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Ineffective erythropoiesis and its treatment. Blood 2021; 139:2460-2470. [PMID: 34932791 DOI: 10.1182/blood.2021011045] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 01/19/2023] Open
Abstract
The erythroid marrow and circulating red blood cells (RBCs) are the key components of the human erythron. Abnormalities of the erythron that are responsible for anemia can be distinguished into 3 major categories, that is, erythroid hypoproliferation, ineffective erythropoiesis, and peripheral hemolysis. Ineffective erythropoiesis is characterized by erythropoietin-driven expansion of early-stage erythroid precursors, associated with apoptosis of late-stage precursors. This mechanism is primarily responsible for anemia in inherited disorders like β-thalassemia, inherited sideroblastic anemias, and congenital dyserythropoietic anemias, as well as in acquired conditions like some subtypes of myelodysplastic syndromes (MDS). The inherited anemias due to ineffective erythropoiesis are also defined as iron loading anemias because of the associated parenchymal iron loading caused by the release of erythroid factors that suppress hepcidin production. Novel treatments specifically targeting ineffective erythropoiesis are being developed. Iron restriction through enhancement of hepcidin activity or inhibition of ferroportin function has been shown to reduce ineffective erythropoiesis in murine models of β-thalassemia. Luspatercept is a TGF-β ligand trap that inhibits SMAD2/3 signaling. Based on pre-clinical and clinical studies, this compound is now approved for the treatment of anemia in adult patients with β-thalassemia who require regular RBC transfusions. Luspatercept is also approved for the treatment of transfusion-dependent anemia in patients with MDS with ring sideroblasts, most of whom carry a somatic SF3B1mutation. While long-term efficacy and safety of luspatercept need to be evaluated both in β-thalassemia and MDS, defining the molecular mechanisms of ineffective erythropoiesis in different disorders might allow the discovery of new effective compounds.
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Wu K, Nie B, Li L, Yang X, Yang J, He Z, Li Y, Cheng S, Shi M, Zeng Y. Bioinformatics analysis of high frequency mutations in myelodysplastic syndrome-related patients. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1491. [PMID: 34805353 PMCID: PMC8573449 DOI: 10.21037/atm-21-4094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/24/2021] [Indexed: 11/06/2022]
Abstract
Background Myelodysplastic syndrome (MDS) is a group of hematological malignancies that may progress to acute myeloid leukemia (AML). Bioinformatics-based analysis of high-frequency mutation genes in MDS-related patients is still relatively rare, so we conducted our research to explore whether high-frequency mutation genes in MDS-related patients can play a reference role in clinical guidance and prognosis. Methods Next generation sequencing (NGS) technology was used to detect 32 mutations in 64 MDS-related patients. We classified the patients' genes and analyzed them by Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, protein-protein interaction (PPI) analysis, and then calculated the gene survival curve of high-frequency mutations. Results We discovered 32 mutant genes such as ASXL1, DNMT3A, KRAS, NRAS, TP53, SF3B1, and SRSF2. The overall survival (OS) of these genes decreased significantly after DNMT3A, ASXL1, RUNX1, and U2AF1 occurred mutation. These genes play a significant role in biological processes, not only in MDS but also in the occurrence and development of other diseases. Through retrospective analysis, genes associated with MDS-related diseases were identified, and their effects on the disease were predicted. Conclusions Thirty-two mutant genes were determined in MDS and when mutations occur in DNMT3A, ASXL1, RUNX1, and U2AF1, their survival time decreases significantly. This results providing a theoretical basis for clinical and scientific research and broadening the scope of research on MDS.
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Affiliation(s)
- Kun Wu
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Innovation Team of Clinical Laboratory and Diagnosis, Kunming, China
| | - Bo Nie
- Department of Hematology, First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, China
| | - Liyin Li
- Department of Hematology, First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, China
| | - Xin Yang
- Department of Hematology, First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, China
| | - Jinrong Yang
- Department of Hematology, First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, China
| | - Zhenxin He
- Department of Hematology, First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, China
| | - Yanhong Li
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Innovation Team of Clinical Laboratory and Diagnosis, Kunming, China
| | - Shenju Cheng
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Innovation Team of Clinical Laboratory and Diagnosis, Kunming, China
| | - Mingxia Shi
- Department of Hematology, First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, China
| | - Yun Zeng
- Department of Hematology, First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, China
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Karakulak T, Moch H, von Mering C, Kahraman A. Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies. Front Mol Biosci 2021; 8:726902. [PMID: 34888349 PMCID: PMC8650491 DOI: 10.3389/fmolb.2021.726902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/01/2021] [Indexed: 12/03/2022] Open
Abstract
Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances in sequencing technologies and analysis methods led to new insights into the extent and functional impact of disturbed alternative splicing events. In this review, we give a brief overview of the molecular mechanisms driving alternative splicing, highlight the function of alternative splicing in healthy tissues and describe how alternative splicing is disrupted in cancer. We summarize current available computational tools for analyzing differential transcript usage, isoform switching events, and the pathogenic impact of cancer-specific splicing events. Finally, the strategies of three recent pan-cancer studies on isoform switching events are compared. Their methodological similarities and discrepancies are highlighted and lessons learned from the comparison are listed. We hope that our assessment will lead to new and more robust methods for cancer-specific transcript detection and help to produce more accurate functional impact predictions of isoform switching events.
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Affiliation(s)
- Tülay Karakulak
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abdullah Kahraman
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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54
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Zhang B, Ding Z, Li L, Xie LK, Fan YJ, Xu YZ. Two oppositely-charged sf3b1 mutations cause defective development, impaired immune response, and aberrant selection of intronic branch sites in Drosophila. PLoS Genet 2021; 17:e1009861. [PMID: 34723968 PMCID: PMC8559932 DOI: 10.1371/journal.pgen.1009861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
SF3B1 mutations occur in many cancers, and the highly conserved His662 residue is one of the hotspot mutation sites. To address effects on splicing and development, we constructed strains carrying point mutations at the corresponding residue His698 in Drosophila using the CRISPR-Cas9 technique. Two mutations, H698D and H698R, were selected due to their frequent presence in patients and notable opposite charges. Both the sf3b1-H698D and–H698R mutant flies exhibit developmental defects, including less egg-laying, decreased hatching rates, delayed morphogenesis and shorter lifespans. Interestingly, the H698D mutant has decreased resistance to fungal infection, while the H698R mutant shows impaired climbing ability. Consistent with these phenotypes, further analysis of RNA-seq data finds altered expression of immune response genes and changed alternative splicing of muscle and neural-related genes in the two mutants, respectively. Expression of Mef2-RB, an isoform of Mef2 gene that was downregulated due to splicing changes caused by H698R, partly rescues the climbing defects of the sf3b1-H698R mutant. Lariat sequencing reveals that the two sf3b1-H698 mutations cause aberrant selection of multiple intronic branch sites, with the H698R mutant using far upstream branch sites in the changed alternative splicing events. This study provides in vivo evidence from Drosophila that elucidates how these SF3B1 hotspot mutations alter splicing and their consequences in development and in the immune system. In the past decade, one of the important findings in the RNA splicing field has been that somatic SF3B1 mutations widely occur in many cancers. Including R625, H662, K666, K700 and E902, there are five hotspot mutation sites in the highly conserved HEAT repeats of SF3B1. Several kinds of H662 mutations have been found widely in MDS, AML, CLL and breast cancers; however, it remains unclear how these H662 mutations alter splicing and whether they have in vivo effects on development. To address these questions, in this manuscript, we first summarized the H662 mutations in human diseases and constructed two corresponding Drosophila mutant strains, sf3b1-H698D and -H698R using CRISPR-Cas9. Analyses of these two fly strains find that the two oppositely charged Sf3b1-H698 mutants are defective in development. In addition, one mutant has decreased climbing ability, whereas the other mutant has impaired immune response. Further RNA-seq allows us to find responsible genes in each mutant strain, and lariat sequencing reveals that both mutations cause aberrant selection of the intronic branch sites. Our findings provide the first in vivo evidence that Sf3b1 mutations result in defective development, and also reveal a molecular mechanism of these hotspot histidine mutations that enhance the use of cryptic branch sites to alter splicing. Importantly, we demonstrate that the H698R mutant prefers to use far upstream branch sites.
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Affiliation(s)
- Bei Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Zhan Ding
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Liang Li
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Ling-Kun Xie
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
- * E-mail:
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55
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Impact of alternative splicing on mechanisms of resistance to anticancer drugs. Biochem Pharmacol 2021; 193:114810. [PMID: 34673012 DOI: 10.1016/j.bcp.2021.114810] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
A shared characteristic of many tumors is the lack of response to anticancer drugs. Multiple mechanisms of pharmacoresistance (MPRs) are involved in permitting cancer cells to overcome the effect of these agents. Pharmacoresistance can be primary (intrinsic) or secondary (acquired), i.e., triggered or enhanced in response to the treatment. Moreover, MPRs usually result in the lack of sensitivity to several agents, which accounts for diverse multidrug-resistant (MDR) phenotypes. MPRs are based on the dynamic expression of more than one hundred genes, constituting the so-called resistome. Alternative splicing (AS) during pre-mRNA maturation results in changes affecting proteins involved in the resistome. The resulting splicing variants (SVs) reduce the efficacy of anticancer drugs by lowering the intracellular levels of active agents, altering molecular targets, enhancing both DNA repair ability and defensive mechanism of tumors, inducing changes in the balance between pro-survival and pro-apoptosis signals, modifying interactions with the tumor microenvironment, and favoring malignant phenotypic transitions. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the impact of AS on MPR in cancer cells.
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56
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Gallì A, Todisco G, Catamo E, Sala C, Elena C, Pozzi S, Bono E, Ferretti VV, Rizzo E, Molteni E, Zibellini S, Sarchi M, Boveri E, Ferrari J, Fiorelli N, Camaschella C, Gasparini P, Toniolo D, Cazzola M, Malcovati L. Relationship between clone metrics and clinical outcome in clonal cytopenia. Blood 2021; 138:965-976. [PMID: 34255818 DOI: 10.1182/blood.2021011323] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/21/2021] [Indexed: 01/05/2023] Open
Abstract
Clonal cytopenia of undetermined significance (CCUS) is associated with an increased risk of developing a myeloid neoplasm with myelodysplasia (MN). To identify the features of the mutant clone(s) that is associated with clinical phenotype and progression, we studied the following cohorts of individuals: 311 patients with idiopathic cytopenia of undetermined significance (ICUS), 532 community-dwelling individuals without hematologic phenotype (n = 355) or with unexplained anemia (n = 177), and 592 patients with overt MN. Ninety-two of 311 (30%) patients with ICUS carried a somatic genetic lesion that signaled CCUS. Clonal hematopoiesis (CH) was detected in 19.7% and 27.7% of nonanemic and anemic community-dwelling individuals, respectively. Different mutation patterns and variant allele frequencies (VAFs) (clone metrics parameters) were observed in the conditions studied. Recurrent mutation patterns exhibited different VAFs associated with marrow dysplasia (0.17-0.48), indicating variable clinical expressivity of mutant clones. Unsupervised clustering analysis based on mutation profiles identified 2 major clusters, characterized by isolated DNMT3A mutations (CH-like cluster) or combinatorial mutation patterns (MN-like cluster), and showing different overall survival (HR, 1.8). In patients with CCUS, the 2 clusters had different risk of progression to MN (HR, 2.7). Within the MN-like cluster, distinct subsets with different risk of progression to MN were identified based on clone metrics. These findings unveil marked variability in the clinical expressivity of myeloid driver genes and underline the limitations of morphologic dysplasia for clinical staging of mutant hematopoietic clones. Clone metrics appears to be critical for informing clinical decision-making in patients with clonal cytopenia.
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Affiliation(s)
- Anna Gallì
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
| | - Gabriele Todisco
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Eulalia Catamo
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Elena
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
| | - Sara Pozzi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Elisa Bono
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | | | | | - Silvia Zibellini
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
| | - Martina Sarchi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Emanuela Boveri
- Department of Pathology, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Jacqueline Ferrari
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nicolas Fiorelli
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Clara Camaschella
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Gasparini
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Mario Cazzola
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Luca Malcovati
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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Venable ER, Chen D, Chen CP, Bessonen KR, Nguyen PL, Oliveira JL, Reichard KK, Hoyer JD, Althoff SD, Roh DJ, Miller MA, Begna K, Patnaik MM, Litzow MR, Al-Kali A, Viswanatha DS, He R. Pathologic Spectrum and Molecular Landscape of Myeloid Disorders Harboring SF3B1 Mutations. Am J Clin Pathol 2021; 156:679-690. [PMID: 33978189 PMCID: PMC8427737 DOI: 10.1093/ajcp/aqab010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Objectives SF3B1 mutations are the most common mutations in myelodysplastic syndromes (MDS). The International Working Group for the Prognosis of MDS (IWG-PM) recently proposed SF3B1-mutant MDS (SF3B1-mut-MDS) as a distinct disease subtype. We evaluated the spectrum and molecular landscape of SF3B1-mutated myeloid disorders and assessed the prognostication in MDS harboring SF3B1 mutations (MDS-SF3B1). Methods Cases were selected by retrospective review. Clinical course and laboratory and clinical findings were collected by chart review. SF3B1-mut-MDS was classified following IWG-PM criteria. Results SF3B1 mutations were identified in 75 of 955 patients, encompassing a full spectrum of myeloid disorders. In MDS-SF3B1, Revised International Prognostic Scoring System (IPSS-R) score greater than 3 and transcription factor (TF) comutations were adverse prognostic markers by both univariate and multivariate analyses. We confirmed the favorable outcome of IWG-PM-defined SF3B1-mut-MDS. Interestingly, it did not show sharp prognostic differentiation within MDS-SF3B1. Conclusions SF3B1 mutations occur in the full spectrum of myeloid disorders. We independently validated the favorable prognostication of IWG-PM-defined SF3B1-mut-MDS. However it may not provide sharp prognostication within MDS-SF3B1 where IPSS-R and TF comutations were prognostic-informative. Larger cohort studies are warranted to verify these findings and refine MDS-SF3B1 prognostication.
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Affiliation(s)
- Elise R Venable
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Dong Chen
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Constance P Chen
- College of Science, University of Notre Dame, Notre Dame, IN, USA
| | - Kurt R Bessonen
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Phuong L Nguyen
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jennifer L Oliveira
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kaaren K Reichard
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - James D Hoyer
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Simon D Althoff
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Dana J Roh
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mechelle A Miller
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kebede Begna
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mrinal M Patnaik
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mark R Litzow
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - David S Viswanatha
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Rong He
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
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Volpe VO, Garcia-Manero G, Komrokji RS. Myelodysplastic Syndromes: A New Decade. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2021; 22:1-16. [PMID: 34544674 DOI: 10.1016/j.clml.2021.07.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous clonal hematopoietic stem cell disorders. The 2020 Surveillance, Epidemiology, and End Results data demonstrates the incidence rate of MDS increases with age especially in those greater than 70 years of age. Risk stratification that impact prognosis, survival, and rate of acute myeloid leukemia (AML) transformation in MDS is largely dependent on revised International Prognostic Scoring System along with molecular genetic testing as a supplement. Low risk MDS typically have a more indolent disease course in which treatment is only initiated to ameliorate symptoms of cytopenias. In many, anemia is the most common cytopenia requiring treatment and erythroid stimulating agents, are considered first line. In contrast, high risk MDS tend to behave more aggressively for which treatment should be initiated rapidly with Hypomethylating Agents (HMA) being in the frontline. In those with high risk MDS and eligible, evaluation for allogeneic stem cell transplant should be considered as this is the only potential curative option for MDS. With the use of molecular genetic testing, a personalized approach to therapy in MDS has ensued. As the treatment landscape in MDS continues to flourish with novel targeted agents, we ambitiously seek to improve survival rates especially among the relapsed/refractory and transplant ineligible.
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Affiliation(s)
- Virginia O Volpe
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | | | - Rami S Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL.
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Co-mutation pattern, clonal hierarchy, and clone size concur to determine disease phenotype of SRSF2 P95-mutated neoplasms. Leukemia 2021; 35:2371-2381. [PMID: 33349666 DOI: 10.1038/s41375-020-01106-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 10/29/2020] [Accepted: 11/27/2020] [Indexed: 01/29/2023]
Abstract
Somatic mutations in splicing factor genes frequently occur in myeloid neoplasms. While SF3B1 mutations are associated with myelodysplastic syndromes (MDS) with ring sideroblasts, SRSF2P95 mutations are found in different disease categories, including MDS, myeloproliferative neoplasms (MPN), myelodysplastic/myeloproliferative neoplasms (MDS/MPN), and acute myeloid leukemia (AML). To identify molecular determinants of this phenotypic heterogeneity, we explored molecular and clinical features of a prospective cohort of 279 SRSF2P95-mutated cases selected from a population of 2663 patients with myeloid neoplasms. Median number of somatic mutations per subject was 3. Multivariate regression analysis showed associations between co-mutated genes and clinical phenotype, including JAK2 or MPL with myelofibrosis (OR = 26.9); TET2 with monocytosis (OR = 5.2); RAS-pathway genes with leukocytosis (OR = 5.1); and STAG2, RUNX1, or IDH1/2 with blast phenotype (MDS or AML) (OR = 3.4, 1.9, and 2.1, respectively). Within patients with SRSF2-JAK2 co-mutation, JAK2 dominance was invariably associated with clinical feature of MPN, whereas SRSF2 mutation was dominant in MDS/MPN. Within patients with SRSF2-TET2 co-mutation, clinical expressivity of monocytosis was positively associated with co-mutated clone size. This study provides evidence that co-mutation pattern, clone size, and hierarchy concur to determine clinical phenotype, tracing relevant genotype-phenotype associations across disease entities and giving insight on unaccountable clinical heterogeneity within current WHO classification categories.
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60
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Chiereghin C, Travaglino E, Zampini M, Saba E, Saitta C, Riva E, Bersanelli M, Della Porta MG. The Genetics of Myelodysplastic Syndromes: Clinical Relevance. Genes (Basel) 2021; 12:genes12081144. [PMID: 34440317 PMCID: PMC8392119 DOI: 10.3390/genes12081144] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/05/2021] [Accepted: 07/22/2021] [Indexed: 12/27/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a clonal disease arising from hematopoietic stem cells, that are characterized by ineffective hematopoiesis (leading to peripheral blood cytopenia) and by an increased risk of evolution into acute myeloid leukemia. MDS are driven by a complex combination of genetic mutations that results in heterogeneous clinical phenotype and outcome. Genetic studies have enabled the identification of a set of recurrently mutated genes which are central to the pathogenesis of MDS and can be organized into a limited number of cellular pathways, including RNA splicing (SF3B1, SRSF2, ZRSR2, U2AF1 genes), DNA methylation (TET2, DNMT3A, IDH1/2), transcription regulation (RUNX1), signal transduction (CBL, RAS), DNA repair (TP53), chromatin modification (ASXL1, EZH2), and cohesin complex (STAG2). Few genes are consistently mutated in >10% of patients, whereas a long tail of 40-50 genes are mutated in <5% of cases. At diagnosis, the majority of MDS patients have 2-4 driver mutations and hundreds of background mutations. Reliable genotype/phenotype relationships were described in MDS: SF3B1 mutations are associated with the presence of ring sideroblasts and more recent studies indicate that other splicing mutations (SRSF2, U2AF1) may identify distinct disease categories with specific hematological features. Moreover, gene mutations have been shown to influence the probability of survival and risk of disease progression and mutational status may add significant information to currently available prognostic tools. For instance, SF3B1 mutations are predictors of favourable prognosis, while driver mutations of other genes (such as ASXL1, SRSF2, RUNX1, TP53) are associated with a reduced probability of survival and increased risk of disease progression. In this article, we review the most recent advances in our understanding of the genetic basis of myelodysplastic syndromes and discuss its clinical relevance.
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Affiliation(s)
- Chiara Chiereghin
- IRCCS Humanitas Research Hospital, Via Alessandro Manzoni 56, 20089 Rozzano, Italy; (C.C.); (E.T.); (M.Z.); (E.S.); (C.S.); (E.R.)
| | - Erica Travaglino
- IRCCS Humanitas Research Hospital, Via Alessandro Manzoni 56, 20089 Rozzano, Italy; (C.C.); (E.T.); (M.Z.); (E.S.); (C.S.); (E.R.)
| | - Matteo Zampini
- IRCCS Humanitas Research Hospital, Via Alessandro Manzoni 56, 20089 Rozzano, Italy; (C.C.); (E.T.); (M.Z.); (E.S.); (C.S.); (E.R.)
| | - Elena Saba
- IRCCS Humanitas Research Hospital, Via Alessandro Manzoni 56, 20089 Rozzano, Italy; (C.C.); (E.T.); (M.Z.); (E.S.); (C.S.); (E.R.)
| | - Claudia Saitta
- IRCCS Humanitas Research Hospital, Via Alessandro Manzoni 56, 20089 Rozzano, Italy; (C.C.); (E.T.); (M.Z.); (E.S.); (C.S.); (E.R.)
| | - Elena Riva
- IRCCS Humanitas Research Hospital, Via Alessandro Manzoni 56, 20089 Rozzano, Italy; (C.C.); (E.T.); (M.Z.); (E.S.); (C.S.); (E.R.)
| | - Matteo Bersanelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Italy;
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Research Hospital, Via Alessandro Manzoni 56, 20089 Rozzano, Italy; (C.C.); (E.T.); (M.Z.); (E.S.); (C.S.); (E.R.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Italy;
- Correspondence: ; Tel.: +39-0282247668
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Kataoka N, Matsumoto E, Masaki S. Mechanistic Insights of Aberrant Splicing with Splicing Factor Mutations Found in Myelodysplastic Syndromes. Int J Mol Sci 2021; 22:ijms22157789. [PMID: 34360561 PMCID: PMC8346168 DOI: 10.3390/ijms22157789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
Pre-mRNA splicing is an essential process for gene expression in higher eukaryotes, which requires a high order of accuracy. Mutations in splicing factors or regulatory elements in pre-mRNAs often result in many human diseases. Myelodysplastic syndrome (MDS) is a heterogeneous group of chronic myeloid neoplasms characterized by many symptoms and a high risk of progression to acute myeloid leukemia. Recent findings indicate that mutations in splicing factors represent a novel class of driver mutations in human cancers and affect about 50% of Myelodysplastic syndrome (MDS) patients. Somatic mutations in MDS patients are frequently found in genes SF3B1, SRSF2, U2AF1, and ZRSR2. Interestingly, they are involved in the recognition of 3' splice sites and exons. It has been reported that mutations in these splicing regulators result in aberrant splicing of many genes. In this review article, we first describe molecular mechanism of pre-mRNA splicing as an introduction and mainly focus on those four splicing factors to describe their mutations and their associated aberrant splicing patterns.
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Affiliation(s)
- Naoyuki Kataoka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
- Correspondence: ; Tel.: +81-3-5841-5372; Fax: +81-3-5841-8014
| | - Eri Matsumoto
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
| | - So Masaki
- Laboratory of Molecular Medicinal Science, Department of Pharmaceutical Sciences, Ritsumeikan University, Shiga 525-8577, Japan;
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62
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Yang H, Beutler B, Zhang D. Emerging roles of spliceosome in cancer and immunity. Protein Cell 2021; 13:559-579. [PMID: 34196950 PMCID: PMC9232692 DOI: 10.1007/s13238-021-00856-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be general cell “housekeeping” machinery, mutations in core components of the spliceosome frequently correlate with cell- or tissue-specific phenotypes and diseases. In this review, we expound the links between spliceosome mutations, aberrant splicing, and human cancers. Remarkably, spliceosome-targeted therapies (STTs) have become efficient anti-cancer strategies for cancer patients with splicing defects. We also highlight the links between spliceosome and immune signaling. Recent studies have shown that some spliceosome gene mutations can result in immune dysregulation and notable phenotypes due to mis-splicing of immune-related genes. Furthermore, several core spliceosome components harbor splicing-independent immune functions within the cell, expanding the functional repertoire of these diverse proteins.
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Affiliation(s)
- Hui Yang
- Department of Neurosurgery, Huashan Hospital, Shanghai Key laboratory of Brain Function Restoration and Neural Regeneration, MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Duanwu Zhang
- Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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Schulz F, Nachtkamp K, Kasprzak A, Gattermann N, Haas R, Germing U. Luspatercept as a therapy for myelodysplastic syndromes with ring sideroblasts. Expert Rev Hematol 2021; 14:509-516. [PMID: 34161752 DOI: 10.1080/17474086.2021.1947791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic stem cell diseases characterized by cell dysplasia, ineffective hematopoiesis and risk of transformation to acute myeloid leukemia (AML). The median age of 75 years at diagnosis is associated with the presence of comorbidities, which preclude intensive therapies like allogeneic hematopoietic stem cell transplantation in most MDS patients. Risk stratification using the (Revised) International Prognostic Scoring System (IPSS/IPSS-R) is necessary to plan individualized treatment. AREAS COVERED Luspatercept (ACE-536), a specific activin receptor fusion protein, promotes late-stage erythropoiesis. Two clinical trials, PACE-MDS (phase 2) and MEDALIST (phase 3), yielded positive results in terms of improved hemoglobin levels and loss of transfusion dependence, with hardly any side effects. A phase 3 trial to compare luspatercept to ESAs (COMMANDS study) is ongoing. EXPERT OPINION Luspatercept is a promising alternative to ESAs for a subset of transfusion-dependent patients with lower risk MDS, namely those with a sideroblastic phenotype who are either not suitable for or have already failed erythropoietin-based treatment. The favorable safety profile and convenient subcutaneous administration every 3 weeks are more conducive to patients' quality of life than chronic red blood cell transfusion therapy.
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Affiliation(s)
- Felicitas Schulz
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Kathrin Nachtkamp
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Annika Kasprzak
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
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Martínez-Valiente C, Garcia-Ruiz C, Rosón B, Liquori A, González-Romero E, Fernández-González R, Gómez-Redondo I, Cervera J, Gutiérrez-Adán A, Sanjuan-Pla A. Aberrant Alternative Splicing in U2af1/Tet2 Double Mutant Mice Contributes to Major Hematological Phenotypes. Int J Mol Sci 2021; 22:6963. [PMID: 34203454 PMCID: PMC8269301 DOI: 10.3390/ijms22136963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/19/2022] Open
Abstract
Mutations in splicing factors are recurrent somatic alterations identified in myelodysplastic syndromes (MDS) and they frequently coincide with mutations in epigenetic factors. About 25% of patients present concurrent mutations in such pathways, suggesting a cooperative role in the pathogenesis of MDS. We focused on the splicing factor U2AF1 involved in the recognition of the 3' splice site during pre-mRNA splicing. Using a CRISPR/Cas9 system, we created heterozygous mice with a carboxy-terminal truncated U2af1 allele (U2af1mut/+), studied the U2af1mut/+ hematopoietic system, and did not observe any gross differences in both young (12-13 weeks) and old (23 months) U2af1mut/+ mice, except for a reduction in size of approximately 20%. However, hematopoietic stem/progenitor cells lacked reconstitution capacity in transplantation assays and displayed an aberrant RNA splicing by RNA sequencing. We also evaluated U2af1mut/+ in conjunction with Tet2-deficiency. Novel double mutant U2af1mut/+Tet2-/- mice showed increased monogranulocytic precursors. Hematopoietic stem/progenitor cells were also enhanced and presented functional and transcriptomic alterations. Nonetheless, U2af1mut/+Tet2-/- mice did not succumb to MDS disease over a 6-month observation period. Collectively, our data suggest that cooperation between mutant U2af1 and Tet2 loss is not sufficient for MDS initiation in mice.
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Affiliation(s)
- Cristina Martínez-Valiente
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain; (C.M.-V.); (C.G.-R.); (B.R.); (A.L.); (E.G.-R.)
| | - Cristian Garcia-Ruiz
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain; (C.M.-V.); (C.G.-R.); (B.R.); (A.L.); (E.G.-R.)
| | - Beatriz Rosón
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain; (C.M.-V.); (C.G.-R.); (B.R.); (A.L.); (E.G.-R.)
| | - Alessandro Liquori
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain; (C.M.-V.); (C.G.-R.); (B.R.); (A.L.); (E.G.-R.)
| | - Elisa González-Romero
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain; (C.M.-V.); (C.G.-R.); (B.R.); (A.L.); (E.G.-R.)
| | - Raúl Fernández-González
- Animal Reproduction Department, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain; (R.F.-G.); (I.G.-R.); (A.G.-A.)
| | - Isabel Gómez-Redondo
- Animal Reproduction Department, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain; (R.F.-G.); (I.G.-R.); (A.G.-A.)
| | - José Cervera
- Hematology Service, Hospital Universitario y Politécnico La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), Av. Monforte de Lemos, 3-5 Pabellón 11, 28029 Madrid, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Alfonso Gutiérrez-Adán
- Animal Reproduction Department, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain; (R.F.-G.); (I.G.-R.); (A.G.-A.)
| | - Alejandra Sanjuan-Pla
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, Avda. Fernando Abril Martorell 106, 46026 Valencia, Spain; (C.M.-V.); (C.G.-R.); (B.R.); (A.L.); (E.G.-R.)
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Phase I First-in-Human Dose Escalation Study of the oral SF3B1 modulator H3B-8800 in myeloid neoplasms. Leukemia 2021; 35:3542-3550. [PMID: 34172893 PMCID: PMC8632688 DOI: 10.1038/s41375-021-01328-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
We conducted a phase I clinical trial of H3B-8800, an oral small molecule that binds Splicing Factor 3B1 (SF3B1), in patients with MDS, CMML, or AML. Among 84 enrolled patients (42 MDS, 4 CMML and 38 AML), 62 were red blood cell (RBC) transfusion dependent at study entry. Dose escalation cohorts examined two once-daily dosing regimens: schedule I (5 days on/9 days off, range of doses studied 1–40 mg, n = 65) and schedule II (21 days on/7 days off, 7–20 mg, n = 19); 27 patients received treatment for ≥180 days. The most common treatment-related, treatment-emergent adverse events included diarrhea, nausea, fatigue, and vomiting. No complete or partial responses meeting IWG criteria were observed; however, RBC transfusion free intervals >56 days were observed in nine patients who were transfusion dependent at study entry (15%). Of 15 MDS patients with missense SF3B1 mutations, five experienced RBC transfusion independence (TI). Elevated pre-treatment expression of aberrant transcripts of Transmembrane Protein 14C (TMEM14C), an SF3B1 splicing target encoding a mitochondrial porphyrin transporter, was observed in MDS patients experiencing RBC TI. In summary, H3B-8800 treatment was associated with mostly low-grade TAEs and induced RBC TI in a biomarker-defined subset of MDS.
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66
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The K666N mutation in SF3B1 is associated with increased progression of MDS and distinct RNA splicing. Blood Adv 2021; 4:1192-1196. [PMID: 32211880 DOI: 10.1182/bloodadvances.2019001127] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
Key Points
The K666N mutation of SF3B1 has distinct clinicopathologic features in MDS. The K666N mutation of SF3B1 has a distinct RNA splicing profile.
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67
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Chen-Liang TH. Prognosis in Myelodysplastic Syndromes: The Clinical Challenge of Genomic Integration. J Clin Med 2021; 10:2052. [PMID: 34064707 PMCID: PMC8151135 DOI: 10.3390/jcm10102052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 11/17/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of clonal hematopoietic neoplasms characterized by ineffective hematopoiesis and myelodysplasia with a variable spectrum of clinical-biological features that can be used to build a prognostic estimation. This review summarizes the current most widely used prognostic scoring systems and gives a general view of the prognostic impact of somatic mutations in MDS patients.
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Affiliation(s)
- Tzu-Hua Chen-Liang
- Hematology and Oncology Unit, University Hospital Morales Meseguer, Marques de los Velez s/n, 30008 Murcia, Spain
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68
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Butt H, Bazin J, Alshareef S, Eid A, Benhamed M, Reddy ASN, Crespi M, Mahfouz MM. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation. Commun Biol 2021; 4:529. [PMID: 33953336 PMCID: PMC8100303 DOI: 10.1038/s42003-021-02051-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
The SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1GEX1ARESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants. Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Sahar Alshareef
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Moussa Benhamed
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Chang YH. Myelodysplastic syndromes and overlap syndromes. Blood Res 2021; 56:S51-S64. [PMID: 33935036 PMCID: PMC8094000 DOI: 10.5045/br.2021.2021010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/11/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematological neoplasms characterized by ineffective hematopoiesis, morphologic dysplasia, and cytopenia. MDS overlap syndromes include various disorders, such as myelodysplastic/myeloproliferative neoplasms and hypoplastic MDS with aplastic anemia characteristics. MDS overlap syndromes share the characteristics of other diseases, which make differential diagnoses challenging. Advances in genomic studies have led to the discovery of frequent mutations in MDS and overlap syndromes; however, most of the mutations are not specific for the diagnosis of these diseases. The molecular characteristics of the overlap syndromes usually do not show a just "in-between" form but rather heterogeneous features. Established diagnostic criteria for these diseases based on clinical, morphologic, and laboratory features are still useful when combined with genomic data. It is expected that further studies for MDS and overlap syndromes will place emphasis on the roles of mutations as therapeutic targets and prognostic indicators.
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Affiliation(s)
- Yoon Hwan Chang
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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70
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Proximity Biotin Labeling Reveals Kaposi's Sarcoma-Associated Herpesvirus Interferon Regulatory Factor Networks. J Virol 2021; 95:JVI.02049-20. [PMID: 33597212 PMCID: PMC8104114 DOI: 10.1128/jvi.02049-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/10/2021] [Indexed: 01/04/2023] Open
Abstract
Viral protein interaction with a host protein shows at least two sides: (i) taking host protein functions for its own benefit and (ii) disruption of existing host protein complex formation to inhibit undesirable host responses. Due to the use of affinity precipitation approaches, the majority of studies have focused on how the virus takes advantage of the newly formed protein interactions for its own replication. Studies on “hit-and-run” effects by viral proteins are difficult when using traditional affinity precipitation-based techniques under dynamic conditions, because only proteins interacting at a specific instance in time can be precipitated by affinity purification. Recent advances in proximity labeling (PL) have enabled identification of both static and dynamic protein-protein interactions. In this study, we applied a PL method by generating recombinant Kaposi’s sarcoma-associated herpesvirus (KSHV). KSHV, a gammaherpesvirus, uniquely encodes four interferon regulatory factors (IRF-1 to -4) that suppress host interferon responses, and we examined KSHV IRF-1 and IRF-4 neighbor proteins to identify cellular proteins involved in innate immune regulation. PL identified 213 and 70 proteins as neighboring proteins of viral IRF-1 (vIRF-1) and vIRF-4 during viral reactivation, and 47 proteins were shared between the two vIRFs; the list also includes three viral proteins, ORF17, thymidine kinase, and vIRF-4. Functional annotation of respective interacting proteins showed highly overlapping biological roles such as mRNA processing and transcriptional regulation by TP53. Innate immune regulation by these commonly interacting 44 cellular proteins was examined with small interfering RNAs (siRNAs), and the splicing factor 3B family proteins were found to be associated with interferon transcription and to act as suppressors of KSHV reactivation. We propose that recombinant mini-TurboID-KSHV is a powerful tool to probe key cellular proteins that play a role in KSHV replication and that selective splicing factors have a function in the regulation of innate immune responses. IMPORTANCE Viral protein interaction with a host protein shows at least two sides: (i) taking host protein functions for its own benefit and (ii) disruption of existing host protein complex formation to inhibit undesirable host responses. Due to the use of affinity precipitation approaches, the majority of studies have focused on how the virus takes advantage of the newly formed protein interactions for its own replication. Proximity labeling (PL), however, can also highlight transient and negative effects—those interactions which lead to dissociation from the existing protein complex. Here, we highlight the power of PL in combination with recombinant KSHV to study viral host interactions.
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Schejbel L, Novotny GW, Breinholt MF, El Fassi D, Schöllkopf C, Hogdall E, Nørgaard P. Improved Variant Detection in Clinical Myeloid NGS Testing by Supplementing a Commercial Myeloid NGS Assay with Custom or Extended Data Filtering and Accessory Fragment Analysis. Mol Diagn Ther 2021; 25:251-266. [PMID: 33687704 DOI: 10.1007/s40291-021-00519-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Commercial myeloid next-generation sequencing (NGS) panels may facilitate uniform generation of raw data between laboratories. However, different strategies for data filtering and variant annotation may contribute to differences in variant detection and reporting. Here, we present how custom data filtering or the use of Oncomine extended data filtering improve detection of clinically relevant mutations with the Oncomine Myeloid Research Assay. METHODS The study included all patient samples (n = 264) analyzed during the first-year, single-site, clinical use of the Ion Torrent Oncomine Myeloid Research Assay. In data analysis, the default analysis filter was supplemented with our own data filtering algorithm in order to detect additional clinically relevant mutations. In addition, we developed a sensitive supplementary test for the ASXL1 c.1934dupG p.Gly646fs mutation by fragment analysis. RESULTS Using our custom filter chain, we found 96 different reportable variants that were not detected by the default filter chain. Twenty-six of these were classified as variants of strong or potential clinical significance (tier I/tier II variants), and the custom filtering discovered otherwise undetected tier I/tier II variants in 25 of 132 patients with clinically relevant mutations (19%). The remaining 70 variants not detected by the default filter chain were classified as variants of unknown significance. Among these were several unique variants with possible pathogenic potential judged by bioinformatic predictions. The recently launched Oncomine 5.14 extended filter algorithm detects most but not all of the tier I/tier II variants that were not detected by the default filter. The supplementary fragment analysis for the ASXL1 c.1934dupG p.Gly646fs confidently detected a variant allele frequency of down to 4.8% (SD 0.83%). The assay also detected the ASXL1 c.1900_1922del23 mutation. CONCLUSION Detection of clinically relevant variants with the Oncomine Myeloid Research NGS assay can be significantly improved by supplementing the default filter chain with custom data filtering or the recently launched Oncomine 5.14 extended filter algorithm. Our accessory fragment analysis facilitates easy testing for frequent ASXL1 mutations that are poorly or not covered by the NGS assay.
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Affiliation(s)
- Lone Schejbel
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark.
| | - Guy Wayne Novotny
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Marie Fredslund Breinholt
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Daniel El Fassi
- Department of Hematology, Herlev and Gentofte Hospital, Herlev, Denmark
| | | | - Estrid Hogdall
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Peter Nørgaard
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
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Vantyghem S, Peterlin P, Thépot S, Ménard A, Dubruille V, Debord C, Guillaume T, Garnier A, Le Bourgeois A, Wuilleme S, Godon C, Theisen O, Eveillard M, Delaunay J, Maisonneuve H, Morineau N, Villemagne B, Vigouroux S, Subiger F, Lestang E, Loirat M, Parcelier A, Godmer P, Mercier M, Trebouet A, Luque Paz D, Le Calloch R, Le Clech L, Bossard C, Moreau A, Ugo V, Hunault M, Moreau P, Le Gouill S, Chevallier P, Béné MC, Le Bris Y. Diagnosis and prognosis are supported by integrated assessment of next-generation sequencing in chronic myeloid malignancies. A real-life study. Haematologica 2021; 106:701-707. [PMID: 32241844 PMCID: PMC7927891 DOI: 10.3324/haematol.2019.242677] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing (NGS) is used to investigate the presence of somatic mutations. The utility of incorporating routine sequencing to guide diagnosis and therapeutic decisions remains unclear. We report the findings of an observational, multicenter study that aimed to assess the impact of somatic mutation testing by NGS in a reallife setting of chronic myeloid malignancies. A total of 177 patients were enrolled, partitioned into two overlapping groups. In group A (n=94), the indication was to search for clonal hematopoiesis, in a context of suspected myelodysplastic syndrome or myeloproliferative neoplasia. In group B (n=95), the theranostic impact of somatic mutations was studied. A panel of 34 genes was used on DNA extracted from blood or bone marrow samples. Within group A, the detection of clonal hematopoiesis supported the diagnosis of chronic myeloid malignancies for 31 patients while the absence of clonal hematopoiesis ruled out the suspected diagnosis in 47 patients. Within group B, NGS identified prognostically relevant somatic mutations in 32 patients, which had a therapeutic impact in 18 cases. By determining the presence or absence of somatic mutations, the application of NGS in daily practice was found to be useful for an integrated final diagnosis in 83% of the patients. Moreover, the search for somatic mutations had a prognostic impact that led to treatment modification in 19% of the cases. This study outlines the fact that adequate implementation of new investigations may have a significant positive medico-economic impact by enabling appropriate management of patients.
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Affiliation(s)
| | | | - Sylvain Thépot
- Hematology Clinic, Angers University Hospital, Angers,CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire
| | - Audrey Ménard
- Hematology Biology, Nantes University Hospital, Nantes
| | | | | | | | - Alice Garnier
- Hematology Clinic, Nantes University Hospital, Nantes
| | | | | | | | | | - Marion Eveillard
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire,Hematology Biology, Nantes University Hospital, Nantes
| | | | | | | | | | | | | | - Elsa Lestang
- Hematology Clinic, Saint Nazaire Hospital, Saint Nazaire
| | - Marion Loirat
- Hematology Clinic, Saint Nazaire Hospital, Saint Nazaire
| | | | - Pascal Godmer
- Hematology Clinic, Bretagne Atlantique Hospital, Vannes
| | | | | | - Damien Luque Paz
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire,Hematology Biology, Angers University Hospital, Angers
| | | | | | - Céline Bossard
- Pathology Department, Nantes University Hospital, Nantes, France
| | - Anne Moreau
- Pathology Department, Nantes University Hospital, Nantes, France
| | - Valérie Ugo
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire,Hematology Biology, Angers University Hospital, Angers
| | - Mathilde Hunault
- Hematology Clinic, Angers University Hospital, Angers,CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire
| | - Philippe Moreau
- Hematology Clinic, Nantes University Hospital, Nantes,CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire
| | - Steven Le Gouill
- Hematology Clinic, Nantes University Hospital, Nantes,CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire
| | - Patrice Chevallier
- Hematology Clinic, Nantes University Hospital, Nantes,CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire
| | - Marie C Béné
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire,Hematology Biology, Nantes University Hospital, Nantes
| | - Yannick Le Bris
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Pays de la Loire,Hematology Biology, Nantes University Hospital, Nantes
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Hasserjian RP, Buckstein R, Patnaik MM. Navigating Myelodysplastic and Myelodysplastic/Myeloproliferative Overlap Syndromes. Am Soc Clin Oncol Educ Book 2021; 41:328-350. [PMID: 34010050 DOI: 10.1200/edbk_320113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Myelodysplastic syndromes (MDS) and MDS/myeloproliferative neoplasms (MPNs) are clonal diseases that differ in morphologic diagnostic criteria but share some common disease phenotypes that include cytopenias, propensity to acute myeloid leukemia evolution, and a substantially shortened patient survival. MDS/MPNs share many clinical and molecular features with MDS, including frequent mutations involving epigenetic modifier and/or spliceosome genes. Although the current 2016 World Health Organization classification incorporates some genetic features in its diagnostic criteria for MDS and MDS/MPNs, recent accumulation of data has underscored the importance of the mutation profiles on both disease classification and prognosis. Machine-learning algorithms have identified distinct molecular genetic signatures that help refine prognosis and notable associations of these genetic signatures with morphologic and clinical features. Combined geno-clinical models that incorporate mutation data seem to surpass the current prognostic schemes. Future MDS classification and prognostication schema will be based on the portfolio of genetic aberrations and traditional features, such as blast count and clinical factors. Arriving at these systems will require studies on large patient cohorts that incorporate advanced computational analysis. The current treatment algorithm in MDS is based on patient risk as derived from existing prognostic and disease classes. Luspatercept is newly approved for patients with MDS and ring sideroblasts who are transfusion dependent after erythropoietic-stimulating agent failure. Other agents that address red blood cell transfusion dependence in patients with lower-risk MDS and the failure of hypomethylating agents in higher-risk disease are in advanced testing. Finally, a plethora of novel targeted agents and immune checkpoint inhibitors are being evaluated in combination with a hypomethylating agent backbone to augment the depth and duration of response and, we hope, improve overall survival.
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Affiliation(s)
| | - Rena Buckstein
- Division of Hematology/Oncology, Sunnybrook Odette Cancer Center, Toronto, Ontario, Canada
| | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, MN
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Iacobucci I, Mullighan C. Prognostic mutation constellations in acute myeloid leukaemia and myelodysplastic syndrome. Curr Opin Hematol 2021; 28:101-109. [PMID: 33427759 PMCID: PMC8174569 DOI: 10.1097/moh.0000000000000629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW In the past decade, numerous studies analysing the genome and transcriptome of large cohorts of acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS) patients have substantially improved our knowledge of the genetic landscape of these diseases with the identification of heterogeneous constellations of germline and somatic mutations with prognostic and therapeutic relevance. However, inclusion of integrated genetic data into classification schema is still far from a reality. The purpose of this review is to summarize recent insights into the prevalence, pathogenic role, clonal architecture, prognostic impact and therapeutic management of genetic alterations across the spectrum of myeloid malignancies. RECENT FINDINGS Recent multiomic-studies, including analysis of genetic alterations at the single-cell resolution, have revealed a high heterogeneity of lesions in over 200 recurrently mutated genes affecting disease initiation, clonal evolution and clinical outcome. Artificial intelligence and specifically machine learning approaches have been applied to large cohorts of AML and MDS patients to define in an unbiased manner clinically meaningful disease patterns including, disease classification, prognostication and therapeutic vulnerability, paving the way for future use in clinical practice. SUMMARY Integration of genomic, transcriptomic, epigenomic and clinical data coupled to conventional and machine learning approaches will allow refined leukaemia classification and risk prognostication and will identify novel therapeutic targets for these still high-risk leukaemia subtypes.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis (USA)
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis (USA)
- Hematological Malignancies Program, St Jude Children’s Research Hospital, Memphis, TN, United States
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75
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Patnaik MM, Tefferi A. Myelodysplastic syndromes with ring sideroblasts (MDS-RS) and MDS/myeloproliferative neoplasm with RS and thrombocytosis (MDS/MPN-RS-T) - "2021 update on diagnosis, risk-stratification, and management". Am J Hematol 2021; 96:379-394. [PMID: 33428785 DOI: 10.1002/ajh.26090] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
DISEASE OVERVIEW Ring sideroblasts (RS) are erythroid precursors with abnormal perinuclear mitochondrial iron accumulation. Two myeloid neoplasms defined by the presence of RS, include myelodysplastic syndromes with RS (MDS-RS) and MDS/myeloproliferative neoplasm with RS and thrombocytosis (MDS/MPN-RS-T). DIAGNOSIS MDS-RS is a lower risk MDS, with single or multilineage dysplasia (MDS-RS-SLD/MLD), <5% bone marrow (BM) blasts, <1% peripheral blood blasts and ≥15% BM RS (≥5% in the presence of SF3B1 mutations). MDS/MPN-RS-T, now a formal entity in the MDS/MPN overlap syndromes, has diagnostic features of MDS-RS-SLD, along with a platelet count ≥450 × 109 /L and large atypical megakaryocytes. MUTATIONS AND KARYOTYPE Mutations in SF3B1 are seen in ≥80% of patients with MDS-RS-SLD and MDS/MPN-RS-T, and strongly correlate with the presence of BM RS; MDS/MPN-RS-T patients also demonstrate JAK2V617F (50%), DNMT3A, TET2 and ASXL1 mutations. Cytogenetic abnormalities are uncommon in both. RISK STRATIFICATION Most patients with MDS-RS-SLD are stratified into lower risk groups by the revised-IPSS. Disease outcome in MDS/MPN-RS-T is better than that of MDS-RS-SLD, but worse than that of essential thrombocythemia (MPN). Both diseases are associated with a low risk of leukemic transformation. TREATMENT Anemia and iron overload are complications seen in both and are managed similar to lower risk MDS and MPN. Luspatercept, a first-in-class erythroid maturation agent is now approved for the management of anemia in patients with MDS-RS and MDS/MPN-RS-T. Aspirin therapy is reasonable in MDS/MPN-RS-T, especially in the presence of JAK2V617F, but the value of platelet-lowering drugs remains to be defined.
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Affiliation(s)
- Mrinal M. Patnaik
- Division of Hematology, Department of Internal Medicine Mayo Clinic Rochester Minnesota
| | - Ayalew Tefferi
- Division of Hematology, Department of Internal Medicine Mayo Clinic Rochester Minnesota
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77
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Bersanelli M, Travaglino E, Meggendorfer M, Matteuzzi T, Sala C, Mosca E, Chiereghin C, Di Nanni N, Gnocchi M, Zampini M, Rossi M, Maggioni G, Termanini A, Angelucci E, Bernardi M, Borin L, Bruno B, Bonifazi F, Santini V, Bacigalupo A, Voso MT, Oliva E, Riva M, Ubezio M, Morabito L, Campagna A, Saitta C, Savevski V, Giampieri E, Remondini D, Passamonti F, Ciceri F, Bolli N, Rambaldi A, Kern W, Kordasti S, Sole F, Palomo L, Sanz G, Santoro A, Platzbecker U, Fenaux P, Milanesi L, Haferlach T, Castellani G, Della Porta MG. Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes. J Clin Oncol 2021; 39:1223-1233. [PMID: 33539200 PMCID: PMC8078359 DOI: 10.1200/jco.20.01659] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Recurrently mutated genes and chromosomal abnormalities have been identified in myelodysplastic syndromes (MDS). We aim to integrate these genomic features into disease classification and prognostication.
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Affiliation(s)
- Matteo Bersanelli
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,National Institute of Nuclear Physics (INFN), Bologna, Italy
| | - Erica Travaglino
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | | | - Tommaso Matteuzzi
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,National Institute of Nuclear Physics (INFN), Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,National Institute of Nuclear Physics (INFN), Bologna, Italy
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council (CNR), Segrate, Milan, Italy
| | | | - Noemi Di Nanni
- Institute of Biomedical Technologies, National Research Council (CNR), Segrate, Milan, Italy
| | - Matteo Gnocchi
- Institute of Biomedical Technologies, National Research Council (CNR), Segrate, Milan, Italy
| | - Matteo Zampini
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Marianna Rossi
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Giulia Maggioni
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
| | | | - Emanuele Angelucci
- Hematology and Transplant Center, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Massimo Bernardi
- Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, & University Vita-Salute San Raffaele, Milan, Italy
| | | | - Benedetto Bruno
- Stem Cell Transplant Program, Department of Oncology, A.O.U. Città della Salute e della Scienza di Torino.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Francesca Bonifazi
- Hematology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Valeria Santini
- Hematology, Azienda Ospedaliero-Universitaria Careggi & University of Florence, Florence Italy
| | - Andrea Bacigalupo
- Hematology, IRCCS Fondazione Policlinico Universitario Gemelli & Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maria Teresa Voso
- Hematology, Policlinico Tor Vergata & Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Esther Oliva
- Hematology, Grande Ospedale Metropolitano Bianchi Melacrino Morelli, Reggio Calabria, Italy
| | - Marta Riva
- Hematology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Marta Ubezio
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Lucio Morabito
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Alessia Campagna
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Claudia Saitta
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza Italy
| | - Victor Savevski
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Enrico Giampieri
- National Institute of Nuclear Physics (INFN), Bologna, Italy.,Experimental, Diagnostic and Specialty Medicine-DIMES, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,National Institute of Nuclear Physics (INFN), Bologna, Italy
| | - Francesco Passamonti
- Hematology, ASST Sette Laghi, Ospedale di Circolo of Varese & Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Fabio Ciceri
- Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, & University Vita-Salute San Raffaele, Milan, Italy
| | - Niccolò Bolli
- Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | | | - Shahram Kordasti
- Haematology, Guy's Hospital & Comprehensive Cancer Centre, King's College, London, United Kingdom.,Hematology Department & Stem Cell Transplant Unit, DISCLIMO-Università Politecnica delle Marche, Ancona, Italy
| | - Francesc Sole
- Institut de Recerca Contra la Leucèmia Josep Carreras, Ctra de Can Ruti, Badalona-Barcelona, Spain
| | - Laura Palomo
- Institut de Recerca Contra la Leucèmia Josep Carreras, Ctra de Can Ruti, Badalona-Barcelona, Spain
| | - Guillermo Sanz
- Hematology, Hospital Universitario La Fe, Valencia, Spain.,Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Armando Santoro
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University Hospital Leipzig, Leipzig, Germany
| | - Pierre Fenaux
- Service d'Hématologie Séniors, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris and Université Paris, Paris, France
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council (CNR), Segrate, Milan, Italy
| | | | - Gastone Castellani
- National Institute of Nuclear Physics (INFN), Bologna, Italy.,Experimental, Diagnostic and Specialty Medicine-DIMES, Bologna, Italy
| | - Matteo G Della Porta
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
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Patel BJ, Barot SV, Xie Y, Cook JR, Carraway HE, Hsi ED. Impact of next generation sequencing results on clinical management in patients with hematological disorders. Leuk Lymphoma 2021; 62:1702-1710. [PMID: 33533694 DOI: 10.1080/10428194.2021.1876860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Application of next generation sequencing (NGS) has shed light on the molecular heterogeneity of hematological malignancies. NGS panels targeting recurrent mutations have become common in many large centers and commercial laboratories. However, its impact in clinical practice is unclear. We sought to characterize the use of NGS at a tertiary care center in an observational study of 343 patients with suspected hematological malignancies. We found that NGS changed or refined the clinical and pathologic diagnosis in 9% of patients and affected management decisions in 65% (including clinical trial eligibility, targeted therapy selection, and consideration for stem cell transplantation). This study emphasizes early incorporation of NGS in clinical practice while also highlighting the present limitations. As our understanding of these disorders increases and more clinically relevant genetic targets emerge, it will be important to refine the molecular testing strategy to deliver personalized medicine given the high cost associated with this technology.
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Affiliation(s)
- Bhumika J Patel
- Leukemia and Myeloid Disorders Program, Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Shimoli V Barot
- Leukemia and Myeloid Disorders Program, Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Yan Xie
- Department of Laboratory Medicine, Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - James R Cook
- Department of Laboratory Medicine, Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Hetty E Carraway
- Leukemia and Myeloid Disorders Program, Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Eric D Hsi
- Department of Laboratory Medicine, Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
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Leeksma AC, Derks IAM, Kasem MH, Kilic E, de Klein A, Jager MJ, van de Loosdrecht AA, Jansen JH, Navrkalova V, Faber LM, Zaborsky N, Egle A, Zenz T, Pospisilova S, Abdel-Wahab O, Kater AP, Eldering E. The Effect of SF3B1 Mutation on the DNA Damage Response and Nonsense-Mediated mRNA Decay in Cancer. Front Oncol 2021; 10:609409. [PMID: 33585229 PMCID: PMC7880055 DOI: 10.3389/fonc.2020.609409] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/01/2020] [Indexed: 01/08/2023] Open
Abstract
Recurrent mutations in splicing factor 3B subunit 1 (SF3B1) have been identified in several malignancies and are associated with an increased expression of 3' cryptic transcripts as a result of alternative branchpoint recognition. A large fraction of cryptic transcripts associated with SF3B1 mutations is expected to be sensitive for RNA degradation via nonsense-mediated mRNA decay (NMD). Several studies indicated alterations in various signaling pathways in SF3B1-mutated cells, including an impaired DNA damage response (DDR) in chronic lymphocytic leukemia (CLL). In this study, we investigated isogenic cell lines and treatment naïve primary CLL samples without any TP53 and/or ATM defect, and found no significant effects of SF3B1 mutations on the ATM/p53 response, phosphorylation of H2AX and sensitivity to fludarabine. Cryptic transcripts associated with SF3B1 mutation status were observed at relatively low levels compared to the canonical transcripts and were validated as target for mRNA degradation via NMD. Expression of cryptic transcripts increased after NMD inhibition. In conclusion, our results confirm involvement of NMD in the biological effects of SF3B1 mutations. Further studies may elucidate whether SF3B1-mutant patients could benefit from NMD modulatory agents.
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Affiliation(s)
- Alexander C. Leeksma
- Department of Hematology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII), Amsterdam, Netherlands
| | - Ingrid A. M. Derks
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII), Amsterdam, Netherlands
| | - M. Haidar Kasem
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Emine Kilic
- Department of Ophthalmology and Clinical Genetics Erasmus MC, Rotterdam, Netherlands
| | - Annelies de Klein
- Department of Ophthalmology and Clinical Genetics Erasmus MC, Rotterdam, Netherlands
| | | | | | - Joop H. Jansen
- Laboratory of Hematology, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Veronika Navrkalova
- Center of Molecular Biology and Gene Therapy, Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Center of Molecular Medicine, CEITEC, Masaryk University, Brno, Czechia
| | - Laura M. Faber
- Department of Internal Medicine, Rode Kruis Ziekenhuis, Beverwijk, Netherlands
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
- Department of Internal Medicine III with Haematology, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Salzburg, Austria
- Department of Internal Medicine III with Haematology, Cancer Cluster Salzburg, Salzburg, Austria
| | - Alexander Egle
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
- Department of Internal Medicine III with Haematology, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Salzburg, Austria
- Department of Internal Medicine III with Haematology, Cancer Cluster Salzburg, Salzburg, Austria
| | - Thorsten Zenz
- Department of Oncology and Haematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Sarka Pospisilova
- Center of Molecular Biology and Gene Therapy, Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Center of Molecular Medicine, CEITEC, Masaryk University, Brno, Czechia
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Arnon P. Kater
- Department of Hematology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric Eldering
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII), Amsterdam, Netherlands
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Asian Population Is More Prone to Develop High-Risk Myelodysplastic Syndrome, Concordantly with Their Propensity to Exhibit High-Risk Cytogenetic Aberrations. Cancers (Basel) 2021; 13:cancers13030481. [PMID: 33513838 PMCID: PMC7865620 DOI: 10.3390/cancers13030481] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The world population is genetically and environmentally diverse. In particular, genetic differences related to an ethnic factor may underlie differences in cancer phenotypic expression. Therefore, we compared the epidemiology, and the clinical, biological and genetic characteristics of myelodysplastic syndrome (MDS) between Asian and Western countries. Our results show substantial differences in the incidence and age of onset between Asian and Western MDS patients. A higher proportion of Asian MDS patients fall into the high- and very-high risk prognostic MDS groups. This finding is supported by the identification of a higher proportion of high-risk cytogenetic aberrations in Asian MDS patients. However, the survival rate is similar for Western and Asian MDS patients. Our findings may impact the clinical management as well as the strategy of clinical trials targeting those genetic aberrations and mutations depending on the world area where they are run. Abstract This study explores the hypothesis that genetic differences related to an ethnic factor may underlie differences in phenotypic expression of myelodysplastic syndrome (MDS). First, to identify clear ethnic differences, we systematically compared the epidemiology, and the clinical, biological and genetic characteristics of MDS between Asian and Western countries over the last 20 years. Asian MDS cases show a 2- to 4-fold lower incidence and a 10-year younger age of onset compared to the Western cases. A higher proportion of Western MDS patients fall into the very low- and low-risk categories while the intermediate, high and very high-risk groups are more represented in Asian MDS patients according to the Revised International Prognostic Scoring System. Next, we investigated whether differences in prognostic risk scores could find their origin in differential cytogenetic profiles. We found that 5q deletion (del(5q)) aberrations and mutations in TET2, SF3B1, SRSF2 and IDH1/2 are more frequently reported in Western MDS patients while trisomy 8, del(20q), U2AF1 and ETV6 mutations are more frequent in Asian MDS patients. Treatment approaches differ between Western and Asian countries owing to the above discrepancies, but the overall survival rate within each prognostic group is similar for Western and Asian MDS patients. Altogether, our study highlights greater risk MDS in Asians supported by their cytogenetic profile.
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Reilly A, Doulatov S. Induced pluripotent stem cell models of myeloid malignancies and clonal evolution. Stem Cell Res 2021; 52:102195. [PMID: 33592565 PMCID: PMC10115516 DOI: 10.1016/j.scr.2021.102195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Reprogramming of cells from patients with genetic disorders to pluripotency is a promising avenue to understanding disease biology. A number of induced pluripotent stem cell (iPSC) models of inherited monogenic blood disorders have been reported over the past decade. However, the application of iPSCs for modeling of hematological malignancies has only recently been explored. Blood malignancies comprise a spectrum of genetically heterogeneous disorders marked by the acquisition of somatic mutations and chromosomal aberrations. This genetic heterogeneity presents unique challenges for iPSC modeling, but also opportunities to capture genetically distinct states and generate models of stepwise progression from normal to malignant hematopoiesis. Here we briefly review the current state of this field, highlighting current models of acquired pre-malignant and malignant blood disorders and clonal evolution, and challenges including barriers to reprogramming and differentiation of iPSCs into bona fide hematopoietic stem cells.
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Affiliation(s)
- Andreea Reilly
- Division of Hematology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, United States
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, United States.
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Clinical, biological, and prognostic implications of SF3B1 co-occurrence mutations in very low/low- and intermediate-risk MDS patients. Ann Hematol 2021; 100:1995-2004. [PMID: 33409621 DOI: 10.1007/s00277-020-04360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/20/2020] [Indexed: 10/22/2022]
Abstract
SF3B1 is a highly mutated gene in myelodysplastic syndrome (MDS) patients, related to a specific subtype and parameters of good prognosis in MDS without excess blasts. More than 40% of MDS patients carry at least two myeloid-related gene mutations but little is known about the impact of concurrent mutations on the outcome of MDS patients. In applying next-generation sequencing (NGS) with a 117 myeloid gene custom panel, we analyzed the co-occurrence of SF3B1 with other mutations to reveal their clinical, biological, and prognostic implications in very low/low- and intermediate-risk MDS patients. Mutations in addition to those of SF3B1 were present in 80.4% of patients (median of 2 additional mutations/patient, range 0-5). The most frequently mutated genes were as follows: TET2 (39.2%), DNMT3A (25.5%), SRSF2 (10.8%), CDH23 (5.9%), and ASXL1, CUX1, and KMT2D (4.9% each). The presence of at least two mutations concomitant with that of SF3B1 had an adverse impact on survival compared with those with the SF3B1 mutation and fewer than two additional mutations (median of 54 vs. 87 months, respectively: p = 0.007). The co-occurrence of SF3B1 mutations with specific genes is also linked to a dismal prognosis: SRSF2 mutations were associated with shorter overall survival (OS) than SRSF2wt (median, 27 vs. 75 months, respectively; p = 0.001), concomitant IDH2 mutations (median OS, 11 [mut] vs. 75 [wt] months; p = 0.001), BCOR mutations (median OS, 11 [mut] vs. 71 [wt] months; p = 0.036), and NUP98 and STAG2 mutations (median OS, 27 and 11 vs. 71 months, respectively; p = 0.008 and p = 0.002). Mutations in CHIP genes (TET2, DNMT3A) did not significantly affect the clinical features or outcome. Our results suggest that a more comprehensive NGS study in low-risk MDS SF3B1mut patients is essential for a better prognostic evaluation.
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83
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Chronic myeloid neoplasms harboring concomitant mutations in myeloproliferative neoplasm driver genes (JAK2/MPL/CALR) and SF3B1. Mod Pathol 2021; 34:20-31. [PMID: 32694616 DOI: 10.1038/s41379-020-0624-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 01/10/2023]
Abstract
JAK2, CALR, and MPL are myeloproliferative neoplasm (MPN)-driver mutations, whereas SF3B1 is strongly associated with ring sideroblasts (RS) in myelodysplastic syndrome (MDS). Concomitant mutations of SF3B1 and MPN-driver mutations out of the context of MDS/MPN with RS and thrombocytosis (MDS/MPN-RS-T) are not well-studied. From the cases (<5% blasts) tested by NGS panels interrogating at least 42 myeloid neoplasm-related genes, we identified 18 MDS/MPN-RS-T, 42 MPN, 10 MDS, and 6 MDS/MPN-U cases with an SF3B1 and an MPN-driver mutation. Using a 10% VAF difference to define "SF3B1-dominant," "MPN-mutation dominant," and "no dominance," the majority of MDS/MPN-RS-T clustered in "SF3B1-dominant" and "no dominance" regions. Aside from parameters as thrombocytosis and ≥15% RS required for RS-T, MDS also differed in frequent neutropenia, multilineage dysplasia, and notably more cases with <10% VAF of MPN-driver mutations (60%, p = 0.0346); MPN differed in more frequent splenomegaly, myelofibrosis, and higher VAF of "MPN-driver mutations." "Gray zone" cases with features overlapping MDS/MPN-RS-T were observed in over one-thirds of non-RS-T cases. This study shows that concomitant SF3B1 and MPN-driver mutations can be observed in MDS, MPN, and MDS/MPN-U, each showing overlapping but also distinctively different clinicopathological features. Clonal hierarchy, cytogenetic abnormalities, and additional somatic mutations may in part contribute to different disease phenotypes, which may help in the classification of "gray zone" cases.
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84
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Pellagatti A, Boultwood J. SF3B1 mutant myelodysplastic syndrome: Recent advances. Adv Biol Regul 2020; 79:100776. [PMID: 33358369 DOI: 10.1016/j.jbior.2020.100776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022]
Abstract
The myelodysplastic syndromes (MDS) are common myeloid malignancies. Mutations in genes encoding different components of the spliceosome occur in more than half of all MDS patients. SF3B1 is the most frequently mutated splicing factor gene in MDS, and there is a strong association between SF3B1 mutations and the presence of ring sideroblasts in the bone marrow of MDS patients. It has been recently proposed that SF3B1 mutant MDS should be recognized as a distinct nosologic entity. Splicing factor mutations cause aberrant pre-mRNA splicing of many target genes, some of which have been shown to impact on hematopoiesis in functional studies. Emerging data show that some of the downstream effects of different mutated splicing factors converge on common cellular processes, such as hyperactivation of NF-κB signaling and increased R-loops. The aberrantly spliced target genes and the dysregulated pathways and cellular processes associated with splicing factor mutations provided the rationale for new potential therapeutic approaches to target MDS cells with mutations of SF3B1 and other splicing factors.
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Affiliation(s)
- Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, And NIHR Oxford BRC Haematology Theme, Oxford, UK.
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, And NIHR Oxford BRC Haematology Theme, Oxford, UK.
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85
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Jiang W, Chen L. Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing. Comput Struct Biotechnol J 2020; 19:183-195. [PMID: 33425250 PMCID: PMC7772363 DOI: 10.1016/j.csbj.2020.12.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/26/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by allowing one gene to generate multiple distinct protein isoforms. It adds another regulation layer of gene expression. Up to 95% of human multi-exon genes undergo alternative splicing to encode proteins with different functions. Moreover, around 15% of human hereditary diseases and cancers are associated with alternative splicing. Regulation of alternative splicing is attributed to a set of delicate machineries interacting with each other in aid of important biological processes such as cell development and differentiation. Given the importance of alternative splicing events, their accurate mapping and quantification are paramount for downstream analysis, especially for associating disease with alternative splicing. However, deriving accurate isoform expression from high-throughput RNA-seq data remains a challenging task. In this mini-review, we aim to illustrate I) mechanisms and regulation of alternative splicing, II) alternative splicing associated human disease, III) computational tools for the quantification of isoforms and alternative splicing from RNA-seq.
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Affiliation(s)
- Wei Jiang
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States
| | - Liang Chen
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States
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Abstract
In recent years CMML has received increased attention as the most commonly observed MDS/MPN overlap syndrome. Renewed interest has occurred in part due to widespread adoption of next-generation sequencing panels that help render the diagnosis in the absence of morphologic dysplasia. Although most CMML patients exhibit somatic mutations in epigenetic modifiers, spliceosome components, transcription factors and signal transduction genes, it is increasingly clear that a small subset harbors an inherited predisposition to CMML and other myeloid neoplasms. More intriguing is the fact that the mutational spectrum observed in CMML is found in other types of myeloid leukemias, begging the question of how similar genetic backgrounds can lead to such divergent clinical phenotypes. In this review we present a contemporary snapshot of the genetic complexity inherent to CMML, explore the relationship between genotype-phenotype and present a stepwise model of CMML pathogenesis and progression.
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Affiliation(s)
- Ami B Patel
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael W Deininger
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
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Jiang L, Wang L, Shen C, Zhu S, Lang W, Luo Y, Zhang H, Yang W, Han Y, Ma L, Ren Y, Zhou X, Mei C, Ye L, Xu W, Yang H, Lu C, Jin J, Tong H. Impact of mutational variant allele frequency on prognosis in myelodysplastic syndromes. Am J Cancer Res 2020; 10:4476-4487. [PMID: 33415012 PMCID: PMC7783761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023] Open
Abstract
The clinical relevance of variant allele frequency (VAF) of recurrent mutations in myelodysplastic syndromes (MDS) has been increasingly reported. However, the prognostic value of mutational VAF across the genetic spectrum of MDS has not been extensively evaluated. In this study, we profiled the mutational spectrum of 382 newly diagnosed MDS patients using targeted next-generation sequencing. Exploratory analysis found that mutational VAF of some genes including TET2, TP53, and SF3B1 had significant associations with patient survival. Specifically, TET2 VAF ≥ 32% (HR 1.69, P = 0.025) and TP53 VAF ≥ 27% (HR 3.58, P < 0.001) were independently associated with shorter overall survival (OS). In contrast, SF3B1 VAF ≥ 15% had an independent association with better prognosis (HR 0.52, P = 0.048). In addition, high TET2 VAF was associated with an increased response to hypomethylating agents relative to low TET2 VAF (P = 0.009). Patients with high TP53 VAF more often possessed complex karyotypes than those with low VAF (P = 0.034). And patients with high SF3B1 VAF were more frequently classified as MDS with ring sideroblasts (MDS-RS) category than those with low VAF (P = 0.012). Meanwhile, we found that for some other genes like EZH2 and NRAS, once their mutations appeared, it meant poor survival regardless of mutational VAF. These findings suggest that mutational VAF of certain genes should be considered into the routine prognostic prediction and risk stratification of MDS patients.
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Affiliation(s)
- Lingxu Jiang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Lu Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Chuying Shen
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Shuanghong Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Wei Lang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Yingwan Luo
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Hua Zhang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Wenli Yang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Yueyuan Han
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Liya Ma
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Yanling Ren
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Xinping Zhou
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Chen Mei
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Li Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Weilai Xu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Haiyang Yang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Chenxi Lu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
| | - Hongyan Tong
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
- Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, Zhejiang Province, P. R. China
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Garcia‐Manero G, Chien KS, Montalban‐Bravo G. Myelodysplastic syndromes: 2021 update on diagnosis, risk stratification and management. Am J Hematol 2020; 95:1399-1420. [PMID: 32744763 DOI: 10.1002/ajh.25950] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022]
Abstract
DISEASE OVERVIEW The myelodysplastic syndromes (MDS) are a very heterogeneous group of myeloid disorders characterized by peripheral blood cytopenias and increased risk of transformation to acute myelogenous leukemia (AML). Myelodysplastic syndromes occur more frequently in older males and in individuals with prior exposure to cytotoxic therapy. DIAGNOSIS Diagnosis of MDS is based on morphological evidence of dysplasia upon visual examination of a bone marrow aspirate and biopsy. Information obtained from additional studies such as karyotype, flow cytometry and molecular genetics is usually complementary and may help refine diagnosis. RISK-STRATIFICATION Prognosis of patients with MDS can be calculated using a number of scoring systems. In general, all these scoring systems include analysis of peripheral cytopenias, percentage of blasts in the bone marrow and cytogenetic characteristics. The most commonly accepted system is the Revised International Prognostic Scoring System (IPSS-R). Somatic mutations can help define prognosis and therapy. RISK-ADAPTED THERAPY Therapy is selected based on risk, transfusion needs, percent of bone marrow blasts, cytogenetic and mutational profiles, comorbidities, potential for allogeneic stem cell transplantation (alloSCT) and prior exposure to hypomethylating agents (HMA). Goals of therapy are different in lower-risk patients than in higher-risk individuals and in those with HMA failure. In lower-risk MDS, the goal is to decrease transfusion needs and transformation to higher risk disease or AML, as well as to improve survival. In higher-risk disease, the goal is to prolong survival. In 2020, we witnessed an explosion of new agents and investigational approaches. Current available therapies include growth factor support, lenalidomide, HMAs, intensive chemotherapy and alloSCT. Novel therapeutics approved in 2020 are luspatercept and the oral HMA ASTX727. At the present time, there are no approved interventions for patients with progressive or refractory disease particularly after HMA-based therapy. Options include participation in a clinical trial, cytarabine-based therapy or alloSCT.
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Affiliation(s)
- Guillermo Garcia‐Manero
- Section of MDS, Department of Leukemia University of Texas MD Anderson Cancer Center Houston Texas USA
| | - Kelly S. Chien
- Section of MDS, Department of Leukemia University of Texas MD Anderson Cancer Center Houston Texas USA
| | - Guillermo Montalban‐Bravo
- Section of MDS, Department of Leukemia University of Texas MD Anderson Cancer Center Houston Texas USA
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89
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Wan Z, Han B. Comparison and Implications of Mutational Profiles of Myelodysplastic Syndromes, Myeloproliferative Neoplasms, and Myelodysplastic/Myeloproliferative Neoplasms: A Meta-Analysis. Front Oncol 2020; 10:579221. [PMID: 33117717 PMCID: PMC7575718 DOI: 10.3389/fonc.2020.579221] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
Dysplasia and proliferation are histological properties that can be used to diagnose and categorize myeloid tumors in myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN). However, these conditions are not exclusive, and overlap between them leads to another classification, MDS/MPN. As well as phenotype continuity, these three conditions may have genetic relationships that have not yet been identified. This study aimed to obtain their mutational profiles by meta-analysis and explore possible similarities and differences. We reviewed screening studies of gene mutations, published from January 2000 to March 2020, from PubMed and Web of Science. Fifty-three articles were eligible for the meta-analysis, and at most 9,809 cases were involved for any gene. The top mutant genes and their pooled mutation rates were as follows: SF3B1 (20.2% [95% CI 11.6-30.5%]) in MDS, TET2 (39.2% [95% CI 21.7-52.0%]) in MDS/MPN, and JAK2 (67.9% [95% CI 64.1-71.6%]) in MPN. Subgroup analysis revealed that leukemic transformation-related genes were more commonly mutated in high-risk MDS (MDS with multilineage dysplasia and MDS with excess blasts) than that in other MDS entities. Thirteen genes including ASXL1, U2AF1, SRSF2, SF3B1, and ZRSR2 had significantly higher mutation frequencies in primary myelofibrosis (PMF) compared with essential thrombocythemia and polycythemia vera; this difference distinguished PMF from MPN and likened it to MDS. Chronic myelomonocytic leukemia and atypical chronic myeloid leukemia were similar entities but showed several mutational differences. A heat map demonstrated that juvenile myelomonocytic leukemia and MDS/MPN with ring sideroblasts and thrombocytosis were two distinct entities, whereas MDS/MPN-unclassifiable was closest to high-risk MDS. Such genetic closeness or difference reflected features in the pathogenesis, diagnosis, treatment, and progression of these conditions, and could inspire future genetic studies.
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Affiliation(s)
- Ziqi Wan
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Bing Han
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
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Bernard E, Nannya Y, Hasserjian RP, Devlin SM, Tuechler H, Medina-Martinez JS, Yoshizato T, Shiozawa Y, Saiki R, Malcovati L, Levine MF, Arango JE, Zhou Y, Solé F, Cargo CA, Haase D, Creignou M, Germing U, Zhang Y, Gundem G, Sarian A, van de Loosdrecht AA, Jädersten M, Tobiasson M, Kosmider O, Follo MY, Thol F, Pinheiro RF, Santini V, Kotsianidis I, Boultwood J, Santos FPS, Schanz J, Kasahara S, Ishikawa T, Tsurumi H, Takaori-Kondo A, Kiguchi T, Polprasert C, Bennett JM, Klimek VM, Savona MR, Belickova M, Ganster C, Palomo L, Sanz G, Ades L, Della Porta MG, Elias HK, Smith AG, Werner Y, Patel M, Viale A, Vanness K, Neuberg DS, Stevenson KE, Menghrajani K, Bolton KL, Fenaux P, Pellagatti A, Platzbecker U, Heuser M, Valent P, Chiba S, Miyazaki Y, Finelli C, Voso MT, Shih LY, Fontenay M, Jansen JH, Cervera J, Atsuta Y, Gattermann N, Ebert BL, Bejar R, Greenberg PL, Cazzola M, Hellström-Lindberg E, Ogawa S, Papaemmanuil E. Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes. Nat Med 2020; 26:1549-1556. [PMID: 32747829 PMCID: PMC8381722 DOI: 10.1038/s41591-020-1008-z] [Citation(s) in RCA: 344] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/07/2020] [Indexed: 01/19/2023]
Abstract
Tumor protein p53 (TP53) is the most frequently mutated gene in cancer1,2. In patients with myelodysplastic syndromes (MDS), TP53 mutations are associated with high-risk disease3,4, rapid transformation to acute myeloid leukemia (AML)5, resistance to conventional therapies6-8 and dismal outcomes9. Consistent with the tumor-suppressive role of TP53, patients harbor both mono- and biallelic mutations10. However, the biological and clinical implications of TP53 allelic state have not been fully investigated in MDS or any other cancer type. We analyzed 3,324 patients with MDS for TP53 mutations and allelic imbalances and delineated two subsets of patients with distinct phenotypes and outcomes. One-third of TP53-mutated patients had monoallelic mutations whereas two-thirds had multiple hits (multi-hit) consistent with biallelic targeting. Established associations with complex karyotype, few co-occurring mutations, high-risk presentation and poor outcomes were specific to multi-hit patients only. TP53 multi-hit state predicted risk of death and leukemic transformation independently of the Revised International Prognostic Scoring System (IPSS-R)11. Surprisingly, monoallelic patients did not differ from TP53 wild-type patients in outcomes and response to therapy. This study shows that consideration of TP53 allelic state is critical for diagnostic and prognostic precision in MDS as well as in future correlative studies of treatment response.
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Affiliation(s)
- Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | - Sean M Devlin
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Juan S Medina-Martinez
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, IRCCS Fondazione Policlinico S. Matteo, Pavia, Italy
| | - Max F Levine
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yangyu Zhou
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francesc Solé
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Catherine A Cargo
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Detlef Haase
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Maria Creignou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunes Gundem
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Araxe Sarian
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Martin Jädersten
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Tobiasson
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olivier Kosmider
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris, France
| | - Matilde Y Follo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation Hannover Medical School, Hannover, Germany
| | - Ronald F Pinheiro
- Drug Research and Development Center, Federal University of Ceara, Ceara, Brazil
| | - Valeria Santini
- MDS Unit, Hematology, AOU Careggi, University of Florence, Florence, Italy
| | - Ioannis Kotsianidis
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Jacqueline Boultwood
- Radcliffe Department of Medicine, University of Oxford and Oxford BRC Haematology Theme, Oxford, UK
| | - Fabio P S Santos
- Oncology-Hematology Center, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Julie Schanz
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Senji Kasahara
- Department of Hematology, Gifu Municipal Hospital, Gifu, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Hisashi Tsurumi
- Department of Hematology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toru Kiguchi
- Department of Hematology, Chugoku Central Hospital, Fukuyama, Japan
| | - Chantana Polprasert
- Department of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - John M Bennett
- Lab. Medicine and Pathology, Hematology/Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Virginia M Klimek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Christina Ganster
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Laura Palomo
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Guillermo Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Lionel Ades
- Department of Hematology, Hôpital St Louis and Paris University, Paris, France
| | - Matteo Giovanni Della Porta
- Humanitas Clinical and Research Center-IRCCS, Humanitas Cancer Center, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Harold K Elias
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yesenia Werner
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnès Viale
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katelynd Vanness
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Donna S Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly L Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Fenaux
- Department of Hematology, Hôpital St Louis and Paris University, Paris, France
| | - Andrea Pellagatti
- Radcliffe Department of Medicine, University of Oxford and Oxford BRC Haematology Theme, Oxford, UK
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University of Leipzig, Leipzig, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation Hannover Medical School, Hannover, Germany
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology and Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Carlo Finelli
- Institute of Hematology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Teresa Voso
- MDS Cooperative Group GROM-L, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Lee-Yung Shih
- Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan City, Taiwan
| | - Michaela Fontenay
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris, France
| | - Joop H Jansen
- Laboratory Hematology, Department LABGK, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - José Cervera
- Department of Hematology and Genetics Unit, University Hospital La Fe, Valencia, Spain
| | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Nagoya, Japan
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology and Howard Hughes Medical Institute, Dana-Farber Cancer Center, Boston, MA, USA
| | - Rafael Bejar
- UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, IRCCS Fondazione Policlinico S. Matteo, Pavia, Italy
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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91
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Hunter AM, Padron E. Molecular genetics of MDS/MPN overlap syndromes. Best Pract Res Clin Haematol 2020; 33:101195. [DOI: 10.1016/j.beha.2020.101195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/27/2020] [Indexed: 01/05/2023]
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92
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Cai YN, Xu ZF, Li B, Qin TJ, Pan LJ, Qu SQ, Hu NB, Liu D, Huang HJ, Shi ZX, Zhang YD, Xiao ZJ. [Features and clinical significance of gene mutations in patients with myelodysplastic syndromes with ring sideroblasts]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41:379-386. [PMID: 32536134 PMCID: PMC7342062 DOI: 10.3760/cma.j.issn.0253-2727.2020.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Objective: To explore the features and clinical significance of gene mutations in patients with myelodysplastic syndromes with ring sideroblasts (MDS-RS) . Methods: A total of 255 newly diagnosed primary MDS-RS patients were retrospectively reviewed from our center from January2001 to June 2019. SF3B1 gene mutations were detected by Sanger sequencing in 129 patients, and next generation sequencing (NGS) was performed in the other 126 patients using a set of selected 112-genes. Results: A total of 193 (75.7%) patients presented with SF3B1 mutation, predominantly mutant at amino acid position 700 (K700E) (n=147, 76.2%) . Non-SF3B1 gene mutations were TET2 (16.7%) , ASXL1 (14.3%) , U2AF1 (11.1%) , TP53 (7.9%) , SETBP1 (6.3%) , and RUNX1 (6.3%) . RS 5%-<15% patients had a higher SETBP1 mutation frequency than RS≥15% patients (21.4% vs 4.5%, P=0.044) . Mutation frequencies of other genes were similar in both groups (all P>0.05) . SF3B1 variant allele frequencies (VAF) had positive correlation with marrow RS percentage but without statistical significance in RS 5%-<15% group (P=0.078, r=0.486) . SF3B1 mutant patients presented with higher marrow RS percentage compared with wild-type patients[40.0% (15.0%-80.0%) vs 25.5% (15.0%-82.0%) , P<0.001], and SF3B1 VAF positively correlated with RS percentage (P=0.009, rs=0.261) in RS≥15% group. Age, ANC, PLT, mean RBC corpuscular volume, RS percentage, IPSS-R cytogenetics, and IPSS-R risk score were significantly different between patients with SF3B1 mutations and wild-type SF3B1 (all P<0.05) . Multivariable survival analyses adjusted by age and IPSS-R cytogenetics revealed that SF3B1 mutation was an independent favorable prognostic factor (HR=0.265, 95% CI 0.077-0.917, P=0.036) , and TP53 mutation was an adverse variable independent of SF3B1 mutation (HR=6.272, 95% CI 1.725-22.809, P=0.005) . According to the mutant status of SF3B1 and TP53, MDS-RS patients were categorized into 4 groups, namely, with SF3B1 and TP53 mutation, with wild-type SF3B1 and TP53, with wild-type SF3B1 but TP53 mutation, and with SF3B1 mutation but wild-type TP53. There was a significant difference for OS among these 4 groups (P<0.001) . The former 3 groups showed no significant difference in OS in multiple comparisons. However, the SF3B1 mutation but wild-type TP53 group had a better OS than wild-type SF3B1 but TP53 mutation group and wild-type SF3B1 and TP53 group, whereas a similar OS compared with SF3B1 and TP53 mutation group. Conclusion: SF3B1 mutations were prevalent in MDS-RS patients with the most common mutation at amino acid position 700 (K700E) . SF3B1 mutation was an independent favorable prognostic variable, whereas TP53 mutation was an independent adverse variable. SF3B1 mutation could coordinate with TP53 mutation for more sophisticated prognosis stratification in MDS-RS patients.
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Affiliation(s)
- Y N Cai
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - Z F Xu
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - B Li
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - T J Qin
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - L J Pan
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - S Q Qu
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - N B Hu
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - D Liu
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - H J Huang
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - Z X Shi
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - Y D Zhang
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
| | - Z J Xiao
- Institute of Hematology and Blood Diseases Hospital, CAMS & PUMC, the State Key Laboratory of Experimental Hematology, National Clinical Research Centre for Blood Diseases, Tianjin 300020, China
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93
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Hautin M, Mornet C, Chauveau A, Bernard DG, Corcos L, Lippert E. Splicing Anomalies in Myeloproliferative Neoplasms: Paving the Way for New Therapeutic Venues. Cancers (Basel) 2020; 12:E2216. [PMID: 32784800 PMCID: PMC7464941 DOI: 10.3390/cancers12082216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Since the discovery of spliceosome mutations in myeloid malignancies, abnormal pre-mRNA splicing, which has been well studied in various cancers, has attracted novel interest in hematology. However, despite the common occurrence of spliceosome mutations in myelo-proliferative neoplasms (MPN), not much is known regarding the characterization and mechanisms of splicing anomalies in MPN. In this article, we review the current scientific literature regarding "splicing and myeloproliferative neoplasms". We first analyse the clinical series reporting spliceosome mutations in MPN and their clinical correlates. We then present the current knowledge about molecular mechanisms by which these mutations participate in the pathogenesis of MPN or other myeloid malignancies. Beside spliceosome mutations, splicing anomalies have been described in myeloproliferative neoplasms, as well as in acute myeloid leukemias, a dreadful complication of these chronic diseases. Based on splicing anomalies reported in chronic myelogenous leukemia as well as in acute leukemia, and the mechanisms presiding splicing deregulation, we propose that abnormal splicing plays a major role in the evolution of myeloproliferative neoplasms and may be the target of specific therapeutic strategies.
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Affiliation(s)
- Marie Hautin
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Clélia Mornet
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Aurélie Chauveau
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Delphine G. Bernard
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Laurent Corcos
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Eric Lippert
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
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94
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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: 1] [Impact Index Per Article: 0.3] [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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95
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Prognostic Markers of Myelodysplastic Syndromes. ACTA ACUST UNITED AC 2020; 56:medicina56080376. [PMID: 32727068 PMCID: PMC7466347 DOI: 10.3390/medicina56080376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/26/2022]
Abstract
Myelodysplastic syndrome (MDS) is a clonal disease characterized by multilineage dysplasia, peripheral blood cytopenias, and a high risk of transformation to acute myeloid leukemia. In theory, from clonal hematopoiesis of indeterminate potential to hematologic malignancies, there is a complex interplay between genetic and epigenetic factors, including miRNA. In practice, karyotype analysis assigns patients to different prognostic groups, and mutations are often associated with a particular disease phenotype. Among myeloproliferative disorders, secondary MDS is a group of special entities with a typical spectrum of genetic mutations and cytogenetic rearrangements resembling those in de novo MDS. This overview analyzes the present prognostic systems of MDS and the most recent efforts in the search for genetic and epigenetic markers for the diagnosis and prognosis of MDS.
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96
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Komrokji RS. Activin Receptor II Ligand Traps: New Treatment Paradigm for Low-Risk MDS. Curr Hematol Malig Rep 2020; 14:346-351. [PMID: 31203517 DOI: 10.1007/s11899-019-00517-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Alleviating cytopenias, namely anemia, is the main goal of therapy in lower-risk myelodysplastic syndromes (MDS). Current available treatment options remain limited. We review the role of TGF-B pathway in MDS, the current available data on luspatercept and sotatercept development. RECENT FINDINGS TGF-B pathway is overactivated in MDS contributing to observed myelosuppression. SMADs, the downstream proteins of TGF-B pathway, are upregulated. GDF-11 is a negative regulator of terminal erythroid differentiation and an activin receptor ligand. Sotatercept and luspatercept are fusion ligand trap novel agents for activin II receptors A and B, respectively. Early promising results have been reported with those novel agents for treating anemia in lower-risk MDS patients, and higher responses were observed among patients with ring sideroblasts and SF3B1 mutation. A phase III randomized clinical trial with luspatercept was recently conducted. Activin receptor II ligand traps may represent a new paradigm for anemia treatment in MDS.
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Affiliation(s)
- Rami S Komrokji
- Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
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97
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Bondu S, Alary AS, Lefèvre C, Houy A, Jung G, Lefebvre T, Rombaut D, Boussaid I, Bousta A, Guillonneau F, Perrier P, Alsafadi S, Wassef M, Margueron R, Rousseau A, Droin N, Cagnard N, Kaltenbach S, Winter S, Kubasch AS, Bouscary D, Santini V, Toma A, Hunault M, Stamatoullas A, Gyan E, Cluzeau T, Platzbecker U, Adès L, Puy H, Stern MH, Karim Z, Mayeux P, Nemeth E, Park S, Ganz T, Kautz L, Kosmider O, Fontenay M. A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome. Sci Transl Med 2020; 11:11/500/eaav5467. [PMID: 31292266 DOI: 10.1126/scitranslmed.aav5467] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/19/2019] [Accepted: 06/12/2019] [Indexed: 12/21/2022]
Abstract
Myelodysplastic syndromes (MDS) with ring sideroblasts are hematopoietic stem cell disorders with erythroid dysplasia and mutations in the SF3B1 splicing factor gene. Patients with MDS with SF3B1 mutations often accumulate excessive tissue iron, even in the absence of transfusions, but the mechanisms that are responsible for their parenchymal iron overload are unknown. Body iron content, tissue distribution, and the supply of iron for erythropoiesis are controlled by the hormone hepcidin, which is regulated by erythroblasts through secretion of the erythroid hormone erythroferrone (ERFE). Here, we identified an alternative ERFE transcript in patients with MDS with the SF3B1 mutation. Induction of this ERFE transcript in primary SF3B1-mutated bone marrow erythroblasts generated a variant protein that maintained the capacity to suppress hepcidin transcription. Plasma concentrations of ERFE were higher in patients with MDS with an SF3B1 gene mutation than in patients with SF3B1 wild-type MDS. Thus, hepcidin suppression by a variant ERFE is likely responsible for the increased iron loading in patients with SF3B1-mutated MDS, suggesting that ERFE could be targeted to prevent iron-mediated toxicity. The expression of the variant ERFE transcript that was restricted to SF3B1-mutated erythroblasts decreased in lenalidomide-responsive anemic patients, identifying variant ERFE as a specific biomarker of clonal erythropoiesis.
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Affiliation(s)
- Sabrina Bondu
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Anne-Sophie Alary
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'hématologie biologique, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France
| | - Carine Lefèvre
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France
| | - Alexandre Houy
- Institut Curie, PSL Research University, Human Genetics and Oncogenesis, Paris 75005, France
| | - Grace Jung
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Thibaud Lefebvre
- Université de Paris, Paris 75006, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,INSERM, UMR 1149/ERL CNRS 8252, Centre de Recherches sur l'inflammation, Université de Paris, Paris 75018, France
| | - David Rombaut
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Ismael Boussaid
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Abderrahmane Bousta
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - François Guillonneau
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Proteomic platform 3P5, Université de Paris, Paris 75014, France
| | - Prunelle Perrier
- Institut de Recherche en Santé Digestive (IRSD), Université de Toulouse, INSERM U1220, Institut National de la Recherche Agronomique U1416, Ecole Nationale Vétérinaire de Toulouse, Université Paul Sabatier, Toulouse 31024, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Department of Translational Research, Paris 75005, France
| | - Michel Wassef
- Institut Curie, PSL Research University, INSERM 934/UMR 3215, Genetics and biology of Development, Paris 75005 France
| | - Raphaël Margueron
- Institut Curie, PSL Research University, INSERM 934/UMR 3215, Genetics and biology of Development, Paris 75005 France
| | - Alice Rousseau
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Nathalie Droin
- Institut Gustave Roussy, Genomic platform, Villejuif 94805, France
| | - Nicolas Cagnard
- Université de Paris, Paris 75006, France.,Platform Bioinformatics, Université de Paris, Paris 75015, France
| | - Sophie Kaltenbach
- Université de Paris, Paris 75006, France.,Laboratoire de Génétique, AP-HP, Hôpital Necker, Paris 75015, France
| | - Susann Winter
- Medical Clinic und Policlinic 1, Technische Universität Dresden, Dresden 01307, Germany
| | - Anne-Sophie Kubasch
- Medical Clinic und Policlinic 1, Hematology and Cellular Therapy, University Hospital, Leipzig 04103, Germany
| | - Didier Bouscary
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'Hématologie clinique, AP-HP, Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France
| | - Valeria Santini
- MDS unit, Hematology, AOU Careggi, University of Florence, Florence 50134, Italy
| | - Andrea Toma
- Département d'Hématologie, AP-HP, Hôpital Henri-Mondor, Université Paris 12, Créteil 94000, France
| | - Mathilde Hunault
- Service des Maladies du Sang, Centre hospitalo-universitaire, Angers 49100, France
| | | | - Emmanuel Gyan
- Service d'hématologie et thérapie cellulaire, Centre hospitalo-universitaire, CNRS ERL 7001 LNOx, Université de Tours, Tours 37044, France
| | - Thomas Cluzeau
- Côte d'Azur University, CHU of Nice, Hematology department and INSERM U1065, Mediterranean Center of Molecular Medecine, Nice 06204, France
| | - Uwe Platzbecker
- Medical Clinic und Policlinic 1, Hematology and Cellular Therapy, University Hospital, Leipzig 04103, Germany
| | - Lionel Adès
- Université de Paris, Paris 75006, France.,Service d'Hématologie Senior, AP-HP, Hôpital Saint-Louis, Paris 75010, France
| | - Hervé Puy
- Université de Paris, Paris 75006, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,INSERM, UMR 1149/ERL CNRS 8252, Centre de Recherches sur l'inflammation, Université de Paris, Paris 75018, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, INSERM U830, Genetics and biology of cancers, DNA repair and uveal melanoma (D.R.U.M.), Équipe labellisée par la Ligue nationale contre le cancer, Paris 75005, France
| | - Zoubida Karim
- Université de Paris, Paris 75006, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,INSERM, UMR 1149/ERL CNRS 8252, Centre de Recherches sur l'inflammation, Université de Paris, Paris 75018, France
| | - Patrick Mayeux
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,Proteomic platform 3P5, Université de Paris, Paris 75014, France
| | - Elizabeta Nemeth
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Sophie Park
- Département d'Hématologie, Centre Hospitalier Universitaire, Université de Grenoble Alpes, La Tronche 38700, France
| | - Tomas Ganz
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Léon Kautz
- Institut de Recherche en Santé Digestive (IRSD), Université de Toulouse, INSERM U1220, Institut National de la Recherche Agronomique U1416, Ecole Nationale Vétérinaire de Toulouse, Université Paul Sabatier, Toulouse 31024, France
| | - Olivier Kosmider
- Université de Paris, Paris 75006, France. .,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'hématologie biologique, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France
| | - Michaëla Fontenay
- Université de Paris, Paris 75006, France. .,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'hématologie biologique, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France
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98
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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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99
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Lee J, Godfrey AL, Nangalia J. Genomic heterogeneity in myeloproliferative neoplasms and applications to clinical practice. Blood Rev 2020; 42:100708. [PMID: 32571583 DOI: 10.1016/j.blre.2020.100708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/22/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022]
Abstract
The myeloproliferative neoplasms (MPN) polycythaemia vera, essential thrombocythaemia and primary myelofibrosis are chronic myeloid disorders associated most often with mutations in JAK2, MPL and CALR, and in some patients with additional acquired genomic lesions. Whilst the molecular mechanisms downstream of these mutations are now clearer, it is apparent that clinical phenotype in MPN is a product of complex interactions, acting between individual mutations, between disease subclones, and between the tumour and background host factors. In this review we first discuss MPN phenotypic driver mutations and the factors that interact with them to influence phenotype. We consider the importance of ongoing studies of clonal haematopoiesis, which may inform a better understanding of why MPN develop in specific individuals. We then consider how best to deploy genomic testing in a clinical environment and the challenges as well as opportunities that may arise from more routine, comprehensive genomic analysis of patients with MPN.
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Affiliation(s)
- Joe Lee
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anna L Godfrey
- Haematopathology and Oncology Diagnostics Service/ Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Hills Rd, Cambridge CB2 0QQ, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Haematopathology and Oncology Diagnostics Service/ Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Hills Rd, Cambridge CB2 0QQ, UK.
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100
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Chen XX, Zhu JH, Li ZP, Xiao HT, Zhou H. Comprehensive Characterization of the Prognosis Value of Alternative Splicing Events in Acute Myeloid Leukemia. DNA Cell Biol 2020; 39:1243-1255. [PMID: 32543226 DOI: 10.1089/dna.2020.5534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Increasing evidence have demonstrated that dysregulated alternative splicing (AS) events promoted tumor development and was correlated with worse prognosis in the context of certain malignancies. Nevertheless, a comprehensive examination of the prognosis role of AS events in acute myeloid leukemia (AML) has not yet been illuminated. In this study, univariate and multivariate Cox regression analysis were used to identify survival-related AS events and independent prognostic predictors. The interaction between splicing factors (SFs) and AS events was visualized by Cytoscape. A total of 3013 survival-associated AS events in 1977 genes were screened in 151 AML patients. Interestingly, the majority (2031 events) were revealed to be protective factors. Furthermore, the prediction models were constructed for each type of AS and all of them displayed good performance in predicting prognosis, considering their area under curve values of the receiver operating characteristic were all above 0.7. Notably, the splicing regulatory network displayed the underlying interaction networks between SFs and AS events. Taken together, our study demonstrated the survival-related AS events in AML and uncovered the possible association between SFs and prognostic AS events, which provide new prognostic biomarkers and aid to develop novel targets for AML therapy.
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Affiliation(s)
- Xue-Xing Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Hua Zhu
- Laboratory of Clinical Immunology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-Ping Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hai-Tao Xiao
- Department of Anatomy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Zhou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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