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Li M, Freeman S, Franco-Barraza J, Cai KQ, Kim A, Jin S, Cukierman E, Ye K. A bioprinted sea-and-island multicellular model for dissecting human pancreatic tumor-stroma reciprocity and adaptive metabolism. Biomaterials 2024; 310:122631. [PMID: 38815457 PMCID: PMC11186049 DOI: 10.1016/j.biomaterials.2024.122631] [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: 01/11/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) presents a formidable clinical challenge due to its intricate microenvironment characterized by desmoplasia and complex tumor-stroma interactions. Conventional models hinder studying cellular crosstalk for therapeutic development. To recapitulate key features of PDAC masses, this study creates a novel sea-and-island PDAC tumor construct (s&i PTC). The s&i PTC consists of 3D-printed islands of human PDAC cells positioned within an interstitial extracellular matrix (ECM) populated by human cancer-associated fibroblasts (CAFs). This design closely mimics the in vivo desmoplastic architecture and nutrient-poor conditions. The model enables studying dynamic tumor-stroma crosstalk and signaling reciprocity, revealing both known and yet-to-be-discovered multicellular metabolic adaptations. Using the model, we discovered the orchestrated dynamic alterations of CAFs under nutrient stress, resembling critical in vivo human tumor niches, such as the secretion of pro-tumoral inflammatory factors. Additionally, nutrient scarcity induces dynamic alterations in the ECM composition and exacerbates poor cancer cell differentiation-features well-established in PDAC progression. Proteomic analysis unveiled the enrichment of proteins associated with aggressive tumor behavior and ECM remodeling in response to poor nutritional conditions, mimicking the metabolic stresses experienced by avascular pancreatic tumor cores. Importantly, the model's relevance to patient outcomes is evident through an inverse correlation between biomarker expression patterns in the s&i PTCs and PDAC patient survival rates. Key findings include upregulated MMPs and key ECM proteins (such as collagen 11 and TGFβ) under nutrient-avid conditions, known to be regulated by CAFs, alongside the concomitant reduction in E-cadherin expression associated with a poorly differentiated PDAC state under nutrient deprivation. Furthermore, elevated levels of hyaluronic acid (HA) and integrins in response to nutrient deprivation underscore the model's fidelity to the PDAC microenvironment. We also observed increased IL-6 and reduced α-SMA expression under poor nutritional conditions, suggesting a transition of CAFs from myofibroblastic to inflammatory phenotypes under a nutrient stress akin to in vivo niches. In conclusion, the s&i PTC represents a significant advancement in engineering clinically relevant 3D models of PDAC masses. It offers a promising platform for elucidating tumor-stroma interactions and guiding future therapeutic strategies to improve patient outcomes.
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Affiliation(s)
- Ming Li
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Binghamton University, SUNY, Binghamton, NY, USA
| | - Sebastian Freeman
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Binghamton University, SUNY, Binghamton, NY, USA
| | - Janusz Franco-Barraza
- Cancer Signaling and Microenvironment Program, Marvin and Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Lewis Katz Temple School of Medicine, Philadelphia, PA, USA
| | - Kathy Q Cai
- Cancer Signaling and Microenvironment Program, Marvin and Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Lewis Katz Temple School of Medicine, Philadelphia, PA, USA
| | - Amy Kim
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Binghamton University, SUNY, Binghamton, NY, USA
| | - Sha Jin
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Binghamton University, SUNY, Binghamton, NY, USA
| | - Edna Cukierman
- Cancer Signaling and Microenvironment Program, Marvin and Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Lewis Katz Temple School of Medicine, Philadelphia, PA, USA.
| | - Kaiming Ye
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Binghamton University, SUNY, Binghamton, NY, USA.
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Issa A, Schlotter F, Flayac J, Chen J, Wacheul L, Philippe M, Sardini L, Mostefa L, Vandermoere F, Bertrand E, Verheggen C, Lafontaine DL, Massenet S. The nucleolar phase of signal recognition particle assembly. Life Sci Alliance 2024; 7:e202402614. [PMID: 38858088 PMCID: PMC11165425 DOI: 10.26508/lsa.202402614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
The signal recognition particle is essential for targeting transmembrane and secreted proteins to the endoplasmic reticulum. Remarkably, because they work together in the cytoplasm, the SRP and ribosomes are assembled in the same biomolecular condensate: the nucleolus. How important is the nucleolus for SRP assembly is not known. Using quantitative proteomics, we have investigated the interactomes of SRP components. We reveal that SRP proteins are associated with scores of nucleolar proteins important for ribosome biogenesis and nucleolar structure. Having monitored the subcellular distribution of SRP proteins upon controlled nucleolar disruption, we conclude that an intact organelle is required for their proper localization. Lastly, we have detected two SRP proteins in Cajal bodies, which indicates that previously undocumented steps of SRP assembly may occur in these bodies. This work highlights the importance of a structurally and functionally intact nucleolus for efficient SRP production and suggests that the biogenesis of SRP and ribosomes may be coordinated in the nucleolus by common assembly factors.
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Affiliation(s)
- Amani Issa
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Florence Schlotter
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Justine Flayac
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Jing Chen
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | | | - Lucas Sardini
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Lalia Mostefa
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | | | | | | | - Denis Lj Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Séverine Massenet
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
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Song F, Hou C, Huang Y, Liang J, Cai H, Tian G, Jiang Y, Wang Z, Hou J. Lactylome analyses suggest systematic lysine-lactylated substrates in oral squamous cell carcinoma under normoxia and hypoxia. Cell Signal 2024; 120:111228. [PMID: 38750680 DOI: 10.1016/j.cellsig.2024.111228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Cancer cells tend to live in hypoxic environment characterized by enhanced glycolysis and accumulation of lactate. Intracellular lactate is shown to drive a novel type of post-translational modification (PTM), lysine lactylation (Kla). Kla has been confirmed to affect the malignant progression of tumors such as hepatocellular carcinoma (HCC) and colon cancer, whereas the global lactylomic profiling of oral squamous cell carcinoma (OSCC) is unclear. Here, the integrative lactylome and proteome analyses by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 1011 Kla sites within 532 proteins and 1197 Kla sites within 608 proteins in SCC25 cells under normoxic and hypoxic environments, respectively. Among these lactylated proteins, histones accounted for only a small fraction, suggesting the presence of Kla modification of OSCC in a large number of non-histone proteins. Notably, Kla preferred to enrich in spliceosome, ribosome and glycolysis/gluconeogenesis pathway in both normoxic and hypoxic cultures. Compared with normoxia, 589 differential proteins with 898 differentially lactylated sites were detected under hypoxia, which were mainly associated with the glycolysis/gluconeogenesis pathway by KEGG analysis. Importantly, we verified the presence of lactylation modification in the spliceosomal proteins hnRNPA1, SF3A1, hnRNPU and SLU7, as well as in glycolytic enzyme PFKP. In addition, the differential alternative splicing analysis described the divergence of pre-mRNA splicing patterns in the presence or absence of sodium lactate and at different oxygen concentrations. Finally, a negative correlation between tissue Kla levels and the prognosis of OSCC patients was revealed by immunohistochemistry. Our study is the first report to elucidate the lactylome and its biological function in OSCC, which deepens our understanding of the mechanisms underlying OSCC progression and provides a novel strategy for targeted therapy for OSCC.
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Affiliation(s)
- Fan Song
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Chen Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yingzhao Huang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jianfeng Liang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Hongshi Cai
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Guoli Tian
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yaoqi Jiang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Ziyi Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China.
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Yang X, Li X. Oncogenic role of RNA-binding protein GNL2 in glioma: Promotion of tumor development through enhancing protein synthesis. Oncol Lett 2024; 28:307. [PMID: 38779136 PMCID: PMC11110002 DOI: 10.3892/ol.2024.14440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/27/2024] [Indexed: 05/25/2024] Open
Abstract
RNA-binding proteins (RBPs) are aberrantly expressed in various diseases, including glioma. In the present study, the role and mechanism of RBPs in glioma were investigated. Differentially expressed genes (DEGs) in glioma were screened from public databases and overlapping genes between DEGs and RBPs were selected in a bioinformatics analysis to identify the hub gene. Next, evaluation of expression, survival analysis and cell experiments were performed to examine the impact of the hub gene on glioma. Through bioinformatics analysis, G protein nucleolar 2 (GNL2), programmed cell death 11 (PDCD11) and ribosomal protein S6 (RPS6) were identified as potential biomarkers in glioma prognosis and GNL2 was chosen as the hub gene for further investigation. GNL2 was increased in glioma tissues and related to poor survival outcomes. Cell experiments revealed that GNL2 knockdown inhibited glioma cell growth, migration and invasion. In addition, GNL2 was found to affect the overall protein synthesis of ribosomal protein L11 in glioma cells. In conclusion, GNL2, PDCD11 and RPS6 may serve as potential biomarkers in glioma prognosis. Importantly, GNL2 acts as an oncogene in glioma and it enhances protein synthesis to promote the development of brain glioma.
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Affiliation(s)
- Xudong Yang
- Department of Neurosurgery, The First Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215008, P.R. China
| | - Xiangdong Li
- Department of Neurosurgery, The First Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215008, P.R. China
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Jia T, Liu C, Guo P, Xu Y, Wang W, Liu X, Wang S, Zhang X, Guo H. FOXA1 regulates ribosomal RNA transcription in prostate cancer. Prostate 2024; 84:967-976. [PMID: 38632701 DOI: 10.1002/pros.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Ribosome biogenesis is excessively activated in tumor cells, yet it is little known whether oncogenic transcription factors (TFs) are involved in the ribosomal RNA (rRNA) transactivation. METHODS Nucleolar proteomics data and large-scale immunofluorescence were re-analyzed to jointly identify the proteins localized at nucleolus. RNA-Seq data of five prostate cancer (PCa) cohorts were combined and integrated with multi-dimensional data to define the upregulated nucleolar TFs in PCa tissues. Then, ChIP-Seq data of PCa cell lines and two PCa clinical cohorts were re-analyzed to reveal the TF binding patterns at ribosomal DNA (rDNA) repeats. The TF binding at rDNA was validated by ChIP-qPCR. The effect of the TF on rRNA transcription was determined by rDNA luciferase reporter, nascent RNA synthesis, and global protein translation assays. RESULTS In this study, we reveal the role of oncogenic TF FOXA1 in regulating rRNA transcription within nucleolar organization regions. By analyzing human TFs in prostate cancer clinical datasets and nucleolar proteomics data, we identified that FOXA1 is partially localized in the nucleolus and correlated with global protein translation. Our extensive FOXA1 ChIP-Seq analysis provides robust evidence of FOXA1 binding across rDNA repeats in prostate cancer cell lines, primary tumors, and castration-resistant variants. Notably, FOXA1 occupancy at rDNA repeats correlates with histone modifications associated with active transcription, namely H3K27ac and H3K4me3. Reducing FOXA1 expression results in decreased transactivation at rDNA, subsequently diminishing global protein synthesis. CONCLUSIONS Our results suggest FOXA1 regulates aberrant ribosome biogenesis downstream of oncogenic signaling in prostate cancer.
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Affiliation(s)
- Tianwei Jia
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Chenxu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Ping Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Yaning Xu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Wenzheng Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Song Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xianglin Zhang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Haiyang Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
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Chen Y, Chen XS, He RQ, Huang ZG, Lu HP, Huang H, Yang DP, Tang ZQ, Yang X, Zhang HJ, Qv N, Kong JL, Chen G. What enlightenment has the development of lung cancer bone metastasis brought in the last 22 years. World J Clin Oncol 2024; 15:765-782. [PMID: 38946828 PMCID: PMC11212609 DOI: 10.5306/wjco.v15.i6.765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/01/2024] [Accepted: 05/22/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Lung cancer bone metastasis (LCBM) is a disease with a poor prognosis, high risk and large patient population. Although considerable scientific output has accumulated on LCBM, problems have emerged, such as confusing research structures. AIM To organize the research frontiers and body of knowledge of the studies on LCBM from the last 22 years according to their basic research and translation, clinical treatment, and clinical diagnosis to provide a reference for the development of new LCBM clinical and basic research. METHODS We used tools, including R, VOSviewer and CiteSpace software, to measure and visualize the keywords and other metrics of 1903 articles from the Web of Science Core Collection. We also performed enrichment and protein-protein interaction analyses of gene expression datasets from LCBM cases worldwide. RESULTS Research on LCBM has received extensive attention from scholars worldwide over the last 20 years. Targeted therapies and immunotherapies have evolved into the mainstream basic and clinical research directions. The basic aspects of drug resistance mechanisms and parathyroid hormone-related protein may provide new ideas for mechanistic study and improvements in LCBM prognosis. The produced molecular map showed that ribosomes and focal adhesion are possible pathways that promote LCBM occurrence. CONCLUSION Novel therapies for LCBM face animal testing and drug resistance issues. Future focus should centre on advancing clinical therapies and researching drug resistance mechanisms and ribosome-related pathways.
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Affiliation(s)
- Yi Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Song Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Hui-Ping Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Hong Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Da-Ping Yang
- Department of Pathology, Guigang People’s Hospital of Guangxi/The Eighth Affiliated Hospital of Guangxi Medical University, Guigang 537100, Guangxi Zhuang Autonomous Region, China
| | - Zhong-Qing Tang
- Department of Pathology, Wuzhou Gongren Hospital/The Seventh Affiliated Hospital of Guangxi Medical University, Wuzhou 543000, Guangxi Zhuang Autonomous Region, China
| | - Xia Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Han-Jie Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Ning Qv
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Jin-Liang Kong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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Han S, Chen LL. Long non-coding RNAs in the nucleolus: Biogenesis, regulation, and function. Curr Opin Struct Biol 2024; 87:102866. [PMID: 38909586 DOI: 10.1016/j.sbi.2024.102866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/08/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024]
Abstract
The nucleolus functions as a multi-layered regulatory hub for ribosomal RNA (rRNA) biogenesis and ribosome assembly. Long noncoding RNAs (lncRNAs) in the nucleolus, originated from transcription by different RNA polymerases, have emerged as critical players in not only fine-tuning rRNA transcription and processing, but also shaping the organization of the multi-phase nucleolar condensate. Here, we review the diverse molecular mechanisms by which functional lncRNAs operate in the nucleolus, as well as their profound implications in a variety of biological processes. We also highlight the development of emerging molecular tools for characterizing and manipulating RNA function in living cells, and how application of such tools in the nucleolus might enable the discovery of additional insights and potential therapeutic strategies.
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Affiliation(s)
- Shuo Han
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China; New Cornerstone Science Laboratory, Shenzhen, China
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Zhuang Y, Guo X, Razorenova OV, Miles CE, Zhao W, Shi X. Coaching ribosome biogenesis from the nuclear periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.597078. [PMID: 38948754 PMCID: PMC11212990 DOI: 10.1101/2024.06.21.597078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Severe invagination of the nuclear envelope is a hallmark of cancers, aging, neurodegeneration, and infections. However, the outcomes of nuclear invagination remain unclear. This work identified a new function of nuclear invagination: regulating ribosome biogenesis. With expansion microscopy, we observed frequent physical contact between nuclear invaginations and nucleoli. Surprisingly, the higher the invagination curvature, the more ribosomal RNA and pre-ribosomes are made in the contacted nucleolus. By growing cells on nanopillars that generate nuclear invaginations with desired curvatures, we can increase and decrease ribosome biogenesis. Based on this causation, we repressed the ribosome levels in breast cancer and progeria cells by growing cells on low-curvature nanopillars, indicating that overactivated ribosome biogenesis can be rescued by reshaping nuclei. Mechanistically, high-curvature nuclear invaginations reduce heterochromatin and enrich nuclear pore complexes, which promote ribosome biogenesis. We anticipate that our findings will serve as a foundation for further studies on nuclear deformation. Highlights Nuclear invaginations regulate ribosome biogenesis by physically contacting nucleoli.High-curvature nuclear tunnels increase ribosome biogenesis.Nanopillars reduce ribosome biogenesis by transforming high-curvature nuclear invaginations to low-curvature ones.
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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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Park J, Nam DH, Kim D, Chung YJ. RPS24 alternative splicing is a marker of cancer progression and epithelial-mesenchymal transition. Sci Rep 2024; 14:13246. [PMID: 38853173 PMCID: PMC11162997 DOI: 10.1038/s41598-024-63976-y] [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: 11/26/2023] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
Although alternative splicing (AS) is a major mechanism that adds diversity to gene expression patterns, its precise role in generating variability in ribosomal proteins, known as ribosomal heterogeneity, remains unclear. The ribosomal protein S24 (RPS24) gene, encoding a ribosomal component, undergoes AS; however, in-depth studies have been challenging because of three microexons between exons 4 and 6. We conducted a detailed analysis of RPS24 AS isoforms using a direct approach to investigate the splicing junctions related to these microexons, focusing on four AS isoforms. Each of these isoforms showed tissue specificity and relative differences in expression among cancer types. Significant differences in the proportions of these RPS24 AS isoforms between cancerous and normal tissues across diverse cancer types were also observed. Our study highlighted a significant correlation between the expression levels of a specific RPS24 AS isoform and the epithelial-mesenchymal transition process in lung and breast cancers. Our research contributes to a better understanding of the intricate regulatory mechanisms governing AS of ribosomal protein genes and highlights the biological implications of RPS24 AS isoforms in tissue development and tumorigenesis.
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Affiliation(s)
- Jiyeon Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea
| | - Da Hae Nam
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dokyeong Kim
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea.
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, Republic of Korea.
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11
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Anastas V, Chavdoula E, La Ferlita A, Soysal B, Cosentini I, Nigita G, Kearse MG, Tsichlis PN. KDM2B is required for ribosome biogenesis and its depletion unequally affects mRNA translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595403. [PMID: 38826406 PMCID: PMC11142201 DOI: 10.1101/2024.05.22.595403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
KDM2B is a JmjC domain lysine demethylase, which promotes cell immortalization, stem cell self-renewal and tumorigenesis. Here we employed a multi-omics strategy to address its role in ribosome biogenesis and mRNA translation. These processes are required to sustain cell proliferation, an important cancer hallmark. Contrary to earlier observations, KDM2B promotes ribosome biogenesis by stimulating the transcription of genes encoding ribosome biogenesis factors and ribosomal proteins, particularly those involved in the biogenesis of the 40S ribosomal subunits. Knockdown of KDM2B impaired the assembly of the small and large subunit processomes, as evidenced by specific defects in pre-ribosomal RNA processing. The final outcome was a decrease in the rate of ribosome assembly and in the abundance of ribosomes, and inhibition of mRNA translation. The inhibition of translation was distributed unequally among mRNAs with different features, suggesting that mRNA-embedded properties influence how mRNAs interpret ribosome abundance. This study identified a novel mechanism contributing to the regulation of translation and provided evidence for a rich biology elicited by a pathway that depends on KDM2B, and perhaps other regulators of translation.
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Affiliation(s)
- Vollter Anastas
- Tufts Graduate School of Biomedical Sciences, Program in Genetics, Boston, MA, United States
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Evangelia Chavdoula
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Burak Soysal
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Ilaria Cosentini
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Michael G Kearse
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Philip N Tsichlis
- Tufts Graduate School of Biomedical Sciences, Program in Genetics, Boston, MA, United States
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
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12
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Yang L, Zhang Z, Jiang P, Kong D, Yu Z, Shi D, Han Y, Chen E, Zheng W, Sun J, Zhao Y, Luo Y, Shi J, Yao H, Huang H, Qian P. Phase separation-competent FBL promotes early pre-rRNA processing and translation in acute myeloid leukaemia. Nat Cell Biol 2024; 26:946-961. [PMID: 38745030 DOI: 10.1038/s41556-024-01420-z] [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: 02/17/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA-binding proteins (RBPs) are pivotal in acute myeloid leukaemia (AML), a lethal disease. Although specific phase separation-competent RBPs are recognized in AML, the effect of their condensate formation on AML leukaemogenesis, and the therapeutic potential of inhibition of phase separation are underexplored. In our in vivo CRISPR RBP screen, fibrillarin (FBL) emerges as a crucial nucleolar protein that regulates AML cell survival, primarily through its phase separation domains rather than methyltransferase or acetylation domains. These phase separation domains, with specific features, coordinately drive nucleoli formation and early processing of pre-rRNA (including efflux, cleavage and methylation), eventually enhancing the translation of oncogenes such as MYC. Targeting the phase separation capability of FBL with CGX-635 leads to elimination of AML cells, suggesting an additional mechanism of action for CGX-635 that complements its established therapeutic effects. We highlight the potential of PS modulation of critical proteins as a possible therapeutic strategy for AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- RNA Precursors/metabolism
- RNA Precursors/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- RNA Processing, Post-Transcriptional
- Animals
- Cell Line, Tumor
- Protein Biosynthesis
- Cell Nucleolus/metabolism
- Cell Nucleolus/genetics
- Mice
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/genetics
- Gene Expression Regulation, Leukemic
- Phase Separation
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Affiliation(s)
- Lin Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zhaoru Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Penglei Jiang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Delin Kong
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zebin Yu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Danrong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingli Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Ertuo Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Weiyan Zheng
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Sun
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanmin Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Luo
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jimin Shi
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Pengxu Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
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13
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Hwang SP, Denicourt C. The impact of ribosome biogenesis in cancer: from proliferation to metastasis. NAR Cancer 2024; 6:zcae017. [PMID: 38633862 PMCID: PMC11023387 DOI: 10.1093/narcan/zcae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
The dysregulation of ribosome biogenesis is a hallmark of cancer, facilitating the adaptation to altered translational demands essential for various aspects of tumor progression. This review explores the intricate interplay between ribosome biogenesis and cancer development, highlighting dynamic regulation orchestrated by key oncogenic signaling pathways. Recent studies reveal the multifaceted roles of ribosomes, extending beyond protein factories to include regulatory functions in mRNA translation. Dysregulated ribosome biogenesis not only hampers precise control of global protein production and proliferation but also influences processes such as the maintenance of stem cell-like properties and epithelial-mesenchymal transition, contributing to cancer progression. Interference with ribosome biogenesis, notably through RNA Pol I inhibition, elicits a stress response marked by nucleolar integrity loss, and subsequent G1-cell cycle arrest or cell death. These findings suggest that cancer cells may rely on heightened RNA Pol I transcription, rendering ribosomal RNA synthesis a potential therapeutic vulnerability. The review further explores targeting ribosome biogenesis vulnerabilities as a promising strategy to disrupt global ribosome production, presenting therapeutic opportunities for cancer treatment.
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Affiliation(s)
- Sseu-Pei Hwang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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14
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Zang T, Fear MW, Parker TJ, Holland AJA, Martin L, Langley D, Kimble R, Wood FM, Cuttle L. Inflammatory proteins and neutrophil extracellular traps increase in burn blister fluid 24h after burn. Burns 2024; 50:1180-1191. [PMID: 38490838 DOI: 10.1016/j.burns.2024.02.026] [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: 05/16/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024]
Abstract
Burn wound blister fluid is a valuable matrix for understanding the biological pathways associated with burn injury. In this study, 152 blister fluid samples collected from paediatric burn wounds at three different hospitals were analysed using mass spectrometry proteomic techniques. The protein abundance profile at different days after burn indicated more proteins were associated with cellular damage/repair in the first 24 h, whereas after this point more proteins were associated with antimicrobial defence. The inflammatory proteins persisted at a high level in the blister fluid for more than 7 days. This may indicate that removal of burn blisters prior to two days after burn is optimal to prevent excessive or prolonged inflammation in the wound environment. Additionally, many proteins associated with the neutrophil extracellular trap (NET) pathway were increased after burn, further implicating NETs in the post-burn inflammatory response. NET inhibitors may therefore be a potential treatment to reduce post-burn inflammation and coagulation pathology and enhance burn wound healing outcomes.
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Affiliation(s)
- Tuo Zang
- Queensland University of Technology (QUT), Faculty of Health, School of Biomedical Sciences, Centre for Children's Health Research, South Brisbane, Queensland, Australia
| | - Mark W Fear
- Burn Injury Research Unit, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Tony J Parker
- Queensland University of Technology (QUT), School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland, Australia
| | - Andrew J A Holland
- The Children's Hospital at Westmead Burns Unit, Kids Research Institute, Department of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, New South Wales, Australia
| | - Lisa Martin
- Burn Injury Research Unit, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Donna Langley
- Queensland University of Technology (QUT), Faculty of Health, School of Biomedical Sciences, Centre for Children's Health Research, South Brisbane, Queensland, Australia
| | - Roy Kimble
- Children's Health Queensland, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Fiona M Wood
- Burn Injury Research Unit, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia; Burns Service of Western Australia, Perth Children's Hospital and Fiona Stanley Hospital, Perth, WA, Australia
| | - Leila Cuttle
- Queensland University of Technology (QUT), Faculty of Health, School of Biomedical Sciences, Centre for Children's Health Research, South Brisbane, Queensland, Australia.
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15
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Sibai DS, Tremblay MG, Lessard F, Tav C, Sabourin-Félix M, Robinson M, Moss T. TTF1 control of LncRNA synthesis delineates a tumor suppressor pathway directly regulating the ribosomal RNA genes. J Cell Physiol 2024. [PMID: 38764354 DOI: 10.1002/jcp.31303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
The tumor suppressor p14/19ARF regulates ribosomal RNA (rRNA) synthesis by controlling the nucleolar localization of Transcription Termination Factor 1 (TTF1). However, the role played by TTF1 in regulating the rRNA genes and in potentially controlling growth has remained unclear. We now show that TTF1 expression regulates cell growth by determining the cellular complement of ribosomes. Unexpectedly, it achieves this by acting as a "roadblock" to synthesis of the noncoding LncRNA and pRNA that we show are generated from the "Spacer Promoter" duplications present upstream of the 47S pre-rRNA promoter on the mouse and human ribosomal RNA genes. Unexpectedly, the endogenous generation of these noncoding RNAs does not induce CpG methylation or gene silencing. Rather, it acts in cis to suppress 47S preinitiation complex formation and hence de novo pre-rRNA synthesis by a mechanism reminiscent of promoter interference or occlusion. Taken together, our data delineate a pathway from p19ARF to cell growth suppression via the regulation of ribosome biogenesis by noncoding RNAs and validate a key cellular growth law in mammalian cells.
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Affiliation(s)
- Dany S Sibai
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Michel G Tremblay
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Frédéric Lessard
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Christophe Tav
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Marianne Sabourin-Félix
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Mark Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tom Moss
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
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16
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Correll CC, Rudloff U, Schmit JD, Ball DA, Karpova TS, Balzer E, Dundr M. Crossing boundaries of light microscopy resolution discerns novel assemblies in the nucleolus. Histochem Cell Biol 2024:10.1007/s00418-024-02297-7. [PMID: 38758429 DOI: 10.1007/s00418-024-02297-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
The nucleolus is the largest membraneless organelle and nuclear body in mammalian cells. It is primarily involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is evolutionarily conserved and accounts for the most energy-consuming cellular process needed for cell growth, proliferation, and homeostasis. Despite the significance of this process, the substructural mechanistic principles of the nucleolar function in preribosome biogenesis have only recently begun to emerge. Here, we provide a new perspective using advanced super-resolution microscopy and single-molecule MINFLUX nanoscopy on the mechanistic principles governing ribosomal RNA-seeded nucleolar formation and the resulting tripartite suborganization of the nucleolus driven, in part, by liquid-liquid phase separation. With recent advances in the cryogenic electron microscopy (cryoEM) structural analysis of ribosome biogenesis intermediates, we highlight the current understanding of the step-wise assembly of preribosomal subunits in the nucleolus. Finally, we address how novel anticancer drug candidates target early steps in ribosome biogenesis to exploit these essential dependencies for growth arrest and tumor control.
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Affiliation(s)
- Carl C Correll
- Center for Proteomics and Molecular Therapeutics and Biochemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University of Medicine & Science, North Chicago, IL, 60064, USA
| | - Udo Rudloff
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eric Balzer
- Nikon Instruments Inc., Melville, NY, 11747, USA
| | - Miroslav Dundr
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Center for Cancer Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine & Science, North Chicago, IL, 60064, USA.
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17
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Gao M, Liu T, Hu K, Chen S, Wang S, Gan D, Li Z, Lin X. Ribosomal Dysregulation in Metastatic Laryngeal Squamous Cell Carcinoma: Proteomic Insights and CX-5461's Therapeutic Promise. TOXICS 2024; 12:363. [PMID: 38787142 PMCID: PMC11126056 DOI: 10.3390/toxics12050363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
One of the main barriers to the successful treatment of laryngeal squamous cell carcinoma (LSCC) is postoperative progression, primarily due to tumor cell metastasis. To systematically investigate the molecular characteristics and potential mechanisms underlying the metastasis in laryngeal cancer, we carried out a TMT-based proteomic analysis of both cancerous and adjacent non-cancerous tissues from 10 LSCC patients with lymph node metastasis (LNM) and 10 without. A total of 5545 proteins were quantified across all samples. We identified 57 proteins that were downregulated in LSCC with LNM, which were enriched in cell adhesion pathways, and 69 upregulated proteins predominantly enriched in protein production pathways. Importantly, our data revealed a strong correlation between increased ribosomal activity and the presence of LNM, as 18 ribosomal subunit proteins were found to be upregulated, with RPS10 and RPL24 being the most significantly overexpressed. The potential of ribosomal proteins, including RPS10 and RPL24, as biomarkers for LSCC with LNM was confirmed in external validation samples (six with LNM and six without LNM) using Western blotting and immunohistochemistry. Furthermore, we have confirmed that the RNA polymerase I inhibitor CX-5461, which impedes ribosome biogenesis in LSCC, also decreases the expression of RPS10, RPL24, and RPS26. In vitro experiments have revealed that CX-5461 moderately reduces cell viability, while it significantly inhibits the invasion and migration of LSCC cells. It can enhance the expression of the epithelial marker CDH1 and suppress the expression of the mesenchymal markers CDH2, VIM, and FN at a dose that does not affect cell viability. Our study broadens the scope of the proteomic data on laryngeal cancer and suggests that ribosome targeting could be a supplementary therapeutic strategy for metastatic LSCC.
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Affiliation(s)
| | | | | | | | | | | | | | - Xiaohuang Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (M.G.); (T.L.); (K.H.); (S.C.); (S.W.); (D.G.); (Z.L.)
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18
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Metge BJ, Alsheikh HAM, Kammerud SC, Chen D, Das D, Nebane NM, Bostwick JR, Shevde LA, Samant RS. Targeting EMT using low-dose Teniposide by downregulating ZEB2-driven activation of RNA polymerase I in breast cancer. Cell Death Dis 2024; 15:322. [PMID: 38719798 PMCID: PMC11079014 DOI: 10.1038/s41419-024-06694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024]
Abstract
Metastatic dissemination from the primary tumor is a complex process that requires crosstalk between tumor cells and the surrounding milieu and involves the interplay between numerous cellular-signaling programs. Epithelial-mesenchymal transition (EMT) remains at the forefront of orchestrating a shift in numerous cellular programs, such as stemness, drug resistance, and apoptosis that allow for successful metastasis. Till date, there is limited success in therapeutically targeting EMT. Utilizing a high throughput screen of FDA-approved compounds, we uncovered a novel role of the topoisomerase inhibitor, Teniposide, in reversing EMT. Here, we demonstrate Teniposide as a potent modulator of the EMT program, specifically through an IRF7-NMI mediated response. Furthermore, Teniposide significantly reduces the expression of the key EMT transcriptional regulator, Zinc Finger E-Box Binding Homeobox 2 (ZEB2). ZEB2 downregulation by Teniposide inhibited RNA polymerase I (Pol I) activity and rRNA biogenesis. Importantly, Teniposide treatment markedly reduced pulmonary colonization of breast cancer cells. We have uncovered a novel role of Teniposide, which when used at a very low concentration, mitigates mesenchymal-like invasive phenotype. Overall, its ability to target EMT and rRNA biogenesis makes Teniposide a viable candidate to be repurposed as a therapeutic option to restrict breast cancer metastases.
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Affiliation(s)
- Brandon J Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Sarah C Kammerud
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongquan Chen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Devika Das
- Birmingham VA Health Care System, Birmingham, AL, USA
- Parexel Biotech, Waltham, MA, USA
| | - N Miranda Nebane
- High-Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - J Robert Bostwick
- High-Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - Lalita A Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rajeev S Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Birmingham VA Health Care System, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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19
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Vincent A, Krishnakumar S, Parameswaran S. Heterozygous RB1 mutation enhanced ATP production in human iPSC-derived retinal organoids. Mol Biol Rep 2024; 51:606. [PMID: 38704498 DOI: 10.1007/s11033-024-09564-9] [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: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Recent in vitro studies using RB1+/- fibroblasts and MSCs have shown molecular and functional disruptions without the need for biallelic loss of RB1. However, this was not reflected in the recent in vitro studies employing RB1+/- retinal organoids. To gain further insights into the molecular disruptions in the RB1+/- retinal organoids, we performed a high throughput RNA sequencing analysis. METHODS AND RESULTS iPSCs were generated from RB1+/+ and RB1+/- OAMSCs derived from retinoblastoma patients. RB1+/+ and RB1+/- iPSCs were subjected to a step-wise retinal differentiation protocol. Retinal differentiation was evaluated by Real-time PCR and flow cytometry analysis of the retinal markers. To gain further insights into the molecular differences in RB1+/- retinal organoids, a high throughput RNA sequencing followed by differential gene expression analysis and gene set enrichment analysis (GSEA) was performed. The analysis revealed a shift from the regular metabolic process of glycolysis to oxidative phosphorylation in the RB1+/- retinal organoids. To investigate further, we performed assays to determine the levels of pyruvate, lactate and ATP in the retinal organoids. The results revealed significant increase in ATP and pyruvate levels in RB1+/- retinal organoids of day 120 compared to that of the RB1+/+. The results thus revealed enhanced ATP production in the RB1+/- retinal organoids. CONCLUSION The study provides novel insights into the metabolic phenotype of heterozygous RB1 mutant suggesting dysregulation of energy metabolism and glycolytic pathways to be first step even before the changes in cellular proliferation or other phenotypic consequences ensue.
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Affiliation(s)
- Ambily Vincent
- Radheshyam Kanoi Stem Cell Laboratory, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, 41, College Road, Chennai, Tamilnadu, India
- School of Chemical and Biotechnology, SASTRA Deemed-to-Be University, Thanjavur, India
| | - Subramanian Krishnakumar
- Radheshyam Kanoi Stem Cell Laboratory, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, 41, College Road, Chennai, Tamilnadu, India
| | - Sowmya Parameswaran
- Radheshyam Kanoi Stem Cell Laboratory, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, 41, College Road, Chennai, Tamilnadu, India.
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20
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Li X, Liu M, Xing Y, Niu Y, Liu TH, Sun JL, Liu Y, Hemba-Waduge RUS, Ji JY. Distinct effects of CDK8 module subunits on cellular growth and proliferation in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591924. [PMID: 38746212 PMCID: PMC11092604 DOI: 10.1101/2024.04.30.591924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The Mediator complex, composed of about 30 conserved subunits, plays a pivotal role in facilitating RNA polymerase II-dependent transcription in eukaryotes. Within this complex, the CDK8 kinase module (CKM), comprising Med12, Med13, CDK8, and CycC (Cyclin C), serves as a dissociable subcomplex that modulates the activity of the small Mediator complex. Genetic studies in Drosophila have revealed distinct phenotypes of CDK8-CycC and Med12-Med13 mutations, yet the underlying mechanism has remained unknown. Here, using Drosophila as a model organism, we show that depleting CDK8-CycC enhances E2F1 target gene expression and promotes cell-cycle progression. Conversely, depletion of Med12-Med13 affects the expression of ribosomal protein genes and fibrillarin, indicating a more severe reduction in ribosome biogenesis and cellular growth compared to the loss of CDK8-CycC. Moreover, we found that the stability of CDK8 and CycC relies on Med12 and Med13, with a mutually interdependent relationship between Med12 and Med13. Furthermore, CycC stability depends on the other three CKM subunits. These findings reveal distinct roles for CKM subunits in vivo , with Med12-Med13 disruption exerting a more pronounced impact on ribosome biogenesis and cellular growth compared to the loss of CDK8-CycC. Significance The CDK8 kinase module (CKM), comprising CDK8, CycC, Med12, and Med13, is essential in the Mediator complex for RNA polymerase II-dependent transcription in eukaryotes. While expected to function jointly, CKM subunit mutations result in distinct phenotypes in Drosophila . This study investigates the mechanisms driving these differing effects. Our analysis reveals the role of Med12-Med13 pair in regulating ribosomal biogenesis and cellular growth, contrasting with the involvement of CDK8-CycC in E2F1-dependent cell-cycle progression. Additionally, an asymmetric interdependence in the stability of CDK8-CycC and Med12-Med13 was observed. CKM mutations or overexpression are associated with cancers and cardiovascular diseases. Our findings underscore the distinct impacts of CKM mutations on cellular growth and proliferation, advancing our understanding of their diverse consequences in vivo .
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Su MC, Lee AM, Zhang W, Maeser D, Gruener RF, Deng Y, Huang RS. Computational Modeling to Identify Drugs Targeting Metastatic Castration-Resistant Prostate Cancer Characterized by Heightened Glycolysis. Pharmaceuticals (Basel) 2024; 17:569. [PMID: 38794139 PMCID: PMC11124089 DOI: 10.3390/ph17050569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) remains a deadly disease due to a lack of efficacious treatments. The reprogramming of cancer metabolism toward elevated glycolysis is a hallmark of mCRPC. Our goal is to identify therapeutics specifically associated with high glycolysis. Here, we established a computational framework to identify new pharmacological agents for mCRPC with heightened glycolysis activity under a tumor microenvironment, followed by in vitro validation. First, using our established computational tool, OncoPredict, we imputed the likelihood of drug responses to approximately 1900 agents in each mCRPC tumor from two large clinical patient cohorts. We selected drugs with predicted sensitivity highly correlated with glycolysis scores. In total, 77 drugs predicted to be more sensitive in high glycolysis mCRPC tumors were identified. These drugs represent diverse mechanisms of action. Three of the candidates, ivermectin, CNF2024, and P276-00, were selected for subsequent vitro validation based on the highest measured drug responses associated with glycolysis/OXPHOS in pan-cancer cell lines. By decreasing the input glucose level in culture media to mimic the mCRPC tumor microenvironments, we induced a high-glycolysis condition in PC3 cells and validated the projected higher sensitivity of all three drugs under this condition (p < 0.0001 for all drugs). For biomarker discovery, ivermectin and P276-00 were predicted to be more sensitive to mCRPC tumors with low androgen receptor activities and high glycolysis activities (AR(low)Gly(high)). In addition, we integrated a protein-protein interaction network and topological methods to identify biomarkers for these drug candidates. EEF1B2 and CCNA2 were identified as key biomarkers for ivermectin and CNF2024, respectively, through multiple independent biomarker nomination pipelines. In conclusion, this study offers new efficacious therapeutics beyond traditional androgen-deprivation therapies by precisely targeting mCRPC with high glycolysis.
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Affiliation(s)
- Mei-Chi Su
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
| | - Adam M. Lee
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
| | - Weijie Zhang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA; (W.Z.); (D.M.)
| | - Danielle Maeser
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA; (W.Z.); (D.M.)
| | - Robert F. Gruener
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
| | - Yibin Deng
- Department of Urology, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA;
| | - R. Stephanie Huang
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA; (W.Z.); (D.M.)
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22
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Han X, Gao Y, Jiang M, Li Z, Guo J, Li Y, Yi J, Hou L, Cheng J, Feng L, Jin Y, Zhao X, Yue W. Single-cell and spatial transcriptome sequencing uncover a platinum-resistant cluster overexpressed TACSTD2 in high-grade serous ovarian cancer. J Cancer 2024; 15:3427-3440. [PMID: 38817863 PMCID: PMC11134433 DOI: 10.7150/jca.95269] [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: 02/12/2024] [Accepted: 04/20/2024] [Indexed: 06/01/2024] Open
Abstract
Purpose: Platinum-based chemotherapy is effective but limited by resistance in high-grade serous ovarian cancer (HGSOC). Single-cell RNA sequencing (scRNA-seq) can reveal tumour cell heterogeneity and subclonal differentiation. We aimed to analyze resistance mechanisms and potential targets in HGSOC using scRNA-seq. Methods: We performed 10× genomics scRNA-seq sequencing on tumour tissues from 3 platinum-sensitive and 3 platinum-resistant HGSOC patients. We analyzed cell subcluster communication networks and spatial distribution using cellchat. We performed RNA-seq analysis on TACSTD2, a representative resistance gene in the E0 subcluster, to explore its molecular mechanism. Results: Epithelial cells, characterized by distinct chemotherapy resistance traits and highest gene copy number variations, revealed a specific cisplatin-resistant cluster (E0) associated with poor prognosis. E0 exhibited malignant features related to resistance, fostering growth through communication with fibroblasts and endothelial cells. Spatially, E0 promoted fibroblasts to protect tumour cells and impede immune cells infiltration. Furthermore, TACSTD2 was identified as a representative gene of the E0 subcluster, elucidating its role in platinum resistance through the Rap1/PI3K/AKT pathway. Conclusions: Our study reveals a platinum-resistant epithelial cell subcluster E0 and its association with TACSTD2 in HGSOC, uncovers new insights and evidence for the platinum resistance mechanism, and provides new ideas and targets for the development of therapeutic strategies against TACSTD2+ epithelial cancer cells.
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Affiliation(s)
- Xiaoyang Han
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yan Gao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Mei Jiang
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Zhefeng Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jiahao Guo
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yue Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Junjie Yi
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Lisha Hou
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jin Cheng
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Lei Feng
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yulan Jin
- Department of Pathology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Xiaoting Zhao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Wentao Yue
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
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23
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Khashei Varnamkhasti K, Moghanibashi M, Naeimi S. Implications of ZNF334 gene in lymph node metastasis of lung SCC: potential bypassing of cellular senescence. J Transl Med 2024; 22:372. [PMID: 38637790 PMCID: PMC11025273 DOI: 10.1186/s12967-024-05115-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/20/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND The primary goal of this work is to identify biomarkers associated with lung squamous cell carcinoma and assess their potential for early detection of lymph node metastasis. METHODS This study investigated gene expression in lymph node metastasis of lung squamous cell carcinoma using data from the Cancer Genome Atlas and R software. Protein-protein interaction networks, hub genes, and enriched pathways were analyzed. ZNF334 and TINAGL1, two less explored genes, were further examined through in vitro, ex vivo, and in vivo experiments to validate the findings from bioinformatics analyses. The role of ZNF334 and TINAGL1 in senescence induction was assessed after H2O2 and UV induced senescence phenotype determined using β-galactosidase activity and cell cycle status assay. RESULTS We identified a total of 611 up- and 339 down-regulated lung squamous cell carcinoma lymph node metastasis-associated genes (FDR < 0.05). Pathway enrichment analysis highlighted the central respiratory pathway within mitochondria for the subnet genes and the nuclear DNA-directed RNA polymerases for the hub genes. Significantly down regulation of ZNF334 gene was associated with malignancy lymph node progression and senescence induction has significantly altered ZNF334 expression (with consistency in bioinformatics, in vitro, ex vivo, and in vivo results). Deregulation of TINAGL1 expression with inconsistency in bioinformatics, in vitro (different types of lung squamous cancer cell lines), ex vivo, and in vivo results, was also associated with malignancy lymph node progression and altered in senescence phenotype. CONCLUSIONS ZNF334 is a highly generalizable gene to lymph node metastasis of lung squamous cell carcinoma and its expression alter certainly under senescence conditions.
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Affiliation(s)
| | - Mehdi Moghanibashi
- Department of Genetics, Faculty of Medicine, Kazerun Branch, Islamic Azad University, Kazerun, Iran.
| | - Sirous Naeimi
- Department of Genetics, Faculty of Basic Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
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24
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Zeng X, Wang Y, Dai M, Li W, Huang Q, Qin L, Li Y, Yan Y, Xue X, Yi F, Li W, He L, Liu Q, Qi L. Single-cell transcriptomics dissects the transcriptome alterations of hematopoietic stem cells in myelodysplastic neoplasms. J Transl Med 2024; 22:359. [PMID: 38632656 PMCID: PMC11022353 DOI: 10.1186/s12967-024-05165-z] [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: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Myelodysplastic neoplasms (MDS) are myeloid neoplasms characterized by disordered differentiation of hematopoietic stem cells and a predisposition to acute myeloid leukemia (AML). The underline pathogenesis remains unclear. METHODS In this study, the trajectory of differentiation and mechanisms of leukemic transformation were explored through bioinformatics analysis of single-cell RNA-Seq data from hematopoietic stem and progenitor cells (HSPCs) in MDS patients. RESULTS Among the HSPC clusters, the proportion of common myeloid progenitor (CMP) was the main cell cluster in the patients with excess blasts (EB)/ secondary AML. Cell cycle analysis indicated the CMP of MDS patients were in an active proliferative state. The genes involved in the cell proliferation, such as MAML3 and PLCB1, were up-regulated in MDS CMP. Further validation analysis indicated that the expression levels of MAML3 and PLCB1 in patients with MDS-EB were significantly higher than those without EB. Patients with high expression of PLCB1 had a higher risk of transformation to AML. PLCB1 inhibitor can suppress proliferation, induce cell cycle arrest, and activate apoptosis of leukemic cells in vitro. CONCLUSION This study revealed the transcriptomic change of HSPCs in MDS patients along the pseudotime and indicated that PLCB1 plays a key role in the transformation of MDS into leukemia.
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Affiliation(s)
- Xiangzong Zeng
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yichen Wang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Min Dai
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wei Li
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qingtian Huang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Lingsha Qin
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yuquan Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yanwen Yan
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Xiangjun Xue
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Fang Yi
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Wenhao Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Langyu He
- Department of Blood Transfusion, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Ling Qi
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
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25
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Zou C, Li W, Zhang Y, Feng N, Chen S, Yan L, He Q, Wang K, Li W, Li Y, Wang Y, Xu B, Zhang D. Identification of an anaplastic subtype of prostate cancer amenable to therapies targeting SP1 or translation elongation. SCIENCE ADVANCES 2024; 10:eadm7098. [PMID: 38569039 PMCID: PMC10990282 DOI: 10.1126/sciadv.adm7098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Histopathological heterogeneity is a hallmark of prostate cancer (PCa). Using spatial and parallel single-nucleus transcriptomics, we report an androgen receptor (AR)-positive but neuroendocrine-null primary PCa subtype with morphologic and molecular characteristics of small cell carcinoma. Such small cell-like PCa (SCLPC) is clinically aggressive with low AR, but high stemness and proliferation, activity. Molecular characterization prioritizes protein translation, represented by up-regulation of many ribosomal protein genes, and SP1, a transcriptional factor that drives SCLPC phenotype and overexpresses in castration-resistant PCa (CRPC), as two potential therapeutic targets in AR-indifferent CRPC. An SP1-specific inhibitor, plicamycin, effectively suppresses CRPC growth in vivo. Homoharringtonine, a Food And Drug Administration-approved translation elongation inhibitor, impedes CRPC progression in preclinical models and patients with CRPC. We construct an SCLPC-specific signature capable of stratifying patients for drug selectivity. Our studies reveal the existence of SCLPC in admixed PCa pathology, which may mediate tumor relapse, and establish SP1 and translation elongation as actionable therapeutic targets for CRPC.
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Affiliation(s)
- Cheng Zou
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Wenchao Li
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Yuanzhen Zhang
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Ninghan Feng
- Department of Urology and Wuxi School of Medicine, Jiangnan University Medical Center, Wuxi 214002, Jiangsu Province, China
| | - Saisai Chen
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Lianlian Yan
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
| | - Qinju He
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
| | - Kai Wang
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Wenjun Li
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Yingying Li
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Yang Wang
- Department of Urology and Wuxi School of Medicine, Jiangnan University Medical Center, Wuxi 214002, Jiangsu Province, China
| | - Bin Xu
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
- National Medicine-Engineering Interdisciplinary Industry-Education Integration Innovation Platform (Ministry of Education), Basic Medicine Research and Innovation Center, Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Dingxiao Zhang
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
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26
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Derangula S, Nadumane VK. Analysis of the Anticancer Mechanism of OR3 Pigment from Streptomyces coelicolor JUACT03 Against the Human Hepatoma Cell Line Using a Proteomic Approach. Cell Biochem Biophys 2024:10.1007/s12013-024-01258-0. [PMID: 38578403 DOI: 10.1007/s12013-024-01258-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/06/2024]
Abstract
This study assessed OR3 pigment, derived from Streptomyces coelicolor JUACT03, for its anticancer potential on HepG2 liver cancer cells and its safety on HEK293 normal cells. OR3 induced apoptosis and inhibited HepG2 cell proliferation, confirmed by caspase activation, Sub-G1 phase cell cycle arrest, and reduced colony formation. Proteomic analysis revealed altered expression of proteins associated with ribosomal function, mRNA processing, nuclear transport, proteasome activity, carbohydrate metabolism, chaperone function, histone regulation, and vesicle-mediated transport. Downregulation of proteins in MAPKAP kinase1, EIF2, mTOR, and EIF4 pathways contributed to apoptosis and cell cycle arrest. Changes in c-MYC, FUBP1 target proteins and upregulation of Prohibitin-1 (PHB1) were also noted. Western blot analysis supported alterations in eIF2, mTOR, and RAN pathways, including downregulation of RAB 5, c-MYC, p38, MAPK1, and MAPK3. OR3 exhibited significant anti-angiogenic activity in the in ovo CAM assay. In summary, OR3 demonstrated strong anticancer effects, inducing apoptosis, hindering proliferation, and displaying antiangiogenic properties. These findings highlight OR3's potential as an anticancer drug candidate, warranting further in vivo exploration.
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Affiliation(s)
- Somasekhara Derangula
- Department of Biotechnology, Center for Research in Pure and Applied Sciences, School of Sciences, JAIN (Deemed-to-Be-University), Bangalore, Karnataka, 560078, India
| | - Varalakshmi Kilingar Nadumane
- Department of Biotechnology, Center for Research in Pure and Applied Sciences, School of Sciences, JAIN (Deemed-to-Be-University), Bangalore, Karnataka, 560078, India.
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27
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Boutabba A, Missaoui F, Dlala A, Kamoun H, Ben Salem K, Gabsi A, Rejeb H, Letessier A, Miotto B, Marrakchi R. Circulating miR-16-5p, miR-92a-3p and miR-451a are biomarkers of lung cancer in Tunisian patients. BMC Cancer 2024; 24:417. [PMID: 38575987 PMCID: PMC10996140 DOI: 10.1186/s12885-024-12181-1] [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: 09/09/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Lung cancer is one of the most common type of cancer and, despite significant advances in screening and diagnosis approaches, a large proportion of patients at diagnosis still present advanced stages of the disease with distant metastasis and bad prognosis. Finding and validating biomarkers of lung cancer is therefore essential. Such studies are often conducted on European, American and Asian populations and the relevance of these biomarkers in other populations remains less clear. In that prospect, we investigated the expression level of seven microRNAs, chosen from the medical literature (miR-16-5p, miR-92a-3p, miR-103a-3p, miR-375-3p, miR-451a, miR-520-3p and miR-let-7e-5p), in the blood of Tunisian lung cancer patients, treated or not by chemotherapy, and healthy control individuals. We found that high expression levels of circulating miR-16-5p, miR-92a-3p and miR-451a in the plasma of untreated patients discriminate them from healthy control individuals. In addition, miR-16-5p and miR-451a expression levels are significantly reduced in the plasma of chemotherapy-treated patients compared to untreated patients. Our results confirmed previous work in other populations worldwide and provide further evidence that circulating miR-16-5p, miR-92a-3p and miR-451a potentially regulate key pathways involved in the initiation and progression of cancer.
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Affiliation(s)
- Alya Boutabba
- Laboratory of genetics, immunology, and human pathologies, LR05ES05, Faculty of sciences, University of Tunis El-Manar - Campus Universitaire El-Manar, El-Manar Tunis, 2092, Tunisia
| | - Fadoua Missaoui
- Laboratory of genetics, immunology, and human pathologies, LR05ES05, Faculty of sciences, University of Tunis El-Manar - Campus Universitaire El-Manar, El-Manar Tunis, 2092, Tunisia
| | - Akram Dlala
- Laboratory of genetics, immunology, and human pathologies, LR05ES05, Faculty of sciences, University of Tunis El-Manar - Campus Universitaire El-Manar, El-Manar Tunis, 2092, Tunisia
| | - Hela Kamoun
- Ibn Nafiss Pneumology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
- Faculty of medicine, University Tunis El-Manar, Tunis, Tunisia
| | - Khalil Ben Salem
- Laboratory of genetics, immunology, and human pathologies, LR05ES05, Faculty of sciences, University of Tunis El-Manar - Campus Universitaire El-Manar, El-Manar Tunis, 2092, Tunisia
| | - Amira Gabsi
- Laboratory of genetics, immunology, and human pathologies, LR05ES05, Faculty of sciences, University of Tunis El-Manar - Campus Universitaire El-Manar, El-Manar Tunis, 2092, Tunisia
| | - Hadhemi Rejeb
- Ibn Nafiss Pneumology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
- Faculty of medicine, University Tunis El-Manar, Tunis, Tunisia
| | - Anne Letessier
- Université Paris Cité, INSERM, U1016, CNRS, UMR8104, Institut Cochin, Paris, F-75014, France
- Team "Epigenetics, DNA replication and Cancer", Institut Cochin, Paris, France
| | - Benoit Miotto
- Université Paris Cité, INSERM, U1016, CNRS, UMR8104, Institut Cochin, Paris, F-75014, France.
- Team "Epigenetics, DNA replication and Cancer", Institut Cochin, Paris, France.
| | - Raja Marrakchi
- Laboratory of genetics, immunology, and human pathologies, LR05ES05, Faculty of sciences, University of Tunis El-Manar - Campus Universitaire El-Manar, El-Manar Tunis, 2092, Tunisia
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Rajan A, Sivapiromrat AK, McAdams MJ. Immunotherapy for Thymomas and Thymic Carcinomas: Current Status and Future Directions. Cancers (Basel) 2024; 16:1369. [PMID: 38611047 PMCID: PMC11010813 DOI: 10.3390/cancers16071369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Thymic epithelial tumors are a histologically diverse group of cancers arising from the epithelial compartment of the thymus. These tumors are characterized by a low tumor mutation burden, a lack of actionable genomic changes, and, especially with thymomas, defects in immune tolerance. Surgery is the mainstay of the management of resectable disease, whereas advanced, unresectable tumors are treated with platinum-based chemotherapy. Disease recurrence can occur months to years after frontline treatment. Although several options are available for conventional treatment of recurrent thymic tumors, response rates are generally low, and treatment-related toxicity can affect quality of life. A subset of patients benefit from biologic therapies, but there remains an unmet need for the development of new treatments. Immune checkpoint inhibitors are safe, clinically active, and have contributed to an improvement in survival for patients with a wide variety of cancers. However, the application of these revolutionary treatments for thymic cancers is limited to their use for the management of recurrent thymic carcinoma because of the risk of immune toxicity. In this paper, we review the current uses of immunotherapy for the management of thymic epithelial tumors and highlight potential strategies to improve safety and broaden the application of these treatments for patients with thymic cancers.
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Affiliation(s)
- Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Zheng C, Yao H, Lu L, Li H, Zhou L, He X, Xu X, Xia H, Ding S, Yang Y, Wang X, Wu M, Xue L, Chen S, Peng X, Cheng Z, Wang Y, He G, Fu S, Keller ET, Liu S, Jiang YZ, Deng X. Dysregulated Ribosome Biogenesis Is a Targetable Vulnerability in Triple-Negative Breast Cancer: MRPS27 as a Key Mediator of the Stemness-inhibitory Effect of Lovastatin. Int J Biol Sci 2024; 20:2130-2148. [PMID: 38617541 PMCID: PMC11008279 DOI: 10.7150/ijbs.94058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/16/2024] [Indexed: 04/16/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with limited effective therapeutic options readily available. We have previously demonstrated that lovastatin, an FDA-approved lipid-lowering drug, selectively inhibits the stemness properties of TNBC. However, the intracellular targets of lovastatin in TNBC remain largely unknown. Here, we unexpectedly uncovered ribosome biogenesis as the predominant pathway targeted by lovastatin in TNBC. Lovastatin induced the translocation of ribosome biogenesis-related proteins including nucleophosmin (NPM), nucleolar and coiled-body phosphoprotein 1 (NOLC1), and the ribosomal protein RPL3. Lovastatin also suppressed the transcript levels of rRNAs and increased the nuclear protein level and transcriptional activity of p53, a master mediator of nucleolar stress. A prognostic model generated from 10 ribosome biogenesis-related genes showed outstanding performance in predicting the survival of TNBC patients. Mitochondrial ribosomal protein S27 (MRPS27), the top-ranked risky model gene, was highly expressed and correlated with tumor stage and lymph node involvement in TNBC. Mechanistically, MRPS27 knockdown inhibited the stemness properties and the malignant phenotypes of TNBC. Overexpression of MRPS27 attenuated the stemness-inhibitory effect of lovastatin in TNBC cells. Our findings reveal that dysregulated ribosome biogenesis is a targetable vulnerability and targeting MRPS27 could be a novel therapeutic strategy for TNBC patients.
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Affiliation(s)
- Chanjuan Zheng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Hui Yao
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Lu Lu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Hongqi Li
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Lei Zhou
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Xueyan He
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Xi Xu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Hongzhuo Xia
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Siyu Ding
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Yiyuan Yang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Xinyu Wang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Muyao Wu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Lian Xue
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Sisi Chen
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Xiaojun Peng
- Jingjie PTM BioLab Co. Ltd., Hangzhou Economic and Technological Development Area, Hangzhou, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab Co. Ltd., Hangzhou Economic and Technological Development Area, Hangzhou, China
| | - Yian Wang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Guangchun He
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Shujun Fu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Evan T. Keller
- Department of Urology and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Suling Liu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Yi-zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiyun Deng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
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Fu Q, Luo L, Hong R, Zhou H, Xu X, Feng Y, Huang K, Wan Y, Li Y, Gong J, Le X, Liu X, Wang N, Yuan J, Li F. Radiogenomic analysis of ultrasound phenotypic features coupled to proteomes predicts metastatic risk in primary prostate cancer. BMC Cancer 2024; 24:290. [PMID: 38438956 PMCID: PMC10913270 DOI: 10.1186/s12885-024-12028-9] [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: 10/24/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Primary prostate cancer with metastasis has a poor prognosis, so assessing its risk of metastasis is essential. METHODS This study combined comprehensive ultrasound features with tissue proteomic analysis to obtain biomarkers and practical diagnostic image features that signify prostate cancer metastasis. RESULTS In this study, 17 ultrasound image features of benign prostatic hyperplasia (BPH), primary prostate cancer without metastasis (PPCWOM), and primary prostate cancer with metastasis (PPCWM) were comprehensively analyzed and combined with the corresponding tissue proteome data to perform weighted gene co-expression network analysis (WGCNA), which resulted in two modules highly correlated with the ultrasound phenotype. We screened proteins with temporal expression trends based on the progression of the disease from BPH to PPCWOM and ultimately to PPCWM from two modules and obtained a protein that can promote prostate cancer metastasis. Subsequently, four ultrasound image features significantly associated with the metastatic biomarker HNRNPC (Heterogeneous nuclear ribonucleoprotein C) were identified by analyzing the correlation between the protein and ultrasound image features. The biomarker HNRNPC showed a significant difference in the five-year survival rate of prostate cancer patients (p < 0.0053). On the other hand, we validated the diagnostic efficiency of the four ultrasound image features in clinical data from 112 patients with PPCWOM and 150 patients with PPCWM, obtaining a combined diagnostic AUC of 0.904. In summary, using ultrasound imaging features for predicting whether prostate cancer is metastatic has many applications. CONCLUSION The above study reveals noninvasive ultrasound image biomarkers and their underlying biological significance, which provide a basis for early diagnosis, treatment, and prognosis of primary prostate cancer with metastasis.
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Affiliation(s)
- Qihuan Fu
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Li Luo
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Ruixia Hong
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Hang Zhou
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Xinzhi Xu
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Yujie Feng
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Kaifeng Huang
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Yujie Wan
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Ying Li
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Jiaqi Gong
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Xingyan Le
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Xiu Liu
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Na Wang
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Jiangbei Yuan
- Department of Infection, Zhejiang Provincial People's Hospital, 310014, Hangzhou, China.
| | - Fang Li
- Department of Ultrasound, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC) , Chongqing University Cancer Hospital, 400030, Chongqing, China.
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Wang M, Vulcano S, Xu C, Xie R, Peng W, Wang J, Liu Q, Jia L, Li Z, Li Y. Potentials of ribosomopathy gene as pharmaceutical targets for cancer treatment. J Pharm Anal 2024; 14:308-320. [PMID: 38618250 PMCID: PMC11010632 DOI: 10.1016/j.jpha.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/29/2023] [Accepted: 10/07/2023] [Indexed: 04/16/2024] Open
Abstract
Ribosomopathies encompass a spectrum of disorders arising from impaired ribosome biogenesis and reduced functionality. Mutation or dysexpression of the genes that disturb any finely regulated steps of ribosome biogenesis can result in different types of ribosomopathies in clinic, collectively known as ribosomopathy genes. Emerging data suggest that ribosomopathy patients exhibit a significantly heightened susceptibility to cancer. Abnormal ribosome biogenesis and dysregulation of some ribosomopathy genes have also been found to be intimately associated with cancer development. The correlation between ribosome biogenesis or ribosomopathy and the development of malignancies has been well established. This work aims to review the recent advances in the research of ribosomopathy genes among human cancers and meanwhile, to excavate the potential role of these genes, which have not or rarely been reported in cancer, in the disease development across cancers. We plan to establish a theoretical framework between the ribosomopathy gene and cancer development, to further facilitate the potential of these genes as diagnostic biomarker as well as pharmaceutical targets for cancer treatment.
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Affiliation(s)
- Mengxin Wang
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Stephen Vulcano
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery New York, New York, NY, 10021, USA
| | - Changlu Xu
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Renjian Xie
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Weijie Peng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Jie Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Qiaojun Liu
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Lee Jia
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhi Li
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Yumei Li
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
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Hallal SM, Tűzesi Á, Sida LA, Xian E, Madani D, Muralidharan K, Shivalingam B, Buckland ME, Satgunaseelan L, Alexander KL. Glioblastoma biomarkers in urinary extracellular vesicles reveal the potential for a 'liquid gold' biopsy. Br J Cancer 2024; 130:836-851. [PMID: 38212481 PMCID: PMC10912426 DOI: 10.1038/s41416-023-02548-9] [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: 08/14/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Biomarkers that reflect glioblastoma tumour activity and treatment response are urgently needed to help guide clinical management, particularly for recurrent disease. As the urinary system is a major clearance route of circulating extracellular vesicles (EVs; 30-1000 nm nanoparticles) we explored whether sampling urinary-EVs could serve as a simple and non-invasive liquid biopsy approach for measuring glioblastoma-associated biomarkers. METHODS Fifty urine specimens (15-60 ml) were collected from 24 catheterised glioblastoma patients immediately prior to primary (n = 17) and recurrence (n = 7) surgeries, following gross total resection (n = 9), and from age/gender-matched healthy participants (n = 14). EVs isolated by differential ultracentrifugation were characterised and extracted proteomes were analysed by high-resolution data-independent acquisition liquid chromatography tandem mass spectrometry (DIA-LC-MS/MS). RESULTS Overall, 6857 proteins were confidently identified in urinary-EVs (q-value ≤ 0.01), including 94 EV marker proteins. Glioblastoma-specific proteomic signatures were determined, and putative urinary-EV biomarkers corresponding to tumour burden and recurrence were identified (FC ≥ | 2 | , adjust p-val≤0.05, AUC > 0.9). CONCLUSION In-depth DIA-LC-MS/MS characterisation of urinary-EVs substantiates urine as a viable source of glioblastoma biomarkers. The promising 'liquid gold' biomarker panels described here warrant further investigation.
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Affiliation(s)
- Susannah M Hallal
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Ágota Tűzesi
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Liam A Sida
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Elissa Xian
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Daniel Madani
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Krishna Muralidharan
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Brindha Shivalingam
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Michael E Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Laveniya Satgunaseelan
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Kimberley L Alexander
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia.
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia.
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Zacchini F, Barozzi C, Venturi G, Montanaro L. How snoRNAs can contribute to cancer at multiple levels. NAR Cancer 2024; 6:zcae005. [PMID: 38406265 PMCID: PMC10894041 DOI: 10.1093/narcan/zcae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
snoRNAs are a class of non-coding RNAs known to guide site specifically RNA modifications such as 2'-O-methylation and pseudouridylation. Recent results regarding snoRNA alterations in cancer has been made available and suggest their potential evaluation as diagnostic and prognostic biomarkers. A large part of these data, however, was not consistently confirmed and failed to provide mechanistic insights on the contribution of altered snoRNA expression to the neoplastic process. Here, we aim to critically review the available literature on snoRNA in cancer focusing on the studies elucidating the functional consequences of their deregulation. Beyond the canonical guide function in RNA processing and modification we also considered additional roles in which snoRNA, in various forms and through different modalities, are involved and that have been recently reported.
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Affiliation(s)
- Federico Zacchini
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Chiara Barozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
| | - Giulia Venturi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Lorenzo Montanaro
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
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Kluge V, Kappelmann-Fenzl M, Fischer S, Zimmermann T, Pommer M, Kuphal S, Bosserhoff AK. Alternative Wnt-signaling axis leads to a break of oncogene-induced senescence. Cell Death Dis 2024; 15:166. [PMID: 38388496 PMCID: PMC10883971 DOI: 10.1038/s41419-024-06550-8] [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: 11/23/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Oncogene-induced senescence (OIS) is an important process that suppresses tumor development, but the molecular mechanisms of OIS are still under investigation. It is known that BRAFV600E-mutated melanocytes can overcome OIS and develop melanoma, but the underlying mechanism is largely unknown. Using an established OIS model of primary melanocytes transduced with BRAFV600E, YAP activity was shown to be induced in OIS as well as in melanoma cells compared to that in normal epidermal melanocytes. This led to the assumption that YAP activation itself is not a factor involved in the disruption of OIS. However, its role and interaction partners potentially change. As Wnt molecules are known to be important in melanoma progression, these molecules were the focus of subsequent studies. Interestingly, activation of Wnt signaling using AMBMP resulted in a disruption of OIS in BRAFV600E-transduced melanocytes. Furthermore, depletion of Wnt6, Wnt10b or β-catenin expression in melanoma cells resulted in the induction of senescence. Given that melanoma cells do not exhibit canonical Wnt/β-catenin activity, alternative β-catenin signaling pathways may disrupt OIS. Here, we discovered that β-catenin is an interaction partner of YAP on DNA in melanoma cells. Furthermore, the β-catenin-YAP interaction changed the gene expression pattern from senescence-stabilizing genes to tumor-supportive genes. This switch is caused by transcriptional coactivation via the LEF1/TEAD interaction. The target genes with binding sites for LEF1 and TEAD are involved in rRNA processing and are associated with poor prognosis in melanoma patients. This study revealed that an alternative YAP-Wnt signaling axis is an essential molecular mechanism leading to OIS disruption in melanocytes.
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Affiliation(s)
- Viola Kluge
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Melanie Kappelmann-Fenzl
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Faculty of Computer Science, Deggendorf Institute of Technology, Dieter-Görlitz-Platz 1, 94469, Deggendorf, Germany
| | - Stefan Fischer
- Faculty of Computer Science, Deggendorf Institute of Technology, Dieter-Görlitz-Platz 1, 94469, Deggendorf, Germany
| | - Tom Zimmermann
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Michaela Pommer
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Silke Kuphal
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anja-Katrin Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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Liang C, Zhou J, Wang Y, Sun Y, Zhou J, Shao L, Zhang Z, Yan W, Liu Z, Dong Y. Essential genes analysis reveals small ribosomal subunit protein eS28 may be a prognostic factor and potential vulnerability in osteosarcoma. J Bone Oncol 2024; 44:100517. [PMID: 38204480 PMCID: PMC10776981 DOI: 10.1016/j.jbo.2023.100517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Background Osteosarcoma, the most common primary malignant bone tumor, is currently treated with surgery combined with chemotherapy, but the limited availability of targeted drugs contributes to a poor prognosis. Identifying effective therapeutic targets is crucial for improving the prognosis of osteosarcoma patients. Methods We screened the DepMap database to identify essential genes as potential therapeutic targets for osteosarcoma. Gene Set Enrichment Analysis (GSEA) was employed to elucidate the biological roles of these essential genes. Promising candidates were filtered through univariate and multivariate Cox analyses, as well as Kaplan-Meier survival analyses using the GSE21257-OSA and TARGET-OSA datasets. The functional role of the target gene was assessed through cell experiments. Additionally, an in situ nude mice model was established to observe the gene's function, and RNA sequencing was utilized to explore the underlying molecular mechanism. Results A total of 934 essential genes were identified based on their effects (Chronos) using the DepMap database. These genes were primarily enriched in the ribosome pathway according to GSEA analysis. Among them, 195 genes were associated with the ribosome pathway. Rps28, Rps7, and Rps25 were validated as promising candidates following univariate and multivariate Cox analyses of the TARGET-OSA and GSE21257-OSA datasets. Kaplan-Meier survival analyses indicated Rps28 represented an especially promising target, with high expression correlating with poor prognosis. Knockdown of small ribosomal subunit protein eS28, the protein of Rps28, inhibited proliferation, migration, and invasion in both in vitro and in vivo experiments. Silencing RPS28 affected the MAPK signaling pathway in osteosarcoma. Conclusion In summary, Rps28 has been identified as an essential gene for osteosarcoma cell survival and eS28 may serve as a potential vulnerability in osteosarcoma.
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Affiliation(s)
- Chao Liang
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Juan Zhou
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Yongjie Wang
- Department of Orthopedics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, PR China
| | - Yin Sun
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Jin Zhou
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Lan Shao
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Zhichang Zhang
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Zhiyan Liu
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Yang Dong
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
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Zhang Y, Kong Y, Zhang W, He J, Zhang Z, Cai Y, Zhao Y, Xu Q. METTL3 promotes osteoblast ribosome biogenesis and alleviates periodontitis. Clin Epigenetics 2024; 16:18. [PMID: 38267969 PMCID: PMC10809637 DOI: 10.1186/s13148-024-01628-8] [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: 08/29/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Periodontitis is a highly prevalent oral disease characterized by bacterium-induced periodontal inflammation and alveolar bone destruction. Osteoblast function is impaired in periodontitis with a global proteome change. METTL3 is the pivotal methyltransferase of N6-methyladenosine (m6A) that is recently proved to exert a crucial role in osteoblast differentiation. This study aims to investigate the role of METTL3 in osteoblast ribosome biogenesis in periodontitis progression. RESULTS METTL3 was knocked down in osteoblasts, and the downregulated genes were enriched in ribosome and translation. METTL3 knockdown inhibited ribosome biogenesis and oxidative phosphorylation in LPS-stimulated osteoblasts, whereas METTL3 overexpression facilitated ribosomal and mitochondrial function. Mechanistically, METTL3 mediated osteoblast biological behaviors by activating Wnt/β-catenin/c-Myc signaling. METTL3 depletion enhanced the mRNA expression and stability of Dkk3 and Sostdc1 via YTHDF2. In periodontitis mice, METTL3 inhibitor SAH promoted alveolar bone loss and local inflammatory status, which were partially rescued by Wnt/β-catenin pathway activator CHIR-99021 HCl. CONCLUSIONS METTL3 promoted ribosome biogenesis and oxidative phosphorylation by activating Wnt/β-catenin/c-Myc signaling in LPS-treated osteoblasts and alleviated the inflammatory alveolar bone destruction in periodontitis mice.
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Affiliation(s)
- Yiwen Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou, 510055, China
- Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Yiping Kong
- Changsha Stomatological Hospital, Hunan University of Chinese Medicine, Changsha, 410004, China
| | - Wenjie Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou, 510055, China
| | - Jinlin He
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou, 510055, China
| | - Zhanqi Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou, 510055, China
| | - Yongjie Cai
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou, 510055, China
| | - Yiqing Zhao
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou, 510055, China
| | - Qiong Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Ling Yuan Xi Road, Guangzhou, 510055, China.
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Zang Y, Ran X, Yuan J, Wu H, Wang Y, Li H, Teng H, Sun Z. Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer. Brief Bioinform 2024; 25:bbae023. [PMID: 38343327 PMCID: PMC10859687 DOI: 10.1093/bib/bbae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Hyperactive ribosome biogenesis (RiboSis) fuels unrestricted cell proliferation, whereas genomic hallmarks and therapeutic targets of RiboSis in cancers remain elusive, and efficient approaches to quantify RiboSis activity are still limited. Here, we have established an in silico approach to conveniently score RiboSis activity based on individual transcriptome data. By employing this novel approach and RNA-seq data of 14 645 samples from TCGA/GTEx dataset and 917 294 single-cell expression profiles across 13 cancer types, we observed the elevated activity of RiboSis in malignant cells of various human cancers, and high risk of severe outcomes in patients with high RiboSis activity. Our mining of pan-cancer multi-omics data characterized numerous molecular alterations of RiboSis, and unveiled the predominant somatic alteration in RiboSis genes was copy number variation. A total of 128 RiboSis genes, including EXOSC4, BOP1, RPLP0P6 and UTP23, were identified as potential therapeutic targets. Interestingly, we observed that the activity of RiboSis was associated with TP53 mutations, and hyperactive RiboSis was associated with poor outcomes in lung cancer patients without TP53 mutations, highlighting the importance of considering TP53 mutations during therapy by impairing RiboSis. Moreover, we predicted 23 compounds, including methotrexate and CX-5461, associated with the expression signature of RiboSis genes. The current study generates a comprehensive blueprint of molecular alterations in RiboSis genes across cancers, which provides a valuable resource for RiboSis-based anti-tumor therapy.
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Affiliation(s)
- Yue Zang
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences and Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Xia Ran
- Liangzhu Laboratory, Zhejiang University Medical Center, China
| | - Jie Yuan
- BGI Education Center, University of Chinese Academy of Sciences, China
| | - Hao Wu
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Youya Wang
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - He Li
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhongsheng Sun
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Institute of Genomic Medicine, Wenzhou Medical University, and Beijing Institutes of Life Science, Chinese Academy of Sciences, Hangzhou, China
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Skvortsova L, Abdikerim S, Yergali K, Mit N, Perfilyeva A, Omarbayeva N, Zhunussova A, Kachiyeva Z, Sadykova T, Bekmanov B, Kaidarova D, Djansugurova L, Zhunussova G. Association of Genetic Markers with the Risk of Early-Onset Breast Cancer in Kazakh Women. Genes (Basel) 2024; 15:108. [PMID: 38254997 PMCID: PMC10815330 DOI: 10.3390/genes15010108] [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: 12/11/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due to mutations in the BRCA1/BRCA2 genes, and 90% have a more complex genetic background. This poses a significant challenge to timely cancer detection in young women and highlights the need for research and awareness. Therefore, identifying genetic risk factors for eBC is essential to solving these problems. This study represents an association analysis of 144 eBC cases and 163 control participants to identify genetic markers associated with eBC risks in Kazakh women. We performed a two-stage approach in association analysis to assess genetic predisposition to eBC. First-stage genome-wide association analysis revealed two risk intronic loci in the CHI3L2 gene (p = 5.2 × 10-6) and MGAT5 gene (p = 8.4 × 10-6). Second-stage exonic polymorphisms haplotype analysis showed significant risks for seven haplotypes (p < 9.4 × 10-4). These results point to the importance of studying medium- and low-penetrant genetic markers in their haplotype combinations for a detailed understanding of the role of detected genetic markers in eBC development and prediction.
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Affiliation(s)
- Liliya Skvortsova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kanagat Yergali
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Natalya Mit
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Nazgul Omarbayeva
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Aigul Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Zulfiya Kachiyeva
- Research Institute of Applied and Fundamental Medicine, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan;
| | - Tolkyn Sadykova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Bakhytzhan Bekmanov
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Dilyara Kaidarova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
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Gelfo V, Venturi G, Zacchini F, Montanaro L. Decoding Ribosome Heterogeneity: A New Horizon in Cancer Therapy. Biomedicines 2024; 12:155. [PMID: 38255260 PMCID: PMC10813612 DOI: 10.3390/biomedicines12010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The traditional perception of ribosomes as uniform molecular machines has been revolutionized by recent discoveries, revealing a complex landscape of ribosomal heterogeneity. Opposing the conventional belief in interchangeable ribosomal entities, emerging studies underscore the existence of specialized ribosomes, each possessing unique compositions and functions. Factors such as cellular and tissue specificity, developmental and physiological states, and external stimuli, including circadian rhythms, significantly influence ribosome compositions. For instance, muscle cells and neurons are characterized by distinct ribosomal protein sets and dynamic behaviors, respectively. Furthermore, alternative forms of ribosomal RNA (rRNAs) and their post-transcriptional modifications add another dimension to this heterogeneity. These variations, orchestrated by spatial, temporal, and conditional factors, enable the manifestation of a broad spectrum of specialized ribosomes, each tailored for potentially distinct functions. Such specialization not only impacts mRNA translation and gene expression but also holds significant implications for broader biological contexts, notably in the realm of cancer research. As the understanding of ribosomal diversity deepens, it also paves the way for exploring novel avenues in cellular function and offers a fresh perspective on the molecular intricacies of translation.
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Affiliation(s)
- Valerio Gelfo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Giulia Venturi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Federico Zacchini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
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40
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Hsu CH, Liu CY, Lo KY. Mutations of ribosomal protein genes induce overexpression of catalase in Saccharomyces cerevisiae. FEMS Yeast Res 2024; 24:foae005. [PMID: 38271612 PMCID: PMC10855018 DOI: 10.1093/femsyr/foae005] [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: 07/17/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 01/27/2024] Open
Abstract
Ribosome assembly defects result in ribosomopathies, primarily caused by inadequate protein synthesis and induced oxidative stress. This study aimed to investigate the link between deleting one ribosomal protein gene (RPG) paralog and oxidative stress response. Our results indicated that RPG mutants exhibited higher oxidant sensitivity than the wild type (WT). The concentrations of H2O2 were increased in the RPG mutants. Catalase and superoxide dismutase (SOD) activities were generally higher at the stationary phase, with catalase showing particularly elevated activity in the RPG mutants. While both catalase genes, CTT1 and CTA1, consistently exhibited higher transcription in RPG mutants, Ctt1 primarily contributed to the increased catalase activity. Stress-response transcription factors Msn2, Msn4, and Hog1 played a role in regulating these processes. Previous studies have demonstrated that H2O2 can cleave 25S rRNA via the Fenton reaction, enhancing ribosomes' ability to translate mRNAs associated with oxidative stress-related genes. The cleavage of 25S rRNA was consistently more pronounced, and the translation efficiency of CTT1 and CTA1 mRNAs was altered in RPG mutants. Our results provide evidence that the mutations in RPGs increase H2O2 levels in vivo and elevate catalase expression through both transcriptional and translational controls.
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Affiliation(s)
- Ching-Hsiang Hsu
- Department of Agricultural Chemistry National Taiwan University Agricultural Chemistry Building No. 2, Rm. 233 No. 1, Sec. 4, Roosevelt Rd. Taipei 10617, Taiwan
| | - Ching-Yu Liu
- Department of Agricultural Chemistry National Taiwan University Agricultural Chemistry Building No. 2, Rm. 233 No. 1, Sec. 4, Roosevelt Rd. Taipei 10617, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry National Taiwan University Agricultural Chemistry Building No. 2, Rm. 233 No. 1, Sec. 4, Roosevelt Rd. Taipei 10617, Taiwan
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Sullivan MR, White RP, Dashnamoorthy Ravi, Kanetkar N, Fridman IB, Ekenseair A, Evens AM, Konry T. Characterizing influence of rCHOP treatment on diffuse large B-cell lymphoma microenvironment through in vitro microfluidic spheroid model. Cell Death Dis 2024; 15:18. [PMID: 38195589 PMCID: PMC10776622 DOI: 10.1038/s41419-023-06299-6] [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: 05/25/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
For over two decades, Rituximab and CHOP combination treatment (rCHOP) has remained the standard treatment approach for diffuse large B-cell lymphoma (DLBCL). Despite numerous clinical trials exploring treatment alternatives, few options have shown any promise at further improving patient survival and recovery rates. A wave of new therapeutic approaches have recently been in development with the rise of immunotherapy for cancer, however, the cost of clinical trials is prohibitive of testing all promising approaches. Improved methods of early drug screening are essential for expediting the development of the therapeutic approaches most likely to help patients. Microfluidic devices provide a powerful tool for drug testing with enhanced biological relevance, along with multi-parameter data outputs. Here, we describe a hydrogel spheroid-based microfluidic model for screening lymphoma treatments. We utilized primary patient DLBCL cells in combination with NK cells and rCHOP treatment to determine the biological relevance of this approach. We observed cellular viability in response to treatment, rheological properties, and cell surface marker expression levels correlated well with expected in vivo characteristics. In addition, we explored secretory and transcriptomic changes in response to treatment. Our results showed complex changes in phenotype and transcriptomic response to treatment stimuli, including numerous metabolic and immunogenic changes. These findings support this model as an optimal platform for the comparative screening of novel treatments.
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Affiliation(s)
- Matthew R Sullivan
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Rachel P White
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | | | - Ninad Kanetkar
- Chemical Engineering Department, Northeastern University, Boston, MA, USA
| | - Ilana Berger Fridman
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
- Avram and Stella Goldstein-Goren Department of Biotechnology and Regenerative Medicine and Stem Cell Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Adam Ekenseair
- Chemical Engineering Department, Northeastern University, Boston, MA, USA
| | | | - Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.
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Weissmiller AM, Fesik SW, Tansey WP. WD Repeat Domain 5 Inhibitors for Cancer Therapy: Not What You Think. J Clin Med 2024; 13:274. [PMID: 38202281 PMCID: PMC10779565 DOI: 10.3390/jcm13010274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
WDR5 is a conserved nuclear protein that scaffolds the assembly of epigenetic regulatory complexes and moonlights in functions ranging from recruiting MYC oncoproteins to chromatin to facilitating the integrity of mitosis. It is also a high-value target for anti-cancer therapies, with small molecule WDR5 inhibitors and degraders undergoing extensive preclinical assessment. WDR5 inhibitors were originally conceived as epigenetic modulators, proposed to inhibit cancer cells by reversing oncogenic patterns of histone H3 lysine 4 methylation-a notion that persists to this day. This premise, however, does not withstand contemporary inspection and establishes expectations for the mechanisms and utility of WDR5 inhibitors that can likely never be met. Here, we highlight salient misconceptions regarding WDR5 inhibitors as epigenetic modulators and provide a unified model for their action as a ribosome-directed anti-cancer therapy that helps focus understanding of when and how the tumor-inhibiting properties of these agents can best be understood and exploited.
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Affiliation(s)
- April M. Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 32132, USA;
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - William P. Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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43
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Wang X, Xu J, Li Q, Zhang Y, Lin Z, Zhai X, Wang F, Huang J, Gao Q, Wen J, Li L, Feng Y, Luo H, Li Q, Liu X, Li J, Zhao F, Zhang L, Niu T, Sun C, Zheng Y. RNA-binding protein hnRNPU regulates multiple myeloma resistance to selinexor. Cancer Lett 2024; 580:216486. [PMID: 37984724 DOI: 10.1016/j.canlet.2023.216486] [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: 09/01/2023] [Revised: 10/22/2023] [Accepted: 11/04/2023] [Indexed: 11/22/2023]
Abstract
Multiple myeloma (MM) is an incurable haematological cancer. Selinexor is the first-in-class selective inhibitor of nuclear export (SINE) and was newly approved for the treatment of MM. Until now, very few studies have investigated selinexor resistance in MM. Heterogeneous nuclear ribonucleoprotein U (hnRNPU) is an RNA-binding protein and a component of hnRNP complexes. Here we found that hnRNPU regulates MM sensitivity to selinexor. Cell apoptosis assays were performed to compare selinexor-induced cell death in control knockdown (CTR-KD) and hnRNPU knockdown (hnR-KD) MM cells. HnRNPU knockdown-induced nuclear protein retention was examined by proteomics array. HnRNPU-conferred mRNA translation regulation was evaluated by sucrose gradient assay, RNA electrophoresis mobility shift assay, and RNA pull-down assay. We found that hnR-KD MM cells were more sensitive to selinexor-induced cell death in vitro and in mouse model. MM patients who responded to selinexor had relatively low hnRNPU expression. In brief, hnRNPU comprehensively regulated MM sensitivity to selinexor by affecting the localization of LTV1 and NMD3, and mRNA translation of MDM2 and RAN, which were involved in XPO1-mediated nuclear export of ribosome subunits and tumor suppressors. Our discoveries indicate that hnRNPU might be a possible marker to categorize MM patients for the use of Selinexor.
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Affiliation(s)
- Xin Wang
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Juan Xu
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Qun Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology China, China
| | - Yue Zhang
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Zhimei Lin
- Department of Hematology, West China Hospital, Sichuan University, China; Department of Hematology, The Affiliated Hospital of Chengdu University, China
| | - Xinyu Zhai
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Fangfang Wang
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Jingcao Huang
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Qianwen Gao
- Department of Hematology, West China Hospital, Sichuan University, China; School of Life Science, Sichuan University, China
| | - Jingjing Wen
- Department of Hematology, West China Hospital, Sichuan University, China; Department of Hematology, Mian-yang Central Hospital, China
| | - Linfeng Li
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Yu Feng
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Hongmei Luo
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Qian Li
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Xiang Liu
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Junying Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology China, China
| | - Fei Zhao
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology China, China
| | - Li Zhang
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology China, China.
| | - Yuhuan Zheng
- Department of Hematology, West China Hospital, Sichuan University, China.
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Diamantopoulos MA, Georgoulia KK, Levis P, Kotronopoulos G, Stravodimos K, Kontos CK, Avgeris M, Scorilas A. 28S rRNA-Derived Fragments Represent an Independent Molecular Predictor of Short-Term Relapse in Prostate Cancer. Int J Mol Sci 2023; 25:239. [PMID: 38203408 PMCID: PMC10779029 DOI: 10.3390/ijms25010239] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Prostate cancer (PCa) is a global health concern, being a leading cause of cancer-related mortality among males. Early detection and accurate prognosis are crucial for effective management. This study delves into the diagnostic and prognostic potential of 28S rRNA-derived fragments (rRFs) in PCa. Total RNA extracted from 89 PCa and 53 benign prostate hyperplasia (BPH) tissue specimens. After 3'-end polyadenylation, we performed reverse transcription to create first-strand cDNA. Using an in-house quantitative real-time PCR (qPCR) assay, we quantified 28S rRF levels. Post-treatment biochemical relapse served as the clinical endpoint event for survival analysis, which we validated internally through bootstrap analysis. Our results revealed downregulated 28S rRF levels in PCa compared to BPH patients. Additionally, we observed a significant positive correlation between 28S rRF levels and higher Gleason scores and tumor stages. Furthermore, PCa patients with elevated 28S rRF expression had a significantly higher risk of post-treatment disease relapse independently of clinicopathological data. In conclusion, our study demonstrates, for the first time, the prognostic value of 28S rRF in prostate adenocarcinoma. Elevated 28S rRF levels independently predict short-term PCa relapse and enhance risk stratification. This establishes 28S rRF as a potential novel molecular marker for PCa prognosis.
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Affiliation(s)
- Marios A. Diamantopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Konstantina K. Georgoulia
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Panagiotis Levis
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Georgios Kotronopoulos
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Konstantinos Stravodimos
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Christos K. Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, “P. & A. Kyriakou” Children’s Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
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Priyadarshini N, Venkatarama Puppala N, Jayaprakash JP, Khandelia P, Sharma V, Mohannath G. Downregulation of ribosomal RNA (rRNA) genes in human head and neck squamous cell carcinoma (HNSCC) cells correlates with rDNA promoter hypermethylation. Gene 2023; 888:147793. [PMID: 37696422 DOI: 10.1016/j.gene.2023.147793] [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: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Eukaryotes carry hundreds of ribosomal RNA (rRNA) genes as tandem arrays, which generate rRNA for protein synthesis. Humans carry ∼ 400 rRNA gene copies and their expression is epigenetically regulated. Dysregulation of rRNA synthesis and ribosome biogenesis are characteristic features of cancers. Targeting aberrant rRNA expression for cancer therapy is being explored. Head and neck squamous cell carcinoma (HNSCC) is among the most prevalent cancers globally. Using quantitative PCR and bisulfite sequencing, we show that rRNA genes are downregulated and their promoters are hypermethylated in HNSCC cell lines. These findings may have relevance for prognosis and diagnosis of HNSCC.
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Affiliation(s)
- Neha Priyadarshini
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Navinchandra Venkatarama Puppala
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Jayasree Peroth Jayaprakash
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
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Zhang J, Huang X, Yang S, Huang A, Ren J, Luo X, Feng S, Li P, Li Z, Dong P. Endophytic Bacillus subtilis H17-16 effectively inhibits Phytophthora infestans, the pathogen of potato late blight, and its potential application. PEST MANAGEMENT SCIENCE 2023; 79:5073-5086. [PMID: 37572366 DOI: 10.1002/ps.7717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 08/03/2023] [Accepted: 08/13/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND As a highly prevalent epidemic disease of potato, late blight caused by Phytophthora infestans poses a serious threat to potato yield and quality. At present, chemical fungicides are mainly used to control potato late blight, but long-term overuse of chemical fungicides may lead to environmental pollution and human health threats. Endophytes, natural resources for plant diseases control, can promote plant growth, enhance plant resistance, and secrete antifungal substances. Therefore, there is an urgent need to find some beneficial endophytes to control potato late blight. RESULTS We isolated a strain of Bacillus subtilis H17-16 from potato healthy roots. It can significantly inhibit mycelial growth, sporangia germination and the pathogenicity of Phytophthora infestans, induce the resistance of potato to late blight, and promote potato growth. In addition, H17-16 has the ability to produce protease, volatile compounds (VOCs) and form biofilms. After H17-16 treatment, most of the genes involved in metabolism, virulence and drug resistance of Phytophthora infestans were down-regulated significantly, and the genes related to ribosome biogenesis were mainly up-regulated. Moreover, field and postharvest application of H17-16 can effectively reduce the occurrence of potato late blight, and the combination of H17-16 with chitosan or chemical fungicides had a better effect than single H17-16. CONCLUSION Our results reveal that Bacillus subtilis H17-16 has great potential as a natural fungicide for controlling potato late blight, laying a theoretical basis for its development as a biological control agent. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jiaomei Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Xiaoqing Huang
- School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Shidong Yang
- Shandong Nongdeli Biotechnology Co., Ltd, Jinan, China
| | - Airong Huang
- School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Jie Ren
- School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Xunguang Luo
- School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Shun Feng
- School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Peihua Li
- College of Agronomy, Xichang University, Xichang, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, Chongqing, China
| | - Pan Dong
- School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
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Dong L, Han X, Yu P, Zhang W, Wang C, Sun Q, Song F, Zhang H, Zheng G, Mao N, Song X. CT Radiomics-Based Nomogram for Predicting the Lateral Neck Lymph Node Metastasis in Papillary Thyroid Carcinoma: A Prospective Multicenter Study. Acad Radiol 2023; 30:3032-3046. [PMID: 37210266 DOI: 10.1016/j.acra.2023.03.039] [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: 01/16/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/22/2023]
Abstract
RATIONALE AND OBJECTIVES This study is based on multicenter cohorts and aims to utilize computed tomography (CT) images to construct a radiomics nomogram for predicting the lateral neck lymph node (LNLN) metastasis in the papillary thyroid carcinoma (PTC) and further explore the biological basis under its prediction. MATERIALS AND METHODS In the multicenter study, 1213 lymph nodes from 409 patients with PTC who underwent CT examinations and received open surgery and lateral neck dissection were included. A prospective test cohort was used in validating the model. Radiomics features were extracted from the CT images of each patient's LNLNs. Selectkbest, maximum relevance and minimum redundancy and the least absolute shrinkage and selection operator (LASSO) algorithm were used in reducing the dimensionality of radiomics features in the training cohort. Then, a radiomics signature (Rad-score) was calculated as the sum of each feature multiplied by the nonzero coefficient from LASSO. A nomogram was generated using the clinical risk factors of the patients and Rad-score. The nomograms' performance was analyzed in terms of accuracy, sensitivity, specificity, confusion matrix, receiver operating characteristic curves, and areas under the receiver operating characteristic curve (AUCs). The clinical usefulness of the nomogram was evaluated by decision curve analysis. Moreover, three radiologists with different working experiences and nomogram were compared to one another. Whole transcriptomics sequencing was performed in 14 tumor samples; the correlation of biological functions and high and low LNLN samples predicted by the nomogram was further investigated. RESULTS A total of 29 radiomics features were used in constructing the Rad-score. Rad-score and clinical risk factors (age, tumor diameter, location and number of suspected tumors) compose the nomogram. The nomogram exhibited good discrimination performance of the nomogram for predicting LNLN metastasis in the training cohort (AUC, 0.866), internal test cohort (0.845), external test cohort (0.725), and prospective test cohort (0.808) and showed diagnostic capability comparable to senior radiologists, significantly outperforming junior radiologists (p < 0.05). Functional enrichment analysis suggested that the nomogram can reflect the ribosome-related structures of cytoplasmic translation in patients with PTC. CONCLUSION Our radiomics nomogram provides a noninvasive method that incorporates radiomics features and clinical risk factors for predicting LNLN metastasis in patients with PTC.
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Affiliation(s)
- Luchao Dong
- Second Clinical Medicine College, Binzhou Medical University, Yantai, Shandong 264003, People's Republic of China (L.D., F.S.); Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.)
| | - Xiao Han
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.)
| | - Pengyi Yu
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.)
| | - Wenbin Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.)
| | - Cai Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.); School of Clinical Medicine, Weifang Medical University, Weifang, Shandong 261042, People's Republic of China (C.W.)
| | - Qi Sun
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.)
| | - Fei Song
- Second Clinical Medicine College, Binzhou Medical University, Yantai, Shandong 264003, People's Republic of China (L.D., F.S.); Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.)
| | - Haicheng Zhang
- Big Data and Artificial Intelligence Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (H.Z., N.M., X.S.); Department of Radiology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (H.Z., N.M.)
| | - Guibin Zheng
- Department of Thyroid Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (G.Z.)
| | - Ning Mao
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.); Big Data and Artificial Intelligence Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (H.Z., N.M., X.S.); Department of Radiology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (H.Z., N.M.)
| | - Xicheng Song
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., X.S.); Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong 264000, People's Republic of China (L.D., X.H., P.Y., W.Z., C.W., Q.S., F.S., N.M., X.S.); Big Data and Artificial Intelligence Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong 264000, People's Republic of China (H.Z., N.M., X.S.).
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Böğürcü-Seidel N, Ritschel N, Acker T, Németh A. Beyond ribosome biogenesis: noncoding nucleolar RNAs in physiology and tumor biology. Nucleus 2023; 14:2274655. [PMID: 37906621 PMCID: PMC10730139 DOI: 10.1080/19491034.2023.2274655] [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: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The nucleolus, the largest subcompartment of the nucleus, stands out from the nucleoplasm due to its exceptionally high local RNA and low DNA concentrations. Within this central hub of nuclear RNA metabolism, ribosome biogenesis is the most prominent ribonucleoprotein (RNP) biogenesis process, critically determining the structure and function of the nucleolus. However, recent studies have shed light on other roles of the nucleolus, exploring the interplay with various noncoding RNAs that are not directly involved in ribosome synthesis. This review focuses on this intriguing topic and summarizes the techniques to study and the latest findings on nucleolar long noncoding RNAs (lncRNAs) as well as microRNAs (miRNAs) in the context of nucleolus biology beyond ribosome biogenesis. We particularly focus on the multifaceted roles of the nucleolus and noncoding RNAs in physiology and tumor biology.
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Affiliation(s)
| | - Nadja Ritschel
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Attila Németh
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
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Bowley TY, Merkley SD, Lagutina IV, Ortiz MC, Lee M, Tawfik B, Marchetti D. Targeting Translation and the Cell Cycle Inversely Affects CTC Metabolism but Not Metastasis. Cancers (Basel) 2023; 15:5263. [PMID: 37958436 PMCID: PMC10650766 DOI: 10.3390/cancers15215263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Melanoma brain metastasis (MBM) is significantly associated with poor prognosis and is diagnosed in 80% of patients at autopsy. Circulating tumor cells (CTCs) are "seeds" of metastasis and the smallest functional units of cancer. Our multilevel approach has previously identified a CTC RPL/RPS gene signature directly linked to MBM onset. We hypothesized that targeting ribogenesis prevents MBM/metastasis in CTC-derived xenografts. We treated parallel cohorts of MBM mice with FDA-approved protein translation inhibitor omacetaxine with or without CDK4/CDK6 inhibitor palbociclib, and monitored metastatic development and cell proliferation. Necropsies and IVIS imaging showed decreased MBM/extracranial metastasis in drug-treated mice, and RNA-Seq on mouse-blood-derived CTCs revealed downregulation of four RPL/RPS genes. However, mitochondrial stress tests and RT-qPCR showed that omacetaxine and palbociclib inversely affected glycolytic metabolism, demonstrating that dual targeting of cell translation/proliferation is critical to suppress plasticity in metastasis-competent CTCs. Equally relevant, we provide the first-ever functional metabolic characterization of patient-derived circulating neoplastic cells/CTCs.
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Affiliation(s)
- Tetiana Y. Bowley
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (T.Y.B.); (S.D.M.); (M.C.O.); (M.L.)
| | - Seth D. Merkley
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (T.Y.B.); (S.D.M.); (M.C.O.); (M.L.)
| | - Irina V. Lagutina
- Animal Models Shared Resource, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87120, USA;
| | - Mireya C. Ortiz
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (T.Y.B.); (S.D.M.); (M.C.O.); (M.L.)
| | - Margaret Lee
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (T.Y.B.); (S.D.M.); (M.C.O.); (M.L.)
| | - Bernard Tawfik
- Division of Hematology and Oncology, Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87120, USA;
| | - Dario Marchetti
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (T.Y.B.); (S.D.M.); (M.C.O.); (M.L.)
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50
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Jia W, Yuan J, Li S, Cheng B. The role of dysregulated mRNA translation machinery in cancer pathogenesis and therapeutic value of ribosome-inactivating proteins. Biochim Biophys Acta Rev Cancer 2023; 1878:189018. [PMID: 37944831 DOI: 10.1016/j.bbcan.2023.189018] [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: 09/14/2023] [Revised: 10/17/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Dysregulated protein synthesis is a hallmark of tumors. mRNA translation reprogramming contributes to tumorigenesis, which is fueled by abnormalities in ribosome formation, tRNA abundance and modification, and translation factors. Not only malignant cells but also stromal cells within tumor microenvironment can undergo transformation toward tumorigenic phenotypes during translational reprogramming. Ribosome-inactivating proteins (RIPs) have garnered interests for their ability to selectively inhibit protein synthesis and suppress tumor growth. This review summarizes the role of dysregulated translation machinery in tumor development and explores the potential of RIPs in cancer treatment.
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Affiliation(s)
- Wentao Jia
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China
| | - Jiaying Yuan
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Shu Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, China.
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China.
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