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Wu M, Kong C, Cai M, Huang W, Chen Y, Wang B, Liu X. Hsa_circRNA_002144 promotes growth and metastasis of colorectal cancer through regulating miR-615-5p/LARP1/mTOR pathway. Carcinogenesis 2021; 42:601-610. [PMID: 33347535 PMCID: PMC8086769 DOI: 10.1093/carcin/bgaa140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/16/2022] Open
Abstract
CircRNAs (circular RNAs), recently identified as a critical regulator in tumorigenesis, participate in CRC (colorectal cancer) growth. However, the role of hsa_circRNA_002144 in CRC was poorly understood. Firstly, hsa_circRNA_002144 showed significantly elevation in both of CRC tissues and cell lines, and suggested closely associated with poor prognosis in patients. Secondly, data from functional assays revealed that silence of hsa_circRNA_002144 inhibited CRC progression with reduced cell viability, proliferation, migration and invasion, while enhanced cell apoptosis. In addition, in vivo CRC growth and metastasis were also suppressed by knockdown of hsa_circRNA_002144. However, CRC progression was promoted with over-expression of hsa_circRNA_002144. Thirdly, hsa_circRNA_002144 colocalized with miR-615-5p in the cytoplasm of CRC cells, and decreased miR-615-5p expression. Moreover, miR-615-5p could target LARP1 (La ribonucleoprotein 1, translational regulator). Lastly, the suppressive effects of hsa_circRNA_002144 knockdown on CRC progression were reversed by LARP1 over-expression. In conclusion, hsa_circRNA_002144 could sponge miR-615-5p to promote CRC progression through the regulation of LARP1, providing a therapeutic target for cancer intervention.
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Affiliation(s)
- Mengqiong Wu
- Department of GynecologyXiuying District, Haikou City, Hainan Province, China
| | - Cancan Kong
- Department of Endoscopy CenterXiuying District, Haikou City, Hainan Province, China
| | - Manni Cai
- Department of GastroenterologyXiuying District, Haikou City, Hainan Province, China
| | - Weiwei Huang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
| | - Yiming Chen
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
| | - Baochun Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
| | - Xin Liu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
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Ma Y, Yin S, Liu XF, Hu J, Cai N, Zhang XB, Fu L, Cao XC, Yu Y. Comprehensive Analysis of the Functions and Prognostic Value of RNA-Binding Proteins in Thyroid Cancer. Front Oncol 2021; 11:625007. [PMID: 33816259 PMCID: PMC8010172 DOI: 10.3389/fonc.2021.625007] [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: 11/02/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
RNA binding proteins (RBPs) have been proved to play pivotal roles in a variety types of tumors. However, there is no convincible evidence disclosing the functions of RBPs in thyroid cancer (THCA) thoroughly and systematically. Integrated analysis of the functional and prognostic effect of RBPs help better understanding tumorigenesis and development in thyroid and may provide a novel therapeutic method for THCA. In this study, we obtained a list of human RBPs from Gerstberger database, which covered 1,542 genes encoding RBPs. Gene expression data of THCA was downloaded from The Cancer Genome Atlas (TCGA, n = 567), from which we extracted 1,491 RBPs' gene expression data. We analyzed differentially expressed RBPs using R package "limma". Based on differentially expressed RBPs, we constructed protein-protein interaction network and the GO and KEGG pathway enrichment analyses were carried out. We found six RBPs (AZGP1, IGF2BP2, MEX3A, NUDT16, NUP153, USB1) independently associated with prognosis of patients with thyroid cancer according to univariate and multivariate Cox proportional hazards regression models. The survival analysis and risk score analysis achieved good performances from this six-gene prognostic model. Nomogram was constructed to guide clinical decision in practice. Finally, biological experiments disclosed that NUP153 and USB1 can significantly impact cancer cell proliferation and migration. In conclusion, our research provided a new insight of thyroid tumorigenesis and development based on analyses of RBPs. More importantly, the six-gene model may play an important role in clinical practice in the future.
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Affiliation(s)
- Yue Ma
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Shi Yin
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Xiao-feng Liu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jing Hu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Ning Cai
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-bei Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Anesthesiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Li Fu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Xu-chen Cao
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Yue Yu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
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Qi X, Liu Z, Zhang Q, Yang M, Wan Y, Huang J, Xu L. Systematic analysis of the function and prognostic value of RNA binding proteins in Colon Adenocarcinoma. J Cancer 2021; 12:2537-2549. [PMID: 33854615 PMCID: PMC8040719 DOI: 10.7150/jca.50407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/17/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Abnormal expression of RNA-binding proteins (RBPs) is closely related to tumorigenesis, progression, and prognosis. This study performed systematic bioinformatic analysis of RBPs abnormally expressed in colon adenocarcinoma (COAD) using the Cancer Genome Atlas (TCGA) database to screen prognostic markers and potential therapeutic targets. Methods: First, the gene expression data from COAD samples were used to screen out differentially expressed RBPs for functional enrichment analysis and to visualize interaction relationships. Second, RBPs that were significantly related to prognosis were screened through univariate and multivariate Cox regression analysis to construct a prognostic model. The prediction performance of the prognostic model was evaluated by survival analysis and receiver operating characteristic (ROC) curve analysis. It addition, it was verified in the test cohort. The Human Protein Atlas (HPA) online database was used to verify the expression levels of RBPs in the prognostic model. Results: The study identified 181 differentially expressed RBPs and analyzed their interaction and functional enrichment, which were mainly related to non-coding RNA processing, ribosome biogenesis, RNA metabolic processes, RNA phosphodiester bond hydrolysis, and alternative mRNA splicing. Five RBPs related to prognosis were used to construct a prognostic model, and its predictive ability was verified by the test cohort. ROC curve analysis showed that the prognostic model had good sensitivity and specificity. Independent prognostic analysis showed that risk scores could be used as independent prognostic factors for COAD. Conclusion: This study constructed a reliable prognostic model by analyzing COAD differentially expressed RBPs, facilitating the screening of COAD prognostic markers and therapeutic targets.
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Affiliation(s)
- Xuewei Qi
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zeyu Liu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Qiaoli Zhang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ming Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yuxiang Wan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jinchang Huang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China.,Institute of Acupuncture and Moxibustion in Cancer Care, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lin Xu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
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Shen T, Wang M, Wang X. Identification of Prognosis-related Hub RNA Binding Proteins Function through Regulating Metabolic Processes in Tongue Cancer. J Cancer 2021; 12:2230-2242. [PMID: 33758601 PMCID: PMC7974894 DOI: 10.7150/jca.52156] [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] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
RNA binding proteins (RBPs) are dysregulated and associated with the occurrence and development in various malignant tumors. However, the role of RBPs in tongue cancer are largely unclear. Here, by integrating the differential gene expression analysis and the Weighted Gene Co-expression Network Analysis (WGCNA) of TCGA-retrieved RNA-seq data, we identified a total of 171 differential co-expression RBPs. Then, in a protein-protein interaction (PPI) network containing 134 nodes (RBPs) and 315 network edges (RBP-RBP interacting networks), the top 30 hub RBPs were identified using the CytoHubba plugin of Cytoscape. Furthermore, we investigated the expression and prognostic value of these RBPs and their highly correlated networks. Among them, six RBPs (PGK1, SLC20A1, LEPR, CYP19A1, ZC3H12D, and PFKM) were shown to be the prognosis-related hub RBPs (prhRBPs). Based on these hub RBPs, we constructed a prognostic model and found that the patients in the high-risk group had dramatically poor overall survival compared to those in low-risk group. In addition, we validated the prognostic model in GSE41613, another tongue cancer patient cohort from GEO datasets. The time-dependent receiver operating characteristic (ROC) analysis of the prognostic model further confirmed the predictive capability of the risk model for tongue cancer. As suggested in functional annotation analysis, we found an intensive enrichment of these prhRBPs in metabolic pathways, including AMPK, HIF-1 signaling pathway, Glycolysis, and steroid hormone biosynthesis. Together, our study revealed the underlying role of RBP in tongue cancer biology and potentially unveiled novel targets for cancer therapy.
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Affiliation(s)
- Tao Shen
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Meiting Wang
- College of Liren, Yanshan University, Qinhuangdao, 066004, China.,Department of Neurobiology and Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Xiangting Wang
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
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55
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Li M, Yin B, Chen M, Peng J, Mu X, Deng Z, Xiao J, Li W, Fan J. Downregulation of the lncRNA ASB16-AS1 Decreases LARP1 Expression and Promotes Clear Cell Renal Cell Carcinoma Progression via miR-185-5p/miR-214-3p. Front Oncol 2021; 10:617105. [PMID: 33680937 PMCID: PMC7933513 DOI: 10.3389/fonc.2020.617105] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) comprises approximately 75% of renal cell carcinomas, which is one of the most common and lethal urologic cancers, with poor quality of life for patients and is a huge economic burden to health care systems. It is imperative we find novel prognostic and therapeutic targets for ccRCC clinical intervention. In this study, we found that the expression of the long noncoding RNA (lncRNA) ASB16-AS1 was downregulated in ccRCC tissues compared with non-diseased tissues and was also associated with advanced tumor stage and larger tumors. By constructing cell and mouse models, it was found that downregulated lncRNA ASB16-AS1 enhanced cell proliferation, migration, invasion, and promoted tumor growth and metastasis. Furthermore, by performing bioinformatics analysis, biotinylated RNA pull-downs, AGO2-RIP, and luciferase reporter assays, our findings showed that downregulated ASB16-AS1 decreased La-related protein 1 (LARP1) expression by inhibiting miR-185-5p and miR-214-3p. Furthermore, it was found that overexpression of LARP1 reversed the promotive effects of downregulated ASB16-AS1 on ccRCC cellular progression. Our results revealed that downregulated ASB16-AS1 promotes ccRCC progression via a miR-185-5p-miR-214-3p-LARP1 pathway. We suggest that this pathway could be used to monitor prognosis and presents therapeutic targets for ccRCC clinical management.
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Affiliation(s)
- Mingzi Li
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Bingde Yin
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, China
| | - Mulin Chen
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jingtao Peng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyu Mu
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zhen Deng
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jiantao Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Weiguo Li
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jie Fan
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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56
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Jiang S, Ren X, Liu S, Lu Z, Xu A, Qin C, Wang Z. Integrated Analysis of the Prognosis-Associated RNA-Binding Protein Genes and Candidate Drugs in Renal Papillary Cell Carcinoma. Front Genet 2021; 12:627508. [PMID: 33643390 PMCID: PMC7907657 DOI: 10.3389/fgene.2021.627508] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play significant roles in various cancer types. However, the functions of RBPs have not been clarified in renal papillary cell carcinoma (pRCC). In this study, we identified 31 downregulated and 89 upregulated differentially expressed RBPs on the basis of the cancer genome atlas (TCGA) database and performed functional enrichment analyses. Subsequently, through univariate Cox, random survival forest, and multivariate Cox regression analysis, six RBPs of SNRPN, RRS1, INTS8, RBPMS2, IGF2BP3, and PIH1D2 were screened out, and the prognostic model was then established. Further analyses revealed that the high-risk group had poor overall survival. The area under the curve values were 0.87 and 0.75 at 3 years and 0.78 and 0.69 at 5 years in the training set and test set, respectively. We then plotted a nomogram on the basis of the six RBPs and tumor stage with the substantiation in the TCGA cohort. Moreover, we selected two intersectant RBPs and evaluate their biological effects by GSEA and predicted three drugs, including STOCK1N-28457, pyrimethamine, and trapidil by using the Connectivity Map. Our research provided a novel insight into pRCC and improved the determination of prognosis and individualized therapeutic strategies.
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Affiliation(s)
- Silin Jiang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaohan Ren
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shouyong Liu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhongwen Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Aiming Xu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Bitaraf A, Razmara E, Bakhshinejad B, Yousefi H, Vatanmakanian M, Garshasbi M, Cho WC, Babashah S. The oncogenic and tumor suppressive roles of RNA-binding proteins in human cancers. J Cell Physiol 2021; 236:6200-6224. [PMID: 33559213 DOI: 10.1002/jcp.30311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022]
Abstract
Posttranscriptional regulation is a mechanism for the cells to control gene regulation at the RNA level. In this process, RNA-binding proteins (RBPs) play central roles and orchestrate the function of RNA molecules in multiple steps. Accumulating evidence has shown that the aberrant regulation of RBPs makes contributions to the initiation and progression of tumorigenesis via numerous mechanisms such as genetic changes, epigenetic alterations, and noncoding RNA-mediated regulations. In this article, we review the effects caused by RBPs and their functional diversity in the malignant transformation of cancer cells that occurs through the involvement of these proteins in various stages of RNA regulation including alternative splicing, stability, polyadenylation, localization, and translation. Besides this, we review the various interactions between RBPs and other crucial posttranscriptional regulators such as microRNAs and long noncoding RNAs in the pathogenesis of cancer. Finally, we discuss the potential approaches for targeting RBPs in human cancers.
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Affiliation(s)
- Amirreza Bitaraf
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hassan Yousefi
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, Louisiana, USA
| | - Mousa Vatanmakanian
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, Louisiana, USA
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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He C, Huang F, Zhang K, Wei J, Hu K, Liang M. Establishment and validation of an RNA binding protein-associated prognostic model for ovarian cancer. J Ovarian Res 2021; 14:27. [PMID: 33550985 PMCID: PMC7869493 DOI: 10.1186/s13048-021-00777-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Background Ovarian cancer (OC) is one of the most common gynecological malignant tumors worldwide, with high mortality and a poor prognosis. As the early symptoms of malignant ovarian tumors are not obvious, the cause of the disease is still unclear, and the patients’ postoperative quality of life of decreases. Therefore, early diagnosis is a problem requiring an urgent solution. Methods We obtained the gene expression profiles of ovarian cancer and normal samples from TCGA and GTEx databases for differential expression analysis. From existing literature reports, we acquired the RNA-binding protein (RBP) list for the human species. Utilizing the online tool Starbase, we analyzed the interaction relationship between RBPs and their target genes and selected the modules of RBP target genes through Cytoscape. Finally, univariate and multivariate Cox regression analyses were used to determine the prognostic RBP signature. Results We obtained 527 differentially expressed RBPs, which were involved in many important cellular events, such as RNA splicing, the cell cycle, and so on. We predicted several target genes of RBPs, constructed the interaction network of RBPs and their target genes, and obtained many modules from the Cytoscape analysis. Functional enrichment of RBP target genes also includes these important biological processes. Through Cox regression analysis, OC prognostic RBPs were identified and a 10-RBP model constructed. Further analysis showed that the model has high accuracy and sensitivity in predicting the 3/5-year survival rate. Conclusions Our study identified differentially expressed RBPs and their target genes in OC, and the results promote our understanding of the molecular mechanism of ovarian cancer. The current study could develop novel biomarkers for the diagnosis, treatment, and prognosis of OC and provide new ideas and prospects for future clinical research. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00777-1.
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Affiliation(s)
- Chaofan He
- School of Life Science, Bengbu Medical College, Bengbu, 233030, Anhui, People's Republic of China
| | - Fuxin Huang
- School of Life Science, Bengbu Medical College, Bengbu, 233030, Anhui, People's Republic of China
| | - Kejia Zhang
- School of Life Science, Bengbu Medical College, Bengbu, 233030, Anhui, People's Republic of China
| | - Jun Wei
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, People's Republic of China
| | - Ke Hu
- School of Life Science, Bengbu Medical College, Bengbu, 233030, Anhui, People's Republic of China.
| | - Meng Liang
- School of Life Science, Bengbu Medical College, Bengbu, 233030, Anhui, People's Republic of China.
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Chen J, Li X, Yang L, Zhang J. Long Non-coding RNA LINC01969 Promotes Ovarian Cancer by Regulating the miR-144-5p/LARP1 Axis as a Competing Endogenous RNA. Front Cell Dev Biol 2021; 8:625730. [PMID: 33614632 PMCID: PMC7889973 DOI: 10.3389/fcell.2020.625730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022] Open
Abstract
Accumulating evidence has shown that long non-coding RNAs (lncRNAs) can be used as biological markers and treatment targets in cancer and play various roles in cancer-related biological processes. However, the lncRNA expression profiles and their roles and action mechanisms in ovarian cancer (OC) are largely unknown. Here, we assessed the lncRNA expression profiles in OC tissues from The Cancer Genome Atlas (TCGA) database, and one upregulated lncRNA, LINC01969, was selected for further study. LINC01969 expression levels in 41 patients were verified using quantitative real-time polymerase chain reaction (qRT-PCR). The in vitro effects of LINC01969 on OC cell migration, invasion, and proliferation were determined by the CCK-8, ethynyl-2-deoxyuridine (EdU), wound healing, and Transwell assays. Epithelial–mesenchymal transition (EMT) was evaluated using qRT-PCR and Western blotting. The molecular mechanisms of LINC01969 in OC were assessed through bioinformatics analysis, RNA-binding protein immunoprecipitation (RIP), dual luciferase reporter gene assays, and a rescue experiment. Finally, in vivo experiments were conducted to evaluate the functions of LINC01969. The results of the current study showed that LINC01969 was dramatically upregulated in OC, and patients with lower LINC01969 expression levels tended to have better overall survival. Further experiments demonstrated that LINC01969 promoted the migration, invasion, and proliferation of OC cells in vitro and sped up tumor growth in vivo. Additionally, LINC01969, which primarily exists in the cytoplasm, boosted LARP1 expression by sponging miR-144-5p and promoted the malignant phenotypes of OC cells. In conclusion, the LINC01969/miR-144-5p/LARP1 axis is a newly identified regulatory signaling pathway involved in OC progression.
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Affiliation(s)
- Jinxin Chen
- Department of Gynecology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Xiaocen Li
- Department of Graduate School, Dalian Medical University, Dalian, China
| | - Lu Yang
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Jingru Zhang
- Department of Gynecology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
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Berman AJ, Thoreen CC, Dedeic Z, Chettle J, Roux PP, Blagden SP. Controversies around the function of LARP1. RNA Biol 2021; 18:207-217. [PMID: 32233986 PMCID: PMC7928164 DOI: 10.1080/15476286.2020.1733787] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
The RNA-binding protein LARP1 has generated interest in recent years for its role in the mTOR signalling cascade and its regulation of terminal oligopyrimidine (TOP) mRNA translation. Paradoxically, some scientists have shown that LARP1 represses TOP translation while others that LARP1 activates it. Here, we present opinions from four leading scientists in the field to discuss these and other contradictory findings.
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Affiliation(s)
- Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, USA
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, USA
| | - Zinaida Dedeic
- Department of Oncology, University of Oxford, Oxford, UK
| | - James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université De Montréal, Montreal, Quebec, Canada
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Mattijssen S, Kozlov G, Gaidamakov S, Ranjan A, Fonseca BD, Gehring K, Maraia RJ. The isolated La-module of LARP1 mediates 3' poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1. RNA Biol 2021; 18:275-289. [PMID: 33292040 PMCID: PMC7928023 DOI: 10.1080/15476286.2020.1860376] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activity in a specific aspect of RNA metabolism. The La-modules vary among the LARPs in linker length and RRM subtype. The La-modules of La protein and LARP7 bind and protect nuclear RNAs with UUU-3' tails from degradation by 3' exonucleases. LARP4 is an mRNA poly(A) stabilization factor that binds poly(A) and the cytoplasmic poly(A)-binding protein PABPC1 (also known as PABP). LARP1 exhibits poly(A) length protection and mRNA stabilization similar to LARP4. Here, we show that these LARP1 activities are mediated by its La-module and dependent on a PAM2 motif that binds PABP. The isolated La-module of LARP1 is sufficient for PABP-dependent poly(A) length protection and mRNA stabilization in HEK293 cells. A point mutation in the PAM2 motif in the La-module impairs mRNA stabilization and PABP binding in vivo but does not impair oligo(A) RNA binding by the purified recombinant La-module in vitro. We characterize the unusual PAM2 sequence of LARP1 and show it may differentially affect stable and unstable mRNAs. The unique LARP1 La-module can function as an autonomous factor to confer poly(A) protection and stabilization to heterologous mRNAs.
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Affiliation(s)
- Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Amitabh Ranjan
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA
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62
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Schwenzer H, Abdel Mouti M, Neubert P, Morris J, Stockton J, Bonham S, Fellermeyer M, Chettle J, Fischer R, Beggs AD, Blagden SP. LARP1 isoform expression in human cancer cell lines. RNA Biol 2021; 18:237-247. [PMID: 32286153 PMCID: PMC7928056 DOI: 10.1080/15476286.2020.1744320] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/09/2020] [Accepted: 03/14/2020] [Indexed: 01/07/2023] Open
Abstract
LARP1 is an oncogenic RNA-binding protein required for ribosome biogenesis and cancer cell survival. From published in vitro studies, there is disparity over which of two different LARP1 protein isoforms (termed the long LI-LARP1 and short SI-LARP1) is the canonical. Here, after conducting a series of biochemical and cellular assays, we conclude that LI-LARP1 (NM_033551.3 > NP_056130.2) is the dominantly expressed form. We observe that SI-LARP1 (NM_015315.5> NP_056130.2) is epigenetically repressed and that this repression is evolutionarily conserved in all but a small subclade of mammalian species. As with other LARP family members, there are multiple potential LARP1 mRNA isoforms that appear to be censored within the nucleus. The capacity of the cell to modulate splicing and expression of these apparently 'redundant' mRNAs hints at contextually specific mechanisms of LARP1 expression.
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Affiliation(s)
| | | | - Pia Neubert
- Department of Oncology, University of Oxford, Oxford, UK
| | | | - Joanne Stockton
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew D. Beggs
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
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63
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Werneck-de-Castro JP, Peçanha FLM, Silvestre DH, Bernal-Mizrachi E. The RNA-binding protein LARP1 is dispensable for pancreatic β-cell function and mass. Sci Rep 2021; 11:2079. [PMID: 33483593 PMCID: PMC7822907 DOI: 10.1038/s41598-021-81457-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) deficiency or chronic hyperactivation in pancreatic β-cells leads to diabetes. mTORC1 complexes with La-related protein 1 (LARP1) to specifically regulate the expression of 5' terminal oligopyrimidine tract (5'TOP) mRNAs which encode proteins of the translation machinery and ribosome biogenesis. Here we show that LARP1 is the most expressed LARP in mouse islets and human β-cells, being 2-4-fold more abundant than LARP1B, a member of the family that also interacts with mTORC1. Interestingly, β-cells from diabetic patients have higher LARP1 and LARP1B expression. However, specific deletion of Larp1 gene in β-cells (β-Larp1KO mice) did not impair insulin secretion and glucose metabolism in male and female mice. High fat or high branched-chain amino acid (BCAA) diets did not disturb glucose homeostasis compared to control littermates up to 8 weeks; BCAA diet slightly impaired glucose tolerance in the β-Larp1KO mice at 16 weeks. However, no differences in plasma insulin levels, non-fasting glycemia and β-cell mass were observed in the β-Larp1KO mice. In conclusion, LARP1 is the most abundant LARP in mouse islets and human β-cells, and it is upregulated in diabetic subjects. However, genetically disruption of Larp1 gene did not impact glucose homeostasis in basal and diabetogenic conditions, suggesting no major role for LARP1 in β-cells.
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Affiliation(s)
- Joao Pedro Werneck-de-Castro
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Miami VA Health Care System, Miami, FL, 33136, USA
| | - Flavia Leticia Martins Peçanha
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Diego Henrique Silvestre
- Institute of Nutrition Josué de Castro, Federal University of Rio de Janeiro, Rio de Janeiro, 21941090, Brazil
| | - Ernesto Bernal-Mizrachi
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Miami VA Health Care System, Miami, FL, 33136, USA.
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64
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Robles-Fort A, García-Robles I, Fernando W, Hoskin DW, Rausell C, Real MD. Dual Antimicrobial and Antiproliferative Activity of TcPaSK Peptide Derived from a Tribolium castaneum Insect Defensin. Microorganisms 2021; 9:222. [PMID: 33499187 PMCID: PMC7912591 DOI: 10.3390/microorganisms9020222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 02/08/2023] Open
Abstract
Antimicrobial peptides (AMPs) found in the innate immune system of a wide range of organisms might prove useful to fight infections, due to the reported slower development of resistance to AMPs. Increasing the cationicity and keeping moderate hydrophobicity of the AMPs have been described to improve antimicrobial activity. We previously found a peptide derived from the Tribolium castaneum insect defensin 3, exhibiting antrimicrobial activity against several human pathogens. Here, we analyzed the effect against Staphyloccocus aureus of an extended peptide (TcPaSK) containing two additional amino acids, lysine and asparagine, flanking the former peptide fragment in the original insect defensin 3 protein. TcPaSK peptide displayed higher antimicrobial activity against S. aureus, and additionally showed antiproliferative activity against the MDA-MB-231 triple negative breast cancer cell line. A SWATH proteomic analysis revealed the downregulation of proteins involved in cell growth and tumor progression upon TcPaSK cell treatment. The dual role of TcPaSK peptide as antimicrobial and antiproliferative agent makes it a versatile molecule that warrants exploration for its use in novel therapeutic developments as an alternative approach to overcome bacterial antibiotic resistance and to increase the efficacy of conventional cancer treatments.
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Affiliation(s)
- Aida Robles-Fort
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (A.R.-F.); (I.G.-R.); (C.R.)
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (A.R.-F.); (I.G.-R.); (C.R.)
| | - Wasundara Fernando
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada; (W.F.); (D.W.H.)
| | - David W. Hoskin
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada; (W.F.); (D.W.H.)
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Surgery, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (A.R.-F.); (I.G.-R.); (C.R.)
| | - María Dolores Real
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (A.R.-F.); (I.G.-R.); (C.R.)
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Qin X, Liu Z, Yan K, Fang Z, Fan Y. Integral Analysis of the RNA Binding Protein-associated Prognostic Model for Renal Cell Carcinoma. Int J Med Sci 2021; 18:953-963. [PMID: 33456353 PMCID: PMC7807188 DOI: 10.7150/ijms.50704] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
RNA binding protein (RBPs) dysregulation has been reported in various malignant tumors and plays a pivotal role in tumor carcinogenesis and progression. However, the underlying mechanisms in renal cell carcinoma (RCC) are still unknown. In the present study, we performed a bioinformatics analysis using data from TCGA database to explore the expression and prognostic value of RBPs. We identified 125 differently expressed RBPs between tumor and normal tissue in RCC patients, including 87 upregulated and 38 downregulated RBPs. Eight RBPs (RPL22L1, RNASE2, RNASE3, EZH2, DDX25, DQX1, EXOSC5, DDX47) were selected as prognosis-related RBPs and used to construct a risk score model. In the risk score model, the high-risk subgroup had a poorer overall survival (OS) than the low-risk subgroup, and we divided the 539 RCC patients into two groups and conducted a time-dependent receiver operating characteristic (ROC) analysis to further test the prognostic ability of the eight hub RBPs. The area under the curve (AUC) of the ROC curve was 0.728 in train-group and 0.688 in test-group, indicating a good prognostic model. More importantly, we established a nomogram based on the selected eight RBPs. The eight selected RBPS have predictive value for RCC patients, with potential applications in clinical decision-making and individualized treatment.
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Affiliation(s)
- Xin Qin
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
| | - Zhengfang Liu
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
| | - Keqiang Yan
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China.,Department of Medicine, Center for Molecular Medicine (CMM) and Bioclinicum, Karolinska Institute and Karolinska University Hospital Solna, Solna 171 64, Sweden
| | - Yidong Fan
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
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66
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Cottrell KA, Chiou RC, Weber JD. Upregulation of 5'-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor. Sci Rep 2020; 10:22276. [PMID: 33335292 PMCID: PMC7747592 DOI: 10.1038/s41598-020-79379-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/08/2020] [Indexed: 12/28/2022] Open
Abstract
Tumor cells require nominal increases in protein synthesis in order to maintain high proliferation rates. As such, tumor cells must acquire enhanced ribosome production. How the numerous mutations in tumor cells ultimately achieve this aberrant production is largely unknown. The gene encoding ARF is the most commonly deleted gene in human cancer. ARF plays a significant role in regulating ribosomal RNA synthesis and processing, ribosome export into the cytoplasm, and global protein synthesis. Utilizing ribosome profiling, we show that ARF is a major suppressor of 5'-terminal oligopyrimidine mRNA translation. Genes with increased translational efficiency following loss of ARF include many ribosomal proteins and translation factors. Knockout of p53 largely phenocopies ARF loss, with increased protein synthesis and expression of 5'-TOP encoded proteins. The 5'-TOP regulators eIF4G1 and LARP1 are upregulated in Arf- and p53-null cells.
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Affiliation(s)
- Kyle A Cottrell
- Division of Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, 660 South Euclid Avenue, Campus, Box 8069, Saint Louis, MO, 63110, USA
| | - Ryan C Chiou
- Division of Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, 660 South Euclid Avenue, Campus, Box 8069, Saint Louis, MO, 63110, USA
| | - Jason D Weber
- Division of Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, 660 South Euclid Avenue, Campus, Box 8069, Saint Louis, MO, 63110, USA.
- Department of Cell Biology and Physiology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO, USA.
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67
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Guo C, Shao T, Jiang X, Wei D, Wang Z, Li M, Bao G. Comprehensive analysis of the functions and prognostic significance of RNA-binding proteins in bladder urothelial carcinoma. Am J Transl Res 2020; 12:7160-7173. [PMID: 33312357 PMCID: PMC7724358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
Alterations in RNA-binding proteins (RBPs) are reported in various cancer types; however, the role of RBPs in bladder urothelial cancer (BLCA) remains unknown. This study aimed to systematically examine the function and prognostic significance of RBPs in bladder cancer using bioinformatics analyses. RNA sequencing and clinical data for BLCA were downloaded from The Cancer Genome Atlas (TCGA) database, and differentially expressed RBPs (DERBPs) between normal and cancer tissues were identified. A total of 388 DERBPs were identified, including 219 upregulated and 169 downregulated RBPs. All RBPs were screened for the prognostic model establishment and 9 RBPs (TRIM71, YTHDC1, DARS2, XPOT, ZNF106, FTO, IPO7, EFTUD2, and CTU1) were regarded as prognosis-related hub RBPs in BLCA. Further analysis revealed worse overall survival (OS) in the high-risk cohort compared to the model-based low-risk cohort. The area under the receiver operating characteristic (ROC) curve was 0.752 in the training group and 0.701 in the testing group, which supports the strength of its predictive ability. A nomogram was established according to nine prognosis-related RBPs, which showed strong predictive ability for BLCA. The C-indices of the nomogram were 0.7033 in the training group, and 0.6295 in the testing group. The prognosis-related hub RBPs may be involved in oncogenesis, development, and metastasis of BLCA. Our results will be of great significance in revealing the pathogenesis of BLCA, and developing new therapeutic targets and prognostic molecular markers for BLCA.
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Affiliation(s)
- Changgang Guo
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
- Urology Research Center, Chifeng UniversityChifeng 024000, China
| | - Ting Shao
- Department of Gynecology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
| | - Xiling Jiang
- Department of Stomatology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
| | - Dadong Wei
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
| | - Zhanhua Wang
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
| | - Mingyang Li
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
| | - Guochang Bao
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
- Urology Research Center, Chifeng UniversityChifeng 024000, China
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68
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Esparza-Moltó PB, Cuezva JM. Reprogramming Oxidative Phosphorylation in Cancer: A Role for RNA-Binding Proteins. Antioxid Redox Signal 2020; 33:927-945. [PMID: 31910046 DOI: 10.1089/ars.2019.7988] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Cancer is a major disease imposing high personal and economic burden draining large part of National Health Care and Research budgets worldwide. In the last decade, research in cancer has underscored the reprogramming of metabolism to an enhanced aerobic glycolysis as a major trait of the cancer phenotype with great potential for targeted therapy. Recent Advances: Mitochondria are essential organelles in metabolic reprogramming for controlling the production of biological energy through oxidative phosphorylation (OXPHOS) and the supply of metabolic precursors that sustain proliferation. In addition, mitochondria are critical hubs that integrate different signaling pathways that control cellular metabolism and cell fate. The mitochondrial ATP synthase plays a fundamental role in OXPHOS and cellular signaling. Critical Issues: This review overviews mitochondrial metabolism and OXPHOS, and the major changes reported in the expression and function of mitochondrial proteins of OXPHOS in oncogenesis and in cellular differentiation. We summarize the prominent role that RNA-binding proteins (RNABPs) play in the sorting and localized translation of nuclear-encoded mRNAs that help define the mitochondrial cell-type-specific phenotype. Moreover, we emphasize the mechanisms that contribute to restrain the activity and expression of the mitochondrial ATP synthase in carcinomas, and illustrate that the dysregulation of proteins that control energy metabolism correlates with patients' survival. Future Directions: Future research should elucidate the mechanisms and RNABPs that promote the specific alterations of the mitochondrial phenotype in carcinomas arising from different tissues with the final aim of developing new therapeutic strategies to treat cancer.
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Affiliation(s)
- Pau B Esparza-Moltó
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid, Madrid, Spain
| | - José M Cuezva
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid, Madrid, Spain
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69
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Huang X, Tang J. Human La Protein: An RNA-Binding Protein Involved in Ovarian Cancer Development and Multidrug Resistance. Onco Targets Ther 2020; 13:10721-10727. [PMID: 33132701 PMCID: PMC7592153 DOI: 10.2147/ott.s269983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
Multidrug resistance is the main cause of chemotherapy failure and death in patients with advanced ovarian cancer. Drug resistance is a problem that must be solved to improve the survival rate of patients with advanced ovarian cancer. The RNA-binding protein La and the La-related protein family are highly expressed in various malignant tumors, including ovarian cancer. This article reviews the mechanisms of La protein in tumorigenesis, development, and drug resistance. High La protein expression in tumor cells promotes tumor proliferation, invasion, and migration; disrupts cell cycle; and inhibits tumor cell apoptosis caused by chemotherapeutic drugs through various pathways, resulting in chemotherapy resistance in ovarian cancer. Further study of the role of La protein in ovarian cancer multidrug resistance may be conducive to the development of human La protein-specific inhibitors that suppress ovarian cancer drug resistance.
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Affiliation(s)
- Xuan Huang
- Department of Pharmacy, Obstetrics & Gynecology Hospital of Fudan University, Shanghai 200011, People's Republic of China
| | - Jing Tang
- Department of Pharmacy, Obstetrics & Gynecology Hospital of Fudan University, Shanghai 200011, People's Republic of China
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70
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Hua X, Ge S, Chen J, Zhang L, Tai S, Liang C. Effects of RNA Binding Proteins on the Prognosis and Malignant Progression in Prostate Cancer. Front Genet 2020; 11:591667. [PMID: 33193734 PMCID: PMC7606971 DOI: 10.3389/fgene.2020.591667] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is a common lethal malignancy in men. RNA binding proteins (RBPs) have been proven to regulate the biological processes of various tumors, but their roles in PCa remain less defined. In the present study, we used bioinformatics analysis to identify RBP genes with prognostic and diagnostic values. A total of 59 differentially expressed RBPs in PCa were obtained, comprising 28 upregulated and 31 downregulated RBP genes, which may play important roles in PCa. Functional enrichment analyses showed that these RBPs were mainly involved in mRNA processing, RNA splicing, and regulation of RNA splicing. Additionally, we identified nine RBP genes (EXO1, PABPC1L, REXO2, MBNL2, MSI1, CTU1, MAEL, YBX2, and ESRP2) and their prognostic values by a protein-protein interaction network and Cox regression analyses. The expression of these nine RBPs was validated using immunohistochemical staining between the tumor and normal samples. Further, the associations between the expression of these nine RBPs and pathological T staging, Gleason score, and lymph node metastasis were evaluated. Moreover, these nine RBP genes showed good diagnostic values and could categorize the PCa patients into two clusters with different malignant phenotypes. Finally, we constructed a prognostic model based on these nine RBP genes and validated them using three external datasets. The model showed good efficiency in predicting patient survival and was independent of other clinical factors. Therefore, our model could be used as a supplement for clinical factors to predict patient prognosis and thereby improve patient survival.
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Affiliation(s)
- Xiaoliang Hua
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
- The Institute of Urology, Anhui Medical University, Hefei, China
| | - Shengdong Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
- The Institute of Urology, Anhui Medical University, Hefei, China
| | - Juan Chen
- The Ministry of Education Key Laboratory of Clinical Diagnostics, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
- The Institute of Urology, Anhui Medical University, Hefei, China
| | - Sheng Tai
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
- The Institute of Urology, Anhui Medical University, Hefei, China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
- The Institute of Urology, Anhui Medical University, Hefei, China
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71
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He Y, Zeng S, Hu S, Zhang F, Shan N. Development and Validation of an RNA-Binding Protein-Based Prognostic Model for Ovarian Serous Cystadenocarcinoma. Front Genet 2020; 11:584624. [PMID: 33193718 PMCID: PMC7593419 DOI: 10.3389/fgene.2020.584624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/18/2020] [Indexed: 11/13/2022] Open
Abstract
Ribonucleic acid-binding proteins (RBPs) are reportedly involved in tumor progression and recurrence; however, the functions and mechanisms of action of RBPs in ovarian serous cystadenocarcinoma (OSC) are not known. To address these issues, gene expression profiles of OSC tissues from The Cancer Genome Atlas (TCGA) and normal tissues from the Genotype-Tissue Expression database were compared in order to identify RBPs that are differentially expressed in OSC. We also analyzed the biological functions of these RBPs and their relationship to clinical outcome. There were 190 RBPs that were differentially expressed between OSC and normal tissues, including 93 that were upregulated and 97 that were downregulated. Five of the RBPs were used to construct a prediction model that was evaluated by univariate and multivariate Cox regression analyses. TCGA data were randomly divided into training and test cohorts, and further categorized into high- and low-risk groups according to risk score in the model. The overall survival (OS) of the high-risk group was shorter than that of the low-risk group (training cohort P = 0.0007596; test cohort P = 0.002219). The area under the receiver operating characteristic curve of the training and test cohorts was 0.701 and 0.638, respectively, demonstrating that the model had good predictive power. A nomogram was established to quantitatively describe the relationship between the five prognostic RBPs and OS in OSC, which can be useful for developing individualized management strategies for patients.
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Affiliation(s)
- Yunan He
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sen Zeng
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Shunjie Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fengqian Zhang
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Nianchun Shan
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Nianchun Shan,
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Zhang Y, Cai W, Zou Y, Zhang H. Knockdown of KCNQ1OT1 Inhibits Proliferation, Invasion, and Drug Resistance by Regulating miR-129-5p-Mediated LARP1 in Osteosarcoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7698767. [PMID: 32953888 PMCID: PMC7487100 DOI: 10.1155/2020/7698767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 07/26/2020] [Indexed: 12/15/2022]
Abstract
KCNQ1OT1 exerts an important role in various cancers, but its role in osteosarcoma (OS) and the potential mechanism remain to be clarified. In the present research, we aimed to explore the effect of KCNQ1OT1 on osteosarcoma and further explore the special molecular mechanism. The expression of KCNQ1OT1 was analyzed in tumor and adjacent tissues of 30 patients with osteosarcoma by RT-PCR. Cell proliferation and invasion were explored using MTT and transwell assay, respectively. Luciferase reporter analysis and pull-down assay were performed to determine the binding activity of KCNQ1OT1 and miR-129-5p. The result revealed that KCNQ1OT1 was highly expressed in osteosarcoma tissues and cells. KCNQ1OT1-siRNA inhibited the proliferation, invasion, and drug resistance of osteosarcoma cells. The luciferase reporter assay and pull-down assay demonstrated that KCNQ1OT1 directly interact with miR-129-5p. In addition, miR-129-5p binds to LARP1 directly, and LARP1 promoted the proliferation, invasion, and drug resistance of osteosarcoma cells. What is more, KCNQ1OT1 promoted proliferation, invasion, and drug resistance via inhibiting the expression of miR-129-5p and further promoting the expression of miR-129-5p-mediated LARP1. Collectively, it suggests that downregulation of KCNQ1OT1 inhibits proliferation, invasion, and drug resistance by regulating miR-129-5p-mediated LARP1 in osteosarcoma cells.
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Affiliation(s)
- Yunfei Zhang
- Department of Pathology, Affiliated Hospital of Northwest Minzu University, Second Provincial People's Hospital of Gansu, Lanzhou, 73000 Gansu Province, China
| | - Wei Cai
- Department of Pathology, People's Hospital of Gansu Province, Lanzhou, 73000 Gansu Province, China
| | - Yuli Zou
- Department of Emergency, Affiliated Hospital of Northwest Minzu University, Second Provincial People's Hospital of Gansu, Lanzhou, 73000 Gansu Province, China
| | - Hong Zhang
- Department of Pathology, Affiliated Hospital of Northwest Minzu University, Second Provincial People's Hospital of Gansu, Lanzhou, 73000 Gansu Province, China
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73
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Abstract
RNA-binding proteins are important regulators of RNA metabolism and are of critical importance in all steps of the gene expression cascade. The role of aberrantly expressed RBPs in human disease is an exciting research field and the potential application of RBPs as a therapeutic target or a diagnostic marker represents a fast-growing area of research.Aberrant overexpression of the human RNA-binding protein La has been found in various cancer entities including lung, cervical, head and neck, and chronic myelogenous leukaemia. Cancer-associated La protein supports tumour-promoting processes such as proliferation, mobility, invasiveness and tumour growth. Moreover, the La protein maintains the survival of cancer cells by supporting an anti-apoptotic state that may cause resistance to chemotherapeutic therapy.The human La protein represents a multifunctional post-translationally modified RNA-binding protein with RNA chaperone activity that promotes processing of non-coding precursor RNAs but also stimulates the translation of selective messenger RNAs encoding tumour-promoting and anti-apoptotic factors. In our model, La facilitates the expression of those factors and helps cancer cells to cope with cellular stress. In contrast to oncogenes, able to initiate tumorigenesis, we postulate that the aberrantly elevated expression of the human La protein contributes to the non-oncogenic addiction of cancer cells. In this review, we summarize the current understanding about the implications of the RNA-binding protein La in cancer progression and therapeutic resistance. The concept of exploiting the RBP La as a cancer drug target will be discussed.
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Affiliation(s)
- Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
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74
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TOP mRNPs: Molecular Mechanisms and Principles of Regulation. Biomolecules 2020; 10:biom10070969. [PMID: 32605040 PMCID: PMC7407576 DOI: 10.3390/biom10070969] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
The cellular response to changes in the surrounding environment and to stress requires the coregulation of gene networks aiming to conserve energy and resources. This is often achieved by downregulating protein synthesis. The 5’ Terminal OligoPyrimidine (5’ TOP) motif-containing mRNAs, which encode proteins that are essential for protein synthesis, are the primary targets of translational control under stress. The TOP motif is a cis-regulatory RNA element that begins directly after the m7G cap structure and contains the hallmark invariant 5’-cytidine followed by an uninterrupted tract of 4–15 pyrimidines. Regulation of translation via the TOP motif coordinates global protein synthesis with simultaneous co-expression of the protein components required for ribosome biogenesis. In this review, we discuss architecture of TOP mRNA-containing ribonucleoprotein complexes, the principles of their assembly, and the modes of regulation of TOP mRNA translation.
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75
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Li G, Ni A, Tang Y, Li S, Meng L. RNA binding proteins involved in regulation of protein synthesis to initiate biogenesis of secondary tumor in hepatocellular carcinoma in mice. PeerJ 2020; 8:e8680. [PMID: 32219019 PMCID: PMC7087493 DOI: 10.7717/peerj.8680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background The tumor microenvironment (TM) in close contact with cancer cells is highly related to tumor growth and cancer metastasis. This study is to explore the biogenesis mechanism of a secondary hepatocellular carcinoma (HCC) based on the function of RNA binding proteins (RBPs)-encoding genes in the physiological microenvironment (PM). Methods The healthy and HCC mice were used to isolate the PM, pre-tumor microenvironment (PTM), and TM. The samples were analyzed using the technology of RNA-seq and bioinformatics. The differentially expressed RBPs-encoding genes (DERs) and differentially expressed DERs-associated genes (DEDs) were screened to undergo GO and KEGG analysis. Results 18 DERs and DEDs were identified in the PTM vs. PM, 87 in the TM vs. PTM, and 87 in the TM vs. PM. Those DERs and DEDs participated in the regulation of gene expression at the levels of chromatin conformation, gene activation and silencing, splicing and degradation of mRNA, biogenesis of piRNA and miRNA, ribosome assemble, and translation of proteins. Conclusion The genes encoding RBPs and the relevant genes are involved in the transformation from PM to PTM, then constructing the TM by regulating protein synthesis. This regulation included whole process of biological genetic information transmission from chromatin conformation to gene activation and silencing to mRNA splicing to ribosome assemble to translation of proteins and degradation of mRNA. The abnormality of those functions in the organic microenvironments promoted the metastasis of HCC and initiated the biogenesis of a secondary HCC in a PM when the PM encountered the invasion of cancer cells.
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Affiliation(s)
- Genliang Li
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Anni Ni
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Yulian Tang
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Shubo Li
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Lingzhang Meng
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
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76
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Teng H, Wei W, Li Q, Xue M, Shi X, Li X, Mao F, Sun Z. Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types. Nucleic Acids Res 2020; 48:1192-1205. [PMID: 31950163 PMCID: PMC7026592 DOI: 10.1093/nar/gkaa019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Somatic synonymous mutations are one of the most frequent genetic variants occurring in the coding region of cancer genomes, while their contributions to cancer development remain largely unknown. To assess whether synonymous mutations involved in post-transcriptional regulation contribute to the genetic etiology of cancers, we collected whole exome data from 8,320 patients across 22 cancer types. By employing our developed algorithm, PIVar, we identified a total of 22,948 posttranscriptionally impaired synonymous SNVs (pisSNVs) spanning 2,042 genes. In addition, 35 RNA binding proteins impacted by these identified pisSNVs were significantly enriched. Remarkably, we discovered markedly elevated ratio of somatic pisSNVs across all 22 cancer types, and a high pisSNV ratio was associated with worse patient survival in five cancer types. Intriguing, several well-established cancer genes, including PTEN, RB1 and PIK3CA, appeared to contribute to tumorigenesis at both protein function and posttranscriptional regulation levels, whereas some pisSNV-hosted genes, including UBR4, EP400 and INTS1, exerted their function during carcinogenesis mainly via posttranscriptional mechanisms. Moreover, we predicted three drugs associated with two pisSNVs, and numerous compounds associated with expression signature of pisSNV-hosted genes. Our study reveals the prevalence and clinical relevance of pisSNVs in cancers, and emphasizes the importance of considering posttranscriptional impaired synonymous mutations in cancer biology.
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Affiliation(s)
- Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wenqing Wei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiying Xue
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui Shi
- Sino-Danish college, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianfeng Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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77
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Bayfield MA, Kerkhofs K, Mansouri-Noori F. C-lection by the DM15 Motif Gets LARP1 to the TOP. Structure 2020; 27:1737-1739. [PMID: 31801095 DOI: 10.1016/j.str.2019.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
LARP1 proteins integrate the translation and stability of 5'TOP mRNAs with signaling from the mTOR pathway, but the mechanism is not well understood. In this issue of Structure, Cassidy et al. (2019) propose that the LARP1-DM15 motif modulates access to the 5'TOP mRNA's m7G-ppp-Cytosine cap.
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Affiliation(s)
- Mark A Bayfield
- Department of Biology, York University, Toronto, ON, Canada.
| | - Kyra Kerkhofs
- Department of Biology, York University, Toronto, ON, Canada
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78
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Li R, Li H, Ge C, Fu Q, Li Z, Jin Y, Tan Q, Zhu Z, Zhang Z, Dong S, Li G, Song X. Increased expression of the RNA-binding motif protein 47 predicts poor prognosis in non-small-cell lung cancer. Oncol Lett 2020; 19:3111-3122. [PMID: 32218862 PMCID: PMC7068708 DOI: 10.3892/ol.2020.11417] [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: 01/17/2019] [Accepted: 11/01/2019] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the leading cause of cancer-associated mortality worldwide. In China, in particular, lung cancer mortality has markedly increased and is likely to continue to rise. RNA-binding proteins are pivotal to the development and progression of a variety of cancer types, including non-small cell lung cancer (NSCLC). RNA-binding motif protein 47 (RBM47) has been found to act as a tumor suppressor in breast cancer and NSCLC. However, to the best of our knowledge, RBM47 expression in NSCLC tissues has yet to be investigated. Analysis via the online database, Gene Expression Omnibus, revealed that RBM47 was upregulated in NSCLC and associated with pathological type, suggesting that RBM47 may play different roles in lung adenocarcinoma and lung squamous cell carcinoma. In the present study, the expression of RBM47 was examined by immunohistochemistry in 175 pairs of tumor and adjacent non-cancerous tissues resected from patients with NSCLC. The results indicated that the expression of RBM47 was significantly increased in NSCLC samples compared with that in the matched non-cancerous samples. Furthermore, RBM47 expression was higher in Xuanwei compared with that in non-Xuanwei NSCLC, suggesting that RBM47 is a more sensitive biomarker in Xuanwei NSCLC, and that it may serve as a candidate therapeutic target. In addition, RBM47 expression was associated with the pathological type, however not with the age, sex, lymph node metastasis, pT stage or pathological Tumor-Node-Metastasis stage of the patients. The increased expression level of RBM47 may indicate a worse overall survival rate for patients with NSCLC. In addition, multivariate survival analysis showed that the Xuanwei area is associated with poor prognosis for patients with NSCLC. In conclusion, the present study revealed that the upregulation of RBM47 accelerated the malignant progression of NSCLC, indicating that RBM47 may be a potential biomarker for NSCLC progression and a therapeutic target for NSCLC.
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Affiliation(s)
- Ruilei Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Heng Li
- Department of Chest Surgery, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Chunlei Ge
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Qiaofen Fu
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Zhen Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Yarong Jin
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Qinghua Tan
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Zhitao Zhu
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Zhiwei Zhang
- Department of Biotherapy, The Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai 201805, P.R. China
| | - Suwei Dong
- Department of Chest Surgery, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Gaofeng Li
- Department of Chest Surgery, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
| | - Xin Song
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, P.R. China
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79
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The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium. Cells 2019; 8:cells8121634. [PMID: 31847302 PMCID: PMC6953095 DOI: 10.3390/cells8121634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
: Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have on cancer development.
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80
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Naghizadeh S, Mansoori B, Mohammadi A, Sakhinia E, Baradaran B. Gene Silencing Strategies in Cancer Therapy: An Update for Drug Resistance. Curr Med Chem 2019; 26:6282-6303. [DOI: 10.2174/0929867325666180403141554] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/10/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
RNAi, post-transcriptional gene silencing mechanism, could be considered as one of the
most important breakthroughs and rapidly growing fields in science. Researchers are trying to use this
discovery in the treatment of various diseases and cancer is one of them although there are multiple
treatment procedures for treatment-resistant cancers, eradication of resistance remain as an unsolvable
problem yet. The current review summarizes both transcriptional and post-transcriptional gene silencing
mechanisms, and highlights mechanisms leading to drug-resistance such as, drug efflux, drug inactivation,
drug target alteration, DNA damages repair, and the epithelial-mesenchymal transition, as
well as the role of tumor cell heterogeneity and tumor microenvironment, involving genes in these
processes. It ultimately points out the obstacles of RNAi application for in vivo treatment of diseases
and progressions that have been achieved in this field.
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Affiliation(s)
- Sanaz Naghizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Sakhinia
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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81
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Cassidy KC, Lahr RM, Kaminsky JC, Mack S, Fonseca BD, Das SR, Berman AJ, Durrant JD. Capturing the Mechanism Underlying TOP mRNA Binding to LARP1. Structure 2019; 27:1771-1781.e5. [PMID: 31676287 PMCID: PMC7269035 DOI: 10.1016/j.str.2019.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/06/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine (m7G) cap and 5' terminal oligopyrimidine (TOP) motif characteristic of transcripts encoding ribosomal proteins and translation factors. Under the control of mammalian target of rapamycin complex 1 (mTORC1), LARP1 regulates translation of these transcripts. Characterizing the dynamics of DM15-TOP recognition is essential to understanding this fundamental biological process. We use molecular dynamics simulations, biophysical assays, and X-ray crystallography to reveal the mechanism of DM15 binding to TOP transcripts. Residues C-terminal to the m7G-binding site play important roles in cap recognition. Furthermore, we show that the unusually static pocket that recognizes the +1 cytosine characteristic of TOP transcripts drives binding specificity. Finally, we demonstrate that the DM15 pockets involved in TOP-specific m7GpppC-motif recognition are likely druggable. Collectively, these studies suggest unique opportunities for further pharmacological development.
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Affiliation(s)
- Kevin C Cassidy
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jesse C Kaminsky
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Stephanie Mack
- Department of Chemistry and Center for Nucleic Acids Science & Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Bruno D Fonseca
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, K1H 8L1 ON, Canada
| | - Subha R Das
- Department of Chemistry and Center for Nucleic Acids Science & Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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82
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Plissonnier ML, Cottarel J, Piver E, Kullolli M, Centonze FG, Pitteri S, Farhan H, Meunier JC, Zoulim F, Parent R. LARP1 binding to hepatitis C virus particles is correlated with intracellular retention of viral infectivity. Virus Res 2019; 271:197679. [PMID: 31398365 DOI: 10.1016/j.virusres.2019.197679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/27/2019] [Indexed: 12/23/2022]
Abstract
Hepatitis C virus (HCV) virions contain a subset of host liver cells proteome often composed of interesting virus-interacting factors. A proteomic analysis performed on double gradient-purified clinical HCV highlighted the translation regulator LARP1 on these virions. This finding was validated using post-virion capture and immunoelectron microscopy, as well as immunoprecipitation applied to in vitro (Huh7.5 liver cells) grown (Gt2a, JFH1 strain) and patient-derived (Gt1a) HCV particles. Upon HCV infection of Huh7.5 cells, we observed a drastic transfer of LARP1 to lipid droplets, inducing colocalization with core proteins. RNAi-mediated depletion of LARP1 using the C911 control approach decreased extracellular infectivity of HCV Gt1a (H77), Gt2a (JFH1), and Gt3a (S52 chimeric strain), yet increased their intracellular infectivity. This latter effect was unrelated to changes in the hepatocyte secretory pathway, as evidenced using a functional RUSH assay. These results indicate that LARP1 binds to HCV, an event associated with retention of intracellular infectivity.
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Affiliation(s)
- Marie-Laure Plissonnier
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France
| | - Jessica Cottarel
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France
| | - Eric Piver
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, INSERM U966, Université de Tours, F-37000, Tours, France
| | - Majlinda Kullolli
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | | | - Sharon Pitteri
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Hesso Farhan
- Institute of Basic Medical Science, University of Oslo, N-0372, Olso, Norway
| | - Jean-Christophe Meunier
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, INSERM U966, Université de Tours, F-37000, Tours, France
| | - Fabien Zoulim
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France; Lyon University Hospital (Hospices civils de Lyon), Hepatogastroenterology Service, F-69001, Lyon, France
| | - Romain Parent
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France.
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83
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Iadevaia V, Wouters MD, Kanitz A, Matia-González AM, Laing EE, Gerber AP. Tandem RNA isolation reveals functional rearrangement of RNA-binding proteins on CDKN1B/p27Kip1 3'UTRs in cisplatin treated cells. RNA Biol 2019; 17:33-46. [PMID: 31522610 PMCID: PMC6948961 DOI: 10.1080/15476286.2019.1662268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-transcriptional control of gene expression is mediated via RNA-binding proteins (RBPs) that interact with mRNAs in a combinatorial fashion. While recent global RNA interactome capture experiments expanded the repertoire of cellular RBPs quiet dramatically, little is known about the assembly of RBPs on particular mRNAs; and how these associations change and control the fate of the mRNA in drug-treatment conditions. Here we introduce a novel biochemical approach, termed tobramycin-based tandem RNA isolation procedure (tobTRIP), to quantify proteins associated with the 3ʹUTRs of cyclin-dependent kinase inhibitor 1B (CDKN1B/p27Kip1) mRNAs in vivo. P27Kip1 plays an important role in mediating a cell’s response to cisplatin (CP), a widely used chemotherapeutic cancer drug that induces DNA damage and cell cycle arrest. We found that p27Kip1 mRNA is stabilized upon CP treatment of HEK293 cells through elements in its 3ʹUTR. Applying tobTRIP, we further compared the associated proteins in CP and non-treated cells, and identified more than 50 interacting RBPs, many functionally related and evoking a coordinated response. Knock-downs of several of the identified RBPs in HEK293 cells confirmed their involvement in CP-induced p27 mRNA regulation; while knock-down of the KH-type splicing regulatory protein (KHSRP) further enhanced the sensitivity of MCF7 adenocarcinoma cancer cells to CP treatment. Our results highlight the benefit of specific in vivo mRNA-protein interactome capture to reveal post-transcriptional regulatory networks implicated in cellular drug response and adaptation.
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Affiliation(s)
- Valentina Iadevaia
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Maikel D Wouters
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | | | - Ana M Matia-González
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Emma E Laing
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
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84
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Blanchard EL, Argyropoulou D, Zurla C, Bhosle SM, Vanover D, Santangelo PJ. Quantification and Localization of Protein-RNA Interactions in Patient-Derived Archival Tumor Tissue. Cancer Res 2019; 79:5418-5431. [PMID: 31481502 DOI: 10.1158/0008-5472.can-19-1094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/24/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022]
Abstract
Abnormal post-transcriptional regulation induced by alterations of mRNA-protein interactions is critical during tumorigenesis and cancer progression and is a hallmark of cancer cells. A more thorough understanding is needed to develop treatments and foresee outcomes. Cellular and mouse tumor models are insufficient for vigorous investigation as they lack consistency and translatability to humans. Moreover, to date, studies in human tumor tissue are predominately limited to expression analysis of proteins and mRNA, which do not necessarily provide information about the frequency of mRNA-protein interactions. Here, we demonstrate novel optimization of a method that is based on FISH and proximity ligation techniques to quantify mRNA interactions with RNA-binding proteins relevant for tumorigenesis and cancer progression in archival patient-derived tumor tissue. This method was validated for multiple mRNA-protein pairs in several cellular models and in multiple types of archival human tumor samples. Furthermore, this approach allowed high-throughput analysis of mRNA-protein interactions across a wide range of tumor types and stages through tumor microarrays. This method is quantitative, specific, and sensitive for detecting interactions and their localization at both the individual cell and whole-tissue scales with single interaction sensitivity. This work presents an important tool in investigating post-transcriptional regulation in cancer on a high-throughput scale, with great potential for translatability into any applications where mRNA-protein interactions are of interest. SIGNIFICANCE: This work presents an approach to sensitively, specifically, and quantitatively detect and localize native mRNA and protein interactions for analysis of abnormal post-transcriptional regulation in patient-derived archival tumor samples.
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Affiliation(s)
- Emmeline L Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Danae Argyropoulou
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Sushma M Bhosle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
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85
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Vinayak J, Marrella SA, Hussain RH, Rozenfeld L, Solomon K, Bayfield MA. Human La binds mRNAs through contacts to the poly(A) tail. Nucleic Acids Res 2019; 46:4228-4240. [PMID: 29447394 PMCID: PMC5934636 DOI: 10.1093/nar/gky090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
In addition to a role in the processing of nascent RNA polymerase III transcripts, La proteins are also associated with promoting cap-independent translation from the internal ribosome entry sites of numerous cellular and viral coding RNAs. La binding to RNA polymerase III transcripts via their common UUU-3’OH motif is well characterized, but the mechanism of La binding to coding RNAs is poorly understood. Using electromobility shift assays and cross-linking immunoprecipitation, we show that in addition to a sequence specific UUU-3’OH binding mode, human La exhibits a sequence specific and length dependent poly(A) binding mode. We demonstrate that this poly(A) binding mode uses the canonical nucleic acid interaction winged helix face of the eponymous La motif, previously shown to be vacant during uridylate binding. We also show that cytoplasmic, but not nuclear La, engages poly(A) RNA in human cells, that La entry into polysomes utilizes the poly(A) binding mode, and that La promotion of translation from the cyclin D1 internal ribosome entry site occurs in competition with cytoplasmic poly(A) binding protein (PABP). Our data are consistent with human La functioning in translation through contacts to the poly(A) tail.
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Affiliation(s)
- Jyotsna Vinayak
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Stefano A Marrella
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Rawaa H Hussain
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Leonid Rozenfeld
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Karine Solomon
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Mark A Bayfield
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
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86
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Kuciauskas D, Dreize N, Ger M, Kaupinis A, Zemaitis K, Stankevicius V, Suziedelis K, Cicenas J, Graves LM, Valius M. Proteomic Analysis of Breast Cancer Resistance to the Anticancer Drug RH1 Reveals the Importance of Cancer Stem Cells. Cancers (Basel) 2019; 11:E972. [PMID: 31336714 PMCID: PMC6678540 DOI: 10.3390/cancers11070972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
Antitumor drug resistance remains a major challenge in cancer chemotherapy. Here we investigated the mechanism of acquired resistance to a novel anticancer agent RH1 designed to be activated in cancer cells by the NQO1 enzyme. Data show that in some cancer cells RH1 may act in an NQO1-independent way. Differential proteomic analysis of breast cancer cells with acquired resistance to RH1 revealed changes in cell energy, amino acid metabolism and G2/M cell cycle transition regulation. Analysis of phosphoproteomics and protein kinase activity by multiplexed kinase inhibitor beads showed an increase in the activity of protein kinases involved in the cell cycle and stemness regulation and downregulation of proapoptotic kinases such as JNK in RH1-resistant cells. Suppression of JNK leads to the increase of cancer cell resistance to RH1. Moreover, resistant cells have enhanced expression of stem cell factor (SCF) and stem cell markers. Inhibition of SCF receptor c-KIT resulted in the attenuation of cancer stem cell enrichment and decreased amounts of tumor-initiating cells. RH1-resistant cells also acquire resistance to conventional therapeutics while remaining susceptible to c-KIT-targeted therapy. Data show that RH1 can be useful to treat cancers in the NQO1-independent way, and targeting of the cancer stem cells might be an effective approach for combating resistance to RH1 therapy.
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Affiliation(s)
- Dalius Kuciauskas
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Nadezda Dreize
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Marija Ger
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Algirdas Kaupinis
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Kristijonas Zemaitis
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Vaidotas Stankevicius
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania
| | - Kestutis Suziedelis
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania
| | - Jonas Cicenas
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
- MAP Kinase Resource, 3027 Bern, Switzerland
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mindaugas Valius
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania.
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87
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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88
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Wilbertz JH, Voigt F, Horvathova I, Roth G, Zhan Y, Chao JA. Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response. Mol Cell 2019; 73:946-958.e7. [PMID: 30661979 DOI: 10.1016/j.molcel.2018.12.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/24/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022]
Abstract
Biological phase transitions form membrane-less organelles that generate distinct cellular environments. How molecules are partitioned between these compartments and the surrounding cellular space and the functional consequence of this localization is not well understood. Here, we report the localization of mRNA to stress granules (SGs) and processing bodies (PBs) and its effect on translation and degradation during the integrated stress response. Using single mRNA imaging in living human cells, we find that the interactions of mRNAs with SGs and PBs have different dynamics, very few mRNAs directly move between SGs and PBs, and that specific RNA-binding proteins can anchor mRNAs within these compartments. During recovery from stress, we show that mRNAs that were within SGs and PBs are translated and degraded at similar rates as their cytosolic counterparts. Our work provides a framework for using single-molecule measurements to directly investigate the molecular mechanisms of phase-separated compartments within their cellular environment.
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Affiliation(s)
- Johannes H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Ivana Horvathova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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89
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Egiz M, Usui T, Ishibashi M, Zhang X, Shigeta S, Toyoshima M, Kitatani K, Yaegashi N. La-Related Protein 4 as a Suppressor for Motility of Ovarian Cancer Cells. TOHOKU J EXP MED 2019; 247:59-67. [PMID: 30686809 DOI: 10.1620/tjem.247.59] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The La-related proteins (LARPs) are a family of RNA binding proteins that control the degradation and stabilization of RNAs. As emerging research reveals the biology of each LARP, it is evident that LARPs are dysregulated in some types of cancer. Upregulation of cell motility potentiates the metastatic potential of ovarian cancer cells; however, the roles of LARPs in cell motility remain unknown. In the present study, we investigated the roles of LARPs in the progression of ovarian cancer using SKOV3 human ovarian cancer cells and a public database that integrates microarray-based gene expression data and clinical data. To explore the involvement of LARPs in the cell motility, we performed RNA interference screening for LARP mRNAs in SKOV3 cells. The screening identified LARP4 as a potential suppressor of the formation of lamellipodia. Conversely, enforced expression of LARP4 suppressed the formation of lamellipodia. Moreover, cell migration was significantly increased in LARP4-depleted SKOV3 cells. Mechanistically, LARP4 depletion was associated with the decrease in RhoA protein expression. These results suggest that LARP4 may limit RhoA-dependent cell motility. In a mouse xenograft model with SKOV3 cells, LARP4 depletion potentiated peritoneal metastasis. Upon analysis of a public database of patients with ovarian cancer, the LARP4 mRNA-high expression group (n = 166) showed longer overall survival compared with the LARP4 mRNA-low expression group (n = 489), implying a positive correlation of LARP4 mRNA levels in ovarian cancer tissues with patient prognosis. Taken together, we propose that LARP4 could suppress motility and metastatic potential of ovarian cancer cells.
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Affiliation(s)
- Mahy Egiz
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
- Department of Obstetrics and Gynecology, Menoufia University Graduate School of Medicine
| | - Toshinori Usui
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Masumi Ishibashi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Xuewei Zhang
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Shogo Shigeta
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Masafumi Toyoshima
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Kazuyuki Kitatani
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
- Tohoku Medical Megabank Organization, Tohoku University
- Laboratory of Immunopharmacology, Faculty of Pharmaceutical Sciences, Setsunan University
| | - Nobuo Yaegashi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
- Tohoku Medical Megabank Organization, Tohoku University
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90
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Wu G, Cao L, Zhu J, Tan Z, Tang M, Li Z, Hu Y, Yu R, Zhang S, Song L, Li J. Loss of RBMS3 Confers Platinum Resistance in Epithelial Ovarian Cancer via Activation of miR-126-5p/β-catenin/CBP signaling. Clin Cancer Res 2018; 25:1022-1035. [PMID: 30279231 DOI: 10.1158/1078-0432.ccr-18-2554] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/24/2018] [Accepted: 09/27/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE The development of resistance to platinum-based chemotherapy remains the unsurmountable obstacle in cancer treatment and consequently leads to tumor relapse. This study aims to investigate the mechanism by which loss of RBMS3 induced chemoresistance in epithelial ovarian cancer (EOC). EXPERIMENTAL DESIGN FISH and IHC were used to determine deletion frequency and expression of RBMS3 in 15 clinical EOC tissues and 150 clinicopathologically characterized EOC specimens. The effects of RBMS3 deletion and CBP/β-catenin antagonist PRI-724 in chemoresistance were examined by clone formation and Annexin V assays in vitro, and by intraperitoneal tumor model in vivo. The mechanism by which RBMS3 loss sustained activation of miR-126-5p/β-catenin/CBP signaling and the effects of RBMS3 and miR-126-5p competitively regulating DKK3, AXIN1, BACH1, and NFAT5 was explored using CLIP-seq, RIP, electrophoretic mobility shift, and immunoblotting and immunofluorescence assays. RESULTS Loss of RBMS3 in EOC was correlated with the overall and relapse-free survival. Genetic ablation of RBMS3 significantly enhanced, whereas restoration of RBMS3 reduced, the chemoresistance ability of EOC cells both in vitro and in vivo. RBMS3 inhibited β-catenin/CBP signaling through directly associating with and stabilizing multiple negative regulators, including DKK3, AXIN1, BACH1, and NFAT5, via competitively preventing the miR-126-5p-mediated repression of these transcripts. Importantly, cotherapy of CBP/β-catenin antagonist PRI-724 induced sensitization of RBMS3-deleted EOC to platinum therapy. CONCLUSIONS Our results demonstrate that genetic ablation of RBMS3 contributes to chemoresistance and PRI-724 may serve as a potential tailored treatment for patients with RBMS3-deleted EOC.
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Affiliation(s)
- Geyan Wu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Lixue Cao
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jinrong Zhu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhanyao Tan
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Miaoling Tang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Ziwen Li
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yameng Hu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ruyuan Yu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuxia Zhang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Libing Song
- State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jun Li
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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91
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Paclitaxel resistance and the role of miRNAs in prostate cancer cell lines. World J Urol 2018; 37:1117-1126. [DOI: 10.1007/s00345-018-2501-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022] Open
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92
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Han J, Zhao G, Ma X, Dong Q, Zhang H, Wang Y, Cui J. CircRNA circ-BANP-mediated miR-503/LARP1 signaling contributes to lung cancer progression. Biochem Biophys Res Commun 2018; 503:2429-2435. [PMID: 29969631 DOI: 10.1016/j.bbrc.2018.06.172] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 06/30/2018] [Indexed: 11/21/2022]
Abstract
Recently, circular RNAs (circRNAs) attract much attention due to their potential vital functions in multiple human diseases, including cancer. circ-BANP has been reported to modulate colorectal cancer growth. Nevertheless, the relationship between circ-BANP and lung cancer requires to be investigated. In this study, we found circ-BANP was overexpressed in lung cancer tissues. Higher circ-BANP expression was associated with lower survival rate. Moreover, silencing circ-BANP markedly inhibited proliferation, migration and invasion of lung cancer cells in vitro and impaired tumor propagation in vivo. In mechanism, circ-BANP was identified as the sponge of miR-503 while miR-503 targets LARP1. Circ-BANP-induced inhibition of miR-503 led to increased expression of LARP1 in lung cancer. Finally, rescue assays indicated that LARP1 restoration partially reversed the effects of circ-BANP knockdown in lung cancer. In sum, our study illustrated that circ-BANP-mediated miR-503/LARP1 signaling promoted lung cancer growth, migration and invasion, providing a novel insight on the mechanism underlying lung cancer progression.
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Affiliation(s)
- Jingquan Han
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Guibin Zhao
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xiao Ma
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Qing Dong
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Hang Zhang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Yue Wang
- Department of Pharmacology and Toxicology, Wright State University, Fairborn, OH, 45435, USA
| | - Jian Cui
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
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93
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Fonseca BD, Lahr RM, Damgaard CK, Alain T, Berman AJ. LARP1 on TOP of ribosome production. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1480. [PMID: 29722158 PMCID: PMC6214789 DOI: 10.1002/wrna.1480] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
The ribosome is an essential unit of all living organisms that commands protein synthesis, ultimately fuelling cell growth (accumulation of cell mass) and cell proliferation (increase in cell number). The eukaryotic ribosome consists of 4 ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs). Despite its fundamental role in every living organism, our present understanding of how higher eukaryotes produce the various ribosome components is incomplete. Uncovering the mechanisms utilized by human cells to generate functional ribosomes will likely have far-reaching implications in human disease. Recent biochemical and structural studies revealed La-related protein 1 (LARP1) as a key new player in RP production. LARP1 is an RNA-binding protein that belongs to the LARP superfamily; it controls the translation and stability of the mRNAs that encode RPs and translation factors, which are characterized by a 5' terminal oligopyrimidine (5'TOP) motif and are thus known as TOP mRNAs. The activity of LARP1 is regulated by the mammalian target of rapamycin complex 1 (mTORC1): a eukaryotic protein kinase complex that integrates nutrient sensing with mRNA translation, particularly that of TOP mRNAs. In this review, we provide an overview of the role of LARP1 in the control of ribosome production in multicellular eukaryotes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
| | | | | | - Tommy Alain
- Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
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94
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Jiang F, Fang DB, Lin J, Chen Q, Zhu LX, Yu HZ. Correlation of LARP1 and E-cadherin expression with prognosis of intrahepatic cholangiocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3559-3566. [PMID: 31949734 PMCID: PMC6962836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 04/28/2018] [Indexed: 06/10/2023]
Abstract
OBJECTIVE The abnormal expression of LARP1 and E-cadherin (E-cad) is related to tumor occurrence and metastasis. Our study analyzed the expression of LARP1 and E-cad in intrahepatic cholangiocarcinoma (ICC) and investigated the prognostic value of the two proteins. METHODS Immunohistochemistry was performed to detect the expression of LARP1 and E-cad in 50 ICC clinical specimens with adjacent normal tissues and 20 normal bile duct tissues. In situ hybridization was performed to analyze the expression of LARP1 mRNA in all the specimens. RESULTS LARP1 protein and mRNA expression levels in ICC tumor tissues were significantly higher compared with corresponding adjacent normal tissues and normal epithelial tissues (P<0.01). E-cad protein expression in ICC tumor tissues was remarkably lower than that of the adjacent normal tissues and benign bile duct tissues (P<0.01). Correlation analysis demonstrated that LARP1 and E-cad expression levels were significantly related with the tumor-node-metastasis staging and lymph node metastasis (P<0.01), while no correlation was observed with patient age, gender, and tumor size. Moreover, Spearman rank correlation test revealed that LARP1 expression was negatively related to E-cad (P<0.05). More importantly, the patients with higher LARP1 expression or lower E-cad expression had a shorter overall survival postoperatively than those with LARP1 lower expression or E-cad higher expression. Multivariate analysis demonstrated that LARP1 and E-cad were both considered as important prognostic factors for survival time. CONCLUSION These findings suggest that the abnormal expression of LARP1 and E-cad showed a close relationship with the occurrence and metastasis of ICC, leading to poor prognosis indirectly.
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Affiliation(s)
- Fei Jiang
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - De-Bao Fang
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Jie Lin
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Qiang Chen
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Li-Xin Zhu
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Hong-Zhu Yu
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
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95
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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Xiao X, Zou J, Fang Y, Meng Y, Xiao C, Fu J, Liu S, Bai P, Yao Y. Fisetin and polymeric micelles encapsulating fisetin exhibit potent cytotoxic effects towards ovarian cancer cells. Altern Ther Health Med 2018; 18:91. [PMID: 29544480 PMCID: PMC5855937 DOI: 10.1186/s12906-018-2127-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/07/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND The anti-tumor activities of Natural compounds and their derivatives are of great interest to pharmaceutical industries. Fisetin is one of prospective natural compounds in this regard but unfortunately with poor hydrophilicity. METHODS The effects of unmodified and modified fisetin in cultured ovarian cancer cells were compared by transmission electronmicroscopy to determine apoptotic bodies, MTT assay to quantitate cell numbers, and fluorescence activated cell sorting analyse of various markers to determine the apoptotic state. In addition, the efficacy of fisetin and fisetin-micelles in vivo was determined by using immunocompromised mice. Apoptosis was measured by established markers using both western blot analysis and immunochemistry. Angiogenesis in a xenograft mouse model carring SKOV3 cells was evaluated by color Doppler ultrasound and immunohistochemistry. RESULT Multiple lines of evidence indicated that fisetin and fisetin micelles induce apoptosis in ovarian cancer cells in a dose-dependent manner. Histological analysis, terminal deoxynucleotidyltransferase-mediated nick-end labeling assay, western blot, immunohistochemical detection and microvessel density detection demonstrated that fisetin and fisetin micelles induced increased tumor apoptosis, proliferation suppression and antiangiogenesis activities. CONCLUSION As far as we know, the present study is the first time to demonstrate the potency of both fisetin and fisetin micelles inducing apoptosis in ovarian cancer cells. Further studies will be needed to validate the therapeutic potential of fisetin and fisetin micelles in ovarian cancer treatment.
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97
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Post-Transcriptional Regulation of Anti-Apoptotic BCL2 Family Members. Int J Mol Sci 2018; 19:ijms19010308. [PMID: 29361709 PMCID: PMC5796252 DOI: 10.3390/ijms19010308] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/05/2018] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
Anti-apoptotic B cell lymphoma 2 (BCL2) family members (BCL2, MCL1, BCLxL, BCLW, and BFL1) are key players in the regulation of intrinsic apoptosis. Dysregulation of these proteins not only impairs normal development, but also contributes to tumor progression and resistance to various anti-cancer therapies. Therefore, cells maintain strict control over the expression of anti-apoptotic BCL2 family members using multiple mechanisms. Over the past two decades, the importance of post-transcriptional regulation of mRNA in controlling gene expression and its impact on normal homeostasis and disease have begun to be appreciated. In this review, we discuss the RNA binding proteins (RBPs) and microRNAs (miRNAs) that mediate post-transcriptional regulation of the anti-apoptotic BCL2 family members. We describe their roles and impact on alternative splicing, mRNA turnover, and mRNA subcellular localization. We also point out the importance of future studies in characterizing the crosstalk between RBPs and miRNAs in regulating anti-apoptotic BCL2 family member expression and ultimately apoptosis.
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98
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The La protein counteracts cisplatin-induced cell death by stimulating protein synthesis of anti-apoptotic factor Bcl2. Oncotarget 2018; 7:29664-76. [PMID: 27105491 PMCID: PMC5045424 DOI: 10.18632/oncotarget.8819] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/28/2016] [Indexed: 02/06/2023] Open
Abstract
Up-regulation of anti-apoptotic factors is a critical mechanism of cancer cell resistance and often counteracts the success of chemotherapeutic treatment. Herein, we identified the cancer-associated RNA-binding protein La as novel factor contributing to cisplatin resistance. Our data demonstrate that depletion of the RNA-binding protein La in head and neck squamous cell carcinoma cells (HNSCC) increases the sensitivity toward cisplatin-induced cell death paralleled by reduced expression of the anti-apoptotic factor Bcl2. Furthermore, it is shown that transient expression of Bcl2 in La-depleted cells protects against cisplatin-induced cell death. By dissecting the underlying mechanism we report herein, that the La protein is required for Bcl2 protein synthesis in cisplatin-treated cells. The RNA chaperone La binds in close proximity to the authentic translation start site and unwinds a secondary structure embedding the authentic AUG. Altogether, our data support a novel model, whereby cancer-associated La protein contributes to cisplatin resistance by stimulating the translation of anti-apoptotic factor Bcl2 in HNSCC cells.
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99
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Blagden S, Abdel Mouti M, Chettle J. Ancient and modern: hints of a core post-transcriptional network driving chemotherapy resistance in ovarian cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1432. [PMID: 28762650 PMCID: PMC5763387 DOI: 10.1002/wrna.1432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/12/2017] [Accepted: 06/12/2017] [Indexed: 01/04/2023]
Abstract
RNA-binding proteins (RBPs) and noncoding (nc)RNAs (such as microRNAs, long ncRNAs, and others) cooperate within a post-transcriptional network to regulate the expression of genes required for many aspects of cancer behavior including its sensitivity to chemotherapy. Here, using an RBP-centric approach, we explore the current knowledge surrounding contributers to post-transcriptional gene regulation (PTGR) in ovarian cancer and identify commonalities that hint at the existence of an evolutionarily conserved core PTGR network. This network regulates survival and chemotherapy resistance in the contemporary context of the cancer cell. There is emerging evidence that cancers become dependent on PTGR factors for their survival. Further understanding of this network may identify innovative therapeutic targets as well as yield crucial insights into the hard-wiring of many malignancies, including ovarian cancer. WIREs RNA 2018, 9:e1432. doi: 10.1002/wrna.1432 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Mechanisms RNA in Disease and Development > RNA in Disease.
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100
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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