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Gordon BH, Blackford N, Silvers R. Deciphering the Binding of 5' Stem Loop RNA to the La Domain of Human LARP6. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598414. [PMID: 38915490 PMCID: PMC11195269 DOI: 10.1101/2024.06.11.598414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
La-related protein 6 regulates the highly organized biosynthesis of type I procollagen polypeptides and affects proper assembly of procollagen peptides into heterotrimers of type I procollagen. LARP6-mediated regulation of collagen biosynthesis is mediated through interaction with the 5' stem loop motif found in type I and III collagen mRNA. Recent studies highlight the involvement of HsLARP6 in fibroproliferative diseases and its potential as a target for therapeutic intervention. The intrinsic instability of the La domain of HsLARP6 hampers studies probing the molecular basis of biologically- and disease-relevant structure-function relationship, particularly when high concentrations are required. This work provides detailed procedures to produce milligram amounts of RNase-free and functional La domain of HsLARP6. Furthermore, we investigated the effect of the construct length as well as RNA binding on protein stability. N- and C-terminal extensions greatly impact stability based on interactions with the core domain and modulation of the pI. When in complex with its cognate 5'SL RNA, the La domain shows unprecedented stability compared to the aggregation-prone unbound state. The protein-RNA complex remains stable for at least 50x longer than the unbound state, under identical conditions, likely due to a global change in conformational plasticity upon RNA binding. These results provide a foundation for further studies of the molecular recognition of 5'SL by HsLARP6 as well as a platform for refining potential antifibrotic therapeutics.
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Affiliation(s)
- Blaine H. Gordon
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Nolan Blackford
- 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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2
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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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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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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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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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Zhang R, Xia Y, Dong J, Ju X, Zhou K, Cao X, Li J, Ru J, Guo M, Zhang S. Comprehensive Analysis of m7G-Related Genes and Chronic Hepatitis B: Diagnostic Markers, Immune Microenvironment Regulation, Disease Progression. J Immunol Res 2023; 2023:9471520. [PMID: 37206976 PMCID: PMC10191754 DOI: 10.1155/2023/9471520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Chronic hepatitis B (CHB) is a major public health problem in the world. It is the main cause of liver cirrhosis and liver cancer. Although many important roles of RNA modification in stem cells or tumor diseases have been identified, the role of N7-methylguanosine (m7G) modification in the process of chronic HBV infection has not been clearly defined. Therefore, we conducted a systematic analysis on the process of chronic HBV infection. We found that a total of 18 m7G-related genes were altered in chronic HBV infection, and then we screened out CHB potential diagnostic biomarkers using machine learning and random forest methods. RT-qPCR was performed on the samples of healthy people and CHB, which further verified the possibility of being a diagnostic marker. Then, we typed CHB patients based on these 18 genes. We found that the immune microenvironment of different subtypes was different. Among them, patients with subtype-Ⅰ had severe immune response, that is, relatively serious immune cell infiltration, rich immune pathways, relatively many HLA genes, and immune checkpoints. Finally, we conducted an in-depth discussion on our m7G-related genes, and found that m7G gene related to immune cell infiltration may be involved in the disease progression of CHB patients, which was also confirmed in the GSE84044 dataset. In conclusion, m7G-related genes can not only serve as diagnostic markers of CHB, but also participate in the regulation of immune microenvironment and play an important role in the progression of CHB.
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Affiliation(s)
- Rongzheng Zhang
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yan Xia
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianming Dong
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaomei Ju
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kun Zhou
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Clinical Laboratory, Beidahuang Industry Group General Hospital, Harbin, China
| | - Xinyang Cao
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaqi Li
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaqiu Ru
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Mengrui Guo
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuyun Zhang
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Imanishi S, Nagata S, Fujita T, Fujii H. Circular RNAs hsa_circ_0001438 and hsa_circ_0000417 are downregulated and upregulated, respectively, in hepatocellular carcinoma. Int J Exp Pathol 2022; 103:245-251. [PMID: 36153641 PMCID: PMC9664408 DOI: 10.1111/iep.12457] [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: 06/01/2022] [Revised: 07/27/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most predominant type of liver cancer and is frequently fatal. Alpha-fetoprotein, alpha-fetoprotein-L3, and protein induced by vitamin K absence or antagonist-II are used as biomarkers to diagnose HCC. However, these biomarkers are not highly specific, especially for early-stage HCC diagnosis; therefore, more specific biomarkers are needed. Recently, circular RNA (circRNA) biomarkers have been used to diagnose several intractable diseases. In this study, we sought to identify circRNA biomarkers for the specific diagnosis of HCC. To this end, we compared the expression levels of circRNAs in primary HCC and normal tissues using publicly available RNA-seq data. Our analysis revealed that the expression levels of eight circRNAs were altered in primary HCC tissues compared with normal tissues. To confirm our findings, we examined the expression levels of selected circRNAs in HCC cell lines and normal hepatocytes. The expression level of hsa_circ_0001438, a circRNA that was downregulated in primary HCC, was lower in poorly and well-differentiated HCC cell lines than in normal hepatocytes. By contrast, the expression level of hsa_circ_0000417, which was increased in primary HCC, was strongly upregulated in a well-differentiated HCC cell line compared with normal hepatocytes. Thus, hsa_circ_0001438 and hsa_circ_0000417 might be potential biomarkers for the specific diagnosis of HCC. The experimental strategy described here, using publicly available RNA-seq data, is a useful and cost-effective method of identifying circRNA biomarkers.
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Affiliation(s)
- Sachiko Imanishi
- Department of Biochemistry and Genome BiologyHirosaki University Graduate School of MedicineHirosakiJapan
| | - Shoko Nagata
- Department of Biochemistry and Genome BiologyHirosaki University Graduate School of MedicineHirosakiJapan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome BiologyHirosaki University Graduate School of MedicineHirosakiJapan
| | - Hodaka Fujii
- Department of Biochemistry and Genome BiologyHirosaki University Graduate School of MedicineHirosakiJapan
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9
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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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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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11
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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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12
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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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13
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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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14
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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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15
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Ramani K, Robinson AE, Berlind J, Fan W, Abeynayake A, Binek A, Barbier-Torres L, Noureddin M, Nissen NN, Yildirim Z, Erbay E, Mato JM, Van Eyk JE, Lu SC. S-adenosylmethionine inhibits la ribonucleoprotein domain family member 1 in murine liver and human liver cancer cells. Hepatology 2022; 75:280-296. [PMID: 34449924 PMCID: PMC8766892 DOI: 10.1002/hep.32130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND AIMS Methionine adenosyltransferase 1A (MAT1A) is responsible for S-adenosylmethionine (SAMe) biosynthesis in the liver. Mice lacking Mat1a have hepatic SAMe depletion and develop NASH and HCC spontaneously. Several kinases are activated in Mat1a knockout (KO) mice livers. However, characterizing the phospho-proteome and determining whether they contribute to liver pathology remain open for study. Our study aimed to provide this knowledge. APPROACH AND RESULTS We performed phospho-proteomics in Mat1a KO mice livers with and without SAMe treatment to identify SAMe-dependent changes that may contribute to liver pathology. Our studies used Mat1a KO mice at different ages treated with and without SAMe, cell lines, in vitro translation and kinase assays, and human liver specimens. We found that the most striking change was hyperphosphorylation and increased content of La-related protein 1 (LARP1), which, in the unphosphorylated form, negatively regulates translation of 5'-terminal oligopyrimidine (TOP)-containing mRNAs. Consistently, multiple TOP proteins are induced in KO livers. Translation of TOP mRNAs ribosomal protein S3 and ribosomal protein L18 was enhanced by LARP1 overexpression in liver cancer cells. We identified LARP1-T449 as a SAMe-sensitive phospho-site of cyclin-dependent kinase 2 (CDK2). Knocking down CDK2 lowered LARP1 phosphorylation and prevented LARP1-overexpression-mediated increase in translation. LARP1-T449 phosphorylation induced global translation, cell growth, migration, invasion, and expression of oncogenic TOP-ribosomal proteins in HCC cells. LARP1 expression is increased in human NASH and HCC. CONCLUSIONS Our results reveal a SAMe-sensitive mechanism of LARP1 phosphorylation that may be involved in the progression of NASH to HCC.
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Affiliation(s)
- Komal Ramani
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Aaron E. Robinson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Smidt Heart Institute and Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Joshua Berlind
- Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033
| | - Wei Fan
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Aushinie Abeynayake
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Aleksandra Binek
- Smidt Heart Institute and Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Lucía Barbier-Torres
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Mazen Noureddin
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Nicholas N. Nissen
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Zehra Yildirim
- Department of Cardiology, Department of Biomedical Sciences and Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Ebru Erbay
- Department of Cardiology, Department of Biomedical Sciences and Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - José M. Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology, Derio, Bizkaia 48160, Spain
| | - Jennifer E. Van Eyk
- Smidt Heart Institute and Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Shelly C. Lu
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048
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16
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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: 9] [Impact Index Per Article: 3.0] [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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17
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Shen Y, Lin Y, Liu K, Chen J, Zhong J, Gao Y, Yuan C. XIST: A Meaningful Long Noncoding RNA in NSCLC Process. Curr Pharm Des 2021; 27:1407-1417. [PMID: 33267757 DOI: 10.2174/1381612826999201202102413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/01/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND A number of studies have proposed that lncRNA XIST plays a role in the development and chemosensitivity of NSCLC. Besides, XIST may become a potential therapeutic target for NSCLC patients. The aim of this review is to reveal the biological functions and exact mechanisms of XIST in NSCLC. METHODS In this review, relevant researches involving the relationship between XIST and NSCLC are collected through systematic retrieval of PubMed. RESULTS XIST is an oncogene in NSCLC and is abnormally upregulated in NSCLC tissues. Considerable evidence has shown that XIST plays a critical role in the proliferation, invasion, migration, apoptosis and chemosensitivity of NSCLC cells. XIST mainly functions as a ceRNA in the NSCLC process, while XIST also functions at transcriptional levels. CONCLUSION LncRNA XIST has the potential to become a novel biomolecular marker of NSCLC and a therapeutic target for NSCLC.
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Affiliation(s)
- Yujie Shen
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yexiang Lin
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Kai Liu
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Jinlan Chen
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Juanjuan Zhong
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yisong Gao
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Chengfu Yuan
- College of Medical Science, China Three Gorges University, Yichang 443002, China
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18
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Alboushi L, Hackett AP, Naeli P, Bakhti M, Jafarnejad SM. Multifaceted control of mRNA translation machinery in cancer. Cell Signal 2021; 84:110037. [PMID: 33975011 DOI: 10.1016/j.cellsig.2021.110037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
The mRNA translation machinery is tightly regulated through several, at times overlapping, mechanisms that modulate its efficiency and accuracy. Due to their fast rate of growth and metabolism, cancer cells require an excessive amount of mRNA translation and protein synthesis. However, unfavorable conditions, such as hypoxia, amino acid starvation, and oxidative stress, which are abundant in cancer, as well as many anti-cancer treatments inhibit mRNA translation. Cancer cells adapt to the various internal and environmental stresses by employing specialised transcript-specific translation to survive and gain a proliferative advantage. We will highlight the major signaling pathways and mechanisms of translation that regulate the global or mRNA-specific translation in response to the intra- or extra-cellular signals and stresses that are key components in the process of tumourigenesis.
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Affiliation(s)
- Lilas Alboushi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Angela P Hackett
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
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19
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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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20
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Berman AJ, Thoreen CC, Dedeic Z, Chettle J, Roux PP, Blagden SP. Controversies around the function of LARP1. RNA Biol 2021; 18:207-217. [PMID: 32233986 PMCID: PMC7928164 DOI: 10.1080/15476286.2020.1733787] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
The RNA-binding protein LARP1 has generated interest in recent years for its role in the mTOR signalling cascade and its regulation of terminal oligopyrimidine (TOP) mRNA translation. Paradoxically, some scientists have shown that LARP1 represses TOP translation while others that LARP1 activates it. Here, we present opinions from four leading scientists in the field to discuss these and other contradictory findings.
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Affiliation(s)
- Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, USA
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, USA
| | - Zinaida Dedeic
- Department of Oncology, University of Oxford, Oxford, UK
| | - James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université De Montréal, Montreal, Quebec, Canada
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21
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Kalous J, Jansová D, Šušor A. Role of Cyclin-Dependent Kinase 1 in Translational Regulation in the M-Phase. Cells 2020; 9:cells9071568. [PMID: 32605021 PMCID: PMC7408968 DOI: 10.3390/cells9071568] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Cyclin dependent kinase 1 (CDK1) has been primarily identified as a key cell cycle regulator in both mitosis and meiosis. Recently, an extramitotic function of CDK1 emerged when evidence was found that CDK1 is involved in many cellular events that are essential for cell proliferation and survival. In this review we summarize the involvement of CDK1 in the initiation and elongation steps of protein synthesis in the cell. During its activation, CDK1 influences the initiation of protein synthesis, promotes the activity of specific translational initiation factors and affects the functioning of a subset of elongation factors. Our review provides insights into gene expression regulation during the transcriptionally silent M-phase and describes quantitative and qualitative translational changes based on the extramitotic role of the cell cycle master regulator CDK1 to optimize temporal synthesis of proteins to sustain the division-related processes: mitosis and cytokinesis.
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TOP mRNPs: Molecular Mechanisms and Principles of Regulation. Biomolecules 2020; 10:biom10070969. [PMID: 32605040 PMCID: PMC7407576 DOI: 10.3390/biom10070969] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
The cellular response to changes in the surrounding environment and to stress requires the coregulation of gene networks aiming to conserve energy and resources. This is often achieved by downregulating protein synthesis. The 5’ Terminal OligoPyrimidine (5’ TOP) motif-containing mRNAs, which encode proteins that are essential for protein synthesis, are the primary targets of translational control under stress. The TOP motif is a cis-regulatory RNA element that begins directly after the m7G cap structure and contains the hallmark invariant 5’-cytidine followed by an uninterrupted tract of 4–15 pyrimidines. Regulation of translation via the TOP motif coordinates global protein synthesis with simultaneous co-expression of the protein components required for ribosome biogenesis. In this review, we discuss architecture of TOP mRNA-containing ribonucleoprotein complexes, the principles of their assembly, and the modes of regulation of TOP mRNA translation.
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The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium. Cells 2019; 8:cells8121634. [PMID: 31847302 PMCID: PMC6953095 DOI: 10.3390/cells8121634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
: Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have on cancer development.
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Cassidy KC, Lahr RM, Kaminsky JC, Mack S, Fonseca BD, Das SR, Berman AJ, Durrant JD. Capturing the Mechanism Underlying TOP mRNA Binding to LARP1. Structure 2019; 27:1771-1781.e5. [PMID: 31676287 PMCID: PMC7269035 DOI: 10.1016/j.str.2019.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/06/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine (m7G) cap and 5' terminal oligopyrimidine (TOP) motif characteristic of transcripts encoding ribosomal proteins and translation factors. Under the control of mammalian target of rapamycin complex 1 (mTORC1), LARP1 regulates translation of these transcripts. Characterizing the dynamics of DM15-TOP recognition is essential to understanding this fundamental biological process. We use molecular dynamics simulations, biophysical assays, and X-ray crystallography to reveal the mechanism of DM15 binding to TOP transcripts. Residues C-terminal to the m7G-binding site play important roles in cap recognition. Furthermore, we show that the unusually static pocket that recognizes the +1 cytosine characteristic of TOP transcripts drives binding specificity. Finally, we demonstrate that the DM15 pockets involved in TOP-specific m7GpppC-motif recognition are likely druggable. Collectively, these studies suggest unique opportunities for further pharmacological development.
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Affiliation(s)
- Kevin C Cassidy
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jesse C Kaminsky
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Stephanie Mack
- Department of Chemistry and Center for Nucleic Acids Science & Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Bruno D Fonseca
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, K1H 8L1 ON, Canada
| | - Subha R Das
- Department of Chemistry and Center for Nucleic Acids Science & Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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Plissonnier ML, Cottarel J, Piver E, Kullolli M, Centonze FG, Pitteri S, Farhan H, Meunier JC, Zoulim F, Parent R. LARP1 binding to hepatitis C virus particles is correlated with intracellular retention of viral infectivity. Virus Res 2019; 271:197679. [PMID: 31398365 DOI: 10.1016/j.virusres.2019.197679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/27/2019] [Indexed: 12/23/2022]
Abstract
Hepatitis C virus (HCV) virions contain a subset of host liver cells proteome often composed of interesting virus-interacting factors. A proteomic analysis performed on double gradient-purified clinical HCV highlighted the translation regulator LARP1 on these virions. This finding was validated using post-virion capture and immunoelectron microscopy, as well as immunoprecipitation applied to in vitro (Huh7.5 liver cells) grown (Gt2a, JFH1 strain) and patient-derived (Gt1a) HCV particles. Upon HCV infection of Huh7.5 cells, we observed a drastic transfer of LARP1 to lipid droplets, inducing colocalization with core proteins. RNAi-mediated depletion of LARP1 using the C911 control approach decreased extracellular infectivity of HCV Gt1a (H77), Gt2a (JFH1), and Gt3a (S52 chimeric strain), yet increased their intracellular infectivity. This latter effect was unrelated to changes in the hepatocyte secretory pathway, as evidenced using a functional RUSH assay. These results indicate that LARP1 binds to HCV, an event associated with retention of intracellular infectivity.
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Affiliation(s)
- Marie-Laure Plissonnier
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France
| | - Jessica Cottarel
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France
| | - Eric Piver
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, INSERM U966, Université de Tours, F-37000, Tours, France
| | - Majlinda Kullolli
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | | | - Sharon Pitteri
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Hesso Farhan
- Institute of Basic Medical Science, University of Oslo, N-0372, Olso, Norway
| | - Jean-Christophe Meunier
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, INSERM U966, Université de Tours, F-37000, Tours, France
| | - Fabien Zoulim
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France; Lyon University Hospital (Hospices civils de Lyon), Hepatogastroenterology Service, F-69001, Lyon, France
| | - Romain Parent
- Pathogenesis of Hepatitis B and C -DEVweCAN LabEx, INSERM U1052-CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, F-69008, Lyon, France.
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Nyambura LW, Muñoz AA, le Coutre P, Walden P. HLA class I-restricted T cell epitopes isolated and identified from myeloid leukemia cells. Sci Rep 2019; 9:14029. [PMID: 31575892 PMCID: PMC6773711 DOI: 10.1038/s41598-019-50341-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
Leukemia-associated antigens (LAAs) and HLA-I epitopes published previously have shown promise in inducing leukemia-specific T cell responses. However, the clinical responses are limited, and clinical effectiveness is yet to be achieved. Limitations, among others, being the LAAs themselves, the indirect approach to HLA-I epitope identification by reverse immunology, and the use of single or few LAAs and HLA-I epitopes, which limits the spectrum of inducible tumor-specific T cells. Use of a direct approach to identify naturally processed and presented HLA-I epitopes from LAAs, and higher numbers of antigens for T cell-mediated immunotherapy for leukemia may enhance clinical responses and broaden clinical effectiveness. In a prior study we used immunoaffinity purification of HLA-I peptide complexes from the differentiated myeloid tumor cell lines MUTZ3 and THP1 coupled to high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS). From this we identified in the current study seven new HLA-I epitopes and the corresponding LAAs for myeloid leukemia. In comparison, the myeloid HLA-I epitopes reported here were generally stronger HLA-binders that induce stronger T cell responses than those previously published, and their source LAAs had higher immunogenicity, higher expression levels in myeloid tumors cells compared to normal hemopoietin and other major normal tissues, and more protein interaction partners, and they are targeted by CD8 T cells in CML patients. This study analyses and compares the LAAs and HLA-I epitopes based on various immunotherapeutic targets selection criteria, and highlights new targets for T cell-mediated immunotherapy for leukemia.
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Affiliation(s)
- Lydon Wainaina Nyambura
- Department of Dermatology, Venerology and Allergology, Clinical Research Group 'Tumor Immunology', Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10098, Berlin, Germany
| | - Alejandro Azorin Muñoz
- Department of Dermatology, Venerology and Allergology, Clinical Research Group 'Tumor Immunology', Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10098, Berlin, Germany
| | - Philipp le Coutre
- Medical Department, Division of Hematology and Oncology, Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10098, Berlin, Germany
| | - Peter Walden
- Department of Dermatology, Venerology and Allergology, Clinical Research Group 'Tumor Immunology', Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10098, Berlin, Germany.
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Jiang F, Fang DB, Lin J, Chen Q, Zhu LX, Yu HZ. Correlation of LARP1 and E-cadherin expression with prognosis of intrahepatic cholangiocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3559-3566. [PMID: 31949734 PMCID: PMC6962836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 04/28/2018] [Indexed: 06/10/2023]
Abstract
OBJECTIVE The abnormal expression of LARP1 and E-cadherin (E-cad) is related to tumor occurrence and metastasis. Our study analyzed the expression of LARP1 and E-cad in intrahepatic cholangiocarcinoma (ICC) and investigated the prognostic value of the two proteins. METHODS Immunohistochemistry was performed to detect the expression of LARP1 and E-cad in 50 ICC clinical specimens with adjacent normal tissues and 20 normal bile duct tissues. In situ hybridization was performed to analyze the expression of LARP1 mRNA in all the specimens. RESULTS LARP1 protein and mRNA expression levels in ICC tumor tissues were significantly higher compared with corresponding adjacent normal tissues and normal epithelial tissues (P<0.01). E-cad protein expression in ICC tumor tissues was remarkably lower than that of the adjacent normal tissues and benign bile duct tissues (P<0.01). Correlation analysis demonstrated that LARP1 and E-cad expression levels were significantly related with the tumor-node-metastasis staging and lymph node metastasis (P<0.01), while no correlation was observed with patient age, gender, and tumor size. Moreover, Spearman rank correlation test revealed that LARP1 expression was negatively related to E-cad (P<0.05). More importantly, the patients with higher LARP1 expression or lower E-cad expression had a shorter overall survival postoperatively than those with LARP1 lower expression or E-cad higher expression. Multivariate analysis demonstrated that LARP1 and E-cad were both considered as important prognostic factors for survival time. CONCLUSION These findings suggest that the abnormal expression of LARP1 and E-cad showed a close relationship with the occurrence and metastasis of ICC, leading to poor prognosis indirectly.
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Affiliation(s)
- Fei Jiang
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - De-Bao Fang
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Jie Lin
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Qiang Chen
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Li-Xin Zhu
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
| | - Hong-Zhu Yu
- Department of General Surgery, The Affiliated Fuyang Hospital of Anhui Medical University Fuyang, China
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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Ye L, Lin ST, Mi YS, Liu Y, Ma Y, Sun HM, Peng ZH, Fan JW. Overexpression of LARP1 predicts poor prognosis of colorectal cancer and is expected to be a potential therapeutic target. Tumour Biol 2016; 37:14585-14594. [PMID: 27614686 PMCID: PMC5126195 DOI: 10.1007/s13277-016-5332-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/06/2016] [Indexed: 01/30/2023] Open
Abstract
This study investigated the significance of La-related protein 1 (LARP1) in the development and progression of colorectal cancer (CRC). Quantitative real-time polymerase chain reaction and Western blot analyses were carried out to determine the mRNA and protein expression of LARP1 in CRC tumor tissues and paired adjacent normal mucosa. The expression of LARP1 was upregulated in CRC. Immunohistochemical analysis using tissue microarray was performed. A positive correlation between LARP1 and proliferating cell nuclear antigen (PCNA) in the area of proliferation was observed using the Spearman's correlation coefficient test (r = 0.332, P < 0.01). The elevated expression of LARP1 significantly correlated with T stage (P = 0.02), N stage (P = 0.006), M stage (P < 0.001), American Joint Committee on Cancer (AJCC) stage (P = 0.04), differentiation rank (P < 0.001), and PCNA level (P < 0.001). In addition, the inhibitory effect of LARP1 knockdown on CRC cell proliferation was demonstrated using Cell Counting Kit-8 (CCK8) and colony-forming cell (CFC) assays. Multivariate analysis showed that LARP1 was an independent prognostic factor for overall survival (OS; hazard rate (HR) = 0.244; 95 % confidence interval (CI), 0.078-0.769; P = 0.016) and disease-free survival (DFS; HR = 0.281; 95 % CI, 0.086-0.917; P = 0.035) in CRC patients. LARP1 plays an important role in the proliferation of colorectal cancer and represents a new prognostic indicator.
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Affiliation(s)
- Ling Ye
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng-tao Lin
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-shuai Mi
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan Liu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Ma
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui-min Sun
- Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-hai Peng
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun-wei Fan
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Plissonnier ML, Lahlali T, Michelet M, Lebossé F, Cottarel J, Beer M, Neveu G, Durantel D, Bartosch B, Accardi R, Clément S, Paradisi A, Devouassoux-Shisheboran M, Einav S, Mehlen P, Zoulim F, Parent R. Epidermal Growth Factor Receptor-Dependent Mutual Amplification between Netrin-1 and the Hepatitis C Virus. PLoS Biol 2016; 14:e1002421. [PMID: 27031829 PMCID: PMC4816328 DOI: 10.1371/journal.pbio.1002421] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/26/2016] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is an oncogenic virus associated with the onset of hepatocellular carcinoma (HCC). The present study investigated the possible link between HCV infection and Netrin-1, a ligand for dependence receptors that sustains tumorigenesis, in particular in inflammation-associated tumors. We show that Netrin-1 expression is significantly elevated in HCV+ liver biopsies compared to hepatitis B virus (HBV+) and uninfected samples. Furthermore, Netrin-1 was upregulated in all histological stages of HCV+ hepatic lesions, from minimal liver fibrosis to cirrhosis and HCC, compared to histologically matched HCV- tissues. Both cirrhosis and HCV contributed to the induction of Netrin-1 expression, whereas anti-HCV treatment resulted in a reduction of Netrin-1 expression. In vitro, HCV increased the level and translation of Netrin-1 in a NS5A-La-related protein 1 (LARP1)-dependent fashion. Knockdown and forced expression experiments identified the receptor uncoordinated receptor-5 (UNC5A) as an antagonist of the Netrin-1 signal, though it did not affect the death of HCV-infected cells. Netrin-1 enhanced infectivity of HCV particles and promoted viral entry by increasing the activation and decreasing the recycling of the epidermal growth factor receptor (EGFR), a protein that is dysregulated in HCC. Netrin-1 and HCV are, therefore, reciprocal inducers in vitro and in patients, as seen from the increase in viral morphogenesis and viral entry, both phenomena converging toward an increase in the level of infectivity of HCV virions. This functional association involving a cancer-related virus and Netrin-1 argues for evaluating the implication of UNC5 receptor ligands in other oncogenic microbial species.
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Affiliation(s)
- Marie-Laure Plissonnier
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
| | - Thomas Lahlali
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
| | - Maud Michelet
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
| | - Fanny Lebossé
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
- Hospices Civils de Lyon, Service d’Hépatogastroentérologie, F-69001 Lyon, France
| | - Jessica Cottarel
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
| | - Melanie Beer
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Grégory Neveu
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - David Durantel
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
| | - Birke Bartosch
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
| | - Rosita Accardi
- International Agency for Research on Cancer, F-69424 Lyon, France
| | - Sophie Clément
- Division of Clinical Pathology, University Hospital, University of Geneva School of Medicine, Geneva, Switzerland
| | - Andrea Paradisi
- Apoptosis, Cancer and Development Laboratory - Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69008 Lyon, France, Université de Lyon F-69003 Lyon, Centre Léon Bérard, F-69008 Lyon, France
| | | | - Shirit Einav
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory - Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69008 Lyon, France, Université de Lyon F-69003 Lyon, Centre Léon Bérard, F-69008 Lyon, France
| | - Fabien Zoulim
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
- Hospices Civils de Lyon, Service d’Hépatogastroentérologie, F-69001 Lyon, France
| | - Romain Parent
- Pathogenesis of Hepatitis B and C - Equipe labellisée LabEx DEVweCAN, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69003 Lyon, France, Université de Lyon, F-69003 Lyon, Université Lyon 1, ISPB, Lyon, F-69622, France, CNRS UMR5286, F-69083 Lyon, France, Centre Léon Bérard, F-69008 Lyon, France
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Hopkins TG, Mura M, Al-Ashtal HA, Lahr RM, Abd-Latip N, Sweeney K, Lu H, Weir J, El-Bahrawy M, Steel JH, Ghaem-Maghami S, Aboagye EO, Berman AJ, Blagden SP. The RNA-binding protein LARP1 is a post-transcriptional regulator of survival and tumorigenesis in ovarian cancer. Nucleic Acids Res 2016; 44:1227-46. [PMID: 26717985 PMCID: PMC4756840 DOI: 10.1093/nar/gkv1515] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/12/2015] [Accepted: 12/17/2015] [Indexed: 11/25/2022] Open
Abstract
RNA-binding proteins (RBPs) are increasingly identified as post-transcriptional drivers of cancer progression. The RBP LARP1 is an mRNA stability regulator, and elevated expression of the protein in hepatocellular and lung cancers is correlated with adverse prognosis. LARP1 associates with an mRNA interactome that is enriched for oncogenic transcripts. Here we explore the role of LARP1 in epithelial ovarian cancer, a disease characterized by the rapid acquisition of resistance to chemotherapy through the induction of pro-survival signalling. We show, using ovarian cell lines and xenografts, that LARP1 is required for cancer cell survival and chemotherapy resistance. LARP1 promotes tumour formation in vivo and maintains cancer stem cell-like populations. Using transcriptomic analysis following LARP1 knockdown, cross-referenced against the LARP1 interactome, we identify BCL2 and BIK as LARP1 mRNA targets. We demonstrate that, through an interaction with the 3' untranslated regions (3' UTRs) of BCL2 and BIK, LARP1 stabilizes BCL2 but destabilizes BIK with the net effect of resisting apoptosis. Together, our data indicate that by differentially regulating the stability of a selection of mRNAs, LARP1 promotes ovarian cancer progression and chemotherapy resistance.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Autoantigens/genetics
- Autoantigens/metabolism
- Blotting, Western
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Cell Line, Tumor
- Cell Survival/drug effects
- Cell Survival/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- HeLa Cells
- Humans
- Interleukin Receptor Common gamma Subunit/deficiency
- Interleukin Receptor Common gamma Subunit/genetics
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Microscopy, Confocal
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Protein Binding
- RNA Interference
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Survival Analysis
- Transplantation, Heterologous
- SS-B Antigen
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Affiliation(s)
- Thomas G Hopkins
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Manuela Mura
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Hiba A Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Normala Abd-Latip
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Katrina Sweeney
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Haonan Lu
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Justin Weir
- Department of Histopathology, Imperial College Healthcare NHS Trust, London W12 0NN, UK
| | - Mona El-Bahrawy
- Department of Histopathology, Imperial College Healthcare NHS Trust, London W12 0NN, UK
| | - Jennifer H Steel
- Imperial College Experimental Cancer Medicine Centre, Division of Cancer, Imperial College Academic Health Science Centre, London W12 0NN, UK
| | - Sadaf Ghaem-Maghami
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Eric O Aboagye
- Comprehensive Cancer Imaging Centre, Imperial College, Du Cane Road, London W12 0NN, UK
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sarah P Blagden
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK Department of Oncology, University of Oxford, Old Road, Oxford OX3 7LE, UK
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32
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Stavraka C, Blagden S. The La-Related Proteins, a Family with Connections to Cancer. Biomolecules 2015; 5:2701-22. [PMID: 26501340 PMCID: PMC4693254 DOI: 10.3390/biom5042701] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 10/07/2015] [Indexed: 01/09/2023] Open
Abstract
The evolutionarily-conserved La-related protein (LARP) family currently comprises Genuine La, LARP1, LARP1b, LARP4, LARP4b, LARP6 and LARP7. Emerging evidence suggests each LARP has a distinct role in transcription and/or mRNA translation that is attributable to subtle sequence variations within their La modules and specific C-terminal domains. As emerging research uncovers the function of each LARP, it is evident that La, LARP1, LARP6, LARP7 and possibly LARP4a and 4b are dysregulated in cancer. Of these, LARP1 is the first to be demonstrated to drive oncogenesis. Here, we review the role of each LARP and the evidence linking it to malignancy. We discuss a future strategy of targeting members of this protein family as cancer therapy.
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Affiliation(s)
- Chara Stavraka
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
| | - Sarah Blagden
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
- Department of Oncology, University of Oxford, Churchill Hospital, Old Road, Oxford OX3 7LE, UK.
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33
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Mura M, Hopkins TG, Michael T, Abd-Latip N, Weir J, Aboagye E, Mauri F, Jameson C, Sturge J, Gabra H, Bushell M, Willis AE, Curry E, Blagden SP. LARP1 post-transcriptionally regulates mTOR and contributes to cancer progression. Oncogene 2015; 34:5025-36. [PMID: 25531318 PMCID: PMC4430325 DOI: 10.1038/onc.2014.428] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 09/20/2014] [Accepted: 10/21/2014] [Indexed: 12/24/2022]
Abstract
RNA-binding proteins (RBPs) bind to and post-transcriptionally regulate the stability of mRNAs. La-related protein 1 (LARP1) is a conserved RBP that interacts with poly-A-binding protein and is known to regulate 5'-terminal oligopyrimidine tract (TOP) mRNA translation. Here, we show that LARP1 is complexed to 3000 mRNAs enriched for cancer pathways. A prominent member of the LARP1 interactome is mTOR whose mRNA transcript is stabilized by LARP1. At a functional level, we show that LARP1 promotes cell migration, invasion, anchorage-independent growth and in vivo tumorigenesis. Furthermore, we show that LARP1 expression is elevated in epithelial cancers such as cervical and non-small cell lung cancers, where its expression correlates with disease progression and adverse prognosis, respectively. We therefore conclude that, through the post-transcriptional regulation of genes such as mTOR within cancer pathways, LARP1 contributes to cancer progression.
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Affiliation(s)
- M Mura
- Division of Cancer, Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK
| | - T G Hopkins
- Division of Cancer, Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK
| | - T Michael
- Division of Cancer, Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK
| | - N Abd-Latip
- Division of Cancer, Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK
| | - J Weir
- Department of Cellular Pathology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, UK
| | - E Aboagye
- Division of Cancer, Department of Surgery and Cancer, Cancer Research UK Laboratories, Imperial College London, Hammersmith Campus, London, UK
| | - F Mauri
- Department of Histopathology, Centre for Pathology, Imperial College London, Hammersmith Campus, London, UK
| | - C Jameson
- Department of Histopathology, University College Hospital, London, UK
| | - J Sturge
- Division of Cancer, Department of Surgery and Cancer, Cancer Research UK Laboratories, Imperial College London, Hammersmith Campus, London, UK
- School of Biological, Biomedical & Environmental Sciences, The Allam Building, University of Hull, Hull, UK
| | - H Gabra
- Division of Cancer, Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK
| | - M Bushell
- MRC Toxicology Unit, Hodgkin Building, University of Leicester, Leicester, UK
| | - A E Willis
- MRC Toxicology Unit, Hodgkin Building, University of Leicester, Leicester, UK
| | - E Curry
- Division of Cancer, Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK
| | - S P Blagden
- Division of Cancer, Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK
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34
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Lahr RM, Mack SM, Héroux A, Blagden SP, Bousquet-Antonelli C, Deragon JM, Berman AJ. The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence. Nucleic Acids Res 2015; 43:8077-88. [PMID: 26206669 PMCID: PMC4652764 DOI: 10.1093/nar/gkv748] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/09/2015] [Accepted: 07/11/2015] [Indexed: 12/20/2022] Open
Abstract
La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.
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Affiliation(s)
- Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Seshat M Mack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Annie Héroux
- Photon Sciences Directorate, Bldg 745 L107 Brookhaven National Laboratory Upton, NY 11973, USA
| | - Sarah P Blagden
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Cécile Bousquet-Antonelli
- CNRS-UMR5096 LGDP, 66860 Perpignan, France Université de Perpignan-UMR5096 LGDP, 66860 Perpignan, France
| | - Jean-Marc Deragon
- CNRS-UMR5096 LGDP, 66860 Perpignan, France Université de Perpignan-UMR5096 LGDP, 66860 Perpignan, France
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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35
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Kato M, Goto Y, Matsushita R, Kurozumi A, Fukumoto I, Nishikawa R, Sakamoto S, Enokida H, Nakagawa M, Ichikawa T, Seki N. MicroRNA-26a/b directly regulate La-related protein 1 and inhibit cancer cell invasion in prostate cancer. Int J Oncol 2015; 47:710-8. [PMID: 26063484 DOI: 10.3892/ijo.2015.3043] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/25/2015] [Indexed: 11/06/2022] Open
Abstract
Our past studies of microRNA (miRNA) expression signatures of cancers including prostate cancer (PCa) revealed that microRNA-26a and microRNA-26b (miR-26a and miR-26b) were significantly downregulated in cancer tissues. In the present study, we found that restoration of miR-26a or miR-26b significantly inhibited PCa cell invasion. Gene expression data and in silico analysis showed that the gene encoding La-related protein 1 (LARP1) was a putative candidate of miR-26a and miR-26b regulation. Moreover, luciferase reporter assays revealed that LARP1 was a direct target of both miR-26a and miR-26b. Overexpression of LARP1 was observed in PCa clinical specimens and knockdown of LARP1 inhibited cancer cell migration. Therefore, LARP1 acted as an oncogene in PCa cells. Moreover, 'ribosome', 'RNA transport' and 'mTOR signaling pathway' were identified as LARP1-regulated pathways. Our present data suggested that loss of tumor-suppressive miR-26a and miR-26b enhanced cancer cell invasion in PCa through direct regulation of oncogenic LARP1. Elucidation of the molecular networks regulated by tumor-suppressive miRNAs will provide insights into the molecular mechanisms of PCa oncogenesis and metastasis.
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Affiliation(s)
- Mayuko Kato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yusuke Goto
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Ryosuke Matsushita
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Akira Kurozumi
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Ichiro Fukumoto
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Rika Nishikawa
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shinichi Sakamoto
- Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hideki Enokida
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Masayuki Nakagawa
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tomohiko Ichikawa
- Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
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36
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Deragon JM, Bousquet-Antonelli C. The role of LARP1 in translation and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:399-417. [PMID: 25892282 DOI: 10.1002/wrna.1282] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022]
Abstract
The LARP1 proteins form an evolutionarily homogeneous subgroup of the eukaryotic superfamily of La-Motif (LAM) containing factors. Members of the LARP1 family are found in most protists, fungi, plants, and animals. We review here evidence suggesting that LARP1 are key versatile messenger RNA (mRNA)-binding proteins involved in regulating important biological processes such as gametogenesis, embryogenesis, sex determination, and cell division in animals, as well as acclimation to stress in yeasts and plants. LARP1 proteins perform all these essential tasks likely by binding to key mRNAs and regulating their stability and/or translation. In human, the impact of LARP1 over cell division and proliferation is potentially under the control of the TORC1 complex. We review data suggesting that LARP1 is a direct target of this master signaling hub. TOR-dependent LARP1 phosphorylation could specifically enhance the translation of TOP mRNAs providing a way to promote translation, growth, and proliferation. Consequently, LARP1 is found to be significantly upregulated in many malignant cell types. In plants, LARP1 was found to act as a cofactor of the heat-induced mRNA degradation process, an essential acclimation strategy leading to the degradation of more than 4500 mRNAs coding for growth and development housekeeping functions. In Saccharomyces cerevisiae, the LARP1 proteins (Slf1p and Sro9p) are important, among other things, for copper resistance and oxidative stress survival. LARP1 proteins are therefore emerging as critical ancient mRNA-binding factors that evolved common as well as specific targets and regulatory functions in all eukaryotic lineages.
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Affiliation(s)
- Jean-Marc Deragon
- CNRS, LGDP-UMR5096, Perpignan, France.,University of Perpignan, LGDP-UMR5096, Perpignan, France
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37
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Gentilella A, Kozma SC, Thomas G. A liaison between mTOR signaling, ribosome biogenesis and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:812-20. [PMID: 25735853 DOI: 10.1016/j.bbagrm.2015.02.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 01/05/2023]
Abstract
The ability to translate genetic information into functional proteins is considered a landmark in evolution. Ribosomes have evolved to take on this responsibility and, although there are some differences in their molecular make-up, both prokaryotes and eukaryotes share a common structural architecture and similar underlying mechanisms of protein synthesis. Understanding ribosome function and biogenesis has been the focus of extensive research since the early days of their discovery. In the last decade however, new and unexpected roles have emerged that place deregulated ribosome biogenesis and protein synthesis at the crossroads of pathological settings, particularly cancer, revealing a set of novel cellular checkpoints. Moreover, it is also becoming evident that mTOR signaling, which regulates an array of anabolic processes, including ribosome biogenesis, is often exploited by cancer cells to sustain proliferation through the upregulation of global protein synthesis. The use of pharmacological agents that interfere with ribosome biogenesis and mTOR signaling has proven to be an effective strategy to control cancer development clinically. Here we discuss the most recent findings concerning the underlying mechanisms by which mTOR signaling controls ribosome production and the potential impact of ribosome biogenesis in tumor development. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Antonio Gentilella
- Laboratory of Metabolism and Cancer, Catalan Institute of Oncology, ICO, Bellvitge Biomedical Research Institute, IDIBELL, 08908 Barcelona, Spain.
| | - Sara C Kozma
- Laboratory of Metabolism and Cancer, Catalan Institute of Oncology, ICO, Bellvitge Biomedical Research Institute, IDIBELL, 08908 Barcelona, Spain; Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati Medical School, Cincinnati, 45267-0508 OH, USA
| | - George Thomas
- Laboratory of Metabolism and Cancer, Catalan Institute of Oncology, ICO, Bellvitge Biomedical Research Institute, IDIBELL, 08908 Barcelona, Spain; Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati Medical School, Cincinnati, 45267-0508 OH, USA.
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38
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Tcherkezian J, Cargnello M, Romeo Y, Huttlin EL, Lavoie G, Gygi SP, Roux PP. Proteomic analysis of cap-dependent translation identifies LARP1 as a key regulator of 5'TOP mRNA translation. Genes Dev 2014; 28:357-71. [PMID: 24532714 PMCID: PMC3937514 DOI: 10.1101/gad.231407.113] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/06/2014] [Indexed: 12/20/2022]
Abstract
The mammalian target of rapamycin (mTOR) promotes cell growth and proliferation by promoting mRNA translation and increasing the protein synthetic capacity of the cell. Although mTOR globally promotes translation by regulating the mRNA 5' cap-binding protein eIF4E (eukaryotic initiation factor 4E), it also preferentially regulates the translation of certain classes of mRNA via unclear mechanisms. To help fill this gap in knowledge, we performed a quantitative proteomic screen to identify proteins that associate with the mRNA 5' cap in an mTOR-dependent manner. Using this approach, we identified many potential regulatory factors, including the putative RNA-binding protein LARP1 (La-related protein 1). Our results indicate that LARP1 associates with actively translating ribosomes via PABP and that LARP1 stimulates the translation of mRNAs containing a 5' terminal oligopyrimidine (TOP) motif, encoding for components of the translational machinery. We found that LARP1 associates with the mTOR complex 1 (mTORC1) and is required for global protein synthesis as well as cell growth and proliferation. Together, these data reveal important molecular mechanisms involved in TOP mRNA translation and implicate LARP1 as an important regulator of cell growth and proliferation.
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Affiliation(s)
- Joseph Tcherkezian
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Marie Cargnello
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Yves Romeo
- Centre National de la Recherche Scientifique, Laboratoire de Biologie Moléculaire Eucaryote, 31062 Toulouse, Cedex 04, France
- Université de Toulouse, Université Paul Sabatier (UPS), F-31000 Toulouse, France
| | - Edward L. Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Genevieve Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
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