1
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Choi IY, Ling JP, Zhang J, Helmenstine E, Walter W, Tsakiroglou P, Bergman RE, Philippe C, Manley JL, Rouault-Pierre K, Li B, Wiseman DH, Batta K, Ouseph M, Bernard E, Dubner B, Li X, Haferlach T, Koget A, Fazal S, Jain T, Gocke CD, DeZern AE, Dalton WB. The E592K variant of SF3B1 creates unique RNA missplicing and associates with high-risk MDS without ring sideroblasts. Blood Adv 2024; 8:3961-3971. [PMID: 38759096 PMCID: PMC11331715 DOI: 10.1182/bloodadvances.2023011260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 05/19/2024] Open
Abstract
ABSTRACT Among the most common genetic alterations in myelodysplastic syndromes (MDS) are mutations in the spliceosome gene SF3B1. Such mutations induce specific RNA missplicing events, directly promote ring sideroblast (RS) formation, and generally associate with a more favorable prognosis. However, not all SF3B1 mutations are the same, and little is known about how distinct hotspots influence disease. Here, we report that the E592K variant of SF3B1 associates with high-risk disease features in MDS, including a lack of RS, increased myeloblasts, a distinct comutation pattern, and a lack of favorable survival seen with other SF3B1 mutations. Moreover, compared with other hot spot SF3B1 mutations, E592K induces a unique RNA missplicing pattern, retains an interaction with the splicing factor SUGP1, and preserves normal RNA splicing of the sideroblastic anemia genes TMEM14C and ABCB7. These data have implications for our understanding of the functional diversity of spliceosome mutations, as well as the pathobiology, classification, prognosis, and management of SF3B1-mutant MDS.
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Affiliation(s)
- In Young Choi
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jonathan P. Ling
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD
| | - Jian Zhang
- Department of Biological Sciences, Columbia University, New York, NY
| | - Eric Helmenstine
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Panagiotis Tsakiroglou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Riley E. Bergman
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and The Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - James L. Manley
- Department of Biological Sciences, Columbia University, New York, NY
| | | | - Bing Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- MDS and MPN Centre, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Daniel H. Wiseman
- Epigenetics of Haematopoiesis Laboratory, Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
- Department of Haematology, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Kiran Batta
- Epigenetics of Haematopoiesis Laboratory, Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
- Department of Haematology, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Madhu Ouseph
- Division of Pathology & Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Dubner
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xiao Li
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | | | - Anna Koget
- Division of Hematology and Cellular Therapy, Allegheny Health Network Cancer Institute, Pittsburgh, PA
| | - Salman Fazal
- Division of Hematology and Cellular Therapy, Allegheny Health Network Cancer Institute, Pittsburgh, PA
| | - Tania Jain
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher D. Gocke
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Amy E. DeZern
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - William Brian Dalton
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
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Zhang Q, Ai Y, Abdel-Wahab O. Molecular impact of mutations in RNA splicing factors in cancer. Mol Cell 2024:S1097-2765(24)00617-8. [PMID: 39146933 DOI: 10.1016/j.molcel.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024]
Abstract
Somatic mutations in genes encoding components of the RNA splicing machinery occur frequently in multiple forms of cancer. The most frequently mutated RNA splicing factors in cancer impact intronic branch site and 3' splice site recognition. These include mutations in the core RNA splicing factor SF3B1 as well as mutations in the U2AF1/2 heterodimeric complex, which recruits the SF3b complex to the 3' splice site. Additionally, mutations in splicing regulatory proteins SRSF2 and RBM10 are frequent in cancer, and there has been a recent suggestion that variant forms of small nuclear RNAs (snRNAs) may contribute to splicing dysregulation in cancer. Here, we describe molecular mechanisms by which mutations in these factors alter splice site recognition and how studies of this process have yielded new insights into cancer pathogenesis and the molecular regulation of splicing. We also discuss data linking mutant RNA splicing factors to RNA metabolism beyond splicing.
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Affiliation(s)
- Qian Zhang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuxi Ai
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Joshi P, Keyvani Chahi A, Liu L, Moreira S, Vujovic A, Hope KJ. RNA binding protein-directed control of leukemic stem cell evolution and function. Hemasphere 2024; 8:e116. [PMID: 39175825 PMCID: PMC11339706 DOI: 10.1002/hem3.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/06/2024] [Accepted: 05/26/2024] [Indexed: 08/24/2024] Open
Abstract
Strict control over hematopoietic stem cell decision making is essential for healthy life-long blood production and underpins the origins of hematopoietic diseases. Acute myeloid leukemia (AML) in particular is a devastating hematopoietic malignancy that arises from the clonal evolution of disease-initiating primitive cells which acquire compounding genetic changes over time and culminate in the generation of leukemic stem cells (LSCs). Understanding the molecular underpinnings of these driver cells throughout their development will be instrumental in the interception of leukemia, the enabling of effective treatment of pre-leukemic conditions, as well as the development of strategies to target frank AML disease. To this point, a number of precancerous myeloid disorders and age-related alterations are proving as instructive models to gain insights into the initiation of LSCs. Here, we explore this myeloid dysregulation at the level of post-transcriptional control, where RNA-binding proteins (RBPs) function as core effectors. Through regulating the interplay of a myriad of RNA metabolic processes, RBPs orchestrate transcript fates to govern gene expression in health and disease. We describe the expanding appreciation of the role of RBPs and their post-transcriptional networks in sustaining healthy hematopoiesis and their dysregulation in the pathogenesis of clonal myeloid disorders and AML, with a particular emphasis on findings described in human stem cells. Lastly, we discuss key breakthroughs that highlight RBPs and post-transcriptional control as actionable targets for precision therapy of AML.
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Affiliation(s)
- Pratik Joshi
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Ava Keyvani Chahi
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Lina Liu
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Steven Moreira
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Ana Vujovic
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Kristin J. Hope
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
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4
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Park J, Peña-Tauber A, Talozzi L, Greicius MD, Guen YL. Genetic associations with human longevity are enriched for oncogenic genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.30.24311226. [PMID: 39132489 PMCID: PMC11312667 DOI: 10.1101/2024.07.30.24311226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Human lifespan is shaped by both genetic and environmental exposures and their interaction. To enable precision health, it is essential to understand how genetic variants contribute to earlier death or prolonged survival. In this study, we tested the association of common genetic variants and the burden of rare non-synonymous variants in a survival analysis, using age-at-death (N = 35,551, median [min, max] = 72.4 [40.9, 85.2]), and last-known-age (N = 358,282, median [min, max] = 71.9 [52.6, 88.7]), in European ancestry participants of the UK Biobank. The associations we identified seemed predominantly driven by cancer, likely due to the age range of the cohort. Common variant analysis highlighted three longevity-associated loci: APOE, ZSCAN23, and MUC5B. We identified six genes whose burden of loss-of-function variants is significantly associated with reduced lifespan: TET2, ATM, BRCA2, CKMT1B, BRCA1 and ASXL1. Additionally, in eight genes, the burden of pathogenic missense variants was associated with reduced lifespan: DNMT3A, SF3B1, CHL1, TET2, PTEN, SOX21, TP53 and SRSF2. Most of these genes have previously been linked to oncogenic-related pathways and some are linked to and are known to harbor somatic variants that predispose to clonal hematopoiesis. A direction-agnostic (SKAT-O) approach additionally identified significant associations with C1orf52, TERT, IDH2, and RLIM, highlighting a link between telomerase function and longevity as well as identifying additional oncogenic genes. Our results emphasize the importance of understanding genetic factors driving the most prevalent causes of mortality at a population level, highlighting the potential of early genetic testing to identify germline and somatic variants increasing one's susceptibility to cancer and/or early death.
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Affiliation(s)
- Junyoung Park
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Andrés Peña-Tauber
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Lia Talozzi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Michael D. Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Yann Le Guen
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, 94304, USA
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Zhang H, Zhu H, Peng H, Sheng Y. Function of serine/arginine-rich splicing factors in hematopoiesis and hematopoietic malignancies. Cancer Cell Int 2024; 24:257. [PMID: 39034387 PMCID: PMC11265194 DOI: 10.1186/s12935-024-03438-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 07/08/2024] [Indexed: 07/23/2024] Open
Abstract
The serine/arginine-rich splicing factors (SRSFs) play an important role in regulating the alternative splicing of precursor RNA (pre-RNA). During this procedure, introns are removed from the pre-RNA, while the exons are accurately joined together to produce mature mRNA. In addition, SRSFs also involved in DNA replication and transcription, mRNA stability and nuclear export, and protein translation. It is reported that SRSFs participate in hematopoiesis, development, and other important biological process. They are also associated with the development of several diseases, particularly cancers. While the basic physiological functions and the important roles of SRSFs in solid cancer have been extensively reviewed, a comprehensive summary of their significant functions in normal hematopoiesis and hematopoietic malignancies is currently absent. Hence, this review presents a summary of their roles in normal hematopoiesis and hematopoietic malignancies.
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Affiliation(s)
- Huifang Zhang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China.
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China.
| | - Hongkai Zhu
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China
| | - Hongling Peng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China.
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China.
| | - Yue Sheng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China.
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China.
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6
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Zhang F, Sun J, Zhang L, Li R, Wang Y, Geng H, Shen C, Li L, Chen L. PARP inhibition leads to synthetic lethality with key splicing-factor mutations in myelodysplastic syndromes. Br J Cancer 2024; 131:231-242. [PMID: 38806724 PMCID: PMC11263539 DOI: 10.1038/s41416-024-02729-0] [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: 06/15/2023] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Splicing factors are frequently mutated in patients with myelodysplastic syndromes and acute myeloid leukaemia. Recent studies have revealed convergent molecular defects caused by splicing factor mutations, among which R-loop dysregulation and resultant genome instability are suggested as contributing factors to disease progression. On the other hand, understanding how mutant cells survive upon aberrant R-loop formation and genome instability is essential for developing novel therapeutics. METHODS The immunoprecipitation was performed to identify R-loops in association with PARP1/poly-ADP-ribosylation. The western blot, immunofluorescence, and flow cytometry assays were used to test the cell viability, cell cycle arrest, apoptosis, and ATM activation in mutant cells following the treatment of the PARP inhibitor. The Srsf2(P95H) knock-in murine hematopoietic cells and MLL-AF9 transformed leukaemia model were generated to investigate the potential of the PARP inhibitor as a therapy for haematological malignancies. RESULTS The disease-causing mutations in SRSF2 activate PARP and elevate the overall poly-ADP-ribosylation levels of proteins in response to R-loop dysregulation. In accordance, mutant cells are more vulnerable to the PARP inhibitors in comparison to the wild-type counterpart. Notably, the synthetic lethality was further validated in the Srsf2(P95H) knock-in murine hematopoietic cell and MLL-AF9 leukaemia model. CONCLUSIONS Our findings suggest that mutant cells antagonise the genome threat caused by R-loop disruption by PARP activation, thus making PARP targeting a promising therapeutic strategy for myeloid cancers with mutations in SRSF2.
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Affiliation(s)
- Fangliang Zhang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianai Sun
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Ruiqi Li
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yanzhen Wang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huichao Geng
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chao Shen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA.
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
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7
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Gimeno-Valiente F, López-Rodas G, Castillo J, Franco L. The Many Roads from Alternative Splicing to Cancer: Molecular Mechanisms Involving Driver Genes. Cancers (Basel) 2024; 16:2123. [PMID: 38893242 PMCID: PMC11171328 DOI: 10.3390/cancers16112123] [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: 05/05/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer driver genes are either oncogenes or tumour suppressor genes that are classically activated or inactivated, respectively, by driver mutations. Alternative splicing-which produces various mature mRNAs and, eventually, protein variants from a single gene-may also result in driving neoplastic transformation because of the different and often opposed functions of the variants of driver genes. The present review analyses the different alternative splicing events that result in driving neoplastic transformation, with an emphasis on their molecular mechanisms. To do this, we collected a list of 568 gene drivers of cancer and revised the literature to select those involved in the alternative splicing of other genes as well as those in which its pre-mRNA is subject to alternative splicing, with the result, in both cases, of producing an oncogenic isoform. Thirty-one genes fall into the first category, which includes splicing factors and components of the spliceosome and splicing regulators. In the second category, namely that comprising driver genes in which alternative splicing produces the oncogenic isoform, 168 genes were found. Then, we grouped them according to the molecular mechanisms responsible for alternative splicing yielding oncogenic isoforms, namely, mutations in cis splicing-determining elements, other causes involving non-mutated cis elements, changes in splicing factors, and epigenetic and chromatin-related changes. The data given in the present review substantiate the idea that aberrant splicing may regulate the activation of proto-oncogenes or inactivation of tumour suppressor genes and details on the mechanisms involved are given for more than 40 driver genes.
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Affiliation(s)
- Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London WC1E 6DD, UK;
| | - Gerardo López-Rodas
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
| | - Josefa Castillo
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Luis Franco
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
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8
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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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9
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Benbarche S, Pineda JMB, Galvis LB, Biswas J, Liu B, Wang E, Zhang Q, Hogg SJ, Lyttle K, Dahi A, Lewis AM, Sarchi M, Rahman J, Fox N, Ai Y, Mehta S, Garippa R, Ortiz-Pacheco J, Li Z, Monetti M, Stanley RF, Doulatov S, Bradley RK, Abdel-Wahab O. GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies. Mol Cell 2024; 84:1886-1903.e10. [PMID: 38688280 PMCID: PMC11102302 DOI: 10.1016/j.molcel.2024.04.006] [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: 09/26/2023] [Revised: 03/04/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Mutations in the RNA splicing factor gene SF3B1 are common across hematologic and solid cancers and result in widespread alterations in splicing, yet there is currently no therapeutic means to correct this mis-splicing. Here, we utilize synthetic introns uniquely responsive to mutant SF3B1 to identify trans factors required for aberrant mutant SF3B1 splicing activity. This revealed the G-patch domain-containing protein GPATCH8 as required for mutant SF3B1-induced splicing alterations and impaired hematopoiesis. GPATCH8 is involved in quality control of branchpoint selection, interacts with the RNA helicase DHX15, and functionally opposes SURP and G-patch domain containing 1 (SUGP1), a G-patch protein recently implicated in SF3B1-mutant diseases. Silencing of GPATCH8 corrected one-third of mutant SF3B1-dependent splicing defects and was sufficient to improve dysfunctional hematopoiesis in SF3B1-mutant mice and primary human progenitors. These data identify GPATCH8 as a novel splicing factor required for mis-splicing by mutant SF3B1 and highlight the therapeutic impact of correcting aberrant splicing in SF3B1-mutant cancers.
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Affiliation(s)
- Salima Benbarche
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Laura Baquero Galvis
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jeetayu Biswas
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Liu
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qian Zhang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kadeen Lyttle
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariana Dahi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander M Lewis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Sarchi
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nina Fox
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuxi Ai
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Juliana Ortiz-Pacheco
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Mara Monetti
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergei Doulatov
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Liu X, Devadiga SA, Stanley RF, Morrow RM, Janssen KA, Quesnel-Vallières M, Pomp O, Moverley AA, Li C, Skuli N, Carroll M, Huang J, Wallace DC, Lynch KW, Abdel-Wahab O, Klein PS. A mitochondrial surveillance mechanism activated by SRSF2 mutations in hematologic malignancies. J Clin Invest 2024; 134:e175619. [PMID: 38713535 PMCID: PMC11178535 DOI: 10.1172/jci175619] [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: 09/11/2023] [Accepted: 04/25/2024] [Indexed: 05/09/2024] Open
Abstract
Splicing factor mutations are common in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), but how they alter cellular functions is unclear. We show that the pathogenic SRSF2P95H/+ mutation disrupts the splicing of mitochondrial mRNAs, impairs mitochondrial complex I function, and robustly increases mitophagy. We also identified a mitochondrial surveillance mechanism by which mitochondrial dysfunction modifies splicing of the mitophagy activator PINK1 to remove a poison intron, increasing the stability and abundance of PINK1 mRNA and protein. SRSF2P95H-induced mitochondrial dysfunction increased PINK1 expression through this mechanism, which is essential for survival of SRSF2P95H/+ cells. Inhibition of splicing with a glycogen synthase kinase 3 inhibitor promoted retention of the poison intron, impairing mitophagy and activating apoptosis in SRSF2P95H/+ cells. These data reveal a homeostatic mechanism for sensing mitochondrial stress through PINK1 splicing and identify increased mitophagy as a disease marker and a therapeutic vulnerability in SRSF2P95H mutant MDS and AML.
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Affiliation(s)
- Xiaolei Liu
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sudhish A. Devadiga
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert F. Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryan M. Morrow
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kevin A. Janssen
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Oz Pomp
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam A. Moverley
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chenchen Li
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicolas Skuli
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Martin Carroll
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jian Huang
- Coriell Institute for Medical Research, Camden, New Jersey, USA
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Peter S. Klein
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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11
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Bauer M, Schöbel CM, Wickenhauser C, Seliger B, Jasinski-Bergner S. Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies. Front Immunol 2024; 15:1386993. [PMID: 38736877 PMCID: PMC11082354 DOI: 10.3389/fimmu.2024.1386993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Alternative splicing (AS) is an important molecular biological mechanism regulated by complex mechanisms involving a plethora of cis and trans-acting elements. Furthermore, AS is tissue specific and altered in various pathologies, including infectious, inflammatory, and neoplastic diseases. Recently developed immuno-oncological therapies include monoclonal antibodies (mAbs) and chimeric antigen receptor (CAR) T cells targeting, among others, immune checkpoint (ICP) molecules. Despite therapeutic successes have been demonstrated, only a limited number of patients showed long-term benefit from these therapies with tumor entity-related differential response rates were observed. Interestingly, splice variants of common immunotherapeutic targets generated by AS are able to completely escape and/or reduce the efficacy of mAb- and/or CAR-based tumor immunotherapies. Therefore, the analyses of splicing patterns of targeted molecules in tumor specimens prior to therapy might help correct stratification, thereby increasing therapy success by antibody panel selection and antibody dosages. In addition, the expression of certain splicing factors has been linked with the patients' outcome, thereby highlighting their putative prognostic potential. Outstanding questions are addressed to translate the findings into clinical application. This review article provides an overview of the role of AS in (tumor) diseases, its molecular mechanisms, clinical relevance, and therapy response.
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Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Chiara-Maria Schöbel
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
- Department of Good Manufacturing Practice (GMP) Development & Advanced Therapy Medicinal Products (ATMP) Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Institute for Medical Immunology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Simon Jasinski-Bergner
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
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12
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Liu X, Devadiga SA, Stanley RF, Morrow R, Janssen K, Quesnel-Vallières M, Pomp O, Moverley AA, Li C, Skuli N, Carroll MP, Huang J, Wallace DC, Lynch KW, Abdel-Wahab O, Klein PS. A mitochondrial surveillance mechanism activated by SRSF2 mutations in hematologic malignancies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.25.546449. [PMID: 38712254 PMCID: PMC11071312 DOI: 10.1101/2023.06.25.546449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Splicing factor mutations are common in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), but how they alter cellular functions is unclear. We show that the pathogenic SRSF2P95H/+ mutation disrupts the splicing of mitochondrial mRNAs, impairs mitochondrial complex I function, and robustly increases mitophagy. We also identified a mitochondrial surveillance mechanism by which mitochondrial dysfunction modifies splicing of the mitophagy activator PINK1 to remove a poison intron, increasing the stability and abundance of PINK1 mRNA and protein. SRSF2P95H-induced mitochondrial dysfunction increased PINK1 expression through this mechanism, which is essential for survival of SRSF2P95H/+ cells. Inhibition of splicing with a glycogen synthase kinase 3 inhibitor promoted retention of the poison intron, impairing mitophagy and activating apoptosis in SRSF2P95H/+ cells. These data reveal a homeostatic mechanism for sensing mitochondrial stress through PINK1 splicing and identify increased mitophagy as a disease marker and a therapeutic vulnerability in SRSF2P95H mutant MDS and AML.
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Affiliation(s)
- Xiaolei Liu
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Sudhish A. Devadiga
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Robert F. Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Ryan Morrow
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Kevin Janssen
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Mathieu Quesnel-Vallières
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Oz Pomp
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Adam A. Moverley
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Chenchen Li
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Nicolas Skuli
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Martin P. Carroll
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Jian Huang
- Coriell Institute for Medical Research; Camden, NJ, USA
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen W. Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Peter S. Klein
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
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13
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Su M, Fleischer T, Grosheva I, Horev MB, Olszewska M, Mattioli CC, Barr H, Plotnikov A, Carvalho S, Moskovich Y, Minden MD, Chapal-Ilani N, Wainstein A, Papapetrou EP, Dezorella N, Cheng T, Kaushansky N, Geiger B, Shlush LI. Targeting SRSF2 mutations in leukemia with RKI-1447: A strategy to impair cellular division and nuclear structure. iScience 2024; 27:109443. [PMID: 38558935 PMCID: PMC10981050 DOI: 10.1016/j.isci.2024.109443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Spliceosome machinery mutations are common early mutations in myeloid malignancies; however, effective targeted therapies against them are still lacking. In the current study, we used an in vitro high-throughput drug screen among four different isogenic cell lines and identified RKI-1447, a Rho-associated protein kinase inhibitor, as selective cytotoxic effector of SRSF2 mutant cells. RKI-1447 targeted SRSF2 mutated primary human samples in xenografts models. RKI-1447 induced mitotic catastrophe and induced major reorganization of the microtubule system and severe nuclear deformation. Transmission electron microscopy and 3D light microscopy revealed that SRSF2 mutations induce deep nuclear indentation and segmentation that are apparently driven by microtubule-rich cytoplasmic intrusions, which are exacerbated by RKI-1447. The severe nuclear deformation in RKI-1447-treated SRSF2 mutant cells prevents cells from completing mitosis. These findings shed new light on the interplay between microtubules and the nucleus and offers new ways for targeting pre-leukemic SRSF2 mutant cells.
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Affiliation(s)
- Minhua Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Fleischer
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Grosheva
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Melanie Bokstad Horev
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Malgorzata Olszewska
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Plotnikov
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Carvalho
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yoni Moskovich
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON Canada
| | - Noa Chapal-Ilani
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Wainstein
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nili Dezorella
- Electron Microscopy Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Nathali Kaushansky
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Geiger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Liran I. Shlush
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
- Molecular Hematology Clinic, Maccabi Healthcare, Tel Aviv, Israel
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel
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14
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Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, Verma A, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol Cell 2024; 84:1475-1495.e18. [PMID: 38521065 PMCID: PMC11061666 DOI: 10.1016/j.molcel.2024.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
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Affiliation(s)
- Prajwal C Boddu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Rahul Roy
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Bárbara De La Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Anne Olazabal-Herrero
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Namrata S Chandhok
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Darren King
- Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Gary M Kupfer
- Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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15
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Jing Q, Zhou C, Zhang J, Zhang P, Wu Y, Zhou J, Tong X, Li Y, Du J, Wang Y. Role of reactive oxygen species in myelodysplastic syndromes. Cell Mol Biol Lett 2024; 29:53. [PMID: 38616283 PMCID: PMC11017617 DOI: 10.1186/s11658-024-00570-0] [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: 11/09/2023] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
Reactive oxygen species (ROS) serve as typical metabolic byproducts of aerobic life and play a pivotal role in redox reactions and signal transduction pathways. Contingent upon their concentration, ROS production not only initiates or stimulates tumorigenesis but also causes oxidative stress (OS) and triggers cellular apoptosis. Mounting literature supports the view that ROS are closely interwoven with the pathogenesis of a cluster of diseases, particularly those involving cell proliferation and differentiation, such as myelodysplastic syndromes (MDS) and chronic/acute myeloid leukemia (CML/AML). OS caused by excessive ROS at physiological levels is likely to affect the functions of hematopoietic stem cells, such as cell growth and self-renewal, which may contribute to defective hematopoiesis. We review herein the eminent role of ROS in the hematological niche and their profound influence on the progress of MDS. We also highlight that targeting ROS is a practical and reliable tactic for MDS therapy.
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Affiliation(s)
- Qiangan Jing
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
- HEALTH BioMed Research & Development Center, Health BioMed Co., Ltd, Ningbo, 315803, Zhejiang, China
| | - Chaoting Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Junyu Zhang
- Department of Hematology, Lishui Central Hospital, Lishui, 323000, Zhejiang, China
| | - Ping Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Yunyi Wu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Junyu Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Xiangmin Tong
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, 310006, Zhejiang, China
| | - Yanchun Li
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, 310006, Zhejiang, China.
| | - Jing Du
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.
| | - Ying Wang
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, 310006, Zhejiang, China.
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16
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Santoro N, Salutari P, Di Ianni M, Marra A. Precision Medicine Approaches in Acute Myeloid Leukemia with Adverse Genetics. Int J Mol Sci 2024; 25:4259. [PMID: 38673842 PMCID: PMC11050344 DOI: 10.3390/ijms25084259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The treatment of acute myeloid leukemia (AML) with adverse genetics remains unsatisfactory, with very low response rates to standard chemotherapy and shorter durations of remission commonly observed in these patients. The complex biology of AML with adverse genetics is continuously evolving. Herein, we discuss recent advances in the field focusing on the contribution of molecular drivers of leukemia biogenesis and evolution and on the alterations of the immune system that can be exploited with immune-based therapeutic strategies. We focus on the biological rationales for combining targeted therapy and immunotherapy, which are currently being investigated in ongoing trials, and could hopefully ameliorate the poor outcomes of patients affected by AML with adverse genetics.
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Affiliation(s)
- Nicole Santoro
- Hematology Unit, Department of Hematology and Oncology, Ospedale Civile “Santo Spirito”, 65122 Pescara, Italy; (P.S.); (M.D.I.)
| | - Prassede Salutari
- Hematology Unit, Department of Hematology and Oncology, Ospedale Civile “Santo Spirito”, 65122 Pescara, Italy; (P.S.); (M.D.I.)
| | - Mauro Di Ianni
- Hematology Unit, Department of Hematology and Oncology, Ospedale Civile “Santo Spirito”, 65122 Pescara, Italy; (P.S.); (M.D.I.)
- Department of Medicine and Science of Aging, “G.D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Andrea Marra
- Laboratory of Molecular Medicine and Biotechnology, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Institute of Translational Pharmacology, National Research Council of Italy (CNR), 00196 Rome, Italy
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17
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Rombaut D, Lefèvre C, Rached T, Bondu S, Letessier A, Mangione RM, Farhat B, Lesieur-Pasquier A, Castillo-Guzman D, Boussaid I, Friedrich C, Tourville A, De Carvalho M, Levavasseur F, Leduc M, Le Gall M, Battault S, Temple M, Houy A, Bouscary D, Willems L, Park S, Raynaud S, Cluzeau T, Clappier E, Fenaux P, Adès L, Margueron R, Wassef M, Alsafadi S, Chapuis N, Kosmider O, Solary E, Constantinou A, Stern MH, Droin N, Palancade B, Miotto B, Chédin F, Fontenay M. Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation. Nat Commun 2024; 15:3016. [PMID: 38589367 PMCID: PMC11001894 DOI: 10.1038/s41467-024-46547-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/29/2024] [Indexed: 04/10/2024] Open
Abstract
Myelodysplastic syndromes (MDS) with mutated SF3B1 gene present features including a favourable outcome distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we find that SF3B1-mutated MDS show reduced R-loop formation predominating in gene bodies associated with intron retention reduction, not found in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibit augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restores R-loop formation, slows down DNA replication forks and improves SF3B1-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress represents a hallmark of SF3B1-mutated MDS ineffective erythropoiesis, which could be used as a therapeutic target.
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Affiliation(s)
- David Rombaut
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Carine Lefèvre
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
| | - Tony Rached
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Sabrina Bondu
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Anne Letessier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | | | - Batoul Farhat
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Auriane Lesieur-Pasquier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Daisy Castillo-Guzman
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Ismael Boussaid
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Chloé Friedrich
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Aurore Tourville
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Magali De Carvalho
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Françoise Levavasseur
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marjorie Leduc
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Morgane Le Gall
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Sarah Battault
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marie Temple
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Alexandre Houy
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Didier Bouscary
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Lise Willems
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Sophie Park
- Department of Hematology, Centre Hospitalier Universitaire, Université de Grenoble Alpes, Grenoble, France
| | - Sophie Raynaud
- Laboratory of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Thomas Cluzeau
- Clinical Department of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Emmanuelle Clappier
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Laboratory of Hematology, Paris, France
| | - Pierre Fenaux
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Lionel Adès
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Raphael Margueron
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Michel Wassef
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nicolas Chapuis
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Olivier Kosmider
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Eric Solary
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nathalie Droin
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Miotto
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Michaela Fontenay
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France.
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France.
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France.
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France.
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18
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Chang J, Zhang Y, Zhou T, Qiao Q, Shan J, Chen Y, Jiang W, Wang Y, Liu S, Wang Y, Yu Y, Li C, Li X. RBM10 C761Y mutation induced oncogenic ASPM isoforms and regulated β-catenin signaling in cholangiocarcinoma. J Exp Clin Cancer Res 2024; 43:104. [PMID: 38576051 PMCID: PMC10993532 DOI: 10.1186/s13046-024-03030-x] [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: 01/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) comprises a heterogeneous group of biliary tract cancer. Our previous CCA mutation pattern study focused on genes in the post-transcription modification process, among which the alternative splicing factor RBM10 captured our attention. However, the roles of RBM10 wild type and mutations in CCA remain unclear. METHODS RBM10 mutation spectrum in CCA was clarified using our initial data and other CCA genomic datasets from domestic and international sources. Real-time PCR and tissue microarray were used to detect RBM10 clinical association. Function assays were conducted to investigate the effects of RBM10 wild type and mutations on CCA. RNA sequencing was to investigate the changes in alternative splicing events in the mutation group compared to the wild-type group. Minigene splicing reporter and interaction assays were performed to elucidate the mechanism of mutation influence on alternative splicing events. RESULTS RBM10 mutations were more common in Chinese CCA populations and exhibited more protein truncation variants. RBM10 exerted a tumor suppressive effect in CCA and correlated with favorable prognosis of CCA patients. The overexpression of wild-type RBM10 enhanced the ASPM exon18 exon skipping event interacting with SRSF2. The C761Y mutation in the C2H2-type zinc finger domain impaired its interaction with SRSF2, resulting in a loss-of-function mutation. Elevated ASPM203 stabilized DVL2 and enhanced β-catenin signaling, which promoted CCA progression. CONCLUSIONS Our results showed that RBM10C761Y-modulated ASPM203 promoted CCA progression in a Wnt/β-catenin signaling-dependent manner. This study may enhance the understanding of the regulatory mechanisms that link mutation-altering splicing variants to CCA.
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Affiliation(s)
- Jiang Chang
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Yaodong Zhang
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
- Key Laboratory for Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China.
| | - Tao Zhou
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Qian Qiao
- Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, China
| | - Jijun Shan
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Yananlan Chen
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Wangjie Jiang
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
- Key Laboratory for Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Yirui Wang
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Shuochen Liu
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Yuming Wang
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Yue Yu
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
- Key Laboratory for Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Changxian Li
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
- Key Laboratory for Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China.
| | - Xiangcheng Li
- Hepatobiliary Surgery Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
- Key Laboratory for Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China.
- Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, Wuxi, China.
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19
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Nishimura K, Saika W, Inoue D. Minor introns impact on hematopoietic malignancies. Exp Hematol 2024; 132:104173. [PMID: 38309573 DOI: 10.1016/j.exphem.2024.104173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 02/05/2024]
Abstract
In the intricate orchestration of the central dogma, pre-mRNA splicing plays a crucial role in the post-transcriptional process that transforms DNA into mature mRNA. Widely acknowledged as a pivotal RNA processing step, it significantly influences gene expression and alters the functionality of gene product proteins. Although U2-dependent spliceosomes efficiently manage the removal of over 99% of introns, a distinct subset of essential genes undergo splicing with a different intron type, denoted as minor introns, using U12-dependent spliceosomes. Mutations in spliceosome component genes are now recognized as prevalent genetic abnormalities in cancer patients, especially those with hematologic malignancies. Despite the relative rarity of minor introns, genes containing them are evolutionarily conserved and play crucial roles in functions such as the RAS-MAPK pathway. Disruptions in U12-type minor intron splicing caused by mutations in snRNA or its regulatory components significantly contribute to cancer progression. Notably, recurrent mutations associated with myelodysplastic syndrome (MDS) in the minor spliceosome component ZRSR2 underscore its significance. Examination of ZRSR2-mutated MDS cells has revealed that only a subset of minor spliceosome-dependent genes, such as LZTR1, consistently exhibit missplicing. Recent technological advancements have uncovered insights into minor introns, raising inquiries beyond current understanding. This review comprehensively explores the importance of minor intron regulation, the molecular implications of minor (U12-type) spliceosomal mutations and cis-regulatory regions, and the evolutionary progress of studies on minor, aiming to provide a sophisticated understanding of their intricate role in cancer biology.
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Affiliation(s)
- Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
| | - Wataru Saika
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan; Department of Hematology, Shiga University of Medical Science, Ōtsu, Shiga, Japan
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
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20
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Mina A, Pavletic S, Aplan PD. The evolution of preclinical models for myelodysplastic neoplasms. Leukemia 2024; 38:683-691. [PMID: 38396286 PMCID: PMC10997513 DOI: 10.1038/s41375-024-02181-2] [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: 09/20/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024]
Abstract
Myelodysplastic Neoplasms (MDS) are a group of clonal disorders characterized by ineffective hematopoiesis and morphologic dysplasia. Clinical manifestations of MDS vary widely and are dictated in large part by a range of genetic aberrations. The lack of robust in vitro models for MDS has limited the ability to conduct high throughput drug screens, which in turn has hampered the development of novel therapies for MDS. There are very few well-characterized MDS cell lines, and the available cell lines expand poorly in vitro. Conventional xenograft mouse models can provide an in vivo vessel to provide growth of cancer cells, but human MDS cells engraft poorly. Three-dimensional (3D) scaffold models that form human "ossicles" represent a promising new approach and can reproduce the intricate communication between hematopoietic stem and progenitor cells and their environment. Genetically engineered mice utilize specific mutations and may not represent the entire array of human MDS; however, genetically engineered mice provided in vivo proof of principle for novel agents such as luspatercept, demonstrating the clinical utility of this approach. This review offers an overview of available preclinical MDS models and potential approaches to accelerate accurate clinical translation.
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Affiliation(s)
- Alain Mina
- Myeloid Malignancies Program, Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Steven Pavletic
- Myeloid Malignancies Program, Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Aplan
- Myeloid Malignancies Program, Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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21
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Jiang Y, Li H, Li Z, Du S, Zhang R, Zhao Y, Christiani DC, Shen S, Chen F. A cross-trait study of lung cancer and its related respiratory diseases based on large-scale exome sequencing population. Transl Lung Cancer Res 2024; 13:512-525. [PMID: 38601445 PMCID: PMC11002514 DOI: 10.21037/tlcr-24-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/27/2024] [Indexed: 04/12/2024]
Abstract
Background Genome-wide association studies (GWASs) explain the genetic susceptibility between diseases and common variants. Nevertheless, with the appearance of large-scale sequencing profiles, we could explore the rare coding variants in disease pathogenesis. Methods We estimated the genetic correlation of nine respiratory diseases and lung cancer in the UK Biobank (UKB) by linkage disequilibrium score regression (LDSC). Then, we performed exome-wide association studies at single-variant level and gene-level for lung cancer and lung cancer-related respiratory diseases using the whole-exome sequencing (WES) data of 427,934 European participants. Cross-trait meta-analysis was conducted by association analysis based on subsets (ASSET) to identify the pleiotropic variants, while in-silico functional analysis was performed to explore their function. Causal mediation analysis was used to explore whether these pleiotropic variants lead to lung cancer is mediated by affecting the chronic respiratory diseases. Results Five respiratory diseases [emphysema, pneumonia, asthma, chronic obstructive pulmonary disease (COPD), and fibrosis] were genetically correlated with lung cancer. We identified 102 significant independent variants at single-variant levels for lung cancer and five lung cancer-related diseases. 15:78590583:G>A (missense variant in CHRNA5) was shared in lung cancer, emphysema, and COPD. Meanwhile, 14 significant genes and 87 suggestive genes were identified in gene-based association tests, including HSD3B7 (lung cancer), SRSF2 (pneumonia), TNXB (asthma), TERT (fibrosis), MOSPD3 (emphysema). Based on the cross-trait meta-analysis, we detected 145 independent pleiotropic variants. We further identified abundant pathways with significant enrichment effects, demonstrating that these pleiotropic genes were functional. Meanwhile, the proportion of mediation effects of these variants ranged from 6 to 23 (emphysema: 23%; COPD: 20%; pneumonia: 20%; fibrosis: 7%; asthma: 6%) through these five respiratory diseases to the incidence of lung cancer. Conclusions The identified shared genetic variants, genes, biological pathways, and potential intermediate causal pathways provide a basis for further exploration of the relationship between lung cancer and respiratory diseases.
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Affiliation(s)
- Yunke Jiang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hongru Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zaiming Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sha Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing, China
| | - David C. Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing, China
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22
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de Jong MME, Chen L, Raaijmakers MHGP, Cupedo T. Bone marrow inflammation in haematological malignancies. Nat Rev Immunol 2024:10.1038/s41577-024-01003-x. [PMID: 38491073 DOI: 10.1038/s41577-024-01003-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
Tissue inflammation is a hallmark of tumour microenvironments. In the bone marrow, tumour-associated inflammation impacts normal niches for haematopoietic progenitor cells and mature immune cells and supports the outgrowth and survival of malignant cells residing in these niche compartments. This Review provides an overview of our current understanding of inflammatory changes in the bone marrow microenvironment of myeloid and lymphoid malignancies, using acute myeloid leukaemia and multiple myeloma as examples and highlights unique and shared features of inflammation in niches for progenitor cells and plasma cells. Importantly, inflammation exerts profoundly different effects on normal bone marrow niches in these malignancies, and we provide context for possible drivers of these divergent effects. We explore the role of tumour cells in inflammatory changes, as well as the role of cellular constituents of normal bone marrow niches, including myeloid cells and stromal cells. Integrating knowledge of disease-specific dynamics of malignancy-associated bone marrow inflammation will provide a necessary framework for future targeting of these processes to improve patient outcome.
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Affiliation(s)
- Madelon M E de Jong
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Lanpeng Chen
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Tom Cupedo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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23
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Lv Y, Li J, Yu S, Zhang Y, Hu H, Sun K, Jia D, Han Y, Tu J, Huang Y, Liu X, Zhang X, Gao P, Chen X, Shaw Williams MT, Tang Z, Shu X, Liu M, Ren X. The splicing factor Prpf31 is required for hematopoietic stem and progenitor cell expansion during zebrafish embryogenesis. J Biol Chem 2024; 300:105772. [PMID: 38382674 PMCID: PMC10959673 DOI: 10.1016/j.jbc.2024.105772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Pre-mRNA splicing is a precise regulated process and is crucial for system development and homeostasis maintenance. Mutations in spliceosomal components have been found in various hematopoietic malignancies (HMs) and have been considered as oncogenic derivers of HMs. However, the role of spliceosomal components in normal and malignant hematopoiesis remains largely unknown. Pre-mRNA processing factor 31 (PRPF31) is a constitutive spliceosomal component, which mutations are associated with autosomal dominant retinitis pigmentosa. PRPF31 was found to be mutated in several HMs, but the function of PRPF31 in normal hematopoiesis has not been explored. In our previous study, we generated a prpf31 knockout (KO) zebrafish line and reported that Prpf31 regulates the survival and differentiation of retinal progenitor cells by modulating the alternative splicing of genes involved in mitosis and DNA repair. In this study, by using the prpf31 KO zebrafish line, we discovered that prpf31 KO zebrafish exhibited severe defects in hematopoietic stem and progenitor cell (HSPC) expansion and its sequentially differentiated lineages. Immunofluorescence results showed that Prpf31-deficient HSPCs underwent malformed mitosis and M phase arrest during HSPC expansion. Transcriptome analysis and experimental validations revealed that Prpf31 deficiency extensively perturbed the alternative splicing of mitosis-related genes. Collectively, our findings elucidate a previously undescribed role for Prpf31 in HSPC expansion, through regulating the alternative splicing of mitosis-related genes.
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Affiliation(s)
- Yuexia Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Department of Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hualei Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xianghan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mark Thomas Shaw Williams
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xinhua Shu
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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24
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Naro C, Antonioni A, Medici V, Caggiano C, Jolly A, de la Grange P, Bielli P, Paronetto MP, Sette C. Splicing targeting drugs highlight intron retention as an actionable vulnerability in advanced prostate cancer. J Exp Clin Cancer Res 2024; 43:58. [PMID: 38413979 PMCID: PMC10898177 DOI: 10.1186/s13046-024-02986-0] [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: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Advanced prostate cancer (PC) is characterized by insensitivity to androgen deprivation therapy and chemotherapy, resulting in poor outcome for most patients. Thus, advanced PC urgently needs novel therapeutic strategies. Mounting evidence points to splicing dysregulation as a hallmark of advanced PC. Moreover, pharmacologic inhibition of the splicing process is emerging as a promising option for this disease. METHOD By using a representative androgen-insensitive PC cell line (22Rv1), we have investigated the genome-wide transcriptomic effects underlying the cytotoxic effects exerted by three splicing-targeting drugs: Pladienolide B, indisulam and THZ531. Bioinformatic analyses were performed to uncover the gene structural features underlying sensitivity to transcriptional and splicing regulation by these treatments. Biological pathways altered by these treatments were annotated by gene ontology analyses and validated by functional experiments in cell models. RESULTS Although eliciting similar cytotoxic effects on advanced PC cells, Pladienolide B, indisulam and THZ531 modulate specific transcriptional and splicing signatures. Drug sensitivity is associated with distinct gene structural features, expression levels and cis-acting sequence elements in the regulated exons and introns. Importantly, we identified PC-relevant genes (i.e. EZH2, MDM4) whose drug-induced splicing alteration exerts an impact on cell survival. Moreover, computational analyses uncovered a widespread impact of splicing-targeting drugs on intron retention, with enrichment in genes implicated in pre-mRNA 3'-end processing (i.e. CSTF3, PCF11). Coherently, advanced PC cells displayed high sensitivity to a specific inhibitor of the cleavage and polyadenylation complex, which enhances the effects of chemotherapeutic drugs that are already in use for this cancer. CONCLUSIONS Our study uncovers intron retention as an actionable vulnerability for advanced PC, which may be exploited to improve therapeutic management of this currently incurable disease.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | - Ambra Antonioni
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Vanessa Medici
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | | | | | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
- University of Rome Foro Italico, 00135, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy.
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy.
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25
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Liu ZS, Sinha S, Bannister M, Song A, Arriaga-Gomez E, McKeeken AJ, Bonner EA, Hanson BK, Sarchi M, Takashima K, Zong D, Corral VM, Nguyen E, Yoo J, Chiraphapphaiboon W, Leibson C, McMahon MC, Rai S, Swisher EM, Sachs Z, Chatla S, Stirewalt DL, Deeg HJ, Skorski T, Papapetrou EP, Walter MJ, Graubert TA, Doulatov S, Lee SC, Nguyen HD. R-Loop Accumulation in Spliceosome Mutant Leukemias Confers Sensitivity to PARP1 Inhibition by Triggering Transcription-Replication Conflicts. Cancer Res 2024; 84:577-597. [PMID: 37967363 PMCID: PMC10922727 DOI: 10.1158/0008-5472.can-23-3239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023]
Abstract
RNA splicing factor (SF) gene mutations are commonly observed in patients with myeloid malignancies. Here we showed that SRSF2- and U2AF1-mutant leukemias are preferentially sensitive to PARP inhibitors (PARPi), despite being proficient in homologous recombination repair. Instead, SF-mutant leukemias exhibited R-loop accumulation that elicited an R-loop-associated PARP1 response, rendering cells dependent on PARP1 activity for survival. Consequently, PARPi induced DNA damage and cell death in SF-mutant leukemias in an R-loop-dependent manner. PARPi further increased aberrant R-loop levels, causing higher transcription-replication collisions and triggering ATR activation in SF-mutant leukemias. Ultimately, PARPi-induced DNA damage and cell death in SF-mutant leukemias could be enhanced by ATR inhibition. Finally, the level of PARP1 activity at R-loops correlated with PARPi sensitivity, suggesting that R-loop-associated PARP1 activity could be predictive of PARPi sensitivity in patients harboring SF gene mutations. This study highlights the potential of targeting different R-loop response pathways caused by spliceosome gene mutations as a therapeutic strategy for treating cancer. SIGNIFICANCE Spliceosome-mutant leukemias accumulate R-loops and require PARP1 to resolve transcription-replication conflicts and genomic instability, providing rationale to repurpose FDA-approved PARP inhibitors for patients carrying spliceosome gene mutations.
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Affiliation(s)
- Zhiyan Silvia Liu
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- These authors contributed equally
| | - Sayantani Sinha
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Maxwell Bannister
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Axia Song
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erica Arriaga-Gomez
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alexander J. McKeeken
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A. Bonner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Benjamin K. Hanson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Martina Sarchi
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Molecular Medicine, University of Pavia, 27100 Pavia PV, Italy
| | - Kouhei Takashima
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Regenerative Medicine and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawei Zong
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Victor M. Corral
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Evan Nguyen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jennifer Yoo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | | | - Cassandra Leibson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Matthew C. McMahon
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Sumit Rai
- Massachusetts General Hospital Cancer Center, Charlestown, MA
| | - Elizabeth M. Swisher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98195
| | - Zohar Sachs
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Srinivas Chatla
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Derek L. Stirewalt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - H. Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Regenerative Medicine and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J. Walter
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | - Sergei Doulatov
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Stanley C. Lee
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Hai Dang Nguyen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
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26
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Venkatasubramanian M, Schwartz L, Ramachandra N, Bennett J, Subramanian KR, Chen X, Gordon-Mitchell S, Fromowitz A, Pradhan K, Shechter D, Sahu S, Heiser D, Scherle P, Chetal K, Kulkarni A, Myers KC, Weirauch MT, Grimes HL, Starczynowski DT, Verma A, Salomonis N. Broad de-regulated U2AF1 splicing is prognostic and augments leukemic transformation via protein arginine methyltransferase activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578798. [PMID: 38370617 PMCID: PMC10871255 DOI: 10.1101/2024.02.04.578798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations is poorly understood. To reveal complex patient subtypes and putative regulators of pathogenic splicing in Acute Myeloid Leukemia (AML), we developed a new approach called OncoSplice. Among diverse new subtypes, OncoSplice identified a biphasic poor prognosis signature that partially phenocopies U2AF1-mutant splicing, impacting thousands of genes in over 40% of adult and pediatric AML cases. U2AF1-like splicing co-opted a healthy circadian splicing program, was stable over time and induced a leukemia stem cell (LSC) program. Pharmacological inhibition of the implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia mis-splicing and inhibited leukemic cell growth. Genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treated cells, blocked leukemia development in xenograft models and induced differentiation. These analyses reveal a new prognostic alternative-splicing mechanism in malignancy, independent of splicing-factor mutations.
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Affiliation(s)
- Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
| | - Leya Schwartz
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Nandini Ramachandra
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Joshua Bennett
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Krithika R. Subramanian
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Xiaoting Chen
- Divisions of Human Genetics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Shanisha Gordon-Mitchell
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Ariel Fromowitz
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Kith Pradhan
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - David Shechter
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Srabani Sahu
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Diane Heiser
- Prelude Therapeutics Incorporated, Wilmington, DE
| | | | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Aishwarya Kulkarni
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
| | - Kasiani C. Myers
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Matthew T. Weirauch
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Divisions of Human Genetics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - H. Leighton Grimes
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Daniel T. Starczynowski
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Amit Verma
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
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27
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Miano M, Bertola N, Grossi A, Dell’Orso G, Regis S, Rusmini M, Uva P, Vozzi D, Fioredda F, Palmisani E, Lupia M, Lanciotti M, Grilli F, Corsolini F, Arcuri L, Giarratana MC, Ceccherini I, Dufour C, Cappelli E, Ravera S. Impaired Mitochondrial Function and Marrow Failure in Patients Carrying a Variant of the SRSF4 Gene. Int J Mol Sci 2024; 25:2083. [PMID: 38396760 PMCID: PMC10888539 DOI: 10.3390/ijms25042083] [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: 12/12/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Serine/arginine-rich splicing factors (SRSFs) are a family of proteins involved in RNA metabolism, including pre-mRNA constitutive and alternative splicing. The role of SRSF proteins in regulating mitochondrial activity has already been shown for SRSF6, but SRSF4 altered expression has never been reported as a cause of bone marrow failure. An 8-year-old patient admitted to the hematology unit because of leukopenia, lymphopenia, and neutropenia showed a missense variant of unknown significance of the SRSF4 gene (p.R235W) found via whole genome sequencing analysis and inherited from the mother who suffered from mild leuko-neutropenia. Both patients showed lower SRSF4 protein expression and altered mitochondrial function and energetic metabolism in primary lymphocytes and Epstein-Barr-virus (EBV)-immortalized lymphoblasts compared to healthy donor (HD) cells, which appeared associated with low mTOR phosphorylation and an imbalance in the proteins regulating mitochondrial biogenesis (i.e., CLUH) and dynamics (i.e., DRP1 and OPA1). Transfection with the wtSRSF4 gene restored mitochondrial function. In conclusion, this study shows that the described variant of the SRSF4 gene is pathogenetic and causes reduced SRSF4 protein expression, which leads to mitochondrial dysfunction. Since mitochondrial function is crucial for hematopoietic stem cell maintenance and some genetic bone marrow failure syndromes display mitochondrial defects, the SRSF4 mutation could have substantially contributed to the clinical phenotype of our patient.
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Affiliation(s)
- Maurizio Miano
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Nadia Bertola
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Alice Grossi
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.G.); (M.R.); (I.C.)
| | - Gianluca Dell’Orso
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Stefano Regis
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Marta Rusmini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.G.); (M.R.); (I.C.)
| | - Paolo Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Diego Vozzi
- Genomics Facility, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy;
| | - Francesca Fioredda
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Elena Palmisani
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Michela Lupia
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Marina Lanciotti
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Federica Grilli
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Fabio Corsolini
- Laboratory for the Study of Inborn Errors of Metabolism (LABSIEM), Pediatric Clinic and Endocrinology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Luca Arcuri
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Maria Carla Giarratana
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Isabella Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.G.); (M.R.); (I.C.)
| | - Carlo Dufour
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Enrico Cappelli
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Silvia Ravera
- Department of Experimental Medicine, University of Genoa, 16132 Genoa, Italy;
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28
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Sui P, Ge G, Chen S, Bai J, Rubalcava IP, Yang H, Guo Y, Zhang P, Li Y, Medina EA, Xu M, Abdel-Wahab O, Bradley R, Yang FC. SRSF2 mutation cooperates with ASXL1 truncated alteration to accelerate leukemogenesis. Leukemia 2024; 38:408-411. [PMID: 38017104 PMCID: PMC10844088 DOI: 10.1038/s41375-023-02094-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/30/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Affiliation(s)
- Pinpin Sui
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Guo Ge
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Shi Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jiaojiao Bai
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ivan P Rubalcava
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hui Yang
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ying Guo
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Peng Zhang
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ying Li
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Edward A Medina
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Mingjiang Xu
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Feng-Chun Yang
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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29
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Jaiswal AK, Thaxton ML, Scherer GM, Sorrentino JP, Garg NK, Rao DS. Small molecule inhibition of RNA binding proteins in haematologic cancer. RNA Biol 2024; 21:1-14. [PMID: 38329136 PMCID: PMC10857685 DOI: 10.1080/15476286.2024.2303558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
In recent years, advances in biomedicine have revealed an important role for post-transcriptional mechanisms of gene expression regulation in pathologic conditions. In cancer in general and leukaemia specifically, RNA binding proteins have emerged as important regulator of RNA homoeostasis that are often dysregulated in the disease state. Having established the importance of these pathogenetic mechanisms, there have been a number of efforts to target RNA binding proteins using oligonucleotide-based strategies, as well as with small organic molecules. The field is at an exciting inflection point with the convergence of biomedical knowledge, small molecule screening strategies and improved chemical methods for synthesis and construction of sophisticated small molecules. Here, we review the mechanisms of post-transcriptional gene regulation, specifically in leukaemia, current small-molecule based efforts to target RNA binding proteins, and future prospects.
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Affiliation(s)
- Amit K. Jaiswal
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Michelle L. Thaxton
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Georgia M. Scherer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Jacob P. Sorrentino
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Neil K. Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dinesh S. Rao
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
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30
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Zavileyskiy LG, Pervouchine DD. Post-transcriptional Regulation of Gene Expression via Unproductive Splicing. Acta Naturae 2024; 16:4-13. [PMID: 38698955 PMCID: PMC11062102 DOI: 10.32607/actanaturae.27337] [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: 12/03/2023] [Accepted: 03/01/2024] [Indexed: 05/05/2024] Open
Abstract
Unproductive splicing is a mechanism of post-transcriptional gene expression control in which premature stop codons are inserted into protein-coding transcripts as a result of regulated alternative splicing, leading to their degradation via the nonsense-mediated decay pathway. This mechanism is especially characteristic of RNA-binding proteins, which regulate each other's expression levels and those of other genes in multiple auto- and cross-regulatory loops. Deregulation of unproductive splicing is a cause of serious human diseases, including cancers, and is increasingly being considered as a prominent therapeutic target. This review discusses the types of unproductive splicing events, the mechanisms of auto- and cross-regulation, nonsense-mediated decay escape, and problems in identifying unproductive splice isoforms. It also provides examples of deregulation of unproductive splicing in human diseases and discusses therapeutic strategies for its correction using antisense oligonucleotides and small molecules.
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Affiliation(s)
- L. G. Zavileyskiy
- Lomonosov Moscow State University, Moscow, 119192 Russian Federation
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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31
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Malakar P, Shukla S, Mondal M, Kar RK, Siddiqui JA. The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. RNA Biol 2024; 21:1-20. [PMID: 38017665 PMCID: PMC10761143 DOI: 10.1080/15476286.2023.2286099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
The process of alternative splicing (AS) is widely deregulated in a variety of cancers. Splicing is dependent upon splicing factors. Recently, several long noncoding RNAs (lncRNAs) have been shown to regulate AS by directly/indirectly interacting with splicing factors. This review focuses on the regulation of AS by lncRNAs through their interaction with splicing factors. AS mis-regulation caused by either mutation in splicing factors or deregulated expression of splicing factors and lncRNAs has been shown to be involved in cancer development and progression, making aberrant splicing, splicing factors and lncRNA suitable targets for cancer therapy. This review also addresses some of the current approaches used to target AS, splicing factors and lncRNAs. Finally, we discuss research challenges, some of the unanswered questions in the field and provide recommendations to advance understanding of the nexus of lncRNAs, AS and splicing factors in cancer.
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Affiliation(s)
- Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Meghna Mondal
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Rajesh Kumar Kar
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
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32
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Tatwavedi D, Pellagatti A, Boultwood J. Recent advances in the application of induced pluripotent stem cell technology to the study of myeloid malignancies. Adv Biol Regul 2024; 91:100993. [PMID: 37827894 DOI: 10.1016/j.jbior.2023.100993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Acquired myeloid malignancies are a spectrum of clonal disorders known to be caused by sequential acquisition of genetic lesions in hematopoietic stem and progenitor cells, leading to their aberrant self-renewal and differentiation. The increasing use of induced pluripotent stem cell (iPSC) technology to study myeloid malignancies has helped usher a paradigm shift in approaches to disease modeling and drug discovery, especially when combined with gene-editing technology. The process of reprogramming allows for the capture of the diversity of genetic lesions and mutational burden found in primary patient samples into individual stable iPSC lines. Patient-derived iPSC lines, owing to their self-renewal and differentiation capacity, can thus be a homogenous source of disease relevant material that allow for the study of disease pathogenesis using various functional read-outs. Furthermore, genome editing technologies like CRISPR/Cas9 enable the study of the stepwise progression from normal to malignant hematopoiesis through the introduction of specific driver mutations, individually or in combination, to create isogenic lines for comparison. In this review, we survey the current use of iPSCs to model acquired myeloid malignancies including myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), acute myeloid leukemia and MDS/MPN overlap syndromes. The use of iPSCs has enabled the interrogation of the underlying mechanism of initiation and progression driving these diseases. It has also made drug testing, repurposing, and the discovery of novel therapies for these diseases possible in a high throughput setting.
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Affiliation(s)
- Dharamveer Tatwavedi
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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33
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Ma HL, Bizet M, Soares Da Costa C, Murisier F, de Bony EJ, Wang MK, Yoshimi A, Lin KT, Riching KM, Wang X, Beckman JI, Arya S, Droin N, Calonne E, Hassabi B, Zhang QY, Li A, Putmans P, Malbec L, Hubert C, Lan J, Mies F, Yang Y, Solary E, Daniels DL, Gupta YK, Deplus R, Abdel-Wahab O, Yang YG, Fuks F. SRSF2 plays an unexpected role as reader of m 5C on mRNA, linking epitranscriptomics to cancer. Mol Cell 2023; 83:4239-4254.e10. [PMID: 38065062 PMCID: PMC11090011 DOI: 10.1016/j.molcel.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here, we identify serine/arginine-rich splicing factor 2 (SRSF2) as a reader of m5C and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and the impact of the prevalent leukemia-associated mutation SRSF2P95H. We show that SRSF2 binding and m5C colocalize within transcripts. Furthermore, knocking down the m5C writer NSUN2 decreases mRNA m5C, reduces SRSF2 binding, and alters RNA splicing. We also show that the SRSF2P95H mutation impairs the ability of the protein to read m5C-marked mRNA, notably reducing its binding to key leukemia-related transcripts in leukemic cells. In leukemia patients, low NSUN2 expression leads to mRNA m5C hypomethylation and, combined with SRSF2P95H, predicts poor outcomes. Altogether, we highlight an unrecognized mechanistic link between epitranscriptomics and a key oncogenesis driver.
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Affiliation(s)
- Hai-Li Ma
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Christelle Soares Da Costa
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédéric Murisier
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Eric James de Bony
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Meng-Ke Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Akihide Yoshimi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Xing Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - John I Beckman
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Shailee Arya
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nathalie Droin
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Qing-Yang Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Ang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Lionel Malbec
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Céline Hubert
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédérique Mies
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Eric Solary
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | | | - Yogesh K Gupta
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China.
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium.
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Yang Y, Abbas S, Sayem MA, Dutta A, Mohi G. SRSF2 mutation reduces polycythemia and impairs hematopoietic progenitor functions in JAK2V617F-driven myeloproliferative neoplasm. Blood Cancer J 2023; 13:171. [PMID: 38012156 PMCID: PMC10682023 DOI: 10.1038/s41408-023-00947-y] [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: 09/06/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
SRSF2 mutations are found in association with JAK2V617F in myeloproliferative neoplasms (MPN), most frequently in myelofibrosis (MF). However, the contribution of SRSF2 mutation in JAK2V617F-driven MPN remains elusive. To investigate the consequences of SRSF2P95H and JAK2V617F mutations in MPN, we generated Cre-inducible Srsf2P95H/+Jak2V617F/+ knock-in mice. We show that co-expression of Srsf2P95H mutant reduced red blood cell, neutrophil, and platelet counts, attenuated splenomegaly but did not induce bone marrow fibrosis in Jak2V617F/+ mice. Furthermore, co-expression of Srsf2P95H diminished the competitiveness of Jak2V617F mutant hematopoietic stem/progenitor cells. We found that Srsf2P95H mutant reduced the TGF-β levels but increased the expression of S100A8 and S100A9 in Jak2V617F/+ mice. Furthermore, enforced expression of S100A9 in Jak2V617F/+ mice bone marrow significantly reduced the red blood cell, hemoglobin, and hematocrit levels. Overall, these data suggest that concurrent expression of Srsf2P95H and Jak2V617F mutants reduces erythropoiesis but does not promote the development of bone marrow fibrosis in mice.
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Affiliation(s)
- Yue Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Salar Abbas
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Mohammad A Sayem
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Avik Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Golam Mohi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- University of Virginia Cancer Center, Charlottesville, VA, 22908, USA.
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35
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Kfoury YS, Ji F, Jain E, Mazzola M, Schiroli G, Papazian A, Mercier F, Sykes DB, Kiem A, Randolph M, Calvi LM, Abdel-Wahab O, Sadreyev RI, Scadden DT. The bone marrow stroma in human myelodysplastic syndrome reveals alterations that regulate disease progression. Blood Adv 2023; 7:6608-6623. [PMID: 37450380 PMCID: PMC10628805 DOI: 10.1182/bloodadvances.2022008268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 06/14/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Myelodysplastic syndromes (MDSs) are a heterogenous group of diseases affecting the hematopoietic stem cell that are curable only by stem cell transplantation. Both hematopoietic cell intrinsic changes and extrinsic signals from the bone marrow (BM) niche seem to ultimately lead to MDS. Animal models of MDS indicate that alterations in specific mesenchymal progenitor subsets in the BM microenvironment can induce or select for abnormal hematopoietic cells. Here, we identify a subset of human BM mesenchymal cells marked by the expression of CD271, CD146, and CD106. This subset of human mesenchymal cells is comparable with mouse mesenchymal cells that, when perturbed, result in an MDS-like syndrome. Its transcriptional analysis identified Osteopontin (SPP1) as the most overexpressed gene. Selective depletion of Spp1 in the microenvironment of the mouse MDS model, Vav-driven Nup98-HoxD13, resulted in an accelerated progression as demonstrated by increased chimerism, higher mutant myeloid cell burden, and a more pronounced anemia when compared with that in wild-type microenvironment controls. These data indicate that molecular perturbations can occur in specific BM mesenchymal subsets of patients with MDS. However, the niche adaptations to dysplastic clones include Spp1 overexpression that can constrain disease fitness and potentially progression. Therefore, niche changes with malignant disease can also serve to protect the host.
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Affiliation(s)
- Youmna S. Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Esha Jain
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Michael Mazzola
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - Ani Papazian
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - Francois Mercier
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - David B. Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - Anna Kiem
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - Mark Randolph
- Division of Plastic and Reconstructive surgery, Massachusetts General Hospital, Boston, MA
| | - Laura M. Calvi
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY
| | - Omar Abdel-Wahab
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ruslan I. Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - David T. Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
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36
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Tatarian J, Tupper N, Li P, Feusier J, Abdo M, Hyter S, Gonzales PR, Zhang D, Woodroof J, Kelting S, Godwin AK, Cui W. Morphologic, immunophenotypic, molecular genetic, and clinical characterization in patients with SRSF2-mutated acute myeloid leukemia. Am J Clin Pathol 2023; 160:490-499. [PMID: 37458189 PMCID: PMC10629464 DOI: 10.1093/ajcp/aqad077] [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: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 09/21/2023] Open
Abstract
OBJECTIVES SRSF2 mutations are known to be associated with poor outcomes in myelodysplastic neoplasm, but studies on their prognostic impact on acute myeloid leukemia (AML) remain limited. In this retrospective study, we analyzed clinical and pathologic characteristics of patients with AML and correlated the outcomes with SRSF2 mutations. METHODS We characterized the morphologic, immunophenotypic, molecular, and clinical findings in AML with mutated SRSF2 and compared them with SRSF2 wild-type (WT) myeloid neoplasms (MNs). RESULTS Using next-generation sequencing, we identified 134 patients with MNs and SRSF2 mutations (85 with AML and 49 with MNs) in addition to 342 SRSF2-WT AMLs. Fifty-two (62%) patients with altered SRSF2 demonstrated a variable degree of morphologic dysplasia. The most frequent immunophenotypic aberrancies in SRSF2-mutant AML included diminished CD33 expression and overexpression of CD7, CD56, or CD123, similar to WT AML. More IDH1/2 (P = .015) and NPM1 (P = .002) mutations were seen in SRSF2-mutant AML than in SRSF2-mutant non-AML. Further, more IDH1/2, ASXL1, RUNX1, and STAG2 mutations were observed in SRSF2-mutant AML than in SRSF2-WT AML (P < .0001 to P = .001). Finally, patients with SRSF2-mutant AML showed a significantly worse overall survival (OS) than patients with SRSF2-WT AML (P < .0001), but this worse OS appeared to be rescued by allogeneic stem cell transplant (allo-SCT). CONCLUSIONS Acute myeloid leukemia with altered SRSF2 shows a variable degree of morphologic dysplasia without uniform immunophenotypic aberrancies. SRSF2 mutations appear to be independent poor prognostic factors, but allo-SCT has improved the clinical outcomes in patients with SRSF2-mutant AML.
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Affiliation(s)
- Joshua Tatarian
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Natalie Tupper
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Peng Li
- Division of Hematopathology, Department of Pathology, University of Utah, Salt Lake City, UT, US
| | - Julie Feusier
- Division of Hematopathology, Department of Pathology, University of Utah, Salt Lake City, UT, US
| | - Maryam Abdo
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Stephen Hyter
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Patrick R Gonzales
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Da Zhang
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Janet Woodroof
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Sarah Kelting
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Andrew K Godwin
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Wei Cui
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
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Croucher PJP, Ridinger M, Becker PS, Lin TL, Silberman SL, Wang ES, Zeidan AM. Spliceosome mutations are associated with clinical response in a phase 1b/2 study of the PLK1 inhibitor onvansertib in combination with decitabine in relapsed or refractory acute myeloid leukemia. Ann Hematol 2023; 102:3049-3059. [PMID: 37702821 PMCID: PMC10567832 DOI: 10.1007/s00277-023-05442-9] [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: 08/10/2023] [Accepted: 09/03/2023] [Indexed: 09/14/2023]
Abstract
PLK1 is overexpressed in acute myeloid leukemia (AML). A phase 1b trial of the PLK1 inhibitor onvansertib (ONV) combined with decitabine (DAC) demonstrated initial safety and efficacy in patients with relapsed/refractory (R/R) AML. The current study aimed to identify molecular predictors of response to ONV + DAC in R/R AML patients. A total of 44 R/R AML patients were treated with ONV + DAC and considered evaluable for efficacy. Bone marrow (BM) samples were collected at baseline for genomic and transcriptomic analysis (n = 32). A 10-gene expression signature, predictive of response to ONV + DAC, was derived from the leading-edge genes of gene set enrichment analyses (GSEA). The gene signature was evaluated in independent datasets and used to identify associated mutated genes. Twenty percent of the patients achieved complete remission, with or without hematologic count recovery (CR/CRi), and 32% exhibited a ≥50% reduction in bone marrow blasts. Patients who responded to treatment had elevated mitochondrial function and OXPHOS. The gene signature was not associated with response to DAC alone in an independent dataset. By applying the signature to the BeatAML cohort (n = 399), we identified a positive association between predicted ONV + DAC response and mutations in splicing factors (SF). In the phase 1b/2 trial, patients with SF mutations (SRSF2, SF3B1) had a higher CR/CRi rate (50%) compared to those without SF mutations (9%). PLK1 inhibition with ONV in combination with DAC could be a potential therapy in R/R AML patients, particularly those with high OXPHOS gene expression and SF mutations.
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Affiliation(s)
- Peter J P Croucher
- Cardiff Oncology Inc., 11055 Flintkote Avenue, San Diego, CA, 92121, USA
| | - Maya Ridinger
- Cardiff Oncology Inc., 11055 Flintkote Avenue, San Diego, CA, 92121, USA
| | - Pamela S Becker
- Leukemia Division, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Tara L Lin
- Division of Hematologic Malignancies and Cellular Therapeutics, University of Kansas, Kansas City, KS, 66205, USA
| | | | - Eunice S Wang
- Leukemia Service, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Amer M Zeidan
- Yale University and Yale Cancer Center, New Haven, 333 Cedar Street, PO Box 208028, New Haven, CT, 06520-8028, USA.
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38
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Haque T, Cadenas FL, Xicoy B, Alfonso-Pierola A, Platzbecker U, Avivi I, Brunner AM, Chromik J, Morillo D, Patel MR, Falantes J, Leitch HA, Germing U, Preis M, Lenox L, Lauring J, Brown RJ, Kalota A, Mehta J, Pastore F, Gu J, Mistry P, Valcárcel D. Phase 1 study of JNJ-64619178, a protein arginine methyltransferase 5 inhibitor, in patients with lower-risk myelodysplastic syndromes. Leuk Res 2023; 134:107390. [PMID: 37776843 DOI: 10.1016/j.leukres.2023.107390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/22/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023]
Abstract
Splicing factor (SF) gene mutations are frequent in myelodysplastic syndromes (MDS), and agents that modulate RNA splicing are hypothesized to provide clinical benefit. JNJ-64619178, a protein arginine methyltransferase 5 (PRMT5) inhibitor, was evaluated in patients with lower-risk (LR) MDS in a multi-part, Phase 1, multicenter study. The objectives were to determine a tolerable dose and to characterize safety, pharmacokinetics, pharmacodynamics, and preliminary clinical activity. JNJ-64619178 was administered on a 14 days on/7 days off schedule or every day on a 21-day cycle to patients with International Prognostic Scoring System (IPSS) Low or Intermediate-1 risk MDS who were red blood cell transfusion-dependent. Twenty-four patients were enrolled; 15 (62.5 %) patients had low IPSS risk score, while 18 (75.0 %) had an SF3B1 mutation. Median duration of treatment was 3.45 months (range: 0.03-6.93). No dose limiting toxicities were observed. The 0.5 mg once daily dose was considered better tolerated and chosen for dose expansion. Twenty-three (95.8 %) patients experienced treatment-emergent adverse events (TEAE). The most common TEAEs were neutropenia (15 [62.5 %]) and thrombocytopenia (14 [58.3 %]). JNJ-64619178 pharmacokinetics was dose-dependent. Target engagement as measured by plasma symmetric di-methylarginine was observed across all dose levels; however, variant allele frequency of clonal mutations in bone marrow or blood did not show sustained reductions from baseline. No patient achieved objective response or hematologic improvement per International Working Group 2006 criteria, or transfusion independence. A tolerable dose of JNJ-64619178 was identified in patients with LR MDS. However, no evidence of clinical benefit was observed.
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Affiliation(s)
| | | | - Blanca Xicoy
- Institut Català d'Oncologia, Hospital Germans Trias I Pujol, Badalona, Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | | | - Irit Avivi
- Sourasky Medical Center, Tel Aviv, Israel
| | | | | | - Daniel Morillo
- University Hospital Fundación Jiménez Díaz, START Madrid-FJD early phase unit, Spain
| | - Manish R Patel
- Florida Cancer Specialists/Sarah Cannon Research Institute, Sarasota, FL, USA
| | - Jose Falantes
- Servicio de Hematologia, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS) / CSIC, Universidad de Sevilla, Spain
| | - Heather A Leitch
- St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich Germing
- Universitätsklinikum Düsseldorf, Department of Hematology, Oncology and Clinical Immunology, Düsseldorf, Germany
| | | | | | | | | | | | | | | | | | | | - David Valcárcel
- Hematology Department, Vall d'Hebron Institute Oncology (VHIO), Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
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Fontenay M, Boussaid I, Chapuis N. [Pathophysiology of myelodysplastic syndromes]. Bull Cancer 2023; 110:1097-1105. [PMID: 37423830 DOI: 10.1016/j.bulcan.2023.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/15/2023] [Indexed: 07/11/2023]
Abstract
During aging, the onset of mutations at low frequency in hematopoietic cells or clonal hematopoiesis of indeterminate significance favors the evolution towards hemopathies such as myelodysplastic syndromes or acute leukemias, but also cardiovascular diseases and other pathologies. Acute or chronic inflammation related to age influences the clonal evolution and the immune response. Conversely, mutated hematopoietic cells create an inflammatory bone marrow environment facilitating their expansion. Various pathophysiological mechanisms depending on the type of mutation produce the diversity of phenotypes. Identifying factors affecting clonal selection is mandatory to improve patient care.
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Affiliation(s)
- Michaela Fontenay
- Assistance publique-Hôpitaux de Paris, université Paris Cité, hôpital Cochin, laboratoire d'hématologie, Inserm, Institut Cochin, Paris, France.
| | - Ismael Boussaid
- Assistance publique-Hôpitaux de Paris, université Paris Cité, hôpital Cochin, laboratoire d'hématologie, Inserm, Institut Cochin, Paris, France
| | - Nicolas Chapuis
- Assistance publique-Hôpitaux de Paris, université Paris Cité, hôpital Cochin, laboratoire d'hématologie, Inserm, Institut Cochin, Paris, France
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40
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Wallace L, Obeng EA. Noncoding rules of survival: epigenetic regulation of normal and malignant hematopoiesis. Front Mol Biosci 2023; 10:1273046. [PMID: 38028538 PMCID: PMC10644717 DOI: 10.3389/fmolb.2023.1273046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Hematopoiesis is an essential process for organismal development and homeostasis. Epigenetic regulation of gene expression is critical for stem cell self-renewal and differentiation in normal hematopoiesis. Increasing evidence shows that disrupting the balance between self-renewal and cell fate decisions can give rise to hematological diseases such as bone marrow failure and leukemia. Consequently, next-generation sequencing studies have identified various aberrations in histone modifications, DNA methylation, RNA splicing, and RNA modifications in hematologic diseases. Favorable outcomes after targeting epigenetic regulators during disease states have further emphasized their importance in hematological malignancy. However, these targeted therapies are only effective in some patients, suggesting that further research is needed to decipher the complexity of epigenetic regulation during hematopoiesis. In this review, an update on the impact of the epigenome on normal hematopoiesis, disease initiation and progression, and current therapeutic advancements will be discussed.
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Affiliation(s)
| | - Esther A. Obeng
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, United States
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41
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Duan C, Zhang Y, Li L, Liu K, Yao X, Wu X, Li B, Mao X, Wu H, Liu H, Zeng J, Li S, Gong Y, Hu Z, Xu H. Identification of alternative splicing associated with clinical features: from pan-cancers to genitourinary tumors. Front Oncol 2023; 13:1249932. [PMID: 37810965 PMCID: PMC10557043 DOI: 10.3389/fonc.2023.1249932] [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: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 10/10/2023] Open
Abstract
Background Alternative splicing events (ASEs) are vital causes of tumor heterogeneity in genitourinary tumors and many other cancers. However, the clinicopathological relevance of ASEs in cancers has not yet been comprehensively characterized. Methods By analyzing splicing data from the TCGA SpliceSeq database and phenotype data for all TCGA samples from the UCSC Xena database, we identified differential clinical feature-related ASEs in 33 tumors. CIBERSORT immune cell infiltration data from the TIMER2.0 database were used for differential clinical feature-related immune cell infiltration analysis. Gene function enrichment analysis was used to analyze the gene function of ASEs related to different clinical features in tumors. To reveal the regulatory mechanisms of ASEs, we integrated race-related ASEs and splicing quantitative trait loci (sQTLs) data in kidney renal clear cell carcinoma (KIRC) to comprehensively assess the impact of SNPs on ASEs. In addition, we predicted regulatory RNA binding proteins in bladder urothelial carcinoma (BLCA) based on the enrichment of motifs around alternative exons for ASEs. Results Alternative splicing differences were systematically analyzed between different groups of 58 clinical features in 33 cancers, and 30 clinical features in 24 cancer types were identified to be associated with more than 50 ASEs individually. The types of immune cell infiltration were found to be significantly different between subgroups of primary diagnosis and disease type. After integrating ASEs with sQTLs data, we found that 63 (58.9%) of the race-related ASEs were significantly SNP-correlated ASEs in KIRC. Gene function enrichment analyses showed that metastasis-related ASEs in KIRC mainly enriched Rho GTPase signaling pathways. Among those ASEs associated with metastasis, alternative splicing of GIT2 and TUBB3 might play key roles in tumor metastasis in KIRC patients. Finally, we identified several RNA binding proteins such as PCBP2, SNRNP70, and HuR, which might contribute to splicing differences between different groups of neoplasm grade in BLCA. Conclusion We demonstrated the significant clinical relevance of ASEs in multiple cancer types. Furthermore, we identified and validated alternative splicing of TUBB3 and RNA binding proteins such as PCBP2 as critical regulators in the progression of urogenital cancers.
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Affiliation(s)
- Chen Duan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangjun Zhang
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lu Li
- Department of Radiation Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Kai Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiangyang Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bo Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiongmin Mao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huahui Wu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoran Liu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Jin Zeng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Sheng Li
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yan Gong
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hua Xu
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
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Bennett J, Ishikawa C, Agarwal P, Yeung J, Sampson A, Uible E, Vick E, Bolanos LC, Hueneman K, Wunderlich M, Kolt A, Choi K, Volk A, Greis KD, Rosenbaum J, Hoyt SB, Thomas CJ, Starczynowski DT. Paralog-specific signaling by IRAK1/4 maintains MyD88-independent functions in MDS/AML. Blood 2023; 142:989-1007. [PMID: 37172199 PMCID: PMC10517216 DOI: 10.1182/blood.2022018718] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 05/14/2023] Open
Abstract
Dysregulation of innate immune signaling is a hallmark of hematologic malignancies. Recent therapeutic efforts to subvert aberrant innate immune signaling in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) have focused on the kinase IRAK4. IRAK4 inhibitors have achieved promising, though moderate, responses in preclinical studies and clinical trials for MDS and AML. The reasons underlying the limited responses to IRAK4 inhibitors remain unknown. In this study, we reveal that inhibiting IRAK4 in leukemic cells elicits functional complementation and compensation by its paralog, IRAK1. Using genetic approaches, we demonstrate that cotargeting IRAK1 and IRAK4 is required to suppress leukemic stem/progenitor cell (LSPC) function and induce differentiation in cell lines and patient-derived cells. Although IRAK1 and IRAK4 are presumed to function primarily downstream of the proximal adapter MyD88, we found that complementary and compensatory IRAK1 and IRAK4 dependencies in MDS/AML occur via noncanonical MyD88-independent pathways. Genomic and proteomic analyses revealed that IRAK1 and IRAK4 preserve the undifferentiated state of MDS/AML LSPCs by coordinating a network of pathways, including ones that converge on the polycomb repressive complex 2 complex and JAK-STAT signaling. To translate these findings, we implemented a structure-based design of a potent and selective dual IRAK1 and IRAK4 inhibitor KME-2780. MDS/AML cell lines and patient-derived samples showed significant suppression of LSPCs in xenograft and in vitro studies when treated with KME-2780 as compared with selective IRAK4 inhibitors. Our results provide a mechanistic basis and rationale for cotargeting IRAK1 and IRAK4 for the treatment of cancers, including MDS/AML.
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Affiliation(s)
- Joshua Bennett
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH
| | - Chiharu Ishikawa
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH
| | - Puneet Agarwal
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
| | - Jennifer Yeung
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
| | - Avery Sampson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
| | - Emma Uible
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH
| | - Eric Vick
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | - Lyndsey C. Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
| | - Kathleen Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
| | | | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
| | - Andrew Volk
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Kenneth D. Greis
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH
| | | | - Scott B. Hoyt
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD
| | - Craig J. Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Daniel T. Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
- University of Cincinnati Cancer Center, Cincinnati, OH
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43
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Rodriguez Gallo MC, Uhrig RG. Phosphorylation mediated regulation of RNA splicing in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1249057. [PMID: 37780493 PMCID: PMC10539000 DOI: 10.3389/fpls.2023.1249057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
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Affiliation(s)
| | - R. Glen Uhrig
- University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
- University of Alberta, Department of Biochemistry, Edmonton, AB, Canada
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Takahashi K, Tanaka T. Clonal evolution and hierarchy in myeloid malignancies. Trends Cancer 2023; 9:707-715. [PMID: 37302922 PMCID: PMC10766088 DOI: 10.1016/j.trecan.2023.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Myeloid malignancies, a group of hematopoietic disorders that includes acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myeloproliferative neoplasms (MPNs), are caused by the accumulation of genetic and epigenetic changes in hematopoietic stem and progenitor cells (HSPCs) over time. Despite the relatively low number of genomic drivers compared with other forms of cancer, the process by which these changes shape the genomic architecture of myeloid malignancies remains elusive. Recent advancements in clonal hematopoiesis research and the use of cutting-edge single cell technologies have shed new light on the developmental process of myeloid malignancies. In this review, we delve into the intricacies of clonal evolution in myeloid malignancies and its implications for the development of new diagnostic and therapeutic approaches.
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Affiliation(s)
- Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Tomoyuki Tanaka
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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45
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Kaonis S, Smith JL, Katiyar N, Merrill M, Hyelkma T, Namciu S, Le Q, Babaeva E, Ishida T, Morris SM, Girard E, Furuyama S, Ries R, Bernstein I, Meshinchi S, Henikoff S, Meers M, Hadland B, Sarthy JF. Chromatin Profiling of CBFA2T3-GLIS2 AMLs Identifies Key Transcription Factor Dependencies and BRG1 Inhibition as a Novel Therapeutic Strategy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555598. [PMID: 37693371 PMCID: PMC10491196 DOI: 10.1101/2023.08.30.555598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Oncogenic fusions involving transcription factors are present in the majority of pediatric leukemias; however, the context-specific mechanisms they employ to drive cancer remain poorly understood. CBFA2T3-GLIS2 (C/G) fusions occur in treatment-refractory acute myeloid leukemias and are restricted to young children. To understand how the C/G fusion drives oncogenesis we applied CUT&RUN chromatin profiling to an umbilical cord blood/endothelial cell (EC) co-culture model of C/G AML that recapitulates the biology of this malignancy. We find C/G fusion binding is mediated by its zinc finger domains. Integration of fusion binding sites in C/G- transduced cells with Polycomb Repressive Complex 2 (PRC2) sites in control cord blood cells identifies MYCN, ZFPM1, ZBTB16 and LMO2 as direct C/G targets. Transcriptomic analysis of a large pediatric AML cohort shows that these genes are upregulated in C/G patient samples. Single cell RNA-sequencing of umbilical cord blood identifies a population of megakaryocyte precursors that already express many of these genes despite lacking the fusion. By integrating CUT&RUN data with CRISPR dependency screens we identify BRG1/SMARCA4 as a vulnerability in C/G AML. BRG1 profiling in C/G patient-derived cell lines shows that the CBFA2T3 locus is a binding site, and treatment with clinically-available BRG1 inhibitors reduces fusion levels and downstream C/G targets including N-MYC, resulting in C/G leukemia cell death and extending survival in a murine xenograft model.
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Cusan M, Shen H, Zhang B, Liao A, Yang L, Jin M, Fernandez M, Iyer P, Wu Y, Hart K, Gutierrez C, Nik S, Pruett-Miller SM, Stark J, Obeng EA, Bowman TV, Wu CJ, Lin RJ, Wang L. SF3B1 mutation and ATM deletion codrive leukemogenesis via centromeric R-loop dysregulation. J Clin Invest 2023; 133:e163325. [PMID: 37463047 PMCID: PMC10471171 DOI: 10.1172/jci163325] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
RNA splicing factor SF3B1 is recurrently mutated in various cancers, particularly in hematologic malignancies. We previously reported that coexpression of Sf3b1 mutation and Atm deletion in B cells, but not either lesion alone, leads to the onset of chronic lymphocytic leukemia (CLL) with CLL cells harboring chromosome amplification. However, the exact role of Sf3b1 mutation and Atm deletion in chromosomal instability (CIN) remains unclear. Here, we demonstrated that SF3B1 mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segregation, altered spindle architecture, and aneuploidy, which could be alleviated by removal of cen-R-loop and exaggerated by deletion of ATM. Aberrant splicing of key genes involved in R-loop processing underlay augmentation of cen-R-loop, as overexpression of the normal isoform, but not the altered form, mitigated mitotic stress in SF3B1-mutant cells. Our study identifies a critical role of splice variants in linking RNA splicing dysregulation and CIN and highlights cen-R-loop augmentation as a key mechanism for leukemogenesis.
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Affiliation(s)
- Martina Cusan
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Haifeng Shen
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Bo Zhang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Department of Hematology, Union Hospital Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aijun Liao
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Department of Hematology, Affiliated Shengjing Hospital of China Medical University, Shenyang, China
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Meiling Jin
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Mike Fernandez
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Prajish Iyer
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Yiming Wu
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Kevyn Hart
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sara Nik
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jeremy Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Esther A. Obeng
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Teresa V. Bowman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ren-Jang Lin
- Center for RNA Biology and Therapeutics, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
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Konda P, Garinet S, Van Allen EM, Viswanathan SR. Genome-guided discovery of cancer therapeutic targets. Cell Rep 2023; 42:112978. [PMID: 37572322 DOI: 10.1016/j.celrep.2023.112978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
The success of precision oncology-which aims to match the right therapies to the right patients based on molecular status-is predicated on a robust pipeline of molecular targets against which therapies can be developed. Recent advances in genomics and functional genetics have enabled the unbiased discovery of novel molecular targets at scale. We summarize the promise and challenges in integrating genomic and functional genetic landscapes of cancer to establish the next generation of cancer targets.
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Affiliation(s)
- Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon Garinet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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48
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Jin B, Zhu J, Pan T, Yang Y, Liang L, Zhou Y, Zhang T, Teng Y, Wang Z, Wang X, Tian Q, Guo B, Li H, Chen T. MEN1 is a regulator of alternative splicing and prevents R-loop-induced genome instability through suppression of RNA polymerase II elongation. Nucleic Acids Res 2023; 51:7951-7971. [PMID: 37395406 PMCID: PMC10450199 DOI: 10.1093/nar/gkad548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
The fidelity of alternative splicing (AS) patterns is essential for growth development and cell fate determination. However, the scope of the molecular switches that regulate AS remains largely unexplored. Here we show that MEN1 is a previously unknown splicing regulatory factor. MEN1 deletion resulted in reprogramming of AS patterns in mouse lung tissue and human lung cancer cells, suggesting that MEN1 has a general function in regulating alternative precursor mRNA splicing. MEN1 altered exon skipping and the abundance of mRNA splicing isoforms of certain genes with suboptimal splice sites. Chromatin immunoprecipitation and chromosome walking assays revealed that MEN1 favored the accumulation of RNA polymerase II (Pol II) in regions encoding variant exons. Our data suggest that MEN1 regulates AS by slowing the Pol II elongation rate and that defects in these processes trigger R-loop formation, DNA damage accumulation and genome instability. Furthermore, we identified 28 MEN1-regulated exon-skipping events in lung cancer cells that were closely correlated with survival in patients with lung adenocarcinoma, and MEN1 deficiency sensitized lung cancer cells to splicing inhibitors. Collectively, these findings led to the identification of a novel biological role for menin in maintaining AS homeostasis and link this role to the regulation of cancer cell behavior.
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Affiliation(s)
- Bangming Jin
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Jiamei Zhu
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Ting Pan
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yunqiao Yang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Li Liang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yuxia Zhou
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Tuo Zhang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yin Teng
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Ziming Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Xuyan Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Qianting Tian
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Bing Guo
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Haiyang Li
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Tengxiang Chen
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
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49
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Han N, Liu Z. Targeting alternative splicing in cancer immunotherapy. Front Cell Dev Biol 2023; 11:1232146. [PMID: 37635865 PMCID: PMC10450511 DOI: 10.3389/fcell.2023.1232146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Tumor immunotherapy has made great progress in cancer treatment but still faces several challenges, such as a limited number of targetable antigens and varying responses among patients. Alternative splicing (AS) is an essential process for the maturation of nearly all mammalian mRNAs. Recent studies show that AS contributes to expanding cancer-specific antigens and modulating immunogenicity, making it a promising solution to the above challenges. The organoid technology preserves the individual immune microenvironment and reduces the time/economic costs of the experiment model, facilitating the development of splicing-based immunotherapy. Here, we summarize three critical roles of AS in immunotherapy: resources for generating neoantigens, targets for immune-therapeutic modulation, and biomarkers to guide immunotherapy options. Subsequently, we highlight the benefits of adopting organoids to develop AS-based immunotherapies. Finally, we discuss the current challenges in studying AS-based immunotherapy in terms of existing bioinformatics algorithms and biological technologies.
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Affiliation(s)
- Nan Han
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoqi Liu
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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50
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He J, Qiu W, Li Y, Wei C, Bai Z, Jia J, Cai H. Advances in the Application of Apoptotic Proteins and Alternative Splicing in Tumor Therapy: A Narrative Review. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:1311-1319. [PMID: 37593500 PMCID: PMC10430389 DOI: 10.18502/ijph.v52i7.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/18/2023] [Indexed: 08/19/2023]
Abstract
An apoptosis-resistant state determined by apoptotic protein expression is commonly seen in the initiation, progression, and treatment failure stages of human cancer, and anti-tumor drugs targeting apoptotic proteins have been increasingly developed over the past three decades. However, the frequently alternative splicing of apoptotic proteins diminished the ability of targeting drugs to bind to apoptotic proteins and, consequently, limit the drug efficacy. Currently, accumulating evidence has demonstrated that many alternative splicing events have been associated to apoptosis resistance in different cancers. Therefore, the intervention targeting alternative splicing for regulating tumor cell apoptosis is expected to become a new strategy and new direction of antitumor therapy. Here, we present well established alternative splicing events that occur in different apoptosis-related genes and their modification by several approaches with cancer therapeutic purposes.
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Affiliation(s)
- Jin He
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Weitao Qiu
- Gansu Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Yonghong Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Chaojun Wei
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Zhongtian Bai
- The Second Department of General Surgery, Lanzhou University First Hospital, Lanzhou 730000, China
| | - Jing Jia
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Hui Cai
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, China
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