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Gerlevik S, Seymen N, Hama S, Mumtaz W, Thompson IR, Jalili SR, Kaya DE, Iacoangeli A, Pellagatti A, Boultwood J, Napolitani G, Mufti GJ, Karimi MM. Identification of novel myelodysplastic syndromes prognostic subgroups by integration of inflammation, cell-type composition, and immune signatures in the bone marrow. eLife 2024; 13:RP97096. [PMID: 39235452 PMCID: PMC11377035 DOI: 10.7554/elife.97096] [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: 09/06/2024] Open
Abstract
Mutational profiles of myelodysplastic syndromes (MDS) have established that a relatively small number of genetic aberrations, including SF3B1 and SRSF2 spliceosome mutations, lead to specific phenotypes and prognostic subgrouping. We performed a multi-omics factor analysis (MOFA) on two published MDS cohorts of bone marrow mononuclear cells (BMMNCs) and CD34 + cells with three data modalities (clinical, genotype, and transcriptomics). Seven different views, including immune profile, inflammation/aging, retrotransposon (RTE) expression, and cell-type composition, were derived from these modalities to identify the latent factors with significant impact on MDS prognosis. SF3B1 was the only mutation among 13 mutations in the BMMNC cohort, indicating a significant association with high inflammation. This trend was also observed to a lesser extent in the CD34 + cohort. Interestingly, the MOFA factor representing the inflammation shows a good prognosis for MDS patients with high inflammation. In contrast, SRSF2 mutant cases show a granulocyte-monocyte progenitor (GMP) pattern and high levels of senescence, immunosenescence, and malignant myeloid cells, consistent with their poor prognosis. Furthermore, MOFA identified RTE expression as a risk factor for MDS. This work elucidates the efficacy of our integrative approach to assess the MDS risk that goes beyond all the scoring systems described thus far for MDS.
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Affiliation(s)
- Sila Gerlevik
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Nogayhan Seymen
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Shan Hama
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Warisha Mumtaz
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - I Richard Thompson
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Seyed R Jalili
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Deniz E Kaya
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom
- Department of Biostatistics and Health Informatics, King's College London, London, United Kingdom
- NIHR BRC SLAM NHS Foundation Trust, London, United Kingdom
- Perron Institute for Neurological and Translational Science, University of Western Australia Medical School, Perth, Australia
| | - Andrea Pellagatti
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jacqueline Boultwood
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Giorgio Napolitani
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Ghulam J Mufti
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Mohammad M Karimi
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
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Szelest M, Giannopoulos K. Biological relevance of alternative splicing in hematologic malignancies. Mol Med 2024; 30:62. [PMID: 38760666 PMCID: PMC11100220 DOI: 10.1186/s10020-024-00839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024] Open
Abstract
Alternative splicing (AS) is a strictly regulated process that generates multiple mRNA variants from a single gene, thus contributing to proteome diversity. Transcriptome-wide sequencing studies revealed networks of functionally coordinated splicing events, which produce isoforms with distinct or even opposing functions. To date, several mechanisms of AS are deregulated in leukemic cells, mainly due to mutations in splicing and/or epigenetic regulators and altered expression of splicing factors (SFs). In this review, we discuss aberrant splicing events induced by mutations affecting SFs (SF3B1, U2AF1, SRSR2, and ZRSR2), spliceosome components (PRPF8, LUC7L2, DDX41, and HNRNPH1), and epigenetic modulators (IDH1 and IDH2). Finally, we provide an extensive overview of the biological relevance of aberrant isoforms of genes involved in the regulation of apoptosis (e. g. BCL-X, MCL-1, FAS, and c-FLIP), activation of key cellular signaling pathways (CASP8, MAP3K7, and NOTCH2), and cell metabolism (PKM).
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Affiliation(s)
- Monika Szelest
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland.
| | - Krzysztof Giannopoulos
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland
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Li X, Liu D, Wang Y, Chen Y, Wang C, Lin Z, Tian L. PHF5A as a new OncoTarget and therapeutic prospects. Heliyon 2023; 9:e18010. [PMID: 37483794 PMCID: PMC10362332 DOI: 10.1016/j.heliyon.2023.e18010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/24/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023] Open
Abstract
PHF5A (PHD-finger domain protein 5A) is a highly conserved protein comprised of 110 amino acids that belong to PHD zinc finger proteins and is ubiquitously expressed in entire eukaryotic nuclei from yeast to man. PHF5A is an essential component of the SF3B splicing complex regulating protein-protein or protein-DNA interactions; particularly involved in pre-mRNA splicing. Besides its basic spliceosome-associated attributes encompassing the regulation of alternative splicing of specific genes, PHF5A also plays a pivotal role in cell cycle regulation and morphological development of cells along with their differentiation into particular tissues/organs, DNA damage repair, maintenance of pluripotent embryonic stem cells (CSCs) embryogenesis and regulation of chromatin-mediated transcription. Presently identification of spliceosome and non-spliceosome-associated attributes of PHF5A needs great attention based on its key involvement in the pathogenesis of cancer malignancies including the prognosis of lung adenocarcinoma, endometrial adenocarcinoma, breast, and colorectal cancer. PHF5A is an essential splicing factor or cofactor actively participating as an oncogenic protein in tumorigenesis via activation of downstream signaling pathway attributed to its regulation of dysregulated splicing or abnormal alternative splicing of targeted genes. Further, the participation of PHF5A in regulating the growth of cancer stem cells might not be ignored. The current review briefly overviews the structural and functional attributes of PHF5A along with its hitherto described role in the propagation of cancer malignancies and its future concern as a potential therapeutic target for cancer management/treatment.
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Affiliation(s)
- Xiaojiang Li
- Department of Orthopedics, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Dalong Liu
- Department of Orthopedics, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Yun Wang
- Department of Thoracic Surgery, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Yu Chen
- Department of Orthopedics, LiaoYuanCity TCM Hospital, LiaoYuan, 136200, China
| | - Chenyang Wang
- Department of Orthopedics, LiaoYuanCity TCM Hospital, LiaoYuan, 136200, China
| | - Zhicheng Lin
- Department of Internal Medicine, Baishan Hospital of Traditional Chinese Medicine, Baishan, 134300, China
| | - Lin Tian
- Department of Lung Oncology, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
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Jiang M, Chen M, Liu Q, Jin Z, Yang X, Zhang W. SF3B1 mutations in myelodysplastic syndromes: A potential therapeutic target for modulating the entire disease process. Front Oncol 2023; 13:1116438. [PMID: 37007111 PMCID: PMC10063959 DOI: 10.3389/fonc.2023.1116438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are clonal hematologic malignancies characterized by ineffective hematopoiesis and dysplasia of the myeloid cell lineage and are characterized by peripheral blood cytopenia and an increased risk of transformation to acute myeloid leukemia (AML). Approximately half of the patients with MDS have somatic mutations in the spliceosome gene. Splicing Factor 3B Subunit 1A (SF3B1), the most frequently occurring splicing factor mutation in MDS is significantly associated with the MDS-RS subtype. SF3B1 mutations are intimately involved in the MDS regulation of various pathophysiological processes, including impaired erythropoiesis, dysregulated iron metabolism homeostasis, hyperinflammatory features, and R-loop accumulation. In the fifth edition of the World Health Organization (WHO) classification criteria for MDS, MDS with SF3B1 mutations has been classified as an independent subtype, which plays a crucial role in identifying the disease phenotype, promoting tumor development, determining clinical features, and influencing tumor prognosis. Given that SF3B1 has demonstrated therapeutic vulnerability both in early MDS drivers and downstream events, therapy based on spliceosome-associated mutations is considered a novel strategy worth exploring in the future.
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Li J, Pei L, Liang S, Xu S, Wang Y, Wang X, Liao Y, Zhan Q, Cheng W, Yang Z, Tang X, Zhang H, Xiao Q, Chen J, Liu L, Wang L. Gene mutation analysis using next-generation sequencing and its clinical significance in patients with myeloid neoplasm: A multi-center study from China. Cancer Med 2023; 12:9332-9350. [PMID: 36799265 PMCID: PMC10166913 DOI: 10.1002/cam4.5690] [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: 07/16/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Myeloid neoplasms (MN) tend to relapse and deteriorate. Exploring the genomic mutation landscape of MN using next-generation sequencing (NGS) is a great measure to clarify the mechanism of oncogenesis and progression of MN. METHODS This multicenter retrospective study investigated 303 patients with MN using NGS from 2019 to 2021. The characteristics of the mutation landscape in the MN subgroups and the clinical value of gene variants were analyzed. RESULTS At least one mutation was detected in 88.11% of the patients (267/303). TET2 was the most common mutation in the cohort, followed by GATA2, ASXL1, FLT3, DNMT3A, and TP53. Among patients with myeloid leukemia (ML), multivariate analysis showed that patients aged ≥60 years had lower overall survival (OS, p = 0.004). Further analysis showed TET2, NPM1, SRSF2, and IDH1 gene mutations, and epigenetic genes (p < 0.050) presented significantly higher frequency in older patients. In patients with myelodysplastic syndrome (MDS) and myelodysplastic neoplasms (MPN), univariate analysis showed that BCORL1 had a significant impact on OS (p = 0.040); however, in multivariate analysis, there were no factors significantly associated with OS. Differential analysis of genetic mutations showed FLT3, TP53, MUC16, SRSF2, and KDM5A mutated more frequently (p < 0.050) in secondary acute myeloid leukemia (s-AML) than in MDS and MPN. TP53, U2AF1, SRSF2, and KDM5A were mutated more frequently (p < 0.050) in s-AML than in primary AML. KDM5A was observed to be restricted to patients with s-AML in this study, and only co-occurred with MUC16 and TP53 (2/2, 100%). Another mutation was MUC16, and its co-occurrence pattern differed between s-AML and AML. MUC16 mutations co-occurred with KDM5A and TP53 in 66.7% (2/3) of patients with s-AML and co-occurred with CEBPA in 100% (4/4) of patients with AML. CONCLUSIONS Our results demonstrate different genomic mutation patterns in the MN subgroups and highlight the clinical value of genetic variants.
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Affiliation(s)
- Junnan Li
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Li Pei
- Department of Hematology, The First Affiliated Hospital of Army Medical University(Southwest Hospital), Chongqing, China
| | - Simin Liang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shuangnian Xu
- Department of Hematology, The First Affiliated Hospital of Army Medical University(Southwest Hospital), Chongqing, China
| | - Yi Wang
- Department of Hematology, Shaanxi Provincial People's Hospital, Xi'An, Shaanxi, China
| | - Xiao Wang
- Department of Hematology, Shaanxi Provincial People's Hospital, Xi'An, Shaanxi, China
| | - Yi Liao
- Department of Oncology and Hematology, Chongqing University Affiliated Center Hospital, Chongqing, China
| | - Qian Zhan
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Wei Cheng
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zesong Yang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaoqiong Tang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hongbin Zhang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Qing Xiao
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Jianbin Chen
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Lin Liu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Kanagal-Shamanna R, Montalban-Bravo G, Sasaki K, Darbaniyan F, Jabbour E, Bueso-Ramos C, Wei Y, Chien K, Kadia T, Ravandi F, Borthakur G, Soltysiak KA, Routbort M, Patel K, Pierce S, Medeiros LJ, Kantarjian HM, Garcia-Manero G. Only SF3B1 mutation involving K700E independently predicts overall survival in myelodysplastic syndromes. Cancer 2021; 127:3552-3565. [PMID: 34161603 PMCID: PMC10015977 DOI: 10.1002/cncr.33745] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/14/2021] [Accepted: 05/11/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND SF3B1 mutations (SF3B1mut ) in myelodysplastic syndromes (MDS) frequently involve codon K700E and have a favorable prognosis. The prognostic effect of non-K700E SF3B1mut is uncertain. METHODS The authors analyzed the clinicopathological features and outcomes of a single-institution series of 94 treatment-naive SF3B1mut MDS patients (18%) and 415 treatment-naive SF3B1wt MDS patients and explored the differences between K700E and non-K700E SF3B1mut MDS. RESULTS Fifty-five patients (59%) carried K700E. Recurrent non-K700E mutations (39 [41%]) included R625, H662, and K666. Compared with SF3B1mut K700E patients, non-K700E patients had a lower median absolute neutrophil count (1.8 vs 2.4; P = .005) and were frequently "high" according to the Revised International Prognostic Scoring System (19% vs 4%; P = .031). Non-K700E MDS was associated frequently with RUNX1 (26% vs 7%; P = .012) and exclusively with BCOR, IDH2, and SRSF2 mutations. A splicing analysis showed the differential distribution of alternatively spliced events and gene expression profiles between K700 and non-K700E MDS patients. The majority (at least 80%) of SF3B1mut K700E, SF3B1mut non-K700E, and SF3B1wt patients were treated with hypomethylating agents. Over a median follow-up of 16 months, SF3B1mut had superior overall survival (OS) in comparison with SF3B1wt in all MDS patients (not reached vs 25.2 months; P = .0003), in patients with low-grade MDS, and in patients with myelodysplastic syndromes with ring sideroblasts (MDS-RS). Compared with SF3B1wt , SF3B1mut K700E had superior outcomes in all MDS (median OS, 25 months vs not reached; P = .0001), in low-grade MDS (median OS, 41.3 months vs not reached; P = .0015), and in MDS-RS (median OS, 22.3 months vs not reached; P = .0001), but no significant difference was seen between non-K700E and SF3B1wt MDS. By multivariable analysis, the absence of SF3B1mut K700E mutations was independently associated with the prognosis. CONCLUSIONS This study highlights the importance of the SF3B1 mutation subtype in MDS risk assessment. LAY SUMMARY Myelodysplastic syndromes (MDS) with SF3B1 mutations are regarded as having a favorable prognosis by both the World Health Organization and the International Working Group for the Prognosis of Myelodysplastic Syndromes. However, this article shows that only MDS patients with SF3B1 K700E mutations have a favorable prognosis (and not MDS patients with SF3B1 mutations involving other codons). This has important implications for refining future MDS subclassification and risk assessment criteria.
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Koji Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Faezeh Darbaniyan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carlos Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yue Wei
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kelly Chien
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tapan Kadia
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Farhad Ravandi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kelly A Soltysiak
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherry Pierce
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hagop M Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Rosenthal SH, Gerasimova A, Ma C, Li HR, Grupe A, Chong H, Acab A, Smolgovsky A, Owen R, Elzinga C, Chen R, Sugganth D, Freitas T, Graham J, Champion K, Bhattacharya A, Racke F, Lacbawan F. Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms. PLoS One 2021; 16:e0243683. [PMID: 33909614 PMCID: PMC8081174 DOI: 10.1371/journal.pone.0243683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. Various NGS based in-house developed and commercial myeloid neoplasm panels have been integrated into routine clinical practice. However, some genes frequently mutated in myeloid malignancies are particularly difficult to sequence with NGS panels (e.g., CEBPA, CARL, and FLT3). We report development and validation of a 48-gene NGS panel that includes genes that are technically challenging for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies ≥5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n = 2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9-99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n = 2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms even in technically challenging genes.
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Affiliation(s)
- Sun Hee Rosenthal
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Anna Gerasimova
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Charles Ma
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hai-Rong Li
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Andrew Grupe
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hansook Chong
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Allan Acab
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Alla Smolgovsky
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Renius Owen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Christopher Elzinga
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Rebecca Chen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Daniel Sugganth
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Tracey Freitas
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Jennifer Graham
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Kristen Champion
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Anindya Bhattacharya
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Frederick Racke
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Felicitas Lacbawan
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
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8
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Do next-generation sequencing results drive diagnostic and therapeutic decisions in MDS? Blood Adv 2020; 3:3454-3460. [PMID: 31714959 DOI: 10.1182/bloodadvances.2019000680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/05/2019] [Indexed: 02/07/2023] Open
Abstract
This article has a companion Point by Thol and Platzbecker.
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9
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Roles and mechanisms of alternative splicing in cancer - implications for care. Nat Rev Clin Oncol 2020; 17:457-474. [PMID: 32303702 DOI: 10.1038/s41571-020-0350-x] [Citation(s) in RCA: 393] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
Removal of introns from messenger RNA precursors (pre-mRNA splicing) is an essential step for the expression of most eukaryotic genes. Alternative splicing enables the regulated generation of multiple mRNA and protein products from a single gene. Cancer cells have general as well as cancer type-specific and subtype-specific alterations in the splicing process that can have prognostic value and contribute to every hallmark of cancer progression, including cancer immune responses. These splicing alterations are often linked to the occurrence of cancer driver mutations in genes encoding either core components or regulators of the splicing machinery. Of therapeutic relevance, the transcriptomic landscape of cancer cells makes them particularly vulnerable to pharmacological inhibition of splicing. Small-molecule splicing modulators are currently in clinical trials and, in addition to splice site-switching antisense oligonucleotides, offer the promise of novel and personalized approaches to cancer treatment.
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10
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Abstract
Sideroblastic anemias are a heterogeneous group of disorders unified by the presence of abnormal erythroid precursors with perinuclear mitochondrial iron deposition in the bone marrow. Based on etiology, they are classified into clonal and nonclonal. Clonal sideroblastic anemias refer to myeloid neoplasms with ring sideroblasts (RS) and frequently have somatic perturbations in the SF3B1 gene. Anemia is a major cause of morbidity in patients, and restoration of effective erythropoiesis is a major treatment goal. Morbidity includes transfusion and disease-related complications. This article focuses on treatment of acquired sideroblastic anemias and highlights areas of future investigation.
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Affiliation(s)
- Abhishek A Mangaonkar
- Division of Hematology, Department of Medicine, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA.
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11
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Tobiasson M, Kittang AO. Treatment of myelodysplastic syndrome in the era of next-generation sequencing. J Intern Med 2019; 286:41-62. [PMID: 30869816 DOI: 10.1111/joim.12893] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing (NGS) is rapidly changing the clinical care of patients with myelodysplastic syndrome (MDS). NGS can be used for various applications: (i) in the diagnostic process to discriminate between MDS and other diseases such as aplastic anaemia, myeloproliferative disorders and idiopathic cytopenias; (ii) for classification, for example, where the presence of SF3B1 mutation is one criterion for the ring sideroblast anaemia subgroups in the World Health Organization 2016 classification; (iii) for identification of patients suitable for targeted therapy (e.g. IDH1/2 inhibitors); (iv) for prognostication, for example, where specific mutations (e.g. TP53 and RUNX1) are associated with inferior prognosis, whereas others (e.g. SF3B1) are associated with superior prognosis; and (v) to monitor patients for progression or treatment failure. Most commonly, targeted sequencing for genes (normally 50-100 genes) reported to be recurrently mutated in myeloid disease is used. At present, NGS is rarely incorporated into clinical guidelines although an increasing number of studies have demonstrated the benefit of using NGS in the clinical management of MDS patients.
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Affiliation(s)
- M Tobiasson
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden.,Institution of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - A O Kittang
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Section for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Baek DW, Lee YJ, Kim H, Ahn SY, Ahn JS, Shin HJ, Lee WS, Lee SM, Song IC, Lee HS, Park SW, Choi Y, Cho YY, Bae SH, Kim HJ, Sohn SK, Moon JH. Response to hypomethylating agents improves long-term outcomes for lower-risk patients with myelodysplastic syndrome in case-matched cohorts. Ann Hematol 2018; 97:2309-2317. [PMID: 30073392 DOI: 10.1007/s00277-018-3458-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/23/2018] [Indexed: 02/07/2023]
Abstract
Predictive factors for initiating hypomethylating agents' (HMAs) treatment and the survival benefit of HMAs for lower-risk myelodysplastic syndrome (LR-MDS) are still unknown. This study evaluated the factors affecting the use of HMAs and compared long-term outcomes between best supportive care (BSC) and HMA groups after matching baseline clinical factors. Data of 353 patients diagnosed with LR-MDS by International Prognostic Scoring System between October 1992 and July 2013 were retrospectively analyzed. HMAs were administered continuously until a clinical response or progression. HMAs were administered to 243 patients with median 45 days (range 0-7078 days) after diagnosis, while 110 patients were treated with BSC. HMAs were administered over a median of 5 cycles and overall response was achieved in 104 patients (42.8%). The cumulative incidence of HMA treatment increased in higher-risk groups by other risk scoring systems. Three-year overall survival (OS) rate was higher in BSC group (69.1%) than HMA responders (47.4%, p = 0.065) or HMA non-responders (46.3%, p = 0.005). Among 162 case-matched cohorts, 3-year OS rates were comparable between the BSC group (67.1%) and HMA responders (58.1%, p = 0.914), while that of HMA non-responder was low (32.2%, p < 0.001). In the case-matched cohorts, HMA non-responder were associated with inferior OS rate in the multivariate analysis (hazard ratio 3.01, p = 0.001). Higher-risk groups by other clinical risk scoring systems among IPSS lower-risk patients showed an increased incidence of using HMAs. The OS rate of HMA responders among case-matched cohorts showed an improved OS rate similar to the BSC group.
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Affiliation(s)
- Dong Won Baek
- Department of Hematology/Oncology, Kyungpook National University Hospital, 130 Dongdeok-ro, Jung-gu, Daegu, 41944, South Korea
- School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Yoo Jin Lee
- Department of Hematology/Oncology, Kyungpook National University Hospital, 130 Dongdeok-ro, Jung-gu, Daegu, 41944, South Korea
- School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Hyunjeong Kim
- School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Seo Yeon Ahn
- Department of Hematology/Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Jae Sook Ahn
- Department of Hematology/Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Ho Jin Shin
- Busan National University Hospital, Busan, South Korea
| | - Won Sik Lee
- Inje University Busan Baik Hospital, Busan, South Korea
| | - Sang Min Lee
- Inje University Busan Baik Hospital, Busan, South Korea
| | - Ik Chan Song
- Chungnam National University Hospital, Daejeon, South Korea
| | - Ho Sup Lee
- Kosin University Gosper Hospital, Busan, South Korea
| | - Sung Woo Park
- Gyeongsang National University Hospital, Jinju, South Korea
| | - Yunsuk Choi
- Ulsan University Hospital, Ulsan, South Korea
| | - Yoon Young Cho
- Daegu Catholic University Medical Center, Daegu, South Korea
| | - Sung Hwa Bae
- Daegu Catholic University Medical Center, Daegu, South Korea
| | - Hyeoung Joon Kim
- Department of Hematology/Oncology, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Sang Kyun Sohn
- Department of Hematology/Oncology, Kyungpook National University Hospital, 130 Dongdeok-ro, Jung-gu, Daegu, 41944, South Korea
- School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Joon Ho Moon
- Department of Hematology/Oncology, Kyungpook National University Hospital, 130 Dongdeok-ro, Jung-gu, Daegu, 41944, South Korea.
- School of Medicine, Kyungpook National University Hospital, Daegu, South Korea.
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