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Bidikian A, Bewersdorf JP, Shallis RM, Getz TM, Stempel JM, Kewan T, Stahl M, Zeidan AM. Targeted therapies for myelodysplastic Syndromes/Neoplasms (MDS): current landscape and future directions. Expert Rev Anticancer Ther 2024. [PMID: 39367718 DOI: 10.1080/14737140.2024.2414071] [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: 08/28/2024] [Revised: 10/01/2024] [Accepted: 10/04/2024] [Indexed: 10/06/2024]
Abstract
INTRODUCTION Myelodysplastic syndromes/neoplasms (MDS) are a heterogeneous group of hematologic malignancies that are stratified into high-risk (HR-MDS) and low-risk (LR-MDS) categories. Until recently LR-MDS has been typically managed by supportive measures and erythropoiesis-stimulating agents (ESAs); whereas, management of HR-MDS, typically included hypomethylating agents and allogeneic hematopoietic stem cell transplant. However, the limited rates and duration of response observed with these interventions prompted the search for targeted therapies to improve the outcomes among patients with MDS. AREAS COVERED Here we review the current landscape of targeted therapies in MDS. These include pyruvate kinase and hypoxia-inducible factor (HIF) activators; TGF-beta, telomerase, BCL2 and isocitrate dehydrogenase (IDH) inhibitors; as well as novel approaches targeting inflammation, pyroptosis, immune evasion and RNA splicing machinery. EXPERT OPINION This review highlights the progress and challenges in MDS treatment. Despite some promising results, many therapies remain in early development or have faced setbacks, emphasizing the need for a more comprehensive understanding of the disease's pathobiology. Continued research into targeted therapies, homogenous clinical trial designs, as well as increased incorporation of molecular prognostic tools and artificial intelligence into trial design are essential for developing effective treatments for MDS and improving patient outcomes.
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Affiliation(s)
- Aram Bidikian
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Jan P Bewersdorf
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Rory M Shallis
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Ted M Getz
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Jessica M Stempel
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Tariq Kewan
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
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2
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Nguyen JQN, Drabarek W, Leeflang AMCHJ, Brands T, van den Bosch TPP, Verdijk RM, van de Werken HJG, van Riet J, Paridaens D, de Klein A, Brosens E, Kiliç E. The Impact of Spliceosome Inhibition in SF3B1-Mutated Uveal Melanoma. Invest Ophthalmol Vis Sci 2024; 65:11. [PMID: 39374010 PMCID: PMC11463709 DOI: 10.1167/iovs.65.12.11] [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: 05/17/2024] [Accepted: 09/08/2024] [Indexed: 10/08/2024] Open
Abstract
Purpose Unfortunately, treatment of patients with uveal melanoma (UM) with metastatic disease is limited. Twenty percent of patients with UM harbor a mutation in the splicing factor gene SF3B1, suggesting that aberrant spliceosome function plays a vital role in tumorigenesis. Splicing inhibitors exploit the preferential sensitivity of spliceosome-compromised leukemic cells to these compounds. Methods We studied the effect of the splicing inhibitor E7107 using two UM cell lines and ex vivo cultured SF3B1- and BAP1-mutated primary UM tumor slices. These UM cell lines and ex vivo tumor slices were exposed for 24 hours to different concentrations of E7107. Tumor slices were stained with hematoxylin and eosin (H&E) and incubated with BAP1, MelanA, MIB-1, and caspase-3 antisera. Results The E7107-exposed UM cell lines exhibited decreased cell viability and increased apoptosis, with the greatest effect on SF3B1-mutated UM cells. A similar effect on UM tumor slices was observed upon exposure to E7107. Additionally, RNA was isolated for differential isoform expression analysis. No significant difference in isoform usage was found genome-wide. However, specific genes were differentially expressed after E7107 treatment in the SF3B1-mutated samples. Moreover, E7107 had the greatest effect on intron retention. Conclusions This study indicates/suggests that mutated SF3B1 UM cells are more sensitive to the splicing inhibitor E7107 than wild-type SF3B1 UM cells.
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Affiliation(s)
- Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | | | - Aïsha M. C. H. J. Leeflang
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Thierry P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Robert M. Verdijk
- The Rotterdam Eye Hospital, BH Rotterdam, The Netherlands
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, ZA Leiden, The Netherlands
| | - Harmen J. G. van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Job van Riet
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- The Rotterdam Eye Hospital, BH Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - on behalf of the Rotterdam Ocular Melanoma Study Group
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- The Rotterdam Eye Hospital, BH Rotterdam, The Netherlands
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, ZA Leiden, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
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3
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Wang K, Zhang L, Zhang S, Liu Y, Mao J, Liu Z, Xu L, Li K, Wang J, Ma Y, Wang J, Li H, Wang Z, Li G, Cheng H, Ye M. Metabolic labeling based methylome profiling enables functional dissection of histidine methylation in C3H1 zinc fingers. Nat Commun 2024; 15:7459. [PMID: 39198440 PMCID: PMC11358137 DOI: 10.1038/s41467-024-51979-2] [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: 01/07/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024] Open
Abstract
Protein methylation is a functionally important post-translational modification that occurs on diverse amino acid residues. The current proteomics approaches are inefficient to discover the methylation on residues other than Arg and Lys, which hinders the deep understanding of the functional role of rare protein methylation. Herein, we present a methyl-specific metabolic labeling approach for global methylome mapping, which enable the acquisition of methylome dataset covering diverse methylation types. Interestingly, of the identified methylation events, His methylation is found to be preferably occurred in C3H1 zinc fingers (ZFs). These His methylation events are determined to be Nπ specific and catalyzed by CARNMT1. The His methylation is found to stabilize the structure of ZFs. U2AF1 is used as a proof-of-concept to highlight the functional importance of His methylation in ZFs in RNA binding and RNA metabolism. The results of this study enable novel understanding of how protein methylation regulates cellular processes.
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Grants
- This work was supported, in part, by funds from the China State Key Basic Research Program Grants (2021YFA13026012, 2019YFA0709400, 2022YFA1303300), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB37040401, XDB0570100), the National Natural Science Foundation of China (21804131, 92153302, 21933010, 31925008), the innovation program (DICP I202226) of science and research from the DICP, CAS.
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Affiliation(s)
- Keyun Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ye Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiawei Mao
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Xu
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Kejia Li
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianshu Wang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yanni Ma
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiayi Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science, Southern University of Science and Technology, Shenzhen, China.
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Hong Cheng
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Mingliang Ye
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Shukla M, Abdul-Hay M, Choi JH. Molecular Features and Treatment Paradigms of Acute Myeloid Leukemia. Biomedicines 2024; 12:1768. [PMID: 39200232 PMCID: PMC11351617 DOI: 10.3390/biomedicines12081768] [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: 05/07/2024] [Revised: 07/26/2024] [Accepted: 07/31/2024] [Indexed: 09/02/2024] Open
Abstract
Acute myeloid leukemia (AML) is a common hematologic malignancy that is considered to be a disease of aging, and traditionally has been treated with induction chemotherapy, followed by consolidation chemotherapy and/or allogenic hematopoietic stem cell transplantation. More recently, with the use of next-generation sequencing and access to molecular information, targeted molecular approaches to the treatment of AML have been adopted. Molecular targeting is gaining prominence, as AML mostly afflicts the elderly population, who often cannot tolerate traditional chemotherapy. Understanding molecular changes at the gene level is also important for accurate disease classification, risk stratification, and prognosis, allowing for more personalized medicine. Some mutations are well studied and have an established gene-specific therapy, including FLT3 and IDH1/2, while others are being investigated in clinical trials. However, data on most known mutations in AML are still minimal and therapeutic studies are in pre-clinical stages, highlighting the importance of further research and elucidation of the pathophysiology involving these genes. In this review, we aim to highlight the key molecular alterations and chromosomal changes that characterize AML, with a focus on pathophysiology, presently available treatment approaches, and future therapeutic options.
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Affiliation(s)
| | | | - Jun H. Choi
- Department of Hematology and Medical Oncology, NYU Langone Health, Perlmutter Cancer Center, New York, NY 10016, USA; (M.S.)
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5
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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, Montgomery SB. Impact of genome build on RNA-seq interpretation and diagnostics. Am J Hum Genet 2024; 111:1282-1300. [PMID: 38834072 PMCID: PMC11267525 DOI: 10.1016/j.ajhg.2024.05.005] [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: 01/04/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.
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Affiliation(s)
- Rachel A Ungar
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Pagé C Goddard
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Tanner D Jensen
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Christopher A Jin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Devon E Bonner
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Matthew T Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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6
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Yuan X, Sabzvar MK, Patil AD, Chinnaswamy K, Howie KL, Andhavaram R, Wang B, Siegler MA, Dumaz A, Stuckey JA, Corey SJ, Maciejewski JP, Visconte V, Yang CY. Comprehensive Analyses of the Effects of the Small-Molecule Inhibitor of the UHM Domain in the Splicing Factor U2AF1 in Leukemia Cells. RESEARCH SQUARE 2024:rs.3.rs-4477663. [PMID: 38883705 PMCID: PMC11177969 DOI: 10.21203/rs.3.rs-4477663/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mutations in RNA splicing factor genes including SF3B1, U2AF1, SRSF2, and ZRSR2 have been reported to contribute to development of myeloid neoplasms including myelodysplastic syndrome (MDS) and secondary acute myeloid leukemia (sAML). Chemical tools targeting cells carrying these mutant genes remain limited and underdeveloped. Among the four proteins, mutant U2AF1 (U2AF1mut) acquires an altered 3' splice site selection preference and co-operates with the wild-type U2AF1 (U2AF1wt) to change various gene isoform patterns to support MDS cells survival and proliferation. U2AF1 mutations in MDS cells are always heterozygous and the cell viability is reduced when exposed to additional insult affecting U2AF1wt function. To investigate if the pharmacological inhibition of U2AF1wt function can provoke drug-induced vulnerability of cells harboring U2AF1 mut , we conducted a fragment-based library screening campaign to discover compounds targeting the U2AF homology domain (UHM) in U2AF1 that is required for the formation of the U2AF1/U2AF2 complex to define the 3' splice site. The most promising hit (SF1-8) selectively inhibited growth of leukemia cell lines overexpressingU2AF1 mut and human primary MDS cells carrying U2AF1 mut . RNA-seq analysis of K562-U2AF1mut following treatment with SF1-8 further revealed alteration of isoform patterns for a set of proteins that impair or rescue pathways associated with endocytosis, intracellular vesicle transport, and secretion. Our data suggested that further optimization of SF1-8 is warranted to obtain chemical probes that can be used to evaluate the therapeutic concept of inducing lethality to U2AF1 mut cells by inhibiting the U2AF1wt protein.
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Affiliation(s)
- Xinrui Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mona Kazemi Sabzvar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Amol D Patil
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | | | - Kathryn L Howie
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ramaraju Andhavaram
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Borwyn Wang
- Departments of Pediatrics and Cancer Biology, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Maxime A Siegler
- Department of Chemistry, John Hopkins University, Baltimore, MD, 21218, USA
| | - Arda Dumaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seth J Corey
- Departments of Pediatrics and Cancer Biology, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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7
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Jin P, Wang X, Jin Q, Zhang Y, Shen J, Jiang G, Zhu H, Zhao M, Wang D, Li Z, Zhou Y, Li W, Zhang W, Liu Y, Wang S, Jin W, Cao Y, Sheng G, Dong F, Wu S, Li X, Jin Z, He M, Liu X, Chen L, Zhang Y, Wang K, Li J. Mutant U2AF1-Induced Mis-Splicing of mRNA Translation Genes Confers Resistance to Chemotherapy in Acute Myeloid Leukemia. Cancer Res 2024; 84:1583-1596. [PMID: 38417135 DOI: 10.1158/0008-5472.can-23-2543] [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: 08/23/2023] [Revised: 01/07/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Patients with primary refractory acute myeloid leukemia (AML) have a dismal long-term prognosis. Elucidating the resistance mechanisms to induction chemotherapy could help identify strategies to improve AML patient outcomes. Herein, we retrospectively analyzed the multiomics data of more than 1,500 AML cases and found that patients with spliceosome mutations had a higher risk of developing refractory disease. RNA splicing analysis revealed that the mis-spliced genes in refractory patients converged on translation-associated pathways, promoted mainly by U2AF1 mutations. Integrative analyses of binding and splicing in AML cell lines substantiated that the splicing perturbations of mRNA translation genes originated from both the loss and gain of mutant U2AF1 binding. In particular, the U2AF1S34F and U2AF1Q157R mutants orchestrated the inclusion of exon 11 (encoding a premature termination codon) in the eukaryotic translation initiation factor 4A2 (EIF4A2). This aberrant inclusion led to reduced eIF4A2 protein expression via nonsense-mediated mRNA decay. Consequently, U2AF1 mutations caused a net decrease in global mRNA translation that induced the integrated stress response (ISR) in AML cells, which was confirmed by single-cell RNA sequencing. The induction of ISR enhanced the ability of AML cells to respond and adapt to stress, contributing to chemoresistance. A pharmacologic inhibitor of ISR, ISRIB, sensitized U2AF1 mutant cells to chemotherapy. These findings highlight a resistance mechanism by which U2AF1 mutations drive chemoresistance and provide a therapeutic approach for AML through targeting the ISR pathway. SIGNIFICANCE U2AF1 mutations induce the integrated stress response by disrupting splicing of mRNA translation genes that improves AML cell fitness to enable resistance to chemotherapy, which can be targeted to improve AML treatment.
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Affiliation(s)
- Peng Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoling Wang
- Department of Reproductive Medical Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiqi Jin
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Shen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ge Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongming Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Zhao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zeyi Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Zhou
- Department of Reproductive Medical Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenzhu Li
- Department of Reproductive Medical Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yabin Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Siyang Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuncan Cao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guangying Sheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangyi Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shishuang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyang Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengke He
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaxin Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Yunxiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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8
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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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9
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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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10
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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, Montgomery SB. Impact of genome build on RNA-seq interpretation and diagnostics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.11.24301165. [PMID: 38260490 PMCID: PMC10802764 DOI: 10.1101/2024.01.11.24301165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. Combined, we provide a database of genes impacted by build choice, and recommend that transcriptomics-guided analyses and diagnoses are cross-referenced with these data for robustness.
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Affiliation(s)
- Rachel A. Ungar
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | - Pagé C. Goddard
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | - Tanner D. Jensen
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | | | - Kevin S. Smith
- Department of Pathology, School of Medicine, Stanford University
| | | | | | - Devon E. Bonner
- Department of Pediatrics, School of Medicine, Stanford University
- Stanford Center for Undiagnosed Diseases, Stanford University
| | | | - Matthew T. Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University
| | - Stephen B. Montgomery
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
- Department of Biomedical Data Science, Stanford University
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11
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Nian Q, Li Y, Li J, Zhao L, Rodrigues Lima F, Zeng J, Liu R, Ye Z. U2AF1 in various neoplastic diseases and relevant targeted therapies for malignant cancers with complex mutations (Review). Oncol Rep 2024; 51:5. [PMID: 37975232 PMCID: PMC10688450 DOI: 10.3892/or.2023.8664] [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: 10/03/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
U2 small nuclear RNA auxiliary factor 1 (U2AF1) is a multifunctional protein that plays a crucial role in the regulation of RNA splicing during eukaryotic gene expression. U2AF1 belongs to the SR family of splicing factors and is involved in the removal of introns from mRNAs and exon-exon binding. Mutations in U2AF1 are frequently observed in myelodysplastic syndrome, primary myelofibrosis, chronic myelomonocytic leukaemia, hairy cell leukaemia and other solid tumours, particularly in lung, pancreatic, and ovarian carcinomas. Therefore, targeting U2AF1 for therapeutic interventions may be a viable strategy for treating malignant diseases. In the present review, the pathogenic mechanisms associated with U2AF1 in different malignant diseases were summarized, and the potential of related targeting agents was discussed. Additionally, the feasibility of natural product-based therapies directed against U2AF1 was explored.
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Affiliation(s)
- Qing Nian
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Yihui Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing 100730, P.R. China
| | - Jingwei Li
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Liyun Zhao
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France
| | - Jinhao Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610000, P.R. China
| | - Rongxing Liu
- Department of Pharmacy, The Second Affiliated Hospital, Army Medical University, Chongqing 400000, P.R. China
| | - Zhijun Ye
- Department of Clinical Nutrition, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
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12
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Harada K, Carr SM, Shrestha A, La Thangue NB. Citrullination and the protein code: crosstalk between post-translational modifications in cancer. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220243. [PMID: 37778382 PMCID: PMC10542456 DOI: 10.1098/rstb.2022.0243] [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] [Received: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 10/03/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are central to epigenetic regulation and cellular signalling, playing an important role in the pathogenesis and progression of numerous diseases. Growing evidence indicates that protein arginine citrullination, catalysed by peptidylarginine deiminases (PADs), is involved in many aspects of molecular and cell biology and is emerging as a potential druggable target in multiple diseases including cancer. However, we are only just beginning to understand the molecular activities of PADs, and their underlying mechanistic details in vivo under both physiological and pathological conditions. Many questions still remain regarding the dynamic cellular functions of citrullination and its interplay with other types of PTMs. This review, therefore, discusses the known functions of PADs with a focus on cancer biology, highlighting the cross-talk between citrullination and other types of PTMs, and how this interplay regulates downstream biological events. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Koyo Harada
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Simon M. Carr
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Amit Shrestha
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Nicholas B. La Thangue
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
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13
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López-Oreja I, Gohr A, Playa-Albinyana H, Giró A, Arenas F, Higashi M, Tripathi R, López-Guerra M, Irimia M, Aymerich M, Valcárcel J, Bonnal S, Colomer D. SF3B1 mutation-mediated sensitization to H3B-8800 splicing inhibitor in chronic lymphocytic leukemia. Life Sci Alliance 2023; 6:e202301955. [PMID: 37562845 PMCID: PMC10415613 DOI: 10.26508/lsa.202301955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Splicing factor 3B subunit 1 (SF3B1) is involved in pre-mRNA branch site recognition and is the target of antitumor-splicing inhibitors. Mutations in SF3B1 are observed in 15% of patients with chronic lymphocytic leukemia (CLL) and are associated with poor prognosis, but their pathogenic mechanisms remain poorly understood. Using deep RNA-sequencing data from 298 CLL tumor samples and isogenic SF3B1 WT and K700E-mutated CLL cell lines, we characterize targets and pre-mRNA sequence features associated with the selection of cryptic 3' splice sites upon SF3B1 mutation, including an event in the MAP3K7 gene relevant for activation of NF-κB signaling. Using the H3B-8800 splicing modulator, we show, for the first time in CLL, cytotoxic effects in vitro in primary CLL samples and in SF3B1-mutated isogenic CLL cell lines, accompanied by major splicing changes and delayed leukemic infiltration in a CLL xenotransplant mouse model. H3B-8800 displayed preferential lethality towards SF3B1-mutated cells and synergism with the BCL2 inhibitor venetoclax, supporting the potential use of SF3B1 inhibitors as a novel therapeutic strategy in CLL.
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Affiliation(s)
- Irene López-Oreja
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - André Gohr
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Fabian Arenas
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Morihiro Higashi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Rupal Tripathi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Mònica López-Guerra
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
- Universitat Barcelona, Barcelona, Spain
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14
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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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15
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Bonner EA, Lee SC. Therapeutic Targeting of RNA Splicing in Cancer. Genes (Basel) 2023; 14:1378. [PMID: 37510283 PMCID: PMC10379351 DOI: 10.3390/genes14071378] [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] [Received: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
RNA splicing is a key regulatory step in the proper control of gene expression. It is a highly dynamic process orchestrated by the spliceosome, a macro-molecular machinery that consists of protein and RNA components. The dysregulation of RNA splicing has been observed in many human pathologies ranging from neurodegenerative diseases to cancer. The recent identification of recurrent mutations in the core components of the spliceosome in hematologic malignancies has advanced our knowledge of how splicing alterations contribute to disease pathogenesis. This review article will discuss our current understanding of how aberrant RNA splicing regulation drives tumor initiation and progression. We will also review current therapeutic modalities and highlight emerging technologies designed to target RNA splicing for cancer treatment.
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Affiliation(s)
- Elizabeth A. Bonner
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA;
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Stanley C. Lee
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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16
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Bao Y, Zhang S, Zhang X, Pan Y, Yan Y, Wang N, Ren Y, Zuo J, Zong WX, Wang Z, Wang Y. RBM10 Loss Promotes EGFR-Driven Lung Cancer and Confers Sensitivity to Spliceosome Inhibition. Cancer Res 2023; 83:1490-1502. [PMID: 36853175 DOI: 10.1158/0008-5472.can-22-1549] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/01/2023]
Abstract
In lung adenocarcinoma (LUAD), loss-of-function mutations in the splicing factor RBM10 frequently co-occur with oncogenic EGFR mutations. A detailed understanding of the functional consequences and therapeutic impact of RBM10 loss in EGFR-mutant LUAD could help identify more effective treatment strategies. Here, analysis of LUAD data sets indicated that RBM10 mutations are mutually exclusive with mutations in the tumor suppressor gene TP53. In an EGFR-driven LUAD mouse model, lung-specific ablation of either Rbm10 or Trp53 similarly promoted tumor development, leading to overlapping gene expression changes enriched in cancer-related pathways. RBM10 loss induced key RNA splicing changes concordant in mice and LUAD patients. Importantly, RBM10 deficiency conferred high sensitivity to spliceosome inhibition in EGFR-mutated LUAD cells. Combined treatment with spliceosome inhibitor improved the therapeutic efficacy of EGFR tyrosine kinase inhibitor osimertinib and overcame drug resistance, especially in RBM10-deficient LUAD. Together, this study establishes RBM10 as a tumor suppressor akin to p53 and provides a therapeutic strategy of targeting the splicing machinery in EGFR-driven LUAD. SIGNIFICANCE Loss of the splicing factor RBM10 is mutually exclusive with p53 mutations, promotes tumorigenesis, and enhances the efficacy of spliceosome inhibition in EGFR-driven lung cancer.
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Affiliation(s)
- Yufang Bao
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Sirui Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyu Zhang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yunjian Pan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yueren Yan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yunpeng Ren
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ji Zuo
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei-Xing Zong
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers-The State University of New Jersey, Piscataway, New Jersey
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai, China
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17
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Yuan X, Howie KL, Kazemi Sabzvar M, Chinnaswamy K, Stuckey JA, Yang CY. Profiling the Binding Activities of Peptides and Inhibitors to the U2 Auxiliary Factor Homology Motif (UHM) Domains. ACS Med Chem Lett 2023; 14:450-457. [PMID: 37077390 PMCID: PMC10107908 DOI: 10.1021/acsmedchemlett.2c00537] [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: 12/28/2022] [Accepted: 03/17/2023] [Indexed: 04/21/2023] Open
Abstract
RNA splicing is a biological process to generate mature mRNA (mRNA) by removing introns and annexing exons in the nascent RNA transcript and is executed by a multiprotein complex called spliceosome. To aid RNA splicing, a class of splicing factors use an atypical RNA recognition domain (UHM) to bind with U2AF ligand motifs (ULMs) in proteins to form modules that recognize splice sites and splicing regulatory elements on mRNA. Mutations of UHM containing splicing factors have been found frequently in myeloid neoplasms. To profile the selectivity of UHMs for inhibitor development, we established binding assays to measure the binding activities between UHM domains and ULM peptides and a set of small-molecule inhibitors. Additionally, we computationally analyzed the targeting potential of the UHM domains by small-molecule inhibitors. Our study provided the binding assessment of UHM domains to diverse ligands that may guide development of selective UHM domain inhibitors in the future.
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Affiliation(s)
- Xinrui Yuan
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Kathryn L. Howie
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Mona Kazemi Sabzvar
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | - Jeanne A. Stuckey
- Life
Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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18
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Bertoldo JB, Müller S, Hüttelmaier S. RNA-binding proteins in cancer drug discovery. Drug Discov Today 2023; 28:103580. [PMID: 37031812 DOI: 10.1016/j.drudis.2023.103580] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
RNA-binding proteins (RBPs) are crucial players in tumorigenesis and, hence, promising targets in cancer drug discovery. However, they are largely regarded as 'undruggable', because of the often noncatalytic and complex interactions between protein and RNA, which limit the discovery of specific inhibitors. Nonetheless, over the past 10 years, drug discovery efforts have uncovered RBP inhibitors with clinical relevance, highlighting the disruption of RNA-protein networks as a promising avenue for cancer therapeutics. In this review, we discuss the role of structurally distinct RBPs in cancer, and the mechanisms of RBP-directed small-molecule inhibitors (SMOIs) focusing on drug-protein interactions, binding surfaces, potency, and translational potential. Additionally, we underline the limitations of RBP-targeting drug discovery assays and comment on future trends in the field.
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Affiliation(s)
- Jean B Bertoldo
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Simon Müller
- Institute for Molecular Medicine, Faculty of Medicine, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany; New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Stefan Hüttelmaier
- Institute for Molecular Medicine, Faculty of Medicine, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany.
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19
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Abstract
Alternative splicing (AS) of mRNAs is an essential regulatory mechanism in eukaryotic gene expression. AS misregulation, caused by either dysregulation or mutation of splicing factors, has been shown to be involved in cancer development and progression, making splicing factors suitable targets for cancer therapy. In recent years, various types of pharmacological modulators, such as small molecules and oligonucleotides, targeting distinct components of the splicing machinery, have been under development to treat multiple disorders. Although these approaches have promise, targeting the core spliceosome components disrupts the early stages of spliceosome assembly and can lead to nonspecific and toxic effects. New research directions have been focused on targeting specific splicing factors for a more precise effect. In this Perspective, we will highlight several approaches for targeting splicing factors and their functions and suggest ways to improve their specificity.
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Affiliation(s)
- Ariel Bashari
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
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20
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Wedge E, Ahmadov U, Hansen TB, Gao Z, Tulstrup M, Côme C, Nonavinkere Srivatsan S, Ahmed T, Jespersen JS, Schlotmann BC, Schöllkopf C, Raaschou-Jensen K, Ødum N, Kjems J, Bak RO, Walter MJ, Grønbæk K, Kristensen LS. Impact of U2AF1 mutations on circular RNA expression in myelodysplastic neoplasms. Leukemia 2023; 37:1113-1125. [PMID: 36922625 DOI: 10.1038/s41375-023-01866-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/16/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
Mutations in U2AF1 are relatively common in myelodysplastic neoplasms (MDS) and are associated with an inferior prognosis, but the molecular mechanisms underlying this are not fully elucidated. Circular RNAs (circRNAs) have been implicated in cancer, but it is unknown how mutations in splicing factors may impact on circRNA biogenesis. Here, we used RNA-sequencing to investigate the effects of U2AF1 mutations on circRNA expression in K562 cells with a doxycycline-inducible U2AF1S34 mutation, in a mouse model with a doxycycline-inducible U2AF1S34 mutation, and in FACS-sorted CD34+ bone marrow cells from MDS patients with either U2AF1S34 or U2AF1Q157 mutations. In all contexts, we found an increase in global circRNA levels in the U2AF1-mutated setting, which was independent of expression changes in the cognate linear host genes. In patients, the U2AF1S34 and U2AF1Q157 mutations were both associated with an overall increased expression of circRNAs. circRNAs generated by a non-Alu-mediated mechanism generally showed the largest increase in expression levels. Several well-described cancer-associated circRNAs, including circZNF609 and circCSNK1G3, were upregulated in MDS patients with U2AF1 mutations compared to U2AF1-wildtype MDS controls. In conclusion, high circRNA expression is observed in association with U2AF1 mutations in three biological systems, presenting an interesting possibility for biomarker and therapeutic investigation.
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Affiliation(s)
- Eileen Wedge
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
| | - Ulvi Ahmadov
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics, Aarhus, Denmark
| | - Zongliang Gao
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Morten Tulstrup
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
| | - Christophe Côme
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
| | | | - Tanzir Ahmed
- Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Jakob S Jespersen
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital, Copenhagen, Denmark
| | - Balthasar C Schlotmann
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claudia Schöllkopf
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Niels Ødum
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Matthew J Walter
- Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Kirsten Grønbæk
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark.
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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21
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Li Z, He Z, Wang J, Kong G. RNA splicing factors in normal hematopoiesis and hematologic malignancies: novel therapeutic targets and strategies. J Leukoc Biol 2023; 113:149-163. [PMID: 36822179 DOI: 10.1093/jleuko/qiac015] [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: 08/09/2022] [Indexed: 01/18/2023] Open
Abstract
RNA splicing, a crucial transesterification-based process by which noncoding regions are removed from premature RNA to create mature mRNA, regulates various cellular functions, such as proliferation, survival, and differentiation. Clinical and functional studies over the past 10 y have confirmed that mutations in RNA splicing factors are among the most recurrent genetic abnormalities in hematologic neoplasms, including myeloid malignancies, chronic lymphocytic leukemia, mantle cell lymphoma, and clonal hematopoiesis. These findings indicate an important role for splicing factor mutations in the development of clonal hematopoietic disorders. Mutations in core or accessory components of the RNA spliceosome complex alter splicing sites in a manner of change of function. These changes can result in the dysregulation of cancer-associated gene expression and the generation of novel mRNA transcripts, some of which are not only critical to disease development but may be also serving as potential therapeutic targets. Furthermore, multiple studies have revealed that hematopoietic cells bearing mutations in splicing factors depend on the expression of the residual wild-type allele for survival, and these cells are more sensitive to reduced expression of wild-type splicing factors or chemical perturbations of the splicing machinery. These findings suggest a promising possibility for developing novel therapeutic opportunities in tumor cells based on mutations in splicing factors. Here, we combine current knowledge of the mechanistic and functional effects of frequently mutated splicing factors in normal hematopoiesis and the effects of their mutations in hematologic malignancies. Moreover, we discuss the development of potential therapeutic opportunities based on these mutations.
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Affiliation(s)
- Zhenzhen Li
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, No. 127 Youyi West Road, Beilin District, Xi'an, Shaanxi 710072, China
| | - Zhongzheng He
- Department of Neurosurgery, Mini-invasive Neurosurgery and Translational Medical Center, Xi'an Central Hospital, Xi'an Jiaotong University, No. 161 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710003, China
| | - Jihan Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, No. 127 Youyi West Road, Beilin District, Xi'an, Shaanxi 710072, China
| | - Guangyao Kong
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, China
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22
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Splicing Modulation Results in Aberrant Isoforms and Protein Products of p53 Pathway Genes and the Sensitization of B Cells to Non-Genotoxic MDM2 Inhibition. Int J Mol Sci 2023; 24:ijms24032410. [PMID: 36768733 PMCID: PMC9916657 DOI: 10.3390/ijms24032410] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
Several molecular subtypes of cancer are highly dependent on splicing for cell survival. There is a general interest in the therapeutic targeting of splicing by small molecules. E7107, a first-in-class spliceosome inhibitor, showed strong growth inhibitory activities against a large variety of human cancer xenografts. Chronic lymphocytic leukaemia (CLL) is a clinically heterogeneous hematologic malignancy, with approximately 90% of cases being TP53 wild-type at diagnosis. An increasing number of studies are evaluating alternative targeted agents in CLL, including MDM2-p53 binding antagonists. In this study, we report the effect of splicing modulation on key proteins in the p53 signalling pathway, an important cell death pathway in B cells. Splicing modulation by E7107 treatment reduced full-length MDM2 production due to exon skipping, generating a consequent reciprocal p53 increase in TP53WT cells. It was especially noteworthy that a novel p21WAF1 isoform with compromised cyclin-dependent kinase inhibitory activity was produced due to intron retention. E7107 synergized with the MDM2 inhibitor RG7388, via dual MDM2 inhibition; by E7107 at the transcript level and by RG7388 at the protein level, producing greater p53 stabilisation and apoptosis. This study provides evidence for a synergistic MDM2 and spliceosome inhibitor combination as a novel approach to treat CLL and potentially other haematological malignancies.
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23
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Pellagatti A, Boultwood J. Splicing factor mutations in the myelodysplastic syndromes: Role of key aberrantly spliced genes in disease pathophysiology and treatment. Adv Biol Regul 2023; 87:100920. [PMID: 36216757 DOI: 10.1016/j.jbior.2022.100920] [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: 09/22/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 03/01/2023]
Abstract
Mutations of splicing factor genes (including SF3B1, SRSF2, U2AF1 and ZRSR2) occur in more than half of all patients with myelodysplastic syndromes (MDS), a heterogeneous group of myeloid neoplasms. Splicing factor mutations lead to aberrant pre-mRNA splicing of many genes, some of which have been shown in functional studies to impact on hematopoiesis and to contribute to the MDS phenotype. This clearly demonstrates that impaired spliceosome function plays an important role in MDS pathophysiology. Recent studies that harnessed the power of induced pluripotent stem cell (iPSC) and CRISPR/Cas9 gene editing technologies to generate new iPSC-based models of splicing factor mutant MDS, have further illuminated the role of key downstream target genes. The aberrantly spliced genes and the dysregulated pathways associated with splicing factor mutations in MDS represent potential new therapeutic targets. Emerging data has shown that IRAK4 is aberrantly spliced in SF3B1 and U2AF1 mutant MDS, leading to hyperactivation of NF-κB signaling. Pharmacological inhibition of IRAK4 has shown efficacy in pre-clinical studies and in MDS clinical trials, with higher response rates in patients with splicing factor mutations. Our increasing knowledge of the effects of splicing factor mutations in MDS is leading to the development of new treatments that may benefit patients harboring these mutations.
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Affiliation(s)
- Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
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24
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Kontandreopoulou CN, Kalopisis K, Viniou NA, Diamantopoulos P. The genetics of myelodysplastic syndromes and the opportunities for tailored treatments. Front Oncol 2022; 12:989483. [PMID: 36338673 PMCID: PMC9630842 DOI: 10.3389/fonc.2022.989483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic instability, microenvironmental aberrations, and somatic mutations contribute to the phenotype of myelodysplastic syndrome and the risk for transformation to AML. Genes involved in RNA splicing, DNA methylation, histone modification, the cohesin complex, transcription, DNA damage response pathway, signal transduction and other pathways constitute recurrent mutational targets in MDS. RNA-splicing and DNA methylation mutations seem to occur early and are reported as driver mutations in over 50% of MDS patients. The improved understanding of the molecular landscape of MDS has led to better disease and risk classification, leading to novel therapeutic opportunities. Based on these findings, novel agents are currently under preclinical and clinical development and expected to improve the clinical outcome of patients with MDS in the upcoming years. This review provides a comprehensive update of the normal gene function as well as the impact of mutations in the pathogenesis, deregulation, diagnosis, and prognosis of MDS, focuses on the most recent advances of the genetic basis of myelodysplastic syndromes and their clinical relevance, and the latest targeted therapeutic approaches including investigational and approved agents for MDS.
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25
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Zhao Y, Cai W, Hua Y, Yang X, Zhou J. The Biological and Clinical Consequences of RNA Splicing Factor U2AF1 Mutation in Myeloid Malignancies. Cancers (Basel) 2022; 14:4406. [PMID: 36139566 PMCID: PMC9496927 DOI: 10.3390/cancers14184406] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Mutations of spliceosome genes have been frequently identified in myeloid malignancies with the large-scale application of advanced sequencing technology. U2 small nuclear RNA auxiliary factor 1 (U2AF1), an essential component of U2AF heterodimer, plays a pivotal role in the pre-mRNA splicing processes to generate functional mRNAs. Over the past few decades, the mutation landscape of U2AF1 (most frequently involved S34 and Q157 hotspots) has been drawn in multiple cancers, particularly in myeloid malignancies. As a recognized early driver of myelodysplastic syndromes (MDSs), U2AF1 mutates most frequently in MDS, followed by acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPNs). Here, for the first time, we summarize the research progress of U2AF1 mutations in myeloid malignancies, including the correlations between U2AF1 mutations with clinical and genetic characteristics, prognosis, and the leukemic transformation of patients. We also summarize the adverse effects of U2AF1 mutations on hematopoietic function, and the alterations in downstream alternative gene splicing and biological pathways, thus providing comprehensive insights into the roles of U2AF1 mutations in the myeloid malignancy pathogenesis. U2AF1 mutations are expected to be potential novel molecular markers for myeloid malignancies, especially for risk stratification, prognosis assessment, and a therapeutic target of MDS patients.
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Affiliation(s)
- Yangjing Zhao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Weili Cai
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an 223005, China
| | - Ye Hua
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China
| | - Xiaochen Yang
- Department of Thyroid and Breast Surgery, Affiliated Kunshan Hospital of Jiangsu University, Kunshan 215300, China
| | - Jingdong Zhou
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China
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26
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Zhang F, Chen L. Molecular Threat of Splicing Factor Mutations to Myeloid Malignancies and Potential Therapeutic Modulations. Biomedicines 2022; 10:biomedicines10081972. [PMID: 36009519 PMCID: PMC9405558 DOI: 10.3390/biomedicines10081972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022] Open
Abstract
Splicing factors are frequently mutated in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These mutations are presumed to contribute to oncogenic transformation, but the underlying mechanisms remain incompletely understood. While no specific treatment option is available for MDS/AML patients with spliceosome mutations, novel targeting strategies are actively explored, leading to clinical trials of small molecule inhibitors that target the spliceosome, DNA damage response pathway, and immune response pathway. Here, we review recent progress in mechanistic understanding of splicing factor mutations promoting disease progression and summarize potential therapeutic strategies, which, if successful, would provide clinical benefit to patients carrying splicing factor mutations.
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27
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North K, Benbarche S, Liu B, Pangallo J, Chen S, Stahl M, Bewersdorf JP, Stanley RF, Erickson C, Cho H, Pineda JMB, Thomas JD, Polaski JT, Belleville AE, Gabel AM, Udy DB, Humbert O, Kiem HP, Abdel-Wahab O, Bradley RK. Synthetic introns enable splicing factor mutation-dependent targeting of cancer cells. Nat Biotechnol 2022; 40:1103-1113. [PMID: 35241838 PMCID: PMC9288984 DOI: 10.1038/s41587-022-01224-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/17/2022] [Indexed: 11/16/2022]
Abstract
Many cancers carry recurrent, change-of-function mutations affecting RNA splicing factors. Here, we describe a method to harness this abnormal splicing activity to drive splicing factor mutation-dependent gene expression to selectively eliminate tumor cells. We engineered synthetic introns that were efficiently spliced in cancer cells bearing SF3B1 mutations, but unspliced in otherwise isogenic wild-type cells, to yield mutation-dependent protein production. A massively parallel screen of 8,878 introns delineated ideal intronic size and mapped elements underlying mutation-dependent splicing. Synthetic introns enabled mutation-dependent expression of herpes simplex virus-thymidine kinase (HSV-TK) and subsequent ganciclovir (GCV)-mediated killing of SF3B1-mutant leukemia, breast cancer, uveal melanoma and pancreatic cancer cells in vitro, while leaving wild-type cells unaffected. Delivery of synthetic intron-containing HSV-TK constructs to leukemia, breast cancer and uveal melanoma cells and GCV treatment in vivo significantly suppressed the growth of these otherwise lethal xenografts and improved mouse host survival. Synthetic introns provide a means to exploit tumor-specific changes in RNA splicing for cancer gene therapy.
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Affiliation(s)
- Khrystyna North
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Pangallo
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Sisi Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximilian Stahl
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan Philipp Bewersdorf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline Erickson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jacob T Polaski
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrea E Belleville
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Olivier Humbert
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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Sellin M, Mack R, Rhodes MC, Zhang L, Berg S, Joshi K, Liu S, Wei W, S. J. PB, Larsen P, Taylor RE, Zhang J. Molecular mechanisms by which splice modulator GEX1A inhibits leukaemia development and progression. Br J Cancer 2022; 127:223-236. [PMID: 35422078 PMCID: PMC9296642 DOI: 10.1038/s41416-022-01796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/18/2022] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Splice modulators have been assessed clinically in treating haematologic malignancies exhibiting splice factor mutations and acute myeloid leukaemia. However, the mechanisms by which such modulators repress leukaemia remain to be elucidated. OBJECTIVES The primary goal of this assessment was to assess the molecular mechanism by which the natural splice modulator GEX1A kills leukaemic cells in vitro and within in vivo mouse models. METHODS Using human leukaemic cell lines, we assessed the overall sensitivity these cells have to GEX1A via EC50 analysis. We subsequently analysed its effects using in vivo xenograft mouse models and examined whether cell sensitivities were correlated to genetic characteristics or protein expression levels. We also utilised RT-PCR and RNAseq analyses to determine splice change and RNA expression level differences between sensitive and resistant leukaemic cell lines. RESULTS We found that, in vitro, GEX1A induced an MCL-1 isoform shift to pro-apoptotic MCL-1S in all leukaemic cell types, though sensitivity to GEX1A-induced apoptosis was negatively associated with BCL-xL expression. In BCL-2-expressing leukaemic cells, GEX1A induced BCL-2-dependent apoptosis by converting pro-survival BCL-2 into a cell killer. Thus, GEX1A + selective BCL-xL inhibition induced synergism in killing leukaemic cells, while GEX1A + BCL-2 inhibition showed antagonism in BCL-2-expressing leukaemic cells. In addition, GEX1A sensitised FLT3-ITD+ leukaemic cells to apoptosis by inducing aberrant splicing and repressing the expression of FLT3-ITD. Consistently, in in vivo xenografts, GEX1A killed the bulk of leukaemic cells via apoptosis when combined with BCL-xL inhibition. Furthermore, GEX1A repressed leukaemia development by targeting leukaemia stem cells through inhibiting FASTK mitochondrial isoform expression across sensitive and non-sensitive leukaemia types. CONCLUSION Our study suggests that GEX1A is a potent anti-leukaemic agent in combination with BCL-xL inhibitors, which targets leukaemic blasts and leukaemia stem cells through distinct mechanisms.
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Sette C, Paronetto MP. Somatic Mutations in Core Spliceosome Components Promote Tumorigenesis and Generate an Exploitable Vulnerability in Human Cancer. Cancers (Basel) 2022; 14:cancers14071827. [PMID: 35406598 PMCID: PMC8997811 DOI: 10.3390/cancers14071827] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary High throughput exome sequencing approaches have disclosed recurrent cancer-associated mutations in spliceosomal components, which drive aberrant pre-mRNA processing events and support the tumor phenotype. At the same time, mutations in spliceosome genes and aberrant splicing regulation establish a selective vulnerability of cancer cells to splicing-targeting approaches, which could be exploited therapeutically. It is conceivable that a better understanding of the mechanisms and roles of abnormal splicing in tumor metabolism will facilitate the development of a novel generation of tumor-targeting drugs. In this review, we describe recent advances in the elucidation of the biological impact and biochemical effects of somatic mutations in core spliceosome components on splicing choices and their associated targetable vulnerabilities. Abstract Alternative pre-mRNA processing enables the production of distinct mRNA and protein isoforms from a single gene, thus greatly expanding the coding potential of eukaryotic genomes and fine-tuning gene expression programs. Splicing is carried out by the spliceosome, a complex molecular machinery which assembles step-wise on mRNA precursors in the nucleus of eukaryotic cells. In the last decade, exome sequencing technologies have allowed the identification of point mutations in genes encoding splicing factors as a recurrent hallmark of human cancers, with higher incidence in hematological malignancies. These mutations lead to production of splicing factors that reduce the fidelity of the splicing process and yield splicing variants that are often advantageous for cancer cells. However, at the same time, these mutations increase the sensitivity of transformed cells to splicing inhibitors, thus offering a therapeutic opportunity for novel targeted strategies. Herein, we review the recent literature documenting cancer-associated mutations in components of the early spliceosome complex and discuss novel therapeutic strategies based on small-molecule spliceosome inhibitors that exhibit strong anti-tumor effects, particularly against cancer cells harboring mutations in spliceosomal components.
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Affiliation(s)
- Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro De Bosis, 6, 00135 Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, IRCCS, Via del Fosso di Fiorano 64, 00143 Rome, Italy
- Correspondence:
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30
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Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol Cell 2022; 82:1107-1122.e7. [PMID: 35303483 PMCID: PMC8988922 DOI: 10.1016/j.molcel.2022.02.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Splicing factor mutations are common among cancers, recently emerging as drivers of myeloid malignancies. U2AF1 carries hotspot mutations in its RNA-binding motifs; however, how they affect splicing and promote cancer remain unclear. The U2AF1/U2AF2 heterodimer is critical for 3' splice site (3'SS) definition. To specifically unmask changes in U2AF1 function in vivo, we developed a crosslinking and immunoprecipitation procedure that detects contacts between U2AF1 and the 3'SS AG at single-nucleotide resolution. Our data reveal that the U2AF1 S34F and Q157R mutants establish new 3'SS contacts at -3 and +1 nucleotides, respectively. These effects compromise U2AF2-RNA interactions, resulting predominantly in intron retention and exon exclusion. Integrating RNA binding, splicing, and turnover data, we predicted that U2AF1 mutations directly affect stress granule components, which was corroborated by single-cell RNA-seq. Remarkably, U2AF1-mutant cell lines and patient-derived MDS/AML blasts displayed a heightened stress granule response, pointing to a novel role for biomolecular condensates in adaptive oncogenic strategies.
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Affiliation(s)
- Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
| | - Poorval Joshi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Torben Hunck
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yimeng Gao
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Mark D Lessard
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Edward Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Martin Machyna
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Qin
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yuanbin Song
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Hematologic Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lea Kiefer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, 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
| | - 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; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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Chhipi-Shrestha JK, Schneider-Poetsch T, Suzuki T, Mito M, Khan K, Dohmae N, Iwasaki S, Yoshida M. Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns. Cell Chem Biol 2022; 29:259-275.e10. [PMID: 34520743 PMCID: PMC8857039 DOI: 10.1016/j.chembiol.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/10/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022]
Abstract
Chemical splicing modulators that bind to the spliceosome have provided an attractive avenue for cancer treatment. Splicing modulators induce accumulation and subsequent translation of a subset of intron-retained mRNAs. However, the biological effect of proteins containing translated intron sequences remains unclear. Here, we identify a number of truncated proteins generated upon treatment with the splicing modulator spliceostatin A (SSA) via genome-wide ribosome profiling and bio-orthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry. A subset of these truncated proteins has intrinsically disordered regions, forms insoluble cellular condensates, and triggers the proteotoxic stress response through c-Jun N-terminal kinase (JNK) phosphorylation, thereby inhibiting the mTORC1 pathway. In turn, this reduces global translation. These findings indicate that creating an overburden of condensate-prone proteins derived from introns represses translation and prevents further production of harmful truncated proteins. This mechanism appears to contribute to the antiproliferative and proapoptotic activity of splicing modulators.
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Affiliation(s)
- Jagat K. Chhipi-Shrestha
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Khalid Khan
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Wako, Saitama 351-0198, Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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Wu L, Wang D. The "Janus-like" RNA-editing machinery in innate antiviral immunity. CURRENT TRENDS IN IMMUNOLOGY 2022; 23:23-32. [PMID: 36398055 PMCID: PMC9668064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Our innate immune systems are evolved to provide the first line of immune defense against microbial infections. A key effector component is the adenosine deaminase acting on the RNA-1 (ADAR-1)/interferon (IFN) pathway of the innate cytoplasmic immunity that mounts rapid responses to many viral pathogens. As an RNA-editing enzyme, ADAR-1 targets viral RNA intermediates in the cytoplasmic compartment to interfere with the infection. However, ADAR-1 may also edit characteristic RNA structures of certain host genes, notably, the 5-hydroxytryptamine (serotonin) receptor 2C (5-HT2CR). Dysfunction of 5-HT2CR has been linked to the pathology of several human mental conditions, such as Schizophrenia, anxiety, bipolar disorder, major depression, and the mental illnesses of substance use disorders (SUD). Thus, the ADAR-1-mediated RNA editing may be either beneficial or harmful; these effects need to be tightly modulated to sustain innate antiviral immunity while restricting undesired off-target self-reactivity. In this communication, we discuss ideas and tools to identify the orphan drug candidates, including small molecules and biologics that may serve as effective modulators of the ADAR-1/IFN innate immunity and are thereby promising for use in treating or preventing SUD- and/or viral infection-associated mental illnesses.
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Affiliation(s)
- Lisa Wu
- Tumor Glycomics Laboratory, SRI International Biosciences, 333 Ravenswood Ave., Menlo Park, CA, USA
| | - Denong Wang
- Tumor Glycomics Laboratory, SRI International Biosciences, 333 Ravenswood Ave., Menlo Park, CA, USA
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Luo X, Ren C, Liu X, Zhang G, Huang S, Yu L, Li Y. [Screening of drugs that selectively inhibit uveal melanoma cells with SF3B1 mutations]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1835-1842. [PMID: 35012916 DOI: 10.12122/j.issn.1673-4254.2021.12.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To screen compounds that can selectively inhibit uveal melanoma cells with splicing factor 3B subunit 1 (SF3B1) mutations in comparison with isogenic SF3B1 wild-type counterparts in a cell model of SF3B1 mutant allele knockout. METHODS Principal component analysis was used to analyze transcriptome alternative splicing in TCGA cohorts of uveal melanoma with wild-type SF3B1 and SF3B1 mutations, and abnormal alternative splicing events derived from SF3B1 mutations were identified. The SF3B1 mutant allele in Mel202 cells was knocked out using CRISPR-Cas9 technology, and Sanger sequencing was used to verify the edited sequence. MTT and colony formation assays were used to assess the proliferation of Mel202 and Mut-KO cells. RT-PCR agarose electrophoresis combined with Sanger sequencing was used to determine alternative splicing events in Mel202 and Mut-KO cells. MTT assay was performed to screen the compounds that showed selective inhibitory effect against Mel202 cells with SF3B1 mutation. RESULTS Specific knockout of SF3B1 mutant allele in Mel202 cells obviously promoted the cell proliferation and caused changes in alternative splicing of ZDHHC16 and DYNLL1 transcripts. The screening data showed that 13 compounds had selective inhibitory activity against Mel202 cells with SF3B1 mutation (Fold change≥2), and among them, tetrandrine and lapatinib showed good dose-effect curves. CONCLUSION This study provides a cell screening model for identification of potential individualized treatment drugs for patients with uveal melanoma with SF3B1 mutation.
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Affiliation(s)
- X Luo
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - C Ren
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - X Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - G Zhang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - S Huang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - L Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Y Li
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Wadugu BA, Nonavinkere Srivatsan S, Heard A, Alberti MO, Ndonwi M, Liu J, Grieb S, Bradley J, Shao J, Ahmed T, Shirai CL, Khanna A, Fei DL, Miller CA, Graubert TA, Walter MJ. U2af1 is a haplo-essential gene required for hematopoietic cancer cell survival in mice. J Clin Invest 2021; 131:141401. [PMID: 34546980 DOI: 10.1172/jci141401] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Somatic mutations in the spliceosome gene U2AF1 are common in patients with myelodysplastic syndromes. U2AF1 mutations that code for the most common amino acid substitutions are always heterozygous, and the retained WT allele is expressed, suggesting that mutant hematopoietic cells may require the residual WT allele to be viable. We show that hematopoiesis and RNA splicing in U2af1 heterozygous knockout mice were similar to those in control mice, but that deletion of the WT allele in U2AF1(S34F) heterozygous mutant-expressing hematopoietic cells (i.e., hemizygous mutant) was lethal. These results confirm that U2AF1 mutant hematopoietic cells are dependent on the expression of WT U2AF1 for survival in vivo and that U2AF1 is a haplo-essential cancer gene. Mutant U2AF1(S34F)-expressing cells were also more sensitive to reduced expression of WT U2AF1 than nonmutant cells. Furthermore, mice transplanted with leukemia cells expressing mutant U2AF1 had significantly reduced tumor burden and improved survival after the WT U2af1 allele was deleted compared with when it was not deleted. These results suggest that selectively targeting the WT U2AF1 allele in heterozygous mutant cells could induce cancer cell death and be a therapeutic strategy for patients harboring U2AF1 mutations.
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Affiliation(s)
| | | | - Amanda Heard
- Division of Oncology, Department of Medicine and
| | - Michael O Alberti
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Jie Liu
- Division of Oncology, Department of Medicine and
| | - Sarah Grieb
- Division of Oncology, Department of Medicine and
| | | | - Jin Shao
- Division of Oncology, Department of Medicine and
| | - Tanzir Ahmed
- Division of Oncology, Department of Medicine and
| | | | - Ajay Khanna
- Division of Oncology, Department of Medicine and
| | - Dennis L Fei
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA.,Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | - Timothy A Graubert
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
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PRMT5: An Emerging Target for Pancreatic Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13205136. [PMID: 34680285 PMCID: PMC8534199 DOI: 10.3390/cancers13205136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The burden of pancreatic ductal adenocarcinoma (PDAC) increases with rising incidence, yet 5-year overall survival remains poor at 17%. Routine comprehensive genomic profiling of PDAC only finds 2.5% of patients who may benefit and receive matched targeted therapy. Protein arginine methyltransferase 5 (PRMT5) as an anti-cancer target has gained significant interest in recent years and high levels of PRMT5 protein are associated with worse survival outcomes across multiple cancer types. Inhibition of PRMT5 in pre-clinical models can lead to cancer growth inhibition. However, PRMT5 is involved in multiple cellular processes, thus determining its mechanism of action is challenging. While past reviews on PRMT5 have focused on its role in diverse cellular processes and past research studies have focused mainly on haematological malignancies and glioblastoma, this review provides an overview of the possible biological mechanisms of action of PRMT5 inhibition and its potential as a treatment in pancreatic cancer. Abstract The overall survival of pancreatic ductal adenocarcinoma (PDAC) remains poor and its incidence is rising. Targetable mutations in PDAC are rare, thus novel therapeutic approaches are needed. Protein arginine methyltransferase 5 (PRMT5) overexpression is associated with worse survival and inhibition of PRMT5 results in decreased cancer growth across multiple cancers, including PDAC. Emerging evidence also suggests that altered RNA processing is a driver in PDAC tumorigenesis and creates a partial dependency on this process. PRMT5 inhibition induces altered splicing and this vulnerability can be exploited as a novel therapeutic approach. Three possible biological pathways underpinning the action of PRMT5 inhibitors are discussed; c-Myc regulation appears central to its action in the PDAC setting. Whilst homozygous MTAP deletion and symmetrical dimethylation levels are associated with increased sensitivity to PRMT5 inhibition, neither measure robustly predicts its growth inhibitory response. The immunomodulatory effect of PRMT5 inhibitors on the tumour microenvironment will also be discussed, based on emerging evidence that PDAC stroma has a significant bearing on disease behaviour and response to therapy. Lastly, with the above caveats in mind, current knowledge gaps and the implications and rationales for PRMT5 inhibitor development in PDAC will be explored.
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Promoting spliceosome assembly for therapeutic intent. Trends Pharmacol Sci 2021; 42:981-983. [PMID: 34602305 DOI: 10.1016/j.tips.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/23/2022]
Abstract
RNA splicing, the process by which precursor mRNA (pre-mRNA) is processed to mature mRNA, is catalyzed by the spliceosome. Recently, Chatrikhi et al. identified pharmacologic means to perturb splicing by enhancing the spliceosome's binding to pre-mRNA. This represents a novel chemical target and mechanism for therapeutic modulation of splicing.
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A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell Chem Biol 2021; 28:1145-1157.e6. [PMID: 33689684 PMCID: PMC8380659 DOI: 10.1016/j.chembiol.2021.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 12/20/2022]
Abstract
Dysregulated pre-mRNA splicing is an emerging Achilles heel of cancers and myelodysplasias. To expand the currently limited portfolio of small-molecule drug leads, we screened for chemical modulators of the U2AF complex, which nucleates spliceosome assembly and is mutated in myelodysplasias. A hit compound specifically enhances RNA binding by a U2AF2 subunit. Remarkably, the compound inhibits splicing of representative substrates and stalls spliceosome assembly at the stage of U2AF function. Computational docking, together with structure-guided mutagenesis, indicates that the compound bridges the tandem U2AF2 RNA recognition motifs via hydrophobic and electrostatic moieties. Cells expressing a cancer-associated U2AF1 mutant are preferentially killed by treatment with the compound. Altogether, our results highlight the potential of trapping early spliceosome assembly as an effective pharmacological means to manipulate pre-mRNA splicing. By extension, we suggest that stabilizing assembly intermediates may offer a useful approach for small-molecule inhibition of macromolecular machines.
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Therapeutic approaches targeting splicing factor mutations in myelodysplastic syndromes and acute myeloid leukemia. Curr Opin Hematol 2021; 28:73-79. [PMID: 33492002 DOI: 10.1097/moh.0000000000000632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Mutations in components of the spliceosome are the most common acquired lesions in myelodysplastic syndromes (MDS) and are frequently identified in other myeloid malignancies with a high rate of progression to acute myeloid leukemia (AML) including chronic myelomonocytic leukemia and primary myelofibrosis. The only curative option for these disorders remains allogeneic stem-cell transplantation, which is associated with high morbidity and mortality in these patients. The purpose of this review is to highlight the recent therapeutic developments and strategies being pursued for clinical benefit in splicing factor mutant myeloid malignancies. RECENT FINDINGS Cells harboring splicing factor mutations have increased aberrant splicing leading to R-loop formation and cell cycle stalling that create dependencies on Checkpoint kinase 1 (CHK1) activation and canonical splicing maintained by protein arginine methyltransferase activity. Both targeting of the spliceosome and targeting of the downstream consequences of splicing factor mutation expression show promise as selective strategies for the treatment of splicing factor-mutant myeloid malignancies. SUMMARY An improved understanding of the therapeutic vulnerabilities in splicing factor-mutant MDS and AML has led to the development of clinical trials of small molecule inhibitors that target the spliceosome, ataxia telangectasia and Rad3 related (ATR)-CHK1 pathway, and methylation of splicing components.
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U2af1 is required for survival and function of hematopoietic stem/progenitor cells. Leukemia 2021; 35:2382-2398. [PMID: 33414485 PMCID: PMC8283943 DOI: 10.1038/s41375-020-01116-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023]
Abstract
U2AF1 is involved in the recognition of the 3' splice site during pre-mRNA splicing. Mutations in U2AF1 are frequently observed in myelodysplastic syndromes. However, the role of wild-type U2AF1 in normal hematopoiesis has remained elusive. Using a novel conditional U2af1 knockout allele, we have found that deletion of U2af1 results in profound defects in hematopoiesis characterized by pancytopenia, ablation of hematopoietic stem/progenitor cells (HSPC) leading to bone marrow failure and early lethality in mice. U2af1 deletion impairs HSPC function and repopulation capacity. U2af1 deletion also causes increased DNA damage and reduced survival in hematopoietic progenitors. RNA sequencing analysis reveals significant alterations in the expression of genes related to HSC maintenance, cell proliferation, and DNA damage response-related pathways in U2af1-deficient HSPC. U2af1 deficiency also induces splicing alterations in genes important for HSPC function. This includes altered splicing and perturbed expression of Nfya and Pbx1 transcription factors in U2af1-deficient HSPC. Collectively, these results suggest an important role for U2af1 in the maintenance and function of HSPC in normal hematopoiesis. A better understanding of the normal function of U2AF1 in hematopoiesis is important for development of appropriate therapeutic approaches for U2AF1 mutant induced hematologic malignancies.
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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Zhan D, Park CY. Stem Cells in the Myelodysplastic Syndromes. FRONTIERS IN AGING 2021; 2:719010. [PMID: 35822030 PMCID: PMC9261372 DOI: 10.3389/fragi.2021.719010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/02/2021] [Indexed: 01/12/2023]
Abstract
The myelodysplastic syndromes (MDS) represent a group of clonal disorders characterized by ineffective hematopoiesis, resulting in peripheral cytopenias and frequent transformation to acute myeloid leukemia (AML). We and others have demonstrated that MDS arises in, and is propagated by malignant stem cells (MDS-SCs), that arise due to the sequential acquisition of genetic and epigenetic alterations in normal hematopoietic stem cells (HSCs). This review focuses on recent advancements in the cellular and molecular characterization of MDS-SCs, as well as their role in mediating MDS clinical outcomes. In addition to discussing the cell surface proteins aberrantly upregulated on MDS-SCs that have allowed the identification and prospective isolation of MDS-SCs, we will discuss the recurrent cytogenetic abnormalities and genetic mutations present in MDS-SCs and their roles in initiating disease, including recent studies demonstrating patterns of clonal evolution and disease progression from pre-malignant HSCs to MDS-SCs. We also will discuss the pathways that have been described as drivers or promoters of disease, including hyperactivated innate immune signaling, and how the identification of these alterations in MDS-SC have led to investigations of novel therapeutic strategies to treat MDS. It is important to note that despite our increasing understanding of the pathogenesis of MDS, the molecular mechanisms that drive responses to therapy remain poorly understood, especially the mechanisms that underlie and distinguish hematologic improvement from reductions in blast burden. Ultimately, such distinctions will be required in order to determine the shared and/or unique molecular mechanisms that drive ineffective hematopoiesis, MDS-SC maintenance, and leukemic transformation.
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Affiliation(s)
- Di Zhan
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, United States
| | - Christopher Y. Park
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, United States
- *Correspondence: Christopher Y. Park,
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Cheruiyot A, Li S, Nonavinkere Srivatsan S, Ahmed T, Chen Y, Lemacon DS, Li Y, Yang Z, Wadugu BA, Warner WA, Pruett-Miller SM, Obeng EA, Link DC, He D, Xiao F, Wang X, Bailis JM, Walter MJ, You Z. Nonsense-Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells Harboring SF3B1 or U2AF1 Mutations. Cancer Res 2021; 81:4499-4513. [PMID: 34215620 DOI: 10.1158/0008-5472.can-20-4016] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/26/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTC) for degradation, however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system to accurately measure NMD activity in individual cells. A genome-wide CRISPR-Cas9 knockout screen using this reporter system identified novel NMD-promoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, cells with mutations in the spliceosome genes SF3B1 and U2AF1, which are commonly found in myelodysplastic syndrome (MDS) and cancers, have overall attenuated NMD activity. Compared with wild-type (WT) cells, SF3B1- and U2AF1-mutant cells were more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage, and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition was rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, these findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel synthetic lethal strategy for the treatment of MDS and cancers with spliceosome mutations. SIGNIFICANCE: This study has developed a novel NMD reporter system and identified a potential therapeutic approach of targeting the NMD pathway to treat cancer with spliceosome gene mutations.
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Affiliation(s)
- Abigael Cheruiyot
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Shan Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Sridhar Nonavinkere Srivatsan
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Tanzir Ahmed
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Yuhao Chen
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Delphine S Lemacon
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Ying Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Zheng Yang
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Brian A Wadugu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Wayne A Warner
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Esther A Obeng
- Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Daniel C Link
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Dalin He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Fei Xiao
- Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xiaowei Wang
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | | | - Matthew J Walter
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Zhongsheng You
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.
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Splicing factor mutations in hematologic malignancies. Blood 2021; 138:599-612. [PMID: 34157091 DOI: 10.1182/blood.2019004260] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/02/2020] [Indexed: 12/15/2022] Open
Abstract
Mutations in genes encoding RNA splicing factors were discovered nearly ten years ago and are now understood to be amongst the most recurrent genetic abnormalities in patients with all forms of myeloid neoplasms and several types of lymphoproliferative disorders as well as subjects with clonal hematopoiesis. These discoveries implicate aberrant RNA splicing, the process by which precursor RNA is converted into mature messenger RNA, in the development of clonal hematopoietic conditions. Both the protein as well as the RNA components of the splicing machinery are affected by mutations at highly specific residues and a number of these mutations alter splicing in a manner distinct from loss of function. Importantly, cells bearing these mutations have now been shown to generate mRNA species with novel aberrant sequences, some of which may be critical to disease pathogenesis and/or novel targets for therapy. These findings have opened new avenues of research to understand biological pathways disrupted by altered splicing. In parallel, multiple studies have revealed that cells bearing change-of-function mutation in splicing factors are preferentially sensitized to any further genetic or chemical perturbations of the splicing machinery. These discoveries are now being pursued in several early phase clinical trials using molecules with diverse mechanisms of action. Here we review the molecular effects of splicing factor mutations on splicing, mechanisms by which these mutations drive clonal transformation of hematopoietic cells, and the development of new therapeutics targeting these genetic subsets of hematopoietic malignancies.
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Zhang L, Zhang Y, Hu X. Targeting the transcription cycle and RNA processing in cancer treatment. Curr Opin Pharmacol 2021; 58:69-75. [PMID: 33964728 DOI: 10.1016/j.coph.2021.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/24/2022]
Abstract
The transcriptional program and RNA splicing machinery are highly and frequently dysregulated in human cancers due to genomic and epigenomic alterations during tumorigenesis. This leads to cancer-specific dependencies on components of the transcriptional program and RNA splicing machinery, providing alternative and targetable 'Achilles' heels' for cancer treatment in the clinic. To target these vulnerabilities in cancer cells, potent and specific transcriptional CDK inhibitors and chemical compounds that impair splicing have been developed and evaluated in preclinical cancer models. Several novel combination approaches with immune or targeted therapies have also been proposed for cancer treatment. More recently, inhibitors targeting transcriptional CDKs, splicing, or PRMT5 have shown promising therapeutic potential in preclinical studies, and many of them have rapidly advanced into early clinical trials for treatment of human cancer.
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Affiliation(s)
- Lin Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Youyou Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaowen Hu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.
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Kitamura K, Nimura K. Regulation of RNA Splicing: Aberrant Splicing Regulation and Therapeutic Targets in Cancer. Cells 2021; 10:923. [PMID: 33923658 PMCID: PMC8073995 DOI: 10.3390/cells10040923] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/16/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023] Open
Abstract
RNA splicing is a critical step in the maturation of precursor mRNA (pre-mRNA) by removing introns and exons. The combination of inclusion and exclusion of introns and exons in pre-mRNA can generate vast diversity in mature mRNA from a limited number of genes. Cancer cells acquire cancer-specific mechanisms through aberrant splicing regulation to acquire resistance to treatment and to promote malignancy. Splicing regulation involves many factors, such as proteins, non-coding RNAs, and DNA sequences at many steps. Thus, the dysregulation of splicing is caused by many factors, including mutations in RNA splicing factors, aberrant expression levels of RNA splicing factors, small nuclear ribonucleoproteins biogenesis, mutations in snRNA, or genomic sequences that are involved in the regulation of splicing, such as 5' and 3' splice sites, branch point site, splicing enhancer/silencer, and changes in the chromatin status that affect the splicing profile. This review focuses on the dysregulation of RNA splicing related to cancer and the associated therapeutic methods.
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Affiliation(s)
- Koji Kitamura
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan;
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Keisuke Nimura
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan;
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Asian Population Is More Prone to Develop High-Risk Myelodysplastic Syndrome, Concordantly with Their Propensity to Exhibit High-Risk Cytogenetic Aberrations. Cancers (Basel) 2021; 13:cancers13030481. [PMID: 33513838 PMCID: PMC7865620 DOI: 10.3390/cancers13030481] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The world population is genetically and environmentally diverse. In particular, genetic differences related to an ethnic factor may underlie differences in cancer phenotypic expression. Therefore, we compared the epidemiology, and the clinical, biological and genetic characteristics of myelodysplastic syndrome (MDS) between Asian and Western countries. Our results show substantial differences in the incidence and age of onset between Asian and Western MDS patients. A higher proportion of Asian MDS patients fall into the high- and very-high risk prognostic MDS groups. This finding is supported by the identification of a higher proportion of high-risk cytogenetic aberrations in Asian MDS patients. However, the survival rate is similar for Western and Asian MDS patients. Our findings may impact the clinical management as well as the strategy of clinical trials targeting those genetic aberrations and mutations depending on the world area where they are run. Abstract This study explores the hypothesis that genetic differences related to an ethnic factor may underlie differences in phenotypic expression of myelodysplastic syndrome (MDS). First, to identify clear ethnic differences, we systematically compared the epidemiology, and the clinical, biological and genetic characteristics of MDS between Asian and Western countries over the last 20 years. Asian MDS cases show a 2- to 4-fold lower incidence and a 10-year younger age of onset compared to the Western cases. A higher proportion of Western MDS patients fall into the very low- and low-risk categories while the intermediate, high and very high-risk groups are more represented in Asian MDS patients according to the Revised International Prognostic Scoring System. Next, we investigated whether differences in prognostic risk scores could find their origin in differential cytogenetic profiles. We found that 5q deletion (del(5q)) aberrations and mutations in TET2, SF3B1, SRSF2 and IDH1/2 are more frequently reported in Western MDS patients while trisomy 8, del(20q), U2AF1 and ETV6 mutations are more frequent in Asian MDS patients. Treatment approaches differ between Western and Asian countries owing to the above discrepancies, but the overall survival rate within each prognostic group is similar for Western and Asian MDS patients. Altogether, our study highlights greater risk MDS in Asians supported by their cytogenetic profile.
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Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TYT, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XHF, Westbrook TF. Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer. Cell 2021; 184:384-403.e21. [PMID: 33450205 PMCID: PMC8635244 DOI: 10.1016/j.cell.2020.12.031] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022]
Abstract
Many oncogenic insults deregulate RNA splicing, often leading to hypersensitivity of tumors to spliceosome-targeted therapies (STTs). However, the mechanisms by which STTs selectively kill cancers remain largely unknown. Herein, we discover that mis-spliced RNA itself is a molecular trigger for tumor killing through viral mimicry. In MYC-driven triple-negative breast cancer, STTs cause widespread cytoplasmic accumulation of mis-spliced mRNAs, many of which form double-stranded structures. Double-stranded RNA (dsRNA)-binding proteins recognize these endogenous dsRNAs, triggering antiviral signaling and extrinsic apoptosis. In immune-competent models of breast cancer, STTs cause tumor cell-intrinsic antiviral signaling, downstream adaptive immune signaling, and tumor cell death. Furthermore, RNA mis-splicing in human breast cancers correlates with innate and adaptive immune signatures, especially in MYC-amplified tumors that are typically immune cold. These findings indicate that dsRNA-sensing pathways respond to global aberrations of RNA splicing in cancer and provoke the hypothesis that STTs may provide unexplored strategies to activate anti-tumor immune pathways.
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Affiliation(s)
- Elizabeth A Bowling
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jarey H Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fade Gong
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - William Wu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas J Neill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ik Sun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Siddhartha Tyagi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mayra Orellana
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah J Kurley
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rocio Dominguez-Vidaña
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hsiang-Ching Chung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tiffany Y-T Hsu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander B Saltzman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Heyuan Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jitendra K Meena
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gino M Canlas
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swarnima Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Calla M Olson
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - George Miles
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lihua Yu
- H3Biomedicine, Cambridge, MA 02139, USA
| | | | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristen L Karlin
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
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Schneider-Poetsch T, Chhipi-Shrestha JK, Yoshida M. Splicing modulators: on the way from nature to clinic. J Antibiot (Tokyo) 2021; 74:603-616. [PMID: 34345042 PMCID: PMC8472923 DOI: 10.1038/s41429-021-00450-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Over the course of more than two decades, natural products isolated from various microorganisms and plants have built the foundation for chemical biology research into the mechanism of pre-mRNA splicing. Hand in hand with advances in scientific methodology small molecule splicing modulators have become powerful tools for investigating, not just the splicing mechanism, but also the cellular effect of altered mRNA processing. Based on thorough structure-activity studies, synthetic analogues have moved on from scientific tool compounds to experimental drugs. With current advances in drug discovery methodology and new means of attacking targets previously thought undruggable, we can expect further advances in both research and therapeutics based on small molecule splicing modulators.
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Affiliation(s)
- Tilman Schneider-Poetsch
- grid.509461.fChemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan
| | | | - Minoru Yoshida
- grid.509461.fChemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo Japan
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Pellagatti A, Boultwood J. SF3B1 mutant myelodysplastic syndrome: Recent advances. Adv Biol Regul 2020; 79:100776. [PMID: 33358369 DOI: 10.1016/j.jbior.2020.100776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022]
Abstract
The myelodysplastic syndromes (MDS) are common myeloid malignancies. Mutations in genes encoding different components of the spliceosome occur in more than half of all MDS patients. SF3B1 is the most frequently mutated splicing factor gene in MDS, and there is a strong association between SF3B1 mutations and the presence of ring sideroblasts in the bone marrow of MDS patients. It has been recently proposed that SF3B1 mutant MDS should be recognized as a distinct nosologic entity. Splicing factor mutations cause aberrant pre-mRNA splicing of many target genes, some of which have been shown to impact on hematopoiesis in functional studies. Emerging data show that some of the downstream effects of different mutated splicing factors converge on common cellular processes, such as hyperactivation of NF-κB signaling and increased R-loops. The aberrantly spliced target genes and the dysregulated pathways and cellular processes associated with splicing factor mutations provided the rationale for new potential therapeutic approaches to target MDS cells with mutations of SF3B1 and other splicing factors.
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Affiliation(s)
- Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, And NIHR Oxford BRC Haematology Theme, Oxford, UK.
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, And NIHR Oxford BRC Haematology Theme, Oxford, UK.
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Spliceosome Mutations in Uveal Melanoma. Int J Mol Sci 2020; 21:ijms21249546. [PMID: 33333932 PMCID: PMC7765440 DOI: 10.3390/ijms21249546] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy of the eye. It has a high metastatic potential and mainly spreads to the liver. Genetics play a vital role in tumor classification and prognostication of UM metastatic disease. One of the driver genes mutated in metastasized UM is subunit 1 of splicing factor 3b (SF3B1), a component of the spliceosome complex. Recurrent mutations in components of the spliceosome complex are observed in UM and other malignancies, suggesting an important role in tumorigenesis. SF3B1 is the most common mutated spliceosome gene and in UM it is associated with late-onset metastasis. This review summarizes the genetic and epigenetic insights of spliceosome mutations in UM. They form a distinct subgroup of UM and have similarities with other spliceosome mutated malignancies.
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