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Li F, Karimi N, Wang S, Pan T, Dong J, Wang X, Ma S, Shan Q, Liu C, Zhang Y, Li W, Feng G. mRNA isoform switches during mouse zygotic genome activation. Cell Prolif 2024; 57:e13655. [PMID: 38764347 PMCID: PMC11216927 DOI: 10.1111/cpr.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Affiliation(s)
- Fan Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Najmeh Karimi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Tianshi Pan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
| | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Sinan Ma
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Qingtong Shan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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2
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Rouse WB, Tompkins VS, O’Leary CA, Moss WN. The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions. Nucleic Acids Res 2024; 52:6596-6613. [PMID: 38554103 PMCID: PMC11194067 DOI: 10.1093/nar/gkae220] [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: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
The androgen receptor (AR) is a ligand-dependent nuclear transcription factor belonging to the steroid hormone nuclear receptor family. Due to its roles in regulating cell proliferation and differentiation, AR is tightly regulated to maintain proper levels of itself and the many genes it controls. AR dysregulation is a driver of many human diseases including prostate cancer. Though this dysregulation often occurs at the RNA level, there are many unknowns surrounding post-transcriptional regulation of AR mRNA, particularly the role that RNA secondary structure plays. Thus, a comprehensive analysis of AR transcript secondary structure is needed. We address this through the computational and experimental analyses of two key isoforms, full length (AR-FL) and truncated (AR-V7). Here, a combination of in-cell RNA secondary structure probing experiments (targeted DMS-MaPseq) and computational predictions were used to characterize the static structural landscape and conformational dynamics of both isoforms. Additionally, in-cell assays were used to identify functionally relevant structures in the 5' and 3' UTRs of AR-FL. A notable example is a conserved stem loop structure in the 5'UTR of AR-FL that can bind to Poly(RC) Binding Protein 2 (PCBP2). Taken together, our results reveal novel features that regulate AR expression.
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Affiliation(s)
- Warren B Rouse
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Van S Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Collin A O’Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Departments of Biology and Chemistry, Cornell College, Mount Vernon, IA 52314, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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3
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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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4
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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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5
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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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6
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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7
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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: 0] [Impact Index Per Article: 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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8
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Helmold BR, Pauss KE, Ozdinler PH. TDP-43 protein interactome informs about perturbed canonical pathways and may help develop personalized medicine approaches for patients with TDP-43 pathology. Drug Discov Today 2023; 28:103769. [PMID: 37714405 PMCID: PMC10872580 DOI: 10.1016/j.drudis.2023.103769] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/22/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Transactive response DNA binding protein of 43 kDa (TDP-43) pathology is a common proteinopathy observed among a broad spectrum of patients with neurodegenerative disease, regardless of the mutation. This suggests that protein-protein interactions of TDP-43 with other proteins may in part be responsible for the pathology. To gain better insights, we investigated TDP-43-binding proteins in each domain and correlated these interactions with canonical pathways. These investigations revealed key cellular events that are involved and are important at each domain and suggested previously identified compounds to modulate key aspects of these canonical pathways. Our approach proposes that personalized medicine approaches, which focus on perturbed cellular mechanisms would be feasible in the near future.
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Affiliation(s)
- Benjamin R Helmold
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - Kate E Pauss
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - P Hande Ozdinler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA; Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60611, USA; Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Feinberg School of Medicine, Les Turner ALS Center at Northwestern University, Chicago, IL 60611, USA.
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9
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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: 1] [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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10
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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: 1.0] [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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11
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Behl A, Shoaib R, De Leon F, Kumari G, Saini M, Madan E, Kumar V, Singh H, Kumari J, Maurya P, Garg S, Chandra Mishra P, Arenz C, Singh S. Targeting an essential Plasmodium cold shock protein to block growth and transmission of malaria parasite. iScience 2023; 26:106637. [PMID: 37192974 PMCID: PMC10182332 DOI: 10.1016/j.isci.2023.106637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/16/2023] [Accepted: 04/04/2023] [Indexed: 05/18/2023] Open
Abstract
Cold shock proteins are characterized by the presence of one or more cold shock domains that bestow them with nucleic acid binding ability. Although cold shock proteins are well characterized in bacteria, plants and humans, there is no information on their existence and role in malaria parasite. Here, we have identified and delineated the function of a cold shock protein of Plasmodium falciparum (Pf) 'PfCoSP'. We demonstrate that PfCoSP exhibits nucleic acid binding properties and regulates gene expression. PfCoSP promotes microtubule assembly by interacting with Pf α/β tubulin. We identified a human cold shock protein LIN28A inhibitor 'LI71' as a binding partner of PfCoSP which inhibited PfCoSP-DNA and α/β tubulin interactions and, also inhibited the development of asexual blood stages and gametocyte stage of malaria parasite. Because PfCoSP is essential for parasite survival, characterization of its interacting partners may form the basis for development of future anti-malarials.
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Affiliation(s)
- Ankita Behl
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rumaisha Shoaib
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | | | - Geeta Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Monika Saini
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- Department of Life Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Evanka Madan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vikash Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Harshita Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Jyoti Kumari
- Department of Life Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Preeti Maurya
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Swati Garg
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | | | - Christoph Arenz
- Institute for Chemistry, Humboldt University, Berlin, Germany
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- Corresponding author
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12
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Fuller AD, Karami AL, Kabir MF, Klochkova A, Jackson JL, Mu A, Tan Y, Klein-Szanto AJ, Whelan KA. Eosinophilic esophagitis-associated epithelial remodeling may limit esophageal carcinogenesis. FRONTIERS IN ALLERGY 2023; 4:1086032. [PMID: 37064719 PMCID: PMC10090679 DOI: 10.3389/falgy.2023.1086032] [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: 10/31/2022] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Introduction Under homeostatic conditions, esophageal epithelium displays a proliferation/differentiation gradient that is generated as proliferative basal cells give rise to suprabasal cells then terminally differentiated superficial cells. This proliferation/differentiation gradient is often perturbed in esophageal pathologies. Basal cell hyperplasia may occur in patients with gastroesophageal reflux disease (GERD), a condition in which acid from the stomach enters the esophagus, or eosinophilic esophagitis (EoE), an emerging form of food allergy. While GERD is a primary risk factor for esophageal cancer, epidemiological data suggests that EoE patients do not develop esophageal cancer. Methods In order to investigate the impact of EoE and esophageal cancer specifically on the cellular landscape of esophageal epithelium, we perform single cell RNA-sequencing in murine models of EoE and esophageal cancer, specifically esophageal squamous cell carcinoma (ESCC). We further evaluate modules of co-expressed genes in EoE- and ESCC-enriched epithelial cell clusters. Finally, we pair EoE and ESCC murine models to examine the functional relationship between these pathologies. Results In mice with either EoE or ESCC, we find expansion of cell populations as compared to normal esophageal epithelium. In mice with EoE, we detect distinct expansion of 4 suprabasal populations coupled with depletion of 2 basal populations. By contrast, mice with ESCC display unique expansion of 2 basal populations and 1 suprabasal population, as well as depletion of 2 suprabasal populations. Senescence, glucocorticoid receptor signaling, and granulocyte-macrophage colony-stimulating factor pathways are associated with EoE-enriched clusters while pathways associated with cell proliferation and metabolism are identified in ESCC-enriched clusters. Finally, our in vivo data demonstrate that exposure to EoE inflammation limits tumor burden of esophageal carcinogenesis. Discussion Our findings provide the first functional investigation of the relationship between EoE and esophageal cancer and suggest that esophageal epithelial remodeling events occurring in response to EoE inflammation may limit esophageal carcinogenesis. This investigation may have future implications for leveraging allergic inflammation-associated alterations in epithelial biology to prevent and/or treat esophageal cancer.
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Affiliation(s)
- Annie D. Fuller
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Adam L. Karami
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Mohammad Faujul Kabir
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Alena Klochkova
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Jazmyne L. Jackson
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Anbin Mu
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Yinfei Tan
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, United States
| | | | - Kelly A. Whelan
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
- Department of Cancer & Cellular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
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13
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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: 1] [Impact Index Per Article: 1.0] [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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14
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Advances in Adrenal and Extra-adrenal Paraganglioma: Practical Synopsis for Pathologists. Adv Anat Pathol 2023; 30:47-57. [PMID: 36136370 DOI: 10.1097/pap.0000000000000365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adrenal paraganglioma (or "pheochromocytoma") and extra-adrenal paraganglioma, collectively abbreviated PPGL, are rare but spectacular nonepithelial neuroendocrine neoplasms. These are the most inheritable neoplasia of all, with a metastatic potential in a varying degree. As of such, these lesions demand careful histologic, immunohistochemical, and genetic characterization to provide the clinical team with a detailed report taking into account the anticipated prognosis and risk of syndromic/inherited disease. While no histologic algorithm, immunohistochemical biomarker, or molecular aberration single-handedly can identify potentially lethal cases upfront, the combined analysis of various risk parameters may stratify PPGL patients more stringently than previously. Moreover, the novel 2022 WHO Classification of Endocrine and Neuroendocrine Tumors also brings some new concepts into play, not least the reclassification of special neuroendocrine neoplasms (cauda equina neuroendocrine tumor and composite gangliocytoma/neuroma-neuroendocrine tumor) previously thought to belong to the spectrum of PPGL. This review focuses on updated key diagnostic and prognostic concepts that will aid when facing this rather enigmatic tumor entity in clinical practice.
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15
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Andreev DE, Niepmann M, Shatsky IN. Elusive Trans-Acting Factors Which Operate with Type I (Poliovirus-like) IRES Elements. Int J Mol Sci 2022; 23:ijms232415497. [PMID: 36555135 PMCID: PMC9778869 DOI: 10.3390/ijms232415497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
The phenomenon of internal initiation of translation was discovered in 1988 on poliovirus mRNA. The prototypic cis-acting element in the 5' untranslated region (5'UTR) of poliovirus mRNA, which is able to direct initiation at an internal start codon without the involvement of a cap structure, has been called an IRES (Internal Ribosome Entry Site or Segment). Despite its early discovery, poliovirus and other related IRES elements of type I are poorly characterized, and it is not yet clear which host proteins (a.k.a. IRES trans-acting factors, ITAFs) are required for their full activity in vivo. Here we discuss recent and old results devoted to type I IRESes and provide evidence that Poly(rC) binding protein 2 (PCBP2), Glycyl-tRNA synthetase (GARS), and Cold Shock Domain Containing E1 (CSDE1, also known as UNR) are major regulators of type I IRES activity.
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Affiliation(s)
- Dmitry E. Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Michael Niepmann
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Ivan N. Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence:
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16
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Malhotra L, Sharma S, Hariprasad G, Dhingra R, Mishra V, Sharma RS, Kaur P, Ethayathulla AS. Mechanism of apoptosis activation by Curcumin rescued mutant p53Y220C in human pancreatic cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119343. [PMID: 36007676 DOI: 10.1016/j.bbamcr.2022.119343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
The mutant p53Y220C (mutp53Y220C) is frequently observed in numerous tumors, including pancreatic cancer. The mutation creates a crevice in the DNA binding core domain and makes p53 a thermally unstable non-functional protein that assists tumor progression and confers resistance to chemotherapeutic drugs. Restoring mutp53 function to its wild type by selectively targeting this crevice with small molecules is a pivotal strategy to promote apoptosis. In this study, we have shown through different biophysical and cell-based studies that curcumin binds and rescues mutp53Y220C to an active wild-type conformation and restores its apoptotic transcription function in BxPC-3-pancreatic cancer cells. In addition, the curcumin-rescued-p53Y220C (CRp53) showed significant hyperphosphorylation at Ser15, Ser20, and acetylation at Lys382 with an 8-fold increase in transcription activity in the BxPC-3 cell lines. We also observed that the active CRp53 escapes Mdm2-mediated proteasomal degradation and the majority of the proteins were localized inside the nucleus with an increased half-life and transcription restoration compared to untreated BxPC-3 cells. By label-free proteomics analysis, we observed that upon curcumin treatment almost 227 proteins were dysregulated with the majority of them being transcriptional targets of p53. Based on our studies, it reflects that apoptosis in pancreatic cancer cells is mediated by curcumin-rescued mutant p53Y220C.
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Affiliation(s)
- Lakshay Malhotra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Saurabh Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Renu Dhingra
- Department of Anatomy, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vandana Mishra
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Radhey S Sharma
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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17
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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: 6] [Impact Index Per Article: 3.0] [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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18
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Belikov AV, Vyatkin AD, Leonov SV. Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients. PeerJ 2022; 10:e13860. [PMID: 35975235 PMCID: PMC9375969 DOI: 10.7717/peerj.13860] [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: 03/23/2022] [Accepted: 07/18/2022] [Indexed: 01/18/2023] Open
Abstract
Background Cancer driver genes are usually ranked by mutation frequency, which does not necessarily reflect their driver strength. We hypothesize that driver strength is higher for genes preferentially mutated in patients with few driver mutations overall, because these few mutations should be strong enough to initiate cancer. Methods We propose formulas for the Driver Strength Index (DSI) and the Normalized Driver Strength Index (NDSI), the latter independent of gene mutation frequency. We validate them using TCGA PanCanAtlas datasets, established driver prediction algorithms and custom computational pipelines integrating SNA, CNA and aneuploidy driver contributions at the patient-level resolution. Results DSI and especially NDSI provide substantially different gene rankings compared to the frequency approach. E.g., NDSI prioritized members of specific protein families, including G proteins GNAQ, GNA11 and GNAS, isocitrate dehydrogenases IDH1 and IDH2, and fibroblast growth factor receptors FGFR2 and FGFR3. KEGG analysis shows that top NDSI-ranked genes comprise EGFR/FGFR2/GNAQ/GNA11-NRAS/HRAS/KRAS-BRAF pathway, AKT1-MTOR pathway, and TCEB1-VHL-HIF1A pathway. Conclusion Our indices are able to select for driver gene attributes not selected by frequency sorting, potentially for driver strength. Genes and pathways prioritized are likely the strongest contributors to cancer initiation and progression and should become future therapeutic targets.
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19
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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: 0.5] [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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20
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LINC01234 Accelerates the Progression of Breast Cancer via the miR-525-5p/Cold Shock Domain-Containing E1 Axis. DISEASE MARKERS 2022; 2022:6899777. [PMID: 35923244 PMCID: PMC9343190 DOI: 10.1155/2022/6899777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/22/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022]
Abstract
Backgrounds. Long noncoding RNAs (lncRNAs) are strongly associated with the development of breast cancer (BC). As yet, the function of LINC01234 in BC remains unknown. Methods. Using biological information, the potential lncRNA, miRNA, and target gene were predicted. LINC01234 and miR-525-5p expression in BC tissues was detected using quantitative real-time reverse transcription polymerase chain reaction. Fluorescence in situ hybridization was used to determine the distribution of LINC01234. Cell proliferation was analyzed using CCK-8 assay, colony formation, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and apoptosis evaluated using flow cytometry. Western blotting was used to evaluate protein expression. Dual-luciferase® reporter, RNA pull-down, and RNA immunoprecipitation assays were performed to analyze the binding relationships among LINC01234, miR-525-5p, and cold shock domain-containing E1 (CSDE1). Results. We screened out LINC01234, found to be significantly increased in BC tissues, associated with a poor prognosis, and positively correlated with tumor size of BC. Knockdown of LINC01234 suppressed BC cell growth and facilitated apoptosis. Dual-luciferase reporter®, RNA pull-down, and RNA immunoprecipitation assays confirmed that LINC01234 and CSDE1 directly interacted with miR-525-5p. Upregulation of miR-525-5p and suppression of CSDE1 inhibited BC cell growth and induced cell apoptosis. Conclusion. Upregulation of LINC01234 contributes to the development of BC through the miR-525-5p/CSDE1 axis. LINC01234 may be one of the potential diagnostic and treatment targets for BC.
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21
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Sobocki BK, Perdyan A, Szot O, Rutkowski J. Management of Pheochromocytomas and Paragangliomas: A Case-Based Review of Clinical Aspects and Perspectives. J Clin Med 2022; 11:jcm11092591. [PMID: 35566714 PMCID: PMC9103340 DOI: 10.3390/jcm11092591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/30/2022] [Accepted: 05/01/2022] [Indexed: 12/12/2022] Open
Abstract
Paraganglioma and pheochromocytoma are rare medical conditions. Thus, there are still a small number of studies, clinical trials, and evidence-based data in this field. This makes clinical decisions more difficult. In this study, we present a case report enriched with a short review of available essential clinical data, indicating the need for constant metoxycatecholamine level observation and a proper diagnostic imaging approach, especially in terms of ongoing pandemics. Our research also provides a summary of the molecular background of these diseases, indicating their future role in clinical management. We analyzed the ClinicalTrials.gov dataset in order to show future perspectives. In this paper, the use of the PET-CT before MRI or CT is proposed in specific cases during diagnosis processes contrary to the guidelines. PET-CT may be as effective as standard procedures and may provide a faster diagnosis, which is important in periods with more difficult access to health care, such as during the COVID-19 pandemic.
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Affiliation(s)
- Bartosz Kamil Sobocki
- Student Scientific Circle of Oncology and Radiotherapy, Medical University of Gdansk, 80-214 Gdansk, Poland;
- Correspondence: (B.K.S.); (J.R.)
| | - Adrian Perdyan
- International Research Agenda 3P Medicine Laboratory, Medical University of Gdansk, 80-210 Gdansk, Poland;
| | - Olga Szot
- Student Scientific Circle of Oncology and Radiotherapy, Medical University of Gdansk, 80-214 Gdansk, Poland;
| | - Jacek Rutkowski
- Department of Oncology and Radiotherapy, Medical University of Gdansk, 80-214 Gdansk, Poland
- Correspondence: (B.K.S.); (J.R.)
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22
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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: 6] [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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23
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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: 2] [Impact Index Per Article: 1.0] [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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24
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Genetics of Pheochromocytomas and Paragangliomas Determine the Therapeutical Approach. Int J Mol Sci 2022; 23:ijms23031450. [PMID: 35163370 PMCID: PMC8836037 DOI: 10.3390/ijms23031450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/06/2023] Open
Abstract
Pheochromocytomas and paragangliomas are the most heritable endocrine tumors. In addition to the inherited mutation other driver mutations have also been identified in tumor tissues. All these genetic alterations are clustered in distinct groups which determine the pathomechanisms. Most of these tumors are benign and their surgical removal will resolve patient management. However, 5–15% of them are malignant and therapeutical possibilities for them are limited. This review provides a brief insight about the tumorigenesis associated with pheochromocytomas/paragangliomas in order to present them as potential therapeutical targets.
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25
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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: 7] [Impact Index Per Article: 3.5] [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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26
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Li L, Khan S, Li S, Wang S, Wang F. Noncoding RNAs: emerging players in skin cancers pathogenesis. Am J Cancer Res 2021; 11:5591-5608. [PMID: 34873482 PMCID: PMC8640824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023] Open
Abstract
Skin malignancies form in tissues of the skin and are the most frequent cancers in the world, with an increasing incidence and a steady fatality rate. They are classified as melanoma or nonmelanoma cancers, which include basal cell carcinoma and squamous cell carcinoma. Noncoding RNA transcripts have received increased attention after the thorough analysis of the human genome revealed that most of the genomic components are not encoded to protein. MicroRNAs, long noncoding RNAs, and circular RNAs are some of the well-studied types of these noncoding regions. The alteration in any of these members' expression is associated intrinsically with human cancers, including skin malignancies, due to their critical functions in cell processes for normal development. As a result, investigating the noncoding component of the transcriptome opens up the possibility of discovering new therapeutic and diagnostic targets. This review discusses current studies on the involvement of microRNAs, long noncoding RNAs, and circular RNAs in the pathogenesis of human skin cancers.
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Affiliation(s)
- Lin Li
- Department of Dermatology, The Affiliated Children’s Hospital of Zhengzhou UniversityZhengzhou 450053, Henan, China
| | - Suliman Khan
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
- Department of Medical Lab Technology, The University of HaripurPakistan
| | - Song Li
- Department of Dermatology, The Affiliated Children’s Hospital of Zhengzhou UniversityZhengzhou 450053, Henan, China
| | - Shengchun Wang
- Department of Dermatology, The Affiliated Children’s Hospital of Zhengzhou UniversityZhengzhou 450053, Henan, China
| | - Fang Wang
- Department of Dermatology, The Affiliated Children’s Hospital of Zhengzhou UniversityZhengzhou 450053, Henan, China
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27
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Gangfuß A, Lochmüller H, Töpf A, O'Heir E, Horvath R, Kölbel H, Schweiger B, Schara-Schmidt U, Roos A. A de novo CSDE1 variant causing neurodevelopmental delay, intellectual disability, neurologic and psychiatric symptoms in a child of consanguineous parents. Am J Med Genet A 2021; 188:283-291. [PMID: 34519148 DOI: 10.1002/ajmg.a.62494] [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: 04/02/2021] [Revised: 07/02/2021] [Accepted: 08/21/2021] [Indexed: 01/02/2023]
Abstract
CSDE1 encodes the cytoplasmic cold shock domain-containing protein E1 (CSDE1), which is highly conserved across species and functions as an RNA-binding protein involved in translationally coupled mRNA turnover. CSDE1 displays a bidirectional role: promoting and repressing the translation of RNAs but also increasing and decreasing the abundance of RNAs. Preclinical studies highlighted an involvement of CSDE1 in different forms of cancer. Moreover, CSDE1 is highly expressed in human embryonic stem cells and plays a role in neuronal migration and differentiation. A genome-wide association study suggested CSDE1 as a potential autism-spectrum disorder risk gene. A multicenter next generation sequencing approach unraveled likely causative heterozygous variants in CSDE1 in 18 patients, identifying a new autism spectrum disorder-related syndrome consisting of autism, intellectual disability, and neurodevelopmental delay. Since then, no further patients with CSDE1 variants have been reported in the literature. Here, we report a 9.5-year-old girl from a consanguineous family of Turkish origin suffering from profound delayed speech and motor development, moderate intellectual disability, neurologic and psychiatric symptoms as well as hypoplasia of corpus callosum and mildly reduced brain volume on brain magnetic resonance imaging associated with a recurrent de novo mutation in CSDE1 (c.367C > T; p.R123*) expanding the phenotypical spectrum associated with pathogenic CSDE1 variants.
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Affiliation(s)
- Andrea Gangfuß
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, University of Ottawa, Ottawa, Canada.,Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.,Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, New-castle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Heike Kölbel
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Bernd Schweiger
- Department of Radiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Andreas Roos
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
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28
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Rao S, Hoskins I, Tonn T, Garcia PD, Ozadam H, Sarinay Cenik E, Cenik C. Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. RNA (NEW YORK, N.Y.) 2021; 27:1025-1045. [PMID: 34127534 PMCID: PMC8370740 DOI: 10.1261/rna.078661.120] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/08/2021] [Indexed: 05/05/2023]
Abstract
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a nonstructural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation levels. We discover that a functionally coherent subset of human genes is preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5' terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5' UTRs from TOP transcripts can drive preferential expression in the presence of Nsp1. Finally, we found that LARP1, a key effector protein in the mTOR pathway, may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine-tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
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Affiliation(s)
- Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - P Daniela Garcia
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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29
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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: 4] [Impact Index Per Article: 1.3] [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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30
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Abstract
Abdominal paragangliomas and pheochromocytomas (PPGLs) are rare neuroendocrine tumors of the infradiaphragmatic paraganglia and adrenal medulla, respectively. Although few pathologists outside of endocrine tertiary centers will ever diagnose such a lesion, the tumors are well known through the medical community-possible due to a combination of the sheer rarity, their often-spectacular presentation due to excess catecholamine secretion as well as their unrivaled coupling to constitutional susceptibility gene mutations and hereditary syndromes. All PPGLs are thought to harbor malignant potential, and therefore pose several challenges to the practicing pathologist. Specifically, a responsible diagnostician should recognize both the capacity and limitations of histological, immunohistochemical, and molecular algorithms to pinpoint high risk for future metastatic disease. This focused review aims to provide the surgical pathologist with a condensed update regarding the current strategies available in order to deliver an accurate prognostication of these enigmatic lesions.
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Affiliation(s)
- C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.
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31
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Rao S, Hoskins I, Tonn T, Garcia PD, Ozadam H, Cenik ES, Cenik C. Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.09.13.295493. [PMID: 32995776 PMCID: PMC7523102 DOI: 10.1101/2020.09.13.295493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5' terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5' UTRs from TOP transcripts can drive preferential expression in the presence of NSP1. Finally, we found that LARP1, a key effector protein in the mTOR pathway may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
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Affiliation(s)
- Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - P. Daniela Garcia
- 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
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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32
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Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions. Nat Genet 2021; 53:729-741. [PMID: 33821006 PMCID: PMC8825242 DOI: 10.1038/s41588-021-00830-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023]
Abstract
The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5' untranslated regions (UTRs) in noncanonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5' UTRs decreased gene expression, and extremely conserved 5' UTRs possess cis-regulatory elements that promote cell-type-specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a new methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5' UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
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Kottke T, Tonne J, Evgin L, Driscoll CB, van Vloten J, Jennings VA, Huff AL, Zell B, Thompson JM, Wongthida P, Pulido J, Schuelke MR, Samson A, Selby P, Ilett E, McNiven M, Roberts LR, Borad MJ, Pandha H, Harrington K, Melcher A, Vile RG. Oncolytic virotherapy induced CSDE1 neo-antigenesis restricts VSV replication but can be targeted by immunotherapy. Nat Commun 2021; 12:1930. [PMID: 33772027 PMCID: PMC7997928 DOI: 10.1038/s41467-021-22115-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/25/2021] [Indexed: 01/06/2023] Open
Abstract
In our clinical trials of oncolytic vesicular stomatitis virus expressing interferon beta (VSV-IFNβ), several patients achieved initial responses followed by aggressive relapse. We show here that VSV-IFNβ-escape tumors predictably express a point-mutated CSDE1P5S form of the RNA-binding Cold Shock Domain-containing E1 protein, which promotes escape as an inhibitor of VSV replication by disrupting viral transcription. Given time, VSV-IFNβ evolves a compensatory mutation in the P/M Inter-Genic Region which rescues replication in CSDE1P5S cells. These data show that CSDE1 is a major cellular co-factor for VSV replication. However, CSDE1P5S also generates a neo-epitope recognized by non-tolerized T cells. We exploit this predictable neo-antigenesis to drive, and trap, tumors into an escape phenotype, which can be ambushed by vaccination against CSDE1P5S, preventing tumor escape. Combining frontline therapy with escape-targeting immunotherapy will be applicable across multiple therapies which drive tumor mutation/evolution and simultaneously generate novel, targetable immunopeptidomes associated with acquired treatment resistance.
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Affiliation(s)
- Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jason Tonne
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura Evgin
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jacob van Vloten
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Victoria A Jennings
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Amanda L Huff
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brady Zell
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jill M Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jose Pulido
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Adel Samson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Peter Selby
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Elizabeth Ilett
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Mark McNiven
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Mitesh J Borad
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Kevin Harrington
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Alan Melcher
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
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A new horizon for the old antibacterial drug clofoctol. Drug Discov Today 2021; 26:1302-1310. [PMID: 33581321 DOI: 10.1016/j.drudis.2021.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/16/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023]
Abstract
The synthetic antibacterial drug clofoctol (CFT) has long been used to treat respiratory tract infections in Europe. In recent years, the drug was found to target two biologically important proteins, the Cdc7/Dbf4 protein kinase complex and the mRNA-binding protein cold shock domain containing E1 (CSDE1), also known as upstream-of-N-Ras protein (UNR). These interactions are at the origin of the antitumor activity of CFT, recently evidenced in prostate cancer and neuroglioma. Drug-protein binding models provide a structural basis to guide the design of more potent anticancer compounds. A renewed interest in CFT can be anticipated for the treatment of cancers, and possibly Coronavirus 2019 (COVID-19).
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Proteomics analysis of human intestinal organoids during hypoxia and reoxygenation as a model to study ischemia-reperfusion injury. Cell Death Dis 2021; 12:95. [PMID: 33462215 PMCID: PMC7813872 DOI: 10.1038/s41419-020-03379-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022]
Abstract
Intestinal ischemia-reperfusion (IR) injury is associated with high mortality rates, which have not improved in the past decades despite advanced insight in its pathophysiology using in vivo animal and human models. The inability to translate previous findings to effective therapies emphasizes the need for a physiologically relevant in vitro model to thoroughly investigate mechanisms of IR-induced epithelial injury and test potential therapies. In this study, we demonstrate the use of human small intestinal organoids to model IR injury by exposing organoids to hypoxia and reoxygenation (HR). A mass-spectrometry-based proteomics approach was applied to characterize organoid differentiation and decipher protein dynamics and molecular mechanisms of IR injury in crypt-like and villus-like human intestinal organoids. We showed successful separation of organoids exhibiting a crypt-like proliferative phenotype, and organoids exhibiting a villus-like phenotype, enriched for enterocytes and goblet cells. Functional enrichment analysis of significantly changing proteins during HR revealed that processes related to mitochondrial metabolism and organization, other metabolic processes, and the immune response were altered in both organoid phenotypes. Changes in protein metabolism, as well as mitophagy pathway and protection against oxidative stress were more pronounced in crypt-like organoids, whereas cellular stress and cell death associated protein changes were more pronounced in villus-like organoids. Profile analysis highlighted several interesting proteins showing a consistent temporal profile during HR in organoids from different origin, such as NDRG1, SDF4 or DMBT1. This study demonstrates that the HR response in human intestinal organoids recapitulates properties of the in vivo IR response. Our findings provide a framework for further investigations to elucidate underlying mechanisms of IR injury in crypt and/or villus separately, and a model to test therapeutics to prevent IR injury.
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Heinemann U, Roske Y. Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. Cancers (Basel) 2021; 13:cancers13020190. [PMID: 33430354 PMCID: PMC7825780 DOI: 10.3390/cancers13020190] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. Abstract The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.
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Pleiotropic roles of cold shock proteins with special emphasis on unexplored cold shock protein member of Plasmodium falciparum. Malar J 2020; 19:382. [PMID: 33109193 PMCID: PMC7592540 DOI: 10.1186/s12936-020-03448-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
The cold shock domain (CSD) forms the hallmark of the cold shock protein family that provides the characteristic feature of binding with nucleic acids. While much of the information is available on bacterial, plants and human cold shock proteins, their existence and functions in the malaria parasite remains undefined. In the present review, the available information on functions of well-characterized cold shock protein members in different organisms has been collected and an attempt was made to identify the presence and role of cold shock proteins in malaria parasite. A single Plasmodium falciparum cold shock protein (PfCoSP) was found in P. falciparum which is reported to be essential for parasite survival. Essentiality of PfCoSP underscores its importance in malaria parasite life cycle. In silico tools were used to predict the features of PfCoSP and to identify its homologues in bacteria, plants, humans, and other Plasmodium species. Modelled structures of PfCoSP and its homologues in Plasmodium species were compared with human cold shock protein 'YBOX-1' (Y-box binding protein 1) that provide important insights into their functioning. PfCoSP model was subjected to docking with B-form DNA and RNA to reveal a number of residues crucial for their interaction. Transcriptome analysis and motifs identified in PfCoSP implicate its role in controlling gene expression at gametocyte, ookinete and asexual blood stages of malaria parasite. Overall, this review emphasizes the functional diversity of the cold shock protein family by discussing their known roles in gene expression regulation, cold acclimation, developmental processes like flowering transition, and flower and seed development, and probable function in gametocytogenesis in case of malaria parasite. This enables readers to view the cold shock protein family comprehensively.
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