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Ren J, Luo S, Shi H, Wang X. Spatial omics advances for in situ RNA biology. Mol Cell 2024:S1097-2765(24)00656-7. [PMID: 39270643 DOI: 10.1016/j.molcel.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/07/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024]
Abstract
Spatial regulation of RNA plays a critical role in gene expression regulation and cellular function. Understanding spatially resolved RNA dynamics and translation is vital for bringing new insights into biological processes such as embryonic development, neurobiology, and disease pathology. This review explores past studies in subcellular, cellular, and tissue-level spatial RNA biology driven by diverse methodologies, ranging from cell fractionation, in situ and proximity labeling, imaging, spatially indexed next-generation sequencing (NGS) approaches, and spatially informed computational modeling. Particularly, recent advances have been made for near-genome-scale profiling of RNA and multimodal biomolecules at high spatial resolution. These methods enabled new discoveries into RNA's spatiotemporal kinetics, RNA processing, translation status, and RNA-protein interactions in cells and tissues. The evolving landscape of experimental and computational strategies reveals the complexity and heterogeneity of spatial RNA biology with subcellular resolution, heralding new avenues for RNA biology research.
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Affiliation(s)
- Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shuchen Luo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hailing Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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2
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Wang S, Liu S, Zhu Y, Zhang B, Yang Y, Li L, Sun Y, Zhang L, Fan L, Hu X, Huang C. A novel and independent survival prognostic model for OSCC: the functions and prognostic values of RNA-binding proteins. Eur Arch Otorhinolaryngol 2024; 281:397-409. [PMID: 37656222 DOI: 10.1007/s00405-023-08200-9] [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: 04/04/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC), exhibiting high morbidity and malignancy, is the most common type of oral cancer. The abnormal expression of RNA-binding proteins (RBPs) plays important roles in the occurrence and progression of cancer. The objective of the present study was to establish a prognostic assessment model of RBPs and to evaluate the prognosis of OSCC patients. METHODS Gene expression data in The Cancer Genome Atlas (TCGA) were analyzed by univariate Cox regression analysis model that established a novel nine RBPs, which were used to build a prognostic risk model. A multivariate Cox proportional regression model and the survival analysis were used to evaluate the prognostic risk model. Moreover, the receive operator curve (ROC) analysis was tested further the efficiency of prognostic risk model based on data from TCGA database and Gene Expression Omnibus (GEO). RESULTS Nine RBPs' signatures (ACO1, G3BP1, NMD3, RNGTT, ZNF385A, SARS, CARS2, YARS and SMAD6) with prognostic value were identified in OSCC patients. Subsequently, the patients were further categorized into high-risk group and low-risk in the overall survival (OS) and disease-free survival (DFS), and external validation dataset. ROC analysis was significant for both the TCGA and GEO. Moreover, GSEA revealed that patients in the high-risk group significantly enriched in many critical pathways correlated with tumorigenesis than the low, including cell cycle, adheres junctions, oocyte meiosis, spliceosome, ERBB signaling pathway and ubiquitin-mediated proteolysis. CONCLUSIONS Collectively, we developed and validated a novel robust nine RBPs for OSCC prognosis prediction. The nine RBPs could serve as an independent and reliable prognostic biomarker and guiding clinical therapy for OSCC patients.
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Affiliation(s)
- Shanshan Wang
- Shenzhen Stomatology Hospital, Shenzhen, 518001, Guangdong, People's Republic of China
| | - Shuang Liu
- Shenzhen Luohu People's Hospital, Shenzhen, 518001, Guangdong, People's Republic of China
| | - Yaomin Zhu
- Shenzhen Stomatology Hospital, Shenzhen, 518001, Guangdong, People's Republic of China
| | - Baorong Zhang
- Department of Stomatology, University of Chinese Academy of Sciences Shenzhen Hospital, Songbai Road 4253, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Yongtao Yang
- Shenzhen Stomatology Hospital, Shenzhen, 518001, Guangdong, People's Republic of China
| | - Limei Li
- Shenzhen Stomatology Hospital, Shenzhen, 518001, Guangdong, People's Republic of China
| | - Yingying Sun
- Shenzhen Stomatology Hospital, Shenzhen, 518001, Guangdong, People's Republic of China
| | - Long Zhang
- Department of Stomatology, University of Chinese Academy of Sciences Shenzhen Hospital, Songbai Road 4253, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Lina Fan
- Department of Stomatology, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, Fujian, China
| | - Xuegang Hu
- Department of Stomatology, University of Chinese Academy of Sciences Shenzhen Hospital, Songbai Road 4253, Shenzhen, 518107, Guangdong, People's Republic of China.
| | - Chunyu Huang
- Department of Stomatology, University of Chinese Academy of Sciences Shenzhen Hospital, Songbai Road 4253, Shenzhen, 518107, Guangdong, People's Republic of China.
- Medical Affairs Department, University of Chinese Academy of Sciences-Shenzhen Hospital, Songbai Road 4253, Shenzhen, 518107, Guangdong, China.
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3
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Salvato I, Ricciardi L, Nucera F, Nigro A, Dal Col J, Monaco F, Caramori G, Stellato C. RNA-Binding Proteins as a Molecular Link between COPD and Lung Cancer. COPD 2023; 20:18-30. [PMID: 36655862 DOI: 10.1080/15412555.2022.2107500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) represents an independent risk factor for lung cancer development. Accelerated cell senescence, induced by oxidative stress and inflammation, is a common pathogenic determinant of both COPD and lung cancer. The post transcriptional regulation of genes involved in these processes is finely regulated by RNA-binding proteins (RBPs), which regulate mRNA turnover, subcellular localization, splicing and translation. Multiple pro-inflammatory mediators (including cytokines, chemokines, proteins, growth factors and others), responsible of lung microenvironment alteration, are regulated by RBPs. Several mouse models have shown the implication of RBPs in multiple mechanisms that sustain chronic inflammation and neoplastic transformation. However, further studies are required to clarify the role of RBPs in the pathogenic mechanisms shared by lung cancer and COPD, in order to identify novel biomarkers and therapeutic targets. This review will therefore focus on the studies collectively indicating the role of RBPs in oxidative stress and chronic inflammation as common pathogenic mechanisms shared by lung cancer and COPD.
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Affiliation(s)
- Ilaria Salvato
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Luca Ricciardi
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Francesco Monaco
- Chirurgia Toracica, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
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Mancarella C, Giusti V, Caldoni G, Laginestra MA, Parra A, Toracchio L, Giordano G, Roncuzzi L, Piazzi M, Blalock W, Columbaro M, De Feo A, Scotlandi K. Extracellular vesicle-associated IGF2BP3 tunes Ewing sarcoma cell migration and affects PI3K/Akt pathway in neighboring cells. Cancer Gene Ther 2023; 30:1285-1295. [PMID: 37353558 PMCID: PMC10501906 DOI: 10.1038/s41417-023-00637-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023]
Abstract
Ewing sarcoma (EWS) is a challenging pediatric cancer characterized by vast intra-tumor heterogeneity. We evaluated the RNA-binding protein IGF2BP3, whose high expression correlates with a poor prognosis and an elevated tendency of metastases, as a possible soluble mediator of inter-cellular communication in EWS. Our data demonstrate that (i) IGF2BP3 is detected in cell supernatants, and it is released inside extracellular vesicles (EVs); (ii) EVs from IGF2BP3-positive or IGF2BP3-negative EWS cells reciprocally affect cell migration but not the proliferation of EWS recipient cells; (iii) EVs derived from IGF2BP3-silenced cells have a distinct miRNA cargo profile and inhibit the PI3K/Akt pathway in recipient cells; (iv) the 11 common differentially expressed miRNAs associated with IGF2BP3-positive and IGF2BP3-negative EVs correctly group IGF2BP3-positive and IGF2BP3-negative clinical tissue specimens. Overall, our data suggest that IGF2BP3 can participate in the modulation of phenotypic heterogeneity.
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Affiliation(s)
- Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Veronica Giusti
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Giulia Caldoni
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | | | - Alessandro Parra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lisa Toracchio
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Giorgia Giordano
- Sarcoma Unit, Candiolo Cancer Institute, FPO, IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Torino, Italy
| | - Laura Roncuzzi
- Biomedical Science and Technologies and Nanobiotechnology Lab, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Piazzi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), Bologna, Italy
- IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - William Blalock
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), Bologna, Italy
- IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Marta Columbaro
- Piattaforma di Microscopia Elettronica, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandra De Feo
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
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Salvato I, Ricciardi L, Dal Col J, Nigro A, Giurato G, Memoli D, Sellitto A, Lamparelli EP, Crescenzi MA, Vitale M, Vatrella A, Nucera F, Brun P, Caicci F, Dama P, Stiff T, Castellano L, Idrees S, Johansen MD, Faiz A, Wark PA, Hansbro PM, Adcock IM, Caramori G, Stellato C. Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation. Front Immunol 2023; 14:1192028. [PMID: 37483631 PMCID: PMC10360199 DOI: 10.3389/fimmu.2023.1192028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss. Results RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3'-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets' steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature was also significantly represented in multiple transcriptomic COPD databases generated from primary HSAEC, from lung tissue and from single-cell RNA-sequencing, displaying a predominant downregulation of expression. Discussion Loss of intracellular AUF-1 may alter posttranscriptional regulation of targets particularly relevant for protection of genomic integrity and gene regulation, thus concurring to airway epithelial inflammatory responses related to oxidative stress and accelerated aging. Exosomal-associated AUF-1 may in turn preserve bound RNA targets and sustain their function, participating to spreading of inflammation and senescence to neighbouring cells.
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Affiliation(s)
- Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Luca Ricciardi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Assunta Sellitto
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Erwin Pavel Lamparelli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Maria Assunta Crescenzi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Monica Vitale
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Paola Dama
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Thomas Stiff
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Leandro Castellano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Alen Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Peter A. Wark
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, London, United Kingdom
| | - Gaetano Caramori
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
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Fu W, Lei X, Lu Q, Zhang J, Guo J, Zhao J, Tong X, Hu X. UBE2K regulated by IGF2BP3 promotes cell proliferation and stemness in pancreatic ductal adenocarcinoma. Int J Oncol 2023; 62:52. [PMID: 36896783 PMCID: PMC10019758 DOI: 10.3892/ijo.2023.5500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/16/2023] [Indexed: 03/11/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a noteworthy malignant carcinoma with an unsatisfactory prognosis attributed to late diagnosis. Ubiquitin‑conjugating enzyme E2K (UBE2K) has been found to serve important roles in a number of diseases. However, its function and the exact molecular mechanism of UBE2K in PDAC remain to be elucidated. The present study discovered that UBE2K was expressed at high levels and indicated the poor prognosis of patients with PDAC. Following this, the CCK‑8, colony formation, and sphere formation assays showed that UBE2K promoted proliferation and the stemness phenotype of PDAC cells in vitro. Evidence from subcutaneous tumor‑bearing nude mice experiments further confirmed that UBE2K enhanced PDAC cell tumorigenesis in vivo. Additionally, the present study demonstrated that insulin‑like growth factor 2 RNA binding protein 3 (IGF2BP3) functioned as an RNA‑binding protein to increase UBE2K expression by enhancing the RNA stability of UBE2K. The knockdown or overexpression of IGF2BP3 could attenuate the change in cells growth induced by the overexpression or knockdown of UBE2K. In summary, the findings indicated the oncogenic roles of UBE2K in PDAC. In addition, IGF2BP3 and UBE2K constitute a functional axis to regulate the malignant progression of PDAC.
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Affiliation(s)
- Wen Fu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Xiangxiang Lei
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Ji Zhang
- Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P.R. China
| | - Jinhui Guo
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Jie Zhao
- Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P.R. China
| | - Xiangmin Tong
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Xiaoge Hu
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
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7
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Voss PG, Wang JL. Liquid-liquid phase separation: Galectin-3 in nuclear speckles and ribonucleoprotein complexes. Exp Cell Res 2023; 427:113571. [PMID: 37003559 DOI: 10.1016/j.yexcr.2023.113571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
Nuclear speckles are subcellular structures originally characterized by punctate immunofluorescence staining of the monoclonal antibody SC35, which recognizes an epitope on SRRM2 (serine/arginine repetitive matrix protein 2) and Sfrs2, a member of the SR (serine/arginine-rich) family of splicing factors. Galectin-3 co-localizes with SC35 in nuclear speckles, which represent one group of nuclear bodies that include the nucleolus, Cajal bodies and gems, paraspeckles, etc. Although they appear to have well-delineated physical boundaries, these nuclear bodies are not membrane-bound structures but represent macromolecular assemblies arising from a phenomenon called liquid-liquid phase separation. There has been much recent interest in liquid phase condensation as a newly recognized mechanism by which a cell can organize and compartmentalize subcellular structures with distinct composition. The punctate/speckled staining of galectin-3 with SC3 demonstrates their co-localization in a phase-separated body in vivo, under conditions endogenous to the cell. The purpose of the present review is to summarize the studies that document three key features of galectin-3 for its localization in liquid phase condensates: (a) an intrinsically disordered domain; (b) oligomer formation for multivalent binding; and (c) association with RNA and ribonucleoprotein complexes.
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Affiliation(s)
- Patricia G Voss
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - John L Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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8
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The mechanism of BUD13 m6A methylation mediated MBNL1-phosphorylation by CDK12 regulating the vasculogenic mimicry in glioblastoma cells. Cell Death Dis 2022; 13:1017. [PMID: 36463205 PMCID: PMC9719550 DOI: 10.1038/s41419-022-05426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 12/04/2022]
Abstract
Vasculogenic mimicry (VM) is an endothelium-independent tumor microcirculation that provides adequate blood supply for tumor growth. The presence of VM greatly hinders the treatment of glioblastoma (GBM) with anti-angiogenic drugs. Therefore, targeting VM formation may be a feasible therapeutic strategy for GBM. The research aimed to evaluate the roles of BUD13, CDK12, MBNL1 in regulating VM formation of GBM. BUD13 and CDK12 were upregulated and MBNL1 was downregulated in GBM tissues and cells. Knockdown of BUD13, CDK12, or overexpression of MBNL1 inhibited GBM VM formation. METTL3 enhanced the stability of BUD13 mRNA and upregulated its expression through m6A methylation. BUD13 enhanced the stability of CDK12 mRNA and upregulated its expression. CDK12 phosphorylated MBNL1, thereby regulating VM formation of GBM. The simultaneous knockdown of BUD13, CDK12, and overexpression of MBNL1 reduced the volume of subcutaneously transplanted tumors in nude mice and prolonged the survival period. Thus, the BUD13/CDK12/MBNL1 axis plays a crucial role in regulating VM formation of GBM and provides a potential target for GBM therapy.
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Nair RR, Pataki E, Gerst JE. Transperons: RNA operons as effectors of coordinated gene expression in eukaryotes. Trends Genet 2022; 38:1217-1227. [PMID: 35934590 DOI: 10.1016/j.tig.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 01/24/2023]
Abstract
Coordinated gene expression allows spatiotemporal control of cellular processes and is achieved by the cotranscription/translation of functionally related genes/proteins. Prokaryotes evolved polycistronic messages (operons) to confer expression from a single promoter to efficiently cotranslate proteins functioning on the same pathway. Yet, despite having far greater diversity (e.g., gene number, distribution, modes of expression), eukaryotic cells employ individual promoters and monocistronic messages. Although gene expression is modular, it does not account for how eukaryotes achieve coordinated localized translation. The RNA operon theory states that mRNAs derived from different chromosomes assemble into ribonucleoprotein particles (RNPs) that act as functional operons to generate protein cohorts upon cotranslation. Work in yeast has now validated this theory and shown that intergenic associations and noncanonical histone functions create pathway-specific RNA operons (transperons) that regulate cell physiology. Herein the involvement of chromatin organization in transperon formation and programmed gene coexpression is discussed.
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Affiliation(s)
- Rohini R Nair
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emese Pataki
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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10
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Bhattacharya S, Zhang M, Hu W, Qi T, Heisterkamp N. Targeting disordered-structured domain interactions in Galectin-3 based on NMR and enhanced MD. Biophys J 2022; 121:4342-4357. [PMID: 36209362 PMCID: PMC9703043 DOI: 10.1016/j.bpj.2022.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/18/2022] [Accepted: 10/06/2022] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are common and important functional domains in many proteins. However, IDRs are difficult to target for drug development due to the lack of defined structures that would facilitate the identification of possible drug-binding pockets. Galectin-3 is a carbohydrate-binding protein of which overexpression has been implicated in a wide variety of disorders, including cancer and inflammation. Apart from its carbohydrate-recognition/binding domain (CRD), Galectin-3 also contains a functionally important disordered N-terminal domain (NTD) that contacts the C-terminal domain (CTD) and could be a target for drug development. To overcome challenges involved in inhibitor design due to lack of structure and the highly dynamic nature of the NTD, we used a protocol combining nuclear magnetic resonance data from recombinant Galectin-3 with accelerated molecular dynamics (MD) simulations. This approach identified a pocket in the CTD with which the NTD makes frequent contact. In accordance with this model, mutation of residues L131 and L203 in this pocket caused loss of Galectin-3 agglutination ability, signifying the functional relevance of the cavity. In silico screening was used to design candidate inhibitory peptides targeting the newly discovered cavity, and experimental testing of only three of these yielded one peptide that inhibits the agglutination promoted by wild-type Galectin-3. NMR experiments further confirmed that this peptide indeed binds to a cavity in the CTD, not within the actual CRD. Our results show that it is possible to apply a combination of MD simulations and NMR experiments to precisely predict the binding interface of a disordered domain with a structured domain, and furthermore use this predicted interface for designing inhibitors. This procedure can potentially be extended to many other targets in which similar IDR interactions play a vital functional role.
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Affiliation(s)
- Supriyo Bhattacharya
- Integrative Genomics Core, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Mingfeng Zhang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, California
| | - Weidong Hu
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California
| | - Tong Qi
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, California
| | - Nora Heisterkamp
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, California.
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11
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Martinelli M, Mancarella C, Scapoli L, Palmieri A, De Sanctis P, Ferrari C, Pasello M, Zucchini C, Scotlandi K. Polymorphic variants of IGF2BP3 and SENCR have an impact on predisposition and/or progression of Ewing sarcoma. Front Oncol 2022; 12:968884. [PMID: 36338681 PMCID: PMC9634078 DOI: 10.3389/fonc.2022.968884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/26/2022] [Indexed: 11/15/2022] Open
Abstract
Ewing sarcoma (EWS), the second most common malignant bone tumor in children and adolescents, occurs abruptly without clear evidence of tumor history or progression. Previous association studies have identified some inherited variants associated with the risk of developing EWS but a common picture of the germline susceptibility to this tumor remains largely unclear. Here, we examine the association between thirty single nucleotide polymorphisms (SNPs) of the IGF2BP3, a gene that codes for an oncofetal RNA-binding protein demonstrated to be important for EWS patient’s risk stratification, and five SNPs of SENCR, a long non-coding RNA shown to regulate IGF2BP3. An association between polymorphisms and EWS susceptibility was observed for three IGF2BP3 SNPs - rs112316332, rs13242065, rs12700421 - and for four SENCR SNPs - rs10893909, rs11221437, rs12420823, rs4526784 -. In addition, IGF2BP3 rs34033684 and SENCR rs10893909 variants increased the risk for female respect to male subgroup when carried together, while IGF2BP3 rs13242065 or rs76983703 variants reduced the probability of a disease later onset (> 14 years). Moreover, the absence of IGF2BP3 rs10488282 variant and the presence of rs199653 or rs35875486 variant were significantly associated with a worse survival in EWS patients with localized disease at diagnosis. Overall, our data provide the first evidence linking genetic variants of IGF2BP3 and its modulator SENCR to the risk of EWS development and to disease progression, thus supporting the concept that heritable factors can influence susceptibility to EWS and may help to predict patient prognosis.
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Affiliation(s)
- Marcella Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- *Correspondence: Marcella Martinelli, ; Katia Scotlandi,
| | - Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luca Scapoli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Annalisa Palmieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Paola De Sanctis
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Cristina Ferrari
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Michela Pasello
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Cinzia Zucchini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- *Correspondence: Marcella Martinelli, ; Katia Scotlandi,
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12
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Whyte SS, Karns R, Min K, Cho J, Lee S, Lake C, Bondoc A, Yoon J, Shin S. Integrated analysis using ToppMiR uncovers altered miRNA- mRNA regulatory networks in pediatric hepatocellular carcinoma-A pilot study. Cancer Rep (Hoboken) 2022; 6:e1685. [PMID: 35859536 PMCID: PMC9875636 DOI: 10.1002/cnr2.1685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pediatric hepatocellular carcinoma (HCC) is a group of liver cancers whose mechanisms behind their pathogenesis and progression are poorly understood. AIM We aimed to identify alterations in the expression of miRNAs and their putative target mRNAs in not only tumor tissues of patients with pediatric HCC but also in corresponding non-tumorous background livers by using liver tissues without underlying liver disease as a control. METHODS AND RESULTS We performed a small-scale miRNA and mRNA profiling of pediatric HCC (consisting of fibrolamellar carcinoma [FLC] and non-FLC HCC) and paired liver tissues to identify miRNAs whose expression levels differed significantly from control livers without underlying liver disease. ToppMiR was used to prioritize both miRNAs and their putative target mRNAs in a gene-annotation network, and the mRNA profile was used to refine the prioritization. Our analysis generated prioritized lists of miRNAs and mRNAs from the following three sets of analyses: (a) pediatric HCC versus control; (b) FLC versus control; and (c) corresponding non-tumorous background liver tissues from the same patients with pediatric HCC versus control. No liver disease liver tissues were used as the control group for all analyses. Many miRNAs whose expressions were deregulated in pediatric HCC were consistent with their roles in adult HCC and/or other non-hepatic cancers. Our gene ontology analysis of target mRNAs revealed enrichment of biological processes related to the sustenance and propagation of cancer and significant downregulation of metabolic processes. CONCLUSION Our pilot study indicates that alterations in miRNA-mRNA networks were detected in not only tumor tissues but also corresponding non-tumorous liver tissues from patients with pediatric HCC, suggesting multi-faceted roles of miRNAs in disease progression. Our results may lead to novel hypotheses for future large-scale studies.
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Affiliation(s)
- Senyo S. Whyte
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology & NutritionCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Kyung‐Won Min
- Department of BiologyGangneung‐Wonju National UniversityGangneungRepublic of Korea
| | - Jung‐Hyun Cho
- Department of Biochemistry and Molecular BiologyMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Sanghoon Lee
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Charissa Lake
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Alexander Bondoc
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA,Department of SurgeryUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Je‐Hyun Yoon
- Department of Biochemistry and Molecular BiologyMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Soona Shin
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA,Department of SurgeryUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
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13
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Bum-Erdene K, Collins PM, Hugo MW, Tarighat SS, Fei F, Kishor C, Leffler H, Nilsson UJ, Groffen J, Grice ID, Heisterkamp N, Blanchard H. Novel Selective Galectin-3 Antagonists Are Cytotoxic to Acute Lymphoblastic Leukemia. J Med Chem 2022; 65:5975-5989. [DOI: 10.1021/acs.jmedchem.1c01296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Khuchtumur Bum-Erdene
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Patrick M. Collins
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Matthew W. Hugo
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Somayeh S. Tarighat
- Section of Molecular Carcinogenesis, Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, California 90027, United States
| | - Fei Fei
- Section of Molecular Carcinogenesis, Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, California 90027, United States
| | - Chandan Kishor
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University, BMC-C1228b, Klinikgatan 28, 221 84 Lund, Sweden
| | - Ulf. J. Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - John Groffen
- Section of Molecular Carcinogenesis, Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, California 90027, United States
| | - I. Darren Grice
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Nora Heisterkamp
- Section of Molecular Carcinogenesis, Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, California 90027, United States
| | - Helen Blanchard
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
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14
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The nano delivery systems and applications of mRNA. Eur J Med Chem 2022; 227:113910. [PMID: 34689071 PMCID: PMC8497955 DOI: 10.1016/j.ejmech.2021.113910] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 02/06/2023]
Abstract
The current COVID-19 epidemic has greatly accelerated the application of mRNA technology to our real world, and during this battle mRNA has proven it's unique advantages compared to traditional biopharmaceutical and vaccine technology. In order to overcome mRNA instability in human physiological environments, mRNA chemical modifications and nano delivery systems are two key factors for their in vivo applications. In this review, we would like to summarize the challenges for clinical translation of mRNA-based therapeutics, with an emphasis on recent advances in innovative materials and delivery strategies. The nano delivery systems include lipid delivery systems (lipid nanoparticles and liposomes), polymer complexes, micelles, cationic peptides and so on. The similarities and differences of lipid nanoparticles and liposomes are also discussed. In addition, this review also present the applications of mRNA to other areas than COVID-19 vaccine, such as infectious diseases, tumors, and cardiovascular disease, for which a variety of candidate vaccines or drugs have entered clinical trials. Furthermore, mRNA was found that it might be used to treat some genetic disease, overcome the immaturity of the immune system due to the small fetal size in utero, treat some neurological diseases that are difficult to be treated surgically, even be used in advancing the translation of iPSC technology et al. In short, mRNA has a wide range of applications, and its era has just begun.
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15
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Tarighat SS, Fei F, Joo EJ, Abdel-Azim H, Yang L, Geng H, Bum-Erdene K, Grice ID, von Itzstein M, Blanchard H, Heisterkamp N. Overcoming Microenvironment-Mediated Chemoprotection through Stromal Galectin-3 Inhibition in Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:12167. [PMID: 34830047 PMCID: PMC8624256 DOI: 10.3390/ijms222212167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Environmentally-mediated drug resistance in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) significantly contributes to relapse. Stromal cells in the bone marrow environment protect leukemia cells by secretion of chemokines as cues for BCP-ALL migration towards, and adhesion to, stroma. Stromal cells and BCP-ALL cells communicate through stromal galectin-3. Here, we investigated the significance of stromal galectin-3 to BCP-ALL cells. We used CRISPR/Cas9 genome editing to ablate galectin-3 in stromal cells and found that galectin-3 is dispensable for steady-state BCP-ALL proliferation and viability. However, efficient leukemia migration and adhesion to stromal cells are significantly dependent on stromal galectin-3. Importantly, the loss of stromal galectin-3 production sensitized BCP-ALL cells to conventional chemotherapy. We therefore tested novel carbohydrate-based small molecule compounds (Cpd14 and Cpd17) with high specificity for galectin-3. Consistent with results obtained using galectin-3-knockout stromal cells, treatment of stromal-BCP-ALL co-cultures inhibited BCP-ALL migration and adhesion. Moreover, these compounds induced anti-leukemic responses in BCP-ALL cells, including a dose-dependent reduction of viability and proliferation, the induction of apoptosis and, importantly, the inhibition of drug resistance. Collectively, these findings indicate galectin-3 regulates BCP-ALL cell responses to chemotherapy through the interactions between leukemia cells and the stroma, and show that a combination of galectin-3 inhibition with conventional drugs can sensitize the leukemia cells to chemotherapy.
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Affiliation(s)
- Somayeh S. Tarighat
- Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.T.); (F.F.); (E.J.J.); (H.A.-A.)
| | - Fei Fei
- Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.T.); (F.F.); (E.J.J.); (H.A.-A.)
| | - Eun Ji Joo
- Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.T.); (F.F.); (E.J.J.); (H.A.-A.)
- Department of Systems Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA;
| | - Hisham Abdel-Azim
- Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.T.); (F.F.); (E.J.J.); (H.A.-A.)
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA;
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA;
| | - Khuchtumur Bum-Erdene
- Institute for Glycomics, Griffith University, Gold Coast, Southport, QLD 4222, Australia; (K.B.-E.); (I.D.G.); (M.v.I.); (H.B.)
| | - I. Darren Grice
- Institute for Glycomics, Griffith University, Gold Coast, Southport, QLD 4222, Australia; (K.B.-E.); (I.D.G.); (M.v.I.); (H.B.)
- School of Medical Science, Griffith University, Gold Coast, Southport, QLD 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast, Southport, QLD 4222, Australia; (K.B.-E.); (I.D.G.); (M.v.I.); (H.B.)
| | - Helen Blanchard
- Institute for Glycomics, Griffith University, Gold Coast, Southport, QLD 4222, Australia; (K.B.-E.); (I.D.G.); (M.v.I.); (H.B.)
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Nora Heisterkamp
- Division of Hematology/Oncology and Bone Marrow Transplant, The Saban Research Institute of Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.T.); (F.F.); (E.J.J.); (H.A.-A.)
- Department of Systems Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA;
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16
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Lin G, Li J, Cai J, Zhang H, Xin Q, Wang N, Xie W, Zhang Y, Xu N. RNA-binding Protein MBNL2 regulates Cancer Cell Metastasis through MiR-182-MBNL2-AKT Pathway. J Cancer 2021; 12:6715-6726. [PMID: 34659561 PMCID: PMC8518006 DOI: 10.7150/jca.62816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
The aberrant expression of RNA-binding proteins (RBPs) plays important roles in the occurrence and progression of cancer. MBNL2 is a member of the RNA binding protein MBNL family that is widely expressed in mammalian cells. We report here that MBNL2 is downregulated in breast, lung and liver cancer tissues, the promoter methylation levels of MBNL2 are higher in cancer tissues than normal tissues. The enrichment analysis of MBNL2 correlated genes indicates the potential function of MBNL2 on cancer progression. MBNL2 regulates cancer cell migration and invasion by modulating PI3K/AKT-mediated epithelial-mesenchymal transition. PI3K/AKT inhibitor overcomes the promotive effect of shMBNL2 on metastasis. The expression of MBNL2 is directly targeted by miR-182. miR-182 is upregulated in breast, lung and liver cancers and has good potential for cancer diagnosis. miR-182 promotes cancer cell migration and invasion by inhibiting the expression of MBNL2. Re-introduction of exogenous MBNL2 reverses the promotive effect of miR-182 on metastasis. Collectively, these findings suggest that MBNL2 plays a tumor suppressive function through miR-182-MBNL2-AKT-EMT signaling pathways.
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Affiliation(s)
- Guanglan Lin
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiao Li
- Department of Neurology, Wuhan Hankou Hospital, Wuhan 430010, China
| | - Jin Cai
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Haowei Zhang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Qilei Xin
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ningchao Wang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Weidong Xie
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yaou Zhang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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17
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Lou S, Meng F, Yin X, Zhang Y, Han B, Xue Y. Comprehensive Characterization of RNA Processing Factors in Gastric Cancer Identifies a Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses. Front Immunol 2021; 12:719628. [PMID: 34413861 PMCID: PMC8369824 DOI: 10.3389/fimmu.2021.719628] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/20/2021] [Indexed: 01/02/2023] Open
Abstract
RNA processing converts primary transcript RNA into mature RNA. Altered RNA processing drives tumor initiation and maintenance, and may generate novel therapeutic opportunities. However, the role of RNA processing factors in gastric cancer (GC) has not been clearly elucidated. This study presents a comprehensive analysis exploring the clinical, molecular, immune, and drug response features underlying the RNA processing factors in GC. This study included 1079 GC cases from The Cancer Genome Atlas (TCGA, training set), our hospital cohort, and two other external validation sets (GSE15459, GSE62254). We developed an RNA processing-related prognostic signature using Cox regression with the least absolute shrinkage and selection operator (LASSO) penalty. The prognostic value of the signature was evaluated using a multiple-method approach. The genetic variants, pathway activation, immune heterogeneity, drug response, and splicing features associated with the risk signature were explored using bioinformatics methods. Among the tested 819 RNA processing genes, we identified five distinct RNA processing patterns with specific clinical outcomes and biological features. A 10-gene RNA processing-related prognostic signature, involving ZBTB7A, METTL2B, CACTIN, TRUB2, POLDIP3, TSEN54, SUGP1, RBMS1, TGFB1, and PWP2, was further identified. The signature was a powerful and robust prognosis factor in both the training and validation datasets. Notably, it could stratify the survival of patients with GC in specific tumor-node-metastasis (TNM) classification subgroups. We constructed a composite prognostic nomogram to facilitate clinical practice by integrating this signature with other clinical variables (TNM stage, age). Patients with low-risk scores were characterized with good clinical outcomes, proliferation, and metabolism hallmarks. Conversely, poor clinical outcome, invasion, and metastasis hallmarks were enriched in the high-risk group. The RNA processing signature was also involved in tumor microenvironment reprogramming and regulating alternative splicing, causing different drug response features between the two risk groups. The low-risk subgroup was characterized by high genomic instability, high alternative splicing and might benefit from the immunotherapy. Our findings highlight the prognostic value of RNA processing factors for patients with GC and provide insights into the specific clinical and molecular features underlying the RNA processing-related signature, which may be important for patient management and targeting treatment.
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Affiliation(s)
- Shenghan Lou
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fanzheng Meng
- Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Xin Yin
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yao Zhang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bangling Han
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yingwei Xue
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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18
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Liu Y, Liu X, Gu Y, Lu H. A novel RNA binding protein-associated prognostic model to predict overall survival in hepatocellular carcinoma patients. Medicine (Baltimore) 2021; 100:e26491. [PMID: 34398005 PMCID: PMC8294901 DOI: 10.1097/md.0000000000026491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is 1 of the deadliest malignancies worldwide. Despite significant advances in diagnosis and treatment, the mortality rate from HCC persists at a substantial level. Construction of a prognostic model that can reliably predict HCC patients' overall survival is urgently needed.Two RNA-seq dataset (the Cancer Genome Atlas and International Cancer Genome Consortium) and 1 microarray dataset (GSE14520) were included in our study. RNA-binding proteins (RBPs) in HCC patients was examined by differentially expressed genes analysis, functional enrichment analysis and protein-protein interaction network analysis. Subsequently, the Cancer Genome Atlas dataset was randomly divided into training and testing cohort with a prognostic model developed in the training cohort. In order to evaluate the prognostic value of the model, a comprehensive survival assessment was conducted.Five RBPs (ribosomal protein L10-like, enhancer of zeste homolog 2 (EZH2), peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A), zinc finger protein 239, interferon-induced protein with tetratricopeptide repeats 1) were used to construct the model. The model accurately predicted the prognosis of liver cancer patients in both the training cohort and validation cohort. HCC patients could be assigned into a high-risk group and a low-risk group by this model, and the overall survival of these 2 groups was significantly different (P < .05). Furthermore, the risk scores obtained by this model were highly correlated with immune cell infiltration.The prognostic model helps to identify HCC patients at high risk of mortality, which optimizes decision-making for individualized treatment.
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Affiliation(s)
- Ye Liu
- Department of Hepatobiliary and Pancreatic, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Xiaohong Liu
- Department of General Surgery, Wuhan University Zhongnan Hospital, Wuhan, China
| | - Yang Gu
- Department of General Surgery, Wuhan University Zhongnan Hospital, Wuhan, China
| | - Haofeng Lu
- Department of Hepatobiliary and Pancreatic, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
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19
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Vincent A, Delacour D, Pigny P. [Galectin-3, an unexpected mediator at the ER-mitochondria negotiating table]. Med Sci (Paris) 2021; 37:569-571. [PMID: 34180809 DOI: 10.1051/medsci/2021066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Audrey Vincent
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U1277 - CANTHER - Cancer heterogeneity plasticity and resistance to therapies, Place de Verdun, 59000 Lille, France
| | - Delphine Delacour
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U1277 - CANTHER - Cancer heterogeneity plasticity and resistance to therapies, Place de Verdun, 59000 Lille, France
| | - Pascal Pigny
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U1277 - CANTHER - Cancer heterogeneity plasticity and resistance to therapies, Place de Verdun, 59000 Lille, France
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20
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Liang Q, Du X, Mao L, Wang G. Molecular characterization of colorectal cancer: A five-gene prognostic signature based on RNA-binding proteins. Saudi J Gastroenterol 2021; 27:223-233. [PMID: 34169901 PMCID: PMC8448017 DOI: 10.4103/sjg.sjg_530_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers worldwide. RNA-binding proteins (RBPs) regulate essential biological processes and play essential roles in a variety of cancers. The present study screened differentially expressed RBPs, analyzed their function and constructed a prognostic model to predict the overall survival of patients with CRC. METHODS We downloaded CRC RNA-sequencing data from the Cancer Genome Atlas (TCGA) portal and screened differentially expressed RBPs. Then, functional analyses of these genes were performed, and a risk model was established by multivariate Cox regression. RESULTS We obtained 132 differentially expressed RBPs, including 66 upregulated and 66 downregulated RBPs. Functional analysis revealed that these genes were significantly enriched in RNA processing, modification and binding, ribosome biogenesis, post-transcriptional regulation, ribonuclease and nuclease activity. Additionally, some RBPs were significantly related to interferon (IFN)-alpha and IFN-beta biosynthetic processes and the Toll-like receptor signaling pathway. A prognostic model was constructed and included insulin like growth factor 2 messenger ribonucleic acid binding protein 3 (IGF2BP3), poly (A) binding protein cytoplasmic 1 like (PABPC1L), peroxisome proliferator activated receptor gamma coactivator 1 alpha (PPARGC1A), peptidyl- transfer ribonucleic acid hydrolase 1 homolog (PTRH1) and tudor domain containing 7 (TDRD7). The model is an independent risk factor for clinicopathological characteristics. CONCLUSION Our study provided novel insights into the pathogenesis of CRC and constructed a prognostic gene model, which may be helpful for determining the prognosis of CRC.
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Affiliation(s)
- Qiankun Liang
- Gansu University of Chinese Medicine, Lanzhou, China,Address for correspondence: Dr. Qiankun Liang, Gansu University of Chinese Medicine, Lanzhou 730020, China. E-mail:
| | - Xiaojuan Du
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Lanfang Mao
- Gansu University of Chinese Medicine, Lanzhou, China,Affiliated Hospital of Gansu University of Chinese Medicine, Lanzhou, China
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21
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Krismer K, Bird MA, Varmeh S, Handly ED, Gattinger A, Bernwinkler T, Anderson DA, Heinzel A, Joughin BA, Kong YW, Cannell IG, Yaffe MB. Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression. Cell Rep 2021; 32:108064. [PMID: 32846122 PMCID: PMC8204639 DOI: 10.1016/j.celrep.2020.108064] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/28/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. Stimulus-induced alterations in RBP function contribute to global changes in gene expression, but identifying which RBPs are responsible for the observed changes remains an unmet need. Here, we present Transite, a computational approach that systematically infers RBPs influencing gene expression through changes in RNA stability and degradation. As a proof of principle, we apply Transite to RNA expression data from human patients with non-small-cell lung cancer whose tumors were sampled at diagnosis or after recurrence following treatment with platinum-based chemotherapy. Transite implicates known RBP regulators of the DNA damage response and identifies hnRNPC as a new modulator of chemotherapeutic resistance, which we subsequently validated experimentally. Transite serves as a framework for the identification of RBPs that drive cell-state transitions and adds additional value to the vast collection of publicly available gene expression datasets. Krismer et al. present a computational approach to identify RNA-binding proteins (RBPs) that modulate post-transcriptional control of gene expression using RNA expression data as inputs. By applying this approach to publicly available patient datasets, they identify and experimentally confirm that the RBP hnRNPC contributes to chemotherapy resistance in lung cancer.
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Affiliation(s)
- Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Molly A Bird
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shohreh Varmeh
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA
| | - Erika D Handly
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Anna Gattinger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Thomas Bernwinkler
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Daniel A Anderson
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Andreas Heinzel
- Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Brian A Joughin
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA.
| | - Ian G Cannell
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Divisions of Acute Care Surgery, Trauma and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.
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Aboughaleb IH, Matboli M, Shawky SM, El-Sharkawy YH. Integration of transcriptomes analysis with spectral signature of total RNA for generation of affordable remote sensing of Hepatocellular carcinoma in serum clinical specimens. Heliyon 2021; 7:e06388. [PMID: 33748469 PMCID: PMC7972971 DOI: 10.1016/j.heliyon.2021.e06388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a major global health problem with about 841,000 new cases and 782,000 deaths annually, due to lacking early biomarker/s, and centralized diagnosis. Transcriptomes research despite its infancy has proved excellence in its implementation in identifying a coherent specific cancer RNAs differential expression. However, results are sometimes overlapped by other cancer types which negatively affecting specificity, plus the high cost of the equipment used. Hyperspectral imaging (HSI) is an advanced tool with unique, spectroscopic features, is an emerging tool that has widely been used in cancer detection. Herein, a pilot study has been performed for HCC diagnosis, by exploiting HIS properties and the analysis of the transcriptome for the development of non-invasive remote HCC sensing. HSI data cube images of the sera extracted total RNA have been analyzed in HCC, normal subject, liver benign tumor, and chronic HCV with cirrhotic/non-cirrhotic liver groups. Data analyses have revealed a specific spectral signature for all groups and can be easily discriminated; at the computed optimum wavelength. Moreover, we have developed a simple setup based on a commercial laser pointer for sample illumination and a Smartphone CCD camera, with HSI consistent data output. We hypothesized that RNA differential expression and its spatial organization/folding are the key players in the obtained spectral signatures. To the best of our knowledge, we are the first to use HSI for sensing cancer based on total RNA in serum, using a Smartphone CCD camera/laser pointer. The proposed biosensor is simple, rapid (2 min), and affordable with specificity and sensitivity of more than 98% and high accuracy.
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Affiliation(s)
| | - Marwa Matboli
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Sherif M. Shawky
- Center of Genomics, Helmy Medical Institute, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 6th of October City, 12578 Giza, Egypt
- Misr University for Science and Technology, Faculty of Pharmacy, Biochemistry Department, Al-Motamayez District. P.O.BOX: 77, 6thOctober City, Giza, Egypt
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Novel Regulators of the IGF System in Cancer. Biomolecules 2021; 11:biom11020273. [PMID: 33673232 PMCID: PMC7918569 DOI: 10.3390/biom11020273] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
The insulin-like growth factor (IGF) system is a dynamic network of proteins, which includes cognate ligands, membrane receptors, ligand binding proteins and functional downstream effectors. It plays a critical role in regulating several important physiological processes including cell growth, metabolism and differentiation. Importantly, alterations in expression levels or activation of components of the IGF network are implicated in many pathological conditions including diabetes, obesity and cancer initiation and progression. In this review we will initially cover some general aspects of IGF action and regulation in cancer and then focus in particular on the role of transcriptional regulators and novel interacting proteins, which functionally contribute in fine tuning IGF1R signaling in several cancer models. A deeper understanding of the biological relevance of this network of IGF1R modulators might provide novel therapeutic opportunities to block this system in neoplasia.
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Sheng C, Chen Z, Lei J, Zhu J, Song S. Development and Multi-Data Set Verification of an RNA Binding Protein Signature for Prognosis Prediction in Glioma. Front Med (Lausanne) 2021; 8:637803. [PMID: 33634155 PMCID: PMC7900154 DOI: 10.3389/fmed.2021.637803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
Objective: Increasing evidence emphasizes the clinical implications of RNA binding proteins (RBPs) in cancers. This study aimed to develop a RBP signature for predicting prognosis in glioma. Methods: Two glioma datasets as training (n = 693) and validation (n = 325) sets were retrieved from the CGGA database. In the training set, univariate Cox regression analysis was conducted to screen prognosis-related RBPs based on differentially expressed RBPs between WHO grade II and IV. A ten-RBP signature was then established. The predictive efficacy was evaluated by ROCs. The applicability was verified in the validation set. The pathways involving the risk scores were analyzed by ssGSEA. scRNA-seq was utilized for evaluating their expression in different glioma cell types. Moreover, their expression was externally validated between glioma and control samples. Results: Based on 39 prognosis-related RBPs, a ten RBP signature was constructed. High risk score distinctly indicated a poorer prognosis than low risk score. AUCs were separately 0.838 and 0.822 in the training and validation sets, suggesting its well performance for prognosis prediction. Following adjustment of other clinicopathological characteristics, the signature was an independent risk factor. Various cancer-related pathways were significantly activated in samples with high risk score. The scRNA-seq identified that risk RBPs were mainly expressed in glioma malignant cells. Their high expression was also found in glioma than control samples. Conclusion: This study developed a novel RBP signature for robustly predicting prognosis of glioma following multi-data set verification. These RBPs may affect the progression of glioma.
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Affiliation(s)
- Chunpeng Sheng
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhihua Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianwei Lei
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianming Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shuxin Song
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Marondedze C. The increasing diversity and complexity of the RNA-binding protein repertoire in plants. Proc Biol Sci 2020; 287:20201397. [PMID: 32962543 PMCID: PMC7542812 DOI: 10.1098/rspb.2020.1397] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Post-transcriptional regulation has far-reaching implications on the fate of RNAs. It is gaining increasing momentum as a critical component in adjusting global cellular transcript levels during development and in response to environmental stresses. In this process, RNA-binding proteins (RBPs) are indispensable chaperones that naturally bind RNA via one or multiple globular RNA-binding domains (RBDs) changing the function or fate of the bound RNAs. Despite the technical challenges faced in plants in large-scale studies, several hundreds of these RBPs have been discovered and elucidated globally over the past few years. Recent discoveries have more than doubled the number of proteins implicated in RNA interaction, including identification of RBPs lacking classical RBDs. This review will discuss these new emerging classes of RBPs, focusing on the current state of the RBP repertoire in Arabidopsis thaliana, including the diverse functional roles derived from quantitative studies implicating RBPs in abiotic stress responses. Notably, this review highlights that 836 RBPs are enriched as Arabidopsis RBPs while 1865 can be classified as candidate RBPs. The review will also outline outstanding areas within this field that require addressing to advance our understanding and potential biotechnological applications of RBPs.
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Affiliation(s)
- C. Marondedze
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
- Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Biochemistry, Midlands State University, P. Bag 9055, Gweru, Zimbabwe
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Abstract
Objective Alternative splicing can generate various structural and functional protein isoforms. Recently, accumulating evidence shows a relationship between alternative splicing and cancer. Cancer is a complex and chronic disease that involves malignant transformation. In this review, we consider alternative splicing events in relation to the hallmarks of cancer cells, and discuss current therapies to treat cancer-related to alternative splicing. Data sources Data cited in this article are from the PubMed and Embase database, primarily focusing on research published from 2000 to 2018. Study selection Articles were selected with the search terms “alternative splicing,” “cancer cell,” “tumor microenvironment,” and “therapy.” Results Alternative splicing plays an important role in tumorigenesis, development, and escape from cell death. Taking this trait of cancer cells into consideration will allow more definite diagnoses of cancer, and allow the development of more effective medicines to intervene in cancer that could focus on controlling alternative splicing or competitively binding to the final products. Conclusions Alternative splicing is common in cancer cells. Consideration of alternative splicing may allow different strategies for cancer therapy or the identification of novel biomarkers for cancer diagnosis.
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MNDA controls the expression of MCL-1 and BCL-2 in chronic lymphocytic leukemia cells. Exp Hematol 2020; 88:68-82.e5. [PMID: 32682001 DOI: 10.1016/j.exphem.2020.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/23/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023]
Abstract
The myeloid nuclear differentiation antigen (MNDA) is a stress-induced protein that promotes degradation of the anti-apoptotic factor MCL-1 and apoptosis in myeloid cells. MNDA is also expressed in normal lymphoid cells and in B-cell clones isolated from individuals with chronic lymphocytic leukemia (CLL), a disease characterized by abnormal apoptosis control. We found that MNDA expression levels inversely correlate with the amount of the anti-apoptotic proteins MCL-1 and BCL-2 in human CLL samples. We report that in response to chemotherapeutic agents that induce genotoxic stress, MNDA exits its typical nucleolar localization and accumulates in the nucleoplasm of CLL and lymphoid cells. Then, MNDA binds chromatin at Mcl1 and Bcl2 genes and affects the transcriptional competence of RNA polymerase II. Our data also reveal that MNDA specifically associates with Mcl1 and Bcl2 (pre-) mRNAs and favors their rapid turnover as a prompt response to genotoxic stress. We propose that this rapid dynamic tuning of RNA levels, which leads to the destabilization of Mcl1 and Bcl2 transcripts, represents a post-transcriptional mechanism of apoptosis control in CLL cells. These results provide an explanation of previous clinical data and corroborate the finding that higher MNDA expression levels in CLL are associated with a better clinical course.
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Mancarella C, Caldoni G, Ribolsi I, Parra A, Manara MC, Mercurio AM, Morrione A, Scotlandi K. Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 Modulates Aggressiveness of Ewing Sarcoma by Regulating the CD164-CXCR4 Axis. Front Oncol 2020; 10:994. [PMID: 32719743 PMCID: PMC7347992 DOI: 10.3389/fonc.2020.00994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Ewing sarcoma (EWS) is the second most common bone and soft tissue-associated malignancy in children and young adults. It is driven by the fusion oncogene EWS/FLI1 and characterized by rapid growth and early metastasis. We have previously discovered that the mRNA binding protein IGF2BP3 constitutes an important biomarker for EWS as high expression of IGF2BP3 in primary tumors predicts poor prognosis of EWS patients. We additionally demonstrated that IGF2BP3 enhances anchorage-independent growth and migration of EWS cells suggesting that IGF2BP3 might work as molecular driver and predictor of EWS progression. The aim of this study was to further define the role of IGF2BP3 in EWS progression. We demonstrated that high IGF2BP3 mRNA expression levels correlated with EWS metastasis and disease progression in well-characterized EWS tumor specimens. EWS tumors with high IGF2BP3 levels were characterized by a specific gene signature enriched in chemokine-mediated signaling pathways. We also discovered that IGF2BP3 regulated the expression of CXCR4 through CD164. Significantly, CD164 and CXCR4 colocalized at the plasma membrane of EWS cells upon CXCL12 stimulation. We further demonstrated that IGF2BP3, CD164, and CXCR4 expression levels correlated in clinical samples and the IGF2BP3/CD164/CXCR4 signaling pathway promoted motility of EWS cells in response to CXCL12 and under hypoxia conditions. The data presented identified CD164 and CXCR4 as novel IGF2BP3 downstream functional effectors indicating that the IGF2BP3/CD164/CXCR4 oncogenic axis may work as critical modulator of EWS aggressiveness. In addition, IGF2BP3, CD164, and CXCR4 expression levels may constitute a novel biomarker panel predictive of EWS progression.
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Affiliation(s)
- Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Giulia Caldoni
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Irene Ribolsi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandro Parra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Maria Cristina Manara
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Arthur M Mercurio
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Andrea Morrione
- Department of Biology, Center for Biotechnology, College of Science and Technology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, United States.,Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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Sending messages in moving cells: mRNA localization and the regulation of cell migration. Essays Biochem 2020; 63:595-606. [PMID: 31324705 DOI: 10.1042/ebc20190009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
Abstract
Cell migration is a fundamental biological process involved in tissue formation and homeostasis. The correct polarization of motile cells is critical to ensure directed movement, and is orchestrated by many intrinsic and extrinsic factors. Of these, the subcellular distribution of mRNAs and the consequent spatial control of translation are key modulators of cell polarity. mRNA transport is dependent on cis-regulatory elements within transcripts, which are recognized by trans-acting proteins that ensure the efficient delivery of certain messages to the leading edge of migrating cells. At their destination, translation of localized mRNAs then participates in regional cellular responses underlying cell motility. In this review, we summarize the key findings that established mRNA targetting as a critical driver of cell migration and how the characterization of polarized mRNAs in motile cells has been expanded from just a few species to hundreds of transcripts. We also describe the molecular control of mRNA trafficking, subsequent mechanisms of local protein synthesis and how these ultimately regulate cell polarity during migration.
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Galectin-3 modulates epithelial cell adaptation to stress at the ER-mitochondria interface. Cell Death Dis 2020; 11:360. [PMID: 32398681 PMCID: PMC7217954 DOI: 10.1038/s41419-020-2556-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022]
Abstract
Cellular stress response contributes to epithelial defense in adaptation to environment changes. Galectins play a pivotal role in the regulation of this response in malignant cells. However, precise underlying mechanisms are largely unknown. Here we demonstrate that Galectin-3, a pro and anti-apoptotic lectin, is required for setting up a correct cellular response to stress by orchestrating several effects. First, Galectin-3 constitutes a key post-transcriptional regulator of stress-related mRNA regulons coordinating the cell metabolism, the mTORC1 complex or the unfolded protein response (UPR). Moreover, we demonstrated the presence of Galectin-3 with mitochondria-associated membranes (MAM), and its interaction with proteins located at the ER or mitochondrial membranes. There Galectin-3 prevents the activation and recruitment at the mitochondria of the regulator of mitochondria fission DRP-1. Accordingly, loss of Galectin-3 impairs mitochondrial morphology, with more fragmented and round mitochondria, and dynamics both in normal and cancer epithelial cells in basal conditions. Importantly, Galectin-3 deficient cells also display changes of the activity of the mitochondrial respiratory chain complexes, of the mTORC1/S6RP/4EBP1 translation pathway and reactive oxygen species levels. Regarding the ER, Galectin-3 did not modify the activities of the 3 branches of the UPR in basal conditions. However, Galectin-3 favours an adaptative UPR following ER stress induction by Thapsigargin treatment. Altogether, at the ER-mitochondria interface, Galectin-3 coordinates the functioning of the ER and mitochondria, preserves the integrity of mitochondrial network and modulates the ER stress response.
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The PABPC5/HCG15/ZNF331 Feedback Loop Regulates Vasculogenic Mimicry of Glioma via STAU1-Mediated mRNA Decay. MOLECULAR THERAPY-ONCOLYTICS 2020; 17:216-231. [PMID: 32346611 PMCID: PMC7183103 DOI: 10.1016/j.omto.2020.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
Glioma is the most common primary malignancy in the brain, and vasculogenic mimicry (VM) is one of the blood supply methods. Here we investigated the possibility that lncRNAs regulate the stability of transcription factors through the SMD pathway, which affects proliferation, migration, invasion, and the ability to form VMs in glioma. Expression of PABPC5, HCG15, and ZNF331 was detected by real-time qPCR or western blot in glioma. Cell Counting Kit-8, Transwell assays, and in vitro VM tube formation were used to investigate PABPC5, HCG15, and ZNF331 function in cell proliferation, migration, invasion, and VM, respectively. ChIP assays were used to ascertain the interaction betweenZNF331 and LAMC2 or PABPC5. PABPC5 and HCG15 were highly expressed in glioma cells. ZNF331 was lowly expressed. PABPC5 bound HCG15 to increase its stability. Knockdown HCG15 reduced the degradation of ZNF331 mRNA by the SMD pathway. ZNF331 inhibited transcription through binding to the promoter region of LAMC2 and PABPC5 and inhibited the ability to form VMs in glioma cells. The PABPC5/HCG15/ZNF331 feedback loop plays an important role in regulating VM formation in glioma and provides new targets for glioma treatment.
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Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. Genes (Basel) 2020; 11:genes11020231. [PMID: 32098200 PMCID: PMC7074383 DOI: 10.3390/genes11020231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
RNA-binding proteins (RBPs) are important regulators of cellular functions, playing critical roles on the survival of bacteria and in the case of pathogens, on their interaction with the host. RBPs are involved in transcriptional, post-transcriptional, and translational processes. However, except for model organisms like Escherichia coli, there is little information about the identification or characterization of RBPs in other bacteria, namely in members of the Burkholderia cepacia complex (Bcc). Bcc is a group of bacterial species associated with a poor clinical prognosis in cystic fibrosis patients. These species have some of the largest bacterial genomes, and except for the presence of two-distinct Hfq-like proteins, their RBP repertoire has not been analyzed so far. Using in silico approaches, we identified 186 conventional putative RBPs in Burkholderia cenocepacia J2315, an epidemic and multidrug resistant pathogen of cystic fibrosis patients. Here we describe the comparative genomics and phylogenetic analysis of RBPs present in multiple copies and predicted to play a role in transcription, protein synthesis, and RNA decay in Bcc bacteria. In addition to the two different Hfq chaperones, five cold shock proteins phylogenetically close to E. coli CspD protein and three distinct RhlE-like helicases could be found in the B. cenocepacia J2315 genome. No RhlB, SrmB, or DeaD helicases could be found in the genomes of these bacteria. These results, together with the multiple copies of other proteins generally involved in RNA degradation, suggest the existence, in B. cenocepacia and in other Bcc bacteria, of some extra and unexplored functions for the mentioned RBPs, as well as of alternative mechanisms involved in RNA regulation and metabolism in these bacteria.
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Mancarella C, Scotlandi K. IGF2BP3 From Physiology to Cancer: Novel Discoveries, Unsolved Issues, and Future Perspectives. Front Cell Dev Biol 2020; 7:363. [PMID: 32010687 PMCID: PMC6974587 DOI: 10.3389/fcell.2019.00363] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/12/2019] [Indexed: 12/24/2022] Open
Abstract
RNA network control is a key aspect of proper cellular homeostasis. In this context, RNA-binding proteins (RBPs) play a major role as regulators of the RNA life cycle due to their capability to bind to RNA sequences and precisely direct nuclear export, translation/degradation rates, and the intracellular localization of their target transcripts. Alterations in RBP expression or functions result in aberrant RNA translation and may drive the emergence and progression of several pathological conditions, including cancer. Among the RBPs, insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) is of particular interest in tumorigenesis and tumor progression. This review highlights the molecular mechanisms underlying the oncogenic functions of IGF2BP3, summarizes the therapeutic potential related to its inhibition and notes the fundamental issues that remain unanswered. To fully exploit IGF2BP3 for tumor diagnosis and therapy, it is crucial to dissect the mechanisms governing IGF2BP3 re-expression and to elucidate the complex interactions between IGF2BP3 and its target mRNAs as normal cells become tumor cells.
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Affiliation(s)
- Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA (NEW YORK, N.Y.) 2019; 25:1337-1352. [PMID: 31296583 PMCID: PMC6800478 DOI: 10.1261/rna.072157.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/27/2019] [Indexed: 05/10/2023]
Abstract
Proteins bind mRNA through their entire life cycle from transcription to degradation. We analyzed c-Myc mRNA protein interactors in vivo using the HyPR-MS method to capture the crosslinked mRNA by hybridization and then analyzed the bound proteins using mass spectrometry proteomics. Using HyPR-MS, 229 c-Myc mRNA-binding proteins were identified, confirming previously proposed interactors, suggesting new interactors, and providing information related to the roles and pathways known to involve c-Myc. We performed structural and functional analysis of these proteins and validated our findings with a combination of RIP-qPCR experiments, in vitro results released in past studies, publicly available RIP- and eCLIP-seq data, and results from software tools for predicting RNA-protein interactions.
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Affiliation(s)
- Michele Spiniello
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Naples 80138, Italy
- Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, Naples 80131, Italy
| | - Maisie I Steinbrink
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TM. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Nucleic Acids Res 2019; 47:8770-8784. [PMID: 31294800 PMCID: PMC7145691 DOI: 10.1093/nar/gkz583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023] Open
Abstract
PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct architecture and comprise a highly conserved subfamily among fungal species. Puf1/Puf2 proteins contain two types of RNA-binding domain: a divergent PUM-HD and an RNA recognition motif (RRM). They recognize RNAs containing UAAU motifs, often in clusters. Here, we report a crystal structure of the PUM-HD of a fungal Puf1 in complex with a dual UAAU motif RNA. Each of the two UAAU tetranucleotides are bound by a Puf1 PUM-HD forming a 2:1 protein-to-RNA complex. We also determined crystal structures of the Puf1 RRM domain that identified a dimerization interface. The PUM-HD and RRM domains act in concert to determine RNA-binding specificity: the PUM-HD dictates binding to UAAU, and dimerization of the RRM domain favors binding to dual UAAU motifs rather than a single UAAU. Cooperative action of the RRM and PUM-HD identifies a new mechanism by which multiple RNA-binding modules in a single protein collaborate to create a unique RNA-binding specificity.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert C Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yoav Arava
- Department of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Correspondence may also be addressed to Marvin Wickens. Tel: +1 608 263 0858; Fax: +1 608 262 9108;
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA,To whom correspondence should be addressed. Tel: +1 984 287 3556; Fax: +1 310 480 3055;
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Karakostis K, Fåhraeus R. Shaping the regulation of the p53 mRNA tumour suppressor: the co-evolution of genetic signatures. BMC Cancer 2019; 19:915. [PMID: 31519161 PMCID: PMC6743176 DOI: 10.1186/s12885-019-6118-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Structured RNA regulatory motifs exist from the prebiotic stages of the RNA world to the more complex eukaryotic systems. In cases where a functional RNA structure is within the coding sequence a selective pressure drives a parallel co-evolution of the RNA structure and the encoded peptide domain. The p53-MDM2 axis, describing the interactions between the p53 tumor suppressor and the MDM2 E3 ubiquitin ligase, serves as particularly useful model revealing how secondary RNA structures have co-evolved along with corresponding interacting protein motifs, thus having an impact on protein - RNA and protein - protein interactions; and how such structures developed signal-dependent regulation in mammalian systems. The p53(BOX-I) RNA sequence binds the C-terminus of MDM2 and controls p53 synthesis while the encoded peptide domain binds MDM2 and controls p53 degradation. The BOX-I peptide domain is also located within p53 transcription activation domain. The folding of the p53 mRNA structure has evolved from temperature-regulated in pre-vertebrates to an ATM kinase signal-dependent pathway in mammalian cells. The protein - protein interaction evolved in vertebrates and became regulated by the same signaling pathway. At the same time the protein - RNA and protein - protein interactions evolved, the p53 trans-activation domain progressed to become integrated into a range of cellular pathways. We discuss how a single synonymous mutation in the BOX-1, the p53(L22 L), observed in a chronic lymphocyte leukaemia patient, prevents the activation of p53 following DNA damage. The concepts analysed and discussed in this review may serve as a conceptual mechanistic paradigm of the co-evolution and function of molecules having roles in cellular regulation, or the aetiology of genetic diseases and how synonymous mutations can affect the encoded protein.
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Affiliation(s)
| | - Robin Fåhraeus
- Université Paris 7, INSERM UMR 1131, 27 Rue Juliette Dodu, 75010 Paris, France
- Department of Medical Biosciences, Umea University, SE-90185 Umea, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
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Chai RC, Li YM, Zhang KN, Chang YZ, Liu YQ, Zhao Z, Wang ZL, Chang YH, Li GZ, Wang KY, Wu F, Wang YZ. RNA processing genes characterize RNA splicing and further stratify lower-grade glioma. JCI Insight 2019; 5:130591. [PMID: 31408440 DOI: 10.1172/jci.insight.130591] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Aberrant expression of RNA processing genes may drive the alterative RNA profile in lower-grade gliomas (LGGs). Thus, we aimed to further stratify LGGs based on the expression of RNA processing genes. METHODS This study included 446 LGGs from The Cancer Genome Atlas (TCGA, training set) and 171 LGGs from the Chinese Glioma Genome Atlas (CGGA, validation set). The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was conducted to develop a risk-signature. The receiver operating characteristic (ROC) curves and Kaplan-Meier curves were used to study the prognosis value of the risk-signature. RESULTS Among the tested 784 RNA processing genes, 276 were significantly correlated with the OS of LGGs. Further LASSO Cox regression identified a 19-gene risk-signature, whose risk score was also an independently prognosis factor (P<0.0001, multiplex Cox regression) in the validation dataset. The signature had better prognostic value than the traditional factors "age", "grade" and "WHO 2016 classification" for 3- and 5-year survival both two datasets (AUCs > 85%). Importantly, the risk-signature could further stratify the survival of LGGs in specific subgroups of WHO 2016 classification. Furthermore, alternative splicing events for genes such as EGFR and FGFR were found to be associated with the risk score. mRNA expression levels for genes, which participated in cell proliferation and other processes, were significantly correlated to the risk score. CONCLUSIONS Our results highlight the role of RNA processing genes for further stratifying the survival of patients with LGGs and provide insight into the alternative splicing events underlying this role.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,China National Clinical Research Center for Neurological Diseases and
| | - Yi-Ming Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yu-Zhou Chang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Zhi-Liang Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yuan-Hao Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,China National Clinical Research Center for Neurological Diseases and.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Masuda K, Kuwano Y. Diverse roles of RNA-binding proteins in cancer traits and their implications in gastrointestinal cancers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1520. [PMID: 30479000 DOI: 10.1002/wrna.1520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023]
Abstract
Gene expression patterns in cancer cells are strongly influenced by posttranscriptional mechanisms. RNA-binding proteins (RBPs) play key roles in posttranscriptional gene regulation; they can interact with target mRNAs in a sequence- and structure-dependent manner, and determine cellular behavior by manipulating the processing of these mRNAs. Numerous RBPs are aberrantly deregulated in many human cancers and hence, affect the functioning of mRNAs that encode proteins, implicated in carcinogenesis. Here, we summarize the key roles of RBPs in posttranscriptional gene regulation, describe RBPs disrupted in cancer, and lastly focus on RBPs that are responsible for implementing cancer traits in the digestive tract. These evidences may reveal a potential link between changes in expression/function of RBPs and malignant transformation, and a framework for new insights and potential therapeutic applications. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kiyoshi Masuda
- Kawasaki Medical School at Kurashiki-City, Okayama, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School at Tokushima-City, Tokushima, Japan
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