1
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Eldeeb M, Yuan O, Guzzi N, Thi Ngoc PC, Konturek-Ciesla A, Kristiansen TA, Muthukumar S, Magee J, Bellodi C, Yuan J, Bryder D. A fetal tumor suppressor axis abrogates MLL-fusion-driven acute myeloid leukemia. Cell Rep 2023; 42:112099. [PMID: 36763502 DOI: 10.1016/j.celrep.2023.112099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/16/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
MLL-rearrangements (MLL-r) are recurrent genetic events in acute myeloid leukemia (AML) and frequently associate with poor prognosis. In infants, MLL-r can be sufficient to drive transformation. However, despite the prenatal origin of MLL-r in these patients, congenital leukemia is very rare with transformation usually occurring postnatally. The influence of prenatal signals on leukemogenesis, such as those mediated by the fetal-specific protein LIN28B, remains controversial. Here, using a dual-transgenic mouse model that co-expresses MLL-ENL and LIN28B, we investigate the impact of LIN28B on AML. LIN28B impedes the progression of MLL-r AML through compromised leukemia-initiating cell activity and suppression of MYB signaling. Mechanistically, LIN28B directly binds to MYBBP1A mRNA, resulting in elevated protein levels of this MYB co-repressor. Functionally, overexpression of MYBBP1A phenocopies the tumor-suppressor effects of LIN28B, while its perturbation omits it. Thereby, we propose that developmentally restricted expression of LIN28B provides a layer of protection against MYB-dependent AML.
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Affiliation(s)
- Mohamed Eldeeb
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Ouyang Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Anna Konturek-Ciesla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Trine A Kristiansen
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Jeffrey Magee
- Division of Hematology and Oncology, Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Joan Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - David Bryder
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden.
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3
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Eldeeb M, Yuan O, Guzzi N, Ngoc PCT, Kristiansen T, Muthukumar S, Bellodi C, Yuan J, Bryder D. 3077 – FUNCTIONAL AND MOLECULAR IDENTIFICATION OF A FETAL-ASSOCIATED TUMOR SUPPRESSOR AXIS: ABROGATION OF MLL-ENL DRIVEN ACUTE MYELOID LEUKEMIA. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Beneventi G, Munita R, Cao Thi Ngoc P, Madej M, Cieśla M, Muthukumar S, Krogh N, Nielsen H, Swaminathan V, Bellodi C. The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells. NAR Cancer 2021; 3:zcab026. [PMID: 34316713 PMCID: PMC8271217 DOI: 10.1093/narcan/zcab026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell survival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.
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Affiliation(s)
- Giulia Beneventi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Maciej Cieśla
- 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
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Vinay Swaminathan
- Division of Oncology, Department of Clinical Sciences, Lund University, 22184, Lund, 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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5
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Tran NH, Nguyen Thi TH, Tang HS, Hoang LP, Nguyen THL, Tran NT, Trinh THN, Nguyen VT, Nguyen BHH, Nguyen HT, Doan LP, Phan NM, Nguyen KHT, Nguyen HDL, Quach MTT, Nguyen TPT, Tran VU, Tran DV, Nguyen QTT, Do TTT, Lam NV, Cao Thi Ngoc P, Truong DK, Nguyen HN, Phan MD, Giang H. Genetic landscape of recessive diseases in the Vietnamese population from large-scale clinical exome sequencing. Hum Mutat 2021; 42:1229-1238. [PMID: 34233069 DOI: 10.1002/humu.24253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/08/2021] [Accepted: 06/13/2021] [Indexed: 11/10/2022]
Abstract
Accurate profiling of population-specific recessive diseases is essential for the design of cost-effective carrier screening programs. However, minority populations and ethnic groups, including Vietnamese, are still underrepresented in existing genetic studies. Here, we reported the first comprehensive study of recessive diseases in the Vietnamese population. Clinical exome sequencing data of 4503 disease-associated genes obtained from a cohort of 985 Vietnamese individuals was analyzed to identify pathogenic variants, associated diseases and their carrier frequencies in the population. A total of 118 recessive diseases associated with 164 pathogenic or likely pathogenic variants were identified, among which 28 diseases had carrier frequencies of at least 1% (1 in 100 individuals). Three diseases were prevalent in the Vietnamese population with carrier frequencies of 2-12 times higher than in the world populations, including beta-thalassemia (1 in 23), citrin deficiency (1 in 31), and phenylketonuria (1 in 40). Seven novel pathogenic and two likely pathogenic variants associated with nine recessive diseases were discovered. The comprehensive profile of recessive diseases identified in this study enables the design of cost-effective carrier screening programs specific to the Vietnamese population.
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Affiliation(s)
- Ngoc Hieu Tran
- Gene Solutions, Ho Chi Minh City, Vietnam.,David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | | | - Hung-Sang Tang
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Trung-Hieu Le Nguyen
- Department of Neurology, Children Hospital 2, Ho Chi Minh City, Vietnam.,University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | - Ngoc-Minh Phan
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Kim-Huong Thi Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Hong-Dang Luu Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Minh-Tam Thi Quach
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Thanh-Phuong Thi Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Dinh-Vinh Tran
- Da Nang Hospital for Women and Children, Da Nang, Vietnam
| | | | | | - Nien Vinh Lam
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
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6
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Cieśla M, Ngoc PCT, Cordero E, Martinez ÁS, Morsing M, Muthukumar S, Beneventi G, Madej M, Munita R, Jönsson T, Lövgren K, Ebbesson A, Nodin B, Hedenfalk I, Jirström K, Vallon-Christersson J, Honeth G, Staaf J, Incarnato D, Pietras K, Bosch A, Bellodi C. Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer. Mol Cell 2021; 81:1453-1468.e12. [PMID: 33662273 DOI: 10.1016/j.molcel.2021.01.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/02/2020] [Accepted: 01/21/2021] [Indexed: 02/08/2023]
Abstract
Splicing is a central RNA-based process commonly altered in human cancers; however, how spliceosomal components are co-opted during tumorigenesis remains poorly defined. Here we unravel the core splice factor SF3A3 at the nexus of a translation-based program that rewires splicing during malignant transformation. Upon MYC hyperactivation, SF3A3 levels are modulated translationally through an RNA stem-loop in an eIF3D-dependent manner. This ensures accurate splicing of mRNAs enriched for mitochondrial regulators. Altered SF3A3 translation leads to metabolic reprogramming and stem-like properties that fuel MYC tumorigenic potential in vivo. Our analysis reveals that SF3A3 protein levels predict molecular and phenotypic features of aggressive human breast cancers. These findings unveil a post-transcriptional interplay between splicing and translation that governs critical facets of MYC-driven oncogenesis.
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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
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Eugenia Cordero
- Division of Translational Cancer Research, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22363 Lund, Sweden
| | - Álvaro Sejas Martinez
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Mikkel Morsing
- Division of Translational Cancer Research, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22363 Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Giulia Beneventi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Terese Jönsson
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Kristina Lövgren
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Anna Ebbesson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Björn Nodin
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Karin Jirström
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - Gabriella Honeth
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Danny Incarnato
- Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22363 Lund, Sweden
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, 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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7
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Tran NH, Vo TB, Nguyen VT, Tran NT, Trinh THN, Pham HAT, Dao THT, Nguyen NM, Van YLT, Tran VU, Vu HG, Bui QTN, Vo PAN, Nguyen HN, Nguyen QTT, Do TTT, Lam NV, Ngoc PCT, Truong DK, Nguyen HN, Giang H, Phan MD. Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data. Sci Rep 2020; 10:19142. [PMID: 33154511 PMCID: PMC7644705 DOI: 10.1038/s41598-020-76245-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. As one of the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an alternative untapped resource for genetic studies. Here we performed a large-scale genomic analysis of 2683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially 5 pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency distribution of disease-associated genetic variants between the Vietnamese and other populations, thus highlighting a need for genome-wide association studies dedicated to the Vietnamese population. The resulted database of Vietnamese genetic variants, their allele frequency distribution, and their associated diseases presents a valuable resource for future genetic studies.
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Affiliation(s)
- Ngoc Hieu Tran
- Gene Solutions, Ho Chi Minh City, Vietnam.,David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Canada
| | - Thanh Binh Vo
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | | | | | - Hong-Anh Thi Pham
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Thi Hong Thuy Dao
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Ngoc Mai Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Yen-Linh Thi Van
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Vu Uyen Tran
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Hoang Giang Vu
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Quynh-Tram Nguyen Bui
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Phuong-Anh Ngoc Vo
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Huu Nguyen Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | | | - Nien Vinh Lam
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Phuong Cao Thi Ngoc
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | | | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam. .,Medical Genetics Institute, Ho Chi Minh City, Vietnam.
| | - Minh-Duy Phan
- Gene Solutions, Ho Chi Minh City, Vietnam. .,School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia.
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8
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Phung B, Cieśla M, Sanna A, Guzzi N, Beneventi G, Cao Thi Ngoc P, Lauss M, Cabrita R, Cordero E, Bosch A, Rosengren F, Häkkinen J, Griewank K, Paschen A, Harbst K, Olsson H, Ingvar C, Carneiro A, Tsao H, Schadendorf D, Pietras K, Bellodi C, Jönsson G. The X-Linked DDX3X RNA Helicase Dictates Translation Reprogramming and Metastasis in Melanoma. Cell Rep 2020; 27:3573-3586.e7. [PMID: 31216476 DOI: 10.1016/j.celrep.2019.05.069] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/22/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022] Open
Abstract
The X-linked DDX3X gene encodes an ATP-dependent DEAD-box RNA helicase frequently altered in various human cancers, including melanomas. Despite its important roles in translation and splicing, how DDX3X dysfunction specifically rewires gene expression in melanoma remains completely unknown. Here, we uncover a DDX3X-driven post-transcriptional program that dictates melanoma phenotype and poor disease prognosis. Through an unbiased analysis of translating ribosomes, we identified the microphthalmia-associated transcription factor, MITF, as a key DDX3X translational target that directs a proliferative-to-metastatic phenotypic switch in melanoma cells. Mechanistically, DDX3X controls MITF mRNA translation via an internal ribosome entry site (IRES) embedded within the 5' UTR. Through this exquisite translation-based regulatory mechanism, DDX3X steers MITF protein levels dictating melanoma metastatic potential in vivo and response to targeted therapy. Together, these findings unravel a post-transcriptional layer of gene regulation that may provide a unique therapeutic vulnerability in aggressive male melanomas.
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Affiliation(s)
- Bengt Phung
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Maciej Cieśla
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Adriana Sanna
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Nicola Guzzi
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Giulia Beneventi
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Martin Lauss
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Rita Cabrita
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Eugenia Cordero
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Frida Rosengren
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Klaus Griewank
- Department of Dermatology, University Hospital of Essen, Essen, Germany
| | - Annette Paschen
- Department of Dermatology, University Hospital of Essen, Essen, Germany
| | - Katja Harbst
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - Ana Carneiro
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Oncology and Hematology, Skåne University Hospital, Lund, Sweden
| | - Hensin Tsao
- Department of Dermatology, Harvard Medical School, Boston, MA, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital of Essen, Essen, Germany
| | - Kristian Pietras
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden.
| | - Göran Jönsson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.
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9
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Wang L, Tan TK, Durbin AD, Zimmerman MW, Abraham BJ, Tan SH, Ngoc PCT, Weichert-Leahey N, Akahane K, Lawton LN, Rokita JL, Maris JM, Young RA, Look AT, Sanda T. ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry. Nat Commun 2019; 10:5622. [PMID: 31819055 PMCID: PMC6901540 DOI: 10.1038/s41467-019-13515-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022] Open
Abstract
A heritable polymorphism within regulatory sequences of the LMO1 gene is associated with its elevated expression and increased susceptibility to develop neuroblastoma, but the oncogenic pathways downstream of the LMO1 transcriptional co-regulatory protein are unknown. Our ChIP-seq and RNA-seq analyses reveal that a key gene directly regulated by LMO1 and MYCN is ASCL1, which encodes a basic helix-loop-helix transcription factor. Regulatory elements controlling ASCL1 expression are bound by LMO1, MYCN and the transcription factors GATA3, HAND2, PHOX2B, TBX2 and ISL1-all members of the adrenergic (ADRN) neuroblastoma core regulatory circuitry (CRC). ASCL1 is required for neuroblastoma cell growth and arrest of differentiation. ASCL1 and LMO1 directly regulate the expression of CRC genes, indicating that ASCL1 is a member and LMO1 is a coregulator of the ADRN neuroblastoma CRC.
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Affiliation(s)
- Lu Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02216, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02215, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02216, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38102, USA
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Phuong Cao Thi Ngoc
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02216, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02215, USA
| | - Koshi Akahane
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02216, USA
- Department of Pediatrics, School of Medicine, University of Yamanashi, Chuo, 4093898, Japan
| | - Lee N Lawton
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Jo Lynne Rokita
- Oncology Division, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - John M Maris
- Oncology Division, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Biology Department, MIT, Cambridge, MA, 02142, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02216, USA.
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02215, USA.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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10
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Tan SH, Leong WZ, Ngoc PCT, Tan TK, Bertulfo FC, An Ö, Li ZH, Yeoh AEJ, Fullwood M, Tenen D, Sanda T. Identification of Long Non-Coding RNAs Regulated by the TAL1 Complex in T-Cell Acute Lymphoblastic Leukemia. Exp Hematol 2018. [DOI: 10.1016/j.exphem.2018.06.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Leong WZ, Tan SH, Ngoc PCT, Amanda S, Yam AWY, Liau WS, Gong Z, Lawton LN, Tenen DG, Sanda T. Abstract 3336: ARID5B activates the TAL1-induced core regulatory circuit and the oncogene MYC, thereby promoting T-cell leukemogenesis. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The oncogenic transcription factor TAL1/SCL is abnormally expressed in 40-60% cases of T-cell acute lymphoblastic leukemia (T-ALL) cells. It induces an aberrant transcriptional program with its regulatory partners (E-proteins, LMO1/2, GATA3, RUNX1 and MYB) in malignant T cells. However, the critical factors that are directly activated by the TAL1 transcriptional complex and contribute to T-ALL pathogenesis are largely unknown. Here, we identified ARID5B, an AT-rich interactive domain (ARID) family DNA binding protein, as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. Our result indicated that ARID5B expression is downregulated at the CD4, CD8 double negative 2-4 stages in normal thymocytes, while it is activated by the TAL1 complex in human T-ALL cells. The enhancer located approximately 135 kb upstream of the ARID5B gene locus is associated with a super-enhancer in multiple T-ALL samples but not in normal thymus. These data suggested that ARID5B is aberrantly activated in T-ALL cells. Interestingly, ARID5B-bound regions are predominantly associated with active transcription, as shown by the active histone marks (H3K27ac, H3K4me1 and H3K4me3) by ChIP-seq analysis. ARID5B and TAL1 frequently co-occupy target genes and coordinately control their expression. Notably, ARID5B positively regulates the expression of TAL1 and its regulatory partners (GATA3, RUNX1 and MYB). In addition, ARID5B activates the expression of the oncogene MYC. Importantly, ARID5B is required for the survival and growth of T-ALL cells in vitro, and forced expression of ARID5B in immature thymocytes results in thymus retention, radio-resistance and tumor formation in zebrafish. Our results indicate that ARID5B reinforces the oncogenic transcriptional program by positively regulating the core regulatory circuit and the oncogene MYC in T-ALL, thereby contributing to T-cell leukemogenesis.
Citation Format: Wei Zhong Leong, Shi Hao Tan, Phuong Cao Thi Ngoc, Stella Amanda, Alice Wei Yee Yam, Wei-Siang Liau, Zhiyuan Gong, Lee N. Lawton, Daniel G. Tenen, Takaomi Sanda. ARID5B activates the TAL1-induced core regulatory circuit and the oncogene MYC, thereby promoting T-cell leukemogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3336.
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Affiliation(s)
| | - Shi Hao Tan
- National Univ. of Singapore, Singapore, Singapore
| | | | | | | | | | - Zhiyuan Gong
- National Univ. of Singapore, Singapore, Singapore
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12
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Guzzi N, Cieśla M, Ngoc PCT, Lang S, Arora S, Dimitriou M, Pimková K, Sommarin MNE, Munita R, Lubas M, Lim Y, Okuyama K, Soneji S, Karlsson G, Hansson J, Jönsson G, Lund AH, Sigvardsson M, Hellström-Lindberg E, Hsieh AC, Bellodi C. Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells. Cell 2018; 173:1204-1216.e26. [PMID: 29628141 DOI: 10.1016/j.cell.2018.03.008] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/19/2018] [Accepted: 03/01/2018] [Indexed: 12/27/2022]
Abstract
Pseudouridylation (Ψ) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of Ψ remains poorly understood. Here, we show that a Ψ-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the Ψ "writer" PUS7 modifies and activates a novel network of tRNA-derived small fragments (tRFs) targeting the translation initiation complex. PUS7 inactivation in embryonic stem cells impairs tRF-mediated translation regulation, leading to increased protein biosynthesis and defective germ layer specification. Remarkably, dysregulation of this posttranscriptional regulatory circuitry impairs hematopoietic stem cell commitment and is common to aggressive subtypes of human myelodysplastic syndromes. Our findings unveil a critical function of Ψ in directing translation control in stem cells with important implications for development and disease.
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Affiliation(s)
- Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Maciej Cieśla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Stefan Lang
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sonali Arora
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Departments of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Marios Dimitriou
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kristyna Pimková
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Mikael N E Sommarin
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Michal Lubas
- Biotech Research & Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Yiting Lim
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Departments of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kazuki Okuyama
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Shamit Soneji
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Göran Karlsson
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Jenny Hansson
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Anders H Lund
- Biotech Research & Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden; Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Departments of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
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13
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Leong WZ, Tan SH, Ngoc PCT, Amanda S, Yam AWY, Liau WS, Gong Z, Lawton LN, Tenen DG, Sanda T. ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis. Genes Dev 2018; 31:2343-2360. [PMID: 29326336 PMCID: PMC5795782 DOI: 10.1101/gad.302646.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/30/2017] [Indexed: 12/13/2022]
Abstract
Leong et al. identified ARID5B as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B positively regulates the expression of TAL1 and its regulatory partners and also activates the expression of the oncogene MYC. The oncogenic transcription factor TAL1/SCL induces an aberrant transcriptional program in T-cell acute lymphoblastic leukemia (T-ALL) cells. However, the critical factors that are directly activated by TAL1 and contribute to T-ALL pathogenesis are largely unknown. Here, we identified AT-rich interactive domain 5B (ARID5B) as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B expression is down-regulated at the double-negative 2–4 stages in normal thymocytes, while it is induced by the TAL1 complex in human T-ALL cells. The enhancer located 135 kb upstream of the ARID5B gene locus is activated under a superenhancer in T-ALL cells but not in normal T cells. Notably, ARID5B-bound regions are associated predominantly with active transcription. ARID5B and TAL1 frequently co-occupy target genes and coordinately control their expression. ARID5B positively regulates the expression of TAL1 and its regulatory partners. ARID5B also activates the expression of the oncogene MYC. Importantly, ARID5B is required for the survival and growth of T-ALL cells, and forced expression of ARID5B in immature thymocytes results in thymus retention, differentiation arrest, radioresistance, and tumor formation in zebrafish. Our results indicate that ARID5B reinforces the oncogenic transcriptional program by positively regulating the TAL1-induced regulatory circuit and MYC in T-ALL, thereby contributing to T-cell leukemogenesis.
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Affiliation(s)
- Wei Zhong Leong
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Phuong Cao Thi Ngoc
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Stella Amanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Alice Wei Yee Yam
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Wei-Siang Liau
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Lee N Lawton
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.,Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
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14
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Abstract
Enhancers are regulatory elements in genomic DNA that contain specific sequence motifs that are bound by DNA-binding transcription factors. The activity of enhancers is tightly regulated in an integrated and combinatorial manner, thus yielding complex patterns of transcription in different tissues. Identifying enhancers is crucial to understanding the physiological and pathogenic roles of their target genes. The RUNX1 intronic enhancer, eR1, acts in cis to regulate RUNX1 gene expression in hematopoietic stem cells (HSCs) and hemogenic endothelial cells. RUNX1 and other hematopoietic transcription factors TAL1/SCL, GATA2, PU.1, LMO2 and LDB1 bind at this region. Interestingly, recent studies have revealed that this region is involved in a large cluster of enhancers termed a super-enhancer. The RUNX1 super-enhancer is observed in normal HSCs and T-cell acute lymphoblastic leukemia cells. In this review, we describe the discovery of eR1 and its roles in normal development and leukemogenesis, as well as its potential applications in stem cell research.
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Affiliation(s)
- Wei-Siang Liau
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Phuong Cao Thi Ngoc
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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15
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Ngoc PCT, Greenhalgh R, Dermauw W, Rombauts S, Bajda S, Zhurov V, Grbić M, Van de Peer Y, Van Leeuwen T, Rouzé P, Clark RM. Complex Evolutionary Dynamics of Massively Expanded Chemosensory Receptor Families in an Extreme Generalist Chelicerate Herbivore. Genome Biol Evol 2016; 8:3323-3339. [PMID: 27797949 PMCID: PMC5203786 DOI: 10.1093/gbe/evw249] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
While mechanisms to detoxify plant produced, anti-herbivore compounds have been associated with plant host use by herbivores, less is known about the role of chemosensory perception in their life histories. This is especially true for generalists, including chelicerate herbivores that evolved herbivory independently from the more studied insect lineages. To shed light on chemosensory perception in a generalist herbivore, we characterized the chemosensory receptors (CRs) of the chelicerate two-spotted spider mite, Tetranychus urticae, an extreme generalist. Strikingly, T. urticae has more CRs than reported in any other arthropod to date. Including pseudogenes, 689 gustatory receptors were identified, as were 136 degenerin/Epithelial Na+ Channels (ENaCs) that have also been implicated as CRs in insects. The genomic distribution of T. urticae gustatory receptors indicates recurring bursts of lineage-specific proliferations, with the extent of receptor clusters reminiscent of those observed in the CR-rich genomes of vertebrates or C. elegans Although pseudogenization of many gustatory receptors within clusters suggests relaxed selection, a subset of receptors is expressed. Consistent with functions as CRs, the genomic distribution and expression of ENaCs in lineage-specific T. urticae expansions mirrors that observed for gustatory receptors. The expansion of ENaCs in T. urticae to > 3-fold that reported in other animals was unexpected, raising the possibility that ENaCs in T. urticae have been co-opted to fulfill a major role performed by unrelated CRs in other animals. More broadly, our findings suggest an elaborate role for chemosensory perception in generalist herbivores that are of key ecological and agricultural importance.
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Affiliation(s)
- Phuong Cao Thi Ngoc
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Wannes Dermauw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Sabina Bajda
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Vladimir Zhurov
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Miodrag Grbić
- Department of Biology, The University of Western Ontario, London, ON, Canada.,University of La Rioja, Logroño, Spain
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium.,Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Pierre Rouzé
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Richard M Clark
- Department of Biology, University of Utah, Salt Lake City, Utah .,Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah
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