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Cui JJ, Guo CX, Li J, Guo AX, Zhang Z, Li SY, Wang LY, Jia XB, Guo H, Xia K, Hu ZM, Ouyang QY, Wang Y, Xie YT, Liu ZQ, Zhang JT, Wu W, Chen YH, Yin JY. CSDE1 enhances genotoxic drug resistance in cancer by modulating RPA2 through CSDE1-eIF3a regulatory complex. Drug Resist Updat 2025; 81:101249. [PMID: 40398074 DOI: 10.1016/j.drup.2025.101249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2025] [Revised: 04/17/2025] [Accepted: 04/21/2025] [Indexed: 05/23/2025]
Abstract
AIMS Genotoxic drug resistance is one of the major obstacles for cancer treatment. Our previous study demonstrates that cold shock domain containing E1 (CSDE1) is associated with drug resistance. In this study, we aim to demonstrate that CSDE1 regulates cellular response to genotoxic drugs and to investigate its mechanism of action in drug resistance. METHODS Tissues and blood samples from cancer patients were used to evaluate the relationship between CSDE1 and genotoxic drug response. Comet and immunofluorescence assays were conducted to investigate the role of CSDE1 in DNA damage repair. Systematic knockout mouse models were used to study the underlying mechanism involved. Biotin pull-down, EMSA and co-IP assays were used to probe the triplex structure of CSDE1-protein (eIF3a)-RNA (RPA2). RESULTS CSDE1 elevation correlates with poor response in patient and increased resistance in cell lines to genotoxic drugs. CSDE1 upregulated the nucleotide excision repair (NER) and homologous recombination (HR) pathways. In X-ray irradiation or bleomycin-induced DNA damage mouse model, systemic CSDE1 knockout resulted in increased DNA damage. In both a CSDE1 knockout mouse model and cancer cell lines, CSDE1 inhibited the cGAS-STING pathway through RPA2. Mechanistic studies indicated that CSDE1 serves as a hub for the binding of the CSDE1-protein (eIF3a)-RNA (RPA2) ternary complex. CONCLUSIONS This study reveals the new role of CSDE1 in enhancing resistance to genotoxic drugs, and the detailed zipper-like cross ternary structural of CSDE1. It provides a new strategy for enhancing genotoxic drugs sensitivity.
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Affiliation(s)
- Jia-Jia Cui
- Department of Geratic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, Hunan 410008, PR China; Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Shenzhen Key Laboratory of Chinese Medicine Active substance screening and Translational Research, Shenzhen 518000, PR China
| | - Cheng-Xian Guo
- Center of Clinical Pharmacology, the Third Xiangya Hospital, Central South University, Changsha, Hunan 410000, PR China
| | - Jun Li
- Institute of Clinical Medicine, The First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China
| | - Ao-Xiang Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Pharmacy, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China; Shenzhen Key Laboratory of Chinese Medicine Active substance screening and Translational Research, Shenzhen 518000, PR China
| | - Zhao Zhang
- Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, PR China
| | - Si-Yu Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Pharmacy, Wuhan No.1 Hospital, Wuhan, Hubei 430022, PR China
| | - Xiang-Bin Jia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410000, PR China
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410000, PR China
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410000, PR China; MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421000, PR China; NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410000, PR China
| | - Zheng-Mao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410000, PR China
| | - Qian-Ying Ouyang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Yang Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Yu-Ting Xie
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Pharmacy, The First Hospital of Changsha, Changsha, Hunan 410008, PR China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, The University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Wei Wu
- Department of Geratic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Key Laboratory of Biological Nanotechnology of National Health Commission, Changsha, Hunan 410008, PR China.
| | - Yong-Heng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan 410008, PR China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, Hunan 410000, PR China; National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
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2
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Wang J, Zheng L, Chen W, Zhang X, Lv D, Zeng C, Zhang C, Zhang R, Kang T, Zhong L. Targeting RBM39 suppresses tumor growth and sensitizes osteosarcoma cells to cisplatin. Oncogene 2025; 44:575-586. [PMID: 39633066 DOI: 10.1038/s41388-024-03242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 11/19/2024] [Accepted: 11/28/2024] [Indexed: 12/07/2024]
Abstract
Osteosarcoma is one of the most common malignant primary bone tumors and lacks effective therapeutic targets. Recent studies have reported that RNA binding proteins (RBPs) could serve as promising therapeutic targets for cancers, as their critical roles in transcriptional regulation and RNA splicing. Nevertheless, the potential of pharmacologically inhibiting RBPs as a therapeutic strategy for patients with osteosarcoma remains unclear. In this study, we identified the RNA-binding protein RBM39 as a promising therapeutic target for osteosarcoma. RBM39 is essential for cell viability, and a higher expression of RBM39 was associated with poor prognosis in osteosarcoma. Mechanistically, RBM39 served as a coactivator of c-Jun to transcriptionally upregulate DKK1, leading to the activation of the GSK3β-NF-κB pathway. Importantly, our results reveal that the pharmacological depletion of RBM39 by using the anti-cancer aryl sulfonamide (E7820), a drug known for its oral bioavailability and safe administration, effectively represses osteosarcoma growth and sensitizes osteosarcoma cells to cisplatin treatment both in vitro and in vivo. Our findings unveil the crucial role of RBM39 in modulating tumor growth and cisplatin sensitivity in osteosarcoma cells, suggesting that the combination of aryl sulfonamides with cisplatin may benefit patients with osteosarcoma.
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Affiliation(s)
- Jingxuan Wang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanqi Chen
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xia Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongming Lv
- Department of Burns, Wound Repair and Reconstruction, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Cuiling Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Changlin Zhang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li Zhong
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.
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Wei W, Cao Y, Lu X, Wang L, Li J, Deng G, Li D, Xiao L. RBM47 is a novel immunotherapeutic target and prognostic biomarker in gliomas. Sci Rep 2025; 15:854. [PMID: 39757245 PMCID: PMC11701128 DOI: 10.1038/s41598-024-84719-z] [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: 09/27/2024] [Accepted: 12/26/2024] [Indexed: 01/07/2025] Open
Abstract
The role of RBM47, an RNA-binding protein, in shaping the immune landscape of gliomas and tumor immune responses is yet to be fully studied. Therefore, a comprehensive investigation into the immunomodulatory roles of RBM47 in gliomas was conducted, leveraging gene expression data from multi-omic datasets. The prognosis of patients with gliomas considering RBM47 was elucidated using bioinformatics methods and clinical data, with results validated using immunohistochemistry and immunofluorescence analyses. The expression of RBM47 in gliomas was higher than that in normal tissues and was positively correlated with the World Health Organization tumor grade. Increased RBM47 expression is associated with poor prognosis in patients with glioma, serving as an independent predictor of overall survival. The nomogram combining RBM47 expression levels with clinical prognostic factors demonstrated strong predictive accuracy, achieving a C-index of up to 0.863 in both TCGA training and CGGA validation groups. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Variation Analysis indicated that RBM47 is closely related to immunity and inflammation. Single-cell sequencing and immunofluorescence assays confirmed the enrichment of RBM47 in CD163 + macrophages. Therefore, RBM47 plays a vital role in the immune microenvironment of gliomas and may be a potential immunotherapy target.
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Affiliation(s)
- Wei Wei
- Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 17 Yongwai Street, Nanchang, 330006, Jiangxi, China
| | - Yongfu Cao
- Department of Neurosurgery, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong High Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Lu
- Department of Neurosurgery, Jiangxi Cancer Hospital & Institute, Jiangxi Clinical Research Center for Cancer, The Second Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Long Wang
- Department of Neurosurgery, Jiangxi Cancer Hospital & Institute, Jiangxi Clinical Research Center for Cancer, The Second Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Jianbin Li
- Department of Neurosurgery, Jiangxi Cancer Hospital & Institute, Jiangxi Clinical Research Center for Cancer, The Second Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Guojun Deng
- Department of Neurosurgery, Jiangxi Cancer Hospital & Institute, Jiangxi Clinical Research Center for Cancer, The Second Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Donghai Li
- Department of Neurosurgery, Jiangxi Cancer Hospital & Institute, Jiangxi Clinical Research Center for Cancer, The Second Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Limin Xiao
- Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 17 Yongwai Street, Nanchang, 330006, Jiangxi, China.
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4
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Meyer J, Payr M, Duss O, Hennig J. Exploring the dynamics of messenger ribonucleoprotein-mediated translation repression. Biochem Soc Trans 2024; 52:2267-2279. [PMID: 39601754 PMCID: PMC11668304 DOI: 10.1042/bst20231240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 10/14/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024]
Abstract
Translational control is crucial for well-balanced cellular function and viability of organisms. Different mechanisms have evolved to up- and down-regulate protein synthesis, including 3' untranslated region (UTR)-mediated translation repression. RNA binding proteins or microRNAs interact with regulatory sequence elements located in the 3' UTR and interfere most often with the rate-limiting initiation step of translation. Dysregulation of post-transcriptional gene expression leads to various kinds of diseases, emphasizing the significance of understanding the mechanisms of these processes. So far, only limited mechanistic details about kinetics and dynamics of translation regulation are understood. This mini-review focuses on 3' UTR-mediated translational regulation mechanisms and demonstrates the potential of using single-molecule fluorescence-microscopy for kinetic and dynamic studies of translation regulation in vivo and in vitro.
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Affiliation(s)
- Julia Meyer
- Department of Biochemistry IV – Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marco Payr
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Candidate for Joint PhD Degree From EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Olivier Duss
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Janosch Hennig
- Department of Biochemistry IV – Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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5
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Li K, Wang H, Jiang B, Jin X. TRIM28 in cancer and cancer therapy. Front Genet 2024; 15:1431564. [PMID: 39100077 PMCID: PMC11294089 DOI: 10.3389/fgene.2024.1431564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024] Open
Abstract
TRIM28 (tripartite motif protein 28) was initially believed to be a transcription inhibitor that plays an important role in DNA damage repair (DDR) and in maintaining cancer cellular stemness. As research has continued to deepen, several studies have found that TRIM28 not only has ubiquitin E3 ligase activity to promote degradation of substrates, but also can promote SUMOylation of substrates. Although TRIM28 is highly expressed in various cancer tissues and has oncogenic effects, there are still a few studies indicating that TRIM28 has certain anticancer effects. Additionally, TRIM28 is subject to complex upstream regulation. In this review, we have elaborated on the structure and regulation of TRIM28. At the same time, highlighting the functional role of TRIM28 in tumor development and emphasizing its impact on cancer treatment provides a new direction for future clinical antitumor treatment.
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Affiliation(s)
- Kailang Li
- Department of Oncology and Hematology, Beilun District People’s Hospital, Ningbo, China
| | - Haifeng Wang
- Department of Oncology and Hematology, Beilun District People’s Hospital, Ningbo, China
| | - Bitao Jiang
- Department of Oncology and Hematology, Beilun District People’s Hospital, Ningbo, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo, China
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Chacko J, Ozadam H, Cenik C. RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution. Bioinformatics 2024; 40:btae369. [PMID: 38897662 PMCID: PMC11197854 DOI: 10.1093/bioinformatics/btae369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/02/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024] Open
Abstract
MOTIVATION Ribosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses. RESULTS In this study, we introduce RiboGraph, a dedicated visualization tool designed to work with .ribo files, a specialized and efficient format for ribosome occupancy data. Unlike existing solutions that rely on large alignment files and time-consuming preprocessing steps, RiboGraph operates on a purpose designed compact file type. This efficiency allows for interactive, real-time visualization at ribosome-protected fragment length resolution. By providing an integrated toolset, RiboGraph empowers researchers to conduct comprehensive visual analysis of ribosome occupancy data. AVAILABILITY AND IMPLEMENTATION Source code, step-by-step installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling/ribograph. On the same page, we provide test files and a step-by-step tutorial highlighting the key features of RiboGraph.
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Affiliation(s)
- Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States
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7
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Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
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Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
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8
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Saidu NEB, Aarsund M, Sørensen E, Stensland M, Nyman TA, Ulvmoen A, Wu Y, Inngjerdingen M. Identifying a core protein signature of small extracellular vesicles derived from B-cell precursor acute lymphoblastic leukaemia. Scand J Immunol 2024; 99:e13341. [PMID: 38441169 DOI: 10.1111/sji.13341] [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: 08/15/2023] [Revised: 10/09/2023] [Accepted: 11/10/2023] [Indexed: 03/07/2024]
Abstract
Acute paediatric leukaemia is diagnosed and monitored via bone marrow aspirate assessment of blasts as a measure of minimal residual disease. Liquid biopsies in the form of blood samples could greatly reduce the need for invasive bone marrow aspirations, but there are currently no blood markers that match the sensitivity of bone marrow diagnostics. Circulating extracellular vesicles (EVs) represent candidate biomarkers that may reflect the blast burden in bone marrow, and several studies have reported on the utility of EVs as biomarkers for adult haematological malignancies. Increased levels of EVs have been reported for several haematological malignancies, and we similarly report here elevated EV concentrations in plasma from paediatric BCP-ALL patients. Plasma EVs are very heterogeneous in terms of their cellular origin, thus identifying a cancer selective EV-marker is challenging. Here, we undertook a reductionistic approach to identify protein markers selectively associated to plasma EVs derived from BCP-ALL patients. The EV proteome of primary BCP-ALL cell-derived EVs were compared against EVs from healthy donor B cells and the BCP-ALL cell line REH, and further against EVs isolated from plasma of healthy paediatric donors and paediatric BCP-ALL patients. With this approach, we identified a signature of 6 proteins (CD317, CD38, IGF2BP1, PCNA, CSDE1, and GPR116) that were specifically identified in BCP-ALL derived EVs only and not in healthy control EVs, and that could be exploited as diagnostic biomarkers.
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Affiliation(s)
| | - Miriam Aarsund
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Sørensen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Maria Stensland
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Tuula Anneli Nyman
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Aina Ulvmoen
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | - Yunjie Wu
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Marit Inngjerdingen
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Indacochea A, Guitart T, Boada A, Peg V, Quer A, Laayouni H, Condal L, Espinosa P, Manzano JL, Gebauer F. CSDE1 Intracellular Distribution as a Biomarker of Melanoma Prognosis. Int J Mol Sci 2024; 25:2319. [PMID: 38396995 PMCID: PMC10889260 DOI: 10.3390/ijms25042319] [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: 11/22/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
RNA-binding proteins are emerging as critical modulators of oncogenic cell transformation, malignancy and therapy resistance. We have previously found that the RNA-binding protein Cold Shock Domain containing protein E1 (CSDE1) promotes invasion and metastasis of melanoma, the deadliest form of skin cancer and also a highly heterogeneous disease in need of predictive biomarkers and druggable targets. Here, we design a monoclonal antibody useful for IHC in the clinical setting and use it to evaluate the prognosis potential of CSDE1 in an exploratory cohort of 149 whole tissue sections including benign nevi and primary tumors and metastasis from melanoma patients. Contrary to expectations for an oncoprotein, we observed a global decrease in CSDE1 levels with increasing malignancy. However, the CSDE1 cytoplasmic/nuclear ratio exhibited a positive correlation with adverse clinical features of primary tumors and emerged as a robust indicator of progression free survival in cutaneous melanoma, highlighting the potential of CSDE1 as a biomarker of prognosis. Our findings provide a novel feature for prognosis assessment and highlight the intricacies of RNA-binding protein dynamics in cancer progression.
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Affiliation(s)
- Alberto Indacochea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
| | - Aram Boada
- Dermatology Department, Hospital Universitari Germans Trias i Pujol, Institut d’investigació Germans Trias I Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (A.B.); (L.C.)
| | - Vicente Peg
- Pathology Department, Vall d’Hebron University Hospital, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Ariadna Quer
- Pathology Department, Hospital Universitari Germans Trias I Pujol, Institut d’Investigació Germans Trias I Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain;
- Barcelona Beta Brain Research Center, Pasqual Maragall Foundation, C/Wellington 30, 08006 Barcelona, Spain
| | - Laura Condal
- Dermatology Department, Hospital Universitari Germans Trias i Pujol, Institut d’investigació Germans Trias I Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (A.B.); (L.C.)
| | - Pablo Espinosa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
| | - Jose Luis Manzano
- Medical Oncology Department, Catalonian Institute of Oncology, (ICO), Hospital Germans Trias I Pujol, 08916 Badalona, Spain;
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
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10
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Chacko J, Ozadam H, Cenik C. RiboGraph: An interactive visualization system for ribosome profiling data at read length resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575228. [PMID: 38260303 PMCID: PMC10802566 DOI: 10.1101/2024.01.11.575228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Ribosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses. In this study, we introduce RiboGraph, a dedicated visualization tool designed to work with .ribo files, a specialized and efficient format for ribosome occupancy data. Unlike existing solutions that rely on large alignment files and time-consuming preprocessing steps, RiboGraph operates on a purpose designed compact file type and eliminates the need for data preprocessing. This efficiency allows for interactive, real-time visualization at ribosome-protected fragment length resolution. By providing an integrated toolset, RiboGraph empowers researchers to conduct comprehensive visual analysis of ribosome occupancy data. Availability and Implementation Source code, step-by-step installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling/ribograph. On the same page, we provide test files and a step-by-step tutorial highlighting the key features of RiboGraph.
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Affiliation(s)
- Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Present address: Senda Biosciences, Cambridge, MA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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11
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Sherwood DR, Kenny-Ganzert IW, Balachandar Thendral S. Translational regulation of cell invasion through extracellular matrix-an emerging role for ribosomes. F1000Res 2023; 12:1528. [PMID: 38628976 PMCID: PMC11019292 DOI: 10.12688/f1000research.143519.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 04/19/2024] Open
Abstract
Many developmental and physiological processes require cells to invade and migrate through extracellular matrix barriers. This specialized cellular behavior is also misregulated in many diseases, such as immune disorders and cancer. Cell invasive activity is driven by pro-invasive transcriptional networks that activate the expression of genes encoding numerous different proteins that expand and regulate the cytoskeleton, endomembrane system, cell adhesion, signaling pathways, and metabolic networks. While detailed mechanistic studies have uncovered crucial insights into pro-invasive transcriptional networks and the distinct cell biological attributes of invasive cells, less is known about how invasive cells modulate mRNA translation to meet the robust, dynamic, and unique protein production needs of cell invasion. In this review we outline known modes of translation regulation promoting cell invasion and focus on recent studies revealing elegant mechanisms that expand ribosome biogenesis within invasive cells to meet the increased protein production requirements to invade and migrate through extracellular matrix barriers.
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12
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Li Y, Li C, Liu M, Liu S, Liu F, Wang L. The RNA-binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling. Development 2023; 150:dev201890. [PMID: 37874038 PMCID: PMC10652045 DOI: 10.1242/dev.201890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
In vertebrates, the earliest hematopoietic stem and progenitor cells (HSPCs) are derived from a subset of specialized endothelial cells, hemogenic endothelial cells, in the aorta-gonad-mesonephros region through endothelial-to-hematopoietic transition. HSPC generation is efficiently and accurately regulated by a variety of factors and signals; however, the precise control of these signals remains incompletely understood. Post-transcriptional regulation is crucial for gene expression, as the transcripts are usually bound by RNA-binding proteins (RBPs) to regulate RNA metabolism. Here, we report that the RBP protein Csde1-mediated translational control is essential for HSPC generation during zebrafish early development. Genetic mutants and morphants demonstrated that depletion of csde1 impaired HSPC production in zebrafish embryos. Mechanistically, Csde1 regulates HSPC generation through modulating Wnt/β-catenin signaling activity. We demonstrate that Csde1 binds to ctnnb1 mRNAs (encoding β-catenin, an effector of Wnt signaling) and regulates translation but not stability of ctnnb1 mRNA, which further enhances β-catenin protein level and Wnt signal transduction activities. Together, we identify Csde1 as an important post-transcriptional regulator and provide new insights into how Wnt/β-catenin signaling is precisely regulated at the post-transcriptional level.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Can Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Mengyao Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shicheng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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13
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Wardman R, Keles M, Pachkiv I, Hemanna S, Grein S, Schwarz J, Stein F, Ola R, Dobreva G, Hentze MW, Heineke J. RNA-Binding Proteins Regulate Post-Transcriptional Responses to TGF-β to Coordinate Function and Mesenchymal Activation of Murine Endothelial Cells. Arterioscler Thromb Vasc Biol 2023; 43:1967-1989. [PMID: 37650327 PMCID: PMC10521797 DOI: 10.1161/atvbaha.123.319925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Endothelial cells (ECs) are primed to respond to various signaling cues. For example, TGF (transforming growth factor)-β has major effects on EC function and phenotype by driving ECs towards a more mesenchymal state (ie, triggering endothelial to mesenchymal activation), a dynamic process associated with cardiovascular diseases. Although transcriptional regulation triggered by TGF-β in ECs is well characterized, post-transcriptional regulatory mechanisms induced by TGF-β remain largely unknown. METHODS Using RNA interactome capture, we identified global TGF-β driven changes in RNA-binding proteins in ECs. We investigated specific changes in the RNA-binding patterns of hnRNP H1 (heterogeneous nuclear ribonucleoprotein H1) and Csde1 (cold shock domain containing E1) using RNA immunoprecipitation and overlapped this with RNA-sequencing data after knockdown of either protein for functional insight. Using a modified proximity ligation assay, we visualized the specific interactions between hnRNP H1 and Csde1 and target RNAs in situ both in vitro and in mouse heart sections. RESULTS Characterization of TGF-β-regulated RBPs (RNA-binding proteins) revealed hnRNP H1 and Csde1 as key regulators of the cellular response to TGF-β at the post-transcriptional level, with loss of either protein-promoting mesenchymal activation in ECs. We found that TGF-β drives an increase in binding of hnRNP H1 to its target RNAs, offsetting mesenchymal activation, but a decrease in Csde1 RNA-binding, facilitating this process. Both, hnRNP H1 and Csde1, dynamically bind and regulate specific subsets of mRNAs related to mesenchymal activation and endothelial function. CONCLUSIONS Together, we show that RBPs play a key role in the endothelial response to TGF-β stimulation at the post-transcriptional level and that the RBPs hnRNP H1 and Csde1 serve to maintain EC function and counteract mesenchymal activation. We propose that TGF-β profoundly modifies RNA-protein interaction entailing feedback and feed-forward control at the post-transcriptional level, to fine-tune mesenchymal activation in ECs.
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Affiliation(s)
- Rhys Wardman
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Merve Keles
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Ihor Pachkiv
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
| | - Shruthi Hemanna
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Steve Grein
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Jennifer Schwarz
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (J.S., F.S.)
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (J.S., F.S.)
| | - Roxana Ola
- Cardiovascular Pharmacology (R.O.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
| | - Gergana Dobreva
- Cardiovascular Genomics and Epigenomics (G.D.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Matthias W. Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (M.W.H.)
| | - Joerg Heineke
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
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14
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Kakumani PK, Ko Y, Ramakrishna S, Christopher G, Dodgson M, Shrinet J, Harvey LM, Shin C, Simard M. CSDE1 promotes miR-451 biogenesis. Nucleic Acids Res 2023; 51:9385-9396. [PMID: 37493604 PMCID: PMC10516617 DOI: 10.1093/nar/gkad619] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
MicroRNAs are sequentially processed by RNase III enzymes Drosha and Dicer. miR-451 is a highly conserved miRNA in vertebrates which bypasses Dicer processing and instead relies on AGO2 for its maturation. miR-451 is highly expressed in erythrocytes and regulates the differentiation of erythroblasts into mature red blood cells. However, the mechanistic details underlying miR-451 biogenesis in erythrocytes remains obscure. Here, we report that the RNA binding protein CSDE1 which is required for the development of erythroblasts into erythrocytes, controls the expression of miR-451 in erythroleukemia cells. CSDE1 binds miR-451 and regulates AGO2 processing of pre-miR-451 through its N-terminal domains. CSDE1 further interacts with PARN and promotes the trimming of intermediate miR-451 to the mature length. Together, our results demonstrate that CSDE1 promotes biogenesis of miR-451 in erythroid progenitors.
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Affiliation(s)
- Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Yunkoo Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sushmitha Ramakrishna
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Grace Christopher
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Maria Dodgson
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Louis-Mathieu Harvey
- Oncology Division, Centre Hospitalier Universitaire de Québec-Université Laval Research Center (L’Hôtel-Dieu de Québec), Quebec City, Québec G1R 3S3, Canada
- Laval University Cancer Research Centre, Québec City, Québec G1R 3S3, Canada
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Martin J Simard
- Oncology Division, Centre Hospitalier Universitaire de Québec-Université Laval Research Center (L’Hôtel-Dieu de Québec), Quebec City, Québec G1R 3S3, Canada
- Laval University Cancer Research Centre, Québec City, Québec G1R 3S3, Canada
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15
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Laddach A, Chng SH, Lasrado R, Progatzky F, Shapiro M, Erickson A, Sampedro Castaneda M, Artemov AV, Bon-Frauches AC, Amaniti EM, Kleinjung J, Boeing S, Ultanir S, Adameyko I, Pachnis V. A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia. Nat Commun 2023; 14:5904. [PMID: 37737269 PMCID: PMC10516949 DOI: 10.1038/s41467-023-41492-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
Glial cells have been proposed as a source of neural progenitors, but the mechanisms underpinning the neurogenic potential of adult glia are not known. Using single cell transcriptomic profiling, we show that enteric glial cells represent a cell state attained by autonomic neural crest cells as they transition along a linear differentiation trajectory that allows them to retain neurogenic potential while acquiring mature glial functions. Key neurogenic loci in early enteric nervous system progenitors remain in open chromatin configuration in mature enteric glia, thus facilitating neuronal differentiation under appropriate conditions. Molecular profiling and gene targeting of enteric glial cells in a cell culture model of enteric neurogenesis and a gut injury model demonstrate that neuronal differentiation of glia is driven by transcriptional programs employed in vivo by early progenitors. Our work provides mechanistic insight into the regulatory landscape underpinning the development of intestinal neural circuits and generates a platform for advancing glial cells as therapeutic agents for the treatment of neural deficits.
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Affiliation(s)
- Anna Laddach
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Song Hui Chng
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Experimental Drug Development Centre A*STAR 10 Biopolis Road, Chromos, 138670, Singapore
| | - Reena Lasrado
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- COMPASS Pathways PLC, Fora, 33 Broadwick St, London, W1F 0DQ, UK
| | - Fränze Progatzky
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Michael Shapiro
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alek Erickson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Marisol Sampedro Castaneda
- Kinases and Brain Development Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Artem V Artemov
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Bienna, 1090, Austria
- Boehringer Ingelheim RCV, Vienna, Austria
| | - Ana Carina Bon-Frauches
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Eleni-Maria Amaniti
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Sainsbury Wellcome Centre, London, UK
| | - Jens Kleinjung
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Science Technology Platform, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sila Ultanir
- Kinases and Brain Development Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Bienna, 1090, Austria
| | - Vassilis Pachnis
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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16
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Yin Z, Ma Z, Wang S, Hao S, Liu X, Pang Q, Wang X. Expression and tissue distribution analysis of vimentin and transthyretin proteins associated with coat colors in sheep (Ovis aries). Anim Biosci 2023; 36:1367-1375. [PMID: 37402463 PMCID: PMC10472160 DOI: 10.5713/ab.23.0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 07/06/2023] Open
Abstract
OBJECTIVE Pigment production and distribution are controlled through multiple proteins, resulting in different coat color phenotypes of sheep. METHODS The expression distribution of vimentin (VIM) and transthyretin (TTR) in white and black sheep skins was detected by liquid chromatography-electrospray ionization tandem MS (LC-ESI-MS/MS), gene ontology (GO) statistics, immunohistochemistry, Western blot, and quantitative real time polymerase chain reaction (qRT-PCR) to evaluate their role in the coat color formation of sheep. RESULTS LC-ESI-MS/MS results showed VIM and TTR proteins in white and black skin tissues of sheep. Meanwhile, GO functional annotation analysis suggested that VIM and TTR proteins were mainly concentrated in cellular components and biological process, respectively. Further research confirmed that VIM and TTR proteins were expressed at significantly higher levels in black sheep skins than in white sheep skins by Western blot, respectively. Immunohistochemistry notably detected VIM and TTR in hair follicle, dermal papilla, and outer root sheath of white and black sheep skins. qRT-PCR results also revealed that the expression of VIM and TTR mRNAs was higher in black sheep skins than in white sheep skins. CONCLUSION The expression of VIM and TTR were higher in black sheep skins than in white sheep skins and the transcription and translation were unanimous in this study. VIM and TTR proteins were expressed in hair follicles of white and black sheep skins. These results suggested that VIM and TTR were involved in the coat color formation of sheep.
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Affiliation(s)
- Zhihong Yin
- Postdoctoral Research Base, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046,
China
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003,
China
| | - Zhisheng Ma
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003,
China
| | - Siting Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003,
China
| | - Shitong Hao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003,
China
| | - Xinyou Liu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003,
China
| | - Quanhai Pang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801,
China
| | - Xinzhuang Wang
- Postdoctoral Research Base, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046,
China
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17
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Webb MJ, Kottke T, Kendall BL, Swanson J, Uzendu C, Tonne J, Thompson J, Metko M, Moore M, Borad M, Roberts L, Diaz RM, Olin M, Borgatti A, Vile R. Trap and ambush therapy using sequential primary and tumor escape-selective oncolytic viruses. Mol Ther Oncolytics 2023; 29:129-142. [PMID: 37313455 PMCID: PMC10258242 DOI: 10.1016/j.omto.2023.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
In multiple models of oncolytic virotherapy, it is common to see an early anti-tumor response followed by recurrence. We have previously shown that frontline treatment with oncolytic VSV-IFN-β induces APOBEC proteins, promoting the selection of specific mutations that allow tumor escape. Of these mutations in B16 melanoma escape (ESC) cells, a C-T point mutation in the cold shock domain-containing E1 (CSDE1) gene was present at the highest frequency, which could be used to ambush ESC cells by vaccination with the mutant CSDE1 expressed within the virus. Here, we show that the evolution of viral ESC tumor cells harboring the escape-promoting CSDE1C-T mutation can also be exploited by a virological ambush. By sequential delivery of two oncolytic VSVs in vivo, tumors which would otherwise escape VSV-IFN-β oncolytic virotherapy could be cured. This also facilitated the priming of anti-tumor T cell responses, which could be further exploited using immune checkpoint blockade with the CD200 activation receptor ligand (CD200AR-L) peptide. Our findings here are significant in that they offer the possibility to develop oncolytic viruses as highly specific, escape-targeting viro-immunotherapeutic agents to be used in conjunction with recurrence of tumors following multiple different types of frontline cancer therapies.
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Affiliation(s)
- Mason J. Webb
- Division of Hematology/Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Jack Swanson
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chisom Uzendu
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jason Tonne
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jill Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Muriel Metko
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Madelyn Moore
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Mitesh Borad
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Lewis Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Rosa M. Diaz
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael Olin
- Division of Pediatric Hematology and Oncology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Antonella Borgatti
- Department of Veterinary Clinical Sciences, University of Minnesota, St. Paul, MN 55108, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Clinical Investigation Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Richard Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
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18
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García-Cárdenas JM, Armendáriz-Castillo I, García-Cárdenas N, Pesantez-Coronel D, López-Cortés A, Indacochea A, Guerrero S. Data mining identifies novel RNA-binding proteins involved in colon and rectal carcinomas. Front Cell Dev Biol 2023; 11:1088057. [PMID: 37384253 PMCID: PMC10293682 DOI: 10.3389/fcell.2023.1088057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/13/2023] [Indexed: 06/30/2023] Open
Abstract
Colorectal adenocarcinoma (COREAD) is the second most deadly cancer and third most frequently encountered malignancy worldwide. Despite efforts in molecular subtyping and subsequent personalized COREAD treatments, multidisciplinary evidence suggests separating COREAD into colon cancer (COAD) and rectal cancer (READ). This new perspective could improve diagnosis and treatment of both carcinomas. RNA-binding proteins (RBPs), as critical regulators of every hallmark of cancer, could fulfill the need to identify sensitive biomarkers for COAD and READ separately. To detect new RBPs involved in COAD and READ progression, here we used a multidata integration strategy to prioritize tumorigenic RBPs. We analyzed and integrated 1) RBPs genomic and transcriptomic alterations from 488 COAD and 155 READ patients, 2) ∼ 10,000 raw associations between RBPs and cancer genes, 3) ∼ 15,000 immunostainings, and 4) loss-of-function screens performed in 102 COREAD cell lines. Thus, we unraveled new putative roles of NOP56, RBM12, NAT10, FKBP1A, EMG1, and CSE1L in COAD and READ progression. Interestingly, FKBP1A and EMG1 have never been related with any of these carcinomas but presented tumorigenic features in other cancer types. Subsequent survival analyses highlighted the clinical relevance of FKBP1A, NOP56, and NAT10 mRNA expression to predict poor prognosis in COREAD and COAD patients. Further research should be performed to validate their clinical potential and to elucidate their molecular mechanisms underlying these malignancies.
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Affiliation(s)
- Jennyfer M. García-Cárdenas
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Isaac Armendáriz-Castillo
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Facultad de Ingenierías y Ciencias Aplicadas, Universidad Internacional SEK, Quito, Ecuador
| | | | - David Pesantez-Coronel
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Andrés López-Cortés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Alberto Indacochea
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Santiago Guerrero
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
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19
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Toh JY, Nkouawa A, Dong G, Kolev NG, Tschudi C. Two cold shock domain containing proteins trigger the development of infectious Trypanosoma brucei. PLoS Pathog 2023; 19:e1011438. [PMID: 37276216 PMCID: PMC10270622 DOI: 10.1371/journal.ppat.1011438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Cold shock proteins are members of a family of DNA- and RNA-binding proteins with one or more evolutionarily conserved cold shock domain (CSD). These proteins have a wide variety of biological functions, including DNA-damage repair, mRNA stability, and regulation of transcription, splicing and translation. We previously identified two CSD containing proteins, CSD1 and CSD2, in the protozoan parasite Trypanosoma brucei to be required for RBP6-driven metacyclic production, albeit at different steps of the developmental program. During metacyclogenesis T. brucei undergoes major morphological and metabolic changes that culminate in the establishment of quiescent metacyclic parasites and the acquisition of mammalian infectivity. To investigate the specific role of CSD1 and CSD2 in this process, we ectopically expressed CSD1 or CSD2 in non-infectious procyclic parasites and discovered that each protein is sufficient to produce infectious metacyclic parasites in 24 hours. Domain truncation assays determined that the N-terminal domain, but not the C-terminal domain, of CSD1 and CSD2 was required for metacyclic development. Furthermore, conserved amino acid residues in the CSD of CSD1 and CSD2, known to be important for binding nucleic acids, were found to be necessary for metacyclic production. Using single-end enhanced crosslinking and immunoprecipitation (seCLIP) we identified the specific binding motif of CSD1 and CSD2 as "ANACAU" and the bound mRNAs were enriched for biological processes, including lipid metabolism, microtubule-based movement and nucleocytoplasmic transport that are likely involved in the transition to bloodstream form-like cells.
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Affiliation(s)
- Justin Y Toh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Agathe Nkouawa
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Gang Dong
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Nikolay G Kolev
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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20
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Di Fusco D, Di Grazia A, Di Maggio G, Segreto MT, Iannucci A, Maresca C, De Stefano A, Sica G, Stolfi C, Monteleone G, Monteleone I. A novel tumour enhancer function of Insulin-like growth factor II mRNA-binding protein 3 in colorectal cancer. Cell Death Dis 2023; 14:243. [PMID: 37024466 PMCID: PMC10079693 DOI: 10.1038/s41419-023-05772-6] [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: 08/01/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023]
Abstract
CRC cells evolve a variety of strategies to limit or circumvent apoptosis cell death. RNA binding proteins (RBPs) regulate many of the molecular mechanisms that underlie the development of cancer. The insulin-like growth factor II mRNA-binding proteins (IMP) family are oncofoetal RBPs, consisting of IMP1, IMP2 and IMP3, which have an important role in RNA metabolism. IMP3 is highly expressed in colorectal cancer (CRC) tissue, where its expression often correlates with poor prognosis. However, the role of IMP3 in CRC is not fully understood. IMP3 expression was analysed using a public database and by Western blotting and immunohistochemistry in human colon samples derived from patients with sporadic CRC and healthy subjects. To address whether IMP3 controls cancer cell survival, we analysed cell death pathways in in vitro and in vivo experiments after IMP3 downregulation by siRNA or an antisense oligonucleotide. IMP3 was highly expressed in CRC samples compared to normal control tissues. The knockdown of IMP3 enhanced a caspase-independent cell death in CRC cell lines. Furthermore, the treatment of CRC cells with IMP3 siRNA did not alter the expression of GSDMD, GPX-4 and the activated form of RIP3, three key molecules that govern pyroptosis, ferroptosis and necroptosis, respectively. Abrogation of IMP3 in CRC significantly reduced Bcl-2 and Bcl-xL mRNA and was associated with an altered mitochondrial membrane potential that allowed the nuclear migration of the apoptosis-inducing factor (AIF). Moreover, specific immunoprecipitation experiments on CRC human cell lines indicated that IMP3 binds Bcl-2 and Bcl-xL mRNA, suggesting that IMP3 acts as a regulator of the intrinsic apoptotic pathway through the surveillance of anti-apoptotic Bcl mRNA metabolism. Finally, we showed that IMP3 block inhibited the growth of CRC cell lines in vivo after transplantation into immunodeficient mice. Altogether, these data support a novel role for IMP3 in controlling the intrinsic caspase-independent apoptotic pathway in CRC.
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Affiliation(s)
- Davide Di Fusco
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | - Antonio Di Grazia
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | - Giulia Di Maggio
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | | | - Andrea Iannucci
- Department of Biomedicine and Prevention, University of 'Tor Vergata', Rome, Italy
| | - Claudia Maresca
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | | | - Giuseppe Sica
- Department of Surgery, University of 'Tor Vergata', Rome, Italy
| | - Carmine Stolfi
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | | | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of 'Tor Vergata', Rome, Italy.
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21
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Pinto C, Aluai-Cunha C, Santos A. The human and animals' malignant melanoma: comparative tumor models and the role of microbiome in dogs and humans. Melanoma Res 2023; 33:87-103. [PMID: 36662668 DOI: 10.1097/cmr.0000000000000880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Currently, the most progressively occurring incident cancer is melanoma. The mouse is the most popular model in human melanoma research given its various benefits as a laboratory animal. Nevertheless, unlike humans, mice do not develop melanoma spontaneously, so they need to be genetically manipulated. In opposition, there are several reports of other animals, ranging from wild to domesticated animals, that spontaneously develop melanoma and that have cancer pathways that are similar to those of humans. The influence of the gut microbiome on health and disease is being the aim of many recent studies. It has been proven that the microbiome is a determinant of the host's immune status and disease prevention. In human medicine, there is increasing evidence that changes in the microbiome influences malignant melanoma progression and response to therapy. There are several similarities between some animals and human melanoma, especially between canine and human oral malignant melanoma as well as between the gut microbiome of both species. However, microbiome studies are scarce in veterinary medicine, especially in the oncology field. Future studies need to address the relevance of gut and tissue microbiome for canine malignant melanoma development, which results will certainly benefit both species in the context of translational medicine.
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Affiliation(s)
- Catarina Pinto
- Department of Veterinary Clinics, Institute of Biomedical Sciences Abel Salazar of the University of Porto (ICBAS-UP)
| | - Catarina Aluai-Cunha
- Department of Veterinary Clinics, Institute of Biomedical Sciences Abel Salazar of the University of Porto (ICBAS-UP)
| | - Andreia Santos
- Department of Veterinary Clinics, Institute of Biomedical Sciences Abel Salazar of the University of Porto (ICBAS-UP)
- Animal Science and Study Centre (CECA), Food and Agragrian Sciences and Technologies Institute (ICETA), Apartado, Porto, Portugal
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22
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Hollmann NM, Jagtap PKA, Linse JB, Ullmann P, Payr M, Murciano B, Simon B, Hub JS, Hennig J. Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Nucleic Acids Res 2023; 51:1895-1913. [PMID: 36688322 PMCID: PMC9976900 DOI: 10.1093/nar/gkac1277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/24/2023] Open
Abstract
RNA binding proteins (RBPs) often engage multiple RNA binding domains (RBDs) to increase target specificity and affinity. However, the complexity of target recognition of multiple RBDs remains largely unexplored. Here we use Upstream of N-Ras (Unr), a multidomain RBP, to demonstrate how multiple RBDs orchestrate target specificity. A crystal structure of the three C-terminal RNA binding cold-shock domains (CSD) of Unr bound to a poly(A) sequence exemplifies how recognition goes beyond the classical ππ-stacking in CSDs. Further structural studies reveal several interaction surfaces between the N-terminal and C-terminal part of Unr with the poly(A)-binding protein (pAbp). All interactions are validated by mutational analyses and the high-resolution structures presented here will guide further studies to understand how both proteins act together in cellular processes.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Philip Ullmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco Payr
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jochen S Hub
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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23
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Lv J, Zhou Y, Zhou N, Wang Z, Chen J, Chen H, Wang D, Zhou L, Wei K, Zhang H, Tang K, Ma J, Liu Y, Wan Y, Zhang Y, Zhang H, Huang B. Epigenetic modification of CSDE1 locus dictates immune recognition of nascent tumorigenic cells. Sci Transl Med 2023; 15:eabq6024. [PMID: 36724242 DOI: 10.1126/scitranslmed.abq6024] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023]
Abstract
Weak immunogenicity of tumor cells is a root cause for the ultimate failure of immunosurveillance and immunotherapy. Although tumor evolution can be shaped by immunoediting toward a less immunogenic phenotype, mechanisms governing the initial immunogenicity of primordial tumor cells or original cancer stem cells remain obscure. Here, using a single tumor-repopulating cell (TRC) to form tumors in immunodeficient or immunocompetent mice, we demonstrated that immunogenic heterogeneity is an inherent trait of tumorigenic cells defined by the activation status of signal transducer and activator of transcription 1 (STAT1) protein in the absence of immune pressure. Subsequent investigation identified that the RNA binding protein cold shock domain-containing protein E1 (CSDE1) can promote STAT1 dephosphorylation by stabilizing T cell protein tyrosine phosphatase (TCPTP). A methyltransferase SET and MYN domain-containing 3 (SMYD3) was further identified to mediate H3K4 trimethylation of CSDE1 locus, which was under the regulation of mechanotransduction by cell-matrix and cell-cell contacts. Thus, owing to the differential epigenetic modification and subsequent differential expression of CSDE1, nascent tumorigenic cells may exhibit either a high or low immunogenicity. This identified SMYD3-CSDE1 pathway represents a potential prognostic marker for cancer immunotherapy effectiveness that requires further investigation.
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Affiliation(s)
- Jiadi Lv
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Yabo Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Nannan Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Zhenfeng Wang
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Jie Chen
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Haoran Chen
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Dianheng Wang
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Li Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Keke Wei
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huafeng Zhang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Tang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingwei Ma
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuying Liu
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Yonghong Wan
- McMaster Immunology Research Centre and Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Yi Zhang
- Biotherapy Center and Cancer Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haizeng Zhang
- Department of Medical Oncology, National Cancer Center, Cancer Hospital, CAMS and Peking Union Medical College, Beijing 100021, China
| | - Bo Huang
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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24
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Rubio A, Garland GD, Sfakianos A, Harvey RF, Willis AE. Aberrant protein synthesis and cancer development: The role of canonical eukaryotic initiation, elongation and termination factors in tumorigenesis. Semin Cancer Biol 2022; 86:151-165. [PMID: 35487398 DOI: 10.1016/j.semcancer.2022.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023]
Abstract
In tumourigenesis, oncogenes or dysregulated tumour suppressor genes alter the canonical translation machinery leading to a reprogramming of the translatome that, in turn, promotes the translation of selected mRNAs encoding proteins involved in proliferation and metastasis. It is therefore unsurprising that abnormal expression levels and activities of eukaryotic initiation factors (eIFs), elongation factors (eEFs) or termination factors (eRFs) are associated with poor outcome for patients with a wide range of cancers. In this review we discuss how RNA binding proteins (RBPs) within the canonical translation factor machinery are dysregulated in cancers and how targeting such proteins is leading to new therapeutic avenues.
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Affiliation(s)
- Angela Rubio
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Gavin D Garland
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Aristeidis Sfakianos
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Robert F Harvey
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK.
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25
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RNA-binding proteins: Underestimated contributors in tumorigenesis. Semin Cancer Biol 2022; 86:431-444. [PMID: 35124196 DOI: 10.1016/j.semcancer.2022.01.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/17/2022] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
mRNA export, translation, splicing, cleavage or capping determine mRNA stability, which represents one of the primary aspects regulating gene expression and function. RNA-binding proteins (RBPs) bind to their target mRNAs to regulate multiple cell functions by increasing or reducing their stability. In recent decades, studies of the role of RBPs in tumorigenesis have revealed an increasing number of proteins impacting the prognosis, diagnosis and cancer treatment. Several RBPs have been identified based on their interactions with oncogenes or tumor suppressor genes in human cancers, which are involved in apoptosis, the epithelial-mesenchymal transition (EMT), DNA repair, autophagy, cell proliferation, immune response, metabolism, and the regulation of noncoding RNAs. In this review, we propose a model showing how RBP mutations influence tumorigenesis, and we update the current knowledge regarding the molecular mechanism by which RBPs regulate cancer. Special attention is being devoted to RBPs that represent prognostic and diagnostic factors in cancer patients.
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26
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Liu J, Zhang N, Zeng J, Wang T, Shen Y, Ma C, Yang M. N 6 -methyladenosine-modified lncRNA ARHGAP5-AS1 stabilises CSDE1 and coordinates oncogenic RNA regulons in hepatocellular carcinoma. Clin Transl Med 2022; 12:e1107. [PMID: 36354136 PMCID: PMC9647857 DOI: 10.1002/ctm2.1107] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) ranks fourth among the malignancies leading to cancer-related deaths all around the world. It is increasingly evident that long non-coding RNAs (lncRNAs) are a key mode of hepatocarcinogenesis. As the most prevalent mRNA modification form, N6 -methyladenosine (m6 A) regulates gene expression by impacting multiple aspects of mRNA metabolism. However, there are still no reports on genome-wide screening and functional annotation of m6 A-methylated lncRNAs in HCC. METHODS The m6 A modification and biologic functions of ARHGAP5-AS1 in HCC were investigated through a series of biochemical assays. Clinical implications of ARHGAP5-AS1 were examined in tissues from HCC patients. RESULTS After systematically analysing the m6 A-seq data of HCC cells, we identified 22 candidate lncRNAs with evidently dysregulated m6 A levels. Among these lncRNAs, we found that ARHGAP5-AS1 is the lncRNA with the highest levels of m6 A modification and significantly increased expression in HCC specimens. METTL14 acts as the m6 A writer of ARHGAP5-AS1 and IGF2BP2 stabilises the lncRNA as its m6 A reader. ARHGAP5-AS1 remarkably promotes malignant behaviours of HCC cells ex vivo and in vivo. We identified oncoprotein CSDE1 working as the interacting protein of the lncRNA and TRIM28 as the E3 ligase of CSDE1 in HCC. Interestingly, ARHGAP5-AS1 could attenuate interactions between CSDE1 and TRIM28, which prevents the degradation of CSDE1 via the ubiquitin-proteasome pathway. Elevated levels of CSDE1 coordinate oncogenic RNA regulons, promote translation of VIM and RAC1 and activate the ERK pathway, which contributes to HCC prognosis. CONCLUSIONS Our study reveals a new paradigm in m6 A-modified lncRNAs controlling CSDE1-mediated oncogenic RNA regulons and highlights lncRNAs as potential targets for future therapeutics against HCC.
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Affiliation(s)
- Jiandong Liu
- Shandong Provincial Key Laboratory of Radiation OncologyCancer Research CenterShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanShandong ProvinceChina
| | - Nasha Zhang
- Department of Radiation OncologyShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanShandong ProvinceChina
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and TreatmentCollaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingJiangsu ProvinceChina
| | - Jiajia Zeng
- Shandong Provincial Key Laboratory of Radiation OncologyCancer Research CenterShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanShandong ProvinceChina
| | - Teng Wang
- Shandong University Cancer CenterJinanShandong ProvinceChina
| | - Yue Shen
- Shandong University Cancer CenterJinanShandong ProvinceChina
| | - Chi Ma
- Shandong University Cancer CenterJinanShandong ProvinceChina
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation OncologyCancer Research CenterShandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanShandong ProvinceChina
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and TreatmentCollaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingJiangsu ProvinceChina
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27
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Hou L, Huang F, Chen G, Qiu J, Liu Y, Zhao H, Wang Z. Application of RNA processing factors for predicting clinical outcomes in colon cancer. Front Genet 2022; 13:979001. [PMID: 36212157 PMCID: PMC9538339 DOI: 10.3389/fgene.2022.979001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Background: Colon cancer is the fifth most common cause of cancer-related death worldwide, and despite significant advances in related treatment, the prognosis of colon cancer patients remains poor. Objective: This study performs systematic bioinformatics analysis of prognostic-associated RNA processing factor genes in colon cancer using the Cancer Related Genome Atlas database to explore their role in colon carcinogenesis and prognosis and excavate potential therapeutic targets. Methods: Data sets of colon cancer patients were obtained from GEO and TCGA databases. Univariate cox analysis was performed on the GSE39582 training set to identify prognosis-associated RNA processing factor genes and constructed a muticox model. The predictive performance of the model was validated by Correlation curve analysis. Similar results were obtained for the test dataset. Functional analyses were performed to explore the underlying mechanisms of colon carcinogenesis and prognosis. Results: A constructed muticox model consisting of βi and prognosis-related RNA processing factor gene expression levels (Expi) was established to evaluate the risk score of each patient. The subgroup with a higher risk score had lower overall survival (OS), higher risk factor, and mortality. We found that the risk score, age, gender, and TNM Stage were strongly associated with OS, and the 13-gene signature as an independent prognostic factor for colon cancer. The model has good accuracy in predicting patient survival and is superior to traditional pathological staging. Conclusion: This study proposes 13 RNA processing factor genes as a prognostic factor for colon cancer patients, which can independently predict the clinical outcome by risk score. The gene expression profile in this model is closely related to the immune status and prognosis of colon cancer patients. The interaction of the 13 RNA processing factor genes with the immune system during colon carcinogenesis provides new ideas for the molecular mechanisms and targeted therapies for colon cancer.
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28
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Smith GA, Padmanabhan A, Lau BH, Pampana A, Li L, Lee CY, Pelonero A, Nishino T, Sadagopan N, Xia VQ, Jain R, Natarajan P, Wu RS, Black BL, Srivastava D, Shokat KM, Chorba JS. Cold shock domain-containing protein E1 is a posttranscriptional regulator of the LDL receptor. Sci Transl Med 2022; 14:eabj8670. [PMID: 36103516 PMCID: PMC10174261 DOI: 10.1126/scitranslmed.abj8670] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The low-density lipoprotein receptor (LDLR) controls cellular delivery of cholesterol and clears LDL from the bloodstream, protecting against atherosclerotic heart disease, the leading cause of death in the United States. We therefore sought to identify regulators of the LDLR beyond the targets of current therapies and known causes of familial hypercholesterolemia. We found that cold shock domain-containing protein E1 (CSDE1) enhanced hepatic LDLR messenger RNA (mRNA) decay via its 3' untranslated region and regulated atherogenic lipoproteins in vivo. Using parallel phenotypic genome-wide CRISPR interference screens in a tissue culture model, we identified 40 specific regulators of the LDLR that were not previously identified by observational human genetic studies. Among these, we demonstrated that, in HepG2 cells, CSDE1 regulated the LDLR at least as strongly as statins and proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors. In addition, we showed that hepatic gene silencing of Csde1 treated diet-induced dyslipidemia in mice to a similar degree as Pcsk9 silencing. These results suggest the therapeutic potential of targeting CSDE1 to manipulate the posttranscriptional regulation of the LDLR mRNA for the prevention of cardiovascular disease. Our approach of modeling a clinically relevant phenotype in a forward genetic screen, followed by mechanistic pharmacologic dissection and in vivo validation, may serve as a generalizable template for the identification of therapeutic targets in other human disease states.
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Affiliation(s)
- Geoffrey A Smith
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arun Padmanabhan
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Bryan H Lau
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Akhil Pampana
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Li Li
- Department of Medicine and Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clara Y Lee
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Angelo Pelonero
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Tomohiro Nishino
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Nandhini Sadagopan
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Vivian Q Xia
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Cardiology, Zuckerberg San Francisco General Hospital, San Francisco, CA 94110, USA
| | - Rajan Jain
- Department of Medicine and Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Cell and Developmental Biology, Institute of Regenerative Medicine, and Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Roland S Wu
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.,Departments of Pediatrics and Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John S Chorba
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Cardiology, Zuckerberg San Francisco General Hospital, San Francisco, CA 94110, USA
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29
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Jia X, Zhang S, Tan S, Du B, He M, Qin H, Chen J, Duan X, Luo J, Chen F, Ouyang L, Wang J, Chen G, Yu B, Zhang G, Zhang Z, Lyu Y, Huang Y, Jiao J, Chen JY(H, Swoboda KJ, Agolini E, Novelli A, Leoni C, Zampino G, Cappuccio G, Brunetti-Pierri N, Gerard B, Ginglinger E, Richer J, McMillan H, White-Brown A, Hoekzema K, Bernier RA, Kurtz-Nelson EC, Earl RK, Meddens C, Alders M, Fuchs M, Caumes R, Brunelle P, Smol T, Kuehl R, Day-Salvatore DL, Monaghan KG, Morrow MM, Eichler EE, Hu Z, Yuan L, Tan J, Xia K, Shen Y, Guo H. De novo variants in genes regulating stress granule assembly associate with neurodevelopmental disorders. SCIENCE ADVANCES 2022; 8:eabo7112. [PMID: 35977029 PMCID: PMC9385150 DOI: 10.1126/sciadv.abo7112] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/06/2022] [Indexed: 05/25/2023]
Abstract
Stress granules (SGs) are cytoplasmic assemblies in response to a variety of stressors. We report a new neurodevelopmental disorder (NDD) with common features of language problems, intellectual disability, and behavioral issues caused by de novo likely gene-disruptive variants in UBAP2L, which encodes an essential regulator of SG assembly. Ubap2l haploinsufficiency in mouse led to social and cognitive impairments accompanied by disrupted neurogenesis and reduced SG formation during early brain development. On the basis of data from 40,853 individuals with NDDs, we report a nominally significant excess of de novo variants within 29 genes that are not implicated in NDDs, including 3 essential genes (G3BP1, G3BP2, and UBAP2L) in the core SG interaction network. We validated that NDD-related de novo variants in newly implicated and known NDD genes, such as CAPRIN1, disrupt the interaction of the core SG network and interfere with SG formation. Together, our findings suggest the common SG pathology in NDDs.
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Affiliation(s)
- Xiangbin Jia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Shujie Zhang
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Senwei Tan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Bing Du
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Mei He
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Hunan, China
| | - Haisong Qin
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Jia Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Xinyu Duan
- Department of Pediatrics, Daping Hospital, Army Medical University, Chongqing, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Luping Ouyang
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Guodong Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Bin Yu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Ge Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Zimin Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Yongqing Lyu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Yi Huang
- Mental Health Center, West China Hospital of Sichuan University, Chengdu 610000, China
| | - Jian Jiao
- Mental Health Center, West China Hospital of Sichuan University, Chengdu 610000, China
| | - Jin Yun (Helen) Chen
- Massachusetts General Hospital Neurogenetics Unit, Department of Neurology, Massachusetts General Brigham, Boston, MA 02114, USA
| | - Kathryn J. Swoboda
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children’s Hospital, IRCCS, Rome 00165, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children’s Hospital, IRCCS, Rome 00165, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome 00168, Italy
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome 00168, Italy
- Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, Rome 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli Dipartimento Scienze della Salute della Donna e del Bambino, Rome, Italy
- Università Cattolica S. Cuore, Dipartimento Scienze della Vita e Sanità Pubblica, Rome, Italy
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, Federico II University, Naples, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, Federico II University, Naples, Italy
| | - Benedicte Gerard
- Institut de Génétique Médicale d’Alsace (IGMA), Laboratoire de Diagnostic Génétique, Hôpitaux universitaires de Strasbourg, Strasbourg, Alsace, France
| | | | - Julie Richer
- Department of Medical Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Hugh McMillan
- Department of Pediatrics, Neurology and Neurosurgery, Montreal Children’s Hospital, McGill University, Montreal, Canada
| | - Alexandre White-Brown
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Raphael A. Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Rachel K. Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Claartje Meddens
- Amsterdam University Medical Center, Department of Clinical Genetics, Amsterdam, Netherlands
- University Medical Center Utrecht, Department of Paediatrics, Utrecht, Netherlands
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | | | - Roseline Caumes
- CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000 Lille, France
| | - Perrine Brunelle
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000 Lille, France
| | - Thomas Smol
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000 Lille, France
| | - Ryan Kuehl
- Department of Medical Genetics and Genomic Medicine, Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
| | - Debra-Lynn Day-Salvatore
- Department of Medical Genetics and Genomic Medicine, Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
| | | | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Ling Yuan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Jieqiong Tan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai 200000, China
- Hengyang Medical School, University of South China, Hengyang, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan 410078, China
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30
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Tumor Temperature: Friend or Foe of Virus-Based Cancer Immunotherapy. Biomedicines 2022; 10:biomedicines10082024. [PMID: 36009571 PMCID: PMC9405776 DOI: 10.3390/biomedicines10082024] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
The temperature of a solid tumor is often dissimilar to baseline body temperature and, compared to healthy tissues, may be elevated, reduced, or a mix of both. The temperature of a tumor is dependent on metabolic activity and vascularization and can change due to tumor progression, treatment, or cancer type. Despite the need to function optimally within temperature-variable tumors, oncolytic viruses (OVs) are primarily tested at 37 °C in vitro. Furthermore, animal species utilized to test oncolytic viruses, such as mice, dogs, cats, and non-human primates, poorly recapitulate the temperature profile of humans. In this review, we discuss the importance of temperature as a variable for OV immunotherapy of solid tumors. Accumulating evidence supports that the temperature sensitivity of OVs lies on a spectrum, with some OVs likely hindered but others enhanced by elevated temperatures. We suggest that in vitro temperature sensitivity screening be performed for all OVs destined for the clinic to identify potential hinderances or benefits with regard to elevated temperature. Furthermore, we provide recommendations for the clinical use of temperature and OVs.
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31
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Kumar P, Soory A, Mustfa SA, Sarmah DT, Devvanshi H, Chatterjee S, Bossis G, Ratnaparkhi GS, Srikanth CV. Bidirectional regulation between AP-1 and SUMO genes modulates inflammatory signalling during Salmonella infection. J Cell Sci 2022; 135:276158. [PMID: 35904007 DOI: 10.1242/jcs.260096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Post-translational modifications (PTMs), such as SUMOylation, are known to modulate fundamental processes of a cell. Infectious agents such as Salmonella Typhimurium (STm) that causes gastroenteritis, utilizes PTM mechanism SUMOylation to highjack host cell. STm suppresses host SUMO-pathway genes Ubc9 and PIAS1 to perturb SUMOylation for an efficient infection. In the present study, the regulation of SUMO-pathway genes during STm infection was investigated. A direct binding of c-Fos, a component of AP-1 (Activator Protein-1), to promoters of both UBC9 and PIAS1 was observed. Experimental perturbation of c-Fos led to changes in expression of both Ubc9 and PIAS1. STm infection of fibroblasts with SUMOylation deficient c-Fos (c-FOS-KOSUMO-def-FOS) resulted in uncontrolled activation of target genes, resulting in massive immune activation. Infection of c-FOS-KOSUMO-def-FOS cells favored STm replication, indicating misdirected immune mechanisms. Finally, chromatin Immuno-precipitation assays confirmed a context dependent differential binding and release of AP-1 to/from target genes due to its Phosphorylation and SUMOylation respectively. Overall, our data point towards existence of a bidirectional cross-talk between c-Fos and the SUMO pathway and highlighting its importance in AP-1 function relevant to STm infection and beyond.
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Affiliation(s)
- Pharvendra Kumar
- Regional Centre for Biotechnology, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India.,Kalinga Institute of Industrial Technology, Bhubaneshwar, India
| | | | | | - Dipanka Tanu Sarmah
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Himadri Devvanshi
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Samrat Chatterjee
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS, Montpellier, France
| | | | - C V Srikanth
- Regional Centre for Biotechnology, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
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32
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Mestre-Farràs N, Guerrero S, Bley N, Rivero E, Coll O, Borràs E, Sabidó E, Indacochea A, Casillas-Serra C, Järvelin AI, Oliva B, Castello A, Hüttelmaier S, Gebauer F. Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis. Nucleic Acids Res 2022; 50:8207-8225. [PMID: 35848924 PMCID: PMC9371929 DOI: 10.1093/nar/gkac605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture (RIC) to characterize the melanoma RBPome and uncover novel RBPs involved in melanoma progression. Comparison of RIC profiles of a non-tumoral versus a metastatic cell line revealed prevalent changes in RNA-binding capacities that were not associated with changes in RBP levels. Extensive functional validation of a selected group of 24 RBPs using five different in vitro assays unveiled unanticipated roles of RBPs in melanoma malignancy. As proof-of-principle we focused on PDIA6, an ER-lumen chaperone that displayed a novel RNA-binding activity. We show that PDIA6 is involved in metastatic progression, map its RNA-binding domain, and find that RNA binding is required for PDIA6 tumorigenic properties. These results exemplify how RIC technologies can be harnessed to uncover novel vulnerabilities of cancer cells.
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Affiliation(s)
- Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Santiago Guerrero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Nadine Bley
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Ezequiel Rivero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Olga Coll
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alberto Indacochea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Carlos Casillas-Serra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Baldomero Oliva
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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33
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López-Cortés A, Prathap L, Ortiz-Prado E, Kyriakidis NC, León Cáceres Á, Armendáriz-Castillo I, Vera-Guapi A, Yumiceba V, Simbaña-Rivera K, Echeverría-Garcés G, García-Cárdenas JM, Pérez-Villa A, Guevara-Ramírez P, Abad-Sojos A, Bautista J, Puig San Andrés L, Varela N, Guerrero S. The close interaction between hypoxia-related proteins and metastasis in pancarcinomas. Sci Rep 2022; 12:11100. [PMID: 35773405 PMCID: PMC9246854 DOI: 10.1038/s41598-022-15246-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022] Open
Abstract
Many primary-tumor subregions exhibit low levels of molecular oxygen and restricted access to nutrients due to poor vascularization in the tissue, phenomenon known as hypoxia. Hypoxic tumors are able to regulate the expression of certain genes and signaling molecules in the microenvironment that shift it towards a more aggressive phenotype. The transcriptional landscape of the tumor favors malignant transformation of neighboring cells and their migration to distant sites. Herein, we focused on identifying key proteins that participate in the signaling crossroads between hypoxic environment and metastasis progression that remain poorly defined. To shed light on these mechanisms, we performed an integrated multi-omics analysis encompassing genomic/transcriptomic alterations of hypoxia-related genes and Buffa hypoxia scores across 17 pancarcinomas taken from the PanCancer Atlas project from The Cancer Genome Atlas consortium, protein-protein interactome network, shortest paths from hypoxia-related proteins to metastatic and angiogenic phenotypes, and drugs involved in current clinical trials to treat the metastatic disease. As results, we identified 30 hypoxia-related proteins highly involved in metastasis and angiogenesis. This set of proteins, validated with the MSK-MET Project, could represent key targets for developing therapies. The upregulation of mRNA was the most prevalent alteration in all cancer types. The highest frequencies of genomic/transcriptomic alterations and hypoxia score belonged to tumor stage 4 and positive metastatic status in all pancarcinomas. The most significantly associated signaling pathways were HIF-1, PI3K-Akt, thyroid hormone, ErbB, FoxO, mTOR, insulin, MAPK, Ras, AMPK, and VEGF. The interactome network revealed high-confidence interactions among hypoxic and metastatic proteins. The analysis of shortest paths revealed several ways to spread metastasis and angiogenesis from hypoxic proteins. Lastly, we identified 23 drugs enrolled in clinical trials focused on metastatic disease treatment. Six of them were involved in advanced-stage clinical trials: aflibercept, bevacizumab, cetuximab, erlotinib, ipatasertib, and panitumumab.
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Affiliation(s)
- Andrés López-Cortés
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, 170302, Quito, Ecuador.
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas, 170124, Quito, Ecuador.
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain.
| | - Lavanya Prathap
- Department of Anatomy, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, 600077, Chennai, India
| | - Esteban Ortiz-Prado
- One Health Research Group, Universidad de Las Américas, 170124, Quito, Ecuador
| | | | - Ángela León Cáceres
- Heidelberg Institute of Global Health, Faculty of Medicine, University of Heidelberg, 69117, Heidelberg, Germany
| | - Isaac Armendáriz-Castillo
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
- Instituto Nacional de Investigación en Salud Pública, 170136, Quito, Ecuador
- Facultad de Ingenierías y Ciencias Aplicadas, Universidad Internacional SEK, 170302, Quito, Ecuador
| | - Antonella Vera-Guapi
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747, Jena, Germany
| | - Verónica Yumiceba
- Institut Für Humangenetik Lübeck, Universität Zu Lübeck, 23562, Lübeck, Germany
| | - Katherine Simbaña-Rivera
- One Health Research Group, Universidad de Las Américas, 170124, Quito, Ecuador
- Latin American Network for Cancer Research (LAN-CANCER), Lima, Peru
| | - Gabriela Echeverría-Garcés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
| | - Jennyfer M García-Cárdenas
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, 170113, Quito, Ecuador
| | - Andy Pérez-Villa
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
| | - Patricia Guevara-Ramírez
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
| | | | | | | | - Nelson Varela
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, 8320000, Santiago, Chile
| | - Santiago Guerrero
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain.
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, 170113, Quito, Ecuador.
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34
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LINC00518 Promotes Cell Malignant Behaviors via Influencing EIF4A3-Mediated mRNA Stability of MITF in Melanoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3546795. [PMID: 35813236 PMCID: PMC9262545 DOI: 10.1155/2022/3546795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/22/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022]
Abstract
Melanoma has become the most severe sort of skin cancer, deriving from the pigment-producing melanocytes. Existing research has validated that long noncoding RNAs (lncRNAs) have critical function in the progression of cancers. LINC00518 has been studied in cutaneous melanoma; however, the molecular mechanism of LINC00518 in melanoma needs in-depth investigation. In our study, LINC00518 was revealed to be upregulated in melanoma tissues and cells, and melanoma patients in high LINC00518 expression group had poorer prognosis as depicted in GEPIA database. Functional assays revealed that LINC00518 depletion inhibited cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT). Furthermore, MITF was confirmed to be upregulated in melanoma tissues and cells, and melanoma patients in high MITF expression group had poorer prognosis as displayed in GEPIA database. MITF expression was positively connected to LINC00518 expression. Additionally, results of mechanism assays uncovered EIF4A3 could bind with LINC00518 and MITF, and LINC00518 recruited EIF4A3 to stabilize MITF mRNA. Finally, it was demonstrated that upregulation of MITF could partially abrogate the inhibitory impact of LINC00518 knockdown on melanoma cell malignant behaviors. To summarize, LINC00518 promotes the malignant processes of melanoma cells through targeting EIF4A3/MITF axis, which might provide novel potential biomarkers for melanoma prognosis.
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Zhang S, Wu Z, Shi L, Yan S, Huang Z, Lu B, Wang Z, Ji L. 2,3,5,4'-tetrahydroxy-stilbene-2-O-β-D-glucoside ameliorates NAFLD via attenuating hepatic steatosis through inhibiting mitochondrial dysfunction dependent on SIRT5. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 99:153994. [PMID: 35220131 DOI: 10.1016/j.phymed.2022.153994] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/17/2022] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is becoming more and more common in clinic in the world, and the study on its mechanism and treatment strategy has already been a research hotspot. Natural chemical compound 2,3,5,4'-tetrahydroxy-stilbene-2-O-β-d-glucoside (TSG) is isolated from Polygonum multiflorum Thunb. that has already been reported to have the lipid-lowering activity. PURPOSE The purpose of this research was to observe the improvement of TSG on methionine and choline deficient (MCD) diet-induced NAFLD in mice and to further elucidate its engaged mechanism. METHODS NAFLD was induced in mice fed by MCD diet for 6 weeks. The accumulation of lipids in hepatocytes was induced by 0.5 mM non-esterified fatty acid (NEFA). Biochemical parameters in serum or livers from mice were tested. Protein and mRNA expression and stability were measured. Mitochondrial dysfunction was analyzed both in vivo and in vitro. The Label-free quantitative proteomic analysis was used to find potential involved key molecules. RESULTS TSG attenuated hepatic parenchymal cells injury, liver inflammatory responses and hepatic fibrosis, and markedly ameliorated liver steatosis in mice from MCD group. In vitro results indicated that TSG reduced the accumulation of cellular lipids in hepatocytes induced by NEFA. TSG reduced reactive oxygen species (ROS) formation and attenuated mitochondrial dysfunction both in vivo and in vitro. The label-free quantitative proteomic analysis predicted the crucial participation of NAD-dependent protein deacylase sirtuin-5 (SIRT5). Next experimental results further evidenced that TSG enhanced SIRT5 expression in mitochondria both in vitro and in vivo. The TSG-supplied inhibition on ROS formation and mitochondrial dysfunction in hepatocytes was disappeared after the application of SIRT5 siRNA. TSG increased the expression and enzymatic activity of carnitine palmitoyltransferase 1A (CPT1A), but this enhance was diminished in hepatocytes transfected with SIRT5 siRNA. Additionally, the TSG-provided inhibition on cellular lipids accumulation was also disappeared in hepatocytes transfected with SIRT5 siRNA. Further results demonstrated that TSG increased SIRT5 expression by regulating its mRNA stability through enhancing the binding of SIRT5 mRNA with serine/arginine-rich splicing factor 2 (SRSF2), which is an RNA-binding protein (RBP). CONCLUSION TSG attenuated liver steatosis and inhibited NAFLD progression through preventing oxidative stress injury and improving mitochondrial dysfunction, and SIRT5 played a key role in this process.
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Affiliation(s)
- Shaobo Zhang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zeqi Wu
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Liang Shi
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Shihao Yan
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhenlin Huang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Bin Lu
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Ji
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Reduced miR-371b-5p expression drives tumor progression via CSDE1/RAC1 regulation in triple-negative breast cancer. Oncogene 2022; 41:3151-3161. [PMID: 35490208 PMCID: PMC9135623 DOI: 10.1038/s41388-022-02326-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer; however, specific prognostic biomarkers have not yet been developed. In this study, we identified dysregulated microRNAs (miRNAs) in TNBC by profiling miRNA and mRNA expression. In patients with TNBC, miR-371b-5p expression was reduced, and miR-371b-5p overexpression significantly mitigated TNBC cell growth, migration, and invasion. In addition, we found that expression of cold shock domain-containing protein E1 (CSDE1), a direct target gene of miR-371b-5p, was upregulated in TNBC cells, and inhibition of CSDE1 expression alleviated TNBC cell growth by regulating RAC1 transcription. Mechanistically, CSDE1, phosphorylated C-terminal domain (p-CTD) of RNA polymerase II (RNAPII), and CDK7 form a complex, and downregulation of CSDE1 leads to weak interaction between RNAPII p-CTD and CDK7, resulting in a decrease in RNAPII p-CTD expression to reduce RAC1 transcript levels in CSDE1-deficient TNBC cells. Our data demonstrate that miR-371b-5p is a tumor-suppressive miRNA that regulates the CSDE1/Rac1 axis and could be a potential prognostic biomarker for TNBC.
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AGO-RBP crosstalk on target mRNAs: Implications in miRNA-guided gene silencing and cancer. Transl Oncol 2022; 21:101434. [PMID: 35477066 PMCID: PMC9136600 DOI: 10.1016/j.tranon.2022.101434] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) and RNA-binding proteins (RBPs) are important regulators of mRNA translation and stability in eukaryotes. While miRNAs can only bind their target mRNAs in association with Argonaute proteins (AGOs), RBPs directly bind their targets either as single entities or in complex with other RBPs to control mRNA metabolism. miRNA binding in 3' untranslated regions (3' UTRs) of mRNAs facilitates an intricate network of interactions between miRNA-AGO and RBPs, thus determining the fate of overlapping targets. Here, we review the current knowledge on the interplay between miRNA-AGO and multiple RBPs in different cellular contexts, the rules underlying their synergism and antagonism on target mRNAs, as well as highlight the implications of these regulatory modules in cancer initiation and progression.
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Qian Y, Cheng B, Luo J, Hu Y, Gao L, Cheng H. CircRFX3 Up-regulates Its Host Gene RFX3 to Facilitate Tumorigenesis and Progression of Glioma. J Mol Neurosci 2022; 72:1195-1207. [PMID: 35416616 DOI: 10.1007/s12031-022-02005-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 03/22/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Glioma is classified as one of the most common types of primary brain tumors. The high expression of CircRFX3 has been found in glioma. However, its functional roles in glioma and underlying mechanism remain unknown. PURPOSE Our study aimed to explore the function and specific mechanism of circRFX3 in glioma. METHODS RT-qPCR or western blot was applied to examine the expression of RNAs or proteins. Functional assays were carried out to evaluate the influence of circRFX3, RFX3 and PROX1 on glioma cells. In vivo experiments were done to ascertain the impact of circRFX3 on glioma growth. Moreover, mechanism assays were conducted to investigate the molecular relation among circRFX3, RFX3, HNRNPK and PROX1. RESULTS CircRFX3 was highly expressed in glioma cells. CircRFX3 knockdown led to the suppression of glioma cell and tumor growth. CircRFX3 overexpression resulted in the opposite outcomes. Mechanism analyses suggested that circRFX3 recruited HNRNPK to enhance RFX3 mRNA stability, thereby facilitating glioma cell malignant behaviors. RFX3 was also unveiled to affect glioma cells via stimulating PROX1 transcription. CONCLUSION CircRFX3, as a tumor promoter, could recruit HNRNPK to stabilize RFX3 mRNA in glioma cells. Additionally, RFX3 could promote PROX1 transcription to promote glioma progression.
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Affiliation(s)
- Yu Qian
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Baochun Cheng
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Jing Luo
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Yangchun Hu
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Lu Gao
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Hongwei Cheng
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China.
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RNA-binding proteins and cancer metastasis. Semin Cancer Biol 2022; 86:748-768. [PMID: 35339667 DOI: 10.1016/j.semcancer.2022.03.018] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins (RBPs) can regulate gene expression through post-transcriptionally influencing all manner of RNA biology, including alternative splicing (AS), polyadenylation, stability, and translation of mRNAs, as well as microRNAs (miRNAs) and circular RNAs (circRNAs) processing. There is accumulating evidence reinforcing the perception that dysregulation or dysfunction of RBPs can lead to various human diseases, including cancers. RBPs influence diverse cancer-associated cellular phenotypes, such as proliferation, apoptosis, senescence, migration, invasion, and angiogenesis, contributing to the initiation and development of tumors, as well as clinical prognosis. Metastasis is the leading cause of cancer-related recurrence and death. Therefore, it is necessary to elucidate the molecular mechanisms behind tumor metastasis. In fact, a growing body of published research has proved that RBPs play pivotal roles in cancer metastasis. In this review, we will summarize the recent advances for helping us understand the role of RBPs in tumor metastasis, and discuss dysfunctions and dysregulations of RBPs affecting metastasis-associated processes including epithelial-mesenchymal transition (EMT), migration, and invasion of cancer cells. Furthermore, we will discuss emerging RBP-based strategy for the treatment of cancer metastasis.
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García-Cárdenas JM, Armendáriz-Castillo I, Pérez-Villa A, Indacochea A, Jácome-Alvarado A, López-Cortés A, Guerrero S. Integrated In Silico Analyses Identify PUF60 and SF3A3 as New Spliceosome-Related Breast Cancer RNA-Binding Proteins. BIOLOGY 2022; 11:biology11040481. [PMID: 35453681 PMCID: PMC9030152 DOI: 10.3390/biology11040481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/12/2022] [Accepted: 03/18/2022] [Indexed: 12/24/2022]
Abstract
More women are diagnosed with breast cancer (BC) than any other type of cancer. Although large-scale efforts have completely redefined cancer, a cure remains unattainable. In that respect, new molecular functions of the cell should be investigated, such as post-transcriptional regulation. RNA-binding proteins (RBPs) are emerging as critical post-transcriptional modulators of tumorigenesis, but only a few have clear roles in BC. To recognize new putative breast cancer RNA-binding proteins, we performed integrated in silico analyses of all human RBPs (n = 1392) in three major cancer databases and identified five putative BC RBPs (PUF60, TFRC, KPNB1, NSF, and SF3A3), which showed robust oncogenic features related to their genomic alterations, immunohistochemical changes, high interconnectivity with cancer driver genes (CDGs), and tumor vulnerabilities. Interestingly, some of these RBPs have never been studied in BC, but their oncogenic functions have been described in other cancer types. Subsequent analyses revealed PUF60 and SF3A3 as central elements of a spliceosome-related cluster involving RBPs and CDGs. Further research should focus on the mechanisms by which these proteins could promote breast tumorigenesis, with the potential to reveal new therapeutic pathways along with novel drug-development strategies.
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Affiliation(s)
- Jennyfer M. García-Cárdenas
- Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito 170113, Ecuador; (J.M.G.-C.); (A.J.-A.)
- Facultade de Ciencias, Universidade da Coruña, 15071 A Coruna, Spain
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (I.A.-C.); (A.P.-V.)
| | - Isaac Armendáriz-Castillo
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (I.A.-C.); (A.P.-V.)
- Instituto Nacional de Investigación en Salud Pública, Quito 170136, Ecuador
- Facultad de Ingenierías y Ciencias Aplicadas, Universidad Internacional SEK, Quito 170302, Ecuador
| | - Andy Pérez-Villa
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (I.A.-C.); (A.P.-V.)
| | - Alberto Indacochea
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Andrea Jácome-Alvarado
- Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito 170113, Ecuador; (J.M.G.-C.); (A.J.-A.)
| | - Andrés López-Cortés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (I.A.-C.); (A.P.-V.)
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito 170302, Ecuador
- Facultad de Medicina, Universidad de Las Américas, Quito 170124, Ecuador
- Correspondence: (A.L.-C.); (S.G.)
| | - Santiago Guerrero
- Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito 170113, Ecuador; (J.M.G.-C.); (A.J.-A.)
- Facultade de Ciencias, Universidade da Coruña, 15071 A Coruna, Spain
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (I.A.-C.); (A.P.-V.)
- Correspondence: (A.L.-C.); (S.G.)
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Morin C, Moyret-Lalle C, Mertani HC, Diaz JJ, Marcel V. Heterogeneity and dynamic of EMT through the plasticity of ribosome and mRNA translation. Biochim Biophys Acta Rev Cancer 2022; 1877:188718. [PMID: 35304296 DOI: 10.1016/j.bbcan.2022.188718] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Growing evidence exposes translation and its translational machinery as key players in establishing and maintaining physiological and pathological biological processes. Examining translation may not only provide new biological insight but also identify novel innovative therapeutic targets in several fields of biology, including that of epithelial-to-mesenchymal transition (EMT). EMT is currently considered as a dynamic and reversible transdifferentiation process sustaining the transition from an epithelial to mesenchymal phenotype, known to be mainly driven by transcriptional reprogramming. However, it seems that the characterization of EMT plasticity is challenging, relying exclusively on transcriptomic and epigenetic approaches. Indeed, heterogeneity in EMT programs was reported to depend on the biological context. Here, by reviewing the involvement of translational control, translational machinery and ribosome biogenesis characterizing the different types of EMT, from embryonic and adult physiological to pathological contexts, we discuss the added value of integrating translational control and its machinery to depict the heterogeneity and dynamics of EMT programs.
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Affiliation(s)
- Chloé Morin
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Caroline Moyret-Lalle
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France.
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Avolio R, Inglés-Ferrándiz M, Ciocia A, Coll O, Bonnin S, Guitart T, Ribó A, Gebauer F. Coordinated post-transcriptional control of oncogene-induced senescence by UNR/CSDE1. Cell Rep 2022; 38:110211. [PMID: 35021076 DOI: 10.1016/j.celrep.2021.110211] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 08/27/2021] [Accepted: 12/14/2021] [Indexed: 02/06/2023] Open
Abstract
Oncogene-induced senescence (OIS) is a form of stable cell-cycle arrest arising in response to oncogenic stimulation. OIS must be bypassed for transformation, but the mechanisms of OIS establishment and bypass remain poorly understood, especially at the post-transcriptional level. Here, we show that the RNA-binding protein UNR/CSDE1 enables OIS in primary mouse keratinocytes. Depletion of CSDE1 leads to senescence bypass, cell immortalization, and tumor formation, indicating that CSDE1 behaves as a tumor suppressor. Unbiased high-throughput analyses uncovered that CSDE1 promotes OIS by two independent molecular mechanisms: enhancement of the stability of senescence-associated secretory phenotype (SASP) factor mRNAs and repression of Ybx1 mRNA translation. Importantly, depletion of YBX1 from immortal keratinocytes rescues senescence and uncouples proliferation arrest from the SASP, revealing multilayered mechanisms exerted by CSDE1 to coordinate senescence. Our data highlight the relevance of post-transcriptional control in the regulation of senescence.
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Affiliation(s)
- Rosario Avolio
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Marta Inglés-Ferrándiz
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Annagiulia Ciocia
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Olga Coll
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Sarah Bonnin
- Bioinformatics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Anna Ribó
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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Vanner RJ, Dobson SM, Gan OI, McLeod J, Schoof EM, Grandal I, Wintersinger JA, Garcia-Prat L, Hosseini M, Xie SZ, Jin L, Mbong N, Voisin V, Chan-Seng-Yue M, Kennedy JA, Waanders E, Morris Q, Porse B, Chan SM, Guidos CJ, Danska JS, Minden MD, Mullighan CG, Dick JE. Multiomic Profiling of Central Nervous System Leukemia Identifies mRNA Translation as a Therapeutic Target. Blood Cancer Discov 2022; 3:16-31. [PMID: 35019858 PMCID: PMC9783958 DOI: 10.1158/2643-3230.bcd-20-0216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/29/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
Central nervous system (CNS) dissemination of B-precursor acute lymphoblastic leukemia (B-ALL) has poor prognosis and remains a therapeutic challenge. Here we performed targeted DNA sequencing as well as transcriptional and proteomic profiling of paired leukemia-infiltrating cells in the bone marrow (BM) and CNS of xenografts. Genes governing mRNA translation were upregulated in CNS leukemia, and subclonal genetic profiling confirmed this in both BM-concordant and BM-discordant CNS mutational populations. CNS leukemia cells were exquisitely sensitive to the translation inhibitor omacetaxine mepesuccinate, which reduced xenograft leptomeningeal disease burden. Proteomics demonstrated greater abundance of secreted proteins in CNS-infiltrating cells, including complement component 3 (C3), and drug targeting of C3 influenced CNS disease in xenografts. CNS-infiltrating cells also exhibited selection for stemness traits and metabolic reprogramming. Overall, our study identifies targeting of mRNA translation as a potential therapeutic approach for B-ALL leptomeningeal disease. SIGNIFICANCE: Cancer metastases are often driven by distinct subclones with unique biological properties. Here we show that in B-ALL CNS disease, the leptomeningeal environment selects for cells with unique functional dependencies. Pharmacologic inhibition of mRNA translation signaling treats CNS disease and offers a new therapeutic approach for this condition.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Robert J Vanner
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie M Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Ildiko Grandal
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jeff A Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mohsen Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Veronique Voisin
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, University Medical Center, Utrecht, the Netherlands
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quaid Morris
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cynthia J Guidos
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jayne S Danska
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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44
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Ristau J, Watt K, Oertlin C, Larsson O. Polysome Fractionation for Transcriptome-Wide Studies of mRNA Translation. Methods Mol Biol 2022; 2418:223-241. [PMID: 35119669 DOI: 10.1007/978-1-0716-1920-9_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein synthesis and degradation determine the relationship between mRNA and corresponding protein amounts. This relationship can change in a dynamic and selective fashion when translational efficiencies of transcript subsets are altered downstream of, for example, translation factors and/or RNA binding proteins. Notably, even transcription factors such as estrogen receptor alpha (ERα) can modulate mRNA translation in a transcript-selective manner. Yet, despite ample evidence suggesting a key role for mRNA translation in shaping the proteome in health and disease, it remains largely unexplored. Here, we present a guide for the extraction of mRNA engaged in translation using polysome fractionation with linear and optimized sucrose gradients. The isolated polysome-associated RNA is then quantified, in parallel with total mRNA from the same conditions, using methods such as RNA sequencing; and the resulting data set is analyzed to derive transcriptome-wide insights into how mRNA translation is modulated. The methods we describe are applicable to cultured cells, small numbers of FACS-isolated primary cells, and small tissue samples from biobanks or animal studies. Accordingly, this approach can be applied to study in detail how ERα and other factors control gene expression by selectively modulating mRNA translation both in vitro and in vivo.
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Affiliation(s)
- Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Kathleen Watt
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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45
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Grzybowska EA, Wakula M. Protein Binding to Cis-Motifs in mRNAs Coding Sequence Is Common and Regulates Transcript Stability and the Rate of Translation. Cells 2021; 10:2910. [PMID: 34831133 PMCID: PMC8616275 DOI: 10.3390/cells10112910] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/19/2022] Open
Abstract
Protein binding to the non-coding regions of mRNAs is relatively well characterized and its functionality has been described in many examples. New results obtained by high-throughput methods indicate that binding to the coding sequence (CDS) by RNA-binding proteins is also quite common, but the functions thereof are more obscure. As described in this review, CDS binding has a role in the regulation of mRNA stability, but it has also a more intriguing role in the regulation of translational efficiency. Global approaches, which suggest the significance of CDS binding along with specific examples of CDS-binding RBPs and their modes of action, are outlined here, pointing to the existence of a relatively less-known regulatory network controlling mRNA stability and translation on yet another level.
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Affiliation(s)
- Ewa A. Grzybowska
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland;
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46
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Fabbri L, Chakraborty A, Robert C, Vagner S. The plasticity of mRNA translation during cancer progression and therapy resistance. Nat Rev Cancer 2021; 21:558-577. [PMID: 34341537 DOI: 10.1038/s41568-021-00380-y] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2021] [Indexed: 02/07/2023]
Abstract
Translational control of mRNAs during gene expression allows cells to promptly and dynamically adapt to a variety of stimuli, including in neoplasia in response to aberrant oncogenic signalling (for example, PI3K-AKT-mTOR, RAS-MAPK and MYC) and microenvironmental stress such as low oxygen and nutrient supply. Such translational rewiring allows rapid, specific changes in the cell proteome that shape specific cancer phenotypes to promote cancer onset, progression and resistance to anticancer therapies. In this Review, we illustrate the plasticity of mRNA translation. We first highlight the diverse mechanisms by which it is regulated, including by translation factors (for example, eukaryotic initiation factor 4F (eIF4F) and eIF2), RNA-binding proteins, tRNAs and ribosomal RNAs that are modulated in response to aberrant intracellular pathways or microenvironmental stress. We then describe how translational control can influence tumour behaviour by impacting on the phenotypic plasticity of cancer cells as well as on components of the tumour microenvironment. Finally, we highlight the role of mRNA translation in the cellular response to anticancer therapies and its promise as a key therapeutic target.
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Affiliation(s)
- Lucilla Fabbri
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France
| | - Alina Chakraborty
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, Kremlin-Bicêtre, France
- Dermato-Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France.
- Dermato-Oncology, Gustave Roussy Cancer Campus, Villejuif, France.
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47
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Zhang Z, Zhang X. Identification of m6A-Related Biomarkers Associated with Prognosis of Colorectal Cancer. Med Sci Monit 2021; 27:e932370. [PMID: 34373442 PMCID: PMC8364289 DOI: 10.12659/msm.932370] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Colorectal cancer (CRC) is the second most deadly cancer in the world according to GLOBOCAN 2020 data. Accumulating evidence suggests that RNA methylation modification is also misregulated in human cancers and may be a potential ideal target for cancer treatment. Material/Methods m6A-related differentially expressed genes (DEGs) were identified from colon adenocarcinoma and rectum adenocarcinoma esophageal carcinoma patients with different pathological stages. The protein-protein interaction (PPI) network construction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were conducted. Cox regression analysis was applied to the screening of m6A-related DEGs significantly associated with the overall survival (OS), and those selected genes were used for LASSO regression analysis to construct prognostic signature and calculate patients’ risk scores. Results We identified 673 m6A-related DEGs from CRC patients in different pathologic stages, and 146 of them were associated with OS. CTNNB1, TRIM37, RAB7A, CASC5/KNL1, CENPE, CCNB1, UBE2H, HSPA8, KIF1A, and FBXW4 were hub genes of the PPI network. Nine m6A-related genes were screened out to build the prognostic risk model. TNM stage, vascular invasion, and the risk score were independently related to the OS of CRC patients. Conclusions Nine candidate m6A-related mRNA biomarkers (LRRC17, NFKB1, NOS2, PCDHB2, RAB7A, RPS6KA1, RRNAD1, TLE6, and UBE2H) were found to be closely related to the clinicopathology and prognosis of colorectal cancer, indicating that they could be potential prognostic biomarkers for patients with colorectal cancer.
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Affiliation(s)
- Zhiyong Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Xin Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
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48
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Silva J, Nina P, Romão L. Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells. Biomedicines 2021; 9:biomedicines9080911. [PMID: 34440115 PMCID: PMC8389594 DOI: 10.3390/biomedicines9080911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.
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Affiliation(s)
- Joana Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pedro Nina
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-21-750-8155
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El Khouri E, Ghoumid J, Haye D, Giuliano F, Drevillon L, Briand-Suleau A, De La Grange P, Nau V, Gaillon T, Bienvenu T, Jacquemin-Sablon H, Goossens M, Amselem S, Giurgea I. Wnt/β-catenin pathway and cell adhesion deregulation in CSDE1-related intellectual disability and autism spectrum disorders. Mol Psychiatry 2021; 26:3572-3585. [PMID: 33867523 DOI: 10.1038/s41380-021-01072-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
Among the genetic factors playing a key role in the etiology of intellectual disabilities (IDs) and autism spectrum disorders (ASDs), several encode RNA-binding proteins (RBPs). In this study, we deciphered the molecular and cellular bases of ID-ASD in a patient followed from birth to the age of 21, in whom we identified a de novo CSDE1 (Cold Shock Domain-containing E1) nonsense variation. CSDE1 encodes an RBP that regulates multiple cellular pathways by monitoring the translation and abundance of target transcripts. Analyses performed on the patient's primary fibroblasts showed that the identified CSDE1 variation leads to haploinsufficiency. We identified through RNA-seq assays the Wnt/β-catenin signaling and cellular adhesion as two major deregulated pathways. These results were further confirmed by functional studies involving Wnt-specific luciferase and substrate adhesion assays. Additional data support a disease model involving APC Down-Regulated-1 (APCDD1) and cadherin-2 (CDH2), two components of the Wnt/β-catenin pathway, CDH2 being also pivotal for cellular adhesion. Our study, which relies on both the deep phenotyping and long-term follow-up of a patient with CSDE1 haploinsufficiency and on ex vivo studies, sheds new light on the CSDE1-dependent deregulated pathways in ID-ASD.
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Affiliation(s)
- E El Khouri
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - J Ghoumid
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - D Haye
- Service de Génétique Médicale Centre, Hospitalo-Universitaire de Nice, Nice, France
| | - F Giuliano
- Service de Génétique Médicale Centre, Hospitalo-Universitaire de Nice, Nice, France
| | - L Drevillon
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,CHU Caen Normandie, Caen, France
| | - A Briand-Suleau
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,Service de Génétique et Biologie Moléculaires, Hôpital Cochin, INSERM UMR1266 - Institute of Psychiatry and Neuroscience of Paris (IPNP) and University of Paris, Paris, France
| | | | - V Nau
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - T Gaillon
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France
| | - T Bienvenu
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, INSERM UMR1266 - Institute of Psychiatry and Neuroscience of Paris (IPNP) and University of Paris, Paris, France
| | - H Jacquemin-Sablon
- INSERM UMR1053 Bordeaux Research in Translational Oncology, BaRITOn, Bordeaux, France
| | - M Goossens
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France
| | - S Amselem
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - I Giurgea
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France. .,Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.
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50
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Integrated Analysis of the Roles of RNA Binding Proteins and Their Prognostic Value in Clear Cell Renal Cell Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5568411. [PMID: 34306592 PMCID: PMC8263288 DOI: 10.1155/2021/5568411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022]
Abstract
Methods We downloaded the RNA sequencing data of ccRCC from the Cancer Genome Atlas (TCGA) database and identified differently expressed RBPs in different tissues. In this study, we used bioinformatics to analyze the expression and prognostic value of RBPs; then, we performed functional analysis and constructed a protein interaction network for them. We also screened out some RBPs related to the prognosis of ccRCC. Finally, based on the identified RBPs, we constructed a prognostic model that can predict patients' risk of illness and survival time. Also, the data in the HPA database were used for verification. Results In our experiment, we obtained 539 ccRCC samples and 72 normal controls. In the subsequent analysis, 87 upregulated RBPs and 38 downregulated RBPs were obtained. In addition, 9 genes related to the prognosis of patients were selected, namely, RPL36A, THOC6, RNASE2, NOVA2, TLR3, PPARGC1A, DARS, LARS2, and U2AF1L4. We further constructed a prognostic model based on these genes and plotted the ROC curve. This ROC curve performed well in judgement and evaluation. A nomogram that can judge the patient's life span is also made. Conclusion In conclusion, we have identified differentially expressed RBPs in ccRCC and carried out a series of in-depth research studies, the results of which may provide ideas for the diagnosis of ccRCC and the research of new targeted drugs.
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