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Liu H, Ye Z, Wang X, Wu Y, Deng C. Comprehensive analysis of the functions, prognostic and diagnostic values of RNA binding proteins in head and neck squamous cell carcinoma. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2024:101937. [PMID: 38844022 DOI: 10.1016/j.jormas.2024.101937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Accumulating evidence has suggested that RNA binding protein (RBP) dysregulation plays an essential role during tumorigenesis. Here, we sought to explore the potential biological functions and clinical significance of RBP and develop diagnostic and prognostic signatures based on RBP in patients with head and neck squamous cell carcinoma (HNSCC). METHODS The differently expressed RBPs between HNSCC samples and their normal counterparts were identified using the Limma package. The immunohistochemistry (IHC) images of several RBPs were collected from the Human Protein Atlas database. The diagnostic signature based on RBP was built by LASSO-logistic regression and random forest. The prognostic signature based on RBP was constructed by LASSO and stepwise Cox regression analysis in the training cohort and validated in the validation cohort. RESULTS Eighty-four aberrantly expressed RBPs were obtained, comprising 41 up-regulated and 43 down-regulated RBPs. Seven RBP genes (CPEB3, PDCD4, ENDOU, PARP12, DNMT3B, IGF2BP1, EXO1) were identified as diagnostic-related hub genes. They were used to establish a diagnostic RBP signature risk score (DRBPS) model by the coefficients in least absolute shrinkage and selection operator (LASSO)-logistic regression analysis and showed high specificity and sensitivity in the training (area under the receiver operating characteristic curve (AUC) = 0.998), and in all validation cohorts (AUC > 0.95 for all). Similarly, seven RBP genes (MKRN3, ZC3H12D, EIF5A2, AFF3, SIDT1, RBM24, and NR0B1) were identified as prognosis-associated hub genes by LASSO and stepwise multiple Cox regression analyses and were used to construct the prognostic model named as PRBPS. The AUC of the time-dependent receiver operator characteristic curve of the prognostic model was 0.664 at 3 years and 0.635 at 5 years in the training cohort and 0.720, 0.777 in the validation cohort, showing a favorable predictive efficacy for prognosis in HNSCC. CONCLUSIONS Our results demonstrate the value of consideration of RBP in the diagnosis and prognosis for HNSCC and provide a novel insight into understanding the potential role of dysregulated RBP in HNSCC.
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Affiliation(s)
- Hai Liu
- School of Stomatology, Wannan Medical College, Wuhu, China; Anhui Provincial Engineering Research Center for Dental Materials and Application, Wannan Medical College, Wuhu, China
| | - Zhenqi Ye
- School of Stomatology, Wannan Medical College, Wuhu, China; Anhui Provincial Engineering Research Center for Dental Materials and Application, Wannan Medical College, Wuhu, China
| | - Xiaoying Wang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yaping Wu
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.
| | - Chao Deng
- School of Stomatology, Wannan Medical College, Wuhu, China; Anhui Provincial Engineering Research Center for Dental Materials and Application, Wannan Medical College, Wuhu, China.
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Smith BC, Silvers R. 1H, 13C, and 15N resonance assignments of the La Motif of the human La-related protein 1. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:111-118. [PMID: 38691336 DOI: 10.1007/s12104-024-10176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Human La-related protein 1 (HsLARP1) is involved in post-transcriptional regulation of certain 5' terminal oligopyrimidine (5'TOP) mRNAs as well as other mRNAs and binds to both the 5'TOP motif and the 3'-poly(A) tail of certain mRNAs. HsLARP1 is heavily involved in cell proliferation, cell cycle defects, and cancer, where HsLARP1 is significantly upregulated in malignant cells and tissues. Like all LARPs, HsLARP1 contains a folded RNA binding domain, the La motif (LaM). Our current understanding of post-transcriptional regulation that emanates from the intricate molecular framework of HsLARP1 is currently limited to small snapshots, obfuscating our understanding of the full picture on HsLARP1 functionality in post-transcriptional events. Here, we present the nearly complete resonance assignment of the LaM of HsLARP1, providing a significant platform for future NMR spectroscopic studies.
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Affiliation(s)
- Benjamin C Smith
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA
| | - Robert Silvers
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.
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Bley H, Krisp C, Schöbel A, Hehner J, Schneider L, Becker M, Stegmann C, Heidenfels E, Nguyen-Dinh V, Schlüter H, Gerold G, Herker E. Proximity labeling of host factor ANXA3 in HCV infection reveals a novel LARP1 function in viral entry. J Biol Chem 2024; 300:107286. [PMID: 38636657 PMCID: PMC11101947 DOI: 10.1016/j.jbc.2024.107286] [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: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Hepatitis C virus (HCV) infection is tightly connected to the lipid metabolism with lipid droplets (LDs) serving as assembly sites for progeny virions. A previous LD proteome analysis identified annexin A3 (ANXA3) as an important HCV host factor that is enriched at LDs in infected cells and required for HCV morphogenesis. To further characterize ANXA3 function in HCV, we performed proximity labeling using ANXA3-BioID2 as bait in HCV-infected cells. Two of the top proteins identified proximal to ANXA3 during HCV infection were the La-related protein 1 (LARP1) and the ADP ribosylation factor-like protein 8B (ARL8B), both of which have been previously described to act in HCV particle production. In follow-up experiments, ARL8B functioned as a pro-viral HCV host factor without localizing to LDs and thus likely independent of ANXA3. In contrast, LARP1 interacts with HCV core protein in an RNA-dependent manner and is translocated to LDs by core protein. Knockdown of LARP1 decreased HCV spreading without altering HCV RNA replication or viral titers. Unexpectedly, entry of HCV particles and E1/E2-pseudotyped lentiviral particles was reduced by LARP1 depletion, whereas particle production was not altered. Using a recombinant vesicular stomatitis virus (VSV)ΔG entry assay, we showed that LARP1 depletion also decreased entry of VSV with VSV, MERS, and CHIKV glycoproteins. Therefore, our data expand the role of LARP1 as an HCV host factor that is most prominently involved in the early steps of infection, likely contributing to endocytosis of viral particles through the pleiotropic effect LARP1 has on the cellular translatome.
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Affiliation(s)
- Hanna Bley
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Christoph Krisp
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anja Schöbel
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Julia Hehner
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Laura Schneider
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Miriam Becker
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Cora Stegmann
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Elisa Heidenfels
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Van Nguyen-Dinh
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gisa Gerold
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Eva Herker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany.
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Dong D, Wei J, Wang W, Zhou H, Hong L, Ji G, Yang X. YTHDC1 promotes the malignant progression of gastric cancer by promoting ROD1 translocation to the nucleus. Cell Biol Toxicol 2024; 40:19. [PMID: 38573528 PMCID: PMC10995098 DOI: 10.1007/s10565-024-09859-4] [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: 12/17/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
RNA-binding proteins (RBPs) make vital impacts on tumor progression and are important potential targets for tumor treatment. Previous studies have shown that RBP regulator of differentiation 1 (ROD1), enriched in the nucleus, is abnormally expressed and functions as a splicing factor in tumors; however, the mechanism underlying its involvement in gastric cancer (GC) is unknown. In this study, ROD1 is found to stimulate GC cell proliferation and metastasis and is related to poor patient prognosis. In vitro experiments showed that ROD1 influences GC proliferation and metastasis through modulating the imbalance of the level of the oncogenic gene OIP5 and the tumor suppressor gene GPD1L. Further studies showed that the N6-methyladenosine (m6A) "reader" protein YTHDC1 can interact with ROD1 and regulate the balance of the expression of the downstream molecules OIP5/GPD1L by promoting the nuclear enrichment of ROD1. Therefore, YTHDC1 stimulates GC development and progression through modulating nuclear enrichment of the splicing factor ROD1.
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Affiliation(s)
- Danhong Dong
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Jiangpeng Wei
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Weidong Wang
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Haikun Zhou
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Liu Hong
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China.
| | - Gang Ji
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China.
| | - Xisheng Yang
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China.
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Deng HY, Zhang LW, Tang FQ, Zhou M, Li MN, Lu LL, Li YH. Identification and Validation of a Novel Anoikis-Related Gene Signature for Predicting Survival in Patients With Serous Ovarian Cancer. World J Oncol 2024; 15:45-57. [PMID: 38274727 PMCID: PMC10807923 DOI: 10.14740/wjon1714] [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: 09/19/2023] [Accepted: 11/29/2023] [Indexed: 01/27/2024] Open
Abstract
Background Ovarian cancer is an extremely deadly gynecological malignancy, with a 5-year survival rate below 30%. Among the different histological subtypes, serous ovarian cancer (SOC) is the most common. Anoikis significantly contributes to the progression of ovarian cancer. Therefore, identifying an anoikis-related signature that can serve as potential prognostic predictors for SOC is of great significance. Methods We intersected 308 anoikis-related genes (ARGs) and identified those significantly associated with SOC prognosis using univariate Cox regression. A LASSO Cox regression model was constructed and evaluated using Kaplan-Meier and receiver operating characteristic (ROC) analyses in TCGA (The Cancer Genome Atlas) and GSE26193 cohorts. We conducted quantitative real-time polymerase chain reaction (qPCR) to assess mRNA levels and applied bioinformatics to investigate the correlation between risk groups and gene expression, mutations, pathways, tumor immune microenvironment (TIME), and drug sensitivity in SOC. Results Among 308 ARGs, 28 were significantly associated with SOC prognosis. A 13-gene prognostic model was established through LASSO Cox regression in TCGA cohort. High-risk group had poorer prognosis than low-risk group (median overall survival (mOS): 34.2 vs. 57.1 months, hazard ratio (HR): 2.590, 95% confidence interval (CI): 0.159 - 6.00, P < 0.001). The area under the curve (AUC) values of 0.63, 0.65, and 0.74 reflected the predictive performance for 3-, 5-, and 8-year overall survival (OS) in GSE26193 validation cohort. Functional enrichment, pathway analysis, and TIME analysis identified distinct characteristics between risk groups. Drug sensitivity analysis revealed potential drug advantages for each group. Furthermore, qPCR validation once again confirmed the effectiveness of the risk model in SOC patients. Conclusions We developed and validated a robust ARG model, which could be used to predict OS in SOC patients. By systematically analyzing the correlation between the risk score of the ARGs signature model and various patterns, including the TIME and drug sensitivity, our findings suggest that this prognostic model contributes to the advancement of personalized and precise therapeutic strategies. Nevertheless, further validation studies and investigations into the underlying mechanisms are warranted.
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Affiliation(s)
- Hong Yu Deng
- Department of Clinical Laboratory, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- These authors contributed equally to this work
| | - Li Wen Zhang
- Shanghai OrigiMed Co., Ltd., Shanghai 201112, China
- These authors contributed equally to this work
| | - Fa Qing Tang
- Department of Clinical Laboratory, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ming Zhou
- Department of Clinical Laboratory, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Meng Na Li
- Department of Clinical Laboratory, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Lei Lei Lu
- Shanghai OrigiMed Co., Ltd., Shanghai 201112, China
| | - Ying Hua Li
- Gynecological Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
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Liu X, Zhang WM, Meng N, Lin LJ, Tang GD. LARP1 knockdown inhibits cultured gastric carcinoma cell cycle progression and metastatic behavior. Open Life Sci 2024; 19:20220806. [PMID: 38283117 PMCID: PMC10811526 DOI: 10.1515/biol-2022-0806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 01/30/2024] Open
Abstract
This study aimed to clarify the role of la-related protein 1 (LARP1) in cell cycle progression and metastatic behavior of cultured gastric carcinoma (GC) cells. To do that, LARP1 expression was detected in clinical GC tissues and cell lines using quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. The cell viability, apoptosis, cell cycle, migration, invasion, and cell growth were examined using a Cell Counting Kit-8, Annexin V-FITC staining, propidium iodide staining, Transwell migration and invasion assays, and colony formation assays after LARP1 knockdown. Phosphatidyl inositol 3-kinase (PI3K) and AKT1 mRNA and protein expression levels of PI3K, p-AKT1, AKT1, p-BAD, p-mTOR, and p21 in si-LARP1 transfected GC cells were determined using qRT-PCR and western blotting. Here, we've shown that LARP1 expression was upregulated in human GC tissues and KATO III cells. LARP1 knockdown inhibited GC cell proliferation, cell cycle progression, migration, invasion, and colony formation and promoted apoptosis. In si-LARP1-transfected KATO III cells, the mRNA expression levels of PI3K and AKT1, PI3K protein expression, and the p-AKT1/AKT1 ratio were significantly suppressed. p-mTOR and p-BAD were significantly decreased, whereas p21 was significantly increased in si-LARP1-transfected KATO III cells. In conclusion LARP1 knockdown induces apoptosis and inhibits cell cycle progression and metastatic behavior via PI3K/AKT1 signaling in GC cells.
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Affiliation(s)
- Xin Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
- Department of Gastroenterology, Wuming Hospital Affiliated to Guangxi Medical University, Nanning, Guangxi, 530199, P. R. China
| | - Wei-Ming Zhang
- Department of Radiotherapy, Wuming Hospital Affiliated to Guangxi Medical University, Nanning, Guangxi, 530199, P. R. China
| | - Nuo Meng
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
| | - Lian-Jie Lin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
| | - Guo-Du Tang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
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Saba JA, Huang Z, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J, Green R. LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565189. [PMID: 37961604 PMCID: PMC10635049 DOI: 10.1101/2023.11.01.565189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.
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Affiliation(s)
- James A. Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
- These authors contributed equally
| | - Kate L. Schole
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianwen Ye
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Shrey D. Bhatt
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yi Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Mansouri-Noori F, Pircher A, Bilodeau D, Siniavskaia L, Grigull J, Rissland OS, Bayfield MA. The LARP1 homolog Slr1p controls the stability and expression of proto-5'TOP mRNAs in fission yeast. Cell Rep 2023; 42:113226. [PMID: 37851576 DOI: 10.1016/j.celrep.2023.113226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Messenger RNAs (mRNAs) in higher eukaryotes that encode proteins important for the assembly of the translational apparatus (e.g., ribosomal proteins) often harbor a pyrimidine-rich motif at the extreme 5' end known as a 5' terminal oligopyrimidine (5'TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5'TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5'TOP motifs have not been described in many lower organisms, and fission yeast harbors a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5'TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5'TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5'TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1-associated control of gene expression.
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Affiliation(s)
| | | | - Danielle Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jörg Grigull
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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Hao L, Zhang J, Liu Z, Zhang Z, Mao T, Guo J. Role of the RNA-binding protein family in gynecologic cancers. Am J Cancer Res 2023; 13:3799-3821. [PMID: 37693158 PMCID: PMC10492115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
Gynecological cancers pose a threat to women's health. Although early-stage gynecological cancers show good outcomes after standardized treatment, the prognosis of patients with advanced, met-astatic, and recurrent cancers is poor. RNA-binding proteins (RBPs) are important cellular proteins that interact with RNA through RNA-binding domains and participate extensively in post-transcriptional regulatory processes, such as mRNA alternative splicing, polyadenylation, intracellular localization and stability, and translation. Abnormal RBP expression affects the normal function of oncogenes and tumor suppressor genes in many malignancies, thus leading to the occurrence or progression of cancers. Similarly, RBPs play crucial roles in gynecological carcinogenesis. We summarize the role of RBPs in gynecological malignancies and explore their potential in the diagnosis and treatment of cancers. The findings summarized in this review may provide a guide for future research on the functions of RBPs.
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Affiliation(s)
- Linlin Hao
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Jian Zhang
- School of Life Sciences, Department of Biology, Southern University of Science and TechnologyShenzhen 518055, Guangdong, China
| | - Zhongshan Liu
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Zhiliang Zhang
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Tiezhu Mao
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Jie Guo
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
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Zhu X, Du T, Chen X, Hu P. Circ-PDZD8 promotes cell growth and glutamine metabolism in non-small cell lung cancer by enriching LARP1 via sequestering miR-330-5p. Thorac Cancer 2023; 14:2187-2197. [PMID: 37349870 PMCID: PMC10396782 DOI: 10.1111/1759-7714.15006] [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: 04/24/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND The deregulation of circular RNA (circRNA) is widely reported in carcinogenesis. The purpose of this study was to investigate the role of circRNA-PDZ domain containing 8 (circ-PDZD8) in non-small cell lung cancer (NSCLC) progression. METHODS The histological structure of tissues was identified by hematoxylin-eosin (HE) staining analysis. The expression levels of circ-PDZD8, miR-330-5p and la ribonucleoprotein 1 (LARP1) mRNA were ascertained by qPCR. Cell counting kit-8, colony formation, flow cytometry, and transwell assays were employed for functional analysis. Glutamine metabolism was monitored by glutamine consumption, alpha ketoglutarate (α-KG) level and adenosine triphosphate (ATP) level. A xenograft model was established to ascertain the role of circ-PDZD8 in vivo. The putative binding relationships were verified by dual-luciferase and RIP studies. RESULTS Circ-PDZD8 expression was highly increased in NSCLC. Circ-PDZD8 knockdown inhibited cell growth, migratory capacity, invasiveness and glutamine metabolism but enhanced cell apoptosis in NSCLC cells. Circ-PDZD8 blocked miR-330-5p expression, and miR-330-5p inhibition overturned the effects of circ-PDZD8 absence. LARP1 targeted by miR-330-5p, and miR-330-5p upregulation-impaired cell growth, motility and glutamine metabolism were recovered by LARP1 overexpression. Circ-PDZD8 knockdown was also shown to impede solid tumor growth. CONCLUSION Circ-PDZD8 promotes NSCLC cell growth and glutamine metabolism by increasing LARP1 via competitively targeting miR-330-5p.
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Affiliation(s)
- Xiaopeng Zhu
- Department of Medical OncologyHuangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic UniversityHuangshi CityChina
| | - Tianxing Du
- Department of Medical OncologyHuangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic UniversityHuangshi CityChina
| | - Xi Chen
- Department of Medical OncologyHuangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic UniversityHuangshi CityChina
| | - Peng Hu
- Department of Medical OncologyHuangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic UniversityHuangshi CityChina
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Jennings MD, Srivastava P, Kershaw CJ, Talavera D, Grant C, Pavitt G. Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs. Nucleic Acids Res 2023; 51:5755-5773. [PMID: 37070186 PMCID: PMC10287931 DOI: 10.1093/nar/gkad272] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
In response to oxidative stress cells reprogram gene expression to enhance levels of antioxidant enzymes and promote survival. In Saccharomyces cerevisiae the polysome-interacting La-related proteins (LARPs) Slf1 and Sro9 aid adaptation of protein synthesis during stress by undetermined means. To gain insight in their mechanisms of action in stress responses, we determined LARP mRNA binding positions in stressed and unstressed cells. Both proteins bind within coding regions of stress-regulated antioxidant enzyme and other highly translated mRNAs in both optimal and stressed conditions. LARP interaction sites are framed and enriched with ribosome footprints suggesting ribosome-LARP-mRNA complexes are identified. Although stress-induced translation of antioxidant enzyme mRNAs is attenuated in slf1Δ, these mRNAs remain on polysomes. Focusing further on Slf1, we find it binds to both monosomes and disomes following RNase treatment. slf1Δ reduces disome enrichment during stress and alters programmed ribosome frameshifting rates. We propose that Slf1 is a ribosome-associated translational modulator that stabilises stalled/collided ribosomes, prevents ribosome frameshifting and so promotes translation of a set of highly-translated mRNAs that together facilitate cell survival and adaptation to stress.
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Affiliation(s)
- Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Priya Srivastava
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Christopher M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
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12
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Smith BC, Silvers R. NMR Resonance Assignment of the LA Motif of Human LA-Related Protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539749. [PMID: 37214987 PMCID: PMC10197598 DOI: 10.1101/2023.05.09.539749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human La-related protein 1 (HsLARP1) is involved in post-transcriptional regulation of certain 5' s terminal oligopyrimidine (5'TOP) mRNAs as well as other mRNAs and binds to both the 5'TOP motif and the 3'-poly(A) tail of certain mRNAs. HsLARP1 is heavily involved in cell proliferation, cell cycle defects, and cancer, where HsLARP1 is significantly upregulated in malignant cells and tissues. Like all LARPs, HsLARP1 contains a folded RNA binding domain, the La motif (LaM). Our current understanding of post-transcriptional regulation that emanates from the intricate molecular framework of HsLARP1 is currently limited to small snapshots, obfuscating our understanding of the full picture on HsLARP1 functionality in post-transcriptional events. Here, we present the nearly complete resonance assignment of the LaM of HsLARP1, providing a significant platform for future NMR spectroscopic studies.
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13
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Ntostis P, Swanson G, Kokkali G, Iles D, Huntriss J, Pantou A, Tzetis M, Pantos K, Picton HM, Krawetz SA, Miller D. Trophectoderm non-coding RNAs reflect the higher metabolic and more invasive properties of young maternal age blastocysts. Syst Biol Reprod Med 2023; 69:3-19. [PMID: 36576378 DOI: 10.1080/19396368.2022.2153636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Increasing female age is accompanied by a corresponding fall in her fertility. This decline is influenced by a variety of factors over an individual's life course including background genetics, local environment and diet. Studying both coding and non-coding RNAs of the embryo could aid our understanding of the causes and/or effects of the physiological processes accompanying the decline including the differential expression of sub-cellular biomarkers indicative of various diseases. The current study is a post-hoc analysis of the expression of trophectoderm RNA data derived from a previous high throughput study. Its main aim is to determine the characteristics and potential functionalities that characterize long non-coding RNAs. As reported previously, a maternal age-related component is potentially implicated in implantation success. Trophectoderm samples representing the full range of maternal reproductive ages were considered in relation to embryonic implantation potential, trophectoderm transcriptome dynamics and reproductive maternal age. The long non-coding RNA (lncRNA) biomarkers identified here are consistent with the activities of embryo-endometrial crosstalk, developmental competency and implantation and share common characteristics with markers of neoplasia/cancer invasion. Corresponding genes for expressed lncRNAs were more active in the blastocysts of younger women are associated with metabolic pathways including cholesterol biosynthesis and steroidogenesis.
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Affiliation(s)
- Panagiotis Ntostis
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
- Department of Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Grace Swanson
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Georgia Kokkali
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - David Iles
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - John Huntriss
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Agni Pantou
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - Maria Tzetis
- Department of Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Helen M Picton
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - David Miller
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
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14
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Deng J, Lin J, Liu C, Li J, Cai J, Zhou X, Li X. N7-methylguanosine methylation-related regulator genes as biological markers in predicting prognosis for melanoma. Sci Rep 2022; 12:21082. [PMID: 36473947 PMCID: PMC9726938 DOI: 10.1038/s41598-022-25698-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The aim of this study is to find those N7-methylguanosine (m7G) methylation-related regulator genes (m7GMRRGs) which were associated with melanoma prognosis and use them to develop a prognostic prediction model. Clinical information was retrieved online from The Cancer Gene Atlas (TCGA) and the Gene Expression Omnibus (GEO). R software was used to extract m7GMRRGs by differential expression analysis. To create a prognostic risk model, univariate and multivariate Cox regression analyses were employed for the evaluation of the prognostic significance of m7G methylation modifiers. Internal validation using cohort from TCGA (training set) and external validation using cohort from GEO (validation set) of the model were carried out. The model's predictive performance was confirmed by using the Kaplan-Meier, univariate, and multivariate Cox regression, and receiver operating characteristic curve (ROC) by constructing column line plots incorporating clinical factor characteristics. Immune infiltration analyses were performed to assess the immune function of m7GMRRGs. Drug sensitivity analysis was conducted to study chemotherapeutic drug treatment cues. Prognostic models using four m7GMRRGs (EIF4E3, LARP1, NCBP3, and IFIT5) showed good prognostic power in training and validation sets. The area under the curve (AUC) at 1, 3, and 5 years for GEO-melanoma were 0.689, 0.704, and 0.726, respectively. The prediction model could distinctly classify patients with melanoma into different risk subgroups (P < 0.001 for TCGA-melanoma and P < 0.05 for GEO-melanoma). Clinical characteristics were taken into account in Cox regression and AUC analysis, which highlighted that the risk score served as an independent risk factor determining the prognosis of patients with melanoma. Immuno-infiltration analysis showed that m7GMRRGs could potentially regulate CD8+ T cells as well as regulatory T cells (Treg cells). Results of our study indicate a association between m7GMRRGs and melanoma prognosis, and the prognostic prediction model using m7GMRRGs may predict the prognosis of patients with melanoma well. Nevertheless, these results may provide a clue for potential better options of melanoma treatment but need further validation in futural studies.
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Affiliation(s)
- Jiehua Deng
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Jiahua Lin
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 China ,Department of Neurosurgery, The 924th Hospital of the Chinese People’s Liberation Army Joint Logistic Support Force, Guilin, 541002 Guangxi Zhuang Autonomous Region China
| | - Chang Liu
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Jiasong Li
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Jun Cai
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Xiyu Zhou
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Xiong Li
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
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15
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Mehta M, Raguraman R, Ramesh R, Munshi A. RNA binding proteins (RBPs) and their role in DNA damage and radiation response in cancer. Adv Drug Deliv Rev 2022; 191:114569. [PMID: 36252617 PMCID: PMC10411638 DOI: 10.1016/j.addr.2022.114569] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 01/24/2023]
Abstract
Traditionally majority of eukaryotic gene expression is influenced by transcriptional and post-transcriptional events. Alterations in the expression of proteins that act post-transcriptionally can affect cellular signaling and homeostasis. RNA binding proteins (RBPs) are a family of proteins that specifically bind to RNAs and are involved in post-transcriptional regulation of gene expression and important cellular processes such as cell differentiation and metabolism. Deregulation of RNA-RBP interactions and any changes in RBP expression or function can lead to various diseases including cancer. In cancer cells, RBPs play an important role in regulating the expression of tumor suppressors and oncoproteins involved in various cell-signaling pathways. Several RBPs such as HuR, AUF1, RBM38, LIN28, RBM24, tristetrapolin family and Musashi play critical roles in various types of cancers and their aberrant expression in cancer cells makes them an attractive therapeutic target for cancer treatment. In this review we provide an overview of i). RBPs involved in cancer progression and their mechanism of action ii). the role of RBPs, including HuR, in breast cancer progression and DNA damage response and iii). explore RBPs with emphasis on HuR as therapeutic target for breast cancer therapy.
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Affiliation(s)
- Meghna Mehta
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Anupama Munshi
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA.
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16
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Zhao J, Zou J, Jiao W, Lin L, Wang J, Lin Z. Construction of N-7 methylguanine-related mRNA prognostic model in uterine corpus endometrial carcinoma based on multi-omics data and immune-related analysis. Sci Rep 2022; 12:18813. [PMID: 36335189 PMCID: PMC9637130 DOI: 10.1038/s41598-022-22879-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
N-7 methylguanine (m7G) is one of the most common RNA base modifications in post-transcriptional regulation, which participates in multiple processes such as transcription, mRNA splicing and translation during the mRNA life cycle. However, its expression and prognostic value in uterine corpus endometrial carcinoma (UCEC) have not been systematically studied. In this paper, the data such as gene expression profiles, clinical data of UCEC patients, somatic mutations and copy number variants (CNVs) are obtained from the cancer genome atlas (TCGA) and UCSC Xena. By analyzing the expression differences of m7G-related mRNA in UCEC and plotting the correlation network maps, a risk score model composed of four m7G-related mRNAs (NSUN2, NUDT3, LARP1 and NCBP3) is constructed using least absolute shrinkage and selection operator (LASSO), univariate and multivariate Cox regression in order to identify prognosis and immune response. The correlation of clinical prognosis is analyzed between the m7G-related mRNA and UCEC via Kaplan-Meier method, receiver operating characteristic (ROC) curve, principal component analysis (PCA), t-SNE, decision curve analysis (DCA) curve and nomogram etc. It is concluded that the high risk is significantly correlated with (P < 0.001) the poorer overall survival (OS) in patients with UCEC. It is one of the independent risk factors affecting the OS. Differentially expressed genes are identified by R software in the high and low risk groups. The functional analysis and pathway enrichment analysis have been performed. Single sample gene set enrichment analysis (ssGSEA), immune checkpoints, m6A-related genes, tumor mutation burden (TMB), stem cell correlation, tumor immune dysfunction and rejection (TIDE) scores and drug sensitivity are also used to study the risk model. In addition, we have obtained 3 genotypes based on consensus clustering, which are significantly related to (P < 0.001) the OS and progression-free survival (PFS). The deconvolution algorithm (CIBERSORT) is applied to calculate the proportion of 22 tumor infiltrating immune cells (TIC) in UCEC patients and the estimation algorithm (ESTIMATE) is applied to work out the number of immune and matrix components. In summary, m7G-related mRNA may become a potential biomarker for UCEC prognosis, which may promote UCEC occurrence and development by regulating cell cycles and immune cell infiltration. It is expected to become a potential therapeutic target of UECE.
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Affiliation(s)
- Junde Zhao
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Jiani Zou
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Wenjian Jiao
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Lidong Lin
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Jiuling Wang
- grid.452402.50000 0004 1808 3430Office of Medical Insurance Management, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Zhiheng Lin
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
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17
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Targeting the "undruggable": RNA-binding proteins in the spotlight in cancer therapy. Semin Cancer Biol 2022; 86:69-83. [PMID: 35772609 DOI: 10.1016/j.semcancer.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/19/2022] [Accepted: 06/24/2022] [Indexed: 01/27/2023]
Abstract
Tumors refractory to conventional therapy belong to specific subpopulations of cancer cells, which have acquired a higher number of mutations/epigenetic changes than the majority of cancer cells. This property provides them the ability to become resistant to therapy. Aberrant expression of certain RNA-binding proteins (RBPs) can regulate the sensitivity of tumor cells to chemotherapeutic drugs by binding to specific regions present in the 3´-UTR of certain mRNAs to promote or repress mRNA translation or by interacting with other proteins (including RBPs) and non-coding RNAs that are part of ribonucleoprotein complexes. In particular, an increasing interest in the RBPs involved in chemoresistance has recently emerged. In this review, we discuss how RBPs are not only affected by chemotherapeutic treatments, but also play an active role in therapeutic responses via the direct modulation of crucial cancer-related proteins. A special focus is being placed on the development of therapeutic strategies targeting these RBPs.
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18
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Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol 2022; 86:664-677. [PMID: 35381329 PMCID: PMC9526761 DOI: 10.1016/j.semcancer.2022.03.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/10/2023]
Abstract
RNA-binding proteins (RBPs) are key players in cellular physiology through posttranscriptional regulation of the expression of target RNA transcripts. By modulating the processing, stability and translation of cancer-related messenger RNA (mRNA) transcripts, a large set of RBPs play essential roles in various types of cancers. Perturbations in RBP activity have been causally associated with cancer development, tumor metabolism, drug resistance, cancer stem cell self-renewal, and tumor immune evasion. Here, we summarize the recent advances in cancer pathological roles and mechanisms of RBPs in regulating mRNA stability and translation with an emphasis on the emerging category of RNA modification-associated RBPs. The functional diversity of RBPs in different types of cancers and the therapeutic potential of targeting dysregulated RBPs for cancer treatment are also discussed.
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Affiliation(s)
- Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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19
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Tao X, Huang R, Xu R, Zheng S, Yue J. A novel m7G methylation–related signature associated with chromosome homeostasis in patients with lung adenocarcinoma. Front Genet 2022; 13:998258. [DOI: 10.3389/fgene.2022.998258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a malignant tumor of the respiratory system with poor prognosis. Recent studies have revealed that N7-methylguanosine (m7G) methylation is a widespread modification occurring in RNA. But the expression of m7G methylation–related genes in LUAD and their correlations with prognosis are still unclear. In this study, we found 12 m7G methylation–related regulators with differential expression between LUAD and normal lung tissues. According to differentially expressed genes (DEGs), all LUAD cases were separated into two subtypes. The prognostic value of each m7G methylation–related gene for survival was evaluated to construct a multigene signature using The Cancer Genome Atlas (TCGA) cohort. Finally, an m7G methylation–related prognostic signature based on three genes was built to classify LUAD patients into two risk groups. Patients in the high-risk group showed significantly reduced overall survival (OS) when compared with patients in the low-risk group (p < 0.05). The receiver operating characteristic (ROC) curve analysis confirmed the predictive capacity of the signature. The Gene Ontology (GO) functional annotation analysis disclosed that chromosome homeostasis plays an important role in this process. The gene set enrichment analysis (ssGSEA) implied that the immune status was decreased in the high-risk group. To sum up, m7G methylation–related genes play a vital role in tumor immunity and the related signature is a reliable predictor for LUAD prognosis.
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20
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mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading. Cell Rep 2022; 41:111548. [DOI: 10.1016/j.celrep.2022.111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 08/30/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
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21
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Hou L, Huang F, Chen G, Qiu J, Liu Y, Zhao H, Wang Z. Application of RNA processing factors for predicting clinical outcomes in colon cancer. Front Genet 2022; 13:979001. [PMID: 36212157 PMCID: PMC9538339 DOI: 10.3389/fgene.2022.979001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Background: Colon cancer is the fifth most common cause of cancer-related death worldwide, and despite significant advances in related treatment, the prognosis of colon cancer patients remains poor. Objective: This study performs systematic bioinformatics analysis of prognostic-associated RNA processing factor genes in colon cancer using the Cancer Related Genome Atlas database to explore their role in colon carcinogenesis and prognosis and excavate potential therapeutic targets. Methods: Data sets of colon cancer patients were obtained from GEO and TCGA databases. Univariate cox analysis was performed on the GSE39582 training set to identify prognosis-associated RNA processing factor genes and constructed a muticox model. The predictive performance of the model was validated by Correlation curve analysis. Similar results were obtained for the test dataset. Functional analyses were performed to explore the underlying mechanisms of colon carcinogenesis and prognosis. Results: A constructed muticox model consisting of βi and prognosis-related RNA processing factor gene expression levels (Expi) was established to evaluate the risk score of each patient. The subgroup with a higher risk score had lower overall survival (OS), higher risk factor, and mortality. We found that the risk score, age, gender, and TNM Stage were strongly associated with OS, and the 13-gene signature as an independent prognostic factor for colon cancer. The model has good accuracy in predicting patient survival and is superior to traditional pathological staging. Conclusion: This study proposes 13 RNA processing factor genes as a prognostic factor for colon cancer patients, which can independently predict the clinical outcome by risk score. The gene expression profile in this model is closely related to the immune status and prognosis of colon cancer patients. The interaction of the 13 RNA processing factor genes with the immune system during colon carcinogenesis provides new ideas for the molecular mechanisms and targeted therapies for colon cancer.
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22
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Huang X, Zhu J, Li Y, Yu Y, Tang J. La protein regulates protein expression by binding with the mRNAs of target genes and participates the pathological process of ovarian cancer. Front Oncol 2022; 12:763480. [PMID: 36110943 PMCID: PMC9468491 DOI: 10.3389/fonc.2022.763480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 08/08/2022] [Indexed: 12/03/2022] Open
Abstract
Research on the mechanism and new targets of ovarian cancer is of great significance to reduce the high mortality and drug resistance of ovarian cancer. Human La protein has been found to be highly expressed in a variety of malignant tumors and plays a role in tumorigenesis and development through its RNA-binding function. However, its role and mechanism in ovarian cancer are not completely clear. The present study showed that La protein was highly expressed in serum and tissues of patients with ovarian cancer by ELISA and immunohistochemistry, and the high expression of La protein was associated with the increased degree of malignancy and poor prognosis by searching the KM plotter database. Interference of the La gene resulted in a significant decrease in the proliferation, migration, and invasion of ovarian cancer cells with growth block in the G1 phase and increasing apoptosis. By RNA binding protein immunoprecipitation, transcriptome sequencing, and proteomics, 14 downstream target genes were screened. The La protein might affect the protein expression of these 14 genes by binding with the mRNAs. Therefore, it played a role in the pathological process of ovarian cancer.
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23
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Kozlov G, Mattijssen S, Jiang J, Nyandwi S, Sprules T, Iben J, Coon S, Gaidamakov S, Noronha AM, Wilds C, Maraia R, Gehring K. Structural basis of 3'-end poly(A) RNA recognition by LARP1. Nucleic Acids Res 2022; 50:9534-9547. [PMID: 35979957 PMCID: PMC9458460 DOI: 10.1093/nar/gkac696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
La-related proteins (LARPs) comprise a family of RNA-binding proteins involved in a wide range of posttranscriptional regulatory activities. LARPs share a unique tandem of two RNA-binding domains, La motif (LaM) and RNA recognition motif (RRM), together referred to as a La-module, but vary in member-specific regions. Prior structural studies of La-modules reveal they are pliable platforms for RNA recognition in diverse contexts. Here, we characterize the La-module of LARP1, which plays an important role in regulating synthesis of ribosomal proteins in response to mTOR signaling and mRNA stabilization. LARP1 has been well characterized functionally but no structural information exists for its La-module. We show that unlike other LARPs, the La-module in LARP1 does not contain an RRM domain. The LaM alone is sufficient for binding poly(A) RNA with submicromolar affinity and specificity. Multiple high-resolution crystal structures of the LARP1 LaM domain in complex with poly(A) show that it is highly specific for the RNA 3'-end, and identify LaM residues Q333, Y336 and F348 as the most critical for binding. Use of a quantitative mRNA stabilization assay and poly(A) tail-sequencing demonstrate functional relevance of LARP1 RNA binding in cells and provide novel insight into its poly(A) 3' protection activity.
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Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Jianning Jiang
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Samuel Nyandwi
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Tara Sprules
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada,Quebec/Eastern Canada NMR Centre, McGill University, Montréal, Canada
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Steven L Coon
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Anne M Noronha
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Canada
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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Dong Y, Li Y, Yao Y, Song Q. A novel defined m7G regulator signature to investigate the association between molecular characterization and clinical significance in lung adenocarcinoma. Front Oncol 2022; 12:897323. [PMID: 35982949 PMCID: PMC9380062 DOI: 10.3389/fonc.2022.897323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
Abstract
Background About170 chemical modifications to RNAs have been identified, which significantly affect gene expression. Dysregulation of RNA modifications induced by abnormal expression or mutations in RNA modifiers might result in cancer. The most frequent RNA modifications are N6-methyladenosine (m6A), 5-methylcytosine (m5C), and N7-methylguanosine (m7G). Lung cancer is the leading cause of cancer-related deaths globally. The present study aimed to investigate whether the expression of the m7G-related genes is linked to lung cancer cases with lung adenocarcinoma (LUAD), which accounts for about 40% of lung cancer cases. Methods A total of 12 m7G-related differentially expressed genes (DEGs) were identified in LUAD patients by The Cancer Genome Atlas (TCGA). The least absolute shrinkage and selection operator (LASSO) Cox regression method was used to build a four-gene risk model. Then, LUAD patients in the TCGA cohort were divided into low- and high-risk groups based on their risk scores for subsequent molecular and clinical research. Results Compared to the low-risk group, the high-risk group had a decreased overall survival (OS) (P=0.047). The risk score and stage were independent factors for predicting the OS of LUAD (P=0.0004 and P<0.0001, respectively). Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses based on the two groups showed that the DEGs were metabolically and hormonally related. The high-risk group showed a higher mutation rate and lesser immune cell infiltration, especially in TP53, KRAS, and MET. The expression level of PD-L1 and CTLA4 was high in the high-risk group (P<0.05). The high-risk group is more sensitive to anti-cancer therapy with lower IC50 and higher immunophenoscore (IPS). Conclusions In this study, we developed a novel LUAD stratification model based on m7G-related genes that successfully predicts the prognosis of LUAD patients and serves as a guide for clinically personalized treatment.
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Affiliation(s)
| | | | - Yi Yao
- *Correspondence: Yi Yao, ; Qibin Song,
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25
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Lu F, Gao J, Hou Y, Cao K, Xia Y, Chen Z, Yu H, Chang L, Li W. Construction of a Novel Prognostic Model in Lung Adenocarcinoma Based on 7-Methylguanosine-Related Gene Signatures. Front Oncol 2022; 12:876360. [PMID: 35785179 PMCID: PMC9243265 DOI: 10.3389/fonc.2022.876360] [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: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence has implicated the modification of 7-methylguanosine (m7G), a type of RNA modification, in tumor progression. However, no comprehensive analysis to date has summarized the predicted role of m7G-related gene signatures in lung adenocarcinoma (LUAD). Herein, we aimed to develop a novel prognostic model in LUAD based on m7G-related gene signatures. The LUAD transcriptome profiling data and corresponding clinical data were acquired from the Cancer Genome Atlas (TCGA) and two Gene Expression Omnibus datasets. After screening, we first obtained 29 m7G-related genes, most of which were upregulated in tumor tissues and negatively associated with overall survival (OS). According to the expression similarity of m7G-related genes, the combined samples from the TCGA-LUAD and GSE68465 datasets were further classified as two clusters that exhibit distinct OS rates and genetic heterogeneity. Then, we constructed a novel prognostic model involving four genes by using 130 differentially expressed genes among the two clusters. The combined samples were randomly divided into a training cohort and an internal validation cohort in a 1:1 ratio, and the GSE72094 dataset was used as an external validation cohort. The samples were divided into high- and low-risk groups. We demonstrated that a higher risk score was an independent negative prognostic factor and predicted poor OS. A nomogram was further constructed to better predict the survival of LUAD patients. Functional enrichment analyses indicated that cell cycle and DNA replication-related biological processes and pathways were enriched in the high-risk group. More importantly, the low-risk group had greater infiltration and enrichment of most immune cells, as well as higher ESTIMATE, immune, and stromal scores. In addition, the high-risk group had a lower TIDE score and higher expressions of most immune checkpoint-related genes. We finally noticed that patients in the high-risk group were more sensitive to chemotherapeutic agents commonly used in LUAD. In conclusion, we herein summarized for the first time the alterations and prognostic role of m7G-related genes in LUAD and then constructed a prognostic model based on m7G-related gene signatures that could accurately and stably predict survival and guide individualized treatment decision-making in LUAD patients.
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Affiliation(s)
- Fei Lu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- Department of Oncology and Hematology, Southern Central Hospital of Yunnan Province, The First People’s Hospital of Honghe State, Mengzi, China
| | - Jingyan Gao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yu Hou
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Ke Cao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yaoxiong Xia
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Zhengting Chen
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Hui Yu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Li Chang
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
| | - Wenhui Li
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
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Yang M, Lu Y, Piao W, Jin H. The Translational Regulation in mTOR Pathway. Biomolecules 2022; 12:biom12060802. [PMID: 35740927 PMCID: PMC9221026 DOI: 10.3390/biom12060802] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanistic/mammalian target of rapamycin (mTOR) plays a master role in cell proliferation and growth in response to insulin, amino acids, energy levels, and oxygen. mTOR can coordinate upstream signals with downstream effectors, including transcriptional and translational apparatuses to regulate fundamental cellular processes such as energy utilization, protein synthesis, autophagy, cell growth, and proliferation. Of the above, protein synthesis is highly energy-consuming; thus, mRNA translation is under the tight and immediate control of mTOR signaling. The translational regulation driven by mTOR signaling mainly relies on eukaryotic translation initiation factor 4E (eIF4E)-binding protein (4E-BP), ribosomal protein S6 kinase (S6K), and its downstream players, which are significant in rapid cellular response to environmental change. mTOR signaling not only controls the general mRNA translation, but preferential mRNA translation as well. This means that mTOR signaling shows the stronger selectivity to particular target mRNAs. Some evidence has supported the contribution of 4E-BP and La-related proteins 1 (LARP1) to such translational regulation. In this review, we summarize the mTOR pathway and mainly focus on mTOR-mediated mRNA translational regulation. We introduce the major components of mTOR signaling and their functions in translational control in a general or particular manner, and describe how the specificity of regulation is coordinated. Furthermore, we summarize recent research progress and propose additional ideas for reference. Because the mTOR pathway is on the center of cell growth and metabolism, comprehensively understanding this pathway will contribute to the therapy of related diseases, including cancers, type 2 diabetes, obesity, and neurodegeneration.
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Affiliation(s)
| | | | | | - Hua Jin
- Correspondence: (W.P.); (H.J.)
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Comprehensive characterization of posttranscriptional impairment-related 3'-UTR mutations in 2413 whole genomes of cancer patients. NPJ Genom Med 2022; 7:34. [PMID: 35654793 PMCID: PMC9163142 DOI: 10.1038/s41525-022-00305-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
The 3' untranslated region (3'-UTR) is the vital element regulating gene expression, but most studies have focused on variations in RNA-binding proteins (RBPs), miRNAs, alternative polyadenylation (APA) and RNA modifications. To explore the posttranscriptional function of 3'-UTR somatic mutations in tumorigenesis, we collected whole-genome data from 2413 patients across 18 cancer types. Our updated algorithm, PIVar, revealed 25,216 3'-UTR posttranscriptional impairment-related SNVs (3'-UTR piSNVs) spanning 2930 genes; 24 related RBPs were significantly enriched. The somatic 3'-UTR piSNV ratio was markedly increased across all 18 cancer types, which was associated with worse survival for four cancer types. Several cancer-related genes appeared to facilitate tumorigenesis at the protein and posttranscriptional regulation levels, whereas some 3'-UTR piSNV-affected genes functioned mainly via posttranscriptional mechanisms. Moreover, we assessed immune cell and checkpoint characteristics between the high/low 3'-UTR piSNV ratio groups and predicted 80 compounds associated with the 3'-UTR piSNV-affected gene expression signature. In summary, our study revealed the prevalence and clinical relevance of 3'-UTR piSNVs in cancers, and also demonstrates that in addition to affecting miRNAs, 3'-UTR piSNVs perturb RBPs binding, APA and m6A RNA modification, which emphasized the importance of considering 3'-UTR piSNVs in cancer biology.
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Zhang W, Cao C, Shen J, Shan S, Tong Y, Cai H, Han Z, Chai H. Long non-coding RNA LINC01270 is an onco-promotor in lung adenocarcinoma by upregulating LARP1 via sponging miR-326. Bioengineered 2022; 13:14472-14488. [PMID: 36694453 PMCID: PMC9995133 DOI: 10.1080/21655979.2022.2090183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Accumulating evidence have proved the key role of long non-coding RNA in lung adenocarcinoma (LUAD) progression. Bioinformatics analysis is used to seek the differentially expressed lncRNA LINC01270 from TCGA database. The overexpression of LINC01270 was then verified in LUAD tumor tissues and cell lines by qRT-PCR. LINC01270 knockdown resulted in impaired cell proliferative and invasive ability via CCK-8 assay, EdU assay, colony formation assay, transwell assay, while aberrant upregulation of LINC01270 led to enhanced cell growth and invasion. Moreover, LINC01270 was found inhibiting miR-326 and thereby overexpressing the abundance of LARP1 to promote LUAD development via PI3K/AKT pathway. It was also proved that LINC01270 knockdown could suppress LUAD tumor growth in vivo. All of these findings demonstrate thatLINC01270 is a tumor promotor in LUAD via enhancing LARP1 expressed by sponging miR-326 to facilitate the development of LUAD. LINC01270 play a significant role in LUAD, which could serve as biomarkers for early diagnosis and a novel targeted remedy.
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Affiliation(s)
- Weiran Zhang
- Department of Thoracic Surgery, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Cao
- Department of Thoracic Surgery, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jingfu Shen
- Department of Thoracic Surgery, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shaoyin Shan
- Department of Thoracic Surgery, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuanhao Tong
- Department of Thoracic Surgery, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyan Cai
- Department of Gastrology, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhifeng Han
- Department of Thoracic Surgery, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Huiping Chai
- Department of Thoracic Surgery, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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A N7-Methylguanine-Related Gene Signature Applicable for the Prognosis and Microenvironment of Prostate Cancer. JOURNAL OF ONCOLOGY 2022; 2022:8604216. [PMID: 35602299 PMCID: PMC9122703 DOI: 10.1155/2022/8604216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 01/02/2023]
Abstract
Background Despite the constant iteration of small-molecule inhibitors and immune checkpoint inhibitors, PRAD (prostate adenocarcinoma) patients with distant metastases and biochemical recurrence maintain a poor survival outcome along with an increasing morbidity in recent years. N7-Methylguanine, a new-found type of RNA modification, has demonstrated an essential role in tumor progression but has hardly been studied for its effect on prostate carcinoma. The current study aimed to seek m7G (N7-methylguanosine) related prognostic biomarkers and potential targets for PRAD treatment. Methods 42 genes related to m7G were collected from former literatures and GSEA (Gene Set Enrichment Analysis) website. Then, RNA-seq (RNA sequencing) and clinical data from TCGA-PRAD (The Cancer Genome Atlas-Prostate) cohort were retrieved to screen the differentially expressed m7G genes to further construct a multivariate Cox prognostic model for PRAD. Next, GSE116918, a prostate cancer cohort acquired from GEO (Gene Expression Omnibus) database, was analyzed for the external validation group to assess the ability to predict BFFS (biochemical failure-free survival) of our m7G prognostic signature. Kaplan-Meier, ROC (receiver operator characteristic), AUC (areas under ROC curve), and calibration curves were adopted to display the performance of this prognostic signature. In addition, immune infiltration analysis was implemented to evaluate the effect of these m7G genes on immunoinfiltrating cells. Correlation with drug susceptibility of the m7G signature was also analyzed by matching drug information in CellMiner database. Results The m7G-related prognostic signature, including three genes (EIF3D, EIF4A1, LARP1) illustrated superior prognostic ability for PRAD in both training and validation cohorts. The 5-year AUC were 0.768 for TCGA-PRAD and 0.608 for GSE116918. It can well distinguish patients into different risk groups of biochemical recurrence (p =1e-04 for TCGA-PRAD and p =0.0186 for GSE116918). Immune infiltration analysis suggested potential regulation of m7G genes on neutrophils and dendritic cells in PRAD. Conclusions A m7G-related prognostic signature was constructed and validated in the current study, giving new sights of m7G methylation in predicting the prognostic and improving the treatment of PRAD.
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Kovalski JR, Kuzuoglu‐Ozturk D, Ruggero D. Protein synthesis control in cancer: selectivity and therapeutic targeting. EMBO J 2022; 41:e109823. [PMID: 35315941 PMCID: PMC9016353 DOI: 10.15252/embj.2021109823] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Translational control of mRNAs is a point of convergence for many oncogenic signals through which cancer cells tune protein expression in tumorigenesis. Cancer cells rely on translational control to appropriately adapt to limited resources while maintaining cell growth and survival, which creates a selective therapeutic window compared to non-transformed cells. In this review, we first discuss how cancer cells modulate the translational machinery to rapidly and selectively synthesize proteins in response to internal oncogenic demands and external factors in the tumor microenvironment. We highlight the clinical potential of compounds that target different translation factors as anti-cancer therapies. Next, we detail how RNA sequence and structural elements interface with the translational machinery and RNA-binding proteins to coordinate the translation of specific pro-survival and pro-growth programs. Finally, we provide an overview of the current and emerging technologies that can be used to illuminate the mechanisms of selective translational control in cancer cells as well as within the microenvironment.
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Affiliation(s)
- Joanna R Kovalski
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Duygu Kuzuoglu‐Ozturk
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
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Xiao Y, Gu S, Yao W, Qin L, Luo J. Circ_0047921 acts as the sponge of miR-1287-5p to stimulate lung cancer progression by regulating proliferation, migration, invasion, and glycolysis of lung cancer cells. World J Surg Oncol 2022; 20:108. [PMID: 35365169 PMCID: PMC8976346 DOI: 10.1186/s12957-021-02466-1] [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: 09/29/2021] [Accepted: 12/05/2021] [Indexed: 12/24/2022] Open
Abstract
Background Lung cancer is a common respiratory system disease caused by multiple factors. Circular RNAs (circRNAs) play vital roles in tumorigenesis, including lung cancer. This study aimed to clarify the role and underlying molecular mechanisms of circ_0047921 in lung cancer. Methods Real-time quantitative polymerase chain reaction (RT-qPCR) was used to assess the expression levels of circ_0047921, La-related protein 1 (LARP1), and miR-1287-5p. Cell proliferation was analyzed by CCK-8 and EdU assays. Transwell assay was used to assess migration and invasion. Western blot assay was employed to quantify protein expression. Glycolysis ability of cell was determined by measuring glucose consumption and lactate production with matched kits. The relationship between miR-1287-5p and circ_0047921 or LARP1 was confirmed by dual-luciferase reporter assay. In addition, a xenograft model was established to clarify the functional role of circ_0047921 in vivo. Results Circ_0047921 was highly expressed in lung cancer tissues and cells. Circ_0047921 downregulation repressed proliferation, migration, invasion, epithelial-mesenchymal transition (EMT) and glycolysis in lung cancer cells. Circ_0047921 targeted miR-1287-5p to deplete miR-1287-5p expression. The effects caused by circ_0047921 downregulation were reversed by miR-1287-5p inhibition. In addition, LARP1 was a target of miR-1287-5p, and circ_0047921 could directly interact with miR-1287-5p to increase the expression of LARP1. The effects caused by circ_0047921 downregulation were also reversed by LARP1 overexpression. Circ_0047921 silencing impeded the growth of tumor in vivo. Conclusion Circ_0047921 was overexpressed in lung cancer, and circ_0047921 targeted miR-1287-5p to modulate LARP1 expression, thereby facilitating the development of lung cancer. Trial registration The present study was approved by the ethical review committee of The First People’s Hospital of Chenzhou, Southern Medical University with reference no. 20210106. 1. Circ_0047921 was upregulated in lung cancer tissues and cells. 2. Circ_0047921/miR-1287-5p/LARP1 axis played a key role in proliferation, migration, invasion, EMT and glycolysis of lung cancer cells. 3. Circ_0047921 regulated LARP1 by sponging miR-1287-5p in lung cancer.
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Affiliation(s)
- Yuehua Xiao
- The First General Surgery Department of Carcinoma, The First People's Hospital of Chenzhou, Southern Medical University, Chenzhou, Hunan, China
| | - Shequn Gu
- The First Department of Medical Oncology, The First People's Hospital of Chenzhou, Southern Medical University, Chenzhou, Hunan, China.
| | - Wenxiu Yao
- Department of Thoracic Oncology, The Cancer Hospital of Sichuan Province, Chengdu, Sichuan, China
| | - Ling Qin
- The First Department of Medical Oncology, The First People's Hospital of Chenzhou, Southern Medical University, Chenzhou, Hunan, China
| | - Jihui Luo
- The Second General Surgery Department of Carcinoma, The First People's Hospital of Chenzhou, Southern Medical University, Chenzhou, 423000, Hunan, China
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Li P, Chen J, Zou J, Zhu W, Zang Y, Li H. Circular RNA coiled-coil domain containing 66 regulates malignant development of papillary thyroid carcinoma by upregulating La ribonucleoprotein 1 via the sponge effect on miR-129-5p. Bioengineered 2022; 13:7181-7196. [PMID: 35264065 PMCID: PMC8973727 DOI: 10.1080/21655979.2022.2036304] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Circular RNAs (circRNAs) play vital roles in the development and progression of various diseases. CircRNA coiled-coil domain containing 66 (circ-CCDC66) has been reported to be involved in several cancers, but its biological function and underlying mechanism in papillary thyroid carcinoma (PTC) remain unclear. We detected the relative expression level of circ-CCDC66 in PTC specimens and cell lines using real-time reverse transcription PCR. In addition, EdU assay, transwell assay, and xenograft analysis were performed to measure the effect of circ-CCDC66 on the proliferative, migratory, and invasive capacities of PTC cells. We also investigated the potential mechanism of circ-CCDC66 by bioinformatics analysis, RNA immunoprecipitation, and dual-luciferase reporter assay. We observed that circ-CCDC66 expression was upregulated in PTC specimens and cell lines and was correlated with poor clinical characteristics of PTC patients. Moreover, in vitro experiments demonstrated that knockdown of circ-CCDC66 markedly suppressed the proliferative, migratory, and invasive capacities of PTC cells. Mechanistically, miR-129-5p was a target gene of circ-CCDC66 and was downregulated in PTC tissues. LARP1, a downstream target of miR-129-5p, was upregulated in PTC tissues. In addition, we confirmed that inhibition of circ-CCDC66 could repress xenograft tumor growth. Circ-CCDC66 promoted PTC proliferation, migration, invasion, and tumor growth by sponging miR-129-5p and promoting LARP1 expression.
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Affiliation(s)
- Peipei Li
- Department of Otorhinolaryngology Head and Neck Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Neurosurgery, Wuxi Clinical Medical School of Anhui Medical University, 904th Hospital of PLA(Wuxi Taihu Hospital), Wuxi, China
| | - Junhui Chen
- Department of Neurosurgery, Wuxi Clinical Medical School of Anhui Medical University, 904th Hospital of PLA(Wuxi Taihu Hospital), Wuxi, China
| | - Jun Zou
- Department of Otolaryngology, Wuxi No. 5 People's Hospital, Wuxi, China
| | - Wei Zhu
- Department of Otorhinolaryngology Head and Neck Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yan Zang
- Department of Otorhinolaryngology Head and Neck Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hongwu Li
- Department of Otorhinolaryngology Head and Neck Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
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Wang Y, Ye W, Tian G, Zhang Y. Identification of a new RNA-binding proteins-based signature for prognostic prediction in gastric cancer. Medicine (Baltimore) 2022; 101:e28901. [PMID: 35212295 PMCID: PMC8878810 DOI: 10.1097/md.0000000000028901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2022] [Indexed: 01/04/2023] Open
Abstract
Gastric cancer (GC) is one of the most common cancers with high incidence and mortality worldwide. Recently, RNA-binding proteins (RBPs) have drawn more and more attention for its role in cancer pathophysiology. However, the function and clinical implication of RBPs in GC have not been fully elucidated. RNA sequencing data along with the corresponding clinical information of GC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA-binding proteins (DERBPs) between tumor and normal tissues were identified by "limma" package. Functional enrichment analysis and the protein-protein interaction (PPI) network were harnessed to explore the function and interaction of DERBPs. Next, univariate and multiple Cox regression were applied to screen prognosis-related hub RBPs and to construct a signature for GC. Meanwhile, a nomogram was built on the basis of the independent factors. A total of 296 DERBPs were found, and most of them mainly related to post-transcriptional regulation of RNA and ribonucleoprotein. A PPI network of DERBPs was constructed, consisting of 262 nodes and 2567 edges. A prognostic signature was built depending on 7 prognosis-related hub RBPs that could divide GC patients into high-risk and low-risk groups. Survival analysis showed that high-risk group had a worse prognosis compared with the low-risk group and the time-dependent receiver operating characteristic (ROC) curves suggested that signature existed moderate predictive capacities of survival for GC patients. Similar results were obtained from another independent set GSE62254, confirming the robustness of signature. Besides, the genetic variation and immune heterogeneity differences were identified between the high-risk and low-risk groups by bioinformatics methods. These findings would provide evidence of the effect of RBPs and offer a novel potential biomarker in prognostic prediction and clinical decision for GC.
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Affiliation(s)
- Yuzhi Wang
- Department of Laboratory Medicine, People's Hospital of Deyang City, Deyang, Sichuan, China
| | - Weixia Ye
- Department of Gastroenterology, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - Gang Tian
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yi Zhang
- Department of Blood Transfusion, People's Hospital of Deyang City, Deyang, Sichuan, China
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Desi N, Tong QY, Teh V, Chan JJ, Zhang B, Tabatabaeian H, Tan HQ, Kapeli K, Jin W, Lim CY, Kwok ZH, Tan HT, Wang S, Siew BE, Lee KC, Chong CS, Tan KK, Yang H, Kappei D, Yeo GW, Chung MCM, Tay Y. Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis. Cell Mol Life Sci 2022; 79:147. [PMID: 35195778 PMCID: PMC11072786 DOI: 10.1007/s00018-021-04093-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/03/2022]
Abstract
In addition to genomic alterations, aberrant changes in post-transcriptional regulation can modify gene function and drive cancer development. RNA-binding proteins (RBPs) are a large class of post-transcriptional regulators that have been increasingly implicated in carcinogenesis. By integrating multi-omics data, we identify LARP1 as one of the most upregulated RBPs in colorectal cancer (CRC) and demonstrate its oncogenic properties. We perform LARP1:RNA interactome profiling and unveil a previously unexplored role for LARP1 in targeting the 3'UTR of oncogenes in CRC. Notably, we identify the proto-oncogenic transcription factor MYC as a key LARP1-regulated target. Our data show that LARP1 positively modulates MYC expression by associating with its 3'UTR. In addition, antisense oligonucleotide-mediated blocking of the interaction between LARP1 and the MYC 3'UTR reduces MYC expression and in vitro CRC growth. Furthermore, a systematic analysis of LARP1:protein interactions reveals IGF2BP3 and YBX1 as LARP1-interacting proteins that also regulate MYC expression and CRC development. Finally, we demonstrate that MYC reciprocally modulates LARP1 expression by targeting its enhancer. In summary, our data reveal a critical, previously uncharacterized role of LARP1 in promoting CRC tumorigenesis, validate its direct regulation of the proto-oncogene MYC and delineate a model of the positive feedback loop between MYC and LARP1 that promotes CRC growth and development.
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Affiliation(s)
- Ng Desi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Qing Yun Tong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Velda Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Hossein Tabatabaeian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Hui Qing Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Wenhao Jin
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Chun You Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Division of Pulmonary and Critical Care, Boston University, Boston, MA, 02118, USA
| | - Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Bei-En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok-Chung Lee
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Choon-Seng Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Gene W Yeo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, La Jolla, San Diego, USA
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
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Liu F, Liang J, Long P, Zhu L, Hou W, Wu X, Luo C. ZCCHC17 Served as a Predictive Biomarker for Prognosis and Immunotherapy in Hepatocellular Carcinoma. Front Oncol 2022; 11:799566. [PMID: 35071004 PMCID: PMC8770814 DOI: 10.3389/fonc.2021.799566] [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: 10/21/2021] [Accepted: 12/13/2021] [Indexed: 12/01/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the common malignant tumors. The prognosis and five-year survival rate of HCC are not promising due to tumor recurrence and metastasis. Exploring markers that contribute to the early diagnosis of HCC, markers for prognostic evaluation of HCC patients, and effective targets for treating HCC patients are in the spotlight of HCC therapy. Zinc Finger CCHC-Type Containing 17 (ZCCHC17) encodes the RNA binding protein ZCCHC17, but its role in HCC is still unclear. Here, 90 paraffin-embedded specimens combined with bioinformatics were used to comprehensively clarify the value of ZCCHC17 in the diagnosis and prognosis of HCC and its potential functions. Paraffin-embedded specimens were used to assess ZCCHC17 protein expression and its correlation with prognosis in 90 HCC patients. the public data sets of HCC patients from TCGA, ICG, and GEO databases were also used for further analysis. It was found that protein and mRNA levels of ZCCHC17 in HCC tissues were significantly higher than those in normal tissues. The abnormally high expression may be related to the abnormal DNA methylation of ZCCHC17 in tumor tissues. The high expression of ZCCHC17 is related to AFP, histologic grade, tumor status, vascular invasion, and pathological stage. Multi-data set analysis showed that patients with high ZCCHC17 expression had a worse prognosis, and multivariate cox regression analysis showed an independent prognostic significance of ZCCHC17. The results of functional analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA), indicate that ZCCHC17 is mainly involved in immune regulation. Subsequently, further single-sample gene set enrichment analysis (ssGSEA) showed that the expression of ZCCHC17 was related to the infiltration of immune cells. Importantly, we also analyzed the relationship between ZCCHC17 and immune checkpoint genes, tumor mutation burden (TMB), microsatellite instability (MSI) and TP53 status in HCC patients and evaluated the role of ZCCHC17 in cancer immunotherapy. In summary, ZCCHC17 is a novel marker for the diagnosis and prognostic evaluation of HCC. Concurrently, it regulates immune cells in the tumor microenvironment (TME) of HCC patients, which has a specific reference value for the immunotherapy of HCC.
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Affiliation(s)
- Fahui Liu
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jiadong Liang
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Puze Long
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Lilan Zhu
- Undergraduate Clinical Medicine, Youjiang Medical University for Nationalities, Baise, China
| | - Wanyun Hou
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xueming Wu
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chunying Luo
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.,Department of Cell Biology, Medical College of Guangxi University, Nanning, China
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36
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Alternative Splicing, Epigenetic Modifications and Cancer: A Dangerous Triangle, or a Hopeful One? Cancers (Basel) 2022; 14:cancers14030560. [PMID: 35158828 PMCID: PMC8833605 DOI: 10.3390/cancers14030560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Epigenetics studies the alteration of gene expression without changing DNA sequence and very often, epigenetic dysregulation causes cancer. Alternative splicing is a mechanism that results in the production of several mRNA isoforms from a single gene and aberrant splicing is also a frequent cause of cancer. The present review is built on the interrelations of epigenetics and alternative splicing. In an intuitive way, we say that epigenetic modifications and alternative splicing are at two vertices of a triangle, the third vertex being occupied by cancer. Interconnection between alternative splicing and epigenetic modifications occurs backward and forward and the mechanisms involved are widely reviewed. These connections also provide novel diagnostic or prognostic tools, which are listed. Finally, as epigenetic alterations are reversible and aberrant alternative splicing may be corrected, the therapeutic possibilities to break the triangle are discussed. Abstract The alteration of epigenetic modifications often causes cancer onset and development. In a similar way, aberrant alternative splicing may result in oncogenic products. These issues have often been individually reviewed, but there is a growing body of evidence for the interconnection of both causes of cancer. Actually, aberrant splicing may result from abnormal epigenetic signalization and epigenetic factors may be altered by alternative splicing. In this way, the interrelation between epigenetic marks and alternative splicing form the base of a triangle, while cancer may be placed at the vertex. The present review centers on the interconnections at the triangle base, i.e., between alternative splicing and epigenetic modifications, which may result in neoplastic transformations. The effects of different epigenetic factors, including DNA and histone modifications, the binding of non-coding RNAs and the alterations of chromatin organization on alternative splicing resulting in cancer are first considered. Other less-frequently considered questions, such as the epigenetic regulation of the splicing machinery, the aberrant splicing of epigenetic writers, readers and erasers, etc., are next reviewed in their connection with cancer. The knowledge of the above-mentioned relationships has allowed increasing the collection of biomarkers potentially useful as cancer diagnostic and/or prognostic tools. Finally, taking into account on one hand that epigenetic changes are reversible, and some epigenetic drugs already exist and, on the other hand, that drugs intended for reversing aberrations in alternative splicing, therapeutic possibilities for breaking the mentioned cancer-related triangle are discussed.
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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.
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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.
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38
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Guillemin A, Kumar A, Wencker M, Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol 2022; 12:796012. [PMID: 35087521 PMCID: PMC8787094 DOI: 10.3389/fimmu.2021.796012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.
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Affiliation(s)
- Anissa Guillemin
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
| | - Anuj Kumar
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mélanie Wencker
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, ENS de Lyon, CNRS, UMR 5308, INSERM, Lyon, France
| | - Emiliano P. Ricci
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
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Raguraman R, Shanmugarama S, Mehta M, Elle Peterson J, Zhao YD, Munshi A, Ramesh R. Drug delivery approaches for HuR-targeted therapy for lung cancer. Adv Drug Deliv Rev 2022; 180:114068. [PMID: 34822926 PMCID: PMC8724414 DOI: 10.1016/j.addr.2021.114068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/18/2021] [Indexed: 01/03/2023]
Abstract
Lung cancer (LC) is often diagnosed at an advanced stage and conventional treatments for disease management have limitations associated with them. Novel therapeutic targets are thus avidly sought for the effective management of LC. RNA binding proteins (RBPs) have been convincingly established as key players in tumorigenesis, and their dysregulation is linked to multiple cancers, including LC. In this context, we review the role of Human antigen R (HuR), an RBP that is overexpressed in LC, and further associated with various aspects of LC tumor growth and response to therapy. Herein, we describe the role of HuR in LC progression and outline the evidences supporting various pharmacologic and biologic approaches for inhibiting HuR expression and function. These approaches, including use of small molecule inhibitors, siRNAs and shRNAs, have demonstrated favorable results in reducing tumor cell growth, invasion and migration, angiogenesis and metastasis. Hence, HuR has significant potential as a key therapeutic target in LC. Use of siRNA-based approaches, however, have certain limitations that prevent their maximal exploitation as cancer therapies. To address this, in the conclusion of this review, we provide a list of nanomedicine-based HuR targeting approaches currently being employed for siRNA and shRNA delivery, and provide a rationale for the immense potential therapeutic benefits offered by nanocarrier-based HuR targeting and its promise for treating patients with LC.
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Affiliation(s)
- Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Santny Shanmugarama
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Meghna Mehta
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jo Elle Peterson
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yan D Zhao
- Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Anupama Munshi
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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40
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Yi B, Li H, Cai H, Lou X, Yu M, Li Z. LOXL1-AS1 communicating with TIAR modulates vasculogenic mimicry in glioma via regulation of the miR-374b-5p/MMP14 axis. J Cell Mol Med 2021; 26:475-490. [PMID: 34890108 PMCID: PMC8743654 DOI: 10.1111/jcmm.17106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
At present, growing evidence indicates that long non‐coding RNAs (lncRNAs) participate in the progression of glioma. The function of LOXL1‐AS1 in vasculogenic mimicry (VM) in glioma remains unclear. First, the expressions of TIAR, the lncRNA LOXL1‐AS1, miR‐374b‐5p and MMP14 were examined by qRT‐PCR and Western blot in both, glioma tissues and glioma cell lines. Proliferation, migration, invasion and tube formation assays were conducted to evaluate the roles of TIAR, LOXL1‐AS1, miR‐374b‐5p and MMP14 in malignant cellular behaviours in glioma cells. A nude mouse xenograft model and dual staining for CD34 and PAS were used to assess whether VM was affected by TIAR, LOXL1‐AS1 or miR‐374b‐5p in vivo. In this study, low levels of TIAR and high levels of LOXL1‐AS1 were found in glioma cells and tissues. TIAR downregulated the expression of LOXL1‐AS1 by destabilizing it. LOXL1‐AS1 acted like a miRNA sponge towards miR‐374b‐5p so that downregulation of the former greatly inhibited cell proliferation, migration, invasion and VM. Additionally, miR‐374b‐5p overexpression repressed malignant biological behaviours and VM in glioma by modifying MMP14. In summary, we demonstrated that TIAR combined with LOXL1‐AS1 modulates VM in glioma via the miR‐374b‐5p/MMP14 axis, revealing novel targets for glioma therapy.
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Affiliation(s)
- Bolong Yi
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China.,Department of Anesthesiology, General Hospital of Shenyang Commend, Shenyang
| | - Hao Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xin Lou
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Mingjun Yu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
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Fuentes P, Pelletier J, Martinez-Herráez C, Diez-Obrero V, Iannizzotto F, Rubio T, Garcia-Cajide M, Menoyo S, Moreno V, Salazar R, Tauler A, Gentilella A. The 40 S-LARP1 complex reprograms the cellular translatome upon mTOR inhibition to preserve the protein synthetic capacity. SCIENCE ADVANCES 2021; 7:eabg9275. [PMID: 34818049 PMCID: PMC8612684 DOI: 10.1126/sciadv.abg9275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Ribosomes execute the transcriptional program in every cell. Critical to sustain nearly all cellular activities, ribosome biogenesis requires the translation of ~200 factors of which 80 are ribosomal proteins (RPs). As ribosome synthesis depends on RP mRNA translation, a priority within the translatome architecture should exist to ensure the preservation of ribosome biogenesis capacity, particularly under adverse growth conditions. Here, we show that under critical metabolic constraints characterized by mTOR inhibition, LARP1 complexed with the 40S subunit protects from ribophagy the mRNAs regulon for ribosome biogenesis and protein synthesis, acutely preparing the translatome to promptly resume ribosomes production after growth conditions return permissive. Characterizing the LARP1-protected translatome revealed a set of 5′TOP transcript isoforms other than RPs involved in energy production and in mitochondrial function, among other processes, indicating that the mTOR-LARP1-5′TOP axis acts at the translational level as a primary guardian of the cellular anabolic capacity.
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Affiliation(s)
- Pedro Fuentes
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Joffrey Pelletier
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Carolina Martinez-Herráez
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
| | - Virginia Diez-Obrero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL). L’Hospitalet de Llobregat, Barcelona, Spain
| | - Flavia Iannizzotto
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Teresa Rubio
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Marta Garcia-Cajide
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Sandra Menoyo
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Victor Moreno
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL). L’Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Ramón Salazar
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Albert Tauler
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
| | - Antonio Gentilella
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
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Rogoyski O, Gerber AP. RNA-binding proteins modulate drug sensitivity of cancer cells. Emerg Top Life Sci 2021; 5:681-685. [PMID: 34328175 PMCID: PMC8726047 DOI: 10.1042/etls20210193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/16/2022]
Abstract
As our understanding of the complex network of regulatory pathways for gene expression continues to grow, avenues of investigation for how these new findings can be utilised in therapeutics are emerging. The recent growth of interest in the RNA binding protein (RBP) interactome has revealed it to be rich in targets linked to, and causative of diseases. While this is, in and of itself, very interesting, evidence is also beginning to arise for how the RBP interactome can act to modulate the response of diseases to existing therapeutic treatments, especially in cancers. Here we highlight this topic, providing examples of work that exemplifies such modulation of chemotherapeutic sensitivity.
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Affiliation(s)
- Oliver Rogoyski
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, U.K
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, U.K
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Lan Y, Su J, Xue Y, Zeng L, Cheng X, Zeng L. Analysing a Novel RNA-Binding-Protein-Related Prognostic Signature Highly Expressed in Breast Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:9174055. [PMID: 34707800 PMCID: PMC8545572 DOI: 10.1155/2021/9174055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/13/2021] [Accepted: 09/19/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Breast cancer (BRCA) is one of the most common cancers and the leading cause of cancer-related death in women. RNA-binding proteins (RBPs) play an important role in the emergence and pathogenesis of tumors. The target RNAs of RBPs are very diverse; in addition to binding to mRNA, RBPs also bind to noncoding RNA. Noncoding RNA can cause secondary structures that can bind to RBPs and regulate multiple processes such as splicing, RNA modification, protein localization, and chromosomes remodeling, which can lead to tumor initiation, progression, and invasion. METHODS (1) BRCA data were downloaded from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases and were used as training and testing datasets, respectively. (2) The prognostic RBPs-related genes were screened according to the overlapping differentially expressed genes (DEGs) from the TCGA database. (3) Univariate Cox proportional hazard regression was performed to identify the genes with significant prognostic value. (4) Further, we used the LASSO regression to construct a prognostic signature and validated the signature in the TCGA and ICGC cohort. (5) Besides, we also performed prognostic analysis, expression level verification, immune cell correlation analysis, and drug correlation analysis of the genes in the model. RESULTS Four genes (MRPL13, IGF2BP1, BRCA1, and MAEL) were identified as prognostic gene signatures. The prognostic model has been validated in the TCGA and ICGC cohorts. The risk score calculated with four genes signatures could largely predict overall survival for 1, 3, and 5 years in patients with BRCA. The calibration plot demonstrated outstanding consistency between the prediction and actual observation. The findings of online database verification revealed that these four genes were significantly highly expressed in tumors. Also, we observed their significant correlations with some immune cells and also potential correlations with some drugs. CONCLUSION We constructed a 4-RBPs-based prognostic signature to predict the prognosis of BRCA patients, and it has the potential for treating and diagnosing BRCA.
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Affiliation(s)
- Yunyun Lan
- Department of ICU, Zhuzhou Central Hospital, Zhuzhou, China
| | - Juan Su
- Department of Medical Administration, Zhuzhou Central Hospital, Zhuzhou, China
| | - Yaxin Xue
- Zhuzhou Central Hospital, Department of Cardiology, Zhuzhou, China
| | - Lulu Zeng
- Zhuzhou Central Hospital, ICU, Zhuzhou, China
| | - Xun Cheng
- Department of Medical Administration, Zhuzhou Central Hospital, Zhuzhou, China
| | - Liyi Zeng
- Administration Department of Nosocomial Infection, Zhuzhou, China
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Barreiro-Alonso A, Lamas-Maceiras M, Lorenzo-Catoira L, Pardo M, Yu L, Choudhary JS, Cerdán ME. HMGB1 Protein Interactions in Prostate and Ovary Cancer Models Reveal Links to RNA Processing and Ribosome Biogenesis through NuRD, THOC and Septin Complexes. Cancers (Basel) 2021; 13:cancers13184686. [PMID: 34572914 PMCID: PMC8466577 DOI: 10.3390/cancers13184686] [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: 08/17/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary HMGB1 over-expression is associated to prostate and ovary cancers: in this work, using a proteomic approach, we aimed to discover new protein interactions that might contribute to understand the oncogenic function of HMGB1 in cancers models. Our findings show that HMGB1 interacts with components of the NuRD, THOC and septin complexes, revealing new connections of HMGB1 functions to RNA processing and ribosome biogenesis. Results might contribute to consider the components of these interactomes as targets for diagnosis and therapy in future studies. Abstract This study reports the HMGB1 interactomes in prostate and ovary cancer cells lines. Affinity purification coupled to mass spectrometry confirmed that the HMGB1 nuclear interactome is involved in HMGB1 known functions such as maintenance of chromatin stability and regulation of transcription, and also in not as yet reported processes such as mRNA and rRNA processing. We have identified an interaction between HMGB1 and the NuRD complex and validated this by yeast-two-hybrid, confirming that the RBBP7 subunit directly interacts with HMGB1. In addition, we describe for the first time an interaction between two HMGB1 interacting complexes, the septin and THOC complexes, as well as an interaction of these two complexes with Rab11. Analysis of Pan-Cancer Atlas public data indicated that several genes encoding HMGB1-interacting proteins identified in this study are dysregulated in tumours from patients diagnosed with ovary and prostate carcinomas. In PC-3 cells, silencing of HMGB1 leads to downregulation of the expression of key regulators of ribosome biogenesis and RNA processing, namely BOP1, RSS1, UBF1, KRR1 and LYAR. Upregulation of these genes in prostate adenocarcinomas is correlated with worse prognosis, reinforcing their functional significance in cancer progression.
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Affiliation(s)
- Aida Barreiro-Alonso
- EXPRELA Group, Centro de Investigaciones Científicas Avanzadas (CICA), University of A Coruña (UDC), 15008 A Coruña, Spain; (M.L.-M.); (L.L.-C.)
- Instituto de Investigación Biomédica de A Coruña (INIBIC), 15006 A Coruña, Spain
- Department of Biology, Faculty of Sciences, Campus de A Zapateira, University of A Coruña (UDC), 15008 A Coruña, Spain
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK; (M.P.); (L.Y.); (J.S.C.)
- Correspondence: (A.B.-A.); (M.E.C.)
| | - Mónica Lamas-Maceiras
- EXPRELA Group, Centro de Investigaciones Científicas Avanzadas (CICA), University of A Coruña (UDC), 15008 A Coruña, Spain; (M.L.-M.); (L.L.-C.)
- Instituto de Investigación Biomédica de A Coruña (INIBIC), 15006 A Coruña, Spain
- Department of Biology, Faculty of Sciences, Campus de A Zapateira, University of A Coruña (UDC), 15008 A Coruña, Spain
| | - Lidia Lorenzo-Catoira
- EXPRELA Group, Centro de Investigaciones Científicas Avanzadas (CICA), University of A Coruña (UDC), 15008 A Coruña, Spain; (M.L.-M.); (L.L.-C.)
- Instituto de Investigación Biomédica de A Coruña (INIBIC), 15006 A Coruña, Spain
- Department of Biology, Faculty of Sciences, Campus de A Zapateira, University of A Coruña (UDC), 15008 A Coruña, Spain
| | - Mercedes Pardo
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK; (M.P.); (L.Y.); (J.S.C.)
| | - Lu Yu
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK; (M.P.); (L.Y.); (J.S.C.)
| | - Jyoti S. Choudhary
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK; (M.P.); (L.Y.); (J.S.C.)
| | - M. Esperanza Cerdán
- EXPRELA Group, Centro de Investigaciones Científicas Avanzadas (CICA), University of A Coruña (UDC), 15008 A Coruña, Spain; (M.L.-M.); (L.L.-C.)
- Instituto de Investigación Biomédica de A Coruña (INIBIC), 15006 A Coruña, Spain
- Department of Biology, Faculty of Sciences, Campus de A Zapateira, University of A Coruña (UDC), 15008 A Coruña, Spain
- Correspondence: (A.B.-A.); (M.E.C.)
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Liang Q, Du X, Mao L, Wang G. Molecular characterization of colorectal cancer: A five-gene prognostic signature based on RNA-binding proteins. Saudi J Gastroenterol 2021; 27:223-233. [PMID: 34169901 PMCID: PMC8448017 DOI: 10.4103/sjg.sjg_530_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers worldwide. RNA-binding proteins (RBPs) regulate essential biological processes and play essential roles in a variety of cancers. The present study screened differentially expressed RBPs, analyzed their function and constructed a prognostic model to predict the overall survival of patients with CRC. METHODS We downloaded CRC RNA-sequencing data from the Cancer Genome Atlas (TCGA) portal and screened differentially expressed RBPs. Then, functional analyses of these genes were performed, and a risk model was established by multivariate Cox regression. RESULTS We obtained 132 differentially expressed RBPs, including 66 upregulated and 66 downregulated RBPs. Functional analysis revealed that these genes were significantly enriched in RNA processing, modification and binding, ribosome biogenesis, post-transcriptional regulation, ribonuclease and nuclease activity. Additionally, some RBPs were significantly related to interferon (IFN)-alpha and IFN-beta biosynthetic processes and the Toll-like receptor signaling pathway. A prognostic model was constructed and included insulin like growth factor 2 messenger ribonucleic acid binding protein 3 (IGF2BP3), poly (A) binding protein cytoplasmic 1 like (PABPC1L), peroxisome proliferator activated receptor gamma coactivator 1 alpha (PPARGC1A), peptidyl- transfer ribonucleic acid hydrolase 1 homolog (PTRH1) and tudor domain containing 7 (TDRD7). The model is an independent risk factor for clinicopathological characteristics. CONCLUSION Our study provided novel insights into the pathogenesis of CRC and constructed a prognostic gene model, which may be helpful for determining the prognosis of CRC.
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Affiliation(s)
- Qiankun Liang
- Gansu University of Chinese Medicine, Lanzhou, China,Address for correspondence: Dr. Qiankun Liang, Gansu University of Chinese Medicine, Lanzhou 730020, China. E-mail:
| | - Xiaojuan Du
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Lanfang Mao
- Gansu University of Chinese Medicine, Lanzhou, China,Affiliated Hospital of Gansu University of Chinese Medicine, Lanzhou, China
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Wu M, Kong C, Cai M, Huang W, Chen Y, Wang B, Liu X. Hsa_circRNA_002144 promotes growth and metastasis of colorectal cancer through regulating miR-615-5p/LARP1/mTOR pathway. Carcinogenesis 2021; 42:601-610. [PMID: 33347535 PMCID: PMC8086769 DOI: 10.1093/carcin/bgaa140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/16/2022] Open
Abstract
CircRNAs (circular RNAs), recently identified as a critical regulator in tumorigenesis, participate in CRC (colorectal cancer) growth. However, the role of hsa_circRNA_002144 in CRC was poorly understood. Firstly, hsa_circRNA_002144 showed significantly elevation in both of CRC tissues and cell lines, and suggested closely associated with poor prognosis in patients. Secondly, data from functional assays revealed that silence of hsa_circRNA_002144 inhibited CRC progression with reduced cell viability, proliferation, migration and invasion, while enhanced cell apoptosis. In addition, in vivo CRC growth and metastasis were also suppressed by knockdown of hsa_circRNA_002144. However, CRC progression was promoted with over-expression of hsa_circRNA_002144. Thirdly, hsa_circRNA_002144 colocalized with miR-615-5p in the cytoplasm of CRC cells, and decreased miR-615-5p expression. Moreover, miR-615-5p could target LARP1 (La ribonucleoprotein 1, translational regulator). Lastly, the suppressive effects of hsa_circRNA_002144 knockdown on CRC progression were reversed by LARP1 over-expression. In conclusion, hsa_circRNA_002144 could sponge miR-615-5p to promote CRC progression through the regulation of LARP1, providing a therapeutic target for cancer intervention.
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Affiliation(s)
- Mengqiong Wu
- Department of GynecologyXiuying District, Haikou City, Hainan Province, China
| | - Cancan Kong
- Department of Endoscopy CenterXiuying District, Haikou City, Hainan Province, China
| | - Manni Cai
- Department of GastroenterologyXiuying District, Haikou City, Hainan Province, China
| | - Weiwei Huang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
| | - Yiming Chen
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
| | - Baochun Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
| | - Xin Liu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Xiuying District, Haikou City, Hainan Province, China
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Ma Y, Yin S, Liu XF, Hu J, Cai N, Zhang XB, Fu L, Cao XC, Yu Y. Comprehensive Analysis of the Functions and Prognostic Value of RNA-Binding Proteins in Thyroid Cancer. Front Oncol 2021; 11:625007. [PMID: 33816259 PMCID: PMC8010172 DOI: 10.3389/fonc.2021.625007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
RNA binding proteins (RBPs) have been proved to play pivotal roles in a variety types of tumors. However, there is no convincible evidence disclosing the functions of RBPs in thyroid cancer (THCA) thoroughly and systematically. Integrated analysis of the functional and prognostic effect of RBPs help better understanding tumorigenesis and development in thyroid and may provide a novel therapeutic method for THCA. In this study, we obtained a list of human RBPs from Gerstberger database, which covered 1,542 genes encoding RBPs. Gene expression data of THCA was downloaded from The Cancer Genome Atlas (TCGA, n = 567), from which we extracted 1,491 RBPs' gene expression data. We analyzed differentially expressed RBPs using R package "limma". Based on differentially expressed RBPs, we constructed protein-protein interaction network and the GO and KEGG pathway enrichment analyses were carried out. We found six RBPs (AZGP1, IGF2BP2, MEX3A, NUDT16, NUP153, USB1) independently associated with prognosis of patients with thyroid cancer according to univariate and multivariate Cox proportional hazards regression models. The survival analysis and risk score analysis achieved good performances from this six-gene prognostic model. Nomogram was constructed to guide clinical decision in practice. Finally, biological experiments disclosed that NUP153 and USB1 can significantly impact cancer cell proliferation and migration. In conclusion, our research provided a new insight of thyroid tumorigenesis and development based on analyses of RBPs. More importantly, the six-gene model may play an important role in clinical practice in the future.
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Affiliation(s)
- Yue Ma
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Shi Yin
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Xiao-feng Liu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jing Hu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Ning Cai
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-bei Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Anesthesiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Li Fu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Xu-chen Cao
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Yue Yu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
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Qi X, Liu Z, Zhang Q, Yang M, Wan Y, Huang J, Xu L. Systematic analysis of the function and prognostic value of RNA binding proteins in Colon Adenocarcinoma. J Cancer 2021; 12:2537-2549. [PMID: 33854615 PMCID: PMC8040719 DOI: 10.7150/jca.50407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/17/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Abnormal expression of RNA-binding proteins (RBPs) is closely related to tumorigenesis, progression, and prognosis. This study performed systematic bioinformatic analysis of RBPs abnormally expressed in colon adenocarcinoma (COAD) using the Cancer Genome Atlas (TCGA) database to screen prognostic markers and potential therapeutic targets. Methods: First, the gene expression data from COAD samples were used to screen out differentially expressed RBPs for functional enrichment analysis and to visualize interaction relationships. Second, RBPs that were significantly related to prognosis were screened through univariate and multivariate Cox regression analysis to construct a prognostic model. The prediction performance of the prognostic model was evaluated by survival analysis and receiver operating characteristic (ROC) curve analysis. It addition, it was verified in the test cohort. The Human Protein Atlas (HPA) online database was used to verify the expression levels of RBPs in the prognostic model. Results: The study identified 181 differentially expressed RBPs and analyzed their interaction and functional enrichment, which were mainly related to non-coding RNA processing, ribosome biogenesis, RNA metabolic processes, RNA phosphodiester bond hydrolysis, and alternative mRNA splicing. Five RBPs related to prognosis were used to construct a prognostic model, and its predictive ability was verified by the test cohort. ROC curve analysis showed that the prognostic model had good sensitivity and specificity. Independent prognostic analysis showed that risk scores could be used as independent prognostic factors for COAD. Conclusion: This study constructed a reliable prognostic model by analyzing COAD differentially expressed RBPs, facilitating the screening of COAD prognostic markers and therapeutic targets.
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Affiliation(s)
- Xuewei Qi
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zeyu Liu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Qiaoli Zhang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ming Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yuxiang Wan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jinchang Huang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China.,Institute of Acupuncture and Moxibustion in Cancer Care, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lin Xu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
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Shen T, Wang M, Wang X. Identification of Prognosis-related Hub RNA Binding Proteins Function through Regulating Metabolic Processes in Tongue Cancer. J Cancer 2021; 12:2230-2242. [PMID: 33758601 PMCID: PMC7974894 DOI: 10.7150/jca.52156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
RNA binding proteins (RBPs) are dysregulated and associated with the occurrence and development in various malignant tumors. However, the role of RBPs in tongue cancer are largely unclear. Here, by integrating the differential gene expression analysis and the Weighted Gene Co-expression Network Analysis (WGCNA) of TCGA-retrieved RNA-seq data, we identified a total of 171 differential co-expression RBPs. Then, in a protein-protein interaction (PPI) network containing 134 nodes (RBPs) and 315 network edges (RBP-RBP interacting networks), the top 30 hub RBPs were identified using the CytoHubba plugin of Cytoscape. Furthermore, we investigated the expression and prognostic value of these RBPs and their highly correlated networks. Among them, six RBPs (PGK1, SLC20A1, LEPR, CYP19A1, ZC3H12D, and PFKM) were shown to be the prognosis-related hub RBPs (prhRBPs). Based on these hub RBPs, we constructed a prognostic model and found that the patients in the high-risk group had dramatically poor overall survival compared to those in low-risk group. In addition, we validated the prognostic model in GSE41613, another tongue cancer patient cohort from GEO datasets. The time-dependent receiver operating characteristic (ROC) analysis of the prognostic model further confirmed the predictive capability of the risk model for tongue cancer. As suggested in functional annotation analysis, we found an intensive enrichment of these prhRBPs in metabolic pathways, including AMPK, HIF-1 signaling pathway, Glycolysis, and steroid hormone biosynthesis. Together, our study revealed the underlying role of RBP in tongue cancer biology and potentially unveiled novel targets for cancer therapy.
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Affiliation(s)
- Tao Shen
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Meiting Wang
- College of Liren, Yanshan University, Qinhuangdao, 066004, China.,Department of Neurobiology and Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Xiangting Wang
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
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Li M, Yin B, Chen M, Peng J, Mu X, Deng Z, Xiao J, Li W, Fan J. Downregulation of the lncRNA ASB16-AS1 Decreases LARP1 Expression and Promotes Clear Cell Renal Cell Carcinoma Progression via miR-185-5p/miR-214-3p. Front Oncol 2021; 10:617105. [PMID: 33680937 PMCID: PMC7933513 DOI: 10.3389/fonc.2020.617105] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) comprises approximately 75% of renal cell carcinomas, which is one of the most common and lethal urologic cancers, with poor quality of life for patients and is a huge economic burden to health care systems. It is imperative we find novel prognostic and therapeutic targets for ccRCC clinical intervention. In this study, we found that the expression of the long noncoding RNA (lncRNA) ASB16-AS1 was downregulated in ccRCC tissues compared with non-diseased tissues and was also associated with advanced tumor stage and larger tumors. By constructing cell and mouse models, it was found that downregulated lncRNA ASB16-AS1 enhanced cell proliferation, migration, invasion, and promoted tumor growth and metastasis. Furthermore, by performing bioinformatics analysis, biotinylated RNA pull-downs, AGO2-RIP, and luciferase reporter assays, our findings showed that downregulated ASB16-AS1 decreased La-related protein 1 (LARP1) expression by inhibiting miR-185-5p and miR-214-3p. Furthermore, it was found that overexpression of LARP1 reversed the promotive effects of downregulated ASB16-AS1 on ccRCC cellular progression. Our results revealed that downregulated ASB16-AS1 promotes ccRCC progression via a miR-185-5p-miR-214-3p-LARP1 pathway. We suggest that this pathway could be used to monitor prognosis and presents therapeutic targets for ccRCC clinical management.
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Affiliation(s)
- Mingzi Li
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Bingde Yin
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, China
| | - Mulin Chen
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jingtao Peng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyu Mu
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zhen Deng
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jiantao Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Weiguo Li
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jie Fan
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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