51
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Popli P, Richters MM, Chadchan SB, Kim TH, Tycksen E, Griffith O, Thaker PH, Griffith M, Kommagani R. Splicing factor SF3B1 promotes endometrial cancer progression via regulating KSR2 RNA maturation. Cell Death Dis 2020; 11:842. [PMID: 33040078 PMCID: PMC7548007 DOI: 10.1038/s41419-020-03055-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Although endometrial cancer is the most common cancer of the female reproductive tract, we have little understanding of what controls endometrial cancer beyond the transcriptional effects of steroid hormones such as estrogen. As a result, we have limited therapeutic options for the ~62,000 women diagnosed with endometrial cancer each year in the United States. Here, in an attempt to identify new prognostic and therapeutic targets, we focused on a new area for this cancer—alternative mRNA splicing—and investigated whether splicing factor, SF3B1, plays an important role in endometrial cancer pathogenesis. Using a tissue microarray, we found that human endometrial tumors expressed more SF3B1 protein than non-cancerous tissues. Furthermore, SF3B1 knockdown reduced in vitro proliferation, migration, and invasion of the endometrial cancer cell lines Ishikawa and AN3CA. Similarly, the SF3B1 inhibitor, Pladienolide-B (PLAD-B), reduced the Ishikawa and AN3CA cell proliferation and invasion in vitro. Moreover, PLAD-B reduced tumor growth in an orthotopic endometrial cancer mouse model. Using RNA-Seq approach, we identified ~2000 differentially expressed genes (DEGs) with SF3B1 knockdown in endometrial cancer cells. Additionally, alternative splicing (AS) events analysis revealed that SF3B1 depletion led to alteration in multiple categories of AS events including alternative exon skipping (ES), transcript start site usage (TSS), and transcript termination site (TTS) usage. Subsequently, bioinformatics analysis showed KSR2 as a potential candidate for SF3B1-mediated functions in endometrial cancer. Specifically, loss of SF3B1 led to decrease in KSR2 expression, owing to reduced maturation of KSR2 pre-mRNA to a mature RNA. Importantly, we found rescuing the KSR2 expression with SF3B1 knockdown partially restored the cell growth of endometrial cancer cells. Taken together, our data suggest that SF3B1 plays a crucial oncogenic role in the tumorigenesis of endometrial cancer and hence may support the development of SF3B1 inhibitors to treat this disease.
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Affiliation(s)
- Pooja Popli
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Megan M Richters
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sangappa B Chadchan
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tae Hoon Kim
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 48824, USA
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Obi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Premal H Thaker
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ramakrishna Kommagani
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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52
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Petasny M, Bentata M, Pawellek A, Baker M, Kay G, Salton M. Splicing to Keep Cycling: The Importance of Pre-mRNA Splicing during the Cell Cycle. Trends Genet 2020; 37:266-278. [PMID: 32950269 DOI: 10.1016/j.tig.2020.08.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022]
Abstract
Pre-mRNA splicing is a fundamental process in mammalian gene expression, and alternative splicing plays an extensive role in generating protein diversity. Because the majority of genes undergo pre-mRNA splicing, most cellular processes depend on proper spliceosome function. We focus on the cell cycle and describe its dependence on pre-mRNA splicing and accurate alternative splicing. We outline the key cell-cycle factors and their known alternative splicing isoforms. We discuss different levels of pre-mRNA splicing regulation such as post-translational modifications and changes in the expression of splicing factors. We describe the effect of chromatin dynamics on pre-mRNA splicing during the cell cycle. In addition, we focus on spliceosome component SF3B1, which is mutated in many types of cancer, and describe the link between SF3B1 and its inhibitors and the cell cycle.
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Affiliation(s)
- Mayra Petasny
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mercedes Bentata
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Andrea Pawellek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mai Baker
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
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53
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Fagnan A, Bagger FO, Piqué-Borràs MR, Ignacimouttou C, Caulier A, Lopez CK, Robert E, Uzan B, Gelsi-Boyer V, Aid Z, Thirant C, Moll U, Tauchmann S, Kurtovic-Kozaric A, Maciejewski J, Dierks C, Spinelli O, Salmoiraghi S, Pabst T, Shimoda K, Deleuze V, Lapillonne H, Sweeney C, De Mas V, Leite B, Kadri Z, Malinge S, de Botton S, Micol JB, Kile B, Carmichael CL, Iacobucci I, Mullighan CG, Carroll M, Valent P, Bernard OA, Delabesse E, Vyas P, Birnbaum D, Anguita E, Garçon L, Soler E, Schwaller J, Mercher T. Human erythroleukemia genetics and transcriptomes identify master transcription factors as functional disease drivers. Blood 2020; 136:698-714. [PMID: 32350520 PMCID: PMC8215330 DOI: 10.1182/blood.2019003062] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Acute erythroleukemia (AEL or acute myeloid leukemia [AML]-M6) is a rare but aggressive hematologic malignancy. Previous studies showed that AEL leukemic cells often carry complex karyotypes and mutations in known AML-associated oncogenes. To better define the underlying molecular mechanisms driving the erythroid phenotype, we studied a series of 33 AEL samples representing 3 genetic AEL subgroups including TP53-mutated, epigenetic regulator-mutated (eg, DNMT3A, TET2, or IDH2), and undefined cases with low mutational burden. We established an erythroid vs myeloid transcriptome-based space in which, independently of the molecular subgroup, the majority of the AEL samples exhibited a unique mapping different from both non-M6 AML and myelodysplastic syndrome samples. Notably, >25% of AEL patients, including in the genetically undefined subgroup, showed aberrant expression of key transcriptional regulators, including SKI, ERG, and ETO2. Ectopic expression of these factors in murine erythroid progenitors blocked in vitro erythroid differentiation and led to immortalization associated with decreased chromatin accessibility at GATA1-binding sites and functional interference with GATA1 activity. In vivo models showed development of lethal erythroid, mixed erythroid/myeloid, or other malignancies depending on the cell population in which AEL-associated alterations were expressed. Collectively, our data indicate that AEL is a molecularly heterogeneous disease with an erythroid identity that results in part from the aberrant activity of key erythroid transcription factors in hematopoietic stem or progenitor cells.
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Affiliation(s)
- Alexandre Fagnan
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Frederik Otzen Bagger
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
- Swiss Institute of Bioinformatics, Basel, Basel, Switzerland
| | - Maria-Riera Piqué-Borràs
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Cathy Ignacimouttou
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Alexis Caulier
- Equipe d'Accueil (EA) 4666, Hématopoïèse et Immunologie (HEMATIM), Université de Picardie Jules Verne (UPJV), Amiens, France
- Service Hématologie Biologique, Centre Hospitalier Universitaire (CHU) Amiens, Amiens, France
| | - Cécile K Lopez
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Elie Robert
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Benjamin Uzan
- Unité Mixte de Recherche 967 (UMR 967), INSERM-Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF)/Institut de Biologie François Jacob (IBFJ)/Institut de Radiobiologie Cellulaire et Moléculaire (IRCM)/Laboratoire des cellules Souches Hématopoïétiques et des Leucémies (LSHL)-Université Paris-Diderot-Université Paris-Sud, Fontenay-aux-Roses, France
| | - Véronique Gelsi-Boyer
- U1068 and
- UMR7258, Centre de Recherche en Cancérologie de Marseille, Centre National de la Recherche Scientifique (CNRS)/INSERM/Institut Paoli Calmettes/Aix-Marseille Université, Marseille, France
| | - Zakia Aid
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Cécile Thirant
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Ute Moll
- Institute of Molecular Oncology, University Medical Center Göttingen, Göttingen, Germany
- Department of Pathology, Stony Brook University, Stony Brook, NY
| | - Samantha Tauchmann
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Amina Kurtovic-Kozaric
- Clinical Center of the University of Sarajevo, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Jaroslaw Maciejewski
- Department of Translational Hematology and Oncologic Research, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH
| | - Christine Dierks
- Hämatologie, Onkologie und Stammzelltransplantation, Klinik für Innere Medizin I, Freiburg, Germany
| | - Orietta Spinelli
- UOC Ematologia, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Silvia Salmoiraghi
- UOC Ematologia, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII Hospital, Bergamo, Italy
- FROM Research Foundation, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Thomas Pabst
- Department of Oncology, Inselspital, University Hospital Bern/University of Bern, Bern, Switzerland
| | - Kazuya Shimoda
- Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Virginie Deleuze
- IGMM, University of Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | - Hélène Lapillonne
- Centre de Recherche Saint Antoine (CRSA)-Unité INSERM, Sorbonne Université/Assistance Publique-Hôpitaux de Paris (AP-HP)/Hôpital Trousseau, Paris, France
| | - Connor Sweeney
- Medical Research Council Molecular Haematology Unit (MRC MHU), Biomedical Research Centre (BRC) Hematology Theme, Oxford Biomedical Research Centre, Oxford Centre for Haematology, Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Véronique De Mas
- Team 16, Hematology Laboratory, Center of Research of Cancerology of Toulouse, U1037, INSERM/Institut Universitaire du Cancer de Toulouse (IUCT) Oncopole, Toulouse, France
| | - Betty Leite
- Genomic Platform, Unité Mixte de Service - Analyse Moléculaire, Modélisation et Imagerie de la maladie Cancéreuse (UMS AMMICA), Gustave Roussy/Université Paris-Saclay, Villejuif, France
| | - Zahra Kadri
- Division of Innovative Therapies, UMR-1184, Immunologie des Maladies Virales, Auto-immunes, Hématologiques et Bactériennes (IMVA-HB) and Infectious Disease Models and Innovative Therapies (IDMIT) Center, CEA/INSERM/Paris-Saclay University, Fontenay-aux-Roses, France
| | - Sébastien Malinge
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, Australia
| | - Stéphane de Botton
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Jean-Baptiste Micol
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
| | - Benjamin Kile
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | | | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, PA
| | - Peter Valent
- Division of Hematology and Hemostaseology, Department of Internal Medicine I and
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Olivier A Bernard
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Eric Delabesse
- Team 16, Hematology Laboratory, Center of Research of Cancerology of Toulouse, U1037, INSERM/Institut Universitaire du Cancer de Toulouse (IUCT) Oncopole, Toulouse, France
| | - Paresh Vyas
- Medical Research Council Molecular Haematology Unit (MRC MHU), Biomedical Research Centre (BRC) Hematology Theme, Oxford Biomedical Research Centre, Oxford Centre for Haematology, Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Daniel Birnbaum
- U1068 and
- UMR7258, Centre de Recherche en Cancérologie de Marseille, Centre National de la Recherche Scientifique (CNRS)/INSERM/Institut Paoli Calmettes/Aix-Marseille Université, Marseille, France
| | - Eduardo Anguita
- Hematology Department
- Instituto de Medicina de Laboratorio (IML), and
- Instituto de Investigación Sanitaria San Carlos, (IdISSC), Hospital Clínico San Carlos (HCSC), Madrid, Spain; and
- Department of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Loïc Garçon
- Equipe d'Accueil (EA) 4666, Hématopoïèse et Immunologie (HEMATIM), Université de Picardie Jules Verne (UPJV), Amiens, France
- Service Hématologie Biologique, Centre Hospitalier Universitaire (CHU) Amiens, Amiens, France
| | - Eric Soler
- IGMM, University of Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | - Juerg Schwaller
- University Children's Hospital Beider Basel (UKBB), Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Thomas Mercher
- Unité 1170 (U1170), INSERM, Gustave Roussy, Université Paris Diderot, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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54
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Hershberger CE, Moyer DC, Adema V, Kerr CM, Walter W, Hutter S, Meggendorfer M, Baer C, Kern W, Nadarajah N, Twardziok S, Sekeres MA, Haferlach C, Haferlach T, Maciejewski JP, Padgett RA. Complex landscape of alternative splicing in myeloid neoplasms. Leukemia 2020; 35:1108-1120. [PMID: 32753690 PMCID: PMC8101081 DOI: 10.1038/s41375-020-1002-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022]
Abstract
Myeloid neoplasms are characterized by frequent mutations in at least seven components of the spliceosome that have distinct roles in the process of pre-mRNA splicing. Hotspot mutations in SF3B1, SRSF2, U2AF1 and loss of function mutations in ZRSR2 have revealed widely different aberrant splicing signatures with little overlap. However, previous studies lacked the power necessary to identify commonly mis-spliced transcripts in heterogeneous patient cohorts. By performing RNA-Seq on bone marrow samples from 1,258 myeloid neoplasm patients and 63 healthy bone marrow donors, we identified transcripts frequently mis-spliced by mutated splicing factors (SF), rare SF mutations with common alternative splicing (AS) signatures, and SF-dependent neojunctions. We characterized 17,300 dysregulated AS events using a pipeline designed to predict the impact of mis-splicing on protein function. Meta-splicing analysis revealed a pattern of reduced levels of retained introns among disease samples that was exacerbated in patients with splicing factor mutations. These introns share characteristics with “detained introns,” a class of introns that have been shown to promote differentiation by detaining pro-proliferative transcripts in the nucleus. In this study, we have functionally characterized 17,300 targets of mis-splicing by the SF mutations, identifying a common pathway by which AS may promote maintenance of a proliferative state.
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Affiliation(s)
- Courtney E Hershberger
- Cardiovascular and Metabolic Sciences Department, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Devlin C Moyer
- Cardiovascular and Metabolic Sciences Department, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Vera Adema
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Cassandra M Kerr
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | | | | | | | | | | | | | - Mikkael A Sekeres
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Richard A Padgett
- Cardiovascular and Metabolic Sciences Department, Cleveland Clinic Foundation, Cleveland, OH, USA.
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55
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Spliceosomal factor mutations and mis-splicing in MDS. Best Pract Res Clin Haematol 2020; 33:101199. [PMID: 33038983 DOI: 10.1016/j.beha.2020.101199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Somatic, heterozygous missense and nonsense mutations in at least seven proteins that function in the spliceosome are found at high frequency in MDS patients. These proteins act at various steps in the process of splicing by the spliceosome and lead to characteristic alterations in the alternative splicing of a subset of genes. Several studies have investigated the effects of these mutations and have attempted to identify a commonly affected gene or pathway. Here, we summarize what is known about the normal function of these proteins and how the mutations alter the splicing landscape of the genome. We also summarize the commonly mis-spliced gene targets and discuss the state of mechanistic unification that has been achieved. Finally, we discuss alternative mechanisms by which these mutations may lead to disease.
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56
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Malcovati L, Stevenson K, Papaemmanuil E, Neuberg D, Bejar R, Boultwood J, Bowen DT, Campbell PJ, Ebert BL, Fenaux P, Haferlach T, Heuser M, Jansen JH, Komrokji RS, Maciejewski JP, Walter MJ, Fontenay M, Garcia-Manero G, Graubert TA, Karsan A, Meggendorfer M, Pellagatti A, Sallman DA, Savona MR, Sekeres MA, Steensma DP, Tauro S, Thol F, Vyas P, Van de Loosdrecht AA, Haase D, Tüchler H, Greenberg PL, Ogawa S, Hellstrom-Lindberg E, Cazzola M. SF3B1-mutant MDS as a distinct disease subtype: a proposal from the International Working Group for the Prognosis of MDS. Blood 2020; 136:157-170. [PMID: 32347921 PMCID: PMC7362582 DOI: 10.1182/blood.2020004850] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 12/11/2022] Open
Abstract
The 2016 revision of the World Health Organization classification of tumors of hematopoietic and lymphoid tissues is characterized by a closer integration of morphology and molecular genetics. Notwithstanding, the myelodysplastic syndrome (MDS) with isolated del(5q) remains so far the only MDS subtype defined by a genetic abnormality. Approximately half of MDS patients carry somatic mutations in spliceosome genes, with SF3B1 being the most commonly mutated one. SF3B1 mutation identifies a condition characterized by ring sideroblasts (RS), ineffective erythropoiesis, and indolent clinical course. A large body of evidence supports recognition of SF3B1-mutant MDS as a distinct nosologic entity. To further validate this notion, we interrogated the data set of the International Working Group for the Prognosis of MDS (IWG-PM). Based on the findings of our analyses, we propose the following diagnostic criteria for SF3B1-mutant MDS: (1) cytopenia as defined by standard hematologic values, (2) somatic SF3B1 mutation, (3) morphologic dysplasia (with or without RS), and (4) bone marrow blasts <5% and peripheral blood blasts <1%. Selected concomitant genetic lesions represent exclusion criteria for the proposed entity. In patients with clonal cytopenia of undetermined significance, SF3B1 mutation is almost invariably associated with subsequent development of overt MDS with RS, suggesting that this genetic lesion might provide presumptive evidence of MDS in the setting of persistent unexplained cytopenia. Diagnosis of SF3B1-mutant MDS has considerable clinical implications in terms of risk stratification and therapeutic decision making. In fact, this condition has a relatively good prognosis and may respond to luspatercept with abolishment of the transfusion requirement.
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Affiliation(s)
- Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - David T Bowen
- St. James's Institute of Oncology, Leeds Teaching Hospitals, Leeds, United Kingdom
| | | | | | - Pierre Fenaux
- Hôpital St Louis, Assistance Publique-Hôpitaux de Paris and Paris Diderot University, Paris, France
| | | | | | - Joop H Jansen
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rami S Komrokji
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | | | - Michaela Fontenay
- Université Paris Descartes, Hôpital Cochin Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | | | - Aly Karsan
- BC Cancer Research Centre & Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Andrea Pellagatti
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David A Sallman
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | | | | | - Sudhir Tauro
- Dundee Cancer Centre, University of Dundee, Ninewells Hospital, Dundee, United Kingdom
| | | | - Paresh Vyas
- MRC Molecular Hematology Unit, WIMM University of Oxford, Oxford Biomedical Research Centre, Department of Hematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Detlef Haase
- University Medical Center, Georg August University, Göttingen, Germany
| | - Heinz Tüchler
- Ludwig Boltzmann Institute for Leukemia Research, Vienna, Austria
| | | | - Seishi Ogawa
- Department of Tumor Biology, University of Kyoto, Japan; and
| | - Eva Hellstrom-Lindberg
- Division of Hematology, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia & Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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57
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Laaref AM, Manchon L, Bareche Y, Lapasset L, Tazi J. The core spliceosomal factor U2AF1 controls cell-fate determination via the modulation of transcriptional networks. RNA Biol 2020; 17:857-871. [PMID: 32150510 PMCID: PMC7549707 DOI: 10.1080/15476286.2020.1733800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing (AS) plays a central role during cell-fate determination. However, how the core spliceosomal factors (CSFs) are involved in this process is poorly understood. Here, we report the down-regulation of the U2AF1 CSF during stem cell differentiation. To investigate its function in stemness and differentiation, we downregulated U2AF1 in human induced pluripotent stem cells (hiPSCs), using an inducible-shRNA system, to the level found in differentiated ectodermal, mesodermal and endodermal cells. RNA sequencing and computational analysis reveal that U2AF1 down-regulation modulates the expression of development-regulating genes and regulates transcriptional networks involved in cell-fate determination. Furthermore, U2AF1 down-regulation induces a switch in the AS of transcription factors (TFs) required to establish specific cell lineages, and favours the splicing of a differentiated cell-specific isoform of DNMT3B. Our results showed that the differential expression of the core spliceosomal factor U2AF1, between stem cells and the precursors of the three germ layers regulates a cell-type-specific alternative splicing programme and a transcriptional network involved in cell-fate determination via the modulation of gene expression and alternative splicing of transcription regulators.
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Affiliation(s)
| | | | - Yacine Bareche
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Breast Cancer Translational Research Laboratory, J. C. Heuson, Institut Jules Bordet, Université Libre De Bruxelles, Brussels, Belgium
| | - Laure Lapasset
- IGMM, CNRS, University of Montpellier, Montpellier, France
- VP research, CNRS, University of Montpellier, Montpellier, France
| | - Jamal Tazi
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Lead Contact
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58
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Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with acute myeloid leukemia. Leukemia 2020; 34:2621-2634. [PMID: 32358566 DOI: 10.1038/s41375-020-0839-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022]
Abstract
Previous studies demonstrated that splicing factor mutations are recurrent events in hematopoietic malignancies with both clinical and functional implications. However, their aberrant splicing patterns in acute myeloid leukemia remain largely unexplored. In this study, we characterized mutations in SRSF2, U2AF1, and SF3B1, the most commonly mutated splicing factors. In our clinical analysis of 2678 patients, splicing factor mutations showed inferior relapse-free and overall survival, however, these mutations did not represent independent prognostic markers. RNA-sequencing of 246 and independent validation in 177 patients revealed an isoform expression profile which is highly characteristic for each individual mutation, with several isoforms showing a strong dysregulation. By establishing a custom differential splice junction usage pipeline, we accurately detected aberrant splicing in splicing factor mutated samples. A large proportion of differentially used junctions were novel, including several junctions in leukemia-associated genes. In SRSF2(P95H) mutants, we further explored the possibility of a cascading effect through the dysregulation of the splicing pathway. Furthermore, we observed a validated impact on overall survival for two junctions overused in SRSF2(P95H) mutants. We conclude that splicing factor mutations do not represent independent prognostic markers. However, they do have genome-wide consequences on gene splicing leading to dysregulated isoform expression of several genes.
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59
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Anande G, Deshpande NP, Mareschal S, Batcha AMN, Hampton HR, Herold T, Lehmann S, Wilkins MR, Wong JWH, Unnikrishnan A, Pimanda JE. RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia. Clin Cancer Res 2020; 26:3597-3607. [PMID: 32122925 DOI: 10.1158/1078-0432.ccr-20-0184] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/13/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of splicing factor genes are common in some hematologic cancers but are relatively uncommon in acute myeloid leukemia (AML, < 20% of patients). We examined whether RNA splicing differences exist in AML, even in the absence of splicing factor mutations. EXPERIMENTAL DESIGN We developed a bioinformatics pipeline to study alternative RNA splicing in RNA-sequencing data from large cohorts of patients with AML. RESULTS We have identified recurrent differential alternative splicing between patients with poor and good prognosis. These splicing events occurred even in patients without any discernible splicing factor mutations. Alternative splicing recurrently occurred in genes with specific molecular functions, primarily related to protein translation. Developing tools to predict the functional impact of alternative splicing on the translated protein, we discovered that approximately 45% of the splicing events directly affected highly conserved protein domains. Several splicing factors were themselves misspliced and the splicing of their target transcripts were altered. Studying differential gene expression in the same patients, we identified that alternative splicing of protein translation genes in ELNAdv patients resulted in the induction of an integrated stress response and upregulation of inflammation-related genes. Finally, using machine learning techniques, we identified a splicing signature of four genes which refine the accuracy of existing risk prognosis schemes and validated it in a completely independent cohort. CONCLUSIONS Our discoveries therefore identify aberrant alternative splicing as a molecular feature of adverse AML with clinical relevance.See related commentary by Bowman, p. 3503.
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Affiliation(s)
- Govardhan Anande
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia
| | - Nandan P Deshpande
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, New South Wales, Australia
| | - Sylvain Mareschal
- Hematology Centre, Karolinska University Hospital and Department of Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Aarif M N Batcha
- Institute of Medical Data Processing, Biometrics and Epidemiology, Faculty of Medicine, LMU Munich, Munich, Germany.,Data Integration for Future Medicine, LMU Munich, Munich, Germany
| | - Henry R Hampton
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Soren Lehmann
- Hematology Centre, Karolinska University Hospital and Department of Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, New South Wales, Australia
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia.
| | - John E Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia. .,Department of Pathology, School of Medical Sciences, University of New South Wales Sydney, New South Wales, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, New South Wales, Australia
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60
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RUNX1 mutations enhance self-renewal and block granulocytic differentiation in human in vitro models and primary AMLs. Blood Adv 2020; 3:320-332. [PMID: 30709863 DOI: 10.1182/bloodadvances.2018024422] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/24/2018] [Indexed: 12/21/2022] Open
Abstract
To unravel molecular mechanisms by which Runt-related transcription factor 1 (RUNX1) mutations contribute to leukemic transformation, we introduced the RUNX1-S291fs300X mutation in human CD34+ stem/progenitor cells and in human induced pluripotent stem cells (iPSCs). In both models, RUNX1mut overexpression strongly impaired myeloid commitment. Instead, self-renewal was enhanced, as shown, by increased long-term culture-initiating cell frequencies and enhanced colony-forming cell replating capacity. Long-term suspension cultures with RUNX1mut-transduced cord blood (CB) CD34+ cells continued for more than 100 days, during which the cells displayed an immature granulocyte-macrophage progenitor-like CD34+/CD123+/CD45RA+ phenotype. The CD34+/CD38- hematopoietic stem cell (HSC) population most likely acted as cell of origin, as HSCs provided the best long-term proliferative potential on overexpression of RUNX1mut. CEBPA expression was reduced in RUNX1mut cells, and reexpression of CEBPA partly restored differentiation. RNA-seq analysis on CB/iPSC systems and on primary patient samples confirmed that RUNX1 mutations induce a myeloid differentiation block, and that a common set of RUNX1mut-upregulated target genes was strongly enriched for gene ontology terms associated with nucleosome assembly and chromatin structure. Interestingly, in comparison with AML1-ETO binding in acute myeloid leukemias (AMLs), we found significantly distinct genomic distribution and differential expression for RUNX1mut of genes such as TCF4, MEIS1, and HMGA2 that may potentially contribute to the underlying difference in clinical outcomes between RUNX1mut and AML1-ETO patients. In conclusion, RUNX1mut appears to induce a specific transcriptional program that contributes to leukemic transformation.
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61
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Madan V, Li J, Zhou S, Teoh WW, Han L, Meggendorfer M, Malcovati L, Cazzola M, Ogawa S, Haferlach T, Yang H, Koeffler HP. Distinct and convergent consequences of splice factor mutations in myelodysplastic syndromes. Am J Hematol 2020; 95:133-143. [PMID: 31680297 DOI: 10.1002/ajh.25673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/13/2019] [Accepted: 10/30/2019] [Indexed: 01/02/2023]
Abstract
Myelodysplastic syndromes (MDS) are characterized by recurrent somatic alterations often affecting components of RNA splicing machinery. Mutations of splice factors SF3B1, SRSF2, ZRSR2 and U2AF1 occur in >50% of MDS. To assess the impact of spliceosome mutations on splicing and to identify common pathways/genes affected by distinct mutations, we performed RNA-sequencing of MDS bone marrow samples harboring spliceosome mutations (including hotspot alterations of SF3B1, SRSF2 and U2AF1; small deletions of SRSF2 and truncating mutations of ZRSR2), and devoid of other common co-occurring mutations. We uncover the landscape of splicing alterations in each splice factor mutant MDS and demonstrate that small deletions in SRSF2 cause highest number of splicing alterations compared with other spliceosome mutations. Although the mis-spliced events observed in different splice factor mutations were largely non-overlapping, a subset of genes, including EZH2, were aberrantly spliced in multiple mutant groups. We also verified aberrant splicing of key genes USP9X, USP24 (deubiquitinating enzymes), LUC7L2 (splice factor) and EED (PRC2 component) in MDS harboring small deletions of SRSF2. Pathway analysis revealed that mis-spliced genes in different mutant groups were enriched in RNA splicing and transport as well as several signaling cascades, suggesting converging biological consequences downstream of distinct spliceosome mutations. Our study reveals splicing signatures of each splice factor mutation and identifies shared and distinct sets of mis-spliced genes and affected biological processes in different spliceosome mutant MDS.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore Singapore Singapore
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore Singapore Singapore
- Cardiovascular and Metabolic Disorders ProgramDuke‐NUS Medical School Singapore Singapore
| | - Siqin Zhou
- Cancer Science Institute of Singapore, National University of Singapore Singapore Singapore
| | - Weoi Woon Teoh
- Cancer Science Institute of Singapore, National University of Singapore Singapore Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore Singapore Singapore
- Department of MedicineYong Loo Lin School of Medicine, National University of Singapore Singapore Singapore
| | | | - Luca Malcovati
- Department of Molecular MedicineUniversity of Pavia Pavia Italy
- Department of Hematology OncologyFondazione IRCCS Policlinico San Matteo & University of Pavia Pavia Italy
| | - Mario Cazzola
- Department of Molecular MedicineUniversity of Pavia Pavia Italy
- Department of Hematology OncologyFondazione IRCCS Policlinico San Matteo & University of Pavia Pavia Italy
| | - Seishi Ogawa
- Department of Pathology and Tumor BiologyKyoto University Kyoto Japan
| | | | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore Singapore Singapore
| | - H. Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore Singapore Singapore
- Cedars‐Sinai Medical Center, Division of Hematology/OncologyUCLA School of Medicine Los Angeles California
- National University Cancer Institute, National University Hospital Singapore Singapore Singapore
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62
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Picou F, Vignon C, Debeissat C, Lachot S, Kosmider O, Gallay N, Foucault A, Estienne MH, Ravalet N, Bene MC, Domenech J, Gyan E, Fontenay M, Herault O. Bone marrow oxidative stress and specific antioxidant signatures in myelodysplastic syndromes. Blood Adv 2019; 3:4271-4279. [PMID: 31869414 PMCID: PMC6929385 DOI: 10.1182/bloodadvances.2019000677] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal stem cell disorders with an inherent tendency for transformation in secondary acute myeloid leukemia. This study focused on the redox metabolism of bone marrow (BM) cells from 97 patients compared with 25 healthy controls. The level of reactive oxygen species (ROS) was quantified by flow cytometry in BM cell subsets as well as the expression level of 28 transcripts encoding for major enzymes involved in the antioxidant cellular response. Our results highlight increased ROS levels in BM nonlymphoid cells and especially in primitive CD34posCD38low progenitor cells. Moreover, we identified a specific antioxidant signature, dubbed "antioxidogram," for the different MDS subgroups or secondary acute myeloblastic leukemia (sAML). Our results suggest that progression from MDS toward sAML could be characterized by 3 successive molecular steps: (1) overexpression of enzymes reducing proteic disulfide bonds (MDS with <5% BM blasts [GLRX family]); (2) increased expression of enzymes detoxifying H2O2 (MDS with 5% to 19% BM blasts [PRDX and GPX families]); and finally (3) decreased expression of these enzymes in sAML. The antioxidant score (AO-Score) defined by logistic regression from the expression levels of transcripts made it possible to stage disease progression and, interestingly, this AO-Score was independent of the revised International Scoring System. Altogether, this study demonstrates that MDS and sAML present an important disturbance of redox metabolism, especially in BM stem and progenitor cells and that the specific molecular antioxidant response parameters (antioxidogram, AO-Score) could be considered as useful biomarkers for disease diagnosis and follow-up.
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Affiliation(s)
- Frederic Picou
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Christine Vignon
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Christelle Debeissat
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Sébastien Lachot
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Olivier Kosmider
- Service d'Hématologie Biologique, Assistance Publique-Hôpitaux de Paris, Institut Cochin, Paris, France
| | - Nathalie Gallay
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Amelie Foucault
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Marie-Hélène Estienne
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Noémie Ravalet
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Marie C Bene
- Service d'Hématologie Biologique, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Jorge Domenech
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
| | - Emmanuel Gyan
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie et Thérapie Cellulaire, CHRU de Tours, Tours, France; and
| | - Michaela Fontenay
- Service d'Hématologie Biologique, Assistance Publique-Hôpitaux de Paris, Institut Cochin, Paris, France
| | - Olivier Herault
- Centre National de la Recherche Scientifique (CNRS) Equipe de Recherche Labellisée 7001, LNOX "Leukemic Niche and Redox Metabolism," Tours, France
- Equipe d'Accueil 7501, Université de Tours, Tours, France
- Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire (CHRU) de Tours, Tours, France
- CNRS Groupement de Recherche 3697, "Microenvironment of Tumor Niches," Tours, France
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63
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Visconte V, O. Nakashima M, J. Rogers H. Mutations in Splicing Factor Genes in Myeloid Malignancies: Significance and Impact on Clinical Features. Cancers (Basel) 2019; 11:E1844. [PMID: 31766606 PMCID: PMC6966670 DOI: 10.3390/cancers11121844] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 11/16/2022] Open
Abstract
Components of the pre-messenger RNA splicing machinery are frequently mutated in myeloid malignancies. Mutations in LUC7L2, PRPF8, SF3B1, SRSF2, U2AF1, and ZRSR2 genes occur at various frequencies ranging between 40% and 85% in different subtypes of myelodysplastic syndrome (MDS) and 5% and 10% of acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPNs). In some instances, splicing factor (SF) mutations have provided diagnostic utility and information on clinical outcomes as exemplified by SF3B1 mutations associated with increased ring sideroblasts (RS) in MDS-RS or MDS/MPN-RS with thrombocytosis. SF3B1 mutations are associated with better survival outcomes, while SRSF2 mutations are associated with a shorter survival time and increased AML progression, and U2AF1 mutations with a lower remission rate and shorter survival time. Beside the presence of mutations, transcriptomics technologies have shown that one third of genes in AML patients are differentially expressed, leading to altered transcript stability, interruption of protein function, and improper translation compared to those of healthy individuals. The detection of SF mutations demonstrates the importance of splicing abnormalities in the hematopoiesis of MDS and AML patients given the fact that abnormal splicing regulates the function of several transcriptional factors (PU.1, RUNX1, etc.) crucial in hematopoietic function. This review provides a summary of the significance of the most frequently mutated SF genes in myeloid malignancies and an update on novel targeted therapies in experimental and clinical trial stages.
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Affiliation(s)
- Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Megan O. Nakashima
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Heesun J. Rogers
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH 44195, USA;
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64
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Berger G, Gerritsen M, Yi G, Koorenhof-Scheele TN, Kroeze LI, Stevens-Kroef M, Yoshida K, Shiraishi Y, van den Berg E, Schepers H, Huls G, Mulder AB, Ogawa S, Martens JHA, Jansen JH, Vellenga E. Ring sideroblasts in AML are associated with adverse risk characteristics and have a distinct gene expression pattern. Blood Adv 2019; 3:3111-3122. [PMID: 31648334 PMCID: PMC6849935 DOI: 10.1182/bloodadvances.2019000518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/14/2019] [Indexed: 12/24/2022] Open
Abstract
Ring sideroblasts (RS) emerge as result of aberrant erythroid differentiation leading to excessive mitochondrial iron accumulation, a characteristic feature for myelodysplastic syndromes (MDS) with mutations in the spliceosome gene SF3B1. However, RS can also be observed in patients diagnosed with acute myeloid leukemia (AML). The objective of this study was to characterize RS in patients with AML. Clinically, RS-AML is enriched for ELN adverse risk (55%). In line with this finding, 35% of all cases had complex cytogenetic aberrancies, and TP53 was most recurrently mutated in this cohort (37%), followed by DNMT3A (26%), RUNX1 (25%), TET2 (20%), and ASXL1 (19%). In contrast to RS-MDS, the incidence of SF3B1 mutations was low (8%). Whole-exome sequencing and SNP array analysis on a subset of patients did not uncover a single genetic defect underlying the RS phenotype. Shared genetic defects between erythroblasts and total mononuclear cell fraction indicate common ancestry for the erythroid lineage and the myeloid blast cells in patients with RS-AML. RNA sequencing analysis on CD34+ AML cells revealed differential gene expression between RS-AML and non RS-AML cases, including genes involved in megakaryocyte and erythroid differentiation. Furthermore, several heme metabolism-related genes were found to be upregulated in RS- CD34+ AML cells, as was observed in SF3B1mut MDS. These results demonstrate that although the genetic background of RS-AML differs from that of RS-MDS, they have certain downstream effector pathways in common.
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Affiliation(s)
- Gerbrig Berger
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mylene Gerritsen
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Guoqiang Yi
- Department of Molecular Biology, Radboud University, Nijmegen, The Netherlands
| | | | | | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kenichi Yoshida
- Department of Pathology & Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA information Analysis, Human Genome Centre, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Hein Schepers
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Geert Huls
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - André B Mulder
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Seishi Ogawa
- Department of Pathology & Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan; and
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinksa Institute, Stockholm, Sweden
| | - Joost H A Martens
- Department of Molecular Biology, Radboud University, Nijmegen, The Netherlands
| | | | - Edo Vellenga
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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65
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CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing. PLoS Genet 2019; 15:e1008464. [PMID: 31634348 PMCID: PMC6830814 DOI: 10.1371/journal.pgen.1008464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/05/2019] [Accepted: 10/05/2019] [Indexed: 12/23/2022] Open
Abstract
SF3B1 is the most frequently mutated splicing factor in cancer. Mutations in SF3B1 likely confer clonal advantages to cancer cells but they may also confer vulnerabilities that can be therapeutically targeted. SF3B1 cancer mutations can be maintained in homozygosis in C. elegans, allowing synthetic lethal screens with a homogeneous population of animals. These mutations cause alternative splicing (AS) defects in C. elegans, as it occurs in SF3B1-mutated human cells. In a screen, we identified RNAi of U2 snRNP components that cause synthetic lethality with sftb-1/SF3B1 mutations. We also detected synthetic interactions between sftb-1 mutants and cancer-related mutations in uaf-2/U2AF1 or rsp-4/SRSF2, demonstrating that this model can identify interactions between mutations that are mutually exclusive in human tumors. Finally, we have edited an SFTB-1 domain to sensitize C. elegans to the splicing modulators pladienolide B and herboxidiene. Thus, we have established a multicellular model for SF3B1 mutations amenable for high-throughput genetic and chemical screens.
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66
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Splicing factor mutant myelodysplastic syndromes: Recent advances. Adv Biol Regul 2019; 75:100655. [PMID: 31558432 DOI: 10.1016/j.jbior.2019.100655] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 11/23/2022]
Abstract
The myelodysplastic syndromes (MDS) are common myeloid malignancies showing frequent progression to acute myeloid leukemia (AML). Pre-mRNA splicing is an essential cellular process carried out by the spliceosome. Mutations in splicing factor genes (including SF3B1, SRSF2, U2AF1 and ZRSR2) occur in over half of MDS patients and result in aberrant pre-mRNA splicing of many target genes, implicating aberrant spliceosome function in MDS disease pathogenesis. Recent functional studies have illuminated the impact on hematopoiesis of some aberrantly spliced target genes associated with splicing factor mutations. Emerging data show that the commonly mutated splicing factors have convergent effects on aberrant splicing of mRNAs that promote NF-κB signaling and on R-loop elevation leading to DNA damage, providing novel insights into MDS disease pathophysiology. It is recognized that the survival of splicing factor mutant cells is dependent on the presence of the wildtype allele, providing a rationale for the use of spliceosome inhibitors in splicing factor mutant MDS. Pre-clinical studies involving E7107 and H3B-8800 have shown the potential of these spliceosome inhibitors for the treatment of splicing factor mutant MDS and AML.
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67
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Gackowski D, Gawronski M, Kerr C, Radivoyevitch T, Zarakowska E, Starczak M, Abakir A, Ruzov A, Maciejewski JP, Olinski R. 5-formylcytosine and 5-hydroxymethyluracil as surrogate markers of TET2 and SF3B1 mutations in myelodysplastic syndrome, respectively. Haematologica 2019; 105:e213-e215. [PMID: 31488558 DOI: 10.3324/haematol.2019.224030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland
| | - Maciej Gawronski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland
| | - Cassandra Kerr
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland
| | - Abdulkadir Abakir
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Alexey Ruzov
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Torun, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland
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68
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Ohashi R, Schraml P, Batavia A, Angori S, Simmler P, Rupp N, Ajioka Y, Oliva E, Moch H. Allele Loss and Reduced Expression of CYCLOPS Genes is a Characteristic Feature of Chromophobe Renal Cell Carcinoma. Transl Oncol 2019; 12:1131-1137. [PMID: 31200327 PMCID: PMC6563336 DOI: 10.1016/j.tranon.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes have been recently identified as the most enriched class of copy-number associated gene dependencies in human cancer. These genes are cell essential and render tumor cells highly sensitive to the expression of the remaining copy. Chromophobe renal cell carcinoma (chRCC) is characterized by frequent chromosomal deletions, but the relevance of CYCLOPS genes in this tumor subtype is unclear. We found 39 (31%) of 124 recently published candidate CYCLOPS genes (B. Paolella et al., eLife 2017;6:e23268) located on 7 autosomes that are frequently lost in chRCC. GISTIC and RNA-seq data obtained from the TCGA-KICH database showed that 62% of these CYCLOPS genes had significantly lower expression levels in samples with deletion of the respective gene. As copy number (CN) loss of the CYCLOPS gene SF3B1 (Splicing factor 3B subunit 1) has been recently reported in 71% chRCC, we explored the relevance of SF3B1 CN alteration and SF3B1 expression in a set of chRCC and additional oncocytic renal neoplasms. The frequency of SF3B1 CN loss (65%) was similar to that obtained from the TCGA-KICH database and correlated significantly with both lower SF3B1 mRNA (P < .05) and protein expression (P < .001). Other tumor subtypes with oncocytic cytoplasm had normal SF3B1 CN and displayed strong SF3B1 protein expression. These results suggest that CN loss of CYCLOPS genes is a characteristic feature in chRCC. Since many CYCLOPS genes code for components of proteasomes and transcriptional regulation, their alteration could make chRCC vulnerable to targeted drugs.
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Affiliation(s)
- Riuko Ohashi
- Histopathology Core Facility, 1-757 Asahimachi-dori, Niigata University Faculty of Medicine, Chuo-ku, 951-8510 Niigata, Japan; Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Aashil Batavia
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Silvia Angori
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Patrik Simmler
- Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Niels Rupp
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Yoichi Ajioka
- Histopathology Core Facility, 1-757 Asahimachi-dori, Niigata University Faculty of Medicine, Chuo-ku, 951-8510 Niigata, Japan; Division of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, 757 Ichibancho, Asahimachi-dori, Chuo Ward, 951-8510 Niigata, Japan.
| | - Esther Oliva
- Department of Pathology, Warren Building, 55 Fruit Street, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Holger Moch
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
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69
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Foy A, McMullin MF. Somatic SF3B1 mutations in myelodysplastic syndrome with ring sideroblasts and chronic lymphocytic leukaemia. J Clin Pathol 2019; 72:778-782. [DOI: 10.1136/jclinpath-2019-205895] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
SF3B1 is the largest subunit of the Spliceosome Factor 3b (SF3B) complex and part of the U2 small nuclear ribosomal protein. It functions as an important part of spliceosomal assembly, converting precursor messenger RNA (mRNA) to mRNA ready for ribosomal translation. Mutations of SF3B1 are commonly seen in myelodysplastic syndromes with ring sideroblasts (MDS-RS)and MDS/myeloproliferative neoplasm (MPN-RS-T). These mutations are typically heterozygous missense substitutions, of which, 55% involve K700E. MDS-RS and MDS/MPN-RS-T usually carry a more favourable prognosis than other subtypes of MDS. SF3B1 itself does not influence survival in these conditions, but does correlate with increased thrombotic risk. Mutated SF3B1 is present in 9%–15% of chronic lymphocytic leukaemia cases and on its own correlates with improved responsiveness to ibrutinib, but is associated with additional adverse genetic abnormalities including TP53 and ATM mutations, which traditionally confer adverse outcomes.
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70
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Chwalenia K, Qin F, Singh S, Li H. A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes. Nucleic Acids Res 2019; 47:e24. [PMID: 30590765 PMCID: PMC6393300 DOI: 10.1093/nar/gky1288] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 11/14/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
Chimeric RNAs generated by cis-splicing between adjacent genes (cis-SAGe) are increasingly recognized as a widespread phenomenon. These chimeric messenger RNAs are present in normal human cells, and are also detected in various cancers. The mechanisms for how this group of chimeras is formed are not yet clear, in part due to the lack of a tractable system for their experimental investigation. Here we developed a fast, easy and versatile cell-based reporter system to identify regulators of cis-SAGe. The reporter, consisting of four main cassettes, simultaneously measures the effects of a candidate regulator on cis-SAGe and canonical splicing. Using this cell-based assay, we screened 102 candidate factors involved in RNA pol II cleavage and termination, elongation, splicing, alternative splicing and R-loop formation. We discovered that two factors, SRRM1 and SF3B1, affect not only cis-SAGe chimeras, but also other types of chimeric RNAs in a genome-wide fashion. This system can be used for studying trans-acting factors and cis-acting sequence elements and factors, as well as for screening small molecule inhibitors.
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Affiliation(s)
- Katarzyna Chwalenia
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
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71
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Dalton WB, Helmenstine E, Walsh N, Gondek LP, Kelkar DS, Read A, Natrajan R, Christenson ES, Roman B, Das S, Zhao L, Leone RD, Shinn D, Groginski T, Madugundu AK, Patil A, Zabransky DJ, Medford A, Lee J, Cole AJ, Rosen M, Thakar M, Ambinder A, Donaldson J, DeZern AE, Cravero K, Chu D, Madero-Marroquin R, Pandey A, Hurley PJ, Lauring J, Park BH. Hotspot SF3B1 mutations induce metabolic reprogramming and vulnerability to serine deprivation. J Clin Invest 2019; 129:4708-4723. [PMID: 31393856 DOI: 10.1172/jci125022] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer-associated mutations in the spliceosome gene SF3B1 create a neomorphic protein that produces aberrant mRNA splicing in hundreds of genes, but the ensuing biologic and therapeutic consequences of this missplicing are not well understood. Here we have provided evidence that aberrant splicing by mutant SF3B1 altered the transcriptome, proteome, and metabolome of human cells, leading to missplicing-associated downregulation of metabolic genes, decreased mitochondrial respiration, and suppression of the serine synthesis pathway. We also found that mutant SF3B1 induces vulnerability to deprivation of the nonessential amino acid serine, which was mediated by missplicing-associated downregulation of the serine synthesis pathway enzyme PHGDH. This vulnerability was manifest both in vitro and in vivo, as dietary restriction of serine and glycine in mice was able to inhibit the growth of SF3B1MUT xenografts. These findings describe a role for SF3B1 mutations in altered energy metabolism, and they offer a new therapeutic strategy against SF3B1MUT cancers.
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Affiliation(s)
- W Brian Dalton
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Eric Helmenstine
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Noel Walsh
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Lukasz P Gondek
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Dhanashree S Kelkar
- McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail Read
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Eric S Christenson
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | | | - Samarjit Das
- Department of Pathology, Cardiovascular Division.,Department of Anesthesiology and Critical Care Medicine, and
| | - Liang Zhao
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Robert D Leone
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Daniel Shinn
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Taylor Groginski
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Anil K Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Arun Patil
- McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Daniel J Zabransky
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Arielle Medford
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Justin Lee
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Alex J Cole
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Marc Rosen
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Maya Thakar
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Alexander Ambinder
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Joshua Donaldson
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Amy E DeZern
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Karen Cravero
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - David Chu
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and
| | - Rafael Madero-Marroquin
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and.,Department of Medicine, Icahn School of Medicine, Mount Sinai St. Luke's Roosevelt Hospital Center, New York, New York, USA
| | - Akhilesh Pandey
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and.,McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India.,Department of Pathology and
| | - Paula J Hurley
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and.,Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Josh Lauring
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and.,Janssen Research and Development, Spring House, Pennsylvania, USA
| | - Ben Ho Park
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, and.,Department of Chemical and Biomolecular Engineering, The Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA.,Division of Hematology, Oncology, Department of Medicine, Vanderbilt Ingram Cancer Center, Nashville, Tennessee, USA
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72
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Lorenzini PA, Chew RSE, Tan CW, Yong JY, Zhang F, Zheng J, Roca X. Human PRPF40B regulates hundreds of alternative splicing targets and represses a hypoxia expression signature. RNA (NEW YORK, N.Y.) 2019; 25:905-920. [PMID: 31088860 PMCID: PMC6633195 DOI: 10.1261/rna.069534.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Altered splicing contributes to the pathogenesis of human blood disorders including myelodysplastic syndromes (MDS) and leukemias. Here we characterize the transcriptomic regulation of PRPF40B, which is a splicing factor mutated in a small fraction of MDS patients. We generated a full PRPF40B knockout (KO) in the K562 cell line by CRISPR/Cas9 technology and rescued its levels by transient overexpression of wild-type (WT), P383L or P540S MDS alleles. Using RNA sequencing, we identified hundreds of differentially expressed genes and alternative splicing (AS) events in the KO that are rescued by WT PRPF40B, with a majority also rescued by MDS alleles, pointing to mild effects of these mutations. Among the PRPF40B-regulated AS events, we found a net increase in exon inclusion in the KO, suggesting that this splicing factor primarily acts as a repressor. PRPF40B-regulated splicing events are likely cotranscriptional, affecting exons with A-rich downstream intronic motifs and weak splice sites especially for 5' splice sites, consistent with its PRP40 yeast ortholog being part of the U1 small nuclear ribonucleoprotein. Loss of PRPF40B in K562 induces a KLF1 transcriptional signature, with genes involved in iron metabolism and mainly hypoxia, including related pathways like cholesterol biosynthesis and Akt/MAPK signaling. A cancer database analysis revealed that PRPF40B is lowly expressed in acute myeloid leukemia, whereas its paralog PRPF40A expression is high as opposed to solid tumors. Furthermore, these factors negatively or positively correlated with hypoxia regulator HIF1A, respectively. Our data suggest a PRPF40B role in repressing hypoxia in myeloid cells, and that its low expression might contribute to leukemogenesis.
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Affiliation(s)
- Paolo Alberto Lorenzini
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
- Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School (IGS), Nanyang Technological University, 637551 Singapore, Singapore
| | - Resilind Su Ern Chew
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Cheryl Weiqi Tan
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Jing Yen Yong
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Fan Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 637551 Singapore, Singapore
| | - Jie Zheng
- School of Computer Science and Engineering, Nanyang Technological University, 637551 Singapore, Singapore
- School of Information Science and Technology, ShanghaiTech University, Pudong District, Shanghai 201210, China
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
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73
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De La Garza A, Cameron RC, Gupta V, Fraint E, Nik S, Bowman TV. The splicing factor Sf3b1 regulates erythroid maturation and proliferation via TGFβ signaling in zebrafish. Blood Adv 2019; 3:2093-2104. [PMID: 31300417 PMCID: PMC6650725 DOI: 10.1182/bloodadvances.2018027714] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The spliceosomal component Splicing Factor 3B, subunit 1 (SF3B1) is one of the most prevalently mutated factors in the bone marrow failure disorder myelodysplastic syndrome. There is a strong clinical correlation between SF3B1 mutations and erythroid defects, such as refractory anemia with ringed sideroblasts, but the role of SF3B1 in normal erythroid development is largely unknown. Loss-of-function zebrafish mutants for sf3b1 develop a macrocytic anemia. Here, we explore the underlying mechanism for anemia associated with sf3b1 deficiency in vivo. We found that sf3b1 mutant erythroid progenitors display a G0/G1 cell-cycle arrest with mutant erythrocytes showing signs of immaturity. RNA-sequencing analysis of sf3b1 mutant erythroid progenitors revealed normal expression of red blood cell regulators such as gata1, globin genes, and heme biosynthetic factors, but upregulation of genes in the transforming growth factor β (TGFβ) pathway. As TGFβ signaling is a known inducer of quiescence, the data suggest that activation of the pathway could trigger sf3b1 deficiency-induced anemia via cell-cycle arrest. Indeed, we found that inhibition of TGFβ signaling released the G0/G1 block in erythroid progenitors. Surprisingly, removal of this checkpoint enhanced rather than suppressed the anemia, indicating that the TGFβ-mediated cell-cycle arrest is protective for sf3b1-mutant erythrocytes. Together, these data suggest that macrocytic anemia arising from Sf3b1 deficiency is likely due to pleiotropic and distinct effects on cell-cycle progression and maturation.
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Affiliation(s)
- Adriana De La Garza
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
| | - Rosannah C Cameron
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
| | | | - Ellen Fraint
- Department of Pediatrics, Montefiore Hospital, Bronx, NY; and
| | - Sara Nik
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
- Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY
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74
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Li D, Harlan-Williams LM, Kumaraswamy E, Jensen RA. BRCA1-No Matter How You Splice It. Cancer Res 2019; 79:2091-2098. [PMID: 30992324 PMCID: PMC6497576 DOI: 10.1158/0008-5472.can-18-3190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/09/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
BRCA1 (breast cancer 1, early onset), a well-known breast cancer susceptibility gene, is a highly alternatively spliced gene. BRCA1 alternative splicing may serve as an alternative regulatory mechanism for the inactivation of the BRCA1 gene in both hereditary and sporadic breast cancers, and other BRCA1-associated cancers. The alternative transcripts of BRCA1 can mimic known functions, possess unique functions compared with the full-length BRCA1 transcript, and in some cases, appear to function in opposition to full-length BRCA1 In this review, we will summarize the functional "naturally occurring" alternative splicing transcripts of BRCA1 and then discuss the latest next-generation sequencing-based detection methods and techniques to detect alternative BRCA1 splicing patterns and their potential use in cancer diagnosis, prognosis, and therapy.
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Affiliation(s)
- Dan Li
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Lisa M Harlan-Williams
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Easwari Kumaraswamy
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Roy A Jensen
- The University of Kansas Cancer Center, Kansas City, Kansas.
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
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75
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Bataller A, Montalban-Bravo G, Soltysiak KA, Garcia-Manero G. The role of TGFβ in hematopoiesis and myeloid disorders. Leukemia 2019; 33:1076-1089. [PMID: 30816330 DOI: 10.1038/s41375-019-0420-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 02/06/2023]
Abstract
The role of transforming growth factor-β (TGFβ) signaling in embryological development and tissue homeostasis has been thoroughly characterized. Its canonical downstream cascade is well known, even though its true complexity and other non-canonical pathways are still being explored. TGFβ signaling has been described as an important pathway involved in carcinogenesis and cancer progression. In the hematopoietic compartment, the TGFβ pathway is an important regulator of proliferation and differentiation of different cell types and has been implicated in the pathogenesis of a diverse variety of bone marrow disorders. Due to its importance in hematological diseases, novel inhibitors of this pathway are being developed against a number of hematopoietic disorders, including myelodysplastic syndromes (MDS). In this review, we provide an overview of the TGFβ pathway, focusing on its role in hematopoiesis and impact on myeloid disorders. We will discuss therapeutic interventions with promising results against MDS.
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Affiliation(s)
- Alex Bataller
- Hematology Department, IDIBAPS, Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Kelly A Soltysiak
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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76
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Altered splicing and cytoplasmic levels of tRNA synthetases in SF3B1-mutant myelodysplastic syndromes as a therapeutic vulnerability. Sci Rep 2019; 9:2678. [PMID: 30804405 PMCID: PMC6390101 DOI: 10.1038/s41598-019-39591-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/24/2019] [Indexed: 12/19/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are haematopoietic malignancies that are characterised by a heterogeneous clinical course. In recent years, sequencing efforts have uncovered recurrent somatic mutations within RNA splicing factors, including SF3B1, SRSF2, U2AF1 and ZRSR2. The most frequently mutated gene is SF3B1, mutated in 17% of MDS patients. While SF3B1 mutations and their effects on splicing have been well characterised, much remains to be explored about their more far-reaching effects on cellular homeostasis. Given that mRNA splicing and nuclear export are coordinated processes, we hypothesised that SF3B1 mutation might also affect export of certain mRNAs and that this may represent a targetable pathway for the treatment of SF3B1-mutant MDS. We used CRISPR/Cas9-genome editing to create isogenic cellular models. Comprehensive transcriptome and proteome profiling of these cells identified alterations in the splicing and export of components of the translational machinery, primarily tRNA synthetases, in response to the SF3B1 K700E mutation. While steady-state protein synthesis was unaffected, SF3B1 mutant cells were more sensitive to the clinically-relevant purine analogue, 8-azaguanine. In this study, we also demonstrated that 8-azaguanine affects splicing. Our results suggest that the simultaneous targeting of RNA metabolism and splicing by 8-azaguanine represents a therapeutic opportunity for SF3B1-mutant myelodysplastic syndromes.
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77
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Baeza-Centurion P, Miñana B, Schmiedel JM, Valcárcel J, Lehner B. Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing. Cell 2019; 176:549-563.e23. [PMID: 30661752 DOI: 10.1016/j.cell.2018.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/29/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023]
Abstract
Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modeling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighboring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.
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Affiliation(s)
- Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Belén Miñana
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Jörn M Schmiedel
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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78
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Prognostic value and clinical feature of SF3B1 mutations in myelodysplastic syndromes: A meta-analysis. Crit Rev Oncol Hematol 2019; 133:74-83. [DOI: 10.1016/j.critrevonc.2018.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/12/2018] [Accepted: 07/31/2018] [Indexed: 12/22/2022] Open
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79
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Shingai N, Harada Y, Iizuka H, Ogata Y, Doki N, Ohashi K, Hagihara M, Komatsu N, Harada H. Impact of splicing factor mutations on clinical features in patients with myelodysplastic syndromes. Int J Hematol 2018; 108:598-606. [DOI: 10.1007/s12185-018-2551-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 12/15/2022]
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80
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Implication and Regulation of AMPK during Physiological and Pathological Myeloid Differentiation. Int J Mol Sci 2018; 19:ijms19102991. [PMID: 30274374 PMCID: PMC6213055 DOI: 10.3390/ijms19102991] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 12/25/2022] Open
Abstract
AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine kinase consisting of the arrangement of various α β, and γ isoforms that are expressed differently depending on the tissue or the cell lineage. AMPK is one of the major sensors of energy status in mammalian cells and as such plays essential roles in the regulation of cellular homeostasis, metabolism, cell growth, differentiation, apoptosis, and autophagy. AMPK is activated by two upstream kinases, the tumor suppressor liver kinase B1 (LKB1) and the calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) through phosphorylation of the kinase on Thr172, leading to its activation. In addition, AMPK inhibits the mTOR pathway through phosphorylation and activation of tuberous sclerosis protein 2 (TSC2) and causes direct activation of unc-51-like autophagy activating kinase 1 (ULK1) via phosphorylation of Ser555, thus promoting initiation of autophagy. Although it is well established that AMPK can control the differentiation of different cell lineages, including hematopoietic stem cells (HSCs), progenitors, and mature hematopoietic cells, the role of AMPK regarding myeloid cell differentiation is less documented. The differentiation of monocytes into macrophages triggered by colony stimulating factor 1 (CSF-1), a process during which both caspase activation (independently of apoptosis induction) and AMPK-dependent stimulation of autophagy are necessary, is one noticeable example of the involvement of AMPK in the physiological differentiation of myeloid cells. The present review focuses on the role of AMPK in the regulation of the physiological and pathological differentiation of myeloid cells. The mechanisms of autophagy induction by AMPK will also be addressed, as autophagy has been shown to be important for differentiation of hematopoietic cells. In addition, myeloid malignancies (myeloid leukemia or dysplasia) are characterized by profound defects in the establishment of proper differentiation programs. Reinduction of a normal differentiation process in myeloid malignancies has thus emerged as a valuable and promising therapeutic strategy. As AMPK seems to exert a key role in the differentiation of myeloid cells, notably through induction of autophagy, we will also discuss the potential to target this pathway as a pro-differentiating and anti-leukemic strategy in myeloid malignancies.
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81
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Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia. Nat Commun 2018; 9:3649. [PMID: 30194306 PMCID: PMC6128865 DOI: 10.1038/s41467-018-06063-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/30/2018] [Indexed: 12/20/2022] Open
Abstract
Spliceosome mutations are frequently found in myelodysplasia. Splicing alterations induced by these mutations, their precise targets, and the effect at the transcript level have not been fully elucidated. Here we report transcriptomic analyses of 265 bone marrow samples from myelodysplasia patients, followed by a validation using CRISPR/Cas9-mediated gene editing and an assessment of nonsense-mediated decay susceptibility. Small but widespread reduction of intron-retaining isoforms is the most frequent splicing alteration in SF3B1-mutated samples. SF3B1 mutation is also associated with 3′ splice site alterations, leading to the most pronounced reduction of canonical transcripts. Target genes include tumor suppressors and genes of mitochondrial iron metabolism or heme biosynthesis. Alternative exon usage is predominant in SRSF2- and U2AF1-mutated samples. Usage of an EZH2 cryptic exon harboring a premature termination codon is increased in both SRSF2- and U2AF1-mutated samples. Our study reveals a landscape of splicing alterations and precise targets of various spliceosome mutations. Mutations to the splicing machinery may have an important role in myelodysplasia. Here, the authors describe splicing factor gene mutations in myelodysplasia and report tumor suppressor, epigenetic, iron metabolism and heme biosynthesis genes as their targets.
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82
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Liu X, Klein PS. Glycogen synthase kinase-3 and alternative splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1501. [PMID: 30118183 DOI: 10.1002/wrna.1501] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022]
Abstract
Glycogen synthase kinase-3 (GSK-3) is a highly conserved negative regulator of receptor tyrosine kinase, cytokine, and Wnt signaling pathways. Stimulation of these pathways inhibits GSK-3 to modulate diverse downstream effectors that include transcription factors, nutrient sensors, glycogen synthesis, mitochondrial function, circadian rhythm, and cell fate. GSK-3 also regulates alternative splicing in response to T-cell receptor activation, and recent phosphoproteomic studies have revealed that multiple splicing factors and regulators of RNA biosynthesis are phosphorylated in a GSK-3-dependent manner. Furthermore, inhibition of GSK-3 alters the splicing of hundreds of mRNAs, indicating a broad role for GSK-3 in the regulation of RNA processing. GSK-3-regulated phosphoproteins include SF3B1, SRSF2, PSF, RBM8A, nucleophosmin 1 (NPM1), and PHF6, many of which are mutated in leukemia and myelodysplasia. As GSK-3 is inhibited by pathways that are pathologically activated in leukemia and loss of Gsk3 in hematopoietic cells causes a severe myelodysplastic neoplasm in mice, these findings strongly implicate GSK-3 as a critical regulator of mRNA processing in normal and malignant hematopoiesis. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Xiaolei Liu
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter S Klein
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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83
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Lee SCW, North K, Kim E, Jang E, Obeng E, Lu SX, Liu B, Inoue D, Yoshimi A, Ki M, Yeo M, Zhang XJ, Kim MK, Cho H, Chung YR, Taylor J, Durham BH, Kim YJ, Pastore A, Monette S, Palacino J, Seiler M, Buonamici S, Smith PG, Ebert BL, Bradley RK, Abdel-Wahab O. Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations. Cancer Cell 2018; 34:225-241.e8. [PMID: 30107174 PMCID: PMC6373472 DOI: 10.1016/j.ccell.2018.07.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 04/25/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023]
Abstract
Mutations affecting RNA splicing factors are the most common genetic alterations in myelodysplastic syndrome (MDS) patients and occur in a mutually exclusive manner. The basis for the mutual exclusivity of these mutations and how they contribute to MDS is not well understood. Here we report that although different spliceosome gene mutations impart distinct effects on splicing, they are negatively selected for when co-expressed due to aberrant splicing and downregulation of regulators of hematopoietic stem cell survival and quiescence. In addition to this synthetic lethal interaction, mutations in the splicing factors SF3B1 and SRSF2 share convergent effects on aberrant splicing of mRNAs that promote nuclear factor κB signaling. These data identify shared consequences of splicing-factor mutations and the basis for their mutual exclusivity.
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Affiliation(s)
- Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Khrystyna North
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop: M1-B514, Seattle, WA 98109-1024, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Eunhee Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Eunjung Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Esther Obeng
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sydney X Lu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Daichi Inoue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Akihide Yoshimi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Michelle Ki
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Mirae Yeo
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Xiao Jing Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Min Kyung Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Young Rock Chung
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Justin Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Young Joon Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, The Rockefeller University, New York, NY, USA
| | | | | | | | | | - Benjamin L Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop: M1-B514, Seattle, WA 98109-1024, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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84
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El-Athman R, Fuhr L, Relógio A. A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer. EBioMedicine 2018; 33:68-81. [PMID: 29936137 PMCID: PMC6085510 DOI: 10.1016/j.ebiom.2018.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/28/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence points to a significant role of the circadian clock in the regulation of splicing in various organisms, including mammals. Both dysregulated circadian rhythms and aberrant pre-mRNA splicing are frequently implicated in human disease, in particular in cancer. To investigate the role of the circadian clock in the regulation of splicing in a cancer progression context at the systems-level, we conducted a genome-wide analysis and compared the rhythmic transcriptional profiles of colon carcinoma cell lines SW480 and SW620, derived from primary and metastatic sites of the same patient, respectively. We identified spliceosome components and splicing factors with cell-specific circadian expression patterns including SRSF1, HNRNPLL, ESRP1, and RBM 8A, as well as altered alternative splicing events and circadian alternative splicing patterns of output genes (e.g., VEGFA, NCAM1, FGFR2, CD44) in our cellular model. Our data reveals a remarkable interplay between the circadian clock and pre-mRNA splicing with putative consequences in tumor progression and metastasis.
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Affiliation(s)
- Rukeia El-Athman
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Luise Fuhr
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany.
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85
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Hurtado AM, Luengo-Gil G, Chen-Liang TH, Amaral F, Batta K, Palomo L, Lumbreras E, Przychodzen B, Caparros E, Amigo ML, Dıez-Campelo M, Zamora L, Salido Fierrez EJ, Maciejewski JP, Ortuño FJ, Vicente V, Del Canizo M, Sole F, Ferrer-Marin F, Wiseman DH, Jerez A. Transcriptomic rationale for synthetic lethality-targeting ERCC1 and CDKN1A in chronic myelomonocytic leukaemia. Br J Haematol 2018; 182:373-383. [PMID: 29797327 DOI: 10.1111/bjh.15408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022]
Abstract
Despite the absence of mutations in the DNA repair machinery in myeloid malignancies, the advent of high-throughput sequencing and discovery of splicing and epigenetics defects in chronic myelomonocytic leukaemia (CMML) prompted us to revisit a pathogenic role for genes involved in DNA damage response. We screened for misregulated DNA repair genes by enhanced RNA-sequencing on bone marrow from a discovery cohort of 27 CMML patients and 9 controls. We validated 4 differentially expressed candidates in CMML CD34+ bone marrow selected cells and in an independent cohort of 74 CMML patients, mutationally contextualized by targeted sequencing, and assessed their transcriptional behavior in 70 myelodysplastic syndrome, 66 acute myeloid leukaemia and 25 chronic myeloid leukaemia cases. We found BAP1 and PARP1 down-regulation to be specific to CMML compared with other related disorders. Chromatin-regulator mutated cases showed decreased BAP1 dosage. We validated a significant over-expression of the double strand break-fidelity genes CDKN1A and ERCC1, independent of promoter methylation and associated with chemorefractoriness. In addition, patients bearing mutations in the splicing component SRSF2 displayed numerous aberrant splicing events in DNA repair genes, with a quantitative predominance in the single strand break pathway. Our results highlight potential targets in this disease, which currently has few therapeutic options.
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Affiliation(s)
- Ana M Hurtado
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Gines Luengo-Gil
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Tzu H Chen-Liang
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Fabio Amaral
- Leukaemia Biology Laboratory, Cancer Research UK, Manchester Institute, University of Manchester, Manchester, UK
| | - Kiran Batta
- Division of Cancer Sciences, Cancer Research UK, Manchester Institute, University of Manchester, Manchester, UK
| | - Laura Palomo
- Josep Carreras Leukaemia- Research Institute, ICO-Hospital Germans Trias i Pujol, Badalona, Spain
| | - Eva Lumbreras
- Department of Haematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Bartlomiej Przychodzen
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, USA
| | - Eva Caparros
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Marıa L Amigo
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Maria Dıez-Campelo
- Department of Haematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Lurdes Zamora
- Josep Carreras Leukaemia- Research Institute, ICO-Hospital Germans Trias i Pujol, Badalona, Spain
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, USA
| | | | - Vicente Vicente
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Marıa Del Canizo
- Department of Haematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Francesc Sole
- Josep Carreras Leukaemia- Research Institute, ICO-Hospital Germans Trias i Pujol, Badalona, Spain
| | | | - Daniel H Wiseman
- Leukaemia Biology Laboratory, Cancer Research UK, Manchester Institute, University of Manchester, Manchester, UK
| | - Andres Jerez
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
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86
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Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM. The long tail of oncogenic drivers in prostate cancer. Nat Genet 2018; 50:645-651. [PMID: 29610475 PMCID: PMC6107367 DOI: 10.1038/s41588-018-0078-z] [Citation(s) in RCA: 546] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/26/2018] [Indexed: 01/05/2023]
Abstract
Comprehensive genomic characterization of prostate cancer has identified recurrent alterations in genes involved in androgen signaling, DNA repair, and PI3K signaling, among others. However, larger and uniform genomic analysis may identify additional recurrently mutated genes at lower frequencies. Here we aggregate and uniformly analyze exome sequencing data from 1,013 prostate cancers. We identify and validate a new class of E26 transformation-specific (ETS)-fusion-negative tumors defined by mutations in epigenetic regulators, as well as alterations in pathways not previously implicated in prostate cancer, such as the spliceosome pathway. We find that the incidence of significantly mutated genes (SMGs) follows a long-tail distribution, with many genes mutated in less than 3% of cases. We identify a total of 97 SMGs, including 70 not previously implicated in prostate cancer, such as the ubiquitin ligase CUL3 and the transcription factor SPEN. Finally, comparing primary and metastatic prostate cancer identifies a set of genomic markers that may inform risk stratification.
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Affiliation(s)
- Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie A M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jianjiong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Celine Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Christopher E Barbieri
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zafeiris Zafeiriou
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Susana Miranda
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Tolonen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Robert Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Johann S de Bono
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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87
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Whole-exome sequencing identifies recurrent SF3B1 R625 mutation and comutation of NF1 and KIT in mucosal melanoma. Melanoma Res 2018; 27:189-199. [PMID: 28296713 PMCID: PMC5470740 DOI: 10.1097/cmr.0000000000000345] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mucosal melanomas are a rare subtype of melanoma, arising in mucosal tissues, which have a very poor prognosis due to the lack of effective targeted therapies. This study aimed to better understand the molecular landscape of these cancers and find potential new therapeutic targets. Whole-exome sequencing was performed on mucosal melanomas from 19 patients and 135 sun-exposed cutaneous melanomas, with matched peripheral blood samples when available. Mutational profiles were compared between mucosal subgroups and sun-exposed cutaneous melanomas. Comparisons of molecular profiles identified 161 genes enriched in mucosal melanoma (P<0.05). KIT and NF1 were frequently comutated (32%) in the mucosal subgroup, with a significantly higher incidence than that in cutaneous melanoma (4%). Recurrent SF3B1 R625H/S/C mutations were identified and validated in 7 of 19 (37%) mucosal melanoma patients. Mutations in the spliceosome pathway were found to be enriched in mucosal melanomas when compared with cutaneous melanomas. Alternative splicing in four genes were observed in SF3B1-mutant samples compared with the wild-type samples. This study identified potential new therapeutic targets for mucosal melanoma, including comutation of NF1 and KIT, and recurrent R625 mutations in SF3B1. This is the first report of SF3B1 R625 mutations in vulvovaginal mucosal melanoma, with the largest whole-exome sequencing project of mucosal melanomas to date. The results here also indicated that the mutations in SF3B1 lead to alternative splicing in multiple genes. These findings expand our knowledge of this rare disease.
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88
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Wu ZJ, Zhao X, Banaszak LG, Gutierrez-Rodrigues F, Keyvanfar K, Gao SG, Quinones Raffo D, Kajigaya S, Young NS. CRISPR/Cas9-mediated ASXL1 mutations in U937 cells disrupt myeloid differentiation. Int J Oncol 2018. [PMID: 29532865 PMCID: PMC5843401 DOI: 10.3892/ijo.2018.4290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Additional sex combs-like 1 (ASXL1) is a well‑known tumor suppressor gene and epigenetic modifier. ASXL1 mutations are frequent in myeloid malignances; these mutations are risk factors for the development of myelodysplasia and also appear as small clones during normal aging. ASXL1 appears to act as an epigenetic regulator of cell survival and myeloid differentiation; however, the molecular mechanisms underlying the malignant transformation of cells with ASXL1 mutations are not well defined. Using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9) genome editing, heterozygous and homozygous ASXL1 mutations were introduced into human U937 leukemic cells. Comparable cell growth and cell cycle progression were observed between wild-type (WT) and ASXL1-mutated U937 cells. Drug-induced cytotoxicity, as measured by growth inhibition and apoptosis in the presence of the cell-cycle active agent 5-fluorouracil, was variable among the mutated clones but was not significantly different from WT cells. In addition, ASXL1-mutated cells exhibited defects in monocyte/macrophage differentiation. Transcriptome analysis revealed that ASXL1 mutations altered differentiation of U937 cells by disturbing genes involved in myeloid differentiation, including cytochrome B-245 β chain and C-type lectin domain family 5, member A. Dysregulation of numerous gene sets associated with cell death and survival were also observed in ASXL1-mutated cells. These data provide evidence regarding the underlying molecular mechanisms induced by mutated ASXL1 in leukemogenesis.
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Affiliation(s)
- Zhi-Jie Wu
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Xin Zhao
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Lauren G Banaszak
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Fernanda Gutierrez-Rodrigues
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Keyvan Keyvanfar
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Shou-Guo Gao
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
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89
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Fu X, Tian M, Gu J, Cheng T, Ma D, Feng L, Xin X. SF3B1 mutation is a poor prognostic indicator in luminal B and progesterone receptor-negative breast cancer patients. Oncotarget 2017; 8:115018-115027. [PMID: 29383138 PMCID: PMC5777750 DOI: 10.18632/oncotarget.22983] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/16/2017] [Indexed: 01/24/2023] Open
Abstract
The purpose of this study was to explore the relationship between SF3B1 mutations and the prognoses of patients with breast cancer. Clinical and SF3B1 mutation data from The Cancer Genome Atlas were analyzed. SF3B1 mutations were evaluated as prognostic factors in all breast cancer patients and specific subgroups through Cox regression and Kaplan-Meier analyses. We also investigated the relationship between traditional parameters and SF3B1 mutations. Receiver operating characteristics curves were used to analyze common risk factors for their sensitivity and specificity in predicting SF3B1 mutations. SF3B1 mutations were a poor prognostic factor in luminal B and progesterone receptor (PR)-negative breast cancer (P < 0.01). Age at diagnosis and estrogen receptor (ER) status were associated with SF3B1 mutations in all breast cancers (P < 0.01) and in luminal B and PR-negative subgroups (P < 0.01). The age at diagnosis and ER status combined had a higher sensitivity and specificity for predicting SF3B1 mutations than each factor alone. SF3B1 mutations are a poor prognostic factor in luminal B and PR-negative breast cancer patients. These mutations are significantly associated with age at diagnosis and ER status. SF3B1 mutations may therefore be a novel therapeutic target for breast cancer patients.
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Affiliation(s)
- Xing Fu
- Department of Pediatric Hematology, Children's Hospital of Hainan Province, Haikou 570000, Hainan, P.R.China
| | - Ming Tian
- Department of Nephrology, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, P.R.China
| | - Jia Gu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, P.R. China
| | - Teng Cheng
- Department of Breast and Thyroid Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, P.R.China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, P.R.China
| | - Ling Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, P.R.China
| | - Xing Xin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, P.R.China
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90
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Moyo TK, Savona MR. Molecular Testing in Patients with Suspected Myelodysplastic Syndromes. Curr Hematol Malig Rep 2017; 11:441-448. [PMID: 27734261 DOI: 10.1007/s11899-016-0356-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Myelodysplastic syndromes (MDS) comprise a heterogeneous group of clonal hematologic malignancies characterized by a hypercellular bone marrow and morphologic dysplasia in one or more lineage (i.e., myeloid, erythroid, or megakaryocytic), presenting clinically with leukopenia, anemia, and/or thrombocytopenia and with a propensity to transform to acute myelogenous leukemia. Newer technologies such as next-generation sequencing have allowed better understanding of the genetic landscape in MDS. Nearly 80 % of MDS patients have at least one mutation, and approximately 40 recurrent somatic mutations have been identified to occur in >1 % of cases. Many of these mutations are relevant for prognosis, help with selection of therapy, and/or have specific targeted treatment options. In this article, we will explore the impact of molecular testing on diagnosis, prognosis, and treatment decisions in patients with suspected MDS.
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Affiliation(s)
- Tamara K Moyo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, 2220 Pierce Avenue, 777 Preston Research Building, Nashville, TN, 37232, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. .,Vanderbilt-Ingram Cancer Center, 2220 Pierce Avenue, 777 Preston Research Building, Nashville, TN, 37232, USA.
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91
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Mies A, Hermine O, Platzbecker U. Activin Receptor II Ligand Traps and Their Therapeutic Potential in Myelodysplastic Syndromes with Ring Sideroblasts. Curr Hematol Malig Rep 2017; 11:416-424. [PMID: 27595736 DOI: 10.1007/s11899-016-0347-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Distinct subtypes of lower risk myelodysplastic syndromes display ring sideroblasts in the bone marrow, i. e., erythroid progenitors characterized by excessive iron deposited in the mitochondria. This morphological feature is frequently associated with somatic mutations in components of the splicing machinery that constitutes the underlying molecular principle of the disease. Conventional treatment regimen with erythropoiesis-stimulating agents often fails to induce sustained erythroid improvement in these patients that harbor defects in late-stage erythroblasts downstream of erythropoietin action. In the present review, we will discuss activin receptor ligand traps as novel therapeutic strategies particularly for sideroblastic subgroups of myelodysplastic syndromes that were recently shown to alleviate anemia by specifically inhibiting aberrant TGF-β signaling and thereby promoting erythroid differentiation.
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Affiliation(s)
- Anna Mies
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Olivier Hermine
- Department of Hematology, Hôpital Necker, Assistance Publique Hôpitaux de Paris, University Paris Descartes and Imagine Institute, University Sorbonne Paris Cité, 24, boulevard du Montparnasse, 75015, Paris, France
| | - Uwe Platzbecker
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany. .,German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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92
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Bejar R. Splicing Factor Mutations in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 907:215-28. [PMID: 27256388 DOI: 10.1007/978-3-319-29073-7_9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many cancers demonstrate aberrant splicing patterns that contribute to their development and progression. Recently, recurrent somatic mutations of genes encoding core subunits of the spliceosome have been identified in several different cancer types. These mutations are most common in hematologic malignancies like the myelodysplastic syndromes (MDS), acute myeloid leukemia, and chronic lymphocytic leukemia, but also in occur in several solid tumors at lower frequency. The most frequent mutations occur in SF3B1, U2AF1, SRSF2, and ZRSR2 and are largely exclusive of each other. Mutations in SF3B1, U2AF1, and SRSF2 acquire heterozygous missense mutations in specific codons, resembling oncogenes. ZRSR2 mutations include clear loss-of-function variants, a pattern more common to tumor suppressor genes. These splicing factors are associated with distinct clinical phenotypes and patterns of mutation in different malignancies. Mutations have both diagnostic and prognostic relevance. Splicing factor mutations appear to affect only a minority of transcripts which show little overlap by mutation type. How differences in splicing caused by somatic mutations of spliceosome subunits lead to oncogenesis is not clear and may involve different targets in each disease type. However, cells with mutated splicing machinery may be particularly vulnerable to further disruption of the spliceosome suggesting a novel strategy for the targeted therapy of cancers.
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Affiliation(s)
- Rafael Bejar
- Division of Hematology and Oncology, UC San Diego Moores Cancer Center, La Jolla, CA, USA.
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93
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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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94
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Kim Guisbert KS, Guisbert E. SF3B1 is a stress-sensitive splicing factor that regulates both HSF1 concentration and activity. PLoS One 2017; 12:e0176382. [PMID: 28445500 PMCID: PMC5406028 DOI: 10.1371/journal.pone.0176382] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/10/2017] [Indexed: 12/20/2022] Open
Abstract
The heat shock response (HSR) is a well-conserved, cytoprotective stress response that activates the HSF1 transcription factor. During severe stress, cells inhibit mRNA splicing which also serves a cytoprotective function via inhibition of gene expression. Despite their functional interconnectedness, there have not been any previous reports of crosstalk between these two pathways. In a genetic screen, we identified SF3B1, a core component of the U2 snRNP subunit of the spliceosome, as a regulator of the heat shock response in Caenorhabditis elegans. Here, we show that this regulatory connection is conserved in cultured human cells and that there are at least two distinct pathways by which SF3B1 can regulate the HSR. First, inhibition of SF3B1 with moderate levels of Pladienolide B, a previously established small molecule inhibitor of SF3B1, affects the transcriptional activation of HSF1, the transcription factor that mediates the HSR. However, both higher levels of Pladienolide B and SF3B1 siRNA knockdown also change the concentration of HSF1, a form of HSR regulation that has not been previously documented during normal physiology but is observed in some forms of cancer. Intriguingly, mutations in SF3B1 have also been associated with several distinct types of cancer. Finally, we show that regulation of alternative splicing by SF3B1 is sensitive to temperature, providing a new mechanism by which temperature stress can remodel the transcriptome.
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Affiliation(s)
- Karen S. Kim Guisbert
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Eric Guisbert
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
- * E-mail:
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95
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Lytovchenko O, Kunji ERS. Expression and putative role of mitochondrial transport proteins in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:641-654. [PMID: 28342810 DOI: 10.1016/j.bbabio.2017.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/20/2017] [Accepted: 03/21/2017] [Indexed: 02/07/2023]
Abstract
Cancer cells undergo major changes in energy and biosynthetic metabolism. One of them is the Warburg effect, in which pyruvate is used for fermentation rather for oxidative phosphorylation. Another major one is their increased reliance on glutamine, which helps to replenish the pool of Krebs cycle metabolites used for other purposes, such as amino acid or lipid biosynthesis. Mitochondria are central to these alterations, as the biochemical pathways linking these processes run through these organelles. Two membranes, an outer and inner membrane, surround mitochondria, the latter being impermeable to most organic compounds. Therefore, a large number of transport proteins are needed to link the biochemical pathways of the cytosol and mitochondrial matrix. Since the transport steps are relatively slow, it is expected that many of these transport steps are altered when cells become cancerous. In this review, changes in expression and regulation of these transport proteins are discussed as well as the role of the transported substrates. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.
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Affiliation(s)
- Oleksandr Lytovchenko
- Medical Research Council, Mitochondrial Biology Unit, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Edmund R S Kunji
- Medical Research Council, Mitochondrial Biology Unit, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.
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96
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Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K, Manes N, Wright P, Papaemmanuil E, Kent DG, Campbell PC, Buonamici S, Bolli N, Vassiliou GS. Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts. Leukemia 2017; 31:720-727. [PMID: 27604819 PMCID: PMC5336192 DOI: 10.1038/leu.2016.251] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 02/06/2023]
Abstract
Heterozygous somatic mutations affecting the spliceosome gene SF3B1 drive age-related clonal hematopoiesis, myelodysplastic syndromes (MDS) and other neoplasms. To study their role in such disorders, we generated knock-in mice with hematopoietic-specific expression of Sf3b1-K700E, the commonest type of SF3B1 mutation in MDS. Sf3b1K700E/+ animals had impaired erythropoiesis and progressive anemia without ringed sideroblasts, as well as reduced hematopoietic stem cell numbers and host-repopulating fitness. To understand the molecular basis of these observations, we analyzed global RNA splicing in Sf3b1K700E/+ hematopoietic cells. Aberrant splicing was associated with the usage of cryptic 3' splice and branchpoint sites, as described for human SF3B1 mutants. However, we found a little overlap between aberrantly spliced mRNAs in mouse versus human, suggesting that anemia may be a consequence of globally disrupted splicing. Furthermore, the murine orthologues of genes associated with ring sideroblasts in human MDS, including Abcb7 and Tmem14c, were not aberrantly spliced in Sf3b1K700E/+ mice. Our findings demonstrate that, despite significant differences in affected transcripts, there is overlap in the phenotypes associated with SF3B1-K700E between human and mouse. Future studies should focus on understanding the basis of these similarities and differences as a means of deciphering the consequences of spliceosome gene mutations in MDS.
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Affiliation(s)
- A Mupo
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - M Seiler
- H3 Biomedicine, Inc., Cambridge, MA, USA
| | | | - A Pance
- Malaria Programme, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Y Yang
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - F Iorio
- European Bioinformatics, Institute, Hinxton, Cambridge, UK
| | - R Bautista
- LIMS Compute and Infrastructure, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - S Pacharne
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - K Tzelepis
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - N Manes
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - P Wright
- Department of Pathology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - E Papaemmanuil
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D G Kent
- Cambridge Stem Cell Institute, Cambridge, UK
| | - P C Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - N Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Dipartimento di Oncologia ed Onco-Ematologia, Universita' degli Studi di Milano, Milano, Italy
- Dipartimento di Ematologia ed Onco-Ematologia Pediatrica, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - G S Vassiliou
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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97
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Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations. Oncotarget 2017; 7:9951-63. [PMID: 26848861 PMCID: PMC4891095 DOI: 10.18632/oncotarget.7127] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 01/19/2016] [Indexed: 12/12/2022] Open
Abstract
Spliceosome mutations are frequently observed in patients with myelodysplastic syndromes (MDS). However, it is largely unknown how these mutations contribute to the disease. MicroRNAs (miRNAs) are small noncoding RNAs, which have been implicated in most human cancers due to their role in post transcriptional gene regulation. The aim of this study was to analyze the impact of spliceosome mutations on the expression of miRNAs in a cohort of 34 MDS patients. In total, the expression of 76 miRNAs, including mirtrons and splice site overlapping miRNAs, was accurately quantified using reverse transcriptase quantitative PCR. The majority of the studied miRNAs have previously been implicated in MDS. Stably expressed miRNA genes for normalization of the data were identified using GeNorm and NormFinder algorithms. High-resolution melting assays covering all mutational hotspots within SF3B1, SRSF2, and U2AF1 (U2AF35) were developed, and all detected mutations were confirmed by Sanger sequencing. Overall, canonical miRNAs were downregulated in spliceosome mutated samples compared to wild-type (P = 0.002), and samples from spliceosome mutated patients clustered together in hierarchical cluster analyses. Among the most downregulated miRNAs were several tumor-suppressor miRNAs, including several let-7 family members, miR-423, and miR-103a. Finally, we observed that the predicted targets of the most downregulated miRNAs were involved in apoptosis, hematopoiesis, and acute myeloid leukemia among other cancer- and metabolic pathways. Our data indicate that spliceosome mutations may play an important role in MDS pathophysiology by affecting the expression of tumor suppressor miRNA genes involved in the development and progression of MDS.
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98
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Long ZB, Du YL, Han B. [Research progress on clonal acquired sideroblastic anemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2017; 38:83-86. [PMID: 28219236 PMCID: PMC7348407 DOI: 10.3760/cma.j.issn.0253-2727.2017.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 11/05/2022]
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99
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Dujardin G, Daguenet É, Bernard DG, Flodrops M, Durand S, Chauveau A, El Khoury F, Le Jossic-Corcos C, Corcos L. L’épissage des ARN pré-messagers : quand le splicéosome perd pied. Med Sci (Paris) 2017; 32:1103-1110. [DOI: 10.1051/medsci/20163212014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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100
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Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia. Nat Immunol 2016; 18:236-245. [PMID: 28024152 PMCID: PMC5423405 DOI: 10.1038/ni.3654] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/30/2016] [Indexed: 12/24/2022]
Abstract
Toll-like receptor (TLR) activation contributes to premalignant hematologic conditions, such as myelodysplastic syndromes (MDS). TRAF6, a TLR-effector with ubiquitin (Ub) ligase activity, is overexpressed in MDS hematopoietic stem/progenitor cells (HSPC). Here we show that TRAF6 overexpression in mouse HSPC resulted in impaired hematopoiesis and bone marrow failure. Through the use of a global Ub screen, we identified hnRNPA1, an RNA-binding protein and auxiliary splicing factor, as a substrate of TRAF6. TRAF6 ubiquitination of hnRNPA1 regulated alternative splicing of Arhgap1, which resulted in Cdc42 activation and accounted for hematopoietic defects in TRAF6-expressing HSPC. These results implicate Ub signaling in coordinating RNA processing by TLR pathways during an immune response and in premalignant hematologic diseases, such as MDS.
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