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Guha A, Husain MA, Si Y, Nabors LB, Filippova N, Promer G, Smith R, King PH. RNA regulation of inflammatory responses in glia and its potential as a therapeutic target in central nervous system disorders. Glia 2023; 71:485-508. [PMID: 36380708 DOI: 10.1002/glia.24288] [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: 08/17/2022] [Revised: 09/29/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022]
Abstract
A major hallmark of neuroinflammation is the activation of microglia and astrocytes with the induction of inflammatory mediators such as IL-1β, TNF-α, iNOS, and IL-6. Neuroinflammation contributes to disease progression in a plethora of neurological disorders ranging from acute CNS trauma to chronic neurodegenerative disease. Posttranscriptional pathways of mRNA stability and translational efficiency are major drivers for the expression of these inflammatory mediators. A common element in this level of regulation centers around the adenine- and uridine-rich element (ARE) which is present in the 3' untranslated region (UTR) of the mRNAs encoding these inflammatory mediators. (ARE)-binding proteins (AUBPs) such as Human antigen R (HuR), Tristetraprolin (TTP) and KH- type splicing regulatory protein (KSRP) are key nodes for directing these posttranscriptional pathways and either promote (HuR) or suppress (TTP and KSRP) glial production of inflammatory mediators. This review will discuss basic concepts of ARE-mediated RNA regulation and its impact on glial-driven neuroinflammatory diseases. We will discuss strategies to target this novel level of gene regulation for therapeutic effect and review exciting preliminary studies that underscore its potential for treating neurological disorders.
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Affiliation(s)
- Abhishek Guha
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mohammed Amir Husain
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ying Si
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - L Burt Nabors
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Natalia Filippova
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Grace Promer
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Reed Smith
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Peter H King
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Birmingham Department of Veterans Health Care System, Birmingham, Alabama, USA.,Center for Neurodegeneration and Experimental Therapeutics, The University of Alabama at Birmingham, Birmingham, USA
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Two circPPFIA1s negatively regulate liver metastasis of colon cancer via miR-155-5p/CDX1 and HuR/RAB36. Mol Cancer 2022; 21:197. [PMID: 36224588 PMCID: PMC9555114 DOI: 10.1186/s12943-022-01667-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background Circular RNAs (circRNAs) play a critical role in colorectal cancer (CRC) progression, including metastasis. However, the detailed molecular mechanism is not fully understood. Methods Differentially expressed circRNAs between primary KM12C and liver metastatic KM12L4 colon cancer cells were identified by microarray. The expression of circRNAs was measured by semi-quantitative (semi-qPCR) and real time-quantitative PCR (RT-qPCR). Metastatic potential including invasive and migratory abilities, and liver metastasis were examined by transwell assays and intrasplenic injection, respectively. CircPPFIA1-associated microRNA (miRNA) and RNA-binding protein (RBP) were screened by an antisense oligonucleotide (ASO) pulldown experiment. The effects of circPPFIA1 on target gene expression were evaluated by RT-qPCR and western blot analyses. Results By analyzing circRNA microarray data, we identified two anti-metastatic circRNAs generated from PPFIA1 with different length, which named circPPFIA1-L (long) and -S (short). They were significantly downregulated in liver metastatic KM12L4 cells compared to primary KM12C cells. The knockdown of circPPFIA1s in KM12C enhanced metastatic potential and increased liver metastasis. Conversely, overexpression of circPPFIA1s weakened metastatic potential and inhibited liver metastasis. circPPFIA1s were found to function as sponges of oncogenic miR-155-5p and Hu antigen R (HuR) by an ASO pulldown experiment. circPPFIA1s upregulated tumor-suppressing CDX1 expression and conversely downregulated oncogenic RAB36 by decoying miR-155-5p and by sequestering HuR, respectively. Conclusion Our findings demonstrate that circPPFIA1s inhibit the liver metastasis of CRC via the miR-155-5p/CDX1 and HuR/RAB36 pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01667-w.
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Sobolewski C, Dubuquoy L, Legrand N. MicroRNAs, Tristetraprolin Family Members and HuR: A Complex Interplay Controlling Cancer-Related Processes. Cancers (Basel) 2022; 14:cancers14143516. [PMID: 35884580 PMCID: PMC9319505 DOI: 10.3390/cancers14143516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary AU-rich Element Binding Proteins (AUBPs) represent important post-transcriptional regulators of gene expression by regulating mRNA decay and/or translation. Importantly, AUBPs can interfere with microRNA-dependent regulation by (i) competing with the same binding sites on mRNA targets, (ii) sequestering miRNAs, thereby preventing their binding to their specific targets or (iii) promoting miRNA-dependent regulation. These data highlight a new paradigm where both miRNA and RNA binding proteins form a complex regulatory network involved in physiological and pathological processes. However, this interplay is still poorly considered, and our current models do not integrate this level of complexity, thus potentially giving misleading interpretations regarding the role of these regulators in human cancers. This review summarizes the current knowledge regarding the crosstalks existing between HuR, tristetraprolin family members and microRNA-dependent regulation. Abstract MicroRNAs represent the most characterized post-transcriptional regulators of gene expression. Their altered expression importantly contributes to the development of a wide range of metabolic and inflammatory diseases but also cancers. Accordingly, a myriad of studies has suggested novel therapeutic approaches aiming at inhibiting or restoring the expression of miRNAs in human diseases. However, the influence of other trans-acting factors, such as long-noncoding RNAs or RNA-Binding-Proteins, which compete, interfere, or cooperate with miRNAs-dependent functions, indicate that this regulatory mechanism is much more complex than initially thought, thus questioning the current models considering individuals regulators. In this review, we discuss the interplay existing between miRNAs and the AU-Rich Element Binding Proteins (AUBPs), HuR and tristetraprolin family members (TTP, BRF1 and BRF2), which importantly control the fate of mRNA and whose alterations have also been associated with the development of a wide range of chronic disorders and cancers. Deciphering the interplay between these proteins and miRNAs represents an important challenge to fully characterize the post-transcriptional regulation of pro-tumorigenic processes and design new and efficient therapeutic approaches.
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Han W, Fan B, Huang Y, Wang X, Zhang Z, Gu G, Liu Z. Construction and validation of a prognostic model of RNA binding proteins in clear cell renal carcinoma. BMC Nephrol 2022; 23:172. [PMID: 35513791 PMCID: PMC9069774 DOI: 10.1186/s12882-022-02801-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/25/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The dysfunction of RNA binding proteins (RBPs) is associated with various inflammation and cancer. The occurrence and progression of tumors are closely related to the abnormal expression of RBPs. There are few studies on RBPs in clear cell renal carcinoma (ccRCC), which allows us to explore the role of RBPs in ccRCC. METHODS We obtained the gene expression data and clinical data of ccRCC from the Cancer Genome Atlas (TCGA) database and extracted all the information of RBPs. We performed differential expression analysis of RBPs. Risk model were constructed based on the differentially expressed RBPs (DERBPs). The expression levels of model markers were examined by reverse transcription-quantitative PCR (RT-qPCR) and analyzed for model-clinical relevance. Finally, we mapped the model's nomograms to predict the 1, 3 and 5-year survival rates for ccRCC patients. RESULTS The results showed that the five-year survival rate for the high-risk group was 40.2% (95% CI = 0.313 ~ 0.518), while the five-year survival rate for the low-risk group was 84.3% (95% CI = 0.767 ~ 0.926). The ROC curves (AUC = 0.748) also showed that our model had stable predictive power. Further RT-qPCR results were in accordance with our analysis (p < 0.05). The results of the independent prognostic analysis showed that the model could be an independent prognostic factor for ccRCC. The results of the correlation analysis also demonstrated the good predictive ability of the model. CONCLUSION In summary, the 4-RBPs (EZH2, RPL22L1, RNASE2, U2AF1L4) risk model could be used as a prognostic indicator of ccRCC. Our study provides a possibility for predicting the survival of ccRCC.
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Affiliation(s)
- Wenkai Han
- Department of Clinical Medicine, Qingdao University, Qingdao, Shandong, 266000, China
| | - Bohao Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yongshen Huang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiongbao Wang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Zhao Zhang
- Department of Clinical Medicine, Qingdao University, Qingdao, Shandong, 266000, China.,Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Gangli Gu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
| | - Zhao Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
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Zheng Y, Meng XW, Yang JP. Exploring Potential Regulatory Anesthetic Drugs Based on RNA Binding Protein and Constructing CESC Prognosis Model: A Study Based on TCGA Database. Front Surg 2022; 9:823566. [PMID: 35449547 PMCID: PMC9018109 DOI: 10.3389/fsurg.2022.823566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/10/2022] [Indexed: 01/03/2023] Open
Abstract
Objective To investigate the differential expression of RBPs in cervical squamous cell carcinoma (CESC), analyze the regulatory effect of narcotic drugs on RBPs, and establish the prognostic risk model of CESC patients. Methods RNA-SEQ data and clinical case data of cancer and normal samples from CESC patients were obtained from the Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx) database. Differentially expressed RBPs were screened by R language and enriched. The CMAP database is used to predict the anesthetic drugs that regulate the differential expression of RBPs. The prognostic risk score model was constructed by COX regression analysis. Risk score of each CESC patient was calculated and divided into high-risk group and low-risk group according to the median risk score. The prediction efficiency of prognostic risk model was evaluated by Kaplan-Meier (KM) analysis and receiver operating characteristic (ROC) curve, and the correlation between prognostic risk model and clinical characteristics was analyzed. Immunohistochemistry was used to detect the expression of RNASEH2A and HENMT1 in tissues. Results There were 65 differentially expressed RBPs in CESC. Five anesthetics, including benzocaine, procaine, pentoxyverine, and tetracaine were obtained to regulate RBPs. Survival analysis showed that seven genes were related to the prognosis of patients, and the CESC risk score model was constructed by COX regression. The risk score can be used as an independent prognostic factor. RNASEH2A and HENMT1 are up-regulated in tumors, which can effectively distinguish normal tissues from tumor tissues. Conclusion It is found that different anesthetic drugs have different regulatory effects on the differential expression of RBPs. Based on the differentially expressed RBPs, the prognostic risk score model of CESC patients was constructed. To provide ideas for the formulation of individualized precise anesthesia scheme and cancer pain analgesia scheme, which is helpful to improve the perioperative survival rate of cancer patients.
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Assoni G, La Pietra V, Digilio R, Ciani C, Licata NV, Micaelli M, Facen E, Tomaszewska W, Cerofolini L, Pérez-Ràfols A, Varela Rey M, Fragai M, Woodhoo A, Marinelli L, Arosio D, Bonomo I, Provenzani A, Seneci P. HuR-targeted agents: An insight into medicinal chemistry, biophysical, computational studies and pharmacological effects on cancer models. Adv Drug Deliv Rev 2022; 181:114088. [PMID: 34942276 DOI: 10.1016/j.addr.2021.114088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/07/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022]
Abstract
The Human antigen R (HuR) protein is an RNA-binding protein, ubiquitously expressed in human tissues, that orchestrates target RNA maturation and processing both in the nucleus and in the cytoplasm. A survey of known modulators of the RNA-HuR interactions is followed by a description of its structure and molecular mechanism of action - RRM domains, interactions with RNA, dimerization, binding modes with naturally occurring and synthetic HuR inhibitors. Then, the review focuses on HuR as a validated molecular target in oncology and briefly describes its role in inflammation. Namely, we show ample evidence for the involvement of HuR in the hallmarks and enabling characteristics of cancer, reporting findings from in vitro and in vivo studies; and we provide abundant experimental proofs of a beneficial role for the inhibition of HuR-mRNA interactions through silencing (CRISPR, siRNA) or pharmacological inhibition (small molecule HuR inhibitors).
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Affiliation(s)
- Giulia Assoni
- Chemistry Department, University of Milan, Via Golgi 19, I-20133 Milan, Italy; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Valeria La Pietra
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Rosangela Digilio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Caterina Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Nausicaa Valentina Licata
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Mariachiara Micaelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Elisa Facen
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Weronika Tomaszewska
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Anna Pérez-Ràfols
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Marta Varela Rey
- Gene Regulatory Control in Disease Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; Department of Functional Biology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain; Center for Cooperative Research in Biosciences (CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Luciana Marinelli
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "G. Natta" (SCITEC), National Research Council (CNR), Via C. Golgi 19, I-20133 Milan, Italy
| | - Isabelle Bonomo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy.
| | - Pierfausto Seneci
- Chemistry Department, University of Milan, Via Golgi 19, I-20133 Milan, Italy.
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Dolicka D, Foti M, Sobolewski C. The Emerging Role of Stress Granules in Hepatocellular Carcinoma. Int J Mol Sci 2021; 22:ijms22179428. [PMID: 34502337 PMCID: PMC8430939 DOI: 10.3390/ijms22179428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are small membrane-free cytosolic liquid-phase ordered entities in which mRNAs are protected and translationally silenced during cellular adaptation to harmful conditions (e.g., hypoxia, oxidative stress). This function is achieved by structural and functional SG components such as scaffold proteins and RNA-binding proteins controlling the fate of mRNAs. Increasing evidence indicates that the capacity of cells to assemble/disassemble functional SGs may significantly impact the onset and the development of metabolic and inflammatory diseases, as well as cancers. In the liver, the abnormal expression of SG components and formation of SG occur with chronic liver diseases, hepatocellular carcinoma (HCC), and selective hepatic resistance to anti-cancer drugs. Although, the role of SG in these diseases is still debated, the modulation of SG assembly/disassembly or targeting the expression/activity of specific SG components may represent appealing strategies to treat hepatic disorders and potentially cancer. In this review, we discuss our current knowledge about pathophysiological functions of SGs in HCC as well as available molecular tools and drugs capable of modulating SG formation and functions for therapeutic purposes.
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Gong Q, Zhang X, Liang A, Huang S, Tian G, Yuan M, Ke Q, Cai Y, Yan B, Wang J, Wang J. Proteomic screening of potential N-glycoprotein biomarkers for colorectal cancer by TMT labeling combined with LC-MS/MS. Clin Chim Acta 2021; 521:122-130. [PMID: 34242638 DOI: 10.1016/j.cca.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Colorectal cancer (CRC) is part of the most widespread malignant tumors. At present, colonoscopy is a routine procedure in the diagnosis of CRC, but it is traumatic. Carcinoembryonic antigen, CA199, and CA242 are common serum markers for the diagnosis of CRC; however, they do not demonstrate satisfactory specificity and sensitivity for the diagnosis of CRC. Hence, Now it is necessary to screen many valuable serum biomarkers for CRC, proteomics methods have been used to investigate PTMs such as glycosylation of proteins with prominent roles in the occurrence and development of tumors. METHODS This study screens altering glycosylated proteins of CRC tissues using LC-MS/MS quantitative glycoproteomics, and then these candidate biomarkers for CRC are further validated by serum glycoproteomics. RESULTS The results of glycoproteomics in CRC tissues show that the abundance of 160 and 79 glycerogelatin proteins was obviously upregulated and downregulated compared with their adjacent tissues(P < 0.05). Bioinformatics analysis suggests that these molecules are mainly involved in many biological processes, including skeletal system development, collagen fibril organization, and receptor-mediated endocytosis. Results of serum glycoproteomics show that the changing trends of 2 protein glycosylation were consistent with MS results of CRC tissues, including ICAM1and APMAP. Areas under the ROC curve (AUC) results confirm that ICAM1and APMAP as early immune diagnosis markers of CRC has excellent sensitivity and specificity. CONCLUSION The ICAM1 and APMAP may serve as a potential tumor marker for CRC.
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Affiliation(s)
- Qian Gong
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Xiuming Zhang
- Medical Laboratory of Shenzhen Luohu People's Hospital, Shenzhen, PR China
| | - Aifeng Liang
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Sinian Huang
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Guangang Tian
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Mengjiao Yuan
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Qing Ke
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Yijun Cai
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Bin Yan
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China
| | - Jin Wang
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China; Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, PR China.
| | - Jinjin Wang
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai 201700, PR China.
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Integrated Analysis of the Roles of RNA Binding Proteins and Their Prognostic Value in Clear Cell Renal Cell Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5568411. [PMID: 34306592 PMCID: PMC8263288 DOI: 10.1155/2021/5568411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022]
Abstract
Methods We downloaded the RNA sequencing data of ccRCC from the Cancer Genome Atlas (TCGA) database and identified differently expressed RBPs in different tissues. In this study, we used bioinformatics to analyze the expression and prognostic value of RBPs; then, we performed functional analysis and constructed a protein interaction network for them. We also screened out some RBPs related to the prognosis of ccRCC. Finally, based on the identified RBPs, we constructed a prognostic model that can predict patients' risk of illness and survival time. Also, the data in the HPA database were used for verification. Results In our experiment, we obtained 539 ccRCC samples and 72 normal controls. In the subsequent analysis, 87 upregulated RBPs and 38 downregulated RBPs were obtained. In addition, 9 genes related to the prognosis of patients were selected, namely, RPL36A, THOC6, RNASE2, NOVA2, TLR3, PPARGC1A, DARS, LARS2, and U2AF1L4. We further constructed a prognostic model based on these genes and plotted the ROC curve. This ROC curve performed well in judgement and evaluation. A nomogram that can judge the patient's life span is also made. Conclusion In conclusion, we have identified differentially expressed RBPs in ccRCC and carried out a series of in-depth research studies, the results of which may provide ideas for the diagnosis of ccRCC and the research of new targeted drugs.
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Ma Y, Zheng B, Zhang XH, Nie ZY, Yu J, Zhang H, Wang DD, Shi B, Bai Y, Yang Z, Wen JK. circACTA2 mediates Ang II-induced VSMC senescence by modulation of the interaction of ILF3 with CDK4 mRNA. Aging (Albany NY) 2021; 13:11610-11628. [PMID: 33885378 PMCID: PMC8109074 DOI: 10.18632/aging.202855] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 03/13/2021] [Indexed: 04/12/2023]
Abstract
Chronic angiotensin II (Ang II) stimulation induces vascular smooth muscle cell (VSMC) senescence, and circRNAs and members of the ILF3 family are implicated in cellular senescence, but the mechanism underlying regulation of circRNAs and ILF3 by Ang II in VSMCs remains poorly understood. Here, a model of Ang II-induced VSMC senescence and the renal artery of hypertensive patients were used to investigate the roles and mechanisms of circACTA2 and ILF3 in VSMC senescence. We show that circACTA2 expression was elevated in Ang II-stimulated VSMCs and in the vascular walls of hypertensive patients. circACTA2 knockdown largely abrogated Ang II-induced VSMC senescence as shown by decreased p21 expression and increased CDK4 expression as well as by decreased SA β-gal-positive cells. Oligo pull-down and RIP assays revealed that both circACTA2 and CDK4 mRNA could bind with ILF3, and Ang II facilitated circACTA2 association with ILF3 and attenuated ILF3 interaction with CDK4 mRNA. Mechanistically, increased circACTA2 by Ang II reduced ILF3 association with CDK4 mRNA by competing with CDK4 mRNA to bind to ILF3, which decreases CDK4 mRNA stability and protein expression, thus leading to Ang II-induced VSMC senescence. Targeting the circACTA2-ILF3-CDK4 axis may provide a novel therapeutic strategy for VSMC senescence-associated cardiovascular diseases.
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Affiliation(s)
- Ying Ma
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang 050017, China
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Bin Zheng
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang 050017, China
| | - Xin-Hua Zhang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang 050017, China
| | - Zi-Yuan Nie
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Jing Yu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang 050017, China
| | - Hong Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Bei Shi
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Yang Bai
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhan Yang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang 050017, China
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Jin-Kun Wen
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang 050017, China
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Wen X, Shao Z, Chen S, Wang W, Wang Y, Jiang J, Ma Q, Zhang L. Construction of an RNA-Binding Protein-Related Prognostic Model for Pancreatic Adenocarcinoma Based on TCGA and GTEx Databases. Front Genet 2021; 11:610350. [PMID: 33584809 PMCID: PMC7873872 DOI: 10.3389/fgene.2020.610350] [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: 09/28/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
Background: Recently, RNA-binding proteins (RBPs) were reported to interact with target mRNA to regulate gene posttranscriptional expression, and RBP-mediated RNA modification can regulate the expression and function of proto-oncogenes and tumor suppressor genes. We systematically analyzed the expression of RBPs in pancreatic adenocarcinoma (PAAD) and constructed an RBP-associated prognostic risk model. Methods: Gene expression data of normal pancreatic samples as well as PAAD samples were downloaded from TCGA-PAAD and GTEx databases. Wilcoxon test and univariate Cox analysis were, respectively, applied to screen differential expression RBPs (DE-RBPs) and prognostic-associated RBPs (pRBPs). Functional enrichment was analyzed by GO, KEGG, and GSEA. Protein-protein interaction (PPI) network was constructed by STRING online database. Modeling RBPs were selected by multivariate Cox analysis. Kaplan-Meier survival and Cox analysis were applied to evaluate the effects of risk score on the overall survival of PAAD patients. ROC curves and validation cohort were applied to verify the accuracy of the model. Nomogram was applied for predicting 1-, 3-, and 5-year overall survival (OS) of PAAD patients. At last, modeling RBPs were further analyzed to explore their differential expression, prognostic value, as well as enrichment pathways in PAAD. Results: RBPs (453) were differentially expressed in normal and tumor samples, besides, 28 of which were prognostic associated. DE-RBPs (453) are functionally associated with ribosome, ribonuclease, spliceosome, etc. Eight RBPs (PABPC1, PRPF6, OAS1, RBM5, LSM12, IPO7, FXR1, and RBM6) were identified to construct a prognostic risk model. Higher risk score not only predicted poor prognosis but also was an independent poor prognostic indicator, which was verified by ROC curves and validation cohort. Eight modeling RBPs were confirmed to be significantly differentially expressed between normal and tumor samples from RNA and protein level. Besides, all of eight RBPs were related with overall survival of PAAD patients. Conclusions: We successfully constructed an RBP-associated prognostic risk model in PAAD, which has a potential clinical application prospect.
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Affiliation(s)
- Xin Wen
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Zhiying Shao
- Department of Interventional Ultrasound, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Shuyi Chen
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei Wang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yan Wang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Jinghua Jiang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Qinggong Ma
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Longzhen Zhang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Cancer Institute, Xuzhou Medical University, Xuzhou, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou, China
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12
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The Fragile X Mental Retardation Protein Regulates RIPK1 and Colorectal Cancer Resistance to Necroptosis. Cell Mol Gastroenterol Hepatol 2020; 11:639-658. [PMID: 33091622 PMCID: PMC7806864 DOI: 10.1016/j.jcmgh.2020.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND & AIMS The fragile X mental retardation protein (FMRP) affects multiple steps of the mRNA metabolism during brain development and in different neoplastic processes. However, the contribution of FMRP in colon carcinogenesis has not been investigated. METHODS FMR1 mRNA transcript and FMRP protein expression were analyzed in human colon samples derived from patients with sporadic colorectal cancer (CRC) and healthy subjects. We used a well-established mouse model of sporadic CRC induced by azoxymethane to determine the possible role of FMRP in CRC. To address whether FMRP controls cancer cell survival, we analyzed cell death pathway in CRC human epithelial cell lines and in patient-derived colon cancer organoids in presence or absence of a specific FMR1 antisense oligonucleotide or siRNA. RESULTS We document a significant increase of FMRP in human CRC relative to non-tumor tissues. Next, using an inducible mouse model of CRC, we observed a reduction of colonic tumor incidence and size in the Fmr1 knockout mice. The abrogation of FMRP induced spontaneous cell death in human CRC cell lines activating the necroptotic pathway. Indeed, specific immunoprecipitation experiments on human cell lines and CRC samples indicated that FMRP binds receptor-interacting protein kinase 1 (RIPK1) mRNA, suggesting that FMRP acts as a regulator of necroptosis pathway through the surveillance of RIPK1 mRNA metabolism. Treatment of human CRC cell lines and patient-derived colon cancer organoids with the FMR1 antisense resulted in up-regulation of RIPK1. CONCLUSIONS Altogether, these data support a role for FMRP in controlling RIPK1 expression and necroptotic activation in CRC.
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13
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Inhibition of RNA-binding protein HuR reduces glomerulosclerosis in experimental nephritis. Clin Sci (Lond) 2020; 134:1433-1448. [PMID: 32478392 PMCID: PMC8086301 DOI: 10.1042/cs20200193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Abstract
Recent identification of an RNA-binding protein (HuR) that regulates mRNA turnover and translation of numerous transcripts via binding to an ARE in their 3′-UTR involved in inflammation and is abnormally elevated in varied kidney diseases offers a novel target for the treatment of renal inflammation and subsequent fibrosis. Thus, we hypothesized that treatment with a selective inhibition of HuR function with a small molecule, KH-3, would down-regulate HuR-targeted proinflammatory transcripts thereby improving glomerulosclerosis in experimental nephritis, where glomerular cellular HuR is elevated. Three experimental groups included normal and diseased rats treated with or without KH-3. Disease was induced by the monoclonal anti-Thy 1.1 antibody. KH-3 was given via daily intraperitoneal injection from day 1 after disease induction to day 5 at the dose of 50 mg/kg BW/day. At day 6, diseased animals treated with KH-3 showed significant reduction in glomerular HuR levels, proteinuria, podocyte injury determined by ameliorated podocyte loss and podocin expression, glomerular staining for periodic acid-Schiff positive extracellular matrix proteins, fibronectin and collagen IV and mRNA and protein levels of profibrotic markers, compared with untreated disease rats. KH-3 treatment also reduced disease-induced increases in renal TGFβ1 and PAI-1 transcripts. Additionally, a marked increase in renal NF-κB-p65, Nox4, and glomerular macrophage cell infiltration observed in disease control group was largely reversed by KH-3 treatment. These results strongly support our hypothesis that down-regulation of HuR function with KH-3 has therapeutic potential for reversing glomerulosclerosis by reducing abundance of pro-inflammatory transcripts and related inflammation.
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14
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Dolicka D, Sobolewski C, Gjorgjieva M, Correia de Sousa M, Berthou F, De Vito C, Colin DJ, Bejuy O, Fournier M, Maeder C, Blackshear PJ, Rubbia-Brandt L, Foti M. Tristetraprolin Promotes Hepatic Inflammation and Tumor Initiation but Restrains Cancer Progression to Malignancy. Cell Mol Gastroenterol Hepatol 2020; 11:597-621. [PMID: 32987153 PMCID: PMC7806869 DOI: 10.1016/j.jcmgh.2020.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Tristetraprolin (TTP) is a key post-transcriptional regulator of inflammatory and oncogenic transcripts. Accordingly, TTP was reported to act as a tumor suppressor in specific cancers. Herein, we investigated how TTP contributes to the development of liver inflammation and fibrosis, which are key drivers of hepatocarcinogenesis, as well as to the onset and progression of hepatocellular carcinoma (HCC). METHODS TTP expression was investigated in mouse/human models of hepatic metabolic diseases and cancer. The role of TTP in nonalcoholic steatohepatitis and HCC development was further examined through in vivo/vitro approaches using liver-specific TTP knockout mice and a panel of hepatic cancer cells. RESULTS Our data demonstrate that TTP loss in vivo strongly restrains development of hepatic steatosis and inflammation/fibrosis in mice fed a methionine/choline-deficient diet, as well as HCC development induced by the carcinogen diethylnitrosamine. In contrast, low TTP expression fostered migration and invasion capacities of in vitro transformed hepatic cancer cells likely by unleashing expression of key oncogenes previously associated with these cancerous features. Consistent with these data, TTP was significantly down-regulated in high-grade human HCC, a feature further correlating with poor clinical prognosis. Finally, we uncover hepatocyte nuclear factor 4 alpha and early growth response 1, two key transcription factors lost with hepatocyte dedifferentiation, as key regulators of TTP expression. CONCLUSIONS Although TTP importantly contributes to hepatic inflammation and cancer initiation, its loss with hepatocyte dedifferentiation fosters cancer cells migration and invasion. Loss of TTP may represent a clinically relevant biomarker of high-grade HCC associated with poor prognosis.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/immunology
- Carcinogenesis/pathology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Datasets as Topic
- Diethylnitrosamine/administration & dosage
- Diethylnitrosamine/toxicity
- Down-Regulation
- Female
- Gene Expression Regulation, Neoplastic/immunology
- Hepatocytes
- Humans
- Liver/immunology
- Liver/pathology
- Liver Cirrhosis/genetics
- Liver Cirrhosis/immunology
- Liver Cirrhosis/pathology
- Liver Neoplasms/genetics
- Liver Neoplasms/immunology
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Liver Neoplasms, Experimental/chemistry
- Liver Neoplasms, Experimental/genetics
- Liver Neoplasms, Experimental/immunology
- Liver Neoplasms, Experimental/pathology
- Male
- Mice
- Non-alcoholic Fatty Liver Disease
- Primary Cell Culture
- Prognosis
- RNA-Seq
- Survival Analysis
- Tristetraprolin/genetics
- Tristetraprolin/metabolism
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Affiliation(s)
- Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Flavien Berthou
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Claudio De Vito
- Division of Clinical Pathology, University Hospitals, Geneva, Switzerland
| | - Didier J Colin
- Centre for Biomedical Imaging and Preclinical Imaging Platform, University of Geneva, Geneva, Switzerland
| | - Olivia Bejuy
- Centre for Biomedical Imaging and Preclinical Imaging Platform, University of Geneva, Geneva, Switzerland
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Perry J Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Translational Research Centre in Onco-haematology, Faculty of Medicine, University of Geneva, Switzerland.
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15
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mRNA Post-Transcriptional Regulation by AU-Rich Element-Binding Proteins in Liver Inflammation and Cancer. Int J Mol Sci 2020; 21:ijms21186648. [PMID: 32932781 PMCID: PMC7554771 DOI: 10.3390/ijms21186648] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
AU-rich element-binding proteins (AUBPs) represent important post-transcriptional regulators of gene expression. AUBPs can bind to the AU-rich elements present in the 3'-UTR of more than 8% of all mRNAs and are thereby able to control the stability and/or translation of numerous target mRNAs. The regulation of the stability and the translation of mRNA transcripts by AUBPs are highly complex processes that occur through multiple mechanisms depending on the cell type and the cellular context. While AUBPs have been shown to be involved in inflammatory processes and the development of various cancers, their important role and function in the development of chronic metabolic and inflammatory fatty liver diseases (FLDs), as well as in the progression of these disorders toward cancers such as hepatocellular carcinoma (HCC), has recently started to emerge. Alterations of either the expression or activity of AUBPs are indeed significantly associated with FLDs and HCC, and accumulating evidence indicates that several AUBPs are deeply involved in a significant number of cellular processes governing hepatic metabolic disorders, inflammation, fibrosis, and carcinogenesis. Herein, we discuss our current knowledge of the roles and functions of AUBPs in liver diseases and cancer. The relevance of AUBPs as potential biomarkers for different stages of FLD and HCC, or as therapeutic targets for these diseases, are also highlighted.
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16
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Development and validation of a six-RNA binding proteins prognostic signature and candidate drugs for prostate cancer. Genomics 2020; 112:4980-4992. [PMID: 32882325 DOI: 10.1016/j.ygeno.2020.08.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
The dysregulation of RNA binding proteins (RBPs) regulates the progression of several cancers. However, information on the overall functions of RBPs in prostate cancer (PCa) remains largely understudied. Therefore, based on the TCGA dataset, this study identified 144 differentially expressed RBPs in tumors compared to normal tissues. Subsequently, through univariate, LASSO and multivariate Cox regression analysis, 6 RBP genes among them, MSI1, MBNL2, LENG9, REXO2, RNASE1, and PABPC1L were screened as prognostic hub genes and prognostic signature was further identified. Further analysis indicated that the high-risk group was significantly associated with poor RFS, which was validated in the MSKCC cohort. Besides, patients in the high-risk group were closely associated with dysregulation of DNA damage repair pathway, copy number alteration, tumor burden mutation, and low-response to cisplatin (P < 0.001), and bicalutamide (P < 0.001). Using the Connectivity Map, we finally predicted 3 drugs including, ribavirin, carmustine, and carbenoxolone. In summary, we identified six-RBP gene signature and 3 potential drugs against PCa, which might promote the individualized treatment strategies and further improve the quality of life among PCa patients.
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17
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Yan J, Wei R, Li H, Dou Y, Wang J. miR-452-5p and miR-215-5p expression levels in colorectal cancer tissues and their relationship with clinicopathological features. Oncol Lett 2020; 20:2955-2961. [PMID: 32782612 PMCID: PMC7400294 DOI: 10.3892/ol.2020.11845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2020] [Indexed: 01/07/2023] Open
Abstract
The aim of the study was to investigate the expression levels of miR-452-5p and miR-215-5p in colorectal cancer tissues and their relationship with clinicopathological features. A total of 50 specimens of cancerous and adjacent normal tissues were collected from patients with colorectal cancer who underwent surgical resection at the Xingtai People's Hospital from March 2012 to February 2014. All specimens were confirmed by the Department of Pathology. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to measure the expression levels of miR-452-5p and miR-215-5p in cancerous and adjacent normal tissues. Moreover, the relationship of the expression levels of miR-452-5p and miR-215-5p with the clinicopathological features of patients with colorectal cancer was explored. The expression levels of both miR-452-5p and miR-215-5p in colorectal cancer tissues were significantly lower than those in adjacent normal tissues (P<0.05). miR-452-5p expression was related to tumor-node-metastasis (TNM) staging and differentiation degree in colorectal cancer tissues, and the expression of miR-215-5p was associated with TNM staging, lymph node metastasis and infiltration depth (P<0.05). The 5-year overall survival (OS) rate in the miR-452-5p high-expression group was significantly higher than that in the low-expression group (P<0.05). The 5-year OS rates in the miR-215-5p high- and low-expression groups were 53.57% (15/28) and 40.91% (9/22), respectively, indicating that the 5-year OS rate in the miR-215-5p high-expression group was significantly higher than that in the low-expression group. Cox proportional hazards regression model showed that TNM staging, lymph node metastasis, as well as miR-452-5p and miR-215-5p expression levels were independent risk factors affecting colorectal cancer prognosis (P<0.05), whereas the differentiation degree and infiltration depth were not (P>0.05). In conclusion, the expression levels of miR-452-5p and miR-215-5p were significantly downregulated in colorectal cancer tissues promoting the occurrence, progression, invasion and metastasis of colorectal cancer, which suggests that miR-452-5p and miR-215-5p could be used as prognostic indicators for patients with colorectal cancer.
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Affiliation(s)
- Jingbo Yan
- Department of Pathology, Xingtai People's Hospital, Xingtai, Hebei 054031, P.R. China
| | - Ru Wei
- Department of Microbiology and Immunology, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Hui Li
- Department of Surgery, Xingtai People's Hospital, Xingtai, Hebei 054031, P.R. China
| | - Yan Dou
- Department of Pathology, Xingtai People's Hospital, Xingtai, Hebei 054031, P.R. China
| | - Junhui Wang
- Medical Records Room, Xingtai People's Hospital, Xingtai, Hebei 054031, P.R. China
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18
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Chen F, Keleş S. SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins. Genome Biol 2020; 21:139. [PMID: 32532357 PMCID: PMC7291511 DOI: 10.1186/s13059-020-02039-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/08/2020] [Indexed: 01/10/2023] Open
Abstract
Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of data are lacking. We describe SURF, Statistical Utility for RBP Functions, for integrative analysis of large collections of CLIP-seq and RNA-seq data. We demonstrate SURF's ability to accurately detect differential alternative transcriptional regulation events and associate them to local protein-RNA interactions. We apply SURF to ENCODE RBP compendium and carry out downstream analysis with additional reference datasets. The results of this application are browsable at http://www.statlab.wisc.edu/shiny/surf/.
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Affiliation(s)
- Fan Chen
- Department of Statistics, University of Wisconsin-Madison, 1220 Medical Sciences Center, 1300 University Avenue, Madison, 53706 WI USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, 1220 Medical Sciences Center, 1300 University Avenue, Madison, 53706 WI USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, K6/446 Clinical Sciences Center, 600 Highland Avenue, Madison, 53792-4675 WI USA
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19
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Li W, Gao LN, Song PP, You CG. Development and validation of a RNA binding protein-associated prognostic model for lung adenocarcinoma. Aging (Albany NY) 2020; 12:3558-3573. [PMID: 32087603 PMCID: PMC7066909 DOI: 10.18632/aging.102828] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/27/2020] [Indexed: 12/21/2022]
Abstract
RNA binding proteins (RBPs) dysregulation have been reported in various malignant tumors and associated with the occurrence and development of cancer. However, the role of RBPs in lung adenocarcinoma (LUAD) is poorly understood. We downloaded the RNA sequencing data of LUAD from the Cancer Genome Atlas (TCGA) database and determined the differently expressed RBPs between normal and cancer tissues. The study then systemically investigated the expression and prognostic value of these RBPs by a series of bioinformatics analysis. A total of 223 differently expressed RBPs were identified, including 101 up-regulated and 122 down-regulated RBPs. Eight RBPs (IGF2BP1, IFIT1B, PABPC1, TLR8, GAPDH, PIWIL4, RNPC3, and ZC3H12C) were identified as prognosis related hub gene and used to construct a prognostic model. Further analysis indicated that the patients in the high-risk subgroup had poor overall survival(OS) compared to those in low-risk subgroup based on the model. The area under the curve of the time-dependent receiver operator characteristic curve of the prognostic model are 0.775 in TCGA cohort and 0.814 in GSE31210 cohort, confirming a good prognostic model. We also established a nomogram based on eight RBPs mRNA and internal validation in the TCGA cohort, which displayed a favorable discriminating ability for lung adenocarcinoma.
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Affiliation(s)
- Wei Li
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Li-Na Gao
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Pei-Pei Song
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Chong-Ge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
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20
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Li W, Li N, Gao L, You C. Integrated analysis of the roles and prognostic value of RNA binding proteins in lung adenocarcinoma. PeerJ 2020; 8:e8509. [PMID: 32071816 PMCID: PMC7007976 DOI: 10.7717/peerj.8509] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the top cause of carcinoma-associated deaths worldwide. RNA binding proteins (RBPs) dysregulation has been reported in various malignant tumors, and that dysregulation is closely associated with tumorigenesis and tumor progression. However, little is known about the roles of RBPs in lung adenocarcinoma (LUAD). In this study, we downloaded the RNA sequencing data of LUAD from The Cancer Genome Atlas (TCGA) database and determined the differently expressed RBPs between normal and cancer tissues. We then performed an integrative analysis to explore the expression and prognostic significance of these RBPs. A total of 164 differently expressed RBPs were identified, including 40 down-regulated and 124 up-regulated RBPs. Pathway and Gene ontology (GO) analysis indicated that the differently expressed RBPs were mainly related to RNA processing, RNA metabolic process, RNA degradation, RNA transport, splicing, localization, regulation of translation, RNA binding, TGF-beta signaling pathway, mRNA surveillance pathway, and aminoacyl-tRNA biosynthesis. Survival analysis revealed that the high expression of BOP1 or GNL3 or WDR12 or DCAF13 or IGF2BP3 or IGF2BP1 were associated with poor overall survival (OS). Conversely, overexpression of KHDRBS2/SMAD predicted high OS in these patients. ROC curve analysis showed that the eight hub genes with a better diagnostic accuracy to distinguish lung adenocarcinoma. The results provided novel insights into the pathogenesis of LUAD and the development of treatment targets and prognostic molecular markers.
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Affiliation(s)
- Wei Li
- Laboratory Medicine Center, Lanzhou University Second Hospital, Langzhou, China
| | - Na Li
- Department of Pathology, the First Affiliated Hospital of Hunan University of Medicine, Huaihua, China
| | - Lina Gao
- Laboratory Medicine Center, Lanzhou University Second Hospital, Langzhou, China
| | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Langzhou, China
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21
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Inhibition of Caspase-2 Translation by the mRNA Binding Protein HuR: A Novel Path of Therapy Resistance in Colon Carcinoma Cells? Cells 2019; 8:cells8080797. [PMID: 31366165 PMCID: PMC6721497 DOI: 10.3390/cells8080797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/28/2022] Open
Abstract
An increased expression and cytoplasmic abundance of the ubiquitous RNA binding protein human antigen R (HuR) is critically implicated in the dysregulated control of post- transcriptional gene expression during colorectal cancer development and is frequently associated with a high grade of malignancy and therapy resistance. Regardless of the fact that HuR elicits a broad cell survival program by increasing the stability of mRNAs coding for prominent anti-apoptotic factors, recent data suggest that HuR is critically involved in the regulation of translation, particularly, in the internal ribosome entry site (IRES) controlled translation of cell death regulatory proteins. Accordingly, data from human colon carcinoma cells revealed that HuR maintains constitutively reduced protein and activity levels of caspase-2 through negative interference with IRES-mediated translation. This review covers recent advances in the understanding of mechanisms underlying HuR's modulatory activity on IRES-triggered translation. With respect to the unique regulatory features of caspase-2 and its multiple roles (e.g., in DNA-damage-induced apoptosis, cell cycle regulation and maintenance of genomic stability), the pathophysiological consequences of negative caspase-2 regulation by HuR and its impact on therapy resistance of colorectal cancers will be discussed in detail. The negative HuR-caspase-2 axis may offer a novel target for tumor sensitizing therapies.
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