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Ma Y, Li Z, Li D, Zheng B, Xue Y. G0 arrest gene patterns to predict the prognosis and drug sensitivity of patients with lung adenocarcinoma. PLoS One 2024; 19:e0309076. [PMID: 39159158 PMCID: PMC11332951 DOI: 10.1371/journal.pone.0309076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/02/2024] [Indexed: 08/21/2024] Open
Abstract
G0 arrest (G0A) is widely recognized as a crucial factor contributing to tumor relapse. The role of genes related to G0A in lung adenocarcinoma (LUAD) was unclear. This study aimed to develop a gene signature based on for LUAD patients and investigate its relationship with prognosis, tumor immune microenvironment, and therapeutic response in LUAD. We use the TCGA-LUAD database as the discovery cohort, focusing specifically on genes associated with the G0A pathway. We used various statistical methods, including Cox and lasso regression, to develop the model. We validated the model using bulk transcriptome and single-cell transcriptome datasets (GSE50081, GSE72094, GSE127465, GSE131907 and EMTAB6149). We used GSEA enrichment and the CIBERSORT algorithm to gain insight into the annotation of the signaling pathway and the characterization of the tumor microenvironment. We evaluated the response to immunotherapy, chemotherapy, and targeted therapy in these patients. The expression of six genes was validated in cell lines by quantitative real-time PCR (qRT-PCR). Our study successfully established a six-gene signature (CHCHD4, DUT, LARP1, PTTG1IP, RBM14, and WBP11) that demonstrated significant predictive power for overall survival in patients with LUAD. It demonstrated independent prognostic value in LUAD. To enhance clinical applicability, we developed a nomogram based on this gene signature, which showed high reliability in predicting patient outcomes. Furthermore, we observed a significant association between G0A-related risk and tumor microenvironment as well as drug susceptibility, highlighting the potential of the gene signature to guide personalized treatment strategies. The expression of six genes were significantly upregulated in the LUAD cell lines. This signature holds the potential to contribute to improved prognostic prediction and new personalized therapies specifically for LUAD patients.
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Affiliation(s)
- Yong Ma
- Thoracic Surgery Department, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan City, Shanxi, China
| | - Zhilong Li
- Thoracic Surgery Department, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan City, Shanxi, China
| | - Dongbing Li
- Scientific Research Center, Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing, China
| | - Baozhen Zheng
- Radiation Oncology Department, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences / Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanfeng Xue
- Special Need Medical Department, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
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Hochstoeger T, Chao JA. Towards a molecular understanding of the 5'TOP motif in regulating translation of ribosomal mRNAs. Semin Cell Dev Biol 2024; 154:99-104. [PMID: 37316417 DOI: 10.1016/j.semcdb.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Vertebrate cells have evolved a simple, yet elegant, mechanism for coordinated regulation of ribosome biogenesis mediated by the 5' terminal oligopyrimidine motif (5'TOP). This motif allows cells to rapidly adapt to changes in the environment by specifically modulating translation rate of mRNAs encoding the translation machinery. Here, we provide an overview of the origin of this motif, its characterization, and progress in identifying the key regulatory factors involved. We highlight challenges in the field of 5'TOP research, and discuss future approaches that we think will be able to resolve outstanding questions.
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Affiliation(s)
- Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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3
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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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4
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Muller M, Best MG, van der Noort V, Hiltermann TJN, Niemeijer ALN, Post E, Sol N, In 't Veld SGJG, Nogarede T, Visser L, Schouten RD, van den Broek D, Hummelink K, Monkhorst K, de Langen AJ, Schuuring E, Smit EF, Groen HJM, Wurdinger T, van den Heuvel MM. Blood platelet RNA profiles do not enable for nivolumab response prediction at baseline in patients with non-small cell lung cancer. Tumour Biol 2024; 46:S327-S340. [PMID: 37270827 DOI: 10.3233/tub-220037] [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] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Anti-PD-(L)1 immunotherapy has emerged as a promising treatment approach for non-small cell lung cancer (NSCLC), though the response rates remain low. Pre-treatment response prediction may improve patient allocation for immunotherapy. Blood platelets act as active immune-like cells, thereby constraining T-cell activity, propagating cancer metastasis, and adjusting their spliced mRNA content. OBJECTIVE We investigated whether platelet RNA profiles before start of nivolumab anti-PD1 immunotherapy may predict treatment responses. METHODS We performed RNA-sequencing of platelet RNA samples isolated from stage III-IV NSCLC patients before treatment with nivolumab. Treatment response was scored by the RECIST-criteria. Data were analyzed using a predefined thromboSeq analysis including a particle-swarm-enhanced support vector machine (PSO/SVM) classification algorithm. RESULTS We collected and processed a 286-samples cohort, separated into a training/evaluation and validation series and subjected those to training of the PSO/SVM-classification algorithm. We observed only low classification accuracy in the 107-samples validation series (area under the curve (AUC) training series: 0.73 (95% -CI: 0.63-0.84, n = 88 samples), AUC evaluation series: 0.64 (95% -CI: 0.51-0.76, n = 91 samples), AUC validation series: 0.58 (95% -CI: 0.45-0.70, n = 107 samples)), employing a five-RNAs biomarker panel. CONCLUSIONS We concluded that platelet RNA may have minimally discriminative capacity for anti-PD1 nivolumab response prediction, with which the current methodology is insufficient for diagnostic application.
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Affiliation(s)
- Mirte Muller
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Myron G Best
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Boelelaan, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Liquid Biopsy Center, Amsterdam, The Netherlands
- Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | | | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Anna-Larissa N Niemeijer
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Pulmonary Medicine, Boelelaan, Amsterdam, The Netherlands
| | - Edward Post
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Boelelaan, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Liquid Biopsy Center, Amsterdam, The Netherlands
- Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Nik Sol
- Cancer Center Amsterdam and Liquid Biopsy Center, Amsterdam, The Netherlands
- Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
- Department of Neurology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sjors G J G In 't Veld
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Boelelaan, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Liquid Biopsy Center, Amsterdam, The Netherlands
- Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Tineke Nogarede
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lisanne Visser
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Boelelaan, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Liquid Biopsy Center, Amsterdam, The Netherlands
- Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Robert D Schouten
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karlijn Hummelink
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Adrianus J de Langen
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Pulmonary Medicine, Boelelaan, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Egbert F Smit
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Pulmonary Medicine, Boelelaan, Amsterdam, The Netherlands
- Department of Pulmonary Medicine LUMC, Leiden, The Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Thomas Wurdinger
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Boelelaan, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Liquid Biopsy Center, Amsterdam, The Netherlands
- Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Michel M van den Heuvel
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Respiratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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5
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Saba JA, Huang Z, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J, Green R. LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565189. [PMID: 37961604 PMCID: PMC10635049 DOI: 10.1101/2023.11.01.565189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.
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Affiliation(s)
- James A. Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
- These authors contributed equally
| | - Kate L. Schole
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianwen Ye
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Shrey D. Bhatt
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yi Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Mansouri-Noori F, Pircher A, Bilodeau D, Siniavskaia L, Grigull J, Rissland OS, Bayfield MA. The LARP1 homolog Slr1p controls the stability and expression of proto-5'TOP mRNAs in fission yeast. Cell Rep 2023; 42:113226. [PMID: 37851576 DOI: 10.1016/j.celrep.2023.113226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Messenger RNAs (mRNAs) in higher eukaryotes that encode proteins important for the assembly of the translational apparatus (e.g., ribosomal proteins) often harbor a pyrimidine-rich motif at the extreme 5' end known as a 5' terminal oligopyrimidine (5'TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5'TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5'TOP motifs have not been described in many lower organisms, and fission yeast harbors a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5'TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5'TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5'TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1-associated control of gene expression.
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Affiliation(s)
| | | | - Danielle Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jörg Grigull
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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Alternative Splicing, Epigenetic Modifications and Cancer: A Dangerous Triangle, or a Hopeful One? Cancers (Basel) 2022; 14:cancers14030560. [PMID: 35158828 PMCID: PMC8833605 DOI: 10.3390/cancers14030560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Epigenetics studies the alteration of gene expression without changing DNA sequence and very often, epigenetic dysregulation causes cancer. Alternative splicing is a mechanism that results in the production of several mRNA isoforms from a single gene and aberrant splicing is also a frequent cause of cancer. The present review is built on the interrelations of epigenetics and alternative splicing. In an intuitive way, we say that epigenetic modifications and alternative splicing are at two vertices of a triangle, the third vertex being occupied by cancer. Interconnection between alternative splicing and epigenetic modifications occurs backward and forward and the mechanisms involved are widely reviewed. These connections also provide novel diagnostic or prognostic tools, which are listed. Finally, as epigenetic alterations are reversible and aberrant alternative splicing may be corrected, the therapeutic possibilities to break the triangle are discussed. Abstract The alteration of epigenetic modifications often causes cancer onset and development. In a similar way, aberrant alternative splicing may result in oncogenic products. These issues have often been individually reviewed, but there is a growing body of evidence for the interconnection of both causes of cancer. Actually, aberrant splicing may result from abnormal epigenetic signalization and epigenetic factors may be altered by alternative splicing. In this way, the interrelation between epigenetic marks and alternative splicing form the base of a triangle, while cancer may be placed at the vertex. The present review centers on the interconnections at the triangle base, i.e., between alternative splicing and epigenetic modifications, which may result in neoplastic transformations. The effects of different epigenetic factors, including DNA and histone modifications, the binding of non-coding RNAs and the alterations of chromatin organization on alternative splicing resulting in cancer are first considered. Other less-frequently considered questions, such as the epigenetic regulation of the splicing machinery, the aberrant splicing of epigenetic writers, readers and erasers, etc., are next reviewed in their connection with cancer. The knowledge of the above-mentioned relationships has allowed increasing the collection of biomarkers potentially useful as cancer diagnostic and/or prognostic tools. Finally, taking into account on one hand that epigenetic changes are reversible, and some epigenetic drugs already exist and, on the other hand, that drugs intended for reversing aberrations in alternative splicing, therapeutic possibilities for breaking the mentioned cancer-related triangle are discussed.
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8
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Ferguson J, Campos-León K, Pentland I, Stockton JD, Günther T, Beggs AD, Grundhoff A, Roberts S, Noyvert B, Parish JL. The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression. PLoS Pathog 2021; 17:e1010032. [PMID: 34735550 PMCID: PMC8594839 DOI: 10.1371/journal.ppat.1010032] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/16/2021] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have previously demonstrated that CTCF binds to the E2 open reading frame (ORF) of human papillomavirus (HPV) 18 and functions to repress viral oncogene expression in undifferentiated keratinocytes by co-ordinating an epigenetically repressed chromatin loop within HPV episomes. Keratinocyte differentiation disrupts CTCF-dependent chromatin looping of HPV18 episomes promoting induction of enhanced viral oncogene expression. To further characterise CTCF function in HPV transcription control we utilised direct, long-read Nanopore RNA-sequencing which provides information on the structure and abundance of full-length transcripts. Nanopore analysis of primary human keratinocytes containing HPV18 episomes before and after synchronous differentiation allowed quantification of viral transcript species, including the identification of low abundance novel transcripts. Comparison of transcripts produced in wild type HPV18 genome-containing cells to those identified in CTCF-binding deficient genome-containing cells identifies CTCF as a key regulator of differentiation-dependent late promoter activation, required for efficient E1^E4 and L1 protein expression. Furthermore, our data show that CTCF binding at the E2 ORF promotes usage of the downstream weak splice donor (SD) sites SD3165 and SD3284, to the dominant E4 splice acceptor site at nucleotide 3434. These findings demonstrate that in the HPV life cycle both early and late virus transcription programmes are facilitated by recruitment of CTCF to the E2 ORF. Oncogenic human papillomavirus (HPV) infection is the cause of a subset of epithelial cancers of the uterine cervix, other anogenital areas and the oropharynx. HPV infection is established in the basal cells of epithelia where a restricted programme of viral gene expression is required for replication and maintenance of the viral episome. Completion of the HPV life cycle is dependent on the maturation (differentiation) of infected cells which induces enhanced viral gene expression and induction of capsid production. We previously reported that the host cell transcriptional regulator, CTCF, is hijacked by HPV to control viral gene expression. In this study, we use long-read mRNA sequencing to quantitatively map the variety and abundance of HPV transcripts produced in early and late stages of the HPV life cycle and to dissect the function of CTCF in controlling HPV gene expression and transcript processing.
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Affiliation(s)
- Jack Ferguson
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Karen Campos-León
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Ieisha Pentland
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Joanne D. Stockton
- Genomics Birmingham, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Thomas Günther
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
- Genomics Birmingham, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Adam Grundhoff
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sally Roberts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Boris Noyvert
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
- CRUK Birmingham Centre and Centre for Computational Biology, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Joanna L. Parish
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
- * E-mail:
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Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
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Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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10
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Cottrell KA, Chiou RC, Weber JD. Upregulation of 5'-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor. Sci Rep 2020; 10:22276. [PMID: 33335292 PMCID: PMC7747592 DOI: 10.1038/s41598-020-79379-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/08/2020] [Indexed: 12/28/2022] Open
Abstract
Tumor cells require nominal increases in protein synthesis in order to maintain high proliferation rates. As such, tumor cells must acquire enhanced ribosome production. How the numerous mutations in tumor cells ultimately achieve this aberrant production is largely unknown. The gene encoding ARF is the most commonly deleted gene in human cancer. ARF plays a significant role in regulating ribosomal RNA synthesis and processing, ribosome export into the cytoplasm, and global protein synthesis. Utilizing ribosome profiling, we show that ARF is a major suppressor of 5'-terminal oligopyrimidine mRNA translation. Genes with increased translational efficiency following loss of ARF include many ribosomal proteins and translation factors. Knockout of p53 largely phenocopies ARF loss, with increased protein synthesis and expression of 5'-TOP encoded proteins. The 5'-TOP regulators eIF4G1 and LARP1 are upregulated in Arf- and p53-null cells.
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Affiliation(s)
- Kyle A Cottrell
- Division of Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, 660 South Euclid Avenue, Campus, Box 8069, Saint Louis, MO, 63110, USA
| | - Ryan C Chiou
- Division of Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, 660 South Euclid Avenue, Campus, Box 8069, Saint Louis, MO, 63110, USA
| | - Jason D Weber
- Division of Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, 660 South Euclid Avenue, Campus, Box 8069, Saint Louis, MO, 63110, USA.
- Department of Cell Biology and Physiology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO, USA.
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