryn S Potts
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, United States
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16
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Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat Rev Mol Cell Biol 2017; 18:655-670. [DOI: 10.1038/nrm.2017.86] [Citation(s) in RCA: 234] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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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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18
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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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19
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Jiang Q, Crews LA, Holm F, Jamieson CHM. RNA editing-dependent epitranscriptome diversity in cancer stem cells. Nat Rev Cancer 2017; 17:381-392. [PMID: 28416802 PMCID: PMC5665169 DOI: 10.1038/nrc.2017.23] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer stem cells (CSCs) can regenerate all facets of a tumour as a result of their stem cell-like capacity to self-renew, survive and become dormant in protective microenvironments. CSCs evolve during tumour progression in a manner that conforms to Charles Darwin's principle of natural selection. Although somatic DNA mutations and epigenetic alterations promote evolution, post-transcriptional RNA modifications together with RNA binding protein activity (the 'epitranscriptome') might also contribute to clonal evolution through dynamic determination of RNA function and gene expression diversity in response to environmental stimuli. Deregulation of these epitranscriptomic events contributes to CSC generation and maintenance, which governs cancer progression and drug resistance. In this Review, we discuss the role of malignant RNA processing in CSC generation and maintenance, including mechanisms of RNA methylation, RNA editing and RNA splicing, and the functional consequences of their aberrant regulation in human malignancies. Finally, we highlight the potential of these events as novel CSC biomarkers as well as therapeutic targets.
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Affiliation(s)
- Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Frida Holm
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
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20
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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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21
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Tang Q, Rodriguez-Santiago S, Wang J, Pu J, Yuste A, Gupta V, Moldón A, Xu YZ, Query CC. SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing. Genes Dev 2016; 30:2710-2723. [PMID: 28087715 PMCID: PMC5238730 DOI: 10.1101/gad.291872.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/12/2016] [Indexed: 11/25/2022]
Abstract
Mutations in the U2 snRNP component SF3B1 are prominent in myelodysplastic syndromes (MDSs) and other cancers and have been shown recently to alter branch site (BS) or 3' splice site selection in splicing. However, the molecular mechanism of altered splicing is not known. We show here that hsh155 mutant alleles in Saccharomyces cerevisiae, counterparts of SF3B1 mutations frequently found in cancers, specifically change splicing of suboptimal BS pre-mRNA substrates. We found that Hsh155p interacts directly with Prp5p, the first ATPase that acts during spliceosome assembly, and localized the interacting regions to HEAT (Huntingtin, EF3, PP2A, and TOR1) motifs in SF3B1 associated with disease mutations. Furthermore, we show that mutations in these motifs from both human disease and yeast genetic screens alter the physical interaction with Prp5p, alter branch region specification, and phenocopy mutations in Prp5p. These and other data demonstrate that mutations in Hsh155p and Prp5p alter splicing because they change the direct physical interaction between Hsh155p and Prp5p. This altered physical interaction results in altered loading (i.e., "fidelity") of the BS-U2 duplex into the SF3B complex during prespliceosome formation. These results provide a mechanistic framework to explain the consequences of intron recognition and splicing of SF3B1 mutations found in disease.
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Affiliation(s)
- Qing Tang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | | | - Jing Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | - Jia Pu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | - Andrea Yuste
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
| | - Alberto Moldón
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
| | - Yong-Zhen Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032 China
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461 USA
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22
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Cavallini C, Visco C, Putta S, Rossi D, Mimiola E, Purvis N, Lovato O, Perbellini O, Falisi E, Facco M, Trentin L, Romanelli MG, Semenzato G, Ambrosetti A, Gaidano G, Pizzolo G, Cesano A, Scupoli MT. Integration of B-cell receptor-induced ERK1/2 phosphorylation and mutations of SF3B1 gene refines prognosis in treatment-naïve chronic lymphocytic leukemia. Haematologica 2016; 102:e144-e147. [PMID: 27927769 DOI: 10.3324/haematol.2016.154450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
| | - Carlo Visco
- Department of Cell Therapy and Hematology, San Bortolo Hospital, Vicenza, Italy
| | | | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Elda Mimiola
- Department of Medicine, Section of Hematology, University of Verona, Italy
| | | | | | - Omar Perbellini
- Department of Cell Therapy and Hematology, San Bortolo Hospital, Vicenza, Italy
| | - Erika Falisi
- Department of Cell Therapy and Hematology, San Bortolo Hospital, Vicenza, Italy
| | - Monica Facco
- Department of Medicine, Hematology and Clinical Immunology Branch, University of Padua, Italy
| | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology Branch, University of Padua, Italy
| | - Maria G Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy
| | - Gianpietro Semenzato
- Department of Medicine, Hematology and Clinical Immunology Branch, University of Padua, Italy
| | - Achille Ambrosetti
- Department of Medicine, Section of Hematology, University of Verona, Italy
| | - Gianluca Gaidano
- Department of Translational Medicine, Division of Hematology, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Giovanni Pizzolo
- Department of Medicine, Section of Hematology, University of Verona, Italy
| | | | - Maria T Scupoli
- Research Center LURM, University of Verona, Italy .,Department of Medicine, Section of Hematology, University of Verona, Italy
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Helgadottir H, Höiom V. The genetics of uveal melanoma: current insights. APPLICATION OF CLINICAL GENETICS 2016; 9:147-55. [PMID: 27660484 PMCID: PMC5019476 DOI: 10.2147/tacg.s69210] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Uveal melanoma (UM) is the most common malignant eye tumor in adults affecting ~7,000 individuals per year worldwide. UM is a rare subtype of melanoma with distinct clinical and molecular features as compared to other melanoma subtypes. UMs lack the most typical cutaneous melanoma-associated mutations (BRAF, NRAS, and NF1) and are instead characterized by a different set of genes with oncogenic or loss-of-function mutations. By next-generation sequencing efforts on UM tumors, several driver genes have been detected. The most frequent ones are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1. In many cases, mutations in these genes appear in a mutually exclusive manner, have different risk of metastasis, and are consequently of prognostic importance. The majority of UM cases are sporadic but a few percentage of the cases occurs in families with an inherited predisposition for this malignancy. In recent years, germline mutations in the BAP1 gene have been found to segregate in an autosomal dominant pattern with numerous different cancer types including UM in cancer-prone families. This cancer syndrome has been denoted as the tumor predisposition syndrome.
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Affiliation(s)
- Hildur Helgadottir
- Department of Oncology and Pathology, Karolinska institutet; Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Veronica Höiom
- Department of Oncology and Pathology, Karolinska institutet
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24
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Joseph SJ, Marti H, Didelot X, Read TD, Dean D. Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia suis: A Recently Identified Zoonotic Pathogen. Genome Biol Evol 2016; 8:2613-23. [PMID: 27576537 PMCID: PMC5010913 DOI: 10.1093/gbe/evw182] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2016] [Indexed: 12/22/2022] Open
Abstract
Species closely related to the human pathogen Chlamydia trachomatis (Ct) have recently been found to cause zoonotic infections, posing a public health threat especially in the case of tetracycline resistant Chlamydia suis (Cs) strains. These strains acquired a tet(C)-containing cassette via horizontal gene transfer (HGT). Genomes of 11 Cs strains from various tissues were sequenced to reconstruct evolutionary pathway(s) for tet(C) HGT. Cs had the highest recombination rate of Chlamydia species studied to date. Admixture occurred among Cs strains and with Chlamydia muridarum but not with Ct Although in vitro tet(C) cassette exchange with Ct has been documented, in vivo evidence may require examining human samples from Ct and Cs co-infected sites. Molecular-clock dating indicated that ancestral clades of resistant Cs strains predated the 1947 discovery of tetracycline, which was subsequently used in animal feed. The cassette likely spread throughout Cs strains by homologous recombination after acquisition from an external source, and our analysis suggests Betaproteobacteria as the origin. Selective pressure from tetracycline may be responsible for recent bottlenecks in Cs populations. Since tetracycline is an important antibiotic for treating Ct, zoonotic infections at mutual sites of infection indicate the possibility for cassette transfer and major public health repercussions.
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Affiliation(s)
- Sandeep J Joseph
- Department of Medicine, Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Hanna Marti
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Timothy D Read
- Department of Medicine, Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, CA, USA Joint Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA, USA
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25
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Yan C, Wan R, Bai R, Huang G, Shi Y. Structure of a yeast activated spliceosome at 3.5 Å resolution. Science 2016; 353:904-11. [PMID: 27445306 DOI: 10.1126/science.aag0291] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/13/2016] [Indexed: 12/18/2022]
Abstract
Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction.
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Affiliation(s)
- Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Rui Bai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaoxingyu Huang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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26
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Donaires FS, Martelli F, Alves-Paiva RDM, Magalhães SMM, Pinheiro RF, Calado RT. Splicing factor SF3B1 mutations and ring sideroblasts in myelodysplastic syndromes: a Brazilian cohort screening study. Rev Bras Hematol Hemoter 2016; 38:320-324. [PMID: 27863760 PMCID: PMC5119671 DOI: 10.1016/j.bjhh.2016.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 01/06/2023] Open
Abstract
Background Myelodysplastic syndromes (MDS) comprise a group of malignant clonal hematologic disorders characterized by ineffective hematopoiesis and propensity for progression to acute myeloid leukemia. Acquired mutations in the gene encoding RNA splicing factor 3B subunit 1 (SF3B1) are highly associated with the MDS subtypes presenting ring sideroblasts, and represent a specific nosological entity. The effects of these mutations on clinical outcomes are diverse and contrasting. Methods A cohort of 91 Brazilian MDS patients, including patients with ring sideroblasts in the bone marrow, were screened for mutations in the SF3B1 hotspots (exons 12–15) by direct Sanger sequencing. Results SF3B1 heterozygous mutations were identified in six patients (7%), all of them with ring sideroblasts, thus confirming the association between SF3B1 mutations and myelodysplastic syndrome subtypes bearing this morphologic feature (frequency of 6/13, p-value < 0.0001). Conclusion This is the first screening of SF3B1 mutations in a cohort of Brazilian myelodysplastic syndrome patients. Our findings confirm that mutations in this splicing gene correlate with bone marrow ringed sideroblasts.
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De La Garza A, Cameron RC, Nik S, Payne SG, Bowman TV. Spliceosomal component Sf3b1 is essential for hematopoietic differentiation in zebrafish. Exp Hematol 2016; 44:826-837.e4. [PMID: 27260753 DOI: 10.1016/j.exphem.2016.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/29/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
SF3B1 (Splicing factor 3b, subunit 1) is one of the most commonly mutated factors in myelodysplastic syndrome (MDS). Although the genetic correlation between SF3B1 mutations and MDS etiology are quite strong, no in vivo model currently exists to explore how SF3B1 loss alters blood cell development. Using zebrafish mutants, we show here that proper function of Sf3b1 is required for all hematopoietic lineages. As in MDS patients, zebrafish sf3b1 mutants develop a macrocytic-anemia-like phenotype due to a block in maturation at a late progenitor stage. The mutant embryos also develop neutropenia, because their primitive myeloid cells fail to mature and turn on differentiation markers such as l-plastin and myeloperoxidase. In contrast, production of definitive hematopoietic stem and progenitor cells (HSPCs) from hemogenic endothelial cells within the dorsal aorta is greatly diminished, whereas arterial endothelial cells are correctly fated. Notch signaling, imperative for the endothelial-to-hematopoietic transition, is also normal, indicating that HSPC induction is blocked in sf3b1 mutants downstream or independent of Notch signaling. The data demonstrate that Sf3b1 function is necessary during key differentiation fate decisions in multiple blood cell types. Zebrafish sf3b1 mutants offer a novel animal model with which to explore the role of splicing in hematopoietic development and provide an excellent in vivo system with which to delve into the question of why and how Sf3b1 dysfunction is detrimental to hematopoietic differentiation, which could improve MDS diagnosis and treatment.
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Affiliation(s)
- Adriana De La Garza
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rosannah C Cameron
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sara Nik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sara G Payne
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, USA.
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28
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Matutes E, Martínez-Trillos A, Campo E. Hairy cell leukaemia-variant: Disease features and treatment. Best Pract Res Clin Haematol 2015; 28:253-63. [PMID: 26614904 DOI: 10.1016/j.beha.2015.09.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/21/2015] [Accepted: 09/28/2015] [Indexed: 10/22/2022]
Abstract
Hairy cell leukaemia-variant (HCL-V) is a rare B-cell malignancy that affects elderly males and manifests with splenomegaly, lymphocytosis and cytopenias without monocytopenia. The neoplastic cells have morphological features of prolymphocytes and hairy cells. The immunophenotype is that of a clonal B-cell CD11c and CD103 positive but, unlike classical HCL, CD25, CD123 and CD200 negative. The spleen histology is similar to classical HCL and the pattern of bone marrow infiltration is interstitial and/or intrasinusoidal. Mutations of the immunoglobulin heavy chain (IGVH) are seen in two thirds of cases with a preferential VH4-34 family usage. There is no distinct chromosomal abnormality but del17p13 and mutations of the TP53 gene are frequent. Mutations in the MAP2K1 gene have been documented in half of the cases. The course is chronic with median survivals of 7-9 years. Patients are refractory to purine analogues and the most effective therapy is the combination of 2-chlorodeoxyadenosine and Rituximab.
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Affiliation(s)
- Estella Matutes
- Hematopathology Unit, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
| | | | - Elias Campo
- Hematopathology Unit, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
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Negri G, Crescenzi B, Colombo EA, Fontana L, Barba G, Arcioni F, Gervasini C, Mecucci C, Larizza L. Expanding the role of the splicingUSB1gene from Poikiloderma with Neutropenia to acquired myeloid neoplasms. Br J Haematol 2015; 171:557-65. [DOI: 10.1111/bjh.13651] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/22/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Gloria Negri
- Medical Genetics; Department of Health Sciences; University of Milan; Milan Italy
| | | | - Elisa Adele Colombo
- Medical Genetics; Department of Health Sciences; University of Milan; Milan Italy
| | - Laura Fontana
- Medical Genetics; Department of Health Sciences; University of Milan; Milan Italy
| | - Gianluca Barba
- Haematology Unit; Polo Unico S.M. Misericordia; Perugia Italy
| | - Francesco Arcioni
- Pediatric Oncology Haematology Unit; University of Perugia; Polo Unico S.M. Misericordia; Perugia Italy
| | - Cristina Gervasini
- Medical Genetics; Department of Health Sciences; University of Milan; Milan Italy
| | | | - Lidia Larizza
- Medical Cytogenetics and Molecular Genetics Laboratory; Centro di Ricerche e Tecnologie Biomediche IRCCS; Istituto Auxologico Italiano; Milan Italy
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30
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Hahn CN, Venugopal P, Scott HS, Hiwase DK. Splice factor mutations and alternative splicing as drivers of hematopoietic malignancy. Immunol Rev 2015; 263:257-78. [PMID: 25510282 DOI: 10.1111/imr.12241] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Differential splicing contributes to the vast complexity of mRNA transcripts and protein isoforms that are necessary for cellular homeostasis and response to developmental cues and external signals. The hematopoietic system provides an exquisite example of this. Recently, discovery of mutations in components of the spliceosome in various hematopoietic malignancies (HMs) has led to an explosion in knowledge of the role of splicing and splice factors in HMs and other cancers. A better understanding of the mechanisms by which alternative splicing and aberrant splicing contributes to the leukemogenic process will enable more efficacious targeted approaches to tackle these often difficult to treat diseases. The clinical implications are only just starting to be realized with novel drug targets and therapeutic strategies open to exploitation for patient benefit.
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Affiliation(s)
- Christopher N Hahn
- Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia; Department of Molecular Pathology, SA Pathology, Adelaide, SA, Australia; School of Medicine, University of Adelaide, Adelaide, SA, Australia; Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
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31
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Kang MG, Kim HR, Seo BY, Lee JH, Choi SY, Kim SH, Shin JH, Suh SP, Ahn JS, Shin MG. The prognostic impact of mutations in spliceosomal genes for myelodysplastic syndrome patients without ring sideroblasts. BMC Cancer 2015; 15:484. [PMID: 26115659 PMCID: PMC4483202 DOI: 10.1186/s12885-015-1493-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 06/16/2015] [Indexed: 12/22/2022] Open
Abstract
Background Mutations in genes that are part of the splicing machinery for myelodysplastic syndromes (MDS), including MDS without ring sideroblasts (RS), have been widely investigated. The effects of these mutations on clinical outcomes have been diverse and contrasting. Methods We examined a cohort of 129 de novo MDS patients, who did not harbor RS, for mutations affecting three spliceosomal genes (SF3B1, U2AF1, and SRSF2). Results The mutation rates of SF3B1, U2AF1, and SRSF2 were 7.0 %, 7.8 %, and 10.1 %, respectively. Compared with previously reported results, these rates were relatively infrequent. The SRSF2 mutation strongly correlated with old age (P < 0.001), while the mutation status of SF3B1 did not affect overall survival (OS), progression-free survival (PFS), or acute myeloid leukemia (AML) transformation. In contrast, MDS patients with mutations in U2AF1 or SRSF2 exhibited inferior PFS. The U2AF1 mutation was associated with inferior OS in low-risk MDS patients (P = 0.035). The SRSF2 mutation was somewhat associated with AML transformation (P = 0.083). Conclusion Our findings suggest that the frequencies of the SF3B1, U2AF1, and SRSF2 splicing gene mutations in MDS without RS were relatively low. We also demonstrated that the U2AF1 and SRSF2 mutations were associated with an unfavorable prognostic impact in MDS patients without RS. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1493-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min-Gu Kang
- Departments of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
| | - Hye-Ran Kim
- College of Korean Medicine, Dongshin University, 185 Gunjaero, Naju, Jeollanam-do, 520-714, South Korea.
| | - Bo-Young Seo
- Departments of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
| | - Jun Hyung Lee
- Departments of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
| | - Seok-Yong Choi
- Brain Korea 21 Project, Center for Biomedical Human Resources, Chonnam National University Medical School, Gwangju, South Korea.
| | - Soo-Hyun Kim
- Departments of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
| | - Jong-Hee Shin
- Departments of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
| | - Soon-Pal Suh
- Departments of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
| | - Jae-Sook Ahn
- Department of Hematology-Oncology, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
| | - Myung-Geun Shin
- Departments of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea. .,Brain Korea 21 Project, Center for Biomedical Human Resources, Chonnam National University Medical School, Gwangju, South Korea. .,Environmental Health Center for Childhood Leukemia and Cancer, Chonnam National University Hwasun Hospital, 160 Ilsim-ri, Hwasun-eup, Hwasun-gun, Jeollanam-do, 519-809, South Korea.
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32
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Lehalle D, Wieczorek D, Zechi-Ceide RM, Passos-Bueno MR, Lyonnet S, Amiel J, Gordon CT. A review of craniofacial disorders caused by spliceosomal defects. Clin Genet 2015; 88:405-15. [PMID: 25865758 DOI: 10.1111/cge.12596] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/26/2015] [Accepted: 04/07/2015] [Indexed: 02/04/2023]
Abstract
The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNA transcripts. Mutations in EFTUD2, encoding a component of the major spliceosome, have recently been identified as the cause of mandibulofacial dysostosis, Guion-Almeida type (MFDGA), characterized by mandibulofacial dysostosis, microcephaly, external ear malformations and intellectual disability. Mutations in several other genes involved in spliceosomal function or linked aspects of mRNA processing have also recently been identified in human disorders with specific craniofacial malformations: SF3B4 in Nager syndrome, an acrofacial dysostosis (AFD); SNRPB in cerebrocostomandibular syndrome, characterized by Robin sequence and rib defects; EIF4A3 in the AFD Richieri-Costa-Pereira syndrome, characterized by Robin sequence, median mandibular cleft and limb defects; and TXNL4A in Burn-McKeown syndrome, involving specific craniofacial dysmorphisms. Here, we review phenotypic and molecular aspects of these syndromes. Given the apparent sensitivity of craniofacial development to defects in mRNA processing, it is possible that mutations in other proteins involved in spliceosomal function will emerge in the future as causative for related human disorders.
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Affiliation(s)
- D Lehalle
- Department of Genetics, APHP, Hôpital Necker-Enfants Malades, Paris, France
| | - D Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - R M Zechi-Ceide
- Departamento de Genetica Clinica, Hospital de Reabilitacao de Anomalias Craniofaciais, Universidade de Sao Paulo (HRAC-USP), Bauru, Brasil
| | - M R Passos-Bueno
- Centro de Estudos do Genoma Humano, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, Brasil
| | - S Lyonnet
- Department of Genetics, APHP, Hôpital Necker-Enfants Malades, Paris, France.,INSERM UMR 1163, Institut Imagine, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - J Amiel
- Department of Genetics, APHP, Hôpital Necker-Enfants Malades, Paris, France.,INSERM UMR 1163, Institut Imagine, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - C T Gordon
- INSERM UMR 1163, Institut Imagine, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France
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33
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Abstract
Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA-protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.
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Affiliation(s)
- Yeon Lee
- Center for RNA Systems Biology; Division of Biochemistry, Biophysics, and Structural Biology; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204;
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34
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Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood 2014; 124:598-610. [PMID: 24869935 PMCID: PMC4110662 DOI: 10.1182/blood-2013-12-542209] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/16/2014] [Indexed: 12/18/2022] Open
Abstract
The scope and roles of regulated isoform gene expression during erythroid terminal development are poorly understood. We identified hundreds of differentiation-associated isoform changes during terminal erythropoiesis. Sequences surrounding cassette exons of skipped exon events are enriched for motifs bound by the Muscleblind-like (MBNL) family of splicing factors. Knockdown of Mbnl1 in cultured murine fetal liver erythroid progenitors resulted in a strong block in erythroid differentiation and disrupted the developmentally regulated exon skipping of Ndel1 mRNA, which is bound by MBNL1 and critical for erythroid terminal proliferation. These findings reveal an unanticipated scope of the alternative splicing program and the importance of Mbnl1 during erythroid terminal differentiation.
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Affiliation(s)
- Albert W Cheng
- Whitehead Institute for Biomedical Research, Cambridge, MA; Computational and Systems Biology Program, and
| | - Jiahai Shi
- Whitehead Institute for Biomedical Research, Cambridge, MA
| | - Piu Wong
- Whitehead Institute for Biomedical Research, Cambridge, MA
| | - Katherine L Luo
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Paula Trepman
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Eric T Wang
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
| | - Heejo Choi
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Cambridge, MA; Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
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35
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Adler AS, McCleland ML, Yee S, Yaylaoglu M, Hussain S, Cosino E, Quinones G, Modrusan Z, Seshagiri S, Torres E, Chopra VS, Haley B, Zhang Z, Blackwood EM, Singh M, Junttila M, Stephan JP, Liu J, Pau G, Fearon ER, Jiang Z, Firestein R. An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth. Genes Dev 2014; 28:1068-84. [PMID: 24788092 PMCID: PMC4035536 DOI: 10.1101/gad.237206.113] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The spliceosome machinery is composed of multimeric protein complexes that generate a diverse repertoire of mRNA. Here, Adler et al. discover that PRPF6, a member of the tri-snRNP spliceosome complex, drives cancer proliferation. Inhibition of PRPF6 and other tri-snRNP complex proteins selectively abrogated growth in cancer cells with high tri-snRNP levels. Reducing PRPF6 altered the splicing of a discrete number of genes, including an oncogenic isoform of the ZAK kinase. This study identifies an essential role for PRPF6 in cancer via splicing of distinct growth-related gene products. The spliceosome machinery is composed of multimeric protein complexes that generate a diverse repertoire of mRNA through coordinated splicing of heteronuclear RNAs. While somatic mutations in spliceosome components have been discovered in several cancer types, the molecular bases and consequences of spliceosome aberrations in cancer are poorly understood. Here we report for the first time that PRPF6, a member of the tri-snRNP (small ribonucleoprotein) spliceosome complex, drives cancer proliferation by preferential splicing of genes associated with growth regulation. Inhibition of PRPF6 and other tri-snRNP complex proteins, but not other snRNP spliceosome complexes, selectively abrogated growth in cancer cells with high tri-snRNP levels. High-resolution transcriptome analyses revealed that reduced PRPF6 alters the constitutive and alternative splicing of a discrete number of genes, including an oncogenic isoform of the ZAK kinase. These findings implicate an essential role for PRPF6 in cancer via splicing of distinct growth-related gene products.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Eric Torres
- Department of Biochemical and Cellular Pharmacology
| | | | | | - Zemin Zhang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
| | | | | | | | | | - Jinfeng Liu
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
| | - Gregoire Pau
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
| | - Eric R Fearon
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhaoshi Jiang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
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SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample. PLoS One 2014; 9:e89673. [PMID: 24586954 PMCID: PMC3935918 DOI: 10.1371/journal.pone.0089673] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 01/21/2014] [Indexed: 11/28/2022] Open
Abstract
mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood. Because the RNA intermediates in each of these steps have finite lifetimes, extensive mechanistic and dynamical information is encoded in total cellular RNA. Here we report the development of SnapShot-Seq, a set of computational methods that allow the determination of in vivo rates of pre-mRNA synthesis, splicing, intron degradation, and mRNA decay from a single RNA-Seq snapshot of total cellular RNA. SnapShot-Seq can detect in vivo changes in the rates of specific steps of splicing, and it provides genome-wide estimates of pre-mRNA synthesis rates comparable to those obtained via labeling of newly synthesized RNA. We used SnapShot-Seq to investigate the origins of the intrinsic bimodality of metazoan gene expression levels, and our results suggest that this bimodality is partly due to spillover of transcriptional activation from highly expressed genes to their poorly expressed neighbors. SnapShot-Seq dramatically expands the information obtainable from a standard RNA-Seq experiment.
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37
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The leukemogenicity of Hoxa9 depends on alternative splicing. Leukemia 2014; 28:1838-43. [PMID: 24535405 DOI: 10.1038/leu.2014.74] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/03/2014] [Accepted: 02/07/2014] [Indexed: 01/22/2023]
Abstract
Although the transforming potential of Hox genes is known for a long time, it is not precisely understood to which extent splicing is important for the leukemogenicity of this gene family. To test this for Hoxa9, we compared the leukemogenic potential of the wild-type Hoxa9, which undergoes natural splicing, with a full-length Hoxa9 construct, which was engineered to prevent natural splicing (Hoxa9FLim). Inability to undergo splicing significantly reduced in vivo leukemogenicity compared to Hoxa9-wild-typed. Importantly, Hoxa9FLim could compensate for the reduced oncogenicity by collaborating with the natural splice variant Hoxa9T, as co-expression of Hoxa9T and Hoxa9FLim induced acute myeloid leukemia (AML) after a comparable latency time as wild-type Hoxa9. Hoxa9T on its own induced AML after a similar latency as Hoxa9FLim, despite its inability to bind DNA. These data assign splicing a central task in Hox gene mediated leukemogenesis and suggest an important role of homeodomain-less splice variants in hematological neoplasms.
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38
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Waterfall JJ, Arons E, Walker RL, Pineda M, Roth L, Killian JK, Abaan OD, Davis SR, Kreitman RJ, Meltzer PS. High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias. Nat Genet 2013; 46:8-10. [PMID: 24241536 PMCID: PMC3905739 DOI: 10.1038/ng.2828] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/21/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Joshua J Waterfall
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), US National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Evgeny Arons
- Laboratory of Molecular Biology, CCR, NCI, US NIH, Bethesda, Maryland, USA
| | - Robert L Walker
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), US National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Marbin Pineda
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), US National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Laura Roth
- Laboratory of Molecular Biology, CCR, NCI, US NIH, Bethesda, Maryland, USA
| | - J Keith Killian
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), US National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Ogan D Abaan
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), US National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Sean R Davis
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), US National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Robert J Kreitman
- Laboratory of Molecular Biology, CCR, NCI, US NIH, Bethesda, Maryland, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), US National Institutes of Health (NIH), Bethesda, Maryland, USA
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Clinical significance of SF3B1 mutations in Korean patients with myelodysplastic syndromes and myelodysplasia/myeloproliferative neoplasms with ring sideroblasts. Ann Hematol 2013; 93:603-8. [DOI: 10.1007/s00277-013-1915-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/24/2013] [Indexed: 10/26/2022]
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40
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Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat Genet 2013; 45:933-6. [PMID: 23793026 DOI: 10.1038/ng.2674] [Citation(s) in RCA: 364] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 05/29/2013] [Indexed: 12/14/2022]
Abstract
Gene expression profiles and chromosome 3 copy number divide uveal melanomas into two distinct classes correlating with prognosis. Using exome sequencing, we identified recurrent somatic mutations in EIF1AX and SF3B1, specifically occurring in uveal melanomas with disomy 3, which rarely metastasize. Targeted resequencing showed that 24 of 31 tumors with disomy 3 (77%) had mutations in either EIF1AX (15; 48%) or SF3B1 (9; 29%). Mutations were infrequent (2/35; 5.7%) in uveal melanomas with monosomy 3, which are associated with poor prognosis. Resequencing of 13 uveal melanomas with partial monosomy 3 identified 8 tumors with a mutation in either SF3B1 (7; 54%) or EIF1AX (1; 8%). All EIF1AX mutations caused in-frame changes affecting the N terminus of the protein, whereas 17 of 19 SF3B1 mutations encoded an alteration of Arg625. Resequencing of ten uveal melanomas with disomy 3 that developed metastases identified SF3B1 mutations in three tumors, none of which targeted Arg625.
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41
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Hirabayashi R, Hozumi S, Higashijima SI, Kikuchi Y. Ddx46 is required for multi-lineage differentiation of hematopoietic stem cells in zebrafish. Stem Cells Dev 2013; 22:2532-42. [PMID: 23635340 DOI: 10.1089/scd.2012.0623] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Balanced and precisely controlled processes between self-renewal and differentiation of hematopoietic stem cells (HSCs) into all blood lineages are critical for vertebrate definitive hematopoiesis. However, the molecular mechanisms underlying the maintenance and differentiation of HSCs have not been fully elucidated. Here, we show that zebrafish Ddx46, encoding a DEAD-box RNA helicase, is expressed in HSCs of the caudal hematopoietic tissue (CHT). The number of HSCs expressing the molecular markers cmyb or T-cell acute lymphocytic leukemia 1 (tal1) was markedly reduced in Ddx46 mutants. However, massive cell death of HSCs was not detected, and proliferation of HSCs was normal in the CHT of the mutants at 48 h postfertilization. We found that myelopoiesis occurred, but erythropoiesis and lymphopoiesis were suppressed, in Ddx46 mutants. Consistent with these results, the expression of spi1, encoding a regulator of myeloid development, was maintained, but the expression of gata1a, encoding a regulator of erythrocyte development, was downregulated in the mutants. Taken together, our results provide the first genetic evidence that zebrafish Ddx46 is required for the multilineage differentiation of HSCs during development, through the regulation of specific gene expressions.
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Affiliation(s)
- Ryo Hirabayashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
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42
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Keightley MC, Crowhurst MO, Layton JE, Beilharz T, Markmiller S, Varma S, Hogan BM, de Jong-Curtain TA, Heath JK, Lieschke GJ. In vivo mutation of pre-mRNA processing factor 8 (Prpf8) affects transcript splicing, cell survival and myeloid differentiation. FEBS Lett 2013; 587:2150-7. [PMID: 23714367 DOI: 10.1016/j.febslet.2013.05.030] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 05/15/2013] [Accepted: 05/15/2013] [Indexed: 01/09/2023]
Abstract
Mutated spliceosome components are recurrently being associated with perturbed tissue development and disease pathogenesis. Cephalophŏnus (cph), is a zebrafish mutant carrying an early premature STOP codon in the spliceosome component Prpf8 (pre-mRNA processing factor 8). Cph initially develops normally, but then develops widespread cell death, especially in neurons, and is embryonic lethal. Cph mutants accumulate aberrantly spliced transcripts retaining both U2- and U12-type introns. Within early haematopoiesis, myeloid differentiation is impaired, suggesting Prpf8 is required for haematopoietic development. Cph provides an animal model for zygotic PRPF8 dysfunction diseases and for evaluating therapeutic interventions.
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Affiliation(s)
- Maria-Cristina Keightley
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
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43
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Genetic characterization of SF3B1 mutations in single chronic lymphocytic leukemia cells. Leukemia 2013; 27:2264-7. [PMID: 23685408 DOI: 10.1038/leu.2013.155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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44
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Fischer U, Dugas M, Hu J, Borkhardt A. Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia. Genes Chromosomes Cancer 2013; 52:564-79. [DOI: 10.1002/gcc.22054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/29/2013] [Indexed: 01/10/2023] Open
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45
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Filip AA. New boys in town: prognostic role of SF3B1, NOTCH1 and other cryptic alterations in chronic lymphocytic leukemia and how it works. Leuk Lymphoma 2013; 54:1876-81. [PMID: 23343182 DOI: 10.3109/10428194.2013.769049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
B-cell chronic lymphocytic leukemia (B-CLL) is one of the most common leukemias of the elderly. To date, although many prognostic factors are known, none are universal or easily accessible thus allowing for the stratification of patients to slow-go and aggressive-course groups. Recent studies have identified new recurrent mutations in CLL cells, including mutation of the gene encoding one of the spliceosome subunits, SF3B1, mutation or rearrangement of NOTCH1, a gene of well-known tumorigenesis association, and disruption of BIRC3, a member of the inhibitors of apoptosis (IAP) family. This article presents the current state-of-the-art findings concerning the prognostic significance of these new alterations, as well as an explanation of the mechanisms underlying their biological impact on CLL lymphocytes.
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Affiliation(s)
- Agata A Filip
- Department of Cancer Genetics, Medical University of Lublin, Poland.
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46
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Abstract
Several bacterial fermentation products and their synthetic derivatives display antitumour activities and bind tightly to components of the spliceosome, which is the complex molecular machinery involved in the removal of introns from mRNA precursors in eukaryotic cells. The drugs alter gene expression, including alternative splicing, of genes that are important for cancer progression. A flurry of recent reports has revealed that genes encoding splicing factors, including the drug target splicing factor 3B subunit 1 (SF3B1), are among the most highly mutated in various haematological malignancies such as chronic lymphocytic leukaemia and myelodysplastic syndromes. These observations highlight the role of splicing factors in cancer and suggest that an understanding of the molecular effects of drugs targeting these proteins could open new perspectives for studies of the spliceosome and its role in cancer progression, and for the development of novel antitumour therapies.
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47
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Liang WS, Craig DW, Carpten J, Borad MJ, Demeure MJ, Weiss GJ, Izatt T, Sinari S, Christoforides A, Aldrich J, Kurdoglu A, Barrett M, Phillips L, Benson H, Tembe W, Braggio E, Kiefer JA, Legendre C, Posner R, Hostetter GH, Baker A, Egan JB, Han H, Lake D, Stites EC, Ramanathan RK, Fonseca R, Stewart AK, Von Hoff D. Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing. PLoS One 2012; 7:e43192. [PMID: 23071490 PMCID: PMC3468610 DOI: 10.1371/journal.pone.0043192] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 07/19/2012] [Indexed: 12/24/2022] Open
Abstract
Pancreatic adenocarcinoma (PAC) is among the most lethal malignancies. While research has implicated multiple genes in disease pathogenesis, identification of therapeutic leads has been difficult and the majority of currently available therapies provide only marginal benefit. To address this issue, our goal was to genomically characterize individual PAC patients to understand the range of aberrations that are occurring in each tumor. Because our understanding of PAC tumorigenesis is limited, evaluation of separate cases may reveal aberrations, that are less common but may provide relevant information on the disease, or that may represent viable therapeutic targets for the patient. We used next generation sequencing to assess global somatic events across 3 PAC patients to characterize each patient and to identify potential targets. This study is the first to report whole genome sequencing (WGS) findings in paired tumor/normal samples collected from 3 separate PAC patients. We generated on average 132 billion mappable bases across all patients using WGS, and identified 142 somatic coding events including point mutations, insertion/deletions, and chromosomal copy number variants. We did not identify any significant somatic translocation events. We also performed RNA sequencing on 2 of these patients' tumors for which tumor RNA was available to evaluate expression changes that may be associated with somatic events, and generated over 100 million mapped reads for each patient. We further performed pathway analysis of all sequencing data to identify processes that may be the most heavily impacted from somatic and expression alterations. As expected, the KRAS signaling pathway was the most heavily impacted pathway (P<0.05), along with tumor-stroma interactions and tumor suppressive pathways. While sequencing of more patients is needed, the high resolution genomic and transcriptomic information we have acquired here provides valuable information on the molecular composition of PAC and helps to establish a foundation for improved therapeutic selection.
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Affiliation(s)
- Winnie S. Liang
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - David W. Craig
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - John Carpten
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | | | - Michael J. Demeure
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Virginia G. Piper Cancer Center Clinical Trials, Scottsdale Healthcare, Scottsdale, Arizona, United States of America
| | - Glen J. Weiss
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Virginia G. Piper Cancer Center Clinical Trials, Scottsdale Healthcare, Scottsdale, Arizona, United States of America
| | - Tyler Izatt
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Shripad Sinari
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Alexis Christoforides
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Jessica Aldrich
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Ahmet Kurdoglu
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Michael Barrett
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Lori Phillips
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Hollie Benson
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Waibhav Tembe
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | | | - Jeffrey A. Kiefer
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Christophe Legendre
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Richard Posner
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Galen H. Hostetter
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Angela Baker
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Jan B. Egan
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Haiyong Han
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Douglas Lake
- Arizona State University, Tempe, Arizona, United States of America
| | - Edward C. Stites
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Ramesh K. Ramanathan
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Virginia G. Piper Cancer Center Clinical Trials, Scottsdale Healthcare, Scottsdale, Arizona, United States of America
| | - Rafael Fonseca
- Mayo Clinic, Scottsdale, Arizona, United States of America
| | | | - Daniel Von Hoff
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Mayo Clinic, Scottsdale, Arizona, United States of America
- Virginia G. Piper Cancer Center Clinical Trials, Scottsdale Healthcare, Scottsdale, Arizona, United States of America
- * E-mail:
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48
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Liang WS, Craig DW, Carpten J, Borad MJ, Demeure MJ, Weiss GJ, Izatt T, Sinari S, Christoforides A, Aldrich J, Kurdoglu A, Barrett M, Phillips L, Benson H, Tembe W, Braggio E, Kiefer JA, Legendre C, Posner R, Hostetter GH, Baker A, Egan JB, Han H, Lake D, Stites EC, Ramanathan RK, Fonseca R, Stewart AK, Von Hoff D. Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing. PLoS One 2012. [PMID: 23071490 DOI: 10.137/journal.pone.0043192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pancreatic adenocarcinoma (PAC) is among the most lethal malignancies. While research has implicated multiple genes in disease pathogenesis, identification of therapeutic leads has been difficult and the majority of currently available therapies provide only marginal benefit. To address this issue, our goal was to genomically characterize individual PAC patients to understand the range of aberrations that are occurring in each tumor. Because our understanding of PAC tumorigenesis is limited, evaluation of separate cases may reveal aberrations, that are less common but may provide relevant information on the disease, or that may represent viable therapeutic targets for the patient. We used next generation sequencing to assess global somatic events across 3 PAC patients to characterize each patient and to identify potential targets. This study is the first to report whole genome sequencing (WGS) findings in paired tumor/normal samples collected from 3 separate PAC patients. We generated on average 132 billion mappable bases across all patients using WGS, and identified 142 somatic coding events including point mutations, insertion/deletions, and chromosomal copy number variants. We did not identify any significant somatic translocation events. We also performed RNA sequencing on 2 of these patients' tumors for which tumor RNA was available to evaluate expression changes that may be associated with somatic events, and generated over 100 million mapped reads for each patient. We further performed pathway analysis of all sequencing data to identify processes that may be the most heavily impacted from somatic and expression alterations. As expected, the KRAS signaling pathway was the most heavily impacted pathway (P<0.05), along with tumor-stroma interactions and tumor suppressive pathways. While sequencing of more patients is needed, the high resolution genomic and transcriptomic information we have acquired here provides valuable information on the molecular composition of PAC and helps to establish a foundation for improved therapeutic selection.
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Affiliation(s)
- Winnie S Liang
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
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49
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Gaidano G, Foà R, Dalla-Favera R. Molecular pathogenesis of chronic lymphocytic leukemia. J Clin Invest 2012; 122:3432-8. [PMID: 23023714 DOI: 10.1172/jci64101] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults. Here, we highlight important genetic alterations that contribute to tumorigenesis, clinical progression, and chemorefractoriness of CLL. All CLLs share a common gene expression profile that suggests derivation from antigen-experienced B cells, a model supported by frequent B cell receptor repertoire skewing and stereotypy. Many CLL patients carry mutated immuno-globulin heavy-chain variable genes, while approximately 35% harbor unmutated IgV genes, which are associated with an inferior outcome. Deletion of chromosome 13q14, which is the most common genetic mutation at diagnosis, is considered an initiating lesion that frequently results in disruption of the tumor suppressor locus DLEU2/MIR15A/MIR16A. Next-generation sequencing has revealed additional recurrent genetic lesions that are implicated in CLL pathogenesis. These advancements in the molecular genetics of CLL have important implications for stratifying treatment based on molecular prognosticators and for targeted therapy.
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Affiliation(s)
- Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
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50
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Gonzalez-Perez A, Lopez-Bigas N. Functional impact bias reveals cancer drivers. Nucleic Acids Res 2012; 40:e169. [PMID: 22904074 PMCID: PMC3505979 DOI: 10.1093/nar/gks743] [Citation(s) in RCA: 239] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Identifying cancer driver genes and pathways among all somatic mutations detected in a cohort of tumors is a key challenge in cancer genomics. Traditionally, this is done by prioritizing genes according to the recurrence of alterations that they bear. However, this approach has some known limitations, such as the difficulty to correctly estimate the background mutation rate, and the fact that it cannot identify lowly recurrently mutated driver genes. Here we present a novel approach, Oncodrive-fm, to detect candidate cancer drivers which does not rely on recurrence. First, we hypothesized that any bias toward the accumulation of variants with high functional impact observed in a gene or group of genes may be an indication of positive selection and can thus be used to detect candidate driver genes or gene modules. Next, we developed a method to measure this bias (FM bias) and applied it to three datasets of tumor somatic variants. As a proof of concept of our hypothesis we show that most of the highly recurrent and well-known cancer genes exhibit a clear FM bias. Moreover, this novel approach avoids some known limitations of recurrence-based approaches, and can successfully identify lowly recurrent candidate cancer drivers.
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Affiliation(s)
- Abel Gonzalez-Perez
- Research Programme on Biomedical Informatics - GRIB, Universitat Pompeu Fabra - UPF, Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader, 88, E-08003 Barcelona, Spain.
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