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Snyder K, Dixon CE, Henchir J, Gorse K, Vagni VA, Janesko-Feldman K, Kochanek PM, Jackson TC. Gene knockout of RNA binding motif 5 in the brain alters RIMS2 protein homeostasis in the cerebellum and Hippocampus and exacerbates behavioral deficits after a TBI in mice. Exp Neurol 2024; 374:114690. [PMID: 38218585 PMCID: PMC11178365 DOI: 10.1016/j.expneurol.2024.114690] [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: 10/19/2023] [Revised: 12/28/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
RNA binding motif 5 (RBM5) is a tumor suppressor in cancer but its role in the brain is unclear. We used conditional gene knockout (KO) mice to test if RBM5 inhibition in the brain affects chronic cortical brain tissue survival or function after a controlled cortical impact (CCI) traumatic brain injury (TBI). RBM5 KO decreased baseline contralateral hemispheric volume (p < 0.0001) and exacerbated ipsilateral tissue loss at 21 d after CCI in male mice vs. wild type (WT) (p = 0.0019). CCI injury, but not RBM5 KO, impaired beam balance performance (0-5d post-injury) and swim speed on the Morris Water Maze (MWM) (19-20d) (p < 0.0001). RBM5 KO was associated with mild learning impairment in female mice (p = 0.0426), reflected as a modest increase in escape latency early in training (14-18d post-injury). However, KO did not affect spatial memory at 19d post-injury in male or in female mice but it was impaired by CCI in females (p = 0.0061). RBM5 KO was associated with impaired visual function in male mice on the visible platform test at 20d post-injury (p = 0.0256). To explore signaling disturbances in KOs related to behavior, we first cross-referenced known brain-specific RBM5-regulated gene targets with genes in the curated RetNet database that impact vision. We then performed a secondary literature search on RBM5-regulated genes with a putative role in hippocampal function. Regulating synaptic membrane exocytosis 2 (RIMS) 2 was identified as a gene of interest because it regulates both vision and hippocampal function. Immunoprecipitation and western blot confirmed protein expression of a novel ~170 kDa RIMS2 variant in the cerebellum, and in the hippocampus, it was significantly increased in KO vs WT (p < 0.0001), and in a sex-dependent manner (p = 0.0390). Furthermore, male KOs had decreased total canonical RIMS2 levels in the cerebellum (p = 0.0027) and hippocampus (p < 0.0001), whereas female KOs had increased total RIMS1 levels in the cerebellum (p = 0.0389). In summary, RBM5 modulates brain function in mammals. Future work is needed to test if RBM5 dependent regulation of RIMS2 splicing effects vision and cognition, and to verify potential sex differences on behavior in a larger cohort of mice.
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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, United States of America; University of South Florida, Morsani College of Medicine, Department of Molecular Pharmacology & Physiology, 12901 Bruce B Downs Blvd, Tampa, FL 33612, United States of America.
| | - C Edward Dixon
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Rangos Research Center - 6(th) floor, Pittsburgh, PA 15224, United States of America.
| | - Jeremy Henchir
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Rangos Research Center - 6(th) floor, Pittsburgh, PA 15224, United States of America.
| | - Kiersten Gorse
- University of South Florida, Morsani College of Medicine, USF Health Heart Institute, MDD 0630, 560 Channelside Dr, Tampa, FL 33602, United States of America; University of South Florida, Morsani College of Medicine, Department of Molecular Pharmacology & Physiology, 12901 Bruce B Downs Blvd, Tampa, FL 33612, United States of America.
| | - Vincent A Vagni
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Rangos Research Center - 6(th) floor, Pittsburgh, PA 15224, United States of America.
| | - Keri Janesko-Feldman
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Rangos Research Center - 6(th) floor, Pittsburgh, PA 15224, United States of America.
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Rangos Research Center - 6(th) floor, Pittsburgh, PA 15224, United States of America.
| | - Travis C Jackson
- University of South Florida, Morsani College of Medicine, USF Health Heart Institute, MDD 0630, 560 Channelside Dr, Tampa, FL 33602, United States of America; University of South Florida, Morsani College of Medicine, Department of Molecular Pharmacology & Physiology, 12901 Bruce B Downs Blvd, Tampa, FL 33612, United States of America.
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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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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