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Zhang M, Hyle J, Chen X, Xin Y, Jin Y, Zhang J, Yang X, Chen X, Wright S, Liu Z, Rosikiewicz W, Xu B, He L, Liu H, Ping N, Wu D, Wen F, Li C, Xu P. RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9. Genome Biol 2024; 25:16. [PMID: 38216972 PMCID: PMC10785552 DOI: 10.1186/s13059-023-03149-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND The oncogenic protein HOXA9 plays a critical role in leukemia transformation and maintenance, and its aberrant expression is a hallmark of most aggressive acute leukemia. Although inhibiting the upstream regulators of HOXA9 has been proven as a significant therapeutic intervention, the comprehensive regulation network controlling HOXA9 expression in leukemia has not been systematically investigated. RESULTS Here, we perform genome-wide CRISPR/Cas9 screening in the HOXA9-driven reporter acute leukemia cells. We identify a poorly characterized RNA-binding protein, RBM5, as the top candidate gene required to maintain leukemia cell fitness. RBM5 is highly overexpressed in acute myeloid leukemia (AML) patients compared to healthy individuals. RBM5 loss triggered by CRISPR knockout and shRNA knockdown significantly impairs leukemia maintenance in vitro and in vivo. Through domain CRISPR screening, we reveal that RBM5 functions through a noncanonical transcriptional regulation circuitry rather than RNA splicing, such an effect depending on DNA-binding domains. By integrative analysis and functional assays, we identify HOXA9 as the downstream target of RBM5. Ectopic expression of HOXA9 rescues impaired leukemia cell proliferation upon RBM5 loss. Importantly, acute protein degradation of RBM5 through auxin-inducible degron system immediately reduces HOXA9 transcription. CONCLUSIONS We identify RBM5 as a new upstream regulator of HOXA9 and reveal its essential role in controlling the survival of AML. These functional and molecular mechanisms further support RBM5 as a promising therapeutic target for myeloid leukemia treatment.
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Affiliation(s)
- Mengli Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaowen Chen
- Division of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen Institute of Pediatrics, 7019 Yi Tian Road, Shenzhen, 518038, China
| | - Ye Xin
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Yingcai Jin
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Jianxiang Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Xue Yang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Xinfeng Chen
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhenling Liu
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Liusheng He
- Core Facility of Flow Cytometry, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Hong Liu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Nana Ping
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Feiqiu Wen
- Division of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen Institute of Pediatrics, 7019 Yi Tian Road, Shenzhen, 518038, China
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Peng Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, Jiangsu, China.
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Snyder K, Gorse K, Kochanek PM, Jackson TC. Neuronal RBM5 modulates cell signaling responses to traumatic and hypoxic-ischemic injury in a sex-dependent manner. Cell Death Discov 2023; 9:379. [PMID: 37848418 PMCID: PMC10582027 DOI: 10.1038/s41420-023-01677-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023] Open
Abstract
It is not clear if inhibiting the pro-death gene RNA binding motif 5 (RBM5) is neuroprotective in isolated primary neurons or if it regulates cell survival in a sex-dependent manner. Here we established sex-dichotomized primary cortical neuron cultures from transgenic mice harboring a floxed RBM5 gene-trap. Lentivirus-mediated expression of CRE was used to silence RBM5 expression. Male and female neurons were maintained in next-generation Neurobasal-Plus media and subjected to a mechanical stretch-injury (to model traumatic brain injury) or oxygen-glucose deprivation/OGD (to model ischemia). RBM5 KO did not affect 24 h post-injury survival as determined by lactate dehydrogenase (LDH) release, in either paradigm. In contrast, female KO neurons had increased spectrin breakdown products post-insult (in both models). Furthermore, in OGD, RBM5 KO in male neurons exacerbated injury-induced downregulation of pro-survival AKT activation (pAKT473) but conversely led to pAKT473 sparing in female neurons. Moreover, global proteomics identified 19 differentially expressed (DE) proteins in OGD-injured male neurons, and 102 DE proteins in injured female neurons. Two novel RBM5-regulated proteins (PIGQ and EST1C) were identified in injured male KO neurons, and 8 novel proteins identified in injured female KO neurons (S35A5, DHTK1, STX3, IF3M, RN167, K1C14, DYHS, and MED13). In summary, RBM5 inhibition does not modify neuronal survival in primary mouse neurons in 2 clinically relevant models of excitotoxic insult, but RBM5 does regulate intracellular responses to injury in a sex-dependent manner.
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Affiliation(s)
- Kara Snyder
- University of South Florida, Morsani College of Medicine, USF Health Heart Institute, MDD 0630, 560 Channelside Dr, Tampa, FL, 33602, USA
- University of South Florida, Morsani College of Medicine, Department of Molecular Pharmacology & Physiology, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Kiersten Gorse
- University of South Florida, Morsani College of Medicine, USF Health Heart Institute, MDD 0630, 560 Channelside Dr, Tampa, FL, 33602, USA
- University of South Florida, Morsani College of Medicine, Department of Molecular Pharmacology & Physiology, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Rangos Research Center - 6th floor, Pittsburgh, PA, 15224, USA
| | - Travis C Jackson
- University of South Florida, Morsani College of Medicine, USF Health Heart Institute, MDD 0630, 560 Channelside Dr, Tampa, FL, 33602, USA.
- University of South Florida, Morsani College of Medicine, Department of Molecular Pharmacology & Physiology, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA.
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Farooq J, Snyder K, Janesko-Feldman K, Gorse K, Vagni V, Kochanek PM, Jackson TC. RNA Binding Motif 5 Gene Deletion Modulates Cell Signaling in a Sex-Dependent Manner but not Hippocampal Cell Death. J Neurotrauma 2022; 39:577-589. [PMID: 35152732 PMCID: PMC8978574 DOI: 10.1089/neu.2021.0362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA-binding motif 5 (RBM5) is a pro-death tumor suppressor gene in cancer cells. It remains to be determined if it is neurotoxic in the brain or rather if it plays a fundamentally different role in the central nervous system (CNS). Brain-specific RBM5 knockout (KO) mice were given a controlled cortical impact (CCI) traumatic brain injury (TBI). Markers of acute cellular damage and repair were measured in hippocampal homogenates 48 h post-CCI. Hippocampal CA1/CA3 cell counts were assessed 7 days post-CCI to determine if early changes in injury markers were associated with histological outcome. No genotype-dependent differences were found in the levels of apoptotic markers (caspase 3, caspase 6, and caspase 9). However, KO females had a paradoxical increase in markers of pro-death calpain activation (145/150-spectrin and breakdown products [SBDP]) and in DNA repair/survival markers. (pH2A.x and pCREB). CCI-injured male KOs had a significant increase in phosphorylated calcium/calmodulin-dependent protein kinase II (pCaMKII). Despite sex/genotype-dependent differences in KOs in the levels of acute cell signaling targets involved in cell death pathways, 7 day hippocampal neuronal survival did not differ from that of wild types (WTs). Similarly, no differences in astrogliosis were observed. Finally, gene analysis revealed increased estrogen receptor α (ERα) levels in the KO hippocampus in females and may suggest a novel mechanism to explain sex-dimorphic effects on cell signaling. In summary, RBM5 inhibition did not affect hippocampal survival after a TBI in vivo but did modify targets involved in neural signal transduction/Ca2+ signaling pathways. Findings here support the view that RBM5 may serve a purpose in the CNS that is dissimilar from its traditional pro-death role in cancer.
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Affiliation(s)
- Jeffrey Farooq
- University of South Florida, 7831, Molecular Pharmacology and Physiology, Tampa, Florida, United States
- USF Health Morsani College of Medicine, 33697, USF Health Heart Institute, Tampa, Florida, United States
| | - Kara Snyder
- University of South Florida, 7831, Molecular Pharmacology and Physiology, Tampa, Florida, United States
- USF Health Morsani College of Medicine, 33697, USF Health Heart Institute, Tampa, Florida, United States
| | - Keri Janesko-Feldman
- University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States,
| | - Kiersten Gorse
- University of South Florida, 7831, Molecular Pharmacology and Physiology, Tampa, Florida, United States
- USF Health Morsani College of Medicine, 33697, USF Health Heart Institute, Tampa, Florida, United States
| | - Vincent Vagni
- University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States,
| | - Patrick M. Kochanek
- University of Pittsburgh School of Medicine, Critical Care Medicine, John G. Rangos Research Center, Safar Center for Resuscitation Research, 4401 Penn Avenue, Pittsburgh, Pennsylvania, United States, 15224
- United States
| | - Travis C. Jackson
- University of South Florida, 7831, Molecular Pharmacology and Physiology, 4202 E Fowler Ave, Tampa, Florida, United States, 33620-9951
- USF Health Morsani College of Medicine, 33697, USF Health Heart Institute, 560 Channelside Dr, Tampa, Florida, United States, 33602
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Wright DJ, Hall NAL, Irish N, Man AL, Glynn W, Mould A, Angeles ADL, Angiolini E, Swarbreck D, Gharbi K, Tunbridge EM, Haerty W. Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. BMC Genomics 2022; 23:42. [PMID: 35012468 PMCID: PMC8744310 DOI: 10.1186/s12864-021-08261-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/15/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of which isoforms are differentially used or expressed and how this affects cellular differentiation remains unclear. Long read sequencing allows full-length transcript recovery and quantification, enabling transcript-level analysis of alternative splicing processes and how these change with cell state. Here, we utilise Oxford Nanopore Technologies sequencing to produce a custom annotation of a well-studied human neuroblastoma cell line SH-SY5Y, and to characterise isoform expression and usage across differentiation. RESULTS We identify many previously unannotated features, including a novel transcript of the voltage-gated calcium channel subunit gene, CACNA2D2. We show differential expression and usage of transcripts during differentiation identifying candidates for future research into state change regulation. CONCLUSIONS Our work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.
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Affiliation(s)
- David J Wright
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Nicola A L Hall
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Naomi Irish
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Angela L Man
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Will Glynn
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Arne Mould
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Alejandro De Los Angeles
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Emily Angiolini
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK.
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Jackson TC, Kochanek PM. RNA Binding Motif 5 (RBM5) in the CNS-Moving Beyond Cancer to Harness RNA Splicing to Mitigate the Consequences of Brain Injury. Front Mol Neurosci 2020; 13:126. [PMID: 32765218 PMCID: PMC7381114 DOI: 10.3389/fnmol.2020.00126] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
Gene splicing modulates the potency of cell death effectors, alters neuropathological disease processes, influences neuronal recovery, but may also direct distinct mechanisms of secondary brain injury. Therapeutic targeting of RNA splicing is a promising avenue for next-generation CNS treatments. RNA-binding proteins (RBPs) regulate a variety of RNA species and are prime candidates in the hunt for druggable targets to manipulate and tailor gene-splicing responses in the brain. RBPs preferentially recognize unique consensus sequences in targeted mRNAs. Also, RBPs often contain multiple RNA-binding domains (RBDs)—each having a unique consensus sequence—suggesting the possibility that drugs could be developed to block individual functional domains, increasing the precision of RBP-targeting therapies. Empirical characterization of most RBPs is lacking and represents a major barrier to advance this emerging therapeutic area. There is a paucity of data on the role of RBPs in the brain including, identification of their unique mRNA targets, defining how CNS insults affect their levels and elucidating which RBPs (and individual domains within) to target to improve neurological outcomes. This review focuses on the state-of-the-art of the RBP tumor suppressor RNA binding motif 5 (RBM5) in the CNS. We discuss its potent pro-death roles in cancer, which motivated our interest to study it in the brain. We review recent studies showing that RBM5 levels are increased after CNS trauma and that it promotes neuronal death in vitro. Finally, we conclude with recent reports on the first set of RBM5 regulated genes identified in the intact brain, and discuss how those findings provide new clues germane to its potential function(s) in the CNS, and pose new questions on its therapeutic utility to mitigate CNS injury.
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Affiliation(s)
- Travis C Jackson
- Morsani College of Medicine, USF Health Heart Institute, University of South Florida, Tampa, FL, United States.,Morsani College of Medicine, Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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