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Yu Y, Hu J, Wang W, Lei H, Xi Z, Zhang P, Zhao E, Lu C, Chen H, Liu C, Li L. Targeting PSMD14 combined with arachidonic acid induces synthetic lethality via FADS1 m 6A modification in triple-negative breast cancer. SCIENCE ADVANCES 2025; 11:eadr3173. [PMID: 40344056 PMCID: PMC12063657 DOI: 10.1126/sciadv.adr3173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 04/03/2025] [Indexed: 05/11/2025]
Abstract
Dysregulation of deubiquitination is essential for cancer growth. However, the role of 26S proteasome non-ATPase regulatory subunit 14 (PSMD14) in the progression of triple-negative breast cancer (TNBC) remains to be determined. Gain- and loss-of-function experiments showed that silencing PSMD14 notably attenuated the growth, invasion, and metastasis of TNBC cells in vitro and in vivo. Overexpression of PSMD14 produced the opposite results. Mechanistically, PSMD14 decreased K63-linked ubiquitination on SF3B4 protein to de-ubiquitin and stabilize SF3B4 protein. Then, SF3B4/HNRNPC complex bound to FADS1 mRNA and promoted exon inclusion in the target mRNA through m6A site on FADS1 mRNA recognized by HNRNPC, thereby up-regulating the expression of FADS1 and activating Akt/mTOR signaling. Exogenous arachidonic acid supplementation combined with PSMD14 knockdown induced synthetic lethality, which was further confirmed in TNBC organoid (PDO) and TNBC patient-derived xenograft (PDX) mouse models. Overall, our findings reveal an oncogenic role of PSMD14 in TNBC progression, which indicates a potential biomarker and ferroptosis-mediated therapeutic strategy for TNBC.
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Affiliation(s)
- Yuanhang Yu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Jin Hu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Wenwen Wang
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hao Lei
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University and Key Laboratory of Tropical Translational Medicine of Ministry of Education and School of Tropical Medicine, Hainan Medical University, Haikou 570311, China
| | - Zihan Xi
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Peiyi Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Ende Zhao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chong Lu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hengyu Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University and Key Laboratory of Tropical Translational Medicine of Ministry of Education and School of Tropical Medicine, Hainan Medical University, Haikou 570311, China
| | - Chunping Liu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lei Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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Khan S, Tang Y, Guo Y, Feng J, Wu H, Song Z, Zhang C, Qin F. Revealing the role of U2AF1 in splicing regulation and chimeric RNA dynamics. Sci Rep 2025; 15:16235. [PMID: 40346396 PMCID: PMC12064656 DOI: 10.1038/s41598-025-99865-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 04/23/2025] [Indexed: 05/11/2025] Open
Abstract
U2 small nuclear ribonucleoprotein auxiliary factor 1 (U2AF1) gene is a pivotal splicing factor frequently mutated in various malignancies, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). U2AF1 plays a critical role in the recognition and processing of 3' splice sites during pre-mRNA splicing, thereby contributing to the regulation of gene expression and the generation of protein diversity. However, how U2AF1 contributes to the formation and regulation of different categories of chimeric RNAs remains elusive. In this study, we aimed to elucidate the involvement of U2AF1 in chimeric RNA formation and its regulatory impact on different categories of chimeric RNA. Employing knockdown and overexpression strategies in leukemia and esophageal cancer cell lines, we conducted paired-end RNA sequencing following U2AF1 knockdown to assess transcriptomic alterations and their influence on alternative splicing patterns. Subsequently, we utilized the SOAPfuse algorithm to detect and characterize chimeric RNAs from the paired-end RNA sequencing data. Our findings unveiled significant changes in the landscape of chimeric RNA upon U2AF1 knockdown, highlighting its critical role in chimeric RNA formation. This study provides novel insights into how U2AF1 mediates chimeric RNA formation and regulates distinct categories of chimeric RNA within leukemia cell lines. Thereby highlighting its potential as a biomarker for leukemia and other malignancies, promising avenues for future diagnostic and therapeutic developments.
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Affiliation(s)
- Sangeen Khan
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yue Tang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yangyang Guo
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Clinical Laboratory, Zhenjiang Center for Disease Control and Prevention, Zhenjiang, 212000, Jiangsu, China
| | - Jing Feng
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
- School of Medicine Laboratory, North Henan Medical University, Xinxiang, 453003, Henan, China
| | - Hui Wu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhenguo Song
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, Henan, China
| | - Chengjuan Zhang
- Center of Bio-Repository, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, Henan, China
| | - Fujun Qin
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- State Key Laboratory of Metabolic Dysregulation & Prevention and Treatment of Esophageal Cancer, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- School of Medicine Laboratory, North Henan Medical University, Xinxiang, 453003, Henan, China.
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3
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Li D, Shao F, Li X, Yu Q, Wu R, Wang J, Wang Z, Wusiman D, Ye L, Guo Y, Tuo Z, Wei W, Yoo KH, Cho WC, Feng D. Advancements and challenges of R-loops in cancers: Biological insights and future directions. Cancer Lett 2025; 610:217359. [PMID: 39613219 DOI: 10.1016/j.canlet.2024.217359] [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: 10/08/2024] [Revised: 11/24/2024] [Accepted: 11/25/2024] [Indexed: 12/01/2024]
Abstract
R-loops involve in various biological processes under human normal physiological conditions. Disruption of R-loops can lead to disease onset and affect the progression of illnesses, particularly in cancers. Herein, we summarized and discussed the regulative networks, phenotypes and future directions of R-loops in cancers. In this review, we highlighted the following insights: (1) R-loops significantly influence cancer development, progression and treatment efficiency by regulating key genes, such as PARPs, BRCA1/2, sex hormone receptors, DHX9, and TOP1. (2) Currently, the ATM, ATR, cGAS/STING, and noncanonical pathways are the main pathways that involve in the regulatory network of R-loops in cancer. (3) Cancer biology can be modulated by R-loops-regulated phenotypes, including RNA methylation, DNA and histone methylation, oxidative stress, immune and inflammation regulation, and senescence. (4) Regulation of R-loops induces kinds of drug resistance in various cancers, suggesting that targeting R-loops maybe a promising way to overcome treatment resistance. (5) The role of R-loops in tumorigenesis remains controversial, and senescence may be a crucial research direction to unravel the mechanism of R-loop-induced tumorigenesis. Looking forward, further studies are needed to elucidate the specific mechanisms of R-loops in cancer, laying the groundwork for preclinical and clinical research.
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Affiliation(s)
- Dengxiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fanglin Shao
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Xinrui Li
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Qingxin Yu
- Department of Pathology, Ningbo Clinical Pathology Diagnosis Center, Ningbo City, Zhejiang Province, 315211, China
| | - Ruicheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhipeng Wang
- Department of Urology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Dilinaer Wusiman
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Luxia Ye
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Yiqing Guo
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Zhouting Tuo
- Department of Urological Surgery, Daping Hospital, Army Medical Center of PLA, Army Medical University, Chongqing, China
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Koo Han Yoo
- Department of Urology, Kyung Hee University, South Korea.
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region of China.
| | - Dechao Feng
- Division of Surgery & Interventional Science, University College London, London, W1W 7TS, UK.
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4
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Scott KA, Kojima H, Ropek N, Warren CD, Zhang TL, Hogg SJ, Sanford H, Webster C, Zhang X, Rahman J, Melillo B, Cravatt BF, Lyu J, Abdel-Wahab O, Vinogradova EV. Covalent targeting of splicing in T cells. Cell Chem Biol 2025; 32:201-218.e17. [PMID: 39591969 PMCID: PMC12068509 DOI: 10.1016/j.chembiol.2024.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 10/21/2024] [Accepted: 10/24/2024] [Indexed: 11/28/2024]
Abstract
Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and extensive ITK mRNA alternative splicing. We further introduce the most comprehensive list to date of proteins involved in splicing and leverage cysteine- and protein-directed activity-based protein profiling with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.
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Affiliation(s)
- Kevin A Scott
- Department of Chemical Immunology and Proteomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hiroyuki Kojima
- Department of Chemical Immunology and Proteomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Nathalie Ropek
- Department of Chemical Immunology and Proteomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Charles D Warren
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY 10021, USA
| | - Tiffany L Zhang
- Department of Chemical Immunology and Proteomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY 10021, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Henry Sanford
- Department of Chemical Immunology and Proteomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Caroline Webster
- Department of Chemical Immunology and Proteomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Xiaoyu Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiankun Lyu
- The Evnin Family Laboratory of Computational Molecular Discovery, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ekaterina V Vinogradova
- Department of Chemical Immunology and Proteomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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5
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Chen MX, Tian Y, Zhu FY, Fan T, Yan HX, Sun PC, Li M, Hou XX, Lin P, Song YC, Yang X, Lu CM, Yang JC, Reddy ASN, Zhang JH, Liu YG. Alternative splicing of VRF1 acts as a molecular switch to regulate stress-induced early flowering. Cell Rep 2024; 43:114918. [PMID: 39488828 DOI: 10.1016/j.celrep.2024.114918] [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: 11/01/2023] [Revised: 06/13/2024] [Accepted: 10/11/2024] [Indexed: 11/05/2024] Open
Abstract
Plants frequently evade extreme environmental stress by initiating early flowering, yet the underlying mechanisms remain incompletely understood. Here, through extensive mutant screening, we identify a vegetative growth to reproductive growth transition factor (vrf1) mutant, which exhibits a deficiency in drought escape. Alternative splicing of VRF1 generates four isoforms, of which two encode functional proteins, VRF1-AS1 and VRF1-AS3. The proportions of VRF1-AS1 and VRF1-AS3 are modulated by environmental factors, serving as a molecular switch mediating the transition from tolerance to early flowering, irrespective of their absolute abundance. VRF1-AS1 and VRF1-AS3 competitively bind to MKK1, resulting in MKK1 phosphorylation at different sites, which opens two distinct regulatory pathways. The role of VRF1 is conserved across various conditions, and 66 Arabidopsis ecotypes suggest its central function in stress avoidance through premature flowering. In summary, our findings show that plants respond precisely and effectively to dynamic environmental changes by modulating their isoform ratios.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Yuan Tian
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Fu-Yuan Zhu
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Tao Fan
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Hong-Xue Yan
- College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Peng-Cheng Sun
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Min Li
- College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Xuan-Xuan Hou
- College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Ping Lin
- College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Yu-Chen Song
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Xue Yang
- College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Cong-Ming Lu
- College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Jian-Chang Yang
- College of Agriculture, Yangzhou University, Yangzhou 225000, Jiangsu Province, China
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jian-Hua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ying-Gao Liu
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, China; College of Life Science, Shandong Agricultural University, Taian, Shandong, China.
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6
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De Sousa SMC, McCormack A, Orsmond A, Shen A, Yates CJ, Clifton-Bligh R, Santoreneos S, King J, Feng J, Toubia J, Torpy DJ, Scott HS. Increased Prevalence of Germline Pathogenic CHEK2 Variants in Individuals With Pituitary Adenomas. J Clin Endocrinol Metab 2024; 109:2720-2728. [PMID: 38651569 PMCID: PMC11479685 DOI: 10.1210/clinem/dgae268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
CONTEXT CHEK2 is a cell cycle checkpoint regulator gene with a long-established role as a clinically relevant, moderate risk breast cancer predisposition gene, with greater risk ascribed to truncating variants than missense variants. OBJECTIVE To assess the rate and pathogenicity of CHEK2 variants amongst individuals with pituitary adenomas (PAs). METHODS We assessed 165 individuals with PAs for CHEK2 variants. The study population comprised a primary cohort of 29 individuals who underwent germline and tumor whole-exome sequencing, and a second, independent cohort of 136 individuals who had a targeted next-generation sequencing panel performed on both germline and tumor DNA (n = 52) or germline DNA alone (n = 84). RESULTS We identified rare, coding, nonsynonymous germline CHEK2 variants amongst 3 of 29 (10.3%) patients in our primary cohort, and in 5 of 165 (3.0%) patients overall, with affected patients having a range of PA types (prolactinoma, thyrotropinoma, somatotropinoma, and nonfunctioning PA). No somatic variants were identified. Two variants were definitive null variants (c.1100delC, c.444 + 1G > A), classified as pathogenic. Two variants were missense variants (p.Asn186His, p.Thr476Met), classified as likely pathogenic. Even when considering the null variants only, the rate of CHEK2 variants was higher in our cohort compared to national control data (1.8% vs 0.5%; P = .049). CONCLUSION This is the first study to suggest a role for the breast cancer predisposition gene, CHEK2, in pituitary tumorigenesis, with pathogenic/likely pathogenic variants found in 3% of patients with PAs. As PAs are relatively common and typically lack classic autosomal dominant family histories, risk alleles-such as these variants found in CHEK2-might be a significant contributor to PA risk in the general population.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- South Australian Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Ann McCormack
- Department of Endocrinology, St Vincent's Hospital, Sydney, NSW 2000, Australia
- Hormones and Cancer Group, Garvan Institute of Medical Research, Sydney, NSW 2000, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2000, Australia
| | - Andreas Orsmond
- Hormones and Cancer Group, Garvan Institute of Medical Research, Sydney, NSW 2000, Australia
| | - Angeline Shen
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Christopher J Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Roderick Clifton-Bligh
- Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, Sydney, NSW 2000, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
- Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW 2000, Australia
| | - Stephen Santoreneos
- Department of Neurosurgery, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - James King
- Department of Surgery, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jinghua Feng
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - John Toubia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - David J Torpy
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Hamish S Scott
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
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7
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Hluchý M, Blazek D. CDK11, a splicing-associated kinase regulating gene expression. Trends Cell Biol 2024:S0962-8924(24)00161-2. [PMID: 39245599 DOI: 10.1016/j.tcb.2024.08.004] [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: 05/16/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
The ability of a cell to properly express its genes depends on optimal transcription and splicing. RNA polymerase II (RNAPII) transcribes protein-coding genes and produces pre-mRNAs, which undergo, largely co-transcriptionally, intron excision by the spliceosome complex. Spliceosome activation is a major control step, leading to a catalytically active complex. Recent work has showed that cyclin-dependent kinase (CDK)11 regulates spliceosome activation via the phosphorylation of SF3B1, a core spliceosome component. Thus, CDK11 arises as a major coordinator of gene expression in metazoans due to its role in the rate-limiting step of pre-mRNA splicing. This review outlines the evolution of CDK11 and SF3B1 and their emerging roles in splicing regulation. It also discusses how CDK11 and its inhibition affect transcription and cell cycle progression.
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Affiliation(s)
- Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic.
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8
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Bertazzon M, Hurtado-Pico A, Plaza-Sirvent C, Schuster M, Preußner M, Kuropka B, Liu F, Kirsten AZA, Schmitt XJ, König B, Álvaro-Benito M, Abualrous ET, Albert GI, Kliche S, Heyd F, Schmitz I, Freund C. The nuclear GYF protein CD2BP2/U5-52K is required for T cell homeostasis. Front Immunol 2024; 15:1415839. [PMID: 39308865 PMCID: PMC11412891 DOI: 10.3389/fimmu.2024.1415839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/11/2024] [Indexed: 09/25/2024] Open
Abstract
The question whether interference with the ubiquitous splicing machinery can lead to cell-type specific perturbation of cellular function is addressed here by T cell specific ablation of the general U5 snRNP assembly factor CD2BP2/U5-52K. This protein defines the family of nuclear GYF domain containing proteins that are ubiquitously expressed in eukaryotes with essential functions ascribed to early embryogenesis and organ function. Abrogating CD2BP2/U5-52K in T cells, allows us to delineate the consequences of splicing machinery interferences for T cell development and function. Increased T cell lymphopenia and T cell death are observed upon depletion of CD2BP2/U5-52K. A substantial increase in exon skipping coincides with the observed defect in the proliferation/differentiation balance in the absence of CD2BP2/U5-52K. Prominently, skipping of exon 7 in Mdm4 is observed, coinciding with upregulation of pro-apoptotic gene expression profiles upon CD2BP2/U5-52K depletion. Furthermore, we observe enhanced sensitivity of naïve T cells compared to memory T cells to changes in CD2BP2/U5-52K levels, indicating that depletion of this general splicing factor leads to modulation of T cell homeostasis. Given the recent structural characterization of the U5 snRNP and the crosslinking mass spectrometry data given here, design of inhibitors of the U5 snRNP conceivably offers new ways to manipulate T cell function in settings of disease.
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Affiliation(s)
- Miriam Bertazzon
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Almudena Hurtado-Pico
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | | | - Marc Schuster
- Systems-Oriented Immunology and Inflammation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marco Preußner
- Department of Chemistry and Biochemistry, RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Fan Liu
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | | | - Xiao Jakob Schmitt
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benjamin König
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Miguel Álvaro-Benito
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
- School of Medicine, Universidad Complutense de Madrid, 12 de Octubre Health Research Institute, Madrid, Spain
| | - Esam T. Abualrous
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- Department of Physics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Gesa I. Albert
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Stefanie Kliche
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation GCI3, Otto-von-Guericke-University, Magdeburg, Germany
| | - Florian Heyd
- Department of Chemistry and Biochemistry, RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Ingo Schmitz
- Department of Molecular Immunology, Ruhr-University Bochum, Bochum, Germany
| | - Christian Freund
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
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9
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Xu W, Tian F, Tai X, Song G, Liu Y, Fan L, Weng X, Yang E, Wang M, Bornhäuser M, Zhang C, Lock RB, Wong JWH, Wang J, Jing D, Mi JQ. ETV6::ACSL6 translocation-driven super-enhancer activation leads to eosinophilia in acute lymphoblastic leukemia through IL-3 overexpression. Haematologica 2024; 109:2445-2458. [PMID: 38356460 PMCID: PMC11290521 DOI: 10.3324/haematol.2023.284121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
ETV6::ACSL6 represents a rare genetic aberration in hematopoietic neoplasms and is often associated with severe eosinophilia, which confers an unfavorable prognosis requiring additional anti-inflammatory treatment. However, since the translocation is unlikely to produce a fusion protein, the mechanism of ETV6::ACSL6 action remains unclear. Here, we performed multi-omics analyses of primary leukemia cells and patient-derived xenografts from an acute lymphoblastic leukemia (ALL) patient with ETV6::ACSL6 translocation. We identified a super-enhancer located within the ETV6 gene locus, and revealed translocation and activation of the super-enhancer associated with the ETV6::ACSL6 fusion. The translocated super-enhancer exhibited intense interactions with genomic regions adjacent to and distal from the breakpoint at chromosomes 5 and 12, including genes coding inflammatory factors such as IL-3. This led to modulations in DNA methylation, histone modifications, and chromatin structures, triggering transcription of inflammatory factors leading to eosinophilia. Furthermore, the bromodomain and extraterminal domain (BET) inhibitor synergized with standard-of-care drugs for ALL, effectively reducing IL-3 expression and inhibiting ETV6::ACSL6 ALL growth in vitro and in vivo. Overall, our study revealed for the first time a cis-regulatory mechanism of super-enhancer translocation in ETV6::ACSL6ALL, leading to an ALL-accompanying clinical syndrome. These findings may stimulate novel treatment approaches for this challenging ALL subtype.
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Affiliation(s)
- Wenqian Xu
- 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 200025
| | - Feng Tian
- Hebei Key Laboratory of Medical Data Science, Institute of Biomedical Informatics, School of Medicine, Hebei University of Engineering, Handan, Hebei Province, 056038
| | - Xiaolu Tai
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai
| | - Gaoxian Song
- 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 200025
| | - Yuanfang 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 200025
| | - Liquan Fan
- 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 200025
| | - Xiangqin Weng
- 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 200025
| | - Eunjeong Yang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong
| | - Meng Wang
- Songjiang Research Institute, Songjiang District Central Hospital, Institute of Autism and MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai.
| | - Martin Bornhäuser
- Medical Clinic I, University Hospital Carl Gustav Carus, TU Dresden, Dresden
| | - Chao Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine and Health, UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW
| | - Jason W H Wong
- School of Biomedical Sciences, University of Hong Kong, Hong Kong
| | - Jin 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 200025
| | - Duohui Jing
- 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 200025.
| | - Jian-Qing Mi
- 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 200025.
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10
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Ji T, Yang Y, Yu J, Yin H, Chu X, Yang P, Xu L, Wang X, Hu S, Li Y, Wu X, Liu W, Zhou B, Wang W, Zhang S, Cheng W, Chen Y, Shi L, Li Z, Zhuo R, Zhang Y, Tao Y, Wu D, Li X, Zhang Z, Fan JJ, Pan J, Lu J. Targeting RBM39 through indisulam induced mis-splicing of mRNA to exert anti-cancer effects in T-cell acute lymphoblastic leukemia. J Exp Clin Cancer Res 2024; 43:205. [PMID: 39044280 PMCID: PMC11267830 DOI: 10.1186/s13046-024-03130-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Despite the use of targeted therapeutic approaches, T-cell acute lymphoblastic leukemia (T-ALL) is still associated with a high incidence of complications and a poor prognosis. Indisulam (also known as E7070), a newly identified molecular glue compound, has demonstrated increased therapeutic efficacy in several types of cancer through the rapid degradation of RBM39. This study aimed to evaluate the therapeutic potential of indisulam in T-ALL, elucidate its underlying mechanisms and explore the role of the RBM39 gene. METHODS We verified the anticancer effects of indisulam in both in vivo and in vitro models. Additionally, the construction of RBM39-knockdown cell lines using shRNA confirmed that the malignant phenotype of T-ALL cells was dependent on RBM39. Through RNA sequencing, we identified indisulam-induced splicing anomalies, and proteomic analysis helped pinpoint protein changes caused by the drug. Comprehensive cross-analysis of these findings facilitated the identification of downstream effectors and subsequent validation of their functional roles. RESULTS Indisulam has significant antineoplastic effects on T-ALL. It attenuates cell proliferation, promotes apoptosis and interferes with cell cycle progression in vitro while facilitating tumor remission in T-ALL in vivo models. This investigation provides evidence that the downregulation of RBM39 results in the restricted proliferation of T-ALL cells both in vitro and in vivo, suggesting that RBM39 is a potential target for T-ALL treatment. Indisulam's efficacy is attributed to its ability to induce RBM39 degradation, causing widespread aberrant splicing and abnormal translation of the critical downstream effector protein, THOC1, ultimately leading to protein depletion. Moreover, the presence of DCAF15 is regarded as critical for the effectiveness of indisulam, and its absence negates the ability of indisulam to induce the desired functional alterations. CONCLUSION Our study revealed that indisulam, which targets RBM39 to induce tumor cell apoptosis, is an effective drug for treating T-ALL. Targeting RBM39 through indisulam leads to mis-splicing of pre-mRNAs, resulting in the loss of key effectors such as THOC1.
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Affiliation(s)
- Tongting Ji
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yang Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Juanjuan Yu
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Hongli Yin
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xinran Chu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, Jiangsu, 215003, China
| | - Pengju Yang
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Ling Xu
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatric, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xiaodong Wang
- Department of Orthopaedics, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Shaoyan Hu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, Jiangsu, 215003, China
| | - Yizhen Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xiaochen Wu
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Wengyuan Liu
- Department of Pediatrics, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei City, 230601, China
| | - Bi Zhou
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatric, Suzhou Hospital of AnHui Medical University, Suzhou, 234000, China
| | - Wenjuan Wang
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, China
| | - Shuqi Zhang
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatrics, The First Affiliated Hospital of Wannan Medical College, Wuhu, 241002, China
| | - Wei Cheng
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatrics, The First Affiliated Hospital of Wannan Medical College, Wuhu, 241002, China
| | - Yanling Chen
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Lei Shi
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhiheng Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Ran Zhuo
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yongping Zhang
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, Jiangsu, 215003, China
| | - Yanfang Tao
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Di Wu
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xiaolu Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Zimu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Jun-Jie Fan
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, Jiangsu, 215003, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.
| | - Jun Lu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, Jiangsu, 215003, China.
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11
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Dias MH, Liudkovska V, Montenegro Navarro J, Giebel L, Champagne J, Papagianni C, Bleijerveld OB, Velds A, Agami R, Bernards R, Cieśla M. The phosphatase inhibitor LB-100 creates neoantigens in colon cancer cells through perturbation of mRNA splicing. EMBO Rep 2024; 25:2220-2238. [PMID: 38600345 PMCID: PMC11094086 DOI: 10.1038/s44319-024-00128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024] Open
Abstract
Perturbation of protein phosphorylation represents an attractive approach to cancer treatment. Besides kinase inhibitors, protein phosphatase inhibitors have been shown to have anti-cancer activity. A prime example is the small molecule LB-100, an inhibitor of protein phosphatases 2A/5 (PP2A/PP5), enzymes that affect cellular physiology. LB-100 has proven effective in pre-clinical models in combination with immunotherapy, but the molecular underpinnings of this synergy remain understood poorly. We report here a sensitivity of the mRNA splicing machinery to phosphorylation changes in response to LB-100 in colorectal adenocarcinoma. We observe enrichment for differentially phosphorylated sites within cancer-critical splicing nodes of U2 snRNP, SRSF and hnRNP proteins. Altered phosphorylation endows LB-100-treated colorectal adenocarcinoma cells with differential splicing patterns. In PP2A-inhibited cells, over 1000 events of exon skipping and intron retention affect regulators of genomic integrity. Finally, we show that LB-100-evoked alternative splicing leads to neoantigens that are presented by MHC class 1 at the cell surface. Our findings provide a potential explanation for the pre-clinical and clinical observations that LB-100 sensitizes cancer cells to immune checkpoint blockade.
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Affiliation(s)
- Matheus H Dias
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Jasmine Montenegro Navarro
- Division of Oncogenomics and Oncode institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lisanne Giebel
- Division of Oncogenomics and Oncode institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julien Champagne
- Division of Oncogenomics and Oncode institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Chrysa Papagianni
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Arno Velds
- Central Genomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Reuven Agami
- Division of Oncogenomics and Oncode institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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12
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Mukhopadhyay P, Miller H, Stoja A, Bishop AJR. Approaches for Mapping and Analysis of R-loops. Curr Protoc 2024; 4:e1037. [PMID: 38666626 PMCID: PMC11840513 DOI: 10.1002/cpz1.1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
R-loops are nucleic acid structures composed of a DNA:RNA hybrid with a displaced non-template single-stranded DNA. Current approaches to identify and map R-loop formation across the genome employ either an antibody targeted against R-loops (S9.6) or a catalytically inactivated form of RNase H1 (dRNH1), a nuclease that can bind and resolve DNA:RNA hybrids via RNA exonuclease activity. This overview article outlines several ways to map R-loops using either methodology, explaining the differences and similarities among the approaches. Bioinformatic analysis of R-loops involves several layers of quality control and processing before visualizing the data. This article provides resources and tools that can be used to accurately process R-loop mapping data and explains the advantages and disadvantages of the resources as compared to one another. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Pramiti Mukhopadhyay
- Greehey Children’s Cancer Research Institute, UT Health San
Antonio, 8403 Floyd Curl Dr, San Antonio, TX 78229
| | - Henry Miller
- Altos Labs, 1300 Island Dr Redwood City, CA 94065
| | - Aiola Stoja
- Greehey Children’s Cancer Research Institute, UT Health San
Antonio, 8403 Floyd Curl Dr, San Antonio, TX 78229
| | - Alexander J. R. Bishop
- Greehey Children’s Cancer Research Institute, UT Health San
Antonio, 8403 Floyd Curl Dr, San Antonio, TX 78229
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13
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Scott KA, Kojima H, Ropek N, Warren CD, Zhang TL, Hogg SJ, Webster C, Zhang X, Rahman J, Melillo B, Cravatt BF, Lyu J, Abdel-Wahab O, Vinogradova EV. Covalent Targeting of Splicing in T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572199. [PMID: 38187674 PMCID: PMC10769204 DOI: 10.1101/2023.12.18.572199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide chemical probe EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and availability of functional mRNA pools that can be depleted due to extensive alternative splicing. We further introduce a comprehensive list of proteins involved in splicing and leverage both cysteine- and protein-directed activity-based protein profiling (ABPP) data with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in primary human T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.
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14
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Xie J, Wang L, Lin RJ. Variations of intronic branchpoint motif: identification and functional implications in splicing and disease. Commun Biol 2023; 6:1142. [PMID: 37949953 PMCID: PMC10638238 DOI: 10.1038/s42003-023-05513-7] [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: 07/28/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The branchpoint (BP) motif is an essential intronic element for spliceosomal pre-mRNA splicing. In mammals, its sequence composition, distance to the downstream exon, and number of BPs per 3´ splice site are highly variable, unlike the GT/AG dinucleotides at the intron ends. These variations appear to provide evolutionary advantages for fostering alternative splicing, satisfying more diverse cellular contexts, and promoting resilience to genetic changes, thus contributing to an extra layer of complexity for gene regulation. Importantly, variants in the BP motif itself or in genes encoding BP-interacting factors cause human genetic diseases or cancers, highlighting the critical function of BP motif and the need to precisely identify functional BPs for faithful interpretation of their roles in splicing. In this perspective, we will succinctly summarize the major findings related to BP motif variations, discuss the relevant issues/challenges, and provide our insights.
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Affiliation(s)
- Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Ren-Jang Lin
- Center for RNA Biology & Therapeutics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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15
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Cao L, Ruiz Buendía GA, Fournier N, Liu Y, Armand F, Hamelin R, Pavlou M, Radtke F. Resistance mechanism to Notch inhibition and combination therapy in human T-cell acute lymphoblastic leukemia. Blood Adv 2023; 7:6240-6252. [PMID: 37358480 PMCID: PMC10589794 DOI: 10.1182/bloodadvances.2023010380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/26/2023] [Accepted: 06/19/2023] [Indexed: 06/27/2023] Open
Abstract
Gain-of-function mutations in NOTCH1 are among the most frequent genetic alterations in T-cell acute lymphoblastic leukemia (T-ALL), highlighting the Notch signaling pathway as a promising therapeutic target for personalized medicine. Yet, a major limitation for long-term success of targeted therapy is relapse due to tumor heterogeneity or acquired resistance. Thus, we performed a genome-wide CRISPR-Cas9 screen to identify prospective resistance mechanisms to pharmacological NOTCH inhibitors and novel targeted combination therapies to efficiently combat T-ALL. Mutational loss of phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1) causes resistance to Notch inhibition. PIK3R1 deficiency leads to increased PI3K/AKT signaling, which regulates cell cycle and the spliceosome machinery, both at the transcriptional and posttranslational level. Moreover, several therapeutic combinations have been identified, in which simultaneous targeting of the cyclin-dependent kinases 4 and 6 (CDK4/6) and NOTCH proved to be the most efficacious in T-ALL xenotransplantation models.
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Affiliation(s)
- Linlin Cao
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Swiss Institute for Experimental Cancer Research, Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Gustavo A. Ruiz Buendía
- Translational Data Science, Swiss Institute of Bioinformatics, AGORA Cancer Research Center, Lausanne, Switzerland
| | - Nadine Fournier
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Swiss Institute for Experimental Cancer Research, Swiss Cancer Center Leman, Lausanne, Switzerland
- Translational Data Science, Swiss Institute of Bioinformatics, AGORA Cancer Research Center, Lausanne, Switzerland
| | - Yuanlong Liu
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Florence Armand
- Proteomics Core Facility, École Polytechnique Fédérale de Lausanne, School of Life Sciences, Lausanne, Switzerland
| | - Romain Hamelin
- Proteomics Core Facility, École Polytechnique Fédérale de Lausanne, School of Life Sciences, Lausanne, Switzerland
| | - Maria Pavlou
- Proteomics Core Facility, École Polytechnique Fédérale de Lausanne, School of Life Sciences, Lausanne, Switzerland
| | - Freddy Radtke
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Swiss Institute for Experimental Cancer Research, Swiss Cancer Center Leman, Lausanne, Switzerland
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16
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Wojtyś W, Oroń M. How Driver Oncogenes Shape and Are Shaped by Alternative Splicing Mechanisms in Tumors. Cancers (Basel) 2023; 15:cancers15112918. [PMID: 37296881 DOI: 10.3390/cancers15112918] [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: 04/28/2023] [Revised: 05/20/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The development of RNA sequencing methods has allowed us to study and better understand the landscape of aberrant pre-mRNA splicing in tumors. Altered splicing patterns are observed in many different tumors and affect all hallmarks of cancer: growth signal independence, avoidance of apoptosis, unlimited proliferation, invasiveness, angiogenesis, and metabolism. In this review, we focus on the interplay between driver oncogenes and alternative splicing in cancer. On one hand, oncogenic proteins-mutant p53, CMYC, KRAS, or PI3K-modify the alternative splicing landscape by regulating expression, phosphorylation, and interaction of splicing factors with spliceosome components. Some splicing factors-SRSF1 and hnRNPA1-are also driver oncogenes. At the same time, aberrant splicing activates key oncogenes and oncogenic pathways: p53 oncogenic isoforms, the RAS-RAF-MAPK pathway, the PI3K-mTOR pathway, the EGF and FGF receptor families, and SRSF1 splicing factor. The ultimate goal of cancer research is a better diagnosis and treatment of cancer patients. In the final part of this review, we discuss present therapeutic opportunities and possible directions of further studies aiming to design therapies targeting alternative splicing mechanisms in the context of driver oncogenes.
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Affiliation(s)
- Weronika Wojtyś
- Laboratory of Human Disease Multiomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Magdalena Oroń
- Laboratory of Human Disease Multiomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
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17
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Popli P, Chadchan SB, Dias M, Deng X, Gunderson SJ, Jimenez P, Yalamanchili H, Kommagani R. SF3B1-dependent alternative splicing is critical for maintaining endometrial homeostasis and the establishment of pregnancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541590. [PMID: 37292891 PMCID: PMC10245700 DOI: 10.1101/2023.05.20.541590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The remarkable potential of human endometrium to undergo spontaneous remodeling is shaped by controlled spatiotemporal gene expression patterns. Although hormone-driven transcription shown to govern these patterns, the post-transcriptional processing of these mRNA transcripts, including the mRNA splicing in the endometrium is not studied yet. Here, we report that the splicing factor, SF3B1 is central in driving alternative splicing (AS) events that are vital for physiological responses of the endometrium. We show that loss of SF3B1 splicing activity impairs stromal cell decidualization as well as embryo implantation. Transcriptomic analysis revealed that SF3B1 depletion decidualizing stromal cells led to differential mRNA splicing. Specifically, a significant upregulation in mutually exclusive AS events (MXEs) with SF3B1 loss resulted in the generation of aberrant transcripts. Further, we found that some of these candidate genes phenocopy SF3B1 function in decidualization. Importantly, we identify progesterone as a potential upstream regulator of SF3B1-mediated functions in endometrium possibly via maintaining its persistently high levels, in coordination with deubiquitinating enzymes. Collectively, our data suggest that SF3B1-driven alternative splicing plays a critical role in mediating the endometrial-specific transcriptional paradigms. Thus, the identification of novel mRNA variants associated with successful pregnancy establishment may help to develop new strategies to diagnose or prevent early pregnancy loss.
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18
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Cieśla M, Ngoc PCT, Muthukumar S, Todisco G, Madej M, Fritz H, Dimitriou M, Incarnato D, Hellström-Lindberg E, Bellodi C. m 6A-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis. Mol Cell 2023; 83:1165-1179.e11. [PMID: 36944332 DOI: 10.1016/j.molcel.2023.02.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 01/07/2023] [Accepted: 02/20/2023] [Indexed: 03/22/2023]
Abstract
SF3B1 is the most mutated splicing factor (SF) in myelodysplastic syndromes (MDSs), which are clonal hematopoietic disorders with variable risk of leukemic transformation. Although tumorigenic SF3B1 mutations have been extensively characterized, the role of "non-mutated" wild-type SF3B1 in cancer remains largely unresolved. Here, we identify a conserved epitranscriptomic program that steers SF3B1 levels to counteract leukemogenesis. Our analysis of human and murine pre-leukemic MDS cells reveals dynamic regulation of SF3B1 protein abundance, which affects MDS-to-leukemia progression in vivo. Mechanistically, ALKBH5-driven 5' UTR m6A demethylation fine-tunes SF3B1 translation directing splicing of central DNA repair and epigenetic regulators during transformation. This impacts genome stability and leukemia progression in vivo, supporting an integrative analysis in humans that SF3B1 molecular signatures may predict mutational variability and poor prognosis. These findings highlight a post-transcriptional gene expression nexus that unveils unanticipated SF3B1-dependent cancer vulnerabilities.
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Affiliation(s)
- Maciej Cieśla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden; International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland.
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Gabriele Todisco
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Helena Fritz
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Marios Dimitriou
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden.
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19
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Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
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Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
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20
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Wang E, Pineda JMB, Kim WJ, Chen S, Bourcier J, Stahl M, Hogg SJ, Bewersdorf JP, Han C, Singer ME, Cui D, Erickson CE, Tittley SM, Penson AV, Knorr K, Stanley RF, Rahman J, Krishnamoorthy G, Fagin JA, Creger E, McMillan E, Mak CC, Jarvis M, Bossard C, Beaupre DM, Bradley RK, Abdel-Wahab O. Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia. Cancer Cell 2023; 41:164-180.e8. [PMID: 36563682 PMCID: PMC9839614 DOI: 10.1016/j.ccell.2022.12.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR-Cas9 screens across a broad range of therapies used in acute myeloid leukemia to identify genomic determinants of drug response. Our screens uncover a selective dependency on RNA splicing factors whose loss preferentially enhances response to the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augments response to venetoclax in leukemia yet is completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition leads to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. Inhibition of splicing kinase families CLKs (CDC-like kinases) and DYRKs (dual-specificity tyrosine-regulated kinases) leads to aberrant splicing of key splicing and apoptotic factors that synergize with venetoclax, and overcomes resistance to BCL2 inhibition. Our findings underscore the importance of splicing in modulating response to therapies and provide a strategy to improve venetoclax-based treatments.
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Affiliation(s)
- Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, 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
| | - Won Jun Kim
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sisi Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessie Bourcier
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan Phillipp Bewersdorf
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cuijuan Han
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael E Singer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Cui
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline E Erickson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven M Tittley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine Knorr
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gnana Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Division of Endocrinology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Division of Endocrinology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | | | | | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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21
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De Kesel J, Fijalkowski I, Taylor J, Ntziachristos P. Splicing dysregulation in human hematologic malignancies: beyond splicing mutations. Trends Immunol 2022; 43:674-686. [PMID: 35850914 DOI: 10.1016/j.it.2022.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Splicing is a fundamental process in pre-mRNA maturation. Whereas alternative splicing (AS) enriches the diversity of the proteome, its aberrant regulation can drive oncogenesis. So far, most attention has been given to spliceosome mutations (SMs) in the context of splicing dysregulation in hematologic diseases. However, in recent years, post-translational modifications (PTMs) and transcriptional alterations of splicing factors (SFs), just as epigenetic signatures, have all been shown to contribute to global splicing dysregulation as well. In addition, the contribution of aberrant splicing to the neoantigen repertoire of cancers has been recognized. With the pressing need for novel therapeutics to combat blood cancers, this article provides an overview of emerging mechanisms that contribute to aberrant splicing, as well as their clinical potential.
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Affiliation(s)
- Jonas De Kesel
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Igor Fijalkowski
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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22
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Zhang T, Wang Z, Liu M, Liu L, Yang X, Zhang Y, Bie J, Li Y, Ren M, Song C, Wang W, Tan H, Luo J. Acetylation dependent translocation of EWSR1 regulates CHK2 alternative splicing in response to DNA damage. Oncogene 2022; 41:3694-3704. [PMID: 35732801 DOI: 10.1038/s41388-022-02383-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/09/2022]
Abstract
Ewing sarcoma breakpoint region 1 (EWSR1) is a member of FET (FUS/EWSR1/TAF15) RNA-binding family of proteins. The Ewing sarcoma oncoprotein EWS-FLI1 has been extensively studied, while much less is known about EWSR1 itself, especially the potential role of EWSR1 in response to DNA damage. Here, we found that UV irradiation induces acetylation of EWSR1, which is required for its nucleoli translocation. We identified K423, K432, K438, K640, and K643 as the major acetylation sites, p300/CBP and HDAC3/HDAC10 as the major acetyltransferases and deacetylases, respectively. Mechanically, UV-induced EWSR1 acetylation repressed its interaction with spliceosomal component U1C, which caused abnormal splicing of CHK2, suppressing the activity of CHK2 in response to UV irradiation. Taken together, our findings uncover acetylation as a novel regulatory modification of EWSR1, and is essential for its function in DNA damage response.
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Affiliation(s)
- Tianzhuo Zhang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China.,Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing, 100191, China
| | - Zhe Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Minghui Liu
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Lu Liu
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Xin Yang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Yu Zhang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Juntao Bie
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Yutong Li
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Mengmeng Ren
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Chen Song
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Wengong Wang
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing, 100191, China
| | - Hongyu Tan
- Department of Anesthesiology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| | - Jianyuan Luo
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China. .,Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing, 100191, China.
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23
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Interplay between A-to-I Editing and Splicing of RNA: A Potential Point of Application for Cancer Therapy. Int J Mol Sci 2022; 23:ijms23095240. [PMID: 35563631 PMCID: PMC9105294 DOI: 10.3390/ijms23095240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Adenosine-to-inosine RNA editing is a system of post-transcriptional modification widely distributed in metazoans which is catalyzed by ADAR enzymes and occurs mostly in double-stranded RNA (dsRNA) before splicing. This type of RNA editing changes the genetic code, as inosine generally pairs with cytosine in contrast to adenosine, and this expectably modulates RNA splicing. We review the interconnections between RNA editing and splicing in the context of human cancer. The editing of transcripts may have various effects on splicing, and resultant alternatively spliced isoforms may be either tumor-suppressive or oncogenic. Dysregulated RNA splicing in cancer often causes the release of excess amounts of dsRNA into cytosol, where specific dsRNA sensors provoke antiviral-like responses, including type I interferon signaling. These responses may arrest cell division, causing apoptosis and, externally, stimulate antitumor immunity. Thus, small-molecule spliceosome inhibitors have been shown to facilitate the antiviral-like signaling and are considered to be potential cancer therapies. In turn, a cytoplasmic isoform of ADAR can deaminate dsRNA in cytosol, thereby decreasing its levels and diminishing antitumor innate immunity. We propose that complete or partial inhibition of ADAR may enhance the proapoptotic and cytotoxic effects of splicing inhibitors and that it may be considered a promising addition to cancer therapies targeting RNA splicing.
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