1
|
Chen W, Guo L, Xu H, Dai Y, Yao J, Wang L. NAC1 transcriptional activation of LDHA induces hepatitis B virus immune evasion leading to cirrhosis and hepatocellular carcinoma development. Oncogenesis 2024; 13:15. [PMID: 38704368 PMCID: PMC11069585 DOI: 10.1038/s41389-024-00515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024] Open
Abstract
Our study aimed to elucidate the molecular mechanisms underlying NAC1 (nucleus accumbens associated 1) transcriptional regulation of LDHA and its role in HBV immune evasion, thus contributing to the development of cirrhosis and hepatocellular carcinoma (HCC). Utilizing public datasets, we performed differential gene expression and weighted gene co-expression network analysis (WGCNA) on HBV-induced cirrhosis/HCC data. We identified candidate genes by intersecting differentially expressed genes with co-expression modules. We validated these genes using the TCGA database, conducting survival analysis to pinpoint key genes affecting HBV-HCC prognosis. We also employed the TIMER database for immune cell infiltration data and analyzed correlations with identified key genes to uncover potential immune escape pathways. In vitro, we investigated the impact of NAC1 and LDHA on immune cell apoptosis and HBV immune evasion. In vivo, we confirmed these findings using an HBV-induced cirrhosis model. Bioinformatics analysis revealed 676 genes influenced by HBV infection, with 475 genes showing differential expression in HBV-HCC. NAC1 emerged as a key gene, potentially mediating HBV immune escape through LDHA transcriptional regulation. Experimental data demonstrated that NAC1 transcriptionally activates LDHA, promoting immune cell apoptosis and HBV immune evasion. Animal studies confirmed these findings, linking NAC1-mediated LDHA activation to cirrhosis and HCC development. NAC1, highly expressed in HBV-infected liver cells, likely drives HBV immune escape by activating LDHA expression, inhibiting CD8 + T cells, and promoting cirrhosis and HCC development.
Collapse
Affiliation(s)
- Wenbiao Chen
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Liliangzi Guo
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Huixuan Xu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China.
| | - Lisheng Wang
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China.
| |
Collapse
|
2
|
Sun J, Luo J, Jiang F, Zhao J, Zhou S, Wang L, Zhang D, Ding Y, Li X. Exploring the cross-cancer effect of circulating proteins and discovering potential intervention targets for 13 site-specific cancers. J Natl Cancer Inst 2024; 116:565-573. [PMID: 38039160 DOI: 10.1093/jnci/djad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The proteome is an important reservoir of potential therapeutic targets for cancer. This study aimed to examine the causal associations between plasma proteins and cancer risk and to identify proteins with cross-cancer effects. METHODS Genetic instruments for 3991 plasma proteins were extracted from a large-scale proteomic study. Summary-level data of 13 site-specific cancers were derived from publicly available datasets. Proteome-wide Mendelian randomization and colocalization analyses were used to investigate the causal effect of circulating proteins on cancers. Protein-protein interactions and druggability assessment were conducted to prioritize potential therapeutic targets. Finally, systematical Mendelian randomization analysis between healthy lifestyle factors and cancer-related proteins was conducted to identify which proteins could act as interventional targets by lifestyle changes. RESULTS Genetically determined circulating levels of 58 proteins were statistically significantly associated with 7 site-specific cancers. A total of 39 proteins were prioritized by colocalization, of them, 11 proteins (ADPGK, CD86, CLSTN3, CSF2RA, CXCL10, GZMM, IL6R, NCR3, SIGLEC5, SIGLEC14, and TAPBP) were observed to have cross-cancer effects. Notably, 5 of these identified proteins (CD86, CSF2RA, CXCL10, IL6R, and TAPBP) have been targeted for drug development in cancer therapy; 8 proteins (ADPGK, CD86, CXCL10, GZMM, IL6R, SIGLEC5, SIGLEC14, TAPBP) could be modulated by healthy lifestyles. CONCLUSION Our study identified 39 circulating protein biomarkers with convincing causal evidence for 7 site-specific cancers, with 11 proteins demonstrating cross-cancer effects, and prioritized the proteins as potential intervention targets by either drugs or lifestyle changes, which provided new insights into the etiology, prevention, and treatment of cancers.
Collapse
Affiliation(s)
- Jing Sun
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jia Luo
- Department of Epidemiology and Health Statistics, the School of Public Health of Qingdao University, Qingdao, Shandong Province, China
| | - Fangyuan Jiang
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianhui Zhao
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siyun Zhou
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lijuan Wang
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, the School of Public Health of Qingdao University, Qingdao, Shandong Province, China
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| |
Collapse
|
3
|
Hao J, Liu Y, Guo F, Fu G, Ning J, Ruan X, Zheng X, Gao M. Lnc-SNHG5 Promoted Hepatocellular Carcinoma Progression Through the RPS3-NFκB Pathway. Int J Gen Med 2023; 16:5651-5664. [PMID: 38059157 PMCID: PMC10697148 DOI: 10.2147/ijgm.s442937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Background We planned to explore the underlying mechanism and clinical significance of lnc-SNHG5 and RPS3 in hepatocellular carcinoma in this current study. Methods The expression of Lnc-SNHG5 and RPS3 in HCC tissues and several cell lines were affirmed, respectively, using UALCAN, TIMER, TCGA and RT-qPCR assay. Cell proliferation ability was detected by colony formation assay and CCK8 assay. Cell apoptosis was monitored by flow cytometry assay. Next, the RPS3 expression levels and the related proteins in NFκB pathway were examined using Western blot analysis. The role of lnc-SNHG5 and RPS3 in vivo was identified by subcutaneous tumor bearing experiment. Results Lnc-SNHG5 was significantly increased in hepatocellular carcinoma tissues and in hepatocellular carcinoma cells. Further investigation showed that up-regulated lnc-SNHG5 promoted cell viability and cell proliferation ability of SMMC-7721 cells by regulating the cell apoptosis, while down-regulation of lnc-SNHG5 revealed opposite results in QGY-7703 cells. In terms of mechanism, we found that lnc-SNHG5 interacted with RPS3. Lnc-SNHG5 regulated the NFκB pathway through RPS3 in vitro and in vivo. Conclusion This study suggested that lnc-SNHG5 expression was signally up-regulated in hepatocellular carcinoma, and lnc-SNHG5 promoted the malignant phenotypes in vitro and in vivo via directly regulating RPS3-NFκB pathway. Lnc-SNHG5 might be a target for molecular targeted therapy, a potential and novel diagnostic marker for HCC patients.
Collapse
Affiliation(s)
- Jie Hao
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Department of Breast and Thyroid Surgery, Tianjin Union Medical Center of Nankai University, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center Nankai University, Tianjin, People’s Republic of China
| | - Yu Liu
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
| | - Fengli Guo
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital, Binzhou, People’s Republic of China
| | - Guiming Fu
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Thyroid-Otolaryngology Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Junya Ning
- Department of Breast and Thyroid Surgery, Tianjin Union Medical Center of Nankai University, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center Nankai University, Tianjin, People’s Republic of China
| | - Xianhui Ruan
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
| | - Ming Gao
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Department of Breast and Thyroid Surgery, Tianjin Union Medical Center of Nankai University, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center Nankai University, Tianjin, People’s Republic of China
| |
Collapse
|
4
|
Wang J, Huang J, Ding H, Ma J, Zhong H, Wang F, Chen Y, Peng H. Functional analysis of tumor-derived immunoglobulin lambda and its interacting proteins in cervical cancer. BMC Cancer 2023; 23:929. [PMID: 37784026 PMCID: PMC10544594 DOI: 10.1186/s12885-023-11426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Immunoglobulin lambda (Igλ) has been reported to be expressed in many normal and tumor tissues and cells. However, the function and clinical significance of tumor-derived Igλ remain unclear. METHODS The differential expressions of Immunoglobulin Lambda Constants (IGLCs) in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) were examined with The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Human Protein Atlas (HPA) databases. The effects of IGLCs on patient clinical phenotypes and prognosis were explored via bioinformatics analyses based on the TCGA databases. We used the bioinformatics analyses based on the TCGA and GTEx databases to elucidate the correlations among IGLC expressions, immunomodulator expressions, tumor stemness, and infiltration scores of tumor infiltrating immune cells. Co-immunoprecipitation (Co-IP) and silver staining combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to obtain potential tumor-derived Igλ-interacting proteins. Functional annotation of candidate proteins identified by LC-MS/MS was performed in Database for Annotation, Visualization and Integrated Discovery (DAVID). The bioinformatics analyses of 7 IGLCs in CESC and normal cervical tissues were performed based on TCGA, GTEx, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) databases. Protein-protein interaction (PPI) network was analyzed based on tumor-derived Igλ-interacting proteins in Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Immunohistochemistry (IHC) was used to validate the expressions of IGLCs in CESC. RESULTS We found that the expressions of the majority of IGLCs (IGLC1, IGLC2, IGLC3, IGLC4, IGLC5, IGLC6, and IGLC7) were upregulated in CESC tissues, compared with those in normal cervical tissues. The expressions of IGLC5 and IGLC7 had significant difference in different pathologic metastasis (M), one of tumor, node, and metastasis (TNM) staging system, categories of CESC. Except for disease-free interval (DFI), 4 IGLC (IGLC1, IGLC2, IGLC3, and IGLC7) expression levels were positively associated with patient overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) respectively in CESC tissues. 5 IGLC (IGLC1, IGLC2, IGLC3, IGLC6, and IGLC7) expressions were positively correlated with the expressions of a majority of immunomodulators respectively in CESC tissues. Tumor stemness was negatively correlated with the expressions of 4 IGLCs (IGLC1, IGLC2, IGLC3, and IGLC7) respectively in CESC tissues. Except for IGLC4, IGLC5, and IGLC7, 4 IGLC (IGLC1, IGLC2, IGLC3, and IGLC6) expressions were positively correlated with infiltration scores of 6 tumor-infiltrating immune cells (B cell, T cell CD4, T cell CD8, neutrophil, macrophage, and DC). After analyses of the above bioinformatics data of tumor-derived Igλ, Co-IP and LC-MS/MS were used to confirm that 4 proteins (RPL7, RPS3, H1-5, and H1-6) might interact with tumor-derived Igλ in cervical cancer cells. Functional analyses of these candidate proteins showed that they interacted with many proteins and were involved in various cellular biological processes. Finally, IHC was used to further confirm the above bioinformatics results, it was indicated that the expression level of Igλ in cervical adenocarcinoma and cervical squamous cell carcinoma was higher than that in normal cervical tissue. CONCLUSION This study comprehensively investigated the functions of tumor-derived Igλ and its interacting proteins based on bioinformatics analysis and the potential value of Igλ as a prognostic and therapeutic marker for CESC, providing new direction and evidence for CESC therapy.
Collapse
Affiliation(s)
- Juping Wang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
- Department of Pathology, Binhai Branch of National Regional Medical Center, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Jiangni Huang
- Department of Pathophysiology, School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Hao Ding
- Department of Pathophysiology, School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Jing Ma
- Department of Pathophysiology, School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Haohua Zhong
- Department of Pathophysiology, School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Fanlu Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Yupeng Chen
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hui Peng
- Fujian Provincial Institutes of Brain Disorders and Brain Sciences, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
- Department of Neurosurgery, The First Affiliated Hospital, Neurosurgery Research Institute, Fujian Medical University, Fuzhou, China.
| |
Collapse
|
5
|
Wang W, Zhang R, Feng N, Zhang L, Liu N. Overexpression of RBM34 Promotes Tumor Progression and Correlates with Poor Prognosis of Hepatocellular Carcinoma. J Clin Transl Hepatol 2023; 11:369-381. [PMID: 36643033 PMCID: PMC9817046 DOI: 10.14218/jcth.2022.00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND AIMS Emerging evidence suggests that RNA-binding motif (RBM) proteins are involved in hepatocarcinogenesis and act either as oncogenes or tumor suppressors. The objective of this study was to investigate the role of RBM34, an RBM protein, in hepatocellular carcinoma (HCC). METHODS We first examined the expression of RBM34 across cancers. The correlation of RBM34 with clinicopathological features and the prognostic value of RBM34 for HCC was then investigated. Functional enrichment analysis of RBM34-related differentially expressed genes (DEGs) was performed to explore its biological function. RNA sequencing (RNA-seq) was applied to identify downstream genes and pathways affected upon RBM34 knockout. The correlation of RBM34 with immune characteristics was also analyzed. The oncogenic function of RBM34 was examined in in vitro and in vivo experiments. RESULTS RBM34 was highly expressed in hepatocellular carcinoma and correlated with poor clinicopathological features and prognosis. RBM34 was positively associated with tumor immune cell infiltration, biomarkers of immune cells, and immune checkpoint expression. A positive correlation was also observed between RBM34, T cell exhaustion, and regulatory T cell marker genes. Knockout of RBM34 significantly inhibited cell proliferation, migration, and xenograft tumor growth, and sensitized HCC cells to sorafenib treatment. RBM34 inhibition reduced FGFR2 expression and affected PI3K-AKT pathway activation in HCC cells. CONCLUSIONS Our study suggests that RBM34 may serve as a new prognostic marker and therapeutic target of HCC.
Collapse
Affiliation(s)
- Wei Wang
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Rui Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ning Feng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Longzhen Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Correspondence to: Nianli Liu and Longzhen Zhang, Cancer Institute of Xuzhou Medical University, No.84 West Huaihai Road, Xuzhou, Jiangsu 221000, China. ORCID: https://orcid.org/0000-0002-0602-6709 (NL). Tel/Fax: +86-516-5582530, E-mail: (NL), (LZ)
| | - Nianli Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Correspondence to: Nianli Liu and Longzhen Zhang, Cancer Institute of Xuzhou Medical University, No.84 West Huaihai Road, Xuzhou, Jiangsu 221000, China. ORCID: https://orcid.org/0000-0002-0602-6709 (NL). Tel/Fax: +86-516-5582530, E-mail: (NL), (LZ)
| |
Collapse
|
6
|
Xu K, Zheng S, Li B, Shao Y, Yin X. Molecular characterization of colorectal mucinous adenocarcinoma and adenocarcinoma, not otherwise specified, identified by multiomic data analysis. Front Mol Biosci 2023; 10:1150362. [PMID: 37091868 PMCID: PMC10114614 DOI: 10.3389/fmolb.2023.1150362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
Adenocarcinoma not otherwise specified (AC) and mucinous adenocarcinoma (MC) have different biological behaviors and clinical features. We utilized our previous proteomic data and public transcriptome, single-cell transcriptome, and spatial transcriptome databases to profile the molecular atlas of the tumor microenvironments of MC, AC, and normal colon tissues. By exploring the general and specific molecular features of AC and MC, we found that AC was immune-active but exposed to a hypoxic microenvironment. MC cells could protect against DNA damage, and the microenvironment was unfavorable to leukocyte transendothelial migration. We identified several potential molecular and cellular targets of AC and MC for future research. We also highlighted that the major difference between AC and MC was not the variety of cell types and functions but possibly cell interactions. Stromal and epithelial cell interactions play important roles in both MC and AC, but different regulatory pathways were involved.
Collapse
Affiliation(s)
- Kailun Xu
- Department of Breast Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Shu Zheng
- Department of Breast Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Baosheng Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yingkuan Shao
- Department of Breast Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
- *Correspondence: Yingkuan Shao, ; Xiaoyang Yin,
| | - Xiaoyang Yin
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- *Correspondence: Yingkuan Shao, ; Xiaoyang Yin,
| |
Collapse
|
7
|
Chen XX, Zhang BH, Lu YC, Li ZQ, Chen CY, Yang YC, Chen YJ, Ma D. A novel 16-gene alternative mRNA splicing signature predicts tumor relapse and indicates immune activity in stage I–III hepatocellular carcinoma. Front Pharmacol 2022; 13:939912. [PMID: 36147313 PMCID: PMC9485890 DOI: 10.3389/fphar.2022.939912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a lethal disease with high relapse and dismal survival rates. Alternative splicing (AS) plays a crucial role in tumor progression. Herein, we aim to integratedly analyze the relapse-associated AS events and construct a signature predicting tumor relapse in stage I–III HCC. Methods: AS events of stage I–III HCC with tumor relapse or long-term relapse-free survival were profiled to identify the relapse-associated AS events. A splicing network was set up to analyze the correlation between the relapse-associated AS events and splicing factors. Cox regression analysis and receiver operating characteristic curve were performed to develop and validate the relapse-predictive AS signature. Single-sample gene set enrichment analysis (ssGSEA) and the ESTIMATE algorithm were used to assess the immune infiltration status of the HCC microenvironment between different risk subgroups. Unsupervised cluster analysis was conducted to assess the relationship between molecular subtypes and local immune status and clinicopathological features. Results: In total, 2441 ASs derived from 1634 mRNA were identified as relapse-associated AS events. By analyzing the proteins involved in the relapse-associated AS events, 1573 proteins with 11590 interactions were included in the protein–protein interaction (PPI) network. In total, 16 splicing factors and 61 relapse-associated AS events with 85 interactions were involved in the splicing network. The relevant genes involved in the PPI network and splicing network were also analyzed by Gene Ontology enrichment analysis. Finally, we established a robust 16-gene AS signature for predicting tumor relapse in stage I–III HCC with considerable AUC values in all of the training cohort, testing cohort, and entire cohort. The ssGSEA and ESTIMATE analyses showed that the AS signature was significantly associated with the immune status of the HCC microenvironment. Moreover, four molecular subgroups with distinguishing tumor relapse modes and local immune status were also revealed. Conclusion: Our study built a novel 16-gene AS signature that robustly predicts tumor relapse and indicates immune activity in stage I–III HCC, which may facilitate the deep mining of the mechanisms associated with tumor relapse and tumor immunity and the development of novel individualized treatment targets for HCC.
Collapse
Affiliation(s)
- Xu-Xiao Chen
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xu-Xiao Chen, ; Yong-Jun Chen, ; Di Ma,
| | - Bao-Hua Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Yan-Cen Lu
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zi-Qiang Li
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cong-Yan Chen
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Chen Yang
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong-Jun Chen
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xu-Xiao Chen, ; Yong-Jun Chen, ; Di Ma,
| | - Di Ma
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xu-Xiao Chen, ; Yong-Jun Chen, ; Di Ma,
| |
Collapse
|
8
|
Rui X, Huang Z, Chen R, Chen Y, Wang Y, Huang Z. RPS3 Promotes the Metastasis and Cisplatin Resistance of Adenoid Cystic Carcinoma. Front Oncol 2022; 12:804439. [PMID: 35847905 PMCID: PMC9280127 DOI: 10.3389/fonc.2022.804439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
Background Adenoid cystic carcinoma (ACC) is a malignant tumor in salivary gland tissue, that is characterized by strong invasiveness and lung metastasis, leading to poor survival rates. RPS3 is been reported to be associated with the biological functions of tumor cells. This study explored the regulatory effect of RPS3 in ACC to provide new therapeutic targets for ACC therapy. Methods We reviewed the clinical and pathologic data of 73 ACC patients. The expression of RPS3 was examined in ACC by immunohistochemistry. Transwell, wound healing, half-maximal inhibitory concentration (IC50) and other experiments were used to determine the regulatory effect of RPS3 on ACC functions. Coimmunoprecipitation and mass spectrometry analysis were used to detect the binding proteins of RPS3, mechanisms by which RPS3/STAT1/NF-kB signaling regulates ACC behavior were assessed using western blotting (WB), qPCR, etc. To explore the regulatory effect of RPS3 on ACC in vivo, we constructed nude mouse sciatic nerve infiltration model and a lung metastasis model for studies. Results High RPS3 expression was associated with metastasis and a poor prognosis in ACC patients. Inhibition of RPS3 expression reduced ACC migration, invasion and cisplatin resistance, and overexpression of RPS3 promoted ACC migration, invasion and cisplatin resistance. Further experiments revealed that RPS3 can activate the STAT1/NF-kB signaling pathway and regulate ACC behavior through binding to STAT1. The incidence of sciatic nerve infiltration and lung metastasis in nude mice after RPS3 knockdown was lower than that of the control group in vivo. Conclusion RPS3 is highly expressed and associated with the prognosis and survival of ACC patients. The RPS3/STAT1/NF-kB pathway may play an important regulatory role in ACC migration, invasion and chemoresistance. As a new therapeutic target of ACC, its clinical application value is worthy of attention and further exploration.
Collapse
Affiliation(s)
- Xi Rui
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zixian Huang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Chen
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongju Chen
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Wang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Zhiquan Huang, ; ; Yan Wang,
| | - Zhiquan Huang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Zhiquan Huang, ; ; Yan Wang,
| |
Collapse
|
9
|
Li JR, Tang M, Li Y, Amos CI, Cheng C. Genetic variants associated mRNA stability in lung. BMC Genomics 2022; 23:196. [PMID: 35272635 PMCID: PMC8915503 DOI: 10.1186/s12864-022-08405-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Background Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs). Results Here, we presented a computational framework that takes advantage of recently developed methods to infer the mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3942 genes and 186,132 eQTLs for 4751 genes from 15,122,700 genetic variants for 13,476 genes on the autosomes, respectively. Interestingly, our results indicated that stQTLs were enriched in the CDS and 3’UTR regions, while eQTLs are enriched in the CDS, 3’UTR, 5’UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08405-y.
Collapse
Affiliation(s)
- Jian-Rong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Mabel Tang
- Department of BioSciences, Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Yafang Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
10
|
Ramani K, Robinson AE, Berlind J, Fan W, Abeynayake A, Binek A, Barbier-Torres L, Noureddin M, Nissen NN, Yildirim Z, Erbay E, Mato JM, Van Eyk JE, Lu SC. S-adenosylmethionine inhibits la ribonucleoprotein domain family member 1 in murine liver and human liver cancer cells. Hepatology 2022; 75:280-296. [PMID: 34449924 PMCID: PMC8766892 DOI: 10.1002/hep.32130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND AIMS Methionine adenosyltransferase 1A (MAT1A) is responsible for S-adenosylmethionine (SAMe) biosynthesis in the liver. Mice lacking Mat1a have hepatic SAMe depletion and develop NASH and HCC spontaneously. Several kinases are activated in Mat1a knockout (KO) mice livers. However, characterizing the phospho-proteome and determining whether they contribute to liver pathology remain open for study. Our study aimed to provide this knowledge. APPROACH AND RESULTS We performed phospho-proteomics in Mat1a KO mice livers with and without SAMe treatment to identify SAMe-dependent changes that may contribute to liver pathology. Our studies used Mat1a KO mice at different ages treated with and without SAMe, cell lines, in vitro translation and kinase assays, and human liver specimens. We found that the most striking change was hyperphosphorylation and increased content of La-related protein 1 (LARP1), which, in the unphosphorylated form, negatively regulates translation of 5'-terminal oligopyrimidine (TOP)-containing mRNAs. Consistently, multiple TOP proteins are induced in KO livers. Translation of TOP mRNAs ribosomal protein S3 and ribosomal protein L18 was enhanced by LARP1 overexpression in liver cancer cells. We identified LARP1-T449 as a SAMe-sensitive phospho-site of cyclin-dependent kinase 2 (CDK2). Knocking down CDK2 lowered LARP1 phosphorylation and prevented LARP1-overexpression-mediated increase in translation. LARP1-T449 phosphorylation induced global translation, cell growth, migration, invasion, and expression of oncogenic TOP-ribosomal proteins in HCC cells. LARP1 expression is increased in human NASH and HCC. CONCLUSIONS Our results reveal a SAMe-sensitive mechanism of LARP1 phosphorylation that may be involved in the progression of NASH to HCC.
Collapse
Affiliation(s)
- Komal Ramani
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Aaron E. Robinson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Smidt Heart Institute and Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Joshua Berlind
- Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033
| | - Wei Fan
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Aushinie Abeynayake
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Aleksandra Binek
- Smidt Heart Institute and Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Lucía Barbier-Torres
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Mazen Noureddin
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Nicholas N. Nissen
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Zehra Yildirim
- Department of Cardiology, Department of Biomedical Sciences and Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Ebru Erbay
- Department of Cardiology, Department of Biomedical Sciences and Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - José M. Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology, Derio, Bizkaia 48160, Spain
| | - Jennifer E. Van Eyk
- Smidt Heart Institute and Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Shelly C. Lu
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| |
Collapse
|
11
|
Wu J, Wu Y, Guo Q, Wang S, Wu X. RNA-binding proteins in ovarian cancer: a novel avenue of their roles in diagnosis and treatment. J Transl Med 2022; 20:37. [PMID: 35062979 PMCID: PMC8783520 DOI: 10.1186/s12967-022-03245-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/11/2022] [Indexed: 12/18/2022] Open
Abstract
Ovarian cancer (OC), an important cause of cancer-related death in women worldwide, is one of the most malignant cancers and is characterized by a poor prognosis. RNA-binding proteins (RBPs), a class of endogenous proteins that can bind to mRNAs and modify (or even determine) the amount of protein they can generate, have attracted great attention in the context of various diseases, especially cancers. Compelling studies have suggested that RBPs are aberrantly expressed in different cancer tissues and cell types, including OC tissues and cells. More specifically, RBPs can regulate proliferation, apoptosis, invasion, metastasis, tumorigenesis and chemosensitivity and serve as potential therapeutic targets in OC. Herein, we summarize what is currently known about the biogenesis, molecular functions and potential roles of human RBPs in OC and their prospects for application in the clinical treatment of OC.
Collapse
Affiliation(s)
- Jiangchun Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, People's Republic of China
| | - Yong Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, People's Republic of China
| | - Qinhao Guo
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, People's Republic of China
| | - Simin Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xiaohua Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, People's Republic of China.
| |
Collapse
|
12
|
Zhang Q, Zhang Y, Guo Y, Tang H, Li M, Liu L. A novel machine learning derived RNA-binding protein gene-based score system predicts prognosis of hepatocellular carcinoma patients. PeerJ 2022; 9:e12572. [PMID: 35036125 PMCID: PMC8697767 DOI: 10.7717/peerj.12572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023] Open
Abstract
Background Although the expression of RNA-binding protein (RBP) genes in hepatocellular carcinoma (HCC) varies and is associated with tumor progression, there has been no overview study with multiple cohorts and large samples. The HCC-associated RBP genes need to be more accurately identified, and their clinical application value needs to be further explored. Methods First, we used the robust rank aggregation (RRA) algorithm to extract HCC-associated RBP genes from nine HCC microarray datasets and verified them in The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) cohort and International Cancer Genome Consortium (ICGC) Japanese liver cancer (ICGC-LIRI-JP) cohort. In addition, the copy number variation (CNV), single-nucleotide variant (SNV), and promoter-region methylation data of HCC-associated RBP genes were analyzed. Using the random forest algorithm, we constructed an RBP gene–based prognostic score system (RBP-score). We then evaluated the ability of RBP-score to predict the prognosis of patients. The relationships between RBP-score and other clinical characteristics of patients were analyzed. Results The RRA algorithm identified 30 RBP mRNAs with consistent expression patterns across the nine HCC microarray datasets. These 30 RBP genes were defined as HCC-associated RBP genes. Their mRNA expression patterns were further verified in the TCGA-LIHC and ICGC-LIRI-JP cohorts. Among these 30 RBP genes, some showed significant copy number gain or loss, while others showed differences in the methylation levels of their promoter regions. Some RBP genes were risk factors or protective factors for the prognosis of patients. We extracted 10 key HCC-associated RBP genes using the random forest algorithm and constructed an RBP-score system. RBP-score effectively predicted the overall survival (OS) and disease-free survival (DFS) of HCC patients and was associated with the tumor, node, metastasis (TNM) stage, α-fetoprotein (AFP), and metastasis risk. The clinical value of RBP-score was validated in datasets from different platforms. Cox analysis suggested that a high RBP-score was an independent risk factor for poor prognosis in HCC patients. We also successfully established a combined RBP-score+TNM LASSO-Cox model that more accurately predicted the prognosis. Conclusion The RBP-score system constructed based on HCC-associated RBP genes is a simple and highly effective prognostic evaluation tool. It is suitable for different subgroups of HCC patients and has cross-platform characteristics. Combining RBP-score with the TNM staging system or other clinical parameters can lead to an even greater clinical benefit. In addition, the identified HCC-associated RBP genes may serve as novel targets for HCC treatment.
Collapse
Affiliation(s)
- Qiangnu Zhang
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital).,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | | | | | | | - Mingyue Li
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital).,Shenzhen People's Hospital, Shenzhen, China
| | - Liping Liu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital).,Shenzhen People's Hospital, Shenzhen, China
| |
Collapse
|
13
|
Deregulation of ribosomal proteins in human cancers. Biosci Rep 2021; 41:230380. [PMID: 34873618 PMCID: PMC8685657 DOI: 10.1042/bsr20211577] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ribosome, the site for protein synthesis, is composed of ribosomal RNAs (rRNAs) and ribosomal proteins (RPs). The latter have been shown to have many ribosomal and extraribosomal functions. RPs are implicated in a variety of pathological processes, especially tumorigenesis and cell transformation. In this review, we will focus on the recent advances that shed light on the effects of RPs deregulation in different types of cancer and their roles in regulating the tumor cell fate.
Collapse
|
14
|
Niu M, Wu J, Zou Q, Liu Z, Xu L. rBPDL:Predicting RNA-Binding Proteins Using Deep Learning. IEEE J Biomed Health Inform 2021; 25:3668-3676. [PMID: 33780344 DOI: 10.1109/jbhi.2021.3069259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
RNA-binding protein (RBP) is a powerful and wide-ranging regulator that plays an important role in cell development, differentiation, metabolism, health and disease. The prediction of RBPs provides valuable guidance for biologists. Although experimental methods have made great progress in predicting RBP, they are time-consuming and not flexible. Therefore, we developed a network model, rBPDL, by combining a convolutional neural network and long short-term memory for multilabel classification of RBPs. Moreover, to achieve better prediction results, we used a voting algorithm for ensemble learning of the model. We compared rBPDL with state-of-the-art methods and found that rBPDL significantly improved identification performance for the RBP68 dataset, with a macro-Area Under Curve (AUC), micro-AUC, and weighted AUC of 0.936, 0.962, and 0.946, respectively. Furthermore, through AUC statistical analysis of the RBP domain, we analyzed the performance of rBPDL and found that the RBP identification performance in the same domain was similar. In addition, we analyzed the performance preferences and physicochemical properties of the binding protein amino acids and explored the characteristics that affect the binding by using the RBP86 dataset.
Collapse
|
15
|
Li M, Liu Z, Wang J, Liu H, Gong H, Li S, Jia M, Mao Q. Systematic Analysis Identifies a Specific RNA-Binding Protein-Related Gene Model for Prognostication and Risk-Adjustment in HBV-Related Hepatocellular Carcinoma. Front Genet 2021; 12:707305. [PMID: 34422009 PMCID: PMC8371711 DOI: 10.3389/fgene.2021.707305] [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: 05/09/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
Objective Increasing evidence shows that dysregulated RNA binding proteins (RBPs) modulate the progression of several malignancies. Nevertheless, their clinical implications of RBPs in HBV-related hepatocellular carcinoma (HCC) remain largely undefined. Here, this study systematically analyzed the associations of RBPs with HBV-related HCC prognosis. Methods Based on differentially expressed RBPs between HBV-related HCC and control specimens, prognosis-related RBPs were screened by univariate analyses. A LASSO model was then created. Kaplan-Meier curves, ROCs, multivariate analyses, subgroup analyses and external verification were separately applied to assess the efficacy of this model in predicting prognosis and recurrence of patients. A nomogram was created by incorporating the model and clinical indicators, which was verified by ROCs, calibration curves and decision curve analyses. By CIBERSORT algorithm, the association between the risk score and immune cell infiltrations was evaluated. Results Totally, 54 RBPs were distinctly correlated to prognosis of HBV-related HCC. An 11-RBP model was created, containing POLR2L, MRPS12, DYNLL1, ZFP36, PPIH, RARS, SRP14, DDX41, EIF2B4, and NOL12. This risk score sensitively and accurately predicted one-, three- and five-year overall survival, disease-free survival, and progression-free interval. Compared to other clinical parameters, this risk score had the best predictive efficacy. Also, the clinical generalizability of the model was externally verified in the GSE14520 dataset. The nomogram may predict patients' survival probabilities. Also, the risk score was related to the components in the immune microenvironment. Conclusion Collectively, RBPs may act as critical elements in the malignant progression of HBV-related HCC and possess potential implications on prognostication and therapy decision.
Collapse
Affiliation(s)
- Maoshi Li
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Zhongwei Liu
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Jing Wang
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Huimin Liu
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Hongmei Gong
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Shilian Li
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Ming Jia
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Qing Mao
- Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| |
Collapse
|
16
|
Zhao D, Qian L, Zhuang D, Wang L, Cao Y, Zhou F, Zhang S, Liu Y, Liang Y, Zhang W, Kang W, Zhang M, Wang Y, Zhang F, Zhang W, Xiao J, Xu G, Lv Y, Zou X, Zhuge Y, Zhang B. Inhibition of ribosomal RNA processing 15 Homolog (RRP15), which is overexpressed in hepatocellular carcinoma, suppresses tumour growth via induction of senescence and apoptosis. Cancer Lett 2021; 519:315-327. [PMID: 34343634 DOI: 10.1016/j.canlet.2021.07.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 01/10/2023]
Abstract
Recent studies suggest that RRP15 (Ribosomal RNA Processing 15 Homolog) might be a potential target for cancer therapy. However, the role of RRP15 in hepatocarcinogenesis remains poorly delineated. In this study, we aimed to evaluate the expression and biological function of RRP15 in human hepatocellular carcinoma (HCC). We show that RRP15 was up regulated in HCC cell lines and tumours. Up-regulation of RRP15 in HCC tumours was also correlated with unfavorable prognosis. We further show that the frequent up-regulation of RRP15 in HCCs is at least partly driven by recurrent gene copy gain at chromosome 1q41. Functional studies indicated that RRP15 knockdown suppresses HCC proliferation and growth both in vitro and in vivo. Mechanistically, RRP15 depletion in p53-wild-type HepG2 cells induced senescence via activation of the p53-p21 signalling pathway through enhanced interaction of RPL11 with MDM2, as well as inhibition of SIRT1-mediated p53 deacetylation. Moreover, RRP15 depletion in p53-mutant PLC5 and p53-deleted Hep3B cells induced metabolic shift from the glycolytic pentose-phosphate to mitochondrial oxidative phosphorylation via regulating a series of key genes such as HK2 and TIGAR, and thus, promoted the generation of ROS and apoptosis. Taken together, our findings provide evidence for an important role of the RRP15 gene in hepatocarcinogenesis through regulation of HCC proliferation and growth, raising the possibility that targeting RRP15 may represent a potential therapeutic strategy for HCC treatment.
Collapse
Affiliation(s)
- Dian Zhao
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Liping Qian
- Centre for Experimental Animal, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Duanming Zhuang
- Department of Gastroenterology, Gaochun People's Hospital, Nanjing, Jiangsu, China
| | - Lei Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yu Cao
- Department of Gastroenterology, Changhai Hospital, The Second Military Medical University/Naval Medical University, Shanghai, China
| | - Fan Zhou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Shu Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Ying Liu
- Department of Ultrasound Diagnostics, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Ying Liang
- Department of Anesthesiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Wenjie Zhang
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ming Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yi Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Feng Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Wei Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jiangqiang Xiao
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Guifang Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Ying Lv
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaoping Zou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China.
| | - Yuzheng Zhuge
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China.
| | - Bin Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China; Department of Gastroenterology, Gaochun People's Hospital, Nanjing, Jiangsu, China; Department of Gastroenterology, Yining People's Hospital, Yining, China.
| |
Collapse
|
17
|
Lu Y, Yan Y, Li B, Liu M, Liang Y, Ye Y, Cheng W, Li J, Jiao J, Chang S. A Novel Prognostic Model for Oral Squamous Cell Carcinoma: The Functions and Prognostic Values of RNA-Binding Proteins. Front Oncol 2021; 11:592614. [PMID: 34395233 PMCID: PMC8362834 DOI: 10.3389/fonc.2021.592614] [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: 08/07/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The biological roles and clinical significance of RNA-binding proteins (RBPs) in oral squamous cell carcinoma (OSCC) are not fully understood. We investigated the prognostic value of RBPs in OSCC using several bioinformatic strategies. MATERIALS AND METHODS OSCC data were obtained from a public online database, the Limma R package was used to identify differentially expressed RBPs, and functional enrichment analysis was performed to elucidate the biological functions of the above RBPs in OSCC. We performed protein-protein interaction (PPI) network and Cox regression analyses to extract prognosis-related hub RBPs. Next, we established and validated a prognostic model based on the hub RBPs using Cox regression and risk score analyses. RESULTS We found that the differentially expressed RBPs were closely related to the defense response to viruses and multiple RNA processes. We identified 10 prognosis-related hub RBPs (ZC3H12D, OAS2, INTS10, ACO1, PCBP4, RNASE3, PTGES3L-AARSD1, RNASE13, DDX4, and PCF11) and effectively predicted the overall survival of OSCC patients. The area under the receiver operating characteristic (ROC) curve (AUC) of the risk score model was 0.781, suggesting that our model exhibited excellent prognostic performance. Finally, we built a nomogram integrating the 10 RBPs. The internal validation cohort results showed a reliable predictive capability of the nomogram for OSCC. CONCLUSION We established a novel 10-RBP-based model for OSCC that could enable precise individual treatment and follow-up management strategies in the future.
Collapse
Affiliation(s)
- Yingjuan Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yongcong Yan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Hepatobiliary Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bowen Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mo Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yancan Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yushan Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Weiqi Cheng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jinsong Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiuyang Jiao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shaohai Chang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| |
Collapse
|
18
|
Chen C, Zheng Q, Pan S, Chen W, Huang J, Cao Y, Tu Y, Li Z, Yu C, Jie Z. The RNA-Binding Protein NELFE Promotes Gastric Cancer Growth and Metastasis Through E2F2. Front Oncol 2021; 11:677111. [PMID: 34295816 PMCID: PMC8290256 DOI: 10.3389/fonc.2021.677111] [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: 03/07/2021] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
Worldwide, the incidence rate of gastric cancer ranks fifth, and the mortality rate of gastric cancer ranks third among all malignant tumors. However, the pathogenesis of gastric cancer remains poorly understood. In this study, we demonstrated that the expression level of NELFE is higher in human gastric cancer tissues than in adjacent nontumor tissues. A high level of NELFE is associated with worse postoperative overall survival (OS) and relapse-free survival (RFS) rates in patients with gastric cancer. Moreover, the expression of NELFE is correlated with high tumor grade and lymph node metastasis in gastric cancer patients. Knockdown of NELFE dramatically inhibits the cell proliferation and metastasis of gastric cancer xenografts in vivo. Furthermore, we found that NELFE binding to the 3'UTR of E2F2 affects the mRNA stability of E2F2 to regulate the expression level of E2F2. In gastric cancer, E2F2 also acts as an oncogene to inhibit the proliferation and migration of gastric cancer cells by knocking down the expression level of E2F2. However, overexpressing E2F2 in cells with NELFE knockdown significantly reverses the inhibition of cell proliferation and migration induced by NELFE knockdown. Therefore, NELFE at least partially functions as an oncogene through E2F2. Moreover, CIBERSORTx analysis of the proportion of tumor-infiltrating immune cells (TICs) revealed that immune cells are correlated with NELFE and E2F2 expression, suggesting that NELFE and E2F2 might be responsible for the preservation of the immunodominant status for gastric cancer. In conclusion, NELFE acts as an oncogene in gastric cancer and can be used as a potential therapeutic target.
Collapse
Affiliation(s)
- Changyu Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qiang Zheng
- Department of Anesthesiology (High-Tech Branch), The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shubo Pan
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wenzheng Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianfeng Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi Tu
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhengrong Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Changjun Yu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhigang Jie
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| |
Collapse
|
19
|
Wu ZH, Huang HM, Yang DL. Integrated analysis of the functions and prognostic values of RNA binding proteins in hepatocellular carcinoma. BMC Gastroenterol 2021; 21:265. [PMID: 34130650 PMCID: PMC8204501 DOI: 10.1186/s12876-021-01843-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC), one of the most common malignant tumors worldwide, ranks as the fifth most common cancer and has been the second most frequent cause of cancer-related death. RNA binding proteins (RBPs) are proteins that interact with different classes of RNA and are commonly detected in cells. Methods We used RNA sequencing data from TCGA to display dysfunctional RBPs microenvironments and provide potential useful biomarkers for HCC diagnosis and prognosis. Results 330 differently expressed RBPs (208 upregulated and 122 downregulated) were identified. KEGG were mainly enriched in RNA degradation, Influenza A, Hepatitis C, RIG-I-like receptor signaling pathway, Herpes simplex virus 1 infection and RNA transport. CBioPortal results demonstrated that these genes were altered in 50 samples out of 357 HCC patients (14%) and the amplification of BRCA1 was the largest frequent copy-number alteration. Conclusion Based on the online database, we identified novel RBPs markers for the prognosis of hepatocellular carcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-021-01843-0.
Collapse
Affiliation(s)
- Zeng-Hong Wu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hong-Ming Huang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Dong-Liang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| |
Collapse
|
20
|
Retraction of 'RNA-binding protein RPS3 contributes to hepatocarcinogenesis by post-transcriptionally up-regulating SIRT1'. Nucleic Acids Res 2021; 49:6004. [PMID: 33959772 PMCID: PMC8191794 DOI: 10.1093/nar/gkab403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
21
|
Kan G, Wang Z, Sheng C, Chen G, Yao C, Mao Y, Chen S. Dual Inhibition of DKC1 and MEK1/2 Synergistically Restrains the Growth of Colorectal Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004344. [PMID: 34026451 PMCID: PMC8132060 DOI: 10.1002/advs.202004344] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/28/2021] [Indexed: 05/09/2023]
Abstract
Colorectal cancer, one of the most commonly diagnosed cancers worldwide, is often accompanied by uncontrolled proliferation of tumor cells. Dyskerin pseudouridine synthase 1 (DKC1), screened using the genome-wide RNAi strategy, is a previously unidentified key regulator that promotes colorectal cancer cell proliferation. Enforced expression of DKC1, but not its catalytically inactive mutant D125A, accelerates cell growth in vitro and in vivo. DKC1 knockdown or its inhibitor pyrazofurin attenuates cell proliferation. Proteomics, RNA immunoprecipitation (RIP)-seq, and RNA decay analyses reveal that DKC1 binds to and stabilizes the mRNA of several ribosomal proteins (RPs), including RPL10A, RPL22L1, RPL34, and RPS3. DKC1 depletion significantly accelerates mRNA decay of these RPs, which mediates the oncogenic function of DKC1. Interestingly, these DKC1-regulated RPs also interact with HRAS and suppress the RAS/RAF/MEK/ERK pathway. Pyrazofurin and trametinib combination synergistically restrains colorectal cancer cell growth in vitro and in vivo. Furthermore, DKC1 is markedly upregulated in colorectal cancer tissues compared to adjacent normal tissues. Colorectal cancer patients with higher DKC1 expression has consistently poorer overall survival and progression-free survival outcomes. Taken together, these data suggest that DKC1 is an essential gene and candidate therapeutic target for colorectal cancer.
Collapse
Affiliation(s)
- Guangyan Kan
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Ziyang Wang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Chunjie Sheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Gong Chen
- Department of Colorectal SurgeryState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Chen Yao
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Yizhi Mao
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Shuai Chen
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| |
Collapse
|
22
|
Du X, Zhang C, Yin C, Wang W, Yan X, Xie D, Zheng X, Zheng Q, Li M, Song Z. High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma. Front Oncol 2021; 11:633899. [PMID: 33828983 PMCID: PMC8019910 DOI: 10.3389/fonc.2021.633899] [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: 11/26/2020] [Accepted: 02/09/2021] [Indexed: 12/24/2022] Open
Abstract
Molecular mechanisms underlying the tumorigenesis of a highly malignant cancer, cholangiocarcinoma (CCA), are still obscure. In our study, the CCA expression profile data were acquired from The Cancer Genome Atlas (TCGA) database, and differentially expressed genes (DEGs) in the TCGA-Cholangiocarcinoma (TCGA-CHOL) data set were utilized to construct a co-expression network via weighted gene co-expression network analysis (WGCNA). The blue gene module associated with the histopathologic grade of CCA was screened. Then, five candidate hub genes were screened by combining the co-expression network with protein–protein interaction (PPI) network. After progression and survival analyses, bloom syndrome helicase (BLM) was ultimately identified as a real hub gene. Moreover, the receiver operating characteristic (ROC) curve analysis suggested that BLM had a favorable diagnostic and predictive recurrence value for CCA. The gene set enrichment analysis (GSEA) results for a single hub gene revealed the importance of cell cycle-related pathways in the CCA progression and prognosis. Furthermore, we detected the BLM expression in vitro, and the results demonstrated that the expression level of BLM was much higher in the CCA tissues and cells relative to adjacent non-tumor samples and normal bile duct epithelial cells. Additionally, after further silencing the BLM expression by small interfering RNA (siRNA), the proliferation and migration ability of CCA cells were all inhibited, and the cell cycle was arrested. Altogether, a real hub gene (BLM) and cell cycle-related pathways were identified in the present study, and the gene BLM may be involved in the CCA progression and could act as a reliable biomarker for potential diagnosis and prognostic evaluation.
Collapse
Affiliation(s)
- Xiaolong Du
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Zhang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuanzheng Yin
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueke Yan
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dawei Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xichuan Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qichang Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Li
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zifang Song
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
23
|
Man Z, Chen Y, Gao L, Xei G, Li Q, Lu Q, Yan J. A Prognostic Model Based on RNA Binding Protein Predicts Clinical Outcomes in Hepatocellular Carcinoma Patients. Front Oncol 2021; 10:613102. [PMID: 33643914 PMCID: PMC7907500 DOI: 10.3389/fonc.2020.613102] [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: 10/01/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022] Open
Abstract
Dysregulation of RNA binding proteins (RBPs) is closely associated with tumor events. However, the function of RBPs in hepatocellular carcinoma (HCC) has not been fully elucidated. The RNA sequences and relevant clinical data of HCC were retrieved from the The Cancer Genome Atlas (TCGA) database to identify distinct RBPs. Subsequently, univariate and multivariate cox regression analysis was performed to evaluate the overall survival (OS)-associated RBPs. The expression levels of prognostic RBP genes and survival information were analyzed using a series of bioinformatics tool. A total of 365 samples with 1,542 RBPs were included in this study. One hundred and eighty-seven differently RBPs were screened, including 175 up-regulated and 12 down-regulated. The independent OS-associated RBPs of NHP2, UPF3B, and SMG5 were used to develop a prognostic model. Survival analysis showed that low-risk patients had a significantly longer OS and disease-free survival (DFS) when compared to high-risk patients (HR: 2.577, 95% CI: 1.793-3.704, P < 0.001 and HR: 1.599, 95% CI: 1.185-2.159, P = 0.001, respectively). The International Cancer Genome Consortium (ICGC) database was used to externally validate the model, and the OS of low-risk patients were found to be longer than that of high-risk patients (P < 0.001). The Nomograms of OS and DFS were plotted to help in clinical decision making. These results showed that the model was effective and may help in prognostic stratification of HCC patients. The prognostic prediction model based on RBPs provides new insights for HCC diagnosis and personalized treatment.
Collapse
Affiliation(s)
- Zhongsong Man
- Center of Hepatobiliary Pancreatic Disease, XuZhou Central Hospital, Jiangsu, China
| | - Yongqiang Chen
- Department of Clinical Laboratory, XuZhou Central Hospital, Jiangsu, China
| | - Lu Gao
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing, China
| | - Guowei Xei
- Center of Hepatobiliary Pancreatic Disease, The Affiliated Hospital of Qinghai University, Qinghai, China
| | - Quanfu Li
- Center of Hepatobiliary Pancreatic Disease, The Second Hospital, Baoding, China
| | - Qian Lu
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing, China
| | - Jun Yan
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing, China
| |
Collapse
|
24
|
Sun MY, Xu B, Wu QX, Chen WL, Cai S, Zhang H, Tang QF. Cisplatin-Resistant Gastric Cancer Cells Promote the Chemoresistance of Cisplatin-Sensitive Cells via the Exosomal RPS3-Mediated PI3K-Akt-Cofilin-1 Signaling Axis. Front Cell Dev Biol 2021; 9:618899. [PMID: 33644057 PMCID: PMC7905060 DOI: 10.3389/fcell.2021.618899] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Cisplatin is an important agent in first-line chemotherapy against gastric cancer (GC). However, consequential drug resistance limits its effectiveness for the treatment of GC. In this study, a cisplatin resistant gastric cancer cell line SGC7901R was determined by LC-MS/MS with increased exosomal levels of RPS3 protein. SGC7901R cell-derived exosomes were readily taken up by cisplatin-sensitive SGC7901S cells, thus triggering off a phenotype of chemoresistance in the receptor cells. Subsequently, it was demonstrated that exosomal RPS3 was essential for inducing chemoresistance of receptor cells as shown by the acquisition of this phenotype in SGC7901S cells with enforced expression of RPS3. Further mechanism study demonstrated that cisplatin-resistant gastric cancer cell-derived exosomal RPS3 enhanced the chemoresistance of cisplatin-sensitive gastric cancer cells through the PI3K-Akt-cofilin-1 signaling pathway. All these findings demonstrated that cisplatin-resistant gastric cancer cells communicate with sensitive cells through the intercellular delivery of exosomal RPS3 and activation of the PI3K-Akt-cofilin-1 signaling pathway. Targeting exosomal RPS3 protein in cisplatin-resistant gastric cancer cells may thus be a promising strategy to overcome cisplatin resistance in gastric cancer.
Collapse
Affiliation(s)
- Meng-Yao Sun
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bo Xu
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qiu-Xue Wu
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wen-Lian Chen
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Si Cai
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hui Zhang
- Research Center for Traditional Chinese Medicine Complexity System, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing-Feng Tang
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Clinical Laboratory, Jiading Branch of Shanghai General Hospital, Shanghai, China
| |
Collapse
|
25
|
Tian S, Liu J, Sun K, Liu Y, Yu J, Ma S, Zhang M, Jia G, Zhou X, Shang Y, Han Y. Systematic Construction and Validation of an RNA-Binding Protein-Associated Model for Prognosis Prediction in Hepatocellular Carcinoma. Front Oncol 2021; 10:597996. [PMID: 33575212 PMCID: PMC7870868 DOI: 10.3389/fonc.2020.597996] [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: 08/23/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Evidence from prevailing studies show that hepatocellular carcinoma (HCC) is among the top cancers with high mortality globally. Gene regulation at post-transcriptional level orchestrated by RNA-binding proteins (RBPs) is an important mechanism that modifies various biological behaviors of HCC. Currently, it is not fully understood how RBPs affects the prognosis of HCC. In this study, we aimed to construct and validate an RBP-related model to predict the prognosis of HCC patients. METHODS Differently expressed RBPs were identified in HCC patients based on the GSE54236 dataset from the Gene Expression Omnibus (GEO) database. Integrative bioinformatics analyses were performed to select hub genes. Gene expression patterns were validated in The Cancer Genome Atlas (TCGA) database, after which univariate and multivariate Cox regression analyses, as well as Kaplan-Meier analysis were performed to develop a prognostic model. Then, the performance of the prognostic model was assessed using receiver operating characteristic (ROC) curves and clinicopathological correlation analysis. Moreover, data from the International Cancer Genome Consortium (ICGC) database were used for external validation. Finally, a nomogram combining clinicopathological parameters and prognostic model was established for the individual prediction of survival probability. RESULTS The prognostic risk model was finally constructed based on two RBPs (BOP1 and EZH2), facilitating risk-stratification of HCC patients. Survival was markedly higher in the low-risk group relative to the high-risk group. Moreover, higher risk score was associated with advanced pathological grade and late clinical stage. Besides, the risk score was found to be an independent prognosis factor based on multivariate analysis. Nomogram including the risk score and clinical stage proved to perform better in predicting patient prognosis. CONCLUSIONS The RBP-related prognostic model established in this study may function as a prognostic indicator for HCC, which could provide evidence for clinical decision making.
Collapse
Affiliation(s)
- Siyuan Tian
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Jingyi Liu
- Department of Radiation Oncology, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Keshuai Sun
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Yansheng Liu
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Jiahao Yu
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Shuoyi Ma
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Miao Zhang
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Gui Jia
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Xia Zhou
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Yulong Shang
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| | - Ying Han
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi’an, China
| |
Collapse
|
26
|
Xiong W, Lan T, Mo B. Extraribosomal Functions of Cytosolic Ribosomal Proteins in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:607157. [PMID: 33968093 PMCID: PMC8096920 DOI: 10.3389/fpls.2021.607157] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/29/2021] [Indexed: 05/20/2023]
Abstract
Ribosomes are basic translational machines in all living cells. The plant cytosolic ribosome is composed of four rRNAs and approximately 81 ribosomal proteins (RPs). In addition to the fundamental functions of RPs in the messenger RNA decoding process as well as in polypeptide synthesis and ribosome assembly, extraribosomal functions of RPs that occur in the absence of the ribosome have been proposed and studied with respect to RPs' ability to interact with RNAs and non-ribosomal proteins. In a few cases, extraribosomal functions of several RPs have been demonstrated with solid evidences in plants, including microRNA biogenesis, anti-virus defenses, and plant immunity, which have fascinated biologists. We believe that the widespread duplication of RP genes in plants may increase the potential of extraribosomal functions of RPs and more extraribosomal functions of plant RPs will be discovered in the future. In this article we review the current knowledge concerning the extraribosomal functions of RPs in plants and described the prospects for future research in this fascinating area.
Collapse
Affiliation(s)
- Wei Xiong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Beixin Mo,
| |
Collapse
|
27
|
Integrated bioinformatic analysis of RNA binding proteins in hepatocellular carcinoma. Aging (Albany NY) 2020; 13:2480-2505. [PMID: 33411682 PMCID: PMC7880356 DOI: 10.18632/aging.202281] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
RNA binding proteins (RBPs) are aberrantly expressed in a tissue-specific manner across many tumors. These proteins, which play a vital role in post-transcriptional gene regulation, are involved in RNA splicing, maturation, transport, stability, degradation, and translation. We set out to establish an accurate risk score model based on RBPs to estimate prognosis in hepatocellular carcinoma (HCC). RNA-sequencing data, proteomic data and corresponding clinical information were acquired from the Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database respectively. We identified 406 differentially expressed RBPs between HCC tumor and normal tissues at the transcriptional and protein level. Overall, 11 RBPs (BRIX1, DYNC1H1, GTPBP4, PRKDC, RAN, RBM19, SF3B4, SMG5, SPATS2, TAF9, and THOC5) were selected to establish a risk score model. We divided HCC patients into low-risk and high-risk groups based on the median of risk score values. The survival analysis indicated that patients in the high-risk group had poorer overall survival compared to patients in the low-risk group. Our study demonstrated that 11 RBPs were associated with the overall survival of HCC patients. These RBPs may represent potential drug targets and can help optimize future clinical treatment.
Collapse
|
28
|
Wang M, Huang S, Chen Z, Han Z, Li K, Chen C, Wu G, Zhao Y. Development and validation of an RNA binding protein-associated prognostic model for hepatocellular carcinoma. BMC Cancer 2020; 20:1136. [PMID: 33228611 PMCID: PMC7684760 DOI: 10.1186/s12885-020-07625-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/10/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is among the deadliest forms of cancer. While RNA-binding proteins (RBPs) have been shown to be key regulators of oncogenesis and tumor progression, their dysregulation in the context of HCC remains to be fully characterized. METHODS Data from the Cancer Genome Atlas - liver HCC (TCGA-LIHC) database were downloaded and analyzed in order to identify RBPs that were differentially expressed in HCC tumors relative to healthy normal tissues. Functional enrichment analyses of these RBPs were then conducted using the GO and KEGG databases to understand their mechanistic roles. Central hub RBPs associated with HCC patient prognosis were then detected through Cox regression analyses, and were incorporated into a prognostic model. The prognostic value of this model was then assessed through the use of Kaplan-Meier curves, time-related ROC analyses, univariate and multivariate Cox regression analyses, and nomograms. Lastly, the relationship between individual hub RBPs and HCC patient overall survival (OS) was evaluated using Kaplan-Meier curves. Finally, find protein-coding genes (PCGs) related to hub RBPs were used to construct a hub RBP-PCG co-expression network. RESULTS In total, we identified 81 RBPs that were differentially expressed in HCC tumors relative to healthy tissues (54 upregulated, 27 downregulated). Seven prognostically-relevant hub RBPs (SMG5, BOP1, LIN28B, RNF17, ANG, LARP1B, and NR0B1) were then used to generate a prognostic model, after which HCC patients were separated into high- and low-risk groups based upon resultant risk score values. In both the training and test datasets, we found that high-risk HCC patients exhibited decreased OS relative to low-risk patients, with time-dependent area under the ROC curve values of 0.801 and 0.676, respectively. This model thus exhibited good prognostic performance. We additionally generated a prognostic nomogram based upon these seven hub RBPs and found that four other genes were significantly correlated with OS. CONCLUSION We herein identified a seven RBP signature that can reliably be used to predict HCC patient OS, underscoring the prognostic relevance of these genes.
Collapse
Affiliation(s)
- Min Wang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Shan Huang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Zefeng Chen
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Zhiwei Han
- Department of Chinese Medicine, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Kezhi Li
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Chuang Chen
- Department of Chinese Medicine, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Guobin Wu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yinnong Zhao
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.
| |
Collapse
|
29
|
Graifer D, Karpova G. Ribosomal protein uS3 in cell biology and human disease: Latest insights and prospects. Bioessays 2020; 42:e2000124. [PMID: 33179285 DOI: 10.1002/bies.202000124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/14/2020] [Indexed: 12/20/2022]
Abstract
The conserved ribosomal protein uS3 in eukaryotes has long been known as one of the essential components of the small (40S) ribosomal subunit, which is involved in the structure of the 40S mRNA entry pore, ensuring the functioning of the 40S subunit during translation initiation. Besides, uS3, being outside the ribosome, is engaged in various cellular processes related to DNA repair, NF-kB signaling pathway and regulation of apoptosis. This review is devoted to recent data opening new horizons in understanding the roles of uS3 in such processes as the assembly and maturation of 40S subunits, ensuring proper structure of 48S pre-initiation complexes, regulation of initiation and ribosome-based RNA quality control pathways. Besides, we summarize novel results on the participation of the protein in processes beyond translation and consider biomedical implications of previously known and recently found extra-ribosomal functions of uS3, primarily, in oncogenesis.
Collapse
Affiliation(s)
- Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Galina Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| |
Collapse
|
30
|
Huang Y, Chen S, Qin W, Wang Y, Li L, Li Q, Yuan X. A Novel RNA Binding Protein-Related Prognostic Signature for Hepatocellular Carcinoma. Front Oncol 2020; 10:580513. [PMID: 33251144 PMCID: PMC7673432 DOI: 10.3389/fonc.2020.580513] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant and aggressive cancer with high recurrence rates and mortality. Some studies have illustrated that RNA binding proteins (RBPs) were involved in the carcinogenesis and development of multiple cancers, but the roles in HCC were still unclear. We downloaded the RNA-seq and corresponding clinical information of HCC from The Cancer Genome Atlas (TCGA) database, and 330 differentially expressed RBPs were identified between normal and HCC tissues. Through series of the univariate, the least absolute shrinkage selection operator (LASSO), and the stepwise multivariate Cox regression analyses, six prognosis-related key RBPs (CNOT6, UPF3B, MRPL54, ZC3H13, IFIT5, and PPARGC1A) were screened out from DE RBPs, and a six-RBP gene risk score signature was constructed in training set. Survival analysis indicated that HCC patients with high-risk scores had significantly worse overall survival than low-risk patients, and furthermore, the signature can be used as an independent prognostic indicator. The good accuracy of this prognostic signature was confirmed by the ROC curve analysis and was further validated in the International Cancer Genome Consortium (ICGC) HCC cohort. Besides, a nomogram based on six RBP genes was established and internally validated in the TCGA cohort. Gene set enrichment analysis demonstrated some cancer-related phenotypes were significantly gathered in the high-risk group. Overall, our study first identified an RBP-related six-gene prognostic signature, which could serve as a promising prognostic biomarker and provide some potential therapeutic targets for HCC.
Collapse
Affiliation(s)
- Yongbiao Huang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
31
|
Ren R, Wang Z, Wu M, Wang H. Emerging Roles of SIRT1 in Alcoholic Liver Disease. Int J Biol Sci 2020; 16:3174-3183. [PMID: 33162823 PMCID: PMC7645991 DOI: 10.7150/ijbs.49535] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Alcoholic liver disease (ALD) is the most prevalent type of chronic liver disease worldwide with a wide spectrum of liver pathologies ranging from simple steatosis to steatohepatitis, cirrhosis, and even hepatocellular carcinoma. It has been demonstrated that ALD is mediated in whole or in part by a central signaling molecule sirtuin 1 (SIRT1), a conserved class III histone deacetylase.SIRT1 plays beneficial roles in regulating hepatic lipid metabolism, inhibiting hepatic inflammation, controlling hepatic fibrosis and mediating hepatocellular carcinoma in ALD. However, underlying molecular mechanisms are complex and remain incompletely understood. The aim of this review was to highlight the latest advances in understanding of SIRT1 regulatory mechanisms in ALD and discuss their unique potential role as novel therapeutic target for ALD treatment.
Collapse
Affiliation(s)
- Ruixue Ren
- Department of Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Ziming Wang
- Department of Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Miaomiao Wu
- School of Pharmacy, Institute of Liver Diseases, Anhui Medical University, Hefei 230032, Anhui, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, Anhui, China
| | - Hua Wang
- Department of Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China.,School of Pharmacy, Institute of Liver Diseases, Anhui Medical University, Hefei 230032, Anhui, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, Anhui, China
| |
Collapse
|
32
|
Xie J, Zhang W, Liang X, Shuai C, Zhou Y, Pan H, Yang Y, Han W. RPL32 Promotes Lung Cancer Progression by Facilitating p53 Degradation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:75-85. [PMID: 32516735 PMCID: PMC7281510 DOI: 10.1016/j.omtn.2020.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/25/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide, and the overall survival rate of advanced lung cancer patients is unsatisfactory. Ribosomal proteins (RPs) play important roles in carcinogenesis. However, the role of RPL32 in lung cancer has not been demonstrated. Here, we report that RPL32 is aberrantly, highly expressed in lung cancer tissues and that the overexpression of RPL32 is correlated with the poor prognosis of these patients. RPL32 silencing significantly inhibited the proliferation of lung cancer cells, with an observed p53 accumulation and cell-cycle arrest. Mechanistically, knockdown of RPL32 resulted in ribosomal stress and affected rRNA maturation. RPL5 and RPL11 sensed stress and translocated from the nucleus to the nucleoplasm, where they bound to murine double minute 2 (MDM2), an important p53 E3 ubiquitin ligase, which resulted in p53 accumulation and inhibition of cancer cell proliferation. As lung cancer cells usually express high levels of Toll-like receptor 9 (TLR9), we conjugated RPL32 small interfering RNA (siRNA) to the TLR9 ligand CpG to generate CpG-RPL32 siRNA, which could stabilize and guide RPL32 siRNA to lung cancer cells. Excitingly, CpG-RPL32 siRNA displayed strong anticancer abilities in lung cancer xenografts. Therefore, RPL32 is expected to be a potential target for lung cancer treatment.
Collapse
Affiliation(s)
- Jiansheng Xie
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Zhang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaojing Liang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chong Shuai
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Yunhai Yang
- Cancer Center of Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| |
Collapse
|
33
|
Alam E, Maaliki L, Nasr Z. Ribosomal protein S3 selectively affects colon cancer growth by modulating the levels of p53 and lactate dehydrogenase. Mol Biol Rep 2020; 47:6083-6090. [PMID: 32748020 DOI: 10.1007/s11033-020-05683-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/26/2020] [Indexed: 01/10/2023]
Abstract
Ribosomal protein S3 (RPS3) is a component of the 40S ribosomal subunit. It is known to function in ribosome biogenesis and as an endonuclease. RPS3 has been shown to be over expressed in colon adenocarcinoma but its role in colon cancer is still unknown. In this study, we aim at determining the expression levels of RPS3 in a colon cancer cell line Caco-2 compared to a normal colon mucosa cell line NCM-460 and study the effects of targeting this protein by siRNA on cellular behavior. RPS3 was found to be expressed in both cell lines. However, siRNA treatment showed a more protruding effect on Caco-2 cells compared to NCM-460 cells. RPS3 knockdown led to a significant decrease in the proliferation, survival, migration and invasion and an increase in the apoptosis of Caco-2 cells. Western blot analysis demonstrated that these effects correlated with an increase in the level of the tumor suppressor p53 and a decrease in the level and activity of lactate dehydrogenase (LDH), an enzyme involved in the metabolism of cancer cells. No significant effect was shown in normal colon NCM-460 cells. Targeting p53 by siRNA did not affect RPS3 levels indicating that p53 may be a downstream target of RPS3. However, the concurrent knockdown of RPS3 and p53 showed no change in LDH level in Caco-2 cells suggesting an interesting interplay among the three proteins. These findings might present RPS3 as a selective molecular marker in colon cancer and an attractive target for colon cancer therapy.
Collapse
Affiliation(s)
- Elie Alam
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, P.O.B. 100, Tripoli, Lebanon
| | - Lama Maaliki
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, P.O.B. 100, Tripoli, Lebanon
| | - Zeina Nasr
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, P.O.B. 100, Tripoli, Lebanon.
| |
Collapse
|
34
|
RNA-binding motif protein 43 (RBM43) suppresses hepatocellular carcinoma progression through modulation of cyclin B1 expression. Oncogene 2020; 39:5495-5506. [PMID: 32632220 DOI: 10.1038/s41388-020-1380-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 06/12/2020] [Accepted: 06/25/2020] [Indexed: 11/08/2022]
Abstract
RNA-binding proteins play key roles in the posttranscriptional regulation of mRNA during cancer progression. Here, we show that RNA-binding motif protein 43 (RBM43) is significantly downregulated in human tumors, and its low expression is correlated with poor prognosis in patients with HCC. Overexpression of RBM43 suppressed cell proliferation in culture and resulted in the growth arrest of tumor xenografts, whereas downregulating RBM43 played an opposite role. We have also demonstrated that overexpression or knockdown of RBM43 affects the cell-cycle progression of liver cancer cells. Mechanistically, RBM43 directly associated with the 3'UTR of Cyclin B1 mRNA and regulated its expression. Moreover, loss of Rbm43 in mice promoted liver carcinogenesis and HCC development after diethylnitrosamine (DEN)-carbon tetrachloride (CCl4) treatment. Taken together, our data indicate that RBM43 is a tumor suppressor that controls the cell cycle through modulation of Cyclin B1 expression, providing evidence that RBM43 is particularly important in HCC.
Collapse
|
35
|
Identification of prognostic alternative splicing signatures in hepatitis B or/and C viruses related hepatocellular carcinoma. Genomics 2020; 112:3396-3406. [PMID: 32525024 DOI: 10.1016/j.ygeno.2020.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Alternative splicing (AS) takes a crucial part in tumor process. We aim to analyze AS in Hepatitis B virus (HBV) or/and hepatitis C virus (HCV) related hepatocellular carcinoma (HCC). METHODS Cox regression analysis was conducted to screen survival-associated AS events. The receiver operating characteristic curve used to evaluate the predictive accuracy. Splicing network was built to investigate the relationship between splicing factors and AS events. RESULTS Ninety-six survival-associated AS events were obtained by univariate Cox regression. Final prognostic model could significantly distinguish the prognosis. We identified RBFOX2 as the hub gene in splicing network based on differentially expressed splicing factors, and obtained MAP3K13_AT as the key AS event in survival-related splicing network. CONCLUSION Our results highlight the AS signatures in HCC patients with HBV or/and HCV infection. Meanwhile, AS events and splicing factors in different virus-infected HCC subgroups can provide novel perspectives as biomarkers and individualized therapeutic targets.
Collapse
|
36
|
Bi N, Sun Y, Lei S, Zeng Z, Zhang Y, Sun C, Yu C. Identification of 40S ribosomal protein S8 as a novel biomarker for alcohol‑associated hepatocellular carcinoma using weighted gene co‑expression network analysis. Oncol Rep 2020; 44:611-627. [PMID: 32627011 PMCID: PMC7336510 DOI: 10.3892/or.2020.7634] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022] Open
Abstract
Alcohol‑associated hepatocellular carcinoma (HCC) is a subtype of HCC with poor prognosis. The present study aimed to identify key biomarkers for alcohol‑associated HCC. The gene data profiles and corresponding clinical traits of patients with alcohol‑associated HCC were downloaded from The Cancer Genome Atlas (TCGA) database. Firstly, good genes and good samples were identified, which were subsequently used to conduct weighted gene co‑expression network analysis (WGCNA). Hub genes in the significant modules were selected following Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and from constructing a protein‑protein interaction (PPI) network. Real hub genes among hub genes were determined following progression, survival analysis and gene set enrichment analysis (GSEA), as well as reverse transcription‑quantitative PCR and immunohistochemical staining of non‑alcohol‑ and alcohol‑associated HCC samples. In total, 64 good samples of alcohol‑associated HCC with height score <160 were selected, from which 15,195 good genes were identified and used to conduct WGCNA; 8 gene co‑expressed modules were identified using WGCNA, while 3 modules (including pink, magenta and turquoise) were significantly associated with Child‑Pugh score, T‑stage and body weight. Following GO and KEGG analysis and construction of the PPI network, a total of 30 hub genes were identified in the aforementioned 3 gene co‑expressed modules, while 16 hub genes (including AURKB, BUB1, BUB1B, CCNB1, CCNB2, CDC20, CDCA8, CDK1, PLK1, RPS5, RPS7, RPS8, RPS14, RPS27, RPSA and TOP2A) were associated with the development of alcohol‑associated HCC, and had a significant prognosis value. Among these genes, only RPS8 was highly expressed in alcohol‑associated HCC, but not in non‑alcohol‑associated HCC, while RPS5 was not significantly associated in either alcohol‑ or non‑alcohol‑associated HCC. GSEA demonstrated that 10 pathways, including RNA polymerase and ribosome pathways were enriched in alcohol‑associated HCC samples where RPS8 was highly expressed. Taken together, the results of the present study demonstrate that RPS8 may be a novel biomarker for the diagnosis of patients with alcohol‑associated HCC.
Collapse
Affiliation(s)
- Ningrui Bi
- Department of Liver‑Biliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550009, P.R. China
| | - Yuanmei Sun
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guiyang, Guizhou 550009, P.R. China
| | - Shan Lei
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guiyang, Guizhou 550009, P.R. China
| | - Zhirui Zeng
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guiyang, Guizhou 550009, P.R. China
| | - Yan Zhang
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550009, P.R. China
| | - Chengyi Sun
- Department of Liver‑Biliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550009, P.R. China
| | - Chao Yu
- Department of Liver‑Biliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550009, P.R. China
| |
Collapse
|
37
|
Xu C, Xie N, Su Y, Sun Z, Liang Y, Zhang N, Liu D, Jia S, Xing X, Han L, Li G, Tong T, Chen J. HnRNP F/H associate with hTERC and telomerase holoenzyme to modulate telomerase function and promote cell proliferation. Cell Death Differ 2019; 27:1998-2013. [PMID: 31863069 PMCID: PMC7244589 DOI: 10.1038/s41418-019-0483-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Human telomerase RNA component hTERC comprises multiple motifs that contribute to hTERC biogenesis, holoenzyme activity, and enzyme recruitment to telomeres. hTERC contains several guanine tracts (G-tracts) at its 5′-end, but its associated proteins and potential roles in telomerase function are still poorly understood. The heterogeneous nuclear ribonucleoproteins F, H1, and H2 (hnRNP F/H) are splicing factors that preferentially bind to poly(G)-rich sequences RNA. Here, we demonstrate that hnRNP F/H associate with both hTERC and telomerase holoenzyme to regulate telomerase activity. We reveal hnRNP F/H bind to the 5′-end region of hTERC in vitro and in vivo, and identify the first three G-tracts of hTERC and qRRM1 domain of hnRNP F/H are required for their interaction. Furthermore, hnRNP F/H also directly interact with telomerase holoenzyme. Functionally, we show that hnRNP F/H plays important roles in modulating telomerase activity and telomere length. Moreover, hnRNP F/H deletion greatly impair cancer and stem cell proliferation, and induce stem cell senescence, while hnRNP F/H overexpression delay stem cell senescence. Collectively, our findings unveil a novel role of hnRNP F/H as the binding partners of hTERC and telomerase holoenzyme to regulate telomerase function.
Collapse
Affiliation(s)
- Chenzhong Xu
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Nan Xie
- Department of Physiology and Pathophysiology, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Yuanyuan Su
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Zhaomeng Sun
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Yao Liang
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Na Zhang
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Doudou Liu
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Shuqin Jia
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaofang Xing
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Limin Han
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Guodong Li
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Tanjun Tong
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China
| | - Jun Chen
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China.
| |
Collapse
|
38
|
Han L, Huang C, Zhang S. The RNA-binding protein SORBS2 suppresses hepatocellular carcinoma tumourigenesis and metastasis by stabilizing RORA mRNA. Liver Int 2019; 39:2190-2203. [PMID: 31365778 DOI: 10.1111/liv.14202] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/13/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Numerous studies have revealed that dysregulation of RNA-binding protein (RBP) expression is causally linked with human cancer tumourigenesis. However, the detailed biological effect and underlying mechanisms of most RBPs remain unclear. METHODS Expression of sorbin and SH3 domain-containing 2 (SORBS2) in hepatocellular carcinoma (HCC) was detected by qRT-PCR, immunohistochemistry assay and Western blot assay. Proliferation, migration, invasion and cell cycle progression of HCC cells were measured by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, colony-forming assay, Transwell assay and flow cytometry assay respectively. A xenograft model and metastatic model were established to evaluate the proliferation and metastasis of HCC cells in vivo. Western blot assays were performed to assess the expression of epithelial-mesenchymal transition markers. Luciferase reporter assay, RNA immunoprecipitation and pull-down assay elucidated the effect of SORBS2 on one of its downstream genes. RESULTS The expression of SORBS2 was significantly decreased in HCC and was associated with metastasis, advanced TNM clinical stage and poor clinical outcome of HCC patients. Furthermore, our results suggested that SORBS2 inhibited HCC cell proliferation, invasion, migration and EMT both in vivo and in vitro. Mechanistically, we revealed that retinoic acid receptor-related orphan receptor (RORA) was a major target of SORBS2 and was critical to sustaining the antitumour effect of SORBS2 on HCC cells. SORBS2 reduced RORA mRNA degradation by directly binding to the 3'UTR of RORA mRNA. CONCLUSIONS In this study, we found for the first time that SORBS2 contributed to the suppression of HCC tumourigenesis and metastasis via post-transcriptional regulation of RORA expression as an RBP.
Collapse
Affiliation(s)
- Lili Han
- Department of Oncology, College of Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Chen Huang
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
| | - Shuqun Zhang
- Department of Oncology, College of Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| |
Collapse
|
39
|
Zhou H, Su L, Liu C, Li B, Li H, Xie Y, Sun D. CTHRC1 May Serve As A Prognostic Biomarker For Hepatocellular Carcinoma. Onco Targets Ther 2019; 12:7823-7831. [PMID: 31576140 PMCID: PMC6765327 DOI: 10.2147/ott.s219429] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
Background Hepatocellular carcinoma is a common malignant cancer and the second most common cause of cancer-related deaths worldwide. Collagen triple helix repeat containing 1 (CTHRC1) has been increasingly reported to be involved in tumorigenesis and/or tumor progression. However, limited data are available regarding the role of CTHRC1 in hepatocellular carcinoma. Methods Paraffin-embedded specimens from a total of 29 patients with HCC were collected in our study. The expression of CTHRC1 in hepatocellular carcinoma was evaluated using immunohistochemistry and bioinformatics analysis. Furthermore, Spearman analysis was performed to identify factors of correlation between CTHRC1 and clinicopathological features. Survival curves for hepatocellular carcinoma were produced using the Kaplan-Meier method and the log rank test. Results In this study, we confirmed that CTHRC1 is highly expressed in tissues and hepatoma cell lines. The statistical analysis revealed that the levels of CTHRC1 were significantly correlated with cirrhosis (P=0.024), tumor size (P=0.006), vascular invasion (P<0.001), TNM stage (P<0.001), and BCLC stage (P<0.001). High expression of CTHRC1 in hepatocellular carcinoma tissues is significantly associated with poor survival. Conclusion CTHRC1 may serve as a prognostic biomarker for hepatocellular carcinoma.
Collapse
Affiliation(s)
- Huifang Zhou
- Graduate School of Hebei Medical University, Hebei Medical University, Shijiazhuang, People's Republic of China.,The Liver Disease Center of PLA, The 980th Hospital of PLA Joint Logistics Support Force, Shijiazhuang, People's Republic of China
| | - Libo Su
- Hebei Key Laboratory of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Chao Liu
- Hebei Key Laboratory of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Baosheng Li
- The Liver Disease Center of PLA, The 980th Hospital of PLA Joint Logistics Support Force, Shijiazhuang, People's Republic of China
| | - Hui Li
- Department of Pathology, The 980th Hospital of PLA Joint Logistics Support Force, Shijiazhuang, People's Republic of China
| | - Ying Xie
- Hebei Key Laboratory of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Dianxing Sun
- Graduate School of Hebei Medical University, Hebei Medical University, Shijiazhuang, People's Republic of China.,The Liver Disease Center of PLA, The 980th Hospital of PLA Joint Logistics Support Force, Shijiazhuang, People's Republic of China
| |
Collapse
|