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Cheng Y, Song Z. The identification of hub genes associated with pure ground glass nodules using weighted gene co-expression network analysis. BMC Pulm Med 2024; 24:275. [PMID: 38858671 PMCID: PMC11165796 DOI: 10.1186/s12890-024-03072-z] [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: 11/14/2023] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Whether there are invasive components in pure ground glass nodules(pGGNs) in the lungs is still a huge challenge to forecast. The objective of our study is to investigate and identify the potential biomarker genes for pure ground glass nodule(pGGN) based on the method of bioinformatics analysis. METHODS To investigate differentially expressed genes (DEGs), firstly the data obtained from the gene expression omnibus (GEO) database was used.Next Weighted gene co-expression network analysis (WGCNA) investigate the co-expression network of DEGs. The black key module was chosen as the key one in correlation with pGGN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses were done. Then STRING was uesd to create a protein-protein interaction (PPI) network, and the chosen module genes were analyzed by Cytoscape software.In addition the polymerase chain reaction (PCR) was used to evaluate the value of these hub genes in pGGN patients' tumor tissues compared to controls. RESULTS A total of 4475 DEGs were screened out from GSE193725, then 225 DEGs were identified in black key module, which were found to be enriched for various functions and pathways, such as extracellular exosome, vesicle, ribosome and so on. Among these DEGs, 6 overlapped hub genes with high degrees of stress method were selected. These hub genes include RPL4, RPL8, RPLP0, RPS16, RPS2 and CCT3.At last relative expression levels of CCT3 and RPL8 mRNA were both regulated in pGGN patients' tumor tissues compared to controls. CONCLUSIONS To summarize, the determined DEGs, pathways, modules, and overlapped hub genes can throw light on the potential molecular mechanisms of pGGN.
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Affiliation(s)
- Yuan Cheng
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
- Department of Thoracic Surgery, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, 063000, China
| | - Zuoqing Song
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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2
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Yang X, Tao L, Zhou J, Zhang K, Wang H. Ribosome RNA modification in cancer: Biological functions and therapeutic targets. Sci Bull (Beijing) 2024; 69:722-726. [PMID: 38245449 DOI: 10.1016/j.scib.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Affiliation(s)
- Xianyuan Yang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lijun Tao
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiawang Zhou
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Kun Zhang
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu Seventh People's Hospital, Affiliated Cancer Hospital of Chengdu Medical College, School of Biological Sciences and Technology, Chengdu Medical College, Chengdu 610500, China.
| | - Hongsheng Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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3
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Paraqindes H, Mourksi NEH, Ballesta S, Hedjam J, Bourdelais F, Fenouil T, Picart T, Catez F, Combe T, Ferrari A, Kielbassa J, Thomas E, Tonon L, Viari A, Attignon V, Carrere M, Perrossier J, Giraud S, Vanbelle C, Gabut M, Bergeron D, Scott MS, Castro Vega L, Magne N, Huillard E, Sanson M, Meyronet D, Diaz JJ, Ducray F, Marcel V, Durand S. Isocitrate dehydrogenase wt and IDHmut adult-type diffuse gliomas display distinct alterations in ribosome biogenesis and 2'O-methylation of ribosomal RNA. Neuro Oncol 2023; 25:2191-2206. [PMID: 37531290 PMCID: PMC10708943 DOI: 10.1093/neuonc/noad140] [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: 03/01/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND High-grade adult-type diffuse gliomas (HGGs) constitute a heterogeneous group of aggressive tumors that are mostly incurable. Recent advances highlighting the contribution of ribosomes to cancer development have offered new clinical perspectives. Here, we uncovered that isocitrate dehydrogenase (IDH)wt and IDHmut HGGs display distinct alterations of ribosome biology, in terms of rRNA epitranscriptomics and ribosome biogenesis, which could constitute novel hallmarks that can be exploited for the management of these pathologies. METHODS We analyzed (1) the ribosomal RNA 2'O-ribose methylation (rRNA 2'Ome) using RiboMethSeq and in-house developed bioinformatics tools (https://github.com/RibosomeCRCL/ribomethseq-nfandrRMSAnalyzer) on 3 independent cohorts compiling 71 HGGs (IDHwt n = 30, IDHmut n = 41) and 9 non-neoplastic samples, (2) the expression of ribosome biogenesis factors using medium throughput RT-qPCR as a readout of ribosome biogenesis, and (3) the sensitivity of 5 HGG cell lines to RNA Pol I inhibitors (CX5461, BMH-21). RESULTS Unsupervised analysis demonstrated that HGGs could be distinguished based on their rRNA 2'Ome epitranscriptomic profile, with IDHwt glioblastomas displaying the most significant alterations of rRNA 2'Ome at specific sites. In contrast, IDHmut HGGs are largely characterized by an overexpression of ribosome biogenesis factors compared to non-neoplastic tissues or IDHwt glioblastomas. Finally, IDHmut HGG-derived spheroids display higher cytotoxicity to CX5461 than IDHwt glioblastoma, while all HGG spheroids display a similar cytotoxicity to BMH-21. CONCLUSIONS In HGGs, IDH mutational status is associated with specific alterations of the ribosome biology and with distinct sensitivities to RNA Pol I inhibitors.
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Affiliation(s)
- Hermes Paraqindes
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Nour-El-Houda Mourksi
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Samantha Ballesta
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Plateforme 3D-ONCO, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Jordan Hedjam
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Fleur Bourdelais
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Tanguy Fenouil
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Thiébaud Picart
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Frédéric Catez
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Théo Combe
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Anthony Ferrari
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Emilie Thomas
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Laurie Tonon
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Alain Viari
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
- INRIA Grenoble Rhône-Alpes, Montbonnot-Saint-Martin, France
| | - Valéry Attignon
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Marjorie Carrere
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Jessie Perrossier
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Stéphane Giraud
- Plateforme 3D-ONCO, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Christophe Vanbelle
- Plateforme d’Imagerie Cellulaire, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Mathieu Gabut
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Danny Bergeron
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Luis Castro Vega
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Nathalie Magne
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Emmanuelle Huillard
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - David Meyronet
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Jean-Jacques Diaz
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - François Ducray
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Service de neuro-oncologie, Hôpital Pierre Wertheimer, Lyon, France
| | - Virginie Marcel
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Sébastien Durand
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
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4
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Albaret MA, Aïmontché E, Bendriss-Vermare N, Diaz JJ, Gil C, Hedjam J, Ichim G, Morin C, Mourksi NEH, Nguyen TTM, Picant V, Picard E, Popgeorgiev N, Tirode F, Vanacker H, Puisieux A, Mehlen P. [Oncology research congress: The essentials of the fifth International Symposium 2022 of the Cancer Research Center of Lyon]. Bull Cancer 2023; 110:1332-1342. [PMID: 37806862 DOI: 10.1016/j.bulcan.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/09/2023] [Indexed: 10/10/2023]
Affiliation(s)
- Marie Alexandra Albaret
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France.
| | - Eliezer Aïmontché
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Nathalie Bendriss-Vermare
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Jean-Jacques Diaz
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Clara Gil
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Jordan Hedjam
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Gabriel Ichim
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Chloé Morin
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Nour-El-Houda Mourksi
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Trang Thi Minh Nguyen
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Valentin Picant
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Emilie Picard
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Nikolay Popgeorgiev
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Franck Tirode
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Hélène Vanacker
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
| | - Alain Puisieux
- Institut Curie, 73, rue Claude-Bernard, Paris 5(e) arrondissement, France
| | - Patrick Mehlen
- UnivLyon, université Claude-Bernard Lyon 1, CNRS 5286, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, Inserm 1052, 28, rue Laennec, Lyon, France
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5
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Gao Y, Wang H. Ribosome Heterogeneity in Development and Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550527. [PMID: 37546733 PMCID: PMC10402066 DOI: 10.1101/2023.07.25.550527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The functional ribosome is composed of ∼80 ribosome proteins. With the intensity-based absolute quantification (iBAQ) value, we calculate the stoichiometry ratio of each ribosome protein. We analyze the ribosome ratio-omics (Ribosome R ), which reflects the holistic signature of ribosome composition, in various biological samples with distinct functions, developmental stages, and pathological outcomes. The Ribosome R reveals significant ribosome heterogeneity among different tissues of fat, spleen, liver, kidney, heart, and skeletal muscles. During tissue development, testes at various stages of spermatogenesis show distinct Ribosome R signatures. During in vitro neuronal maturation, the Ribosome R changes reveal functional association with certain molecular aspects of neurodevelopment. Regarding ribosome heterogeneity associated with pathological conditions, the Ribosome R signature of gastric tumors is functionally linked to pathways associated with tumorigenesis. Moreover, the Ribosome R undergoes dynamic changes in macrophages following immune challenges. Taken together, with the examination of a broad spectrum of biological samples, the Ribosome R barcode reveals ribosome heterogeneity and specialization in cell function, development, and disease. One-Sentence Summary Ratio-omics signature of ribosome deciphers functionally relevant heterogeneity in development and disease.
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Costa DS, Kenny-Ganzert IW, Chi Q, Park K, Kelley LC, Garde A, Matus DQ, Park J, Yogev S, Goldstein B, Gibney TV, Pani AM, Sherwood DR. The Caenorhabditis elegans anchor cell transcriptome: ribosome biogenesis drives cell invasion through basement membrane. Development 2023; 150:dev201570. [PMID: 37039075 PMCID: PMC10259517 DOI: 10.1242/dev.201570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/27/2023] [Indexed: 04/12/2023]
Abstract
Cell invasion through basement membrane (BM) barriers is important in development, immune function and cancer progression. As invasion through BM is often stochastic, capturing gene expression profiles of actively invading cells in vivo remains elusive. Using the stereotyped timing of Caenorhabditis elegans anchor cell (AC) invasion, we generated an AC transcriptome during BM breaching. Through a focused RNAi screen of transcriptionally enriched genes, we identified new invasion regulators, including translationally controlled tumor protein (TCTP). We also discovered gene enrichment of ribosomal proteins. AC-specific RNAi, endogenous ribosome labeling and ribosome biogenesis analysis revealed that a burst of ribosome production occurs shortly after AC specification, which drives the translation of proteins mediating BM removal. Ribosomes also enrich near the AC endoplasmic reticulum (ER) Sec61 translocon and the endomembrane system expands before invasion. We show that AC invasion is sensitive to ER stress, indicating a heightened requirement for translation of ER-trafficked proteins. These studies reveal key roles for ribosome biogenesis and endomembrane expansion in cell invasion through BM and establish the AC transcriptome as a resource to identify mechanisms underlying BM transmigration.
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Affiliation(s)
- Daniel S. Costa
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27708, USA
| | | | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Kieop Park
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Laura C. Kelley
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Aastha Garde
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Junhyun Park
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shaul Yogev
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Theresa V. Gibney
- Department of Biology, University of Virginia, Charlottesville, VA 29903, USA
| | - Ariel M. Pani
- Department of Biology, University of Virginia, Charlottesville, VA 29903, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 29904, USA
| | - David R. Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
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7
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Decle-Carrasco S, Rodríguez-Piña AL, Rodríguez-Zapata LC, Castano E. Current research on viral proteins that interact with fibrillarin. Mol Biol Rep 2023; 50:4631-4643. [PMID: 36928641 PMCID: PMC10018631 DOI: 10.1007/s11033-023-08343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
The nucleolus is a multifunctional nuclear domain primarily dedicated to ribosome biogenesis. Certain viruses developed strategies to manipulate host nucleolar proteins to facilitate their replication by modulating ribosomal RNA (rRNA) processing. This association interferes with nucleolar functions resulting in overactivation or arrest of ribosome biogenesis, induction or inhibition of apoptosis, and affecting stress response. The nucleolar protein fibrillarin (FBL) is an important target of some plant and animal viruses. FBL is an essential and highly conserved S-adenosyl methionine (SAM) dependent methyltransferase, capable of rRNA degradation by its intrinsically disordered region (IDR), the glycine/arginine-rich (GAR) domain. It forms a ribonucleoprotein complex that directs 2'-O-methylations in more than 100 sites of pre-rRNAs. It is involved in multiple cellular processes, including initiation of transcription, oncogenesis, and apoptosis, among others. The interaction with animal viruses, including human viruses, triggered its redistribution to the nucleoplasm and cytoplasm, interfering with its role in pre-rRNA processing. Viral-encoded proteins with IDRs as nucleocapsids, matrix, Tat protein, and even a viral snoRNA, can associate with FBL, forcing the nucleolar protein to undergo atypical functions. Here we review the molecular mechanisms employed by animal and human viruses to usurp FBL functions and the effect on cellular processes, particularly in ribosome biogenesis.
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Affiliation(s)
- Stefano Decle-Carrasco
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Alma Laura Rodríguez-Piña
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Enrique Castano
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México.
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8
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Corman A, Sirozh O, Lafarga V, Fernandez-Capetillo O. Targeting the nucleolus as a therapeutic strategy in human disease. Trends Biochem Sci 2023; 48:274-287. [PMID: 36229381 DOI: 10.1016/j.tibs.2022.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022]
Abstract
The nucleolus is the site of ribosome biogenesis, one of the most resource-intensive processes in eukaryotic cells. Accordingly, nucleolar morphology and activity are highly responsive to growth signaling and nucleolar insults which are collectively included in the actively evolving concept of nucleolar stress. Importantly, nucleolar alterations are a prominent feature of multiple human pathologies, including cancer and neurodegeneration, as well as being associated with aging. The past decades have seen numerous attempts to isolate compounds targeting different facets of nucleolar activity. We provide an overview of therapeutic opportunities for targeting nucleoli in different pathologies and currently available therapies.
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Affiliation(s)
- Alba Corman
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Oleksandra Sirozh
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Vanesa Lafarga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden; Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
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9
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Jiao L, Liu Y, Yu XY, Pan X, Zhang Y, Tu J, Song YH, Li Y. Ribosome biogenesis in disease: new players and therapeutic targets. Signal Transduct Target Ther 2023; 8:15. [PMID: 36617563 PMCID: PMC9826790 DOI: 10.1038/s41392-022-01285-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
The ribosome is a multi-unit complex that translates mRNA into protein. Ribosome biogenesis is the process that generates ribosomes and plays an essential role in cell proliferation, differentiation, apoptosis, development, and transformation. The mTORC1, Myc, and noncoding RNA signaling pathways are the primary mediators that work jointly with RNA polymerases and ribosome proteins to control ribosome biogenesis and protein synthesis. Activation of mTORC1 is required for normal fetal growth and development and tissue regeneration after birth. Myc is implicated in cancer development by enhancing RNA Pol II activity, leading to uncontrolled cancer cell growth. The deregulation of noncoding RNAs such as microRNAs, long noncoding RNAs, and circular RNAs is involved in developing blood, neurodegenerative diseases, and atherosclerosis. We review the similarities and differences between eukaryotic and bacterial ribosomes and the molecular mechanism of ribosome-targeting antibiotics and bacterial resistance. We also review the most recent findings of ribosome dysfunction in COVID-19 and other conditions and discuss the consequences of ribosome frameshifting, ribosome-stalling, and ribosome-collision. We summarize the role of ribosome biogenesis in the development of various diseases. Furthermore, we review the current clinical trials, prospective vaccines for COVID-19, and therapies targeting ribosome biogenesis in cancer, cardiovascular disease, aging, and neurodegenerative disease.
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Affiliation(s)
- Lijuan Jiao
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yuzhe Liu
- grid.452829.00000000417660726Department of Orthopedics, the Second Hospital of Jilin University, Changchun, Jilin 130000 P. R. China
| | - Xi-Yong Yu
- grid.410737.60000 0000 8653 1072Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 511436 P. R. China
| | - Xiangbin Pan
- grid.506261.60000 0001 0706 7839Department of Structural Heart Disease, National Center for Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China ,Key Laboratory of Cardiovascular Appratus Innovation, Beijing, 100037 P. R. China
| | - Yu Zhang
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Junchu Tu
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China. .,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, P. R. China.
| | - Yangxin Li
- Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
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10
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Mourksi N, Dalban C, Colombe‐Vermorel A, Odeyer L, Simioni V, Frenel J, Fabbro M, Bazan F, Abadie‐Lacourtoisie S, Coquan E, Martinez S, Garin G, Tabone‐Eglinger S, Treilleux I, Chabaud S, Pérol D, Ray‐Coquard I, Heudel P, Diaz J, Marcel V. Ribosome biogenesis-based predictive biomarkers in endocrine therapy (Anastrozole) combined with mTOR inhibitor (Vistusertib) in endometrial cancer: translational study from the VICTORIA trial in collaboration with the GINECO group. Mol Oncol 2022; 17:27-36. [PMID: 36370117 PMCID: PMC9812831 DOI: 10.1002/1878-0261.13340] [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: 06/16/2022] [Revised: 09/17/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022] Open
Abstract
Resistance of advanced hormone-dependent endometrial carcinoma to endocrine therapy remains a worldwide clinical issue. We recently reported that the combination of Vistusertib (V, mTOR inhibitor) and Anastrozole (A, aromatase inhibitor) improves the progression-free rate compared to Anastrozole alone. However, a better patient selection based on biomarkers would improve patient outcome. We evaluate for the first time the usage of ribosome biogenesis (RiBi) factors as a source of innovative markers. Using 47 FFPE tumours (A n = 18; V + A n = 29), 32 blood samples (A n = 13; V + A n = 19) and 30 samples of total RNAs (A n = 12; V + A n = 18) from the VICTORIA clinical trial, we observed an association between RiBi-associated markers and drug activity or prediction of treatment response. NOP10 and NHP2 mRNA levels were significantly higher in non-responders compared to responders in the Vistusertib + Anastrozole arm (P = 0.0194 and P = 0.0002 respectively; i.e. 8 weeks progression-free survival as endpoint). This study provides RiBi-based markers relevant for a better selection of patients with advanced endometrial carcinoma by predicting the response of endocrine therapy combined with mTOR inhibitor.
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Affiliation(s)
- Nour‐El‐Houda Mourksi
- Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Centre Léon BérardUniversité de LyonLyonFrance,Institut Convergence PLAsCANLyonFrance,DevWeCan Labex LaboratoryLyonFrance
| | - Cécile Dalban
- Clinical Research DepartmentCentre Léon BérardLyonFrance
| | | | | | - Valentin Simioni
- Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Centre Léon BérardUniversité de LyonLyonFrance,Institut Convergence PLAsCANLyonFrance,DevWeCan Labex LaboratoryLyonFrance
| | - Jean‐Sébastien Frenel
- Medical Oncology Department, Institut Cancérologie de l'Ouest, and GINEGEPSSt HerblainFrance
| | - Michel Fabbro
- Department of Surgical Oncology, Institut du Cancer de MontpellierUniversity of MontpellierMontpellierFrance
| | - Fernando Bazan
- Department of Medical OncologyUniversity Hospital of BesançonBesançonFrance
| | | | - Elodie Coquan
- Department of Clinical Research, Department of Medical OncologyComprehensive Cancer Centre François BaclesseCaenFrance
| | | | | | | | | | - Sylvie Chabaud
- Clinical Research DepartmentCentre Léon BérardLyonFrance
| | - David Pérol
- Clinical Research DepartmentCentre Léon BérardLyonFrance
| | - Isabelle Ray‐Coquard
- Medical Oncology DepartmentCentre Léon Bérard and University Claude Bernard Lyon 1, GINECOLyonFrance
| | - Pierre‐Etienne Heudel
- Medical Oncology DepartmentCentre Léon Bérard and University Claude Bernard Lyon 1, GINECOLyonFrance
| | - Jean‐Jacques Diaz
- Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Centre Léon BérardUniversité de LyonLyonFrance,Institut Convergence PLAsCANLyonFrance,DevWeCan Labex LaboratoryLyonFrance
| | - Virginie Marcel
- Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université Claude Bernard Lyon 1, Centre Léon BérardUniversité de LyonLyonFrance,Institut Convergence PLAsCANLyonFrance,DevWeCan Labex LaboratoryLyonFrance
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