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Wu J, Sun C, Guan J, Abdullah SW, Wang X, Ren M, Qiao L, Sun S, Guo H. Nuclear ribonucleoprotein RALY downregulates foot-and-mouth disease virus replication but antagonized by viral 3C protease. Microbiol Spectr 2024; 12:e0365823. [PMID: 38323828 PMCID: PMC10913732 DOI: 10.1128/spectrum.03658-23] [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: 10/12/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
The internal ribosome entry site (IRES) element constitutes a cis-acting RNA regulatory sequence that recruits the ribosomal initiation complex in a cap-independent manner, assisted by various RNA-binding proteins and IRES trans-acting factors. Foot-and-mouth disease virus (FMDV) contains a functional IRES element and takes advantage of this element to subvert host translation machinery. Our study identified a novel mechanism wherein RALY, a member of the heterogeneous nuclear ribonucleoproteins (hnRNP) family belonging to RNA-binding proteins, binds to the domain 3 of FMDV IRES via its RNA recognition motif residue. This interaction results in the downregulation of FMDV replication by inhibiting IRES-driven translation. Furthermore, our findings reveal that the inhibitory effect exerted by RALY on FMDV replication is not attributed to the FMDV IRES-mediated assembly of translation initiation complexes but rather to the impediment of 80S ribosome complex formation after binding with 40S ribosomes. Conversely, 3Cpro of FMDV counteracts RALY-mediated inhibition by the ubiquitin-proteasome pathway. Therefore, these results indicate that RALY, as a novel critical IRES-binding protein, inhibits FMDV replication by blocking the formation of 80S ribosome, providing a deeper understanding of how viruses recruit and manipulate host factors. IMPORTANCE The translation of FMDV genomic RNA driven by IRES element is a crucial step for virus infections. Many host proteins are hijacked to regulate FMDV IRES-dependent translation, but the regulatory mechanism remains unknown. Here, we report for the first time that cellular RALY specifically interacts with the IRES of FMDV and negatively regulates viral replication by blocking 80S ribosome assembly on FMDV IRES. Conversely, RALY-mediated inhibition is antagonized by the viral 3C protease by the ubiquitin-proteasome pathway. These results would facilitate further understanding of virus-host interactions and translational control during viral infection.
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Affiliation(s)
- Jin'en Wu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Chao Sun
- Division of Livestock Infectious Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Junyong Guan
- Division of Livestock Infectious Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Sahibzada Waheed Abdullah
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuefei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lu Qiao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shiqi Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huichen Guo
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
- School of Animal Science, Yangtze University, Jingzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
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Cao S, Wang D, Wang P, Liu Y, Dong W, Ruan X, Liu L, Xue Y, E T, Lin H, Liu X. SUMOylation of RALY promotes vasculogenic mimicry in glioma cells via the FOXD1/DKK1 pathway. Cell Biol Toxicol 2023; 39:3323-3340. [PMID: 37906341 PMCID: PMC10693529 DOI: 10.1007/s10565-023-09836-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023]
Abstract
Human malignant gliomas are the most common and aggressive primary malignant tumors of the human central nervous system. Vasculogenic mimicry (VM), which refers to the formation of a tumor blood supply system independently of endothelial cells, contributes to the malignant progression of glioma. Therefore, VM is considered a potential target for glioma therapy. Accumulated evidence indicates that alterations in SUMOylation, a reversible post-translational modification, are involved in tumorigenesis and progression. In the present study, we found that UBA2 and RALY were upregulated in glioma tissues and cell lines. Downregulation of UBA2 and RALY inhibited the migration, invasion, and VM of glioma cells. RALY can be SUMOylated by conjugation with SUMO1, which is facilitated by the overexpression of UBA2. The SUMOylation of RALY increases its stability, which in turn increases its expression as well as its promoting effect on FOXD1 mRNA. The overexpression of FOXD1 promotes DKK1 transcription by activating its promoter, thereby promoting glioma cell migration, invasion, and VM. Remarkably, the combined knockdown of UBA2, RALY, and FOXD1 resulted in the smallest tumor volumes and the longest survivals of nude mice in vivo. UBA2/RALY/FOXD1/DKK1 axis may play crucial roles in regulating VM in glioma, which may contribute to the development of potential strategies for the treatment of gliomas.
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Affiliation(s)
- Shuo Cao
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning Province, China
| | - Di Wang
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Ping Wang
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Yunhui Liu
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Weiwei Dong
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Xuelei Ruan
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Libo Liu
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Yixue Xue
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Tiange E
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Hongda Lin
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Xiaobai Liu
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China.
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China.
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Chien HT, Li CY, Su WH, Chang KC, Chen CS, Liu YT, Chen CY, Dai CY, Wang SC. Multi-omics profiling of chemotactic characteristics of brain microglia and astrocytoma. Life Sci 2023; 330:121855. [PMID: 37419413 DOI: 10.1016/j.lfs.2023.121855] [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: 04/17/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 07/09/2023]
Abstract
Brain cancer is a deadly disease with low survival rates for over 70 % of patients. Therefore, there is a critical need to develop better treatment methods and strategies to improve patient outcomes. In this study, we explored the tumor microenvironment and discovered unique characteristics of microglia to interact with astrocytoma cells and promote proliferation and migration of collisions. The conditioned medium from the collisions expressed cell chemoattraction and anti-inflammatory responses. To further understand the interactions between microglia and astrocytoma cells, we used flow sorting and protein analysis found that the protein alterations were related to biogenesis in the astrocytoma cells and metabolic processes in the microglia. Both types of cells were involved in binding and activity in cell-cell interactions. Using STRING to demonstrate the protein cross-interaction between the cells. Furthermore, PHB and RDX interact with oncogenic proteins, which were significantly expressed in patients with Glioblastoma Multiforme (GBM) and low-grade glioma (LGG) according to GEPIA. To study the role of RDX in chemoattraction, the inhibitor-NSC668394 suppressed collision formation and migration in BV2 cells in vitro by down-regulating F-actin. Additionally, it suppressed macrophage infiltration in infiltrating islands in vivo of intracranial tumor-bearing mice. These findings provide evidence for the role of resident cells in mediating tumor development and invasiveness and suggest that potential interacting molecules may be a strategy for controlling tumor growth by regulating the infiltration of tumor-associated microglia in the brain tumor microenvironment.
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Affiliation(s)
- Hsin-Tung Chien
- Department of Medical Laboratory Science and Biotechnology, Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan.
| | - Wen-Hsiu Su
- Department of Medical Laboratory Science and Biotechnology, Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Kun-Che Chang
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
| | - Chi-Sheng Chen
- Department of Medical Laboratory Science and Biotechnology, Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yi-Ting Liu
- Department of Medical Laboratory Science and Biotechnology, Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chih-Yi Chen
- Department of Medical Laboratory Science and Biotechnology, Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chia-Yen Dai
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan; College of Medicine and Center of Excellence for Metabolic Associated Fatty Liver Disease, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Shu-Chi Wang
- Department of Medical Laboratory Science and Biotechnology, Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan; College of Medicine and Center of Excellence for Metabolic Associated Fatty Liver Disease, National Sun Yat-sen University, Kaohsiung, Taiwan; Institute of precision medicine, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan.
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4
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Hu H, Zhao K, Fang D, Wang Z, Yu N, Yao B, Liu K, Wang F, Mei Y. The RNA binding protein RALY suppresses p53 activity and promotes lung tumorigenesis. Cell Rep 2023; 42:112288. [PMID: 36952348 DOI: 10.1016/j.celrep.2023.112288] [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: 08/19/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/24/2023] Open
Abstract
The tumor suppressor p53 plays a pivotal role in tumor prevention. The activity of p53 is mainly restrained by the ubiquitin E3 ligase Mdm2. However, it is not well understood how the Mdm2-p53 pathway is intricately regulated. Here we report that the RNA binding protein RALY functions as an oncogenic factor in lung cancer. RALY simultaneously binds to Mdm2 and the deubiquitinating enzyme USP7. Via these interactions, RALY not only stabilizes Mdm2 by stimulating the deubiquitinating activity of USP7 toward Mdm2 but also increases the trans-E3 ligase activity of Mdm2 toward p53. Consequently, RALY enhances Mdm2-mediated ubiquitination and degradation of p53. Functionally, RALY promotes lung tumorigenesis, at least partially, via negative regulation of p53. These findings suggest that RALY destabilizes p53 by modulating the function of Mdm2 at multiple levels. Our study also indicates a critical role for RALY in promoting lung tumorigenesis via p53 inhibition.
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Affiliation(s)
- Hao Hu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Kailiang Zhao
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Debao Fang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Zhongyu Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Ning Yu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Bo Yao
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Kaiyue Liu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Fang Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Yide Mei
- Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China; Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China.
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5
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Kiełbowski K, Ptaszyński K, Wójcik J, Wojtyś ME. The role of selected non-coding RNAs in the biology of non-small cell lung cancer. Adv Med Sci 2023; 68:121-137. [PMID: 36933328 DOI: 10.1016/j.advms.2023.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/26/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023]
Abstract
Lung cancer is the second most frequently diagnosed cancer worldwide and a leading cause of cancer-related deaths. Non-small cell lung carcinoma (NSCLC) represents 85% of all cases. Accumulating evidence highlights the outstanding role of non-coding RNA (ncRNA) in regulating the tumorigenesis process by modulating crucial signaling pathways. Micro RNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) are either up- or downregulated in lung cancer patients and can promote or suppress the progression of the disease. These molecules interact with messenger RNA (mRNA) and with each other to regulate gene expression and stimulate proto-oncogenes or silence tumor suppressors. NcRNAs provide a new strategy to diagnose or treat lung cancer patients and multiple molecules have already been identified as potential biomarkers or therapeutic targets. The aim of this review is to summarize the current evidence on the roles of miRNA, lncRNA and circRNA in NSCLC biology and present their clinical potential.
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Affiliation(s)
- Kajetan Kiełbowski
- Department of Thoracic Surgery and Transplantation, Pomeranian Medical University, Szczecin, Poland
| | - Konrad Ptaszyński
- Department of Pathology, Faculty of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Poland
| | - Janusz Wójcik
- Department of Thoracic Surgery and Transplantation, Pomeranian Medical University, Szczecin, Poland
| | - Małgorzata Edyta Wojtyś
- Department of Thoracic Surgery and Transplantation, Pomeranian Medical University, Szczecin, Poland.
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Miao TW, Chen FY, Du LY, Xiao W, Fu JJ. Signature based on RNA-binding protein-related genes for predicting prognosis and guiding therapy in non-small cell lung cancer. Front Genet 2022; 13:930826. [PMID: 36118863 PMCID: PMC9479344 DOI: 10.3389/fgene.2022.930826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Studies have reported that RNA-binding proteins (RBPs) are dysregulated in multiple cancers and are correlated with the progression and prognosis of disease. However, the functions of RBPs in non-small cell lung cancer (NSCLC) remain unclear. The present study aimed to explore the function of RBPs in NSCLC and their prognostic and therapeutic value.Methods: The mRNA expression profiles, DNA methylation data, gene mutation data, copy number variation data, and corresponding clinical information on NSCLC were downloaded from The Cancer Genome Atlas, Gene Expression Omnibus, and the University of California Santa Cruz Xena databases. The differentially expressed RBPs were identified between tumor and control tissues, and the expression and prognostic value of these RBPs were systemically investigated by bioinformatics analysis. A quantitative polymerase chain reaction (qPCR) was performed to validate the dysregulated genes in the prognostic signature.Results: A prognostic RBP-related signature was successfully constructed based on eight RBPs represented as a risk score using least absolute shrinkage and selection operator (LASSO) regression analysis. The high-risk group had a worse overall survival (OS) probability than the low-risk group (p < 0.001) with 1-, 3-, and 5-year area under the receiver operator characteristic curve values of 0.671, 0.638, and 0.637, respectively. The risk score was associated with the stage of disease (p < 0.05) and was an independent prognostic factor for NSCLC when adjusted for age and UICC stage (p < 0.001, hazard ratio (HR): 1.888). The constructed nomogram showed a good predictive value. The P53, focal adhesion, and NOD-like receptor signaling pathways were the primary pathways in the high-risk group (adjusted p value <0.05). The high-risk group was correlated with increased immune infiltration (p < 0.05), upregulated relative expression levels of programmed cell death 1 (PD1) (p = 0.015), cytotoxic T-lymphocyte-associated protein 4 (CTLA4) (p = 0.042), higher gene mutation frequency, higher tumor mutational burden (p = 0.034), and better chemotherapy response (p < 0.001). The signature was successfully validated using the GSE26939, GSE31210, GSE30219, and GSE157009 datasets. Dysregulation of these genes in patients with NSCLC was confirmed using the qPCR in an independent cohort (p < 0.05).Conclusion: An RBP-related signature was successfully constructed to predict prognosis in NSCLC, functioning as a reference for individualized therapy, including immunotherapy and chemotherapy.
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Affiliation(s)
- Ti-Wei Miao
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Fang-Ying Chen
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Long-Yi Du
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Xiao
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Juan-Juan Fu
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Juan-Juan Fu,
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Magnuson B, Bedi K, Narayanan IV, Bartkowiak B, Blinkiewicz H, Paulsen MT, Greenleaf A, Ljungman M. CDK12 regulates co-transcriptional splicing and RNA turnover in human cells. iScience 2022; 25:105030. [PMID: 36111258 PMCID: PMC9468413 DOI: 10.1016/j.isci.2022.105030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
The cyclin-dependent kinase CDK12 has garnered interest as a cancer therapeutic target as DNA damage response genes are particularly suppressed by loss of CDK12 activity. In this study, we assessed the acute effects of CDK12 inhibition on transcription and RNA processing using nascent RNA Bru-seq and BruChase-seq. Acute transcriptional changes were overall small after CDK12 inhibition but over 600 genes showed intragenic premature termination, including DNA repair and cell cycle genes. Furthermore, many genes showed reduced transcriptional readthrough past the end of genes in the absence of CDK12 activity. RNA turnover was dramatically affected by CDK12 inhibition and importantly, caused increased degradation of many transcripts from DNA damage response genes. We also show that co-transcriptional splicing was suppressed by CDK12 inhibition. Taken together, these studies reveal the roles of CDK12 in regulating transcription elongation, transcription termination, co-transcriptional splicing, and RNA turnover. Over 600 genes showed prematurely terminated transcription when CDK12 was inhibited CDK12 promotes transcriptional readthrough past transcription end sites (TESs) CDK12 promotes splicing and affects transcript stability
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Affiliation(s)
- Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karan Bedi
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Bartlomiej Bartkowiak
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hailey Blinkiewicz
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T. Paulsen
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arno Greenleaf
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mats Ljungman
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author
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8
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Nuclear ribonucleoprotein RALY targets virus nucleocapsid protein and induces autophagy to restrict porcine epidemic diarrhea virus replication. J Biol Chem 2022; 298:102190. [PMID: 35753351 PMCID: PMC9287142 DOI: 10.1016/j.jbc.2022.102190] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/24/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) causes diarrhea and dehydration in pigs and leads to great economic losses in the commercial swine industry. However, the underlying molecular mechanisms of host response to viral infection remain unclear. In the present study, we investigated a novel mechanism by which RALY, a member of the heterogeneous nuclear ribonucleoprotein family, significantly promotes the degradation of the PEDV nucleocapsid (N) protein to inhibit viral replication. Furthermore, we identified an interaction between RALY and the E3 ubiquitin ligase MARCH8 (membrane-associated RING-CH 8), as well as the cargo receptor NDP52 (nuclear dot protein 52 kDa), suggesting that RALY could suppress PEDV replication by degrading the viral N protein through a RALY–MARCH8–NDP52–autophagosome pathway. Collectively, these results suggest a preventive role of RALY against PEDV infection via the autophagy pathway and open up the possibility of inducing RALY in vivo as an effective prophylactic and preventive treatment for PEDV infection.
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9
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RALY regulate the proliferation and expression of immune/inflammatory response genes via alternative splicing of FOS. Genes Immun 2022; 23:246-254. [PMID: 35941292 PMCID: PMC9758052 DOI: 10.1038/s41435-022-00178-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
RALY is a multifunctional RNA-binding protein involved in cancer metastasis, prognosis, and chemotherapy resistance in various cancers. However, the molecular mechanism of which is still unclear. We have established RALY overexpression cell lines and studied the effect of RALY on proliferation and apoptosis in HeLa cells. Then we used RNA-seq to analyze the transcriptomes data. Lastly, RT-qPCR experiments had performed to confirm the RNA-seq results. We found that the overexpression of RALY in HeLa cells inhibited proliferation. Moreover, the overexpression of RALY changed the gene expression profile, and the significant upregulation of genes involved immune/inflammatory response related biological process by NOD-like receptor signaling pathway cytokine-cytokine receptor interaction. The significant downregulation genes involved innate immune response by the Primary immunodeficiency pathway. Notably, IFIT1, IFIT2, IFTI3, IFI44, HERC4, and OASL expression had inhibited by the overexpression of RALY. Furthermore, RALY negatively regulates the expression of transcription factors FOS and FOSB. Notably, we found that 645 alternative splicing events had regulated by overexpression of RALY, which is highly enriched in transcription regulation, RNA splicing, and cell proliferation biological process by the metabolic pathway. We show that RALY regulates the expression of immune/inflammatory response-related genes via alternative splicing of FOS in HeLa cells. The novel role of RALY in regulating immune/inflammatory gene expression may explain its function in regulating chemotherapy resistance and provides novel insights into further exploring the molecular mechanism of RALY in regulating cancer immunity and chemo/immune therapies.
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Wippel HH, Fioramonte M, Chavez JD, Bruce JE. Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs. Mol Omics 2021; 17:503-516. [PMID: 34017973 PMCID: PMC8355073 DOI: 10.1039/d1mo00024a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA-binding proteins (RBPs) have conserved domains and consensus sequences that interact with RNAs and other proteins forming ribonucleoprotein (RNP) complexes. RNPs are involved in the regulation of several cellular processes, including transcription, pre-mRNA splicing, mRNA transport, localization, degradation and storage, and ultimately control of translation. Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RBPs that mediate transcription control and nuclear processing of transcripts. Some hnRNPs are part of the spliceosome complex, a dynamic machinery formed by RNPs that regulate alternative splicing of pre-mRNAs. Here, chemical crosslinking of proteins was applied to identify specific interacting regions and protein structural features of hnRNPs: hnRNPA1, hnRNPA2/B1, hnRNPC, and RALY. The results reveal interaction of these proteins within RNA-binding domains and conserved motifs, providing evidence of a coordinated action of known regulatory sequences of RBPs. Moreover, these crosslinking data enable structural model generation for RBPs, illustrating how crosslinking mass spectrometry can complement other structural methods.
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Affiliation(s)
- Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Mariana Fioramonte
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. and University of Campinas, Campinas, SP, Brazil
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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Du JX, Luo YH, Zhang SJ, Wang B, Chen C, Zhu GQ, Zhu P, Cai CZ, Wan JL, Cai JL, Chen SP, Dai Z, Zhu W. Splicing factor SRSF1 promotes breast cancer progression via oncogenic splice switching of PTPMT1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:171. [PMID: 33992102 PMCID: PMC8122567 DOI: 10.1186/s13046-021-01978-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/09/2021] [Indexed: 02/08/2023]
Abstract
Background Intensive evidence has highlighted the effect of aberrant alternative splicing (AS) events on cancer progression when triggered by dysregulation of the SR protein family. Nonetheless, the underlying mechanism in breast cancer (BRCA) remains elusive. Here we sought to explore the molecular function of SRSF1 and identify the key AS events regulated by SRSF1 in BRCA. Methods We conducted a comprehensive analysis of the expression and clinical correlation of SRSF1 in BRCA based on the TCGA dataset, Metabric database and clinical tissue samples. Functional analysis of SRSF1 in BRCA was conducted in vitro and in vivo. SRSF1-mediated AS events and their binding motifs were identified by RNA-seq, RNA immunoprecipitation-PCR (RIP-PCR) and in vivo crosslinking followed by immunoprecipitation (CLIP), which was further validated by the minigene reporter assay. PTPMT1 exon 3 (E3) AS was identified to partially mediate the oncogenic role of SRSF1 by the P-AKT/C-MYC axis. Finally, the expression and clinical significance of these AS events were validated in clinical samples and using the TCGA database. Results SRSF1 expression was consistently upregulated in BRCA samples, positively associated with tumor grade and the Ki-67 index, and correlated with poor prognosis in a hormone receptor-positive (HR+) cohort, which facilitated proliferation, cell migration and inhibited apoptosis in vitro and in vivo. We identified SRSF1-mediated AS events and discovered the SRSF1 binding motif in the regulation of splice switching of PTPMT1. Furthermore, PTPMT1 splice switching was regulated by SRSF1 by binding directly to its motif in E3 which partially mediated the oncogenic role of SRSF1 by the AKT/C-MYC axis. Additionally, PTPMT1 splice switching was validated in tissue samples of BRCA patients and using the TCGA database. The high-risk group, identified by AS of PTPMT1 and expression of SRSF1, possessed poorer prognosis in the stage I/II TCGA BRCA cohort. Conclusions SRSF1 exerts oncogenic roles in BRCA partially by regulating the AS of PTPMT1, which could be a therapeutic target candidate in BRCA and a prognostic factor in HR+ BRCA patient. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01978-8.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Ping Zhu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, No. 130 Dongan Road, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jing-Lei Wan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Shi-Ping Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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12
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Reyes AJF, Kitata RB, Dela Rosa MAC, Wang YT, Lin PY, Yang PC, Friedler A, Yitzchaik S, Chen YJ. Integrating site-specific peptide reporters and targeted mass spectrometry enables rapid substrate-specific kinase assay at the nanogram cell level. Anal Chim Acta 2021; 1155:338341. [PMID: 33766317 DOI: 10.1016/j.aca.2021.338341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 11/25/2022]
Abstract
Dysregulation of phosphorylation-mediated signaling drives the initiation and progression of many diseases. A substrate-specific kinase assay capable of quantifying the altered site-specific phosphorylation of its phenotype-dependent substrates provides better specificity to monitor a disease state. We report a sensitive and rapid substrate-specific kinase assay by integrating site-specific peptide reporter and multiple reaction monitoring (MRM)-MS platform for relative and absolute quantification of substrate-specific kinase activity at the sensitivity of nanomolar kinase and nanogram cell lysate. Using non-small cell lung cancer as a proof-of-concept, three substrate peptides selected from constitutive phosphorylation in tumors (HDGF-S165, RALY-S135, and NRD1-S94) were designed to demonstrate the feasibility. The assay showed good accuracy (<15% nominal deviation) and reproducibility (<15% CV). In PC9 cells, the measured activity for HDGF-S165 was 3.2 ± 0.2 fmol μg-1 min-1, while RALY-S135 and NRD1-S94 showed 4- and 20-fold higher activity at the sensitivity of 25 ng and 5 ng lysate, respectively, suggesting different endogenous kinases for each substrate peptide. Without the conventional shotgun phosphoproteomics workflow, the overall pipeline from cell lysate to MS data acquisition only takes 3 h. The multiplexed analysis revealed differences in the phenotype-dependent substrate phosphorylation profiles across six NSCLC cell lines and suggested a potential association of HDGF-S165 and NRD1-S94 with TKI resistance. With the ease of design, sensitivity, accuracy, and reproducibility, this approach may offer rapid and sensitive assays for targeted quantification of the multiplexed substrate-specific kinase activity of small amounts of sample.
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Affiliation(s)
- Aaron James F Reyes
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taiwan; Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan; Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Mira Anne C Dela Rosa
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Assaf Friedler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Shlomo Yitzchaik
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Yu-Ju Chen
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taiwan; Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan; Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan.
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13
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Xia Y, Ye S, Yang Y, Liu Y, Tong G. Over-expression of RALYL suppresses the progression of ovarian clear cell carcinoma through inhibiting MAPK and CDH1 signaling pathways. Int J Med Sci 2021; 18:785-791. [PMID: 33437214 PMCID: PMC7797558 DOI: 10.7150/ijms.51488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/30/2020] [Indexed: 12/01/2022] Open
Abstract
Background: The molecular mechanism in the progression of ovarian clear cell carcinoma (OCCC) remains unclear. Objective: This study aimed to investigate the potential function of RAYLY in OCCC. Methods: To validate RAYLY expression, immunohistochemistry, quantitative real-time PCR and western blotting were performed in OCCC tissues and the cell lines of OCCC and epithelial ovarian carcinoma (EOC). Subsequently, the biological effects of RALYL were evaluated through colony formation, and cell proliferation, migration and invasion assays. Finally, RNA-sequencing and gene set enrichment analysis (GSEA) were conducted to explore potential mechanism of RALYL in OCCC. Results: In our study, RALYL was significantly down-regulated in a majority of OCCC tissues compared to adjacent non-tumorous tissues, and OCCC cells had a lower expression level of RALYL than that of EOC cells. OCCC patients with high RALYL expression had a better pathological stage and prognosis. In vitro, over-expression of RALYL inhibited cell proliferation, migration and invasion in OCCC. GSEA analysis and western blot indicated an enrichment of MAPK and CDH1 signaling pathways in OCCC cells without RALYL over-expression. Conclusions: RALYL played an important role in the progression of OCCC, and might serve as a potential prognostic biomarker and novel therapeutic target for OCCC.
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Affiliation(s)
- Ye Xia
- Reproductive Medicine Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shanting Ye
- Department of Hepatobiliary Surgery, Shenzhen Second People's Hospital, Clinical Institute of Guangzhou Medical University, Shenzhen 518035, Guangdong Province, China
| | - Yang Yang
- Reproductive Medicine Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuchen Liu
- Department of Hepatobiliary Surgery, Shenzhen Second People's Hospital, Clinical Institute of Guangzhou Medical University, Shenzhen 518035, Guangdong Province, China
| | - Guoqing Tong
- Reproductive Medicine Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Proteomic analysis of hypopharyngeal and laryngeal squamous cell carcinoma sheds light on differences in survival. Sci Rep 2020; 10:19459. [PMID: 33173143 PMCID: PMC7655956 DOI: 10.1038/s41598-020-76626-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022] Open
Abstract
The link between differences in molecular expression and survival among advanced laryngeal (LSCC) and hypopharyngeal squamous carcinoma (HPSCC) remains unclear. Here, we applied the Surveillance, Epidemiology, and End Results (SEER) program, Isobaric tag for relative and absolute quantitation (iTRAQ) with Liquid chromatography-mass spectrometry (LC–MS/MS) proteomics data and The Cancer Genome Atlas (TCGA) related data to discover the possible disparities between HPSCC and LSCC. Our results showed a significantly worse 5-year overall-survival in HPSCC compared with LSCC before and after adjusting for clinical parameters. 240 differentially expressed proteins were enriched in molecular networks of cytoskeleton remodeling and antigen presentation. Moreover, HPSCC consisted of less T-central-memory cells, T-follicular-helper cells, TGF-β response, and CD4 + T memory resting cells, but more wound healing than LSCC. Furthermore, 9 mRNAs expression were significantly and independently correlated to overall survival in 126 HPSCC and LSCC patients, which was further validated in another cohort of head and neck cancers. These findings support that Immunity signatures as well as pathway networks that include cytoskeleton remodeling and antigen presentation may contribute to the observed differences in survival between HPSCC and LSCC.
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