1
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Lawson H, Holt-Martyn JP, Dembitz V, Kabayama Y, Wang LM, Bellani A, Atwal S, Saffoon N, Durko J, van de Lagemaat LN, De Pace AL, Tumber A, Corner T, Salah E, Arndt C, Brewitz L, Bowen M, Dubusse L, George D, Allen L, Guitart AV, Fung TK, So CWE, Schwaller J, Gallipoli P, O'Carroll D, Schofield CJ, Kranc KR. The selective prolyl hydroxylase inhibitor IOX5 stabilizes HIF-1α and compromises development and progression of acute myeloid leukemia. NATURE CANCER 2024; 5:916-937. [PMID: 38637657 PMCID: PMC11208159 DOI: 10.1038/s43018-024-00761-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Acute myeloid leukemia (AML) is a largely incurable disease, for which new treatments are urgently needed. While leukemogenesis occurs in the hypoxic bone marrow, the therapeutic tractability of the hypoxia-inducible factor (HIF) system remains undefined. Given that inactivation of HIF-1α/HIF-2α promotes AML, a possible clinical strategy is to target the HIF-prolyl hydroxylases (PHDs), which promote HIF-1α/HIF-2α degradation. Here, we reveal that genetic inactivation of Phd1/Phd2 hinders AML initiation and progression, without impacting normal hematopoiesis. We investigated clinically used PHD inhibitors and a new selective PHD inhibitor (IOX5), to stabilize HIF-α in AML cells. PHD inhibition compromises AML in a HIF-1α-dependent manner to disable pro-leukemogenic pathways, re-program metabolism and induce apoptosis, in part via upregulation of BNIP3. Notably, concurrent inhibition of BCL-2 by venetoclax potentiates the anti-leukemic effect of PHD inhibition. Thus, PHD inhibition, with consequent HIF-1α stabilization, is a promising nontoxic strategy for AML, including in combination with venetoclax.
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Affiliation(s)
- Hannah Lawson
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - James P Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Vilma Dembitz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Physiology and Immunology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Yuka Kabayama
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Lydia M Wang
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Aarushi Bellani
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Samanpreet Atwal
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Nadia Saffoon
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Jozef Durko
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Louie N van de Lagemaat
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Azzura L De Pace
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Thomas Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Christine Arndt
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Matthew Bowen
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Louis Dubusse
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Derek George
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lewis Allen
- The Institute of Cancer Research, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Amelie V Guitart
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
- Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale INSERM U1035, Bordeaux, France
| | - Tsz Kan Fung
- Leukemia and Stem Cell Biology Group, Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, King's College London, London, UK
| | - Chi Wai Eric So
- Leukemia and Stem Cell Biology Group, Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, King's College London, London, UK
| | - Juerg Schwaller
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Donal O'Carroll
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
| | - Kamil R Kranc
- The Institute of Cancer Research, London, UK.
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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2
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Lavogina D, Krõlov MK, Vellama H, Modhukur V, Di Nisio V, Lust H, Eskla KL, Salumets A, Jaal J. Inhibition of epigenetic and cell cycle-related targets in glioblastoma cell lines reveals that onametostat reduces proliferation and viability in both normoxic and hypoxic conditions. Sci Rep 2024; 14:4303. [PMID: 38383756 PMCID: PMC10881536 DOI: 10.1038/s41598-024-54707-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
The choice of targeted therapies for treatment of glioblastoma patients is currently limited, and most glioblastoma patients die from the disease recurrence. Thus, systematic studies in simplified model systems are required to pinpoint the choice of targets for further exploration in clinical settings. Here, we report screening of 5 compounds targeting epigenetic writers or erasers and 6 compounds targeting cell cycle-regulating protein kinases against 3 glioblastoma cell lines following incubation under normoxic or hypoxic conditions. The viability/proliferation assay indicated that PRMT5 inhibitor onametostat was endowed with high potency under both normoxic and hypoxic conditions in cell lines that are strongly MGMT-positive (T98-G), weakly MGMT-positive (U-251 MG), or MGMT-negative (U-87 MG). In U-251 MG and U-87 MG cells, onametostat also affected the spheroid formation at concentrations lower than the currently used chemotherapeutic drug lomustine. In T98-G cell line, treatment with onametostat led to dramatic changes in the transcriptome profile by inducing the cell cycle arrest, suppressing RNA splicing, and down-regulating several major glioblastoma cell survival pathways. Further validation by immunostaining in three cell lines confirmed that onametostat affects cell cycle and causes reduction in nucleolar protein levels. In this way, inhibition of epigenetic targets might represent a viable strategy for glioblastoma treatment even in the case of decreased chemo- and radiation sensitivity, although further studies in clinically more relevant models are required.
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Affiliation(s)
- Darja Lavogina
- Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia.
- Chair of Bioorganic Chemistry, Institute of Chemistry, University of Tartu, Tartu, Estonia.
- Competence Centre on Health Technologies, Tartu, Estonia.
| | - Mattias Kaspar Krõlov
- Chair of Bioorganic Chemistry, Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Hans Vellama
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Centre of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Valentina Di Nisio
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Helen Lust
- Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia
| | - Kattri-Liis Eskla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Centre of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Jana Jaal
- Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia.
- Department of Radiotherapy and Oncological Therapy, Tartu University Hospital, Tartu, Estonia.
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3
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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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4
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Soulette CM, Hrabeta-Robinson E, Arevalo C, Felton C, Tang AD, Marin MG, Brooks AN. Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations. Life Sci Alliance 2023; 6:e202000641. [PMID: 37487637 PMCID: PMC10366530 DOI: 10.26508/lsa.202000641] [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: 01/08/2020] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
U2AF1 is one of the most recurrently mutated splicing factors in lung adenocarcinoma and has been shown to cause transcriptome-wide pre-mRNA splicing alterations; however, the full-length altered mRNA isoforms associated with the mutation are largely unknown. To better understand the impact U2AF1 has on full-length isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without a U2AF1 S34F mutation. We identified 49,366 multi-exon transcript isoforms, more than half of which did not match GENCODE or short-read-assembled isoforms. We found 198 transcript isoforms with significant expression and usage changes relative to WT, only 68% of which were assembled by short reads. Expression of isoforms from immune-related genes is largely down-regulated in mutant cells and without observed splicing changes. Finally, we reveal that isoforms likely targeted by nonsense-mediated decay are down-regulated in U2AF1 S34F cells, suggesting that isoform changes may alter the translational output of those affected genes. Altogether, our work provides a resource of full-length isoforms associated with U2AF1 S34F in lung cells.
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Affiliation(s)
- Cameron M Soulette
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Carlos Arevalo
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Maximillian G Marin
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
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5
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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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6
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Wang X, Wang J, Raza SHA, Deng J, Ma J, Qu X, Yu S, Zhang D, Alshammari AM, Almohaimeed HM, Zan L. Identification of the hub genes related to adipose tissue metabolism of bovine. Front Vet Sci 2022; 9:1014286. [PMID: 36439361 PMCID: PMC9682410 DOI: 10.3389/fvets.2022.1014286] [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: 08/08/2022] [Accepted: 09/16/2022] [Indexed: 11/11/2022] Open
Abstract
Due to the demand for high-quality animal protein, there has been consistent interest in how to obtain more high-quality beef. As well-known, the adipose content of beef has a close connection with the taste and quality of beef, and cattle with different energy or protein diet have corresponding effects on the lipid metabolism of beef. Thus, we performed weighted gene co-expression network analysis (WGCNA) with subcutaneous adipose genes from Norwegian red heifers fed different diets to identify hub genes regulating bovine lipid metabolism. For this purpose, the RNA sequencing data of subcutaneous adipose tissue of 12-month-old Norwegian red heifers (n = 48) with different energy or protein levels were selected from the GEO database, and 7,630 genes with the largest variation were selected for WGCNA analysis. Then, three modules were selected as hub genes candidate modules according to the correlation between modules and phenotypes, including pink, magenta and grey60 modules. GO and KEGG enrichment analysis showed that genes were related to metabolism, and participated in Rap, MAPK, AMPK, VEGF signaling pathways, and so forth. Combined gene interaction network analysis using Cytoscape software, eight hub genes of lipid metabolism were identified, including TIA1, LOC516108, SNAPC4, CPSF2, ZNF574, CLASRP, MED15 and U2AF2. Further, the expression levels of hub genes in the cattle tissue were also measured to verify the results, and we found hub genes in higher expression in muscle and adipose tissue in adult cattle. In summary, we predicted the key genes of lipid metabolism in the subcutaneous adipose tissue that were affected by the intake of various energy diets to find the hub genes that coordinate lipid metabolism, which provide a theoretical basis for regulating beef quality.
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Affiliation(s)
- Xiaohui Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | | | - Jiahan Deng
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jing Ma
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xiaopeng Qu
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Shengchen Yu
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Dianqi Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | | | - Hailah M. Almohaimeed
- Department of Basic Science, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China
- *Correspondence: Linsen Zan
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7
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Integrative analysis identifies an older female-linked AML patient group with better risk in ECOG-ACRIN Cancer Research Group's clinical trial E3999. Blood Cancer J 2022; 12:137. [PMID: 36151075 PMCID: PMC9508258 DOI: 10.1038/s41408-022-00736-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 01/14/2023] Open
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8
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The Biological and Clinical Consequences of RNA Splicing Factor U2AF1 Mutation in Myeloid Malignancies. Cancers (Basel) 2022; 14:cancers14184406. [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] [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
Simple Summary U2 small nuclear RNA auxiliary factor 1 (U2AF1) is one of the most important RNA splicing genes involved in regulating the alternative splicing of pre-mRNA. U2AF1 mutation is a genetic driver event in the initiation of myelodysplastic syndromes (MDSs) and frequently occurs in myeloid malignancies. U2AF1 mutation can severely impair hematopoiesis, drive tumor progression, adversely affect disease prognosis, and promote leukemic transformation. This review summarizes the biological and clinical implications of the oncogenic role of U2AF1 mutation in myeloid tumors. Our work provides important and comprehensive insights into the development of the U2AF1 mutation as a novel prognostic biomarker and therapeutic target for myeloid malignancies. 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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9
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Glasser E, Maji D, Biancon G, Puthenpeedikakkal A, Cavender C, Tebaldi T, Jenkins J, Mathews D, Halene S, Kielkopf C. Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Nucleic Acids Res 2022; 50:5299-5312. [PMID: 35524551 PMCID: PMC9128377 DOI: 10.1093/nar/gkac287] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/03/2022] [Accepted: 04/12/2022] [Indexed: 11/24/2022] Open
Abstract
The essential pre-mRNA splicing factor U2AF2 (also called U2AF65) identifies polypyrimidine (Py) tract signals of nascent transcripts, despite length and sequence variations. Previous studies have shown that the U2AF2 RNA recognition motifs (RRM1 and RRM2) preferentially bind uridine-rich RNAs. Nonetheless, the specificity of the RRM1/RRM2 interface for the central Py tract nucleotide has yet to be investigated. We addressed this question by determining crystal structures of U2AF2 bound to a cytidine, guanosine, or adenosine at the central position of the Py tract, and compared U2AF2-bound uridine structures. Local movements of the RNA site accommodated the different nucleotides, whereas the polypeptide backbone remained similar among the structures. Accordingly, molecular dynamics simulations revealed flexible conformations of the central, U2AF2-bound nucleotide. The RNA binding affinities and splicing efficiencies of structure-guided mutants demonstrated that U2AF2 tolerates nucleotide substitutions at the central position of the Py tract. Moreover, enhanced UV-crosslinking and immunoprecipitation of endogenous U2AF2 in human erythroleukemia cells showed uridine-sensitive binding sites, with lower sequence conservation at the central nucleotide positions of otherwise uridine-rich, U2AF2-bound splice sites. Altogether, these results highlight the importance of RNA flexibility for protein recognition and take a step towards relating splice site motifs to pre-mRNA splicing efficiencies.
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Affiliation(s)
- Eliezra Glasser
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Debanjana Maji
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
| | | | - Chapin E Cavender
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
- Department of Cellular, Computational and Integrative Biology
(CIBIO), University of
Trento, Trento, Italy
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
- Yale Center for RNA Science and Medicine, Yale University
School of Medicine, New Haven,
CT 06520, USA
- Department of Pathology, Yale University School of
Medicine, New Haven,
CT 06520, USA
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
- Wilmot Cancer Institute, University of Rochester School of
Medicine and Dentistry, Rochester,
NY 14642, USA
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10
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Tran TM, Philipp J, Bassi JS, Nibber N, Draper JM, Lin TL, Palanichamy JK, Jaiswal AK, Silva O, Paing M, King J, Katzman S, Sanford JR, Rao DS. The RNA-binding protein IGF2BP3 is critical for MLL-AF4-mediated leukemogenesis. Leukemia 2022; 36:68-79. [PMID: 34321607 PMCID: PMC8727287 DOI: 10.1038/s41375-021-01346-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/25/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Despite recent advances in therapeutic approaches, patients with MLL-rearranged leukemia still have poor outcomes. Here, we find that the RNA-binding protein IGF2BP3, which is overexpressed in MLL-translocated leukemia, strongly amplifies MLL-Af4-mediated leukemogenesis. Deletion of Igf2bp3 significantly increases the survival of mice with MLL-Af4-driven leukemia and greatly attenuates disease, with a minimal impact on baseline hematopoiesis. At the cellular level, MLL-Af4 leukemia-initiating cells require Igf2bp3 for their function in leukemogenesis. At the molecular level, IGF2BP3 regulates a complex posttranscriptional operon governing leukemia cell survival and proliferation. IGF2BP3-targeted mRNA transcripts include important MLL-Af4-induced genes, such as those in the Hoxa locus, and the Ras signaling pathway. Targeting of transcripts by IGF2BP3 regulates both steady-state mRNA levels and, unexpectedly, pre-mRNA splicing. Together, our findings show that IGF2BP3 represents an attractive therapeutic target in this disease, providing important insights into mechanisms of posttranscriptional regulation in leukemia.
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Affiliation(s)
- Tiffany M Tran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular, Cellular, and Integrative Physiology Interdepartmental Ph.D. Program, UCLA, Los Angeles, CA, 90095, USA
| | - Julia Philipp
- Department of Molecular, Cellular and Developmental Biology, UCSC, Santa Cruz, CA, 95064, USA
| | - Jaspal Singh Bassi
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Neha Nibber
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Jolene M Draper
- Department of Molecular, Cellular and Developmental Biology, UCSC, Santa Cruz, CA, 95064, USA
| | - Tasha L Lin
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Interdepartmental Doctoral Program, UCLA, Los Angeles, CA, 90095, USA
| | - Jayanth Kumar Palanichamy
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Amit Kumar Jaiswal
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Oscar Silva
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - May Paing
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Jennifer King
- Division of Rheumatology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Sol Katzman
- UCSC Genomics Institute, Santa Cruz, CA, 95064, USA
| | - Jeremy R Sanford
- Department of Molecular, Cellular and Developmental Biology, UCSC, Santa Cruz, CA, 95064, USA
| | - Dinesh S Rao
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
- Molecular, Cellular, and Integrative Physiology Interdepartmental Ph.D. Program, UCLA, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center (JCCC), UCLA, Los Angeles, CA, 90095, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, 90095, USA.
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11
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Alayed K, Meyerson HJ. Decreased CD177 pos neutrophils in myeloid neoplasms is associated with NPM1, RUNX1, TET2, and U2AF1 S34F mutations. Leuk Res 2021; 112:106752. [PMID: 34896936 DOI: 10.1016/j.leukres.2021.106752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 11/26/2022]
Abstract
A decreased percentage of CD177pos neutrophils is frequently present in MDS and AML and is a useful flow cytometry (FCM) marker for the identification of MDS. The underlying mechanism leading to the low percentage of CD177pos neutrophils in MDS has not been explained. The aim of this study was to identify whether specific somatic mutations in myeloid neoplasms are associated with the low percentage of CD177pos neutrophils. 507 myeloid neoplasms with one or more pathogenic molecular abnormality identified by NGS and in which CD177 expression was assessed were evaluated. Correlation with CD177 expression was determined for 39 variables (including genes mutated, diagnostic groups and gender) using a 40 % cutoff level for low CD177 expression. In multivariate analysis mutations involving NPM1 (OD 0.26), RUNX1 (OD 0.39), TET2 (OD 0.58), and U2AF1 S34F (OD 0.25) were associated with low percentage of CD177pos neutrophils when all cases were evaluated. JAK2 (OD 2.5) alteration was associated with increased percentage of CD177pos neutrophils. Differences were noted between diagnostic subgroups with no single mutation associated with decreased CD177pos neutrophils in MDS and CCUS. The findings demonstrate an association between the percentage of CD177pos neutrophils and somatically acquired mutations involving several genes.
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Affiliation(s)
- Khaled Alayed
- King Saud University Medical City, Riyadh, Saudi Arabia
| | - Howard J Meyerson
- University Hospitals Cleveland Medical Center/ Case Western Reserve University, Cleveland, OH, United States.
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12
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Floro J, Dai A, Metzger A, Mora-Martin A, Ganem N, Cifuentes D, Wu CS, Dalal J, Lyons S, Labadorf A, Flynn R. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Nucleic Acids Res 2021; 49:9424-9443. [PMID: 34365507 PMCID: PMC8450105 DOI: 10.1093/nar/gkab647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 11/22/2022] Open
Abstract
RNA provides the framework for the assembly of some of the most intricate macromolecular complexes within the cell, including the spliceosome and the mature ribosome. The assembly of these complexes relies on the coordinated association of RNA with hundreds of trans-acting protein factors. While some of these trans-acting factors are RNA-binding proteins (RBPs), others are adaptor proteins, and others still, function as both. Defects in the assembly of these complexes results in a number of human pathologies including neurodegeneration and cancer. Here, we demonstrate that Silencing Defective 2 (SDE2) is both an RNA binding protein and also a trans-acting adaptor protein that functions to regulate RNA splicing and ribosome biogenesis. SDE2 depletion leads to widespread changes in alternative splicing, defects in ribosome biogenesis and ultimately complete loss of cell viability. Our data highlight SDE2 as a previously uncharacterized essential gene required for the assembly and maturation of the complexes that carry out two of the most fundamental processes in mammalian cells.
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Affiliation(s)
- Jess Floro
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anqi Dai
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
- Bioinformatics Program, Boston University, Boston, MA 02118 USA
| | - Abigail Metzger
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Neil J Ganem
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ching-Shyi Wu
- Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Jasbir Dalal
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University, Boston, MA 02118 USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118 USA
| | - Rachel L Flynn
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
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13
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Abstract
Herculean efforts by the Wellcome Sanger Institute, the National Cancer Institute, and the National Human Genome Research Institute to sequence thousands of tumors representing all major cancer types have yielded more than 700 genes that contribute to neoplastic growth when mutated, amplified, or deleted. While some of these genes (now included in the COSMIC Cancer Gene Census) encode proteins previously identified in hypothesis-driven experiments (oncogenic transcription factors, protein kinases, etc.), additional classes of cancer drivers have emerged, perhaps none more surprisingly than RNA-binding proteins (RBPs). Over 40 RBPs responsible for virtually all aspects of RNA metabolism, from synthesis to degradation, are recurrently mutated in cancer, and just over a dozen are considered major cancer drivers. This Review investigates whether and how their RNA-binding activities pertain to their oncogenic functions. Focusing on several well-characterized steps in RNA metabolism, we demonstrate that for virtually all cancer-driving RBPs, RNA processing activities are either abolished (the loss-of-function phenotype) or carried out with low fidelity (the LoFi phenotype). Conceptually, this suggests that in normal cells, RBPs act as gatekeepers maintaining proper RNA metabolism and the "balanced" proteome. From the practical standpoint, at least some LoFi phenotypes create therapeutic vulnerabilities, which are beginning to be exploited in the clinic.
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