1
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Kerry J, Specker EJ, Mizzoni M, Brumwell A, Fell L, Goodbrand J, Rosen MN, Uniacke J. Autophagy-dependent alternative splicing of ribosomal protein S24 produces a more stable isoform that aids in hypoxic cell survival. FEBS Lett 2024; 598:503-520. [PMID: 38281767 DOI: 10.1002/1873-3468.14804] [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: 11/05/2023] [Revised: 12/08/2023] [Accepted: 12/24/2023] [Indexed: 01/30/2024]
Abstract
Cells remodel splicing and translation machineries to mount specialized gene expression responses to stress. Here, we show that hypoxic human cells in 2D and 3D culture models increase the relative abundance of a longer mRNA variant of ribosomal protein S24 (RPS24L) compared to a shorter mRNA variant (RPS24S) by favoring the inclusion of a 22 bp cassette exon. Mechanistically, RPS24L and RPS24S are induced and repressed, respectively, by distinct pathways in hypoxia: RPS24L is induced in an autophagy-dependent manner, while RPS24S is reduced by mTORC1 repression in a hypoxia-inducible factor-dependent manner. RPS24L produces a more stable protein isoform that aids in hypoxic cell survival and growth, which could be exploited by cancer cells in the tumor microenvironment.
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Affiliation(s)
- Jenna Kerry
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Erin J Specker
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Morgan Mizzoni
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Andrea Brumwell
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Leslie Fell
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Jenna Goodbrand
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Michael N Rosen
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - James Uniacke
- Department of Molecular and Cellular Biology, University of Guelph, Canada
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2
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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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3
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Mou Z, Spencer J, McGrath JS, Harries LW. Comprehensive analysis of alternative splicing across multiple transcriptomic cohorts reveals prognostic signatures in prostate cancer. Hum Genomics 2023; 17:97. [PMID: 37924098 PMCID: PMC10623736 DOI: 10.1186/s40246-023-00545-w] [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: 09/06/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) plays a crucial role in transcriptomic diversity and is a hallmark of cancer that profoundly influences the development and progression of prostate cancer (PCa), a prevalent and potentially life-limiting cancer among men. Accumulating evidence has highlighted the association between AS dysregulation and the onset and progression of PCa. However, a comprehensive and integrative analysis of AS profiles at the event level, utilising data from multiple high-throughput cohorts and evaluating the prognosis of PCa progression, remains lacking and calls for thorough exploration. RESULTS We identified a differentially expressed retained intron event in ZWINT across three distinct cohorts, encompassing an original array-based dataset profiled by us previously and two RNA sequencing (RNA-seq) datasets. Subsequent in-depth analyses of these RNA-seq datasets revealed 141 altered events, of which 21 demonstrated a significant association with patients' biochemical recurrence-free survival (BCRFS). We formulated an AS event-based prognostic signature, capturing six pivotal events in genes CYP4F12, NFATC4, PIGO, CYP3A5, ALS2CL, and FXYD3. This signature effectively differentiated high-risk patients diagnosed with PCa, who experienced shorter BCRFS, from their low-risk counterparts. Notably, the signature's predictive power surpassed traditional clinicopathological markers in forecasting 5-year BCRFS, demonstrating robust performance in both internal and external validation sets. Lastly, we constructed a novel nomogram that integrates patients' Gleason scores with pathological tumour stages, demonstrating improved prognostication of BCRFS. CONCLUSIONS Prediction of clinical progression remains elusive in PCa. This research uncovers novel splicing events associated with BCRFS, augmenting existing prognostic tools, thus potentially refining clinical decision-making.
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Affiliation(s)
- Zhuofan Mou
- Clinical and Biomedical Sciences, Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Barrack Road, Exeter, EX2 5DW, UK
| | - Jack Spencer
- Translational Research Exchange at Exeter, Living Systems Institute, University of Exeter, Exeter, UK
| | - John S McGrath
- Clinical and Biomedical Sciences, Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Barrack Road, Exeter, EX2 5DW, UK
- Royal Devon University Healthcare NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Lorna W Harries
- Clinical and Biomedical Sciences, Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Barrack Road, Exeter, EX2 5DW, UK.
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4
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Schäfer M, Schneider M, Müller T, Franz N, Braspenning-Wesch I, Stephan S, Schmidt G, Krijgsveld J, Helm D, Rösl F, Hasche D. Spatial tissue proteomics reveals distinct landscapes of heterogeneity in cutaneous papillomavirus-induced keratinocyte carcinomas. J Med Virol 2023; 95:e28850. [PMID: 37322807 DOI: 10.1002/jmv.28850] [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: 03/20/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
Infection with certain cutaneous human papillomaviruses (HPV), in conjunction with chronic ultraviolet (UV) exposure, are the major cofactors of non-melanoma skin cancer (NMSC), the most frequent cancer type worldwide. Cutaneous squamous cell carcinomas (SCCs) as well as tumors in general represent three-dimensional entities determined by both temporal and spatial constraints. Whole tissue proteomics is a straightforward approach to understand tumorigenesis in better detail, but studies focusing on different progression states toward a dedifferentiated SCC phenotype on a spatial level are rare. Here, we applied an innovative proteomic workflow on formalin-fixed, paraffin-embedded (FFPE) epithelial tumors derived from the preclinical animal model Mastomys coucha. This rodent is naturally infected with its genuine cutaneous papillomavirus and closely mimics skin carcinogenesis in the context of cutaneous HPV infections in humans. We deciphered cellular networks by comparing diverse epithelial tissues with respect to their differentiation level and infection status. Our study reveals novel regulatory proteins and pathways associated with virus-induced tumor initiation and progression of SCCs. This approach provides the basis to better comprehend the multistep process of skin carcinogenesis.
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Affiliation(s)
- Miriam Schäfer
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Torsten Müller
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Natascha Franz
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilona Braspenning-Wesch
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja Stephan
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriele Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hasche
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
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5
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Opposite changes in the expression of clathrin and caveolin-1 in normal and cancerous human prostate tissue: putative clathrin-mediated recycling of EGFR. Histochem Cell Biol 2023:10.1007/s00418-023-02183-8. [PMID: 36869937 DOI: 10.1007/s00418-023-02183-8] [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: 02/17/2023] [Indexed: 03/05/2023]
Abstract
Endocytosis, an important macromolecule uptake process in cells, is known to be dysregulated in cancer. Clathrin and caveolin-1 proteins play a major role in receptor-mediated endocytosis. We have used a quantitative, unbiased and semi-automated method to measure in situ protein expression of clathrin and caveolin-1 in cancerous and paired normal (cancer adjacent, non-cancerous) human prostate tissue. There was a significant (p < 0.0001) increase in the expression of clathrin in prostate cancer samples (N = 29, n = 91) compared to normal tissue (N = 29, n = 67) (N = number of patients, n = number of cores in tissue arrays). Conversely, there was a significant (p < 0.0001) decrease in expression of caveolin-1 in prostate cancer tissue compared to normal prostate tissue. The opposite change in expression of the two proteins was highly correlated to increasing cancer aggressiveness. There was also a concurrent increase in the expression of epidermal growth factor receptor (EGFR), a key receptor in carcinogenesis, with clathrin in prostate cancer tissue, indicating recycling of EGFR through clathrin-mediated endocytosis (CME). These results indicate that in prostate cancer, caveolin-1-mediated endocytosis (CavME) may be acting as a brake and increase in CME may facilitate tumorigenicity and aggressiveness of prostate cancer through recycling of EGFR. Changes in the expression of these proteins can also potentially be used as a biomarker for prostate cancer to aid in diagnosis and prognosis and clinical decision-making.
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6
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Li H, Gao L, Kang X, Wang X, Yu Y, Zhang Y, Chen H. RPS24 Is Associated with a Poor Prognosis and Immune Infiltration in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:ijms24010806. [PMID: 36614249 PMCID: PMC9820840 DOI: 10.3390/ijms24010806] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver malignancy, with increased mortality and morbidity. Accumulating evidence suggested that 40S ribosomal protein S24 (RPS24) is related to malignant outcomes and progression. However, the role of RPS24 remains unclear in HCC. The mRNA and protein expression pattern of RPS24 in HCC was explored and confirmed based on the bioinformatics analysis and histological examination. The correlation between RPS24 expression and clinicopathological features, diagnostic value, prognosis, methylation status, and survival were evaluated. Then, we divided the HCC cohort into two groups based on the expression of RPS24, and performed the functional enrichment and immune cells infiltration analysis of RPS24. Furthermore, in vivo and in vitro experiments were performed to investigate the effect of RPS24 on HCC cells. RPS24 was observed to be elevated in HCC samples. RPS24 overexpression or RPS24 promoter methylation contributed to an unfavorable prognosis for HCC patients. The genes in the high RPS24 expression group were mainly enriched in DNA replication, cell cycle E2F targets, and the G2M checkpoint pathway. Moreover, the expression level of RPS24 was significantly related to immune infiltration and immunotherapy response. Our experiments also demonstrated that RPS24 knockdown suppressed the growth of HCC cells and tumor proliferation of the xenograft model. Therefore, RPS24 can be a potential adverse biomarker of HCC prognosis acting through facilitating cell proliferation and the formation of an immunosuppressive microenvironment in HCC. Targeting RPS24 may offer a promising therapeutic option for HCC management.
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Affiliation(s)
- Haiyuan Li
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Lei Gao
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Xiaojuan Kang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Xueyan Wang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Yang Yu
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Yaqing Zhang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Hao Chen
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
- Department of Tumor Surgery, Lanzhou University Second Hospital, Lanzhou 730030, China
- Correspondence:
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7
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Ribosome-Directed Therapies in Cancer. Biomedicines 2022; 10:biomedicines10092088. [PMID: 36140189 PMCID: PMC9495564 DOI: 10.3390/biomedicines10092088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 12/29/2022] Open
Abstract
The human ribosomes are the cellular machines that participate in protein synthesis, which is deeply affected during cancer transformation by different oncoproteins and is shown to provide cancer cell proliferation and therefore biomass. Cancer diseases are associated with an increase in ribosome biogenesis and mutation of ribosomal proteins. The ribosome represents an attractive anti-cancer therapy target and several strategies are used to identify specific drugs. Here we review the role of different drugs that may decrease ribosome biogenesis and cancer cell proliferation.
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8
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A novel immune-related RNA-binding proteins signature to predict survival and therapeutic responses in prostate cancer. Clin Transl Oncol 2022; 24:1381-1394. [PMID: 35143037 PMCID: PMC8830953 DOI: 10.1007/s12094-022-02782-2] [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: 11/14/2021] [Accepted: 01/17/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The present study aims to identify immune-related RBPs signature to predict prognosis and therapy response in prostate cancer. METHODS Differentially expressed RBPs were compared and visualized using R packages. Immune-related RBPs were selected by Pearson correlation analysis. The prognostic immune-related RBPs were identified using the Kaplan-Meier method and LASSO regression. A multivariable Cox regression model was used to construct immune-related RBPs signature. RESULTS We constructed a prognostic predictive risk model of prostate cancer containing ten immune-related RBP genes. We found that high-risk prostate cancer patients presented poorer prognosis, higher tumor immune cell infiltration, higher rates of genomic alterations, and were more sensitive to targeted and immunotherapy than the low-risk group. CONCLUSIONS The immune-related RBPs' signature is an independent prognostic marker that could help screen patients with advanced prostate cancer who are better suited for targeted and immunotherapy.
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9
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Downregulated long intergenic non-coding RNA 00,174 represses malignant biological behaviors of lung cancer cells by regulating microRNA-584-3p/ribosomal protein S24 axis. Funct Integr Genomics 2022; 22:643-653. [PMID: 35451652 DOI: 10.1007/s10142-022-00855-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
Abstract
The detailed regulatory mechanism of LINC00174 in lung cancer (LC) development remains largely unknown. This research was designed to probe into the impacts of LINC00174 in LC cells through modulating the microRNA (miR)-584-3p/ribosomal protein S24 (RPS24) axis. LINC00174, miR-584-3p, and RPS24 expression levels in LC cells and tissues were examined. The constructs altering LINC00174, miR-584-3p, or RPS24 expression were transfected into LC cells to examine the malignant phenotypes of LC cells. The relations among LINC00174, miR-584-3p, and RPS24 were validated. LINC00174 and RPS24 were high-expressed while miR-584-3p was low-expressed in LC. Downregulated LINC00174 or RPS24 or upregulated miR-584-3p inhibited the malignant biological behaviors of LC cells. The silenced miR-584-3p could reverse the repressive effects of reduced LINC00174 on the development of LC cells; while RPS24 overexpression inverted the repressive effects of miR-584-3p elevation on LC cells. Mechanically, LINC00174 bound to miR-584-3p that targeted RPS24. Repressed LINC00174 can relieve the malignant phenotypes of LC cells via modulating the miR-584-3p/RPS24 axis.
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10
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Zhou J, Li Q, Wu H, Tsai SH, Yeh YT. Effective Inhibition of Mitochondrial Metabolism by Cryptotanshinone in MDA-MB231 cells: A Proteomic Analysis. CURR PROTEOMICS 2022. [DOI: 10.2174/1570164618666210208144542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background :
Triple-negative breast cancer (TNBC) is a subtype of invasive cancer in breast with the symptoms of unfavourable prognosis and limited targeted treatment options. Evidence of changes in the metabolic status of TNBC, characterised by increased glycolysis, mitochondrial oxidative phosphorylation, as well as production and utilization of tricarboxylic acid cycle intermediates.
Objective:
Investigate the proteins altered in cryptotanshinone treated MDA-MB-231 cells and explore the key pathways and specific molecular markers involved in cryptotanshinone treatment.
Method:
We use unlabeled quantitative proteomics to gain insight into the anticancer mechanism of cryptotanshinone on MDA-MB231 triple negative breast cancer cells. And flow cytometry was used to detect apoptosis and changes in cell mitochondrial membrane potential.
Results:
We show that inhibiting the expression of electron transport chain complex proteins, also inhibits mitochondrial oxidative phosphorylation. Additionally, down-regulation of the ribosime biogenesis pathway was found to inhibit cell metabolism.
Conclusion:
In summary, results show that cryptotanshinone can trigger rapid and irreversible apoptosis in MDA-MB-231 cells through effectively inhibiting cell metabolism.
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Affiliation(s)
- Jiefeng Zhou
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University,-
Taipei City, Taiwan
- Ningbo AJcore Biosciences Inc., 3rd Floor, Building One, East District, Ningbo New Materials
Innovation Center, High-Tech Zone, Ningbo, China
| | - Qingcao Li
- Laboratory Department,Ningbo Medical Center Li Huili Eastern Hospital,High-Tech Zone, Bingbo, China
| | - Haoran Wu
- Ningbo AJcore Biosciences Inc., 3rd Floor, Building One, East District, Ningbo New Materials
Innovation Center, High-Tech Zone, Ningbo, China
| | - Shin-Han Tsai
- Department of Emergency Medicine, Shuang Ho Hospital, Taipei Medical
University, Institute of Injury Prevention and Control, Taipei Medical University, Taipei City, Taiwan
| | - Yu-Ting Yeh
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University,-
Taipei City, Taiwan
- Information Technology Office, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
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11
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Deregulation of ribosomal proteins in human cancers. Biosci Rep 2021; 41:230380. [PMID: 34873618 PMCID: PMC8685657 DOI: 10.1042/bsr20211577] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ribosome, the site for protein synthesis, is composed of ribosomal RNAs (rRNAs) and ribosomal proteins (RPs). The latter have been shown to have many ribosomal and extraribosomal functions. RPs are implicated in a variety of pathological processes, especially tumorigenesis and cell transformation. In this review, we will focus on the recent advances that shed light on the effects of RPs deregulation in different types of cancer and their roles in regulating the tumor cell fate.
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12
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Wang Q, Cai Y, Fu X, Chen L. High RPS27A Expression Predicts Poor Prognosis in Patients With HPV Type 16 Cervical Cancer. Front Oncol 2021; 11:752974. [PMID: 34796111 PMCID: PMC8593198 DOI: 10.3389/fonc.2021.752974] [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: 08/04/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022] Open
Abstract
In recent years, the incidence and the mortality rate of cervical cancer have been gradually increasing, becoming one of the major causes of cancer-related death in women. In particular, patients with advanced and recurrent cervical cancers present a very poor prognosis. In addition, the vast majority of cervical cancer cases are caused by human papillomavirus (HPV) infection, of which HPV16 infection is the main cause and squamous cell carcinoma is the main presenting type. In this study, we performed screening of differentially expressed genes (DEGs) based on The Cancer Genome Atlas (TCGA) database and GSE6791, constructed a protein–protein interaction (PPI) network to screen 34 hub genes, filtered to the remaining 10 genes using the CytoHubba plug-in, and used survival analysis to determine that RPS27A was most associated with the prognosis of cervical cancer patients and has prognostic and predictive value for cervical cancer. The most significant biological functions and pathways of RPS27A enrichment were subsequently investigated with gene set enrichment analysis (GSEA), and integration of TCGA and GTEx database analyses revealed that RPS27A was significantly expressed in most cancer types. In this study, our analysis revealed that RPS27A can be used as a prognostic biomarker for HPV16 cervical cancer and has biological significance for the growth of cervical cancer cells.
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Affiliation(s)
- Qiming Wang
- Department of Gynecology, Ningbo Women & Children's Hospital, Ningbo, China
| | - Yan Cai
- Department of Gynecology, Ningbo Women & Children's Hospital, Ningbo, China
| | - Xuewen Fu
- School of Medicine, Ningbo University, Ningbo, China
| | - Liang Chen
- Department of Gynecology, Ningbo Women & Children's Hospital, Ningbo, China
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13
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Arthurs C, Ahmed A. QuArray: an application for tissue array whole slide image export and signal analysis. Bioinformatics 2021; 37:3082-3083. [PMID: 33690813 DOI: 10.1093/bioinformatics/btab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/04/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Tissue array (TA) staining, combined with whole slide imaging (WSI) methods facilitate discovery of biomarkers for diagnosis, prognostication and disease stratification. A key impediment in TA WSI analysis is handling missing tissue and artefacts when identifying tissue cores before quantitative, standardized downstream analysis. There is a need for an open access, user friendly, integrated analysis of the WSI generated using TAs in clinical and scientific research laboratories. RESULTS We have developed QuArray (Quantitative Array Application) for image export and signal analysis of TAs using WSI. The application input is a WSI and a corresponding TA configuration file. QuArray identifies and exports core images and analyses chromogen staining in a simple graphical user interface. Output data is saved to file for further analysis including indexed data. AVAILABILITYAND IMPLEMENTATION Available for download from https://github.com/c-arthurs/QuArray under an MIT licence. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Callum Arthurs
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, SE1 9RT London, UK
| | - Aamir Ahmed
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, SE1 9RT London, UK
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14
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Lari A, Pourbadie HG, Sharifi-Zarchi A, Akhtari M, Samimi LN, Jamshidi A, Mahmoudi M. Dysregulation of ribosome-related genes in ankylosing spondylitis: a systems biology approach and experimental method. BMC Musculoskelet Disord 2021; 22:789. [PMID: 34521416 PMCID: PMC8442383 DOI: 10.1186/s12891-021-04662-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 08/31/2021] [Indexed: 11/10/2022] Open
Abstract
Background Ankylosing spondylitis (AS) is an autoimmune rheumatic disease. Few candidate gene associations have been reported for AS and the current understanding of its pathogenesis remains still poor. Thus, the exact mechanism of AS is needed to urgently be disclosed. The purpose of this study was to identify candidate genes involving in AS disease. Methods and results GSE25101 publicly available microarray and GSE117769 RNA-seq datasets of AS patients were obtained for bioinformatics analyses. Gene set enrichment analysis showed that in the microarray dataset, the ribosome pathway was significantly up-regulated in AS compared with controls. Furthermore, some ribosomal components demonstrated overexpression in patients in the RNA-seq dataset. To confirm the findings, 20 AS patients and 20 matching controls were selected from the Rheumatology Research Center clinic, Shariati Hospital. PBMCs were separated from whole blood and RNA contents were extracted. Following the results of datasets analysis, the expression level of rRNA5.8S pseudogene, rRNA18S pseudogene, RPL23, RPL7, and RPL17 genes were measured through real-time PCR. Our findings showed dysregulation of rRNA5.8S and rRNA18S pseudogenes, and also the RPL17 gene in patients. Conclusion Considering that genes involved in ribosome biogenesis contributed to some AS-associated biological processes as well as diseases that have comorbidities with AS, our results might advance our understanding of the pathological mechanisms of ankylosing spondylitis. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-021-04662-2.
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Affiliation(s)
- Arezou Lari
- Systems Biomedicine Unit, Pasteur Institute of Iran, Tehran, Iran.,Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran
| | | | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Maryam Akhtari
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran.,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Nejatbakhsh Samimi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, PO-BOX: 1411713137, Kargar Ave, Tehran, Iran. .,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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15
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Integrated Analysis of the Roles of RNA Binding Proteins and Their Prognostic Value in Clear Cell Renal Cell Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5568411. [PMID: 34306592 PMCID: PMC8263288 DOI: 10.1155/2021/5568411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022]
Abstract
Methods We downloaded the RNA sequencing data of ccRCC from the Cancer Genome Atlas (TCGA) database and identified differently expressed RBPs in different tissues. In this study, we used bioinformatics to analyze the expression and prognostic value of RBPs; then, we performed functional analysis and constructed a protein interaction network for them. We also screened out some RBPs related to the prognosis of ccRCC. Finally, based on the identified RBPs, we constructed a prognostic model that can predict patients' risk of illness and survival time. Also, the data in the HPA database were used for verification. Results In our experiment, we obtained 539 ccRCC samples and 72 normal controls. In the subsequent analysis, 87 upregulated RBPs and 38 downregulated RBPs were obtained. In addition, 9 genes related to the prognosis of patients were selected, namely, RPL36A, THOC6, RNASE2, NOVA2, TLR3, PPARGC1A, DARS, LARS2, and U2AF1L4. We further constructed a prognostic model based on these genes and plotted the ROC curve. This ROC curve performed well in judgement and evaluation. A nomogram that can judge the patient's life span is also made. Conclusion In conclusion, we have identified differentially expressed RBPs in ccRCC and carried out a series of in-depth research studies, the results of which may provide ideas for the diagnosis of ccRCC and the research of new targeted drugs.
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16
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Sim EUH, Lee CW, Narayanan K. The roles of ribosomal proteins in nasopharyngeal cancer: culprits, sentinels or both. Biomark Res 2021; 9:51. [PMID: 34193301 PMCID: PMC8247250 DOI: 10.1186/s40364-021-00311-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/20/2021] [Indexed: 12/15/2022] Open
Abstract
Ribosomal protein genes encode products that are essential for cellular protein biosynthesis and are major components of ribosomes. Canonically, they are involved in the complex system of ribosome biogenesis pivotal to the catalysis of protein translation. Amid this tightly organised process, some ribosomal proteins have unique spatial and temporal physiological activity giving rise to their extra-ribosomal functions. Many of these extra-ribosomal roles pertain to cellular growth and differentiation, thus implicating the involvement of some ribosomal proteins in organogenesis. Consequently, dysregulated functions of these ribosomal proteins could be linked to oncogenesis or neoplastic transformation of human cells. Their suspected roles in carcinogenesis have been reported but not specifically explained for malignancy of the nasopharynx. This is despite the fact that literature since one and half decade ago have documented the association of ribosomal proteins to nasopharyngeal cancer. In this review, we explain the association and contribution of dysregulated expression among a subset of ribosomal proteins to nasopharyngeal oncogenesis. The relationship of these ribosomal proteins with the cancer are explained. We provide information to indicate that the dysfunctional extra-ribosomal activities of specific ribosomal proteins are tightly involved with the molecular pathogenesis of nasopharyngeal cancer albeit mechanisms yet to be precisely defined. The complete knowledge of this will impact future applications in the effective management of nasopharyngeal cancer.
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Affiliation(s)
- Edmund Ui-Hang Sim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Choon-Weng Lee
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kumaran Narayanan
- School of Science, Monash University, 46150, Bandar Sunway, Selangor, Malaysia.,Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY, 10029, USA
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17
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Deng Y, Zhao H, Ye L, Hu Z, Fang K, Wang J. Correlations Between the Characteristics of Alternative Splicing Events, Prognosis, and the Immune Microenvironment in Breast Cancer. Front Genet 2021; 12:686298. [PMID: 34194482 PMCID: PMC8236959 DOI: 10.3389/fgene.2021.686298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022] Open
Abstract
Objective Alternative splicing (AS) is the mechanism by which a few genes encode numerous proteins, and it redefines the concept of gene expression regulation. Recent studies showed that dysregulation of AS was an important cause of tumorigenesis and microenvironment formation. Therefore, we performed a systematic analysis to examine the role of AS in breast cancer (Breast Cancer, BrCa) progression. Methods The present study included 993 BrCa patients from The Cancer Genome Atlas (TCGA) database in the genome-wide analysis of AS events. We used differential and prognostic analyses and found differentially expressed alternative splicing (DEAS) events and independent prognostic factors related to patients' overall survival (OS) and disease-free survival (DFS). We divided the patients into two groups based on these AS events and analyzed their clinical features, molecular subtyping and immune characteristics. We also constructed a splicing factor (SF) regulation network for key AS events and verified the existence of AS events in tissue samples using real-time quantitative PCR. Results A total of 678 AS events were identified as differentially expressed, of which 13 and 10 AS events were independent prognostic factors of patients' OS and DFS, respectively. Unsupervised clustering analysis based on these prognostic factors indicated that the Cluster 1 group had a better prognosis and more immune cell infiltration. SFs were significantly related to the expression of AS events, and AA-RPS21 was significantly upregulated in tumors. Conclusion Alternative splicing expands the mechanism of breast cancer progression from a new perspective. Notably, alternative splicing may affect the patient's prognosis by affecting the infiltration of immune cells. Our research provides important guidance for subsequent studies of AS in breast cancer.
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Affiliation(s)
- Youyuan Deng
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
| | - Hongjun Zhao
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
| | - Lifen Ye
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
| | - Zhiya Hu
- Department of Pharmacy, Third Hospital of Changsha, Changsha, China
| | - Kun Fang
- Department of Surgery, Yinchuan Maternal and Child Health Hospital, Yinchuan, China
| | - Jianguo Wang
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
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18
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Furlan T, Kirchmair A, Sampson N, Puhr M, Gruber M, Trajanoski Z, Santer FR, Parson W, Handle F, Culig Z. MYC-Mediated Ribosomal Gene Expression Sensitizes Enzalutamide-resistant Prostate Cancer Cells to EP300/CREBBP Inhibitors. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:1094-1107. [PMID: 33705753 DOI: 10.1016/j.ajpath.2021.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/22/2022]
Abstract
Patients with advanced prostate cancer are frequently treated with the antiandrogen enzalutamide. However, resistance eventually develops in virtually all patients, and various mechanisms have been associated with this process. The histone acetyltransferases EP300 and CREBBP are involved in regulation of cellular events in advanced prostate cancer. This study investigated the role of EP300/CREBBP inhibitors in enzalutamide-resistant prostate cancer. EP300/CREBBP inhibitors led to the same inhibition of androgen receptor activity in enzalutamide-resistant and -sensitive cells. However, enzalutamide-resistant cells were more sensitive to these inhibitors in viability assays. As indicated by the RNA-sequencing-based pathway analysis, genes related to the ribosome and MYC activity were significantly altered upon EP300/CREBBP inhibitor treatment. EP300/CREBBP inhibitors led to the down-regulation of ribosomal proteins RPL36 and RPL29. High-level ribosomal proteins amplifications and MYC amplifications were observed in castration-resistant prostate cancer samples of the publicly available Stand Up to Cancer data set. An inhibitor of RNA polymerase I-mediated transcription was used to evaluate the functional implications of these findings. The enzalutamide-resistant cell lines were more sensitive to this treatment. In addition, the migration rate of enzalutamide-resistant cells was strongly inhibited by this treatment. Taken together, the current data show that EP300/CREBBP inhibitors affect the MYC/ribosomal protein axis in enzalutamide-resistant cells and may have promising therapeutic implications.
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Affiliation(s)
- Tobias Furlan
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Kirchmair
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Natalie Sampson
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Puhr
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Gruber
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Frédéric R Santer
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
| | - Florian Handle
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zoran Culig
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria.
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19
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Ribosome Biogenesis and Cancer: Overview on Ribosomal Proteins. Int J Mol Sci 2021; 22:ijms22115496. [PMID: 34071057 PMCID: PMC8197113 DOI: 10.3390/ijms22115496] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022] Open
Abstract
Cytosolic ribosomes (cytoribosomes) are macromolecular ribonucleoprotein complexes that are assembled from ribosomal RNA and ribosomal proteins, which are essential for protein biosynthesis. Mitochondrial ribosomes (mitoribosomes) perform translation of the proteins essential for the oxidative phosphorylation system. The biogenesis of cytoribosomes and mitoribosomes includes ribosomal RNA processing, modification and binding to ribosomal proteins and is assisted by numerous biogenesis factors. This is a major energy-consuming process in the cell and, therefore, is highly coordinated and sensitive to several cellular stressors. In mitochondria, the regulation of mitoribosome biogenesis is essential for cellular respiration, a process linked to cell growth and proliferation. This review briefly overviews the key stages of cytosolic and mitochondrial ribosome biogenesis; summarizes the main steps of ribosome biogenesis alterations occurring during tumorigenesis, highlighting the changes in the expression level of cytosolic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs) in different types of tumors; focuses on the currently available information regarding the extra-ribosomal functions of CRPs and MRPs correlated to cancer; and discusses the role of CRPs and MRPs as biomarkers and/or molecular targets in cancer treatment.
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20
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Dinh TTH, Iseki H, Mizuno S, Iijima-Mizuno S, Tanimoto Y, Daitoku Y, Kato K, Hamada Y, Hasan ASH, Suzuki H, Murata K, Muratani M, Ema M, Kim JD, Ishida J, Fukamizu A, Kato M, Takahashi S, Yagami KI, Wilson V, Arkell RM, Sugiyama F. Disruption of entire Cables2 locus leads to embryonic lethality by diminished Rps21 gene expression and enhanced p53 pathway. eLife 2021; 10:50346. [PMID: 33949947 PMCID: PMC8099427 DOI: 10.7554/elife.50346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
In vivo function of CDK5 and Abl enzyme substrate 2 (Cables2), belonging to the Cables protein family, is unknown. Here, we found that targeted disruption of the entire Cables2 locus (Cables2d) caused growth retardation and enhanced apoptosis at the gastrulation stage and then induced embryonic lethality in mice. Comparative transcriptome analysis revealed disruption of Cables2, 50% down-regulation of Rps21 abutting on the Cables2 locus, and up-regulation of p53-target genes in Cables2d gastrulas. We further revealed the lethality phenotype in Rps21-deleted mice and unexpectedly, the exon 1-deleted Cables2 mice survived. Interestingly, chimeric mice derived from Cables2d ESCs carrying exogenous Cables2 and tetraploid wild-type embryo overcame gastrulation. These results suggest that the diminished expression of Rps21 and the completed lack of Cables2 expression are intricately involved in the embryonic lethality via the p53 pathway. This study sheds light on the importance of Cables2 locus in mouse embryonic development.
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Affiliation(s)
- Tra Thi Huong Dinh
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Ph.D. Program in Human Biology, School of Integrative and Global Majors (SIGMA), University of Tsukuba, Tsukuba, Japan.,Department of Traditional Medicine, University of Medicine and Pharmacy, Ho Chi Minh City, Viet Nam.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hiroyoshi Iseki
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Saori Iijima-Mizuno
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuko Hamada
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ammar Shaker Hamed Hasan
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Doctor's Program in Biomedical Sciences, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
| | - Hayate Suzuki
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Doctor's Program in Biomedical Sciences, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
| | - Kazuya Murata
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masafumi Muratani
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Jun-Dal Kim
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan.,Division of Complex Bioscience Research, Department of Research and Development, Institute of National Medicine, University of Toyama, Toyama, Japan
| | - Junji Ishida
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Mitsuyasu Kato
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Department of Experimental Pathology, Faculty of. Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ken-Ichi Yagami
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, School of Biological Sciences, SCRM Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ruth M Arkell
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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21
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Liyanage C, Malik A, Abeysinghe P, Clements J, Batra J. SWATH-MS Based Proteomic Profiling of Prostate Cancer Cells Reveals Adaptive Molecular Mechanisms in Response to Anti-Androgen Therapy. Cancers (Basel) 2021; 13:715. [PMID: 33572476 PMCID: PMC7916382 DOI: 10.3390/cancers13040715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/15/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) is the second most common cancer affecting men worldwide. PCa shows a broad-spectrum heterogeneity in its biological and clinical behavior. Although androgen targeted therapy (ATT) has been the mainstay therapy for advanced PCa, it inevitably leads to treatment resistance and progression to castration resistant PCa (CRPC). Thus, greater understanding of the molecular basis of treatment resistance and CRPC progression is needed to improve treatments for this lethal phenotype. The current study interrogated both proteomics and transcriptomic alterations stimulated in AR antagonist/anti-androgen (Bicalutamide and Enzalutamide) treated androgen-dependent cell model (LNCaP) in comparison with androgen-independent/castration-resistant cell model (C4-2B). The analysis highlighted the activation of MYC and PSF/SFPQ oncogenic upstream regulators in response to the anti-androgen treatment. Moreover, the study revealed anti-androgen induced genes/proteins related to transcription/translation regulation, energy metabolism, cell communication and signaling cascades promoting tumor growth and proliferation. In addition, these molecules were found dysregulated in PCa clinical proteomic and transcriptomic datasets, suggesting their potential involvement in PCa progression. In conclusion, our study provides key molecular signatures and associated pathways that might contribute to CRPC progression despite treatment with anti-androgens. Such molecular signatures could be potential therapeutic targets to improve the efficacy of existing therapies and/or predictive/prognostic value in CRPC for treatment response.
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Affiliation(s)
- Chamikara Liyanage
- Faculty of Health, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia; (C.L.); (A.M.); (P.A.); (J.C.)
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, QLD 4012, Australia
| | - Adil Malik
- Faculty of Health, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia; (C.L.); (A.M.); (P.A.); (J.C.)
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, QLD 4012, Australia
| | - Pevindu Abeysinghe
- Faculty of Health, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia; (C.L.); (A.M.); (P.A.); (J.C.)
| | - Judith Clements
- Faculty of Health, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia; (C.L.); (A.M.); (P.A.); (J.C.)
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, QLD 4012, Australia
| | - Jyotsna Batra
- Faculty of Health, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia; (C.L.); (A.M.); (P.A.); (J.C.)
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, QLD 4012, Australia
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22
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Reza AMMT, Yuan YG. microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins. Cells 2021; 10:110. [PMID: 33435549 PMCID: PMC7827472 DOI: 10.3390/cells10010110] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022] Open
Abstract
Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3' untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5' untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.
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Affiliation(s)
- Abu Musa Md Talimur Reza
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Yu-Guo Yuan
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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23
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Zhang J, Yang G, Li Q, Xie F. Increased fibrillarin expression is associated with tumor progression and an unfavorable prognosis in hepatocellular carcinoma. Oncol Lett 2020; 21:92. [PMID: 33376525 PMCID: PMC7751345 DOI: 10.3892/ol.2020.12353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common cancer and third most common cause of cancer-associated mortality worldwide. Hepatectomy and liver transplantation are the main treatments for early HCC. Immunotherapy and targeted therapy for advanced HCC have become increasingly popular; however, their clinical benefits are limited. Thus, identification of novel therapeutic targets for advanced HCC remains essential. Fibrillarin (FBL) is an essential nucleolar protein that catalyzes the 2′-O-methylation of ribosomal RNAs. Recently, experimental data have suggested that FBL can influence breast-cancer progression. However, the association between FBL expression and HCC remains known. In the present study, the UALCAN database was used to assess FBL mRNA expression in HCC. Immunohistochemistry analysis was performed to detect FBL protein expression in 139 patients with HCC. In addition, bioinformatic analysis was performed using the UALCAN, the Database for Annotation, Visualization and Integrated Discovery, cBioportal and TargetScan databases. Data were analyzed using Kaplan-Meier curves and the log-rank test, and a Cox proportional hazards regression model. The results demonstrated that FBL expression was significantly higher in tumor tissues compared with para-tumor tissues. Furthermore, high FBL expression was significantly associated with tumor diameter and advanced TNM stage in HCC. High FBL expression also predicted a shorter overall survival time and disease-free survival time in patients with HCC. Bioinformatics analysis demonstrated that FBL may be regulated by methylation modification. In addition, analyses of functional annotations using the Gene Ontology database indicated that FBL-related genes were predominantly enriched in DNA repair and proliferation-related cell-signaling pathways. Notably, high FBL expression signified larger tumor diameter, advanced tumor stage and a poor prognosis. Taken together, the results of the present study suggest that FBL may be a potential target for HCC treatment.
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Affiliation(s)
- Jing Zhang
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Gang Yang
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Qiang Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Fei Xie
- Department of Hepatobiliary Surgery, The First People's Hospital of Neijiang, Neijiang, Sichuan 641000, P.R. China
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Wang T, Wang ZY, Zeng LY, Gao YZ, Yan YX, Zhang Q. Down-Regulation of Ribosomal Protein RPS21 Inhibits Invasive Behavior of Osteosarcoma Cells Through the Inactivation of MAPK Pathway. Cancer Manag Res 2020; 12:4949-4955. [PMID: 32612383 PMCID: PMC7323807 DOI: 10.2147/cmar.s246928] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/27/2020] [Indexed: 01/01/2023] Open
Abstract
Objective The goal of our present study was to explore the expression level, biological function, and underlying molecular mechanism of ribosomal protein s21 (RPS21) in human osteosarcoma (OS). Methods Firstly, we evaluated the expression of RPS21 in OS tissue samples based on the Gene Expression Omnibus (GEO) datasets and also measured the RPS21 expression of OS cell lines (MG63, and U2OS) by quantitative real-time polymerase chain reaction (qRT-PCR). siRNA interference method was used to reduce the expression of RSP21 in the OS cells. Cell Counting Kit-8 (CCK-8), colony formation, wound-healing, and transwell assays were conducted to measure the proliferation, migration, and invasion of OS cells. The mitogen-activated protein kinase (MAPK) pathway-related proteins levels were examined by Western blot. Results Our analyses showed that the expression of RPS21 was significantly increased in OS, compared with normal samples. Upregulation of RPS21 was associated with worse outcomes of OS patients. Knockdown of RPS21 suppressed OS cell proliferation, colony-forming ability, migration, and invasion capacities. Moreover, down-regulation of RPS21 inactivated the MAPK signaling pathway. Conclusion RPS21 plays an oncogenic candidate in OS development via regulating the activity of MAPK pathway; therefore, it may serve as a novel therapeutic target for OS treatment.
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Affiliation(s)
- Tao Wang
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province 030001, People's Republic of China
| | - Zhi-Yong Wang
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province 030001, People's Republic of China
| | - Ling-Yuan Zeng
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province 030001, People's Republic of China
| | - Yao-Zu Gao
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province 030001, People's Republic of China
| | - Yu-Xin Yan
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province 030001, People's Republic of China
| | - Quan Zhang
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province 030001, People's Republic of China
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Arthurs C, Suarez-Bonnet A, Willis C, Xie B, Machulla N, Mair TS, Cao K, Millar M, Thrasivoulou C, Priestnall SL, Ahmed A. Equine penile squamous cell carcinoma: expression of biomarker proteins and EcPV2. Sci Rep 2020; 10:7863. [PMID: 32398763 PMCID: PMC7217868 DOI: 10.1038/s41598-020-64014-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
Equine penile squamous cell carcinoma (EpSCC) is a relatively common cutaneous neoplasm with a poor prognosis. In this study, we aimed to determine the protein expression and colocalisation of FRA1, c-Myc, Cyclin D1, and MMP7 in normal (NT), tumour (T), hyperplastic epidermis and/or squamous papilloma (Hyp/Pap), poorly-differentiated (PDSCC), or well-differentiated (WDSCC) EpSCC using a tissue array approach. Further objectives were to correlate protein expression to (i) levels of inflammation, using a convolutional neural network (ii) equine papillomavirus 2 (EcPV2) infection, detected using PCR amplification. We found an increase in expression of FRA1 in EpSCC compared to NT samples. c-Myc expression was higher in Hyp/Pap and WDSCC but not PDSCC whereas MMP7 was reduced in WDSCC compared with NT. There was a significant increase in the global intersection coefficient (GIC) of FRA1 with MMP7, c-Myc, and Cyclin D1 in EpSCC. Conversely, GIC for MMP7 with c-Myc was reduced in EpSCC tissue. Inflammation was positively associated with EcPV2 infection in both NT and EpSCC but not Hyp/Pap. Changes in protein expression could be correlated with EcPV2 for Cyclin D1 and c-Myc. Our results evaluate novel biomarkers of EpSCC and a putative correlation between the expression of biomarkers, EcPV2 infection and inflammation.
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Affiliation(s)
- Callum Arthurs
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Alejandro Suarez-Bonnet
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, UK
| | - Claire Willis
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, UK
| | - Boyu Xie
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Natalie Machulla
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Tim S Mair
- Bell Equine Veterinary Clinic, Maidstone, UK
| | - Kevin Cao
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Michael Millar
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Christopher Thrasivoulou
- Research Department of Cell and Developmental Biology, The Centre for Cell and Molecular Dynamics, Rockefeller Building, University College London, London, United Kingdom
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, UK
| | - Aamir Ahmed
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom.
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Comprehensive transcriptome profiling of Taiwanese colorectal cancer implicates an ethnic basis for pathogenesis. Sci Rep 2020; 10:4526. [PMID: 32161294 PMCID: PMC7066141 DOI: 10.1038/s41598-020-61273-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While both genetic and environmental factors have been linked to the incidence and mortality associated with CRC, an ethnic aspect of its etiology has also emerged. Since previous large-scale cancer genomics studies are mostly based on samples of European ancestry, the patterns of clinical events and associated mechanisms in other minority ethnic patients suffering from CRC are largely unexplored. We collected 104 paired and adjacent normal tissue and CRC tumor samples from Taiwanese patients and employed an integrated approach - paired expression profiles of mRNAs and microRNAs (miRNAs) combined with transcriptome-wide network analyses - to catalog the molecular signatures of this regional cohort. On the basis of this dataset, which is the largest ever reported for this type of systems analysis, we made the following key discoveries: (1) In comparison to the The Cancer Genome Atlas (TCGA) data, the Taiwanese CRC tumors show similar perturbations in expressed genes but a distinct enrichment in metastasis-associated pathways. (2) Recurrent as well as novel CRC-associated gene fusions were identified based on the sequencing data. (3) Cancer subtype classification using existing tools reveals a comparable distribution of tumor subtypes between Taiwanese cohort and TCGA datasets; however, this similarity in molecular attributes did not translate into the predicted subtype-related clinical outcomes (i.e., death event). (4) To further elucidate the molecular basis of CRC prognosis, we developed a new stratification strategy based on miRNA-mRNA-associated subtyping (MMAS) and consequently showed that repressed WNT signaling activity is associated with poor prognosis in Taiwanese CRC. In summary, our findings of distinct, hitherto unreported biosignatures underscore the heterogeneity of CRC tumorigenesis, support our hypothesis of an ethnic basis of disease, and provide prospects for translational medicine.
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27
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Loveridge CJ, Slater S, Campbell KJ, Nam NA, Knight J, Ahmad I, Hedley A, Lilla S, Repiscak P, Patel R, Salji M, Fleming J, Mitchell L, Nixon C, Strathdee D, Neilson M, Ntala C, Bryson S, Zanivan S, Edwards J, Robson CN, Goodyear CS, Blyth K, Leung HY. BRF1 accelerates prostate tumourigenesis and perturbs immune infiltration. Oncogene 2020; 39:1797-1806. [PMID: 31740786 PMCID: PMC7033044 DOI: 10.1038/s41388-019-1106-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/22/2019] [Accepted: 11/06/2019] [Indexed: 01/10/2023]
Abstract
BRF1 is a rate-limiting factor for RNA Polymerase III-mediated transcription and is elevated in numerous cancers. Here, we report that elevated levels of BRF1 associate with poor prognosis in human prostate cancer. In vitro studies in human prostate cancer cell lines demonstrated that transient overexpression of BRF1 increased cell proliferation whereas the transient downregulation of BRF1 reduced proliferation and mediated cell cycle arrest. Consistent with our clinical observations, BRF1 overexpression in a Pten-deficient mouse (PtenΔ/Δ BRF1Tg) prostate cancer model accelerated prostate carcinogenesis and shortened survival. In PtenΔ/Δ BRF1Tg tumours, immune and inflammatory processes were altered, with reduced tumoral infiltration of neutrophils and CD4 positive T cells, which can be explained by decreased levels of complement factor D (CFD) and C7 components of the complement cascade, an innate immune pathway that influences the adaptive immune response. We tested if the secretome was involved in BRF1-driven tumorigenesis. Unbiased proteomic analysis on BRF1-overexpresing PC3 cells confirmed reduced levels of CFD in the secretome, implicating the complement system in prostate carcinogenesis. We further identify that expression of C7 significantly correlates with expression of CD4 and has the potential to alter clinical outcome in human prostate cancer, where low levels of C7 associate with poorer prognosis.
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Affiliation(s)
- Carolyn J Loveridge
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sarah Slater
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Kirsteen J Campbell
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Noor A Nam
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
- Department of Basic Sciences and Oral Biology, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, Malaysia
| | - John Knight
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Imran Ahmad
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Ann Hedley
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sergio Lilla
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | | | - Rachana Patel
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Mark Salji
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Janis Fleming
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | | | - Colin Nixon
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | | | | | - Chara Ntala
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sheila Bryson
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Sara Zanivan
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Joanne Edwards
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Craig N Robson
- Northern Institute for Cancer Research, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Carl S Goodyear
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Karen Blyth
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK
| | - Hing Y Leung
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK.
- CRUK Beatson Institute, Bearsden, Glasgow, G61 1BD, UK.
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Binal Z, Açıkgöz E, Kızılay F, Öktem G, Altay B. Cross-talk between ribosome biogenesis, translation, and mTOR in CD133+ 4/CD44+ prostate cancer stem cells. Clin Transl Oncol 2019; 22:1040-1048. [PMID: 31630355 DOI: 10.1007/s12094-019-02229-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/04/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To investigate the gene expression profile of CSCs and to explore the key pathways and specific molecular signatures involved in the characteristic of CSCs. MATERIALS AND METHODS CD133+ /CD44+ CSCs and bulk population (non-CSCs) were isolated from DU-145 cells using fluorescence-activated cell sorting (FACS). We used Illumina HumanHT-12 v4 Expression to investigate gene expression profiling of CSCs and non-CSCs. Protein-protein interaction (PPI) network analysis was performed using the STRING database. Biomarkers selected based on gene expression profiling were visually analyzed using immunofluorescence staining method. An image analysis program, ImageJ®, was used for the analysis of fluorescence intensity. RESULTS In microarray analysis, we found that many ribosomal proteins and translation initiation factors that constitute the mTOR complex were highly expressed. PPI analysis using the 33 genes demonstrated that there was a close interaction between ribosome biogenesis, translation, and mTOR signaling. The fluorescence amount of mTOR and MLST8 were higher in CSCs compared to non-CSCs. CONCLUSIONS The increase in a number of genes associated with ribosome biogenesis, translation, and mTOR signaling may be important to evaluate prognosis and determine treatment approach for prostate cancer (PCa). A better understanding of the molecular pathways associated with CSCs may be promising to develop targeted therapies to prolong survival in PCa.
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Affiliation(s)
- Z Binal
- Department of Urology, Faculty of Medicine, Ege University School of Medicine, Ege University, Bornova, PO Box: 35100, 35100, İzmir, Turkey
| | - E Açıkgöz
- Department of Histology and Embryology, Faculty of Medicine, Yuzuncu Yıl University, 65080, Van, Turkey
| | - F Kızılay
- Department of Urology, Faculty of Medicine, Ege University School of Medicine, Ege University, Bornova, PO Box: 35100, 35100, İzmir, Turkey.
| | - G Öktem
- Department of Histology and Embryology, Faculty of Medicine, Ege University, 35100, Izmir, Turkey
| | - B Altay
- Department of Urology, Faculty of Medicine, Ege University School of Medicine, Ege University, Bornova, PO Box: 35100, 35100, İzmir, Turkey
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29
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Fadaka AO, Pretorius A, Klein A. MicroRNA Assisted Gene Regulation in Colorectal Cancer. Int J Mol Sci 2019; 20:E4899. [PMID: 31623294 PMCID: PMC6801675 DOI: 10.3390/ijms20194899] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second-leading cause of cancer death and a major public health problem. Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulation as the sole of RNA induced silencing complex for gene silencing. These non-coding RNA for example microRNA, are thought to play a key role in affecting the efficiency of gene regulation in cancer, especially CRC. Understanding the mechanism at the molecular level could lead to improved diagnosis, treatment, and management decisions for CRC. The study aimed to predict the molecular mechanism of gene regulation based microRNA-mRNA duplex as a lead in the silencing mechanism. Five candidate microRNAs were identified through the in silico approach. The MicroRNA target prediction and subsequent correlation, and prioritization were performed using miRTarBase, gbCRC and CoReCG, and DAVID databases respectively. Protein selection and preparation were carried out using PDB and Schrödinger suits. The molecular docking analysis was performed using PATCHDOCK webserver and visualized by discovery studio visualizer. The results of the study reveal that the candidate microRNAs have strong binding affinity towards their targets suggesting a crucial factor in the silencing mechanism. Furthermore, the molecular docking of the receptor to both the microRNA and microRNA-mRNA duplex were analyzed computationally to understand their interaction at the molecular level. Conclusively, the study provides an explanation for understanding the microRNAs-based gene regulation (silencing mechanism) in CRC.
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Affiliation(s)
- Adewale O Fadaka
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
| | - Ashley Pretorius
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
| | - Ashwil Klein
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
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30
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Ulgen E, Ozisik O, Sezerman OU. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front Genet 2019; 10:858. [PMID: 31608109 PMCID: PMC6773876 DOI: 10.3389/fgene.2019.00858] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
Pathway analysis is often the first choice for studying the mechanisms underlying a phenotype. However, conventional methods for pathway analysis do not take into account complex protein-protein interaction information, resulting in incomplete conclusions. Previously, numerous approaches that utilize protein-protein interaction information to enhance pathway analysis yielded superior results compared to conventional methods. Hereby, we present pathfindR, another approach exploiting protein-protein interaction information and the first R package for active-subnetwork-oriented pathway enrichment analyses for class comparison omics experiments. Using the list of genes obtained from an omics experiment comparing two groups of samples, pathfindR identifies active subnetworks in a protein-protein interaction network. It then performs pathway enrichment analyses on these identified subnetworks. To further reduce the complexity, it provides functionality for clustering the resulting pathways. Moreover, through a scoring function, the overall activity of each pathway in each sample can be estimated. We illustrate the capabilities of our pathway analysis method on three gene expression datasets and compare our results with those obtained from three popular pathway analysis tools. The results demonstrate that literature-supported disease-related pathways ranked higher in our approach compared to the others. Moreover, pathfindR identified additional pathways relevant to the conditions that were not identified by other tools, including pathways named after the conditions.
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Affiliation(s)
- Ege Ulgen
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ozan Ozisik
- Department of Computer Engineering, Electrical & Electronics Faculty, Yildiz Technical University, Istanbul, Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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31
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Stockert JA, Gupta A, Herzog B, Yadav SS, Tewari AK, Yadav KK. Predictive value of pseudouridine in prostate cancer. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2019; 7:262-272. [PMID: 31511832 PMCID: PMC6734038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Recent studies have shown that certain small nucleolar RNAs (H/ACA snoRNAs) and the protein dyskerin (DKC1) are upregulated in prostate cancer and are thought to contribute to progression of disease. These components convert uridine to pseudouridine (abbreviated ψ), a type of post-transcriptional modification of RNA. Given the increased abundance of H/ACA snoRNAs and expression of DKC1 in prostate carcinomas, and because whole-body turnover of RNA increases in support of rapidly-growing cancer cells, we examined the value of pseudouridine as a biomarker for prostate cancer. METHODS Using a monoclonal antibody against pseudouridine, we tested its ability to distinguish between two 25-base RNA oligonucleotide sequences that differed by only one ψ-substitution, and subsequently measured ψ in RNA isolated from several prostate cancer cell lines representing different stages of disease using dot blot assays and pseudouridinylated RNA linked immunosorbent assay (PURLISA). We also performed immunohistochemistry on a tissue micro array (12 cases/24 cores) containing prostate adenocarcinomas and normal adjacent tissue (NAT). RESULTS High levels of pseudouridine were detected in androgen-independent cell lines (PC3 and Du145) compared to androgen-sensitive (LNCaP) and immortalized human prostate (RWPE) cells. Immunohistochemistry of a tissue micro array (TMA) containing normal adjacent and cancerous prostate tissue revealed a significant difference in immunoreactivity between normal and malignant tissue (P ≤ 0.0001). CONCLUSION Our results provide new information on the relationship between pseudouridine expression and clinical progression of prostate cancer.
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Affiliation(s)
- Jennifer A Stockert
- Department of Urology, Icahn School of Medicine at Mount Sinai New York, NY 10029, USA
| | - Akriti Gupta
- Department of Urology, Icahn School of Medicine at Mount Sinai New York, NY 10029, USA
| | - Bryan Herzog
- Department of Urology, Icahn School of Medicine at Mount Sinai New York, NY 10029, USA
| | - Shalini S Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai New York, NY 10029, USA
| | - Ashutosh K Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai New York, NY 10029, USA
| | - Kamlesh K Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai New York, NY 10029, USA
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Zhang Q, Yin X, Pan Z, Cao Y, Han S, Gao G, Gao Z, Pan Z, Feng W. Identification of potential diagnostic and prognostic biomarkers for prostate cancer. Oncol Lett 2019; 18:4237-4245. [PMID: 31579071 PMCID: PMC6757266 DOI: 10.3892/ol.2019.10765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) is one of the most common malignant tumors worldwide. The aim of the present study was to determine potential diagnostic and prognostic biomarkers for PCa. The GSE103512 dataset was downloaded, and the differentially expressed genes (DEGs) were screened. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) analyses of DEGs were performed. The result of GO analysis suggested that the DEGs were mostly enriched in ‘carboxylic acid catabolic process’, ‘cell apoptosis’, ‘cell proliferation’ and ‘cell migration’. KEGG analysis results indicated that the DEGs were mostly concentrated in ‘metabolic pathways’, ‘ECM-receptor interaction’, the ‘PI3K-Akt pathway’ and ‘focal adhesion’. The PPI analysis results showed that Golgi membrane protein 1 (GOLM1), melanoma inhibitory activity member 3 (MIA3), ATP citrate lyase (ACLY) and G protein subunit β2 (GNB2) were the key genes in PCa, and the Module analysis revealed that they were associated with ‘ECM-receptor interaction’, ‘focal adhesion’, the ‘PI3K-Akt pathway’ and the ‘metabolic pathway’. Subsequently, the gene expression was confirmed using Gene Expression Profiling Interactive Analysis and the Human Protein Atlas. The results demonstrated that GOLM1 and ACLY expression was significantly upregulated (P<0.05) in PCa compared with that in normal tissues. Receiver operating characteristic and survival analyses were performed. The results showed that area under the curve values of these genes all exceeded 0.85, and high expression of these genes was associated with poor survival in patients with PCa. In conclusion, this study identified GOLM1 and ACLY in PCa, which may be potential diagnostic and prognostic biomarker of PCa.
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Affiliation(s)
- Qiang Zhang
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Xiujuan Yin
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhiwei Pan
- Department of Medicine, Laizhou Development Zone Hospital, Yantai, Shandong 261400, P.R. China
| | - Yingying Cao
- College of Clinical Medicine, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Shaojie Han
- Changle County Bureau of Animal Health and Production, Weifang, Shandong 261053, P.R. China
| | - Guojun Gao
- Urology Department, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhiqin Gao
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhifang Pan
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Weiguo Feng
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
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Montalbo R, Lozano JJ, Izquierdo L, Ingelmo-Torres M, BaÑos C, Palou J, Van der Heijden AG, Medina R, Schmidbauer J, Prat A, Ribal MJ, Alcaraz A, Mengual L. Ability of a urine gene expression classifier to reduce the number of follow-up cystoscopies in bladder cancer patients. Transl Res 2019; 208:73-84. [PMID: 30771285 DOI: 10.1016/j.trsl.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/18/2019] [Accepted: 02/04/2019] [Indexed: 11/28/2022]
Abstract
This study aimed to improve our previous urine gene expression classifiers focusing on the detection of non-high-risk non-muscle-invasive bladder cancer (NMIBC), and develop a new classifier able to decrease the frequency of cystoscopies during bladder cancer (BC) patients' surveillance. A total of 597 urines from BC patients, controls and patients in follow-up for BC (PFBC) were included. The study has 3 phases. In the urinary biomarker discovery phase, 84 urines from BC and control patients were retrospectively included and analyzed by Ribonucleic Acid (RNA) sequencing. In the classifier development phase, a total of 132 selected genes from previous phase were evaluated by nCounter in 214 prospectively collected urines from PFBC (98 with tumor). A diagnostic classifier was generated by logistic regression. Finally, in the classifier validation phase, a multicentric and international cohort of 248 urines (134 BC and 114 nonrecurrent PFBC) was used to validate classifier performance. A total of 521 genes were found differentially expressed between non-high-risk NMIBC samples and all other groups (P < 0.05). An 8-gene diagnostic classifier with an area under curve (AUC) of 0.893 was developed. Validation of this classifier in a cohort of PFBC achieved an overall sensitivity (SN) and a negative predictive value (NPV) of 96% and 97%, respectively (AUC = 0.823). Notably, this accuracy was maintained in non-high-risk NMIBC group (SN = 94%; NPV = 98%). In conclusion, this 8-gene expression classifier has high SN and NPV in a real clinical scenario. The use of this classifier can reduce the number of follow-up cystoscopies in PFBC, although assessing its final place in clinical setting is necessary.
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Affiliation(s)
- Ruth Montalbo
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | | | - Laura Izquierdo
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Carmen BaÑos
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Joan Palou
- Department of Urology, Fundació Puigvert, Barcelona, Spain
| | | | - Rafael Medina
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Joerg Schmidbauer
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Aleix Prat
- Oncology Department, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Maria J Ribal
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain
| | - Lourdes Mengual
- Department and Laboratory of Urology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre de Recerca Biomèdica CELLEX, Universitat de Barcelona, Barcelona, Spain.
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Liang Z, Mou Q, Pan Z, Zhang Q, Gao G, Cao Y, Gao Z, Pan Z, Feng W. Identification of candidate diagnostic and prognostic biomarkers for human prostate cancer: RPL22L1 and RPS21. Med Oncol 2019; 36:56. [DOI: 10.1007/s12032-019-1283-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022]
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35
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Keil M, Meyer MT, Dannheisig DP, Maerz LD, Philipp M, Pfister AS. Loss of Peter Pan protein is associated with cell cycle defects and apoptotic events. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:882-895. [DOI: 10.1016/j.bbamcr.2019.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/21/2018] [Accepted: 01/23/2019] [Indexed: 12/19/2022]
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36
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Wen Y, An Z, Qiao B, Zhang C, Zhang Z. RPS7 promotes cell migration through targeting epithelial-mesenchymal transition in prostate cancer. Urol Oncol 2019; 37:297.e1-297.e7. [PMID: 30737160 DOI: 10.1016/j.urolonc.2019.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/06/2019] [Accepted: 01/10/2019] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Small ribosomal protein subunit 7 (RPS7) is an important structural components of the ribosome involved in protein synthesis, previous studies demonstrated that RPS7 was associated with several malignancies, but the role of RPS7 in prostate cancer (PCa) remains unclear. To decipher such a puzzle, in the current study, we deciphered the role and mechanism of RPS7 during the progression of PCa. MATERIAL AND METHODS In this study, the expression of mRNA was performed by quantitative real-time PCR. The protein level was identified by Western blotting. Kaplan-Meier survival analysis was demonstrated the relation between the abnormal expression of RPS7 mRNA and the overall survival. Cell proliferation was assessed by MTT assay and cell counting, meanwhile, cell migration was checked by transwell assay. RESULTS RPS7 is higher expressed in PCa (p < 0.001), and the overexpression of RPS7 is closely associated with poor outcome of PCa patients after radical prostatectomy (p < 0.001). Inhibition the expression of RPS7 with a specific RPS7 siRNA could markedly attenuate prostate tumor growth and migration (p < 0.05). Mechanistic data reveals that inhibition of RPS7 could up-regulate the epithelial protein marker, E-cadherin (p < 0.05), and down-regulate the mesenchymal protein markers, such as N-cadherin and Snail (p < 0.001). CONCLUSIONS RPS7 is a newly verified tumor promoter in PCa, and promotes cell migration by targeting epithelial-to-mesenchymal transitionpathway. Thus, inhibition of RPS7-epithelial to-mesenchymal transition signaling might represent a prospective approach toward limiting prostate tumor progression.
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Affiliation(s)
- Yingwu Wen
- Department of Urology, Kailuan General Hospital, Tangshan, China
| | - Zesheng An
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin, China
| | - Baomin Qiao
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin, China
| | - Changwen Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin, China.
| | - Zhihong Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin, China.
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37
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Munkley J, Li L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL, Oltean S, Elliott DJ. Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer. eLife 2019; 8:47678. [PMID: 31478829 PMCID: PMC6788855 DOI: 10.7554/elife.47678] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/02/2019] [Indexed: 12/14/2022] Open
Abstract
Prostate is the most frequent cancer in men. Prostate cancer progression is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription by stimulating androgen receptor (AR) activity, yet also control pre-mRNA splicing through less clear mechanisms. Here we find androgens regulate splicing through AR-mediated transcriptional control of the epithelial-specific splicing regulator ESRP2. Both ESRP2 and its close paralog ESRP1 are highly expressed in primary prostate cancer. Androgen stimulation induces splicing switches in many endogenous ESRP2-controlled mRNA isoforms, including splicing switches correlating with disease progression. ESRP2 expression in clinical prostate cancer is repressed by ADT, which may thus inadvertently dampen epithelial splice programmes. Supporting this, treatment with the AR antagonist bicalutamide (Casodex) induced mesenchymal splicing patterns of genes including FLNB and CTNND1. Our data reveals a new mechanism of splicing control in prostate cancer with important implications for disease progression.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Ling Li
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - S R Gokul Krishnan
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Gerald Hysenaj
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Emma Scott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Caroline Dalgliesh
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Htoo Zarni Oo
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Teresa Mendes Maia
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal,VIB Center for Medical BiotechnologyVIBGhentBelgium,VIB Proteomics CoreVIBGhentBelgium,Department for Biomolecular MedicineGhent UniversityGhentBelgium
| | - Kathleen Cheung
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Ingrid Ehrmann
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Karen E Livermore
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Hanna Zielinska
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Oliver Thompson
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Bridget Knight
- NIHR Exeter Clinical Research FacilityRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Paul McCullagh
- Department of PathologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - John McGrath
- Exeter Surgical Health Services Research UnitRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Malcolm Crundwell
- Department of UrologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Mads Daugaard
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal
| | - Sebastian Oltean
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - David J Elliott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
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38
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Turiák L, Ozohanics O, Tóth G, Ács A, Révész Á, Vékey K, Telekes A, Drahos L. High sensitivity proteomics of prostate cancer tissue microarrays to discriminate between healthy and cancerous tissue. J Proteomics 2018; 197:82-91. [PMID: 30439472 DOI: 10.1016/j.jprot.2018.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/28/2018] [Accepted: 11/09/2018] [Indexed: 01/14/2023]
Abstract
Biopsies, in the form of tissue microarrays (TMAs) were studied to identify anomalies indicative of prostate cancer at the proteome level. TMAs offer a valuable source of well-characterized biological material. However, because of the small tissue sample size method development was essential to provide the sensitivity and reliability necessary for the analysis. Surface digestion of TMA cores was followed by peptide extraction and shotgun proteomics analysis. About 5 times better sensitivity was achieved by the optimized surface digestion compared to bulk digestion of the same TMA spot and it allowed the identification of over 500 proteins from individual prostate TMA cores. Label-free quantitation showed that biological variability among all samples was about 3 times larger than the technical reproducibility. We have identified 189 proteins which showed statistically significant changes (t-test p-value <.05) in abundance between healthy and cancerous tissue samples. The proteomic profile changed according to cancer grade, but did not show a correlation with cancer stage. Results of this pilot study were further evaluated using bioinformatics tools, identifying various protein pathways affected by prostate cancer progression indicating the usefulness of studying TMA cores to identify quantitative changes in tissue proteomics. SIGNIFICANCE: Detailed proteomics analysis of TMAs presents a good alternative for tissue analysis. Here we present a novel method, based on tissue surface digestion and nano-LC-MS measurements, which is capable of identifying and quantifying over 500 proteins from a 1.5 mm diameter tissue section. We compared healthy and cancerous prostate tissue samples, and tissues with various grades and stages of cancer. Tissue proteomics clearly distinguished healthy and cancerous samples, furthermore the results correlated well with cancer grade, but not with cancer stage. Over 100 proteins showed statistically significant abundance changes (t-test p-value <.05) between various groups. This was sufficient for a meaningful bioinformatics evaluation; showing e.g. increased abundance of proteins in cancer in the KEGG ribosome pathway, GO mRNA splicing via spliceosome, and chromatin assembly biological processes. The results highlight the feasibility of the developed method for future large-scale tissue proteomics studies using commercially available TMAs.
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Affiliation(s)
- Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary.
| | - Oliver Ozohanics
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary; Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - András Ács
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary; Semmelweis University, Ph.D. School of Pharmaceutical Sciences, Üllői út 26, H-1085 Budapest, Hungary
| | - Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - András Telekes
- Div. Sect. of Geriatrics, 2nd Department of Internal Medicine, Semmelweis University, Halmi utca 20-22, H-1115 Budapest, Hungary; Dept. of Oncology, St Lazarus County Hospital, Füleki út 54-56, H-1117, Salgótarján, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
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Molavi G, Samadi N, Hosseingholi EZ. The roles of moonlight ribosomal proteins in the development of human cancers. J Cell Physiol 2018; 234:8327-8341. [PMID: 30417503 DOI: 10.1002/jcp.27722] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022]
Abstract
"Moonlighting protein" is a term used to define a single protein with multiple functions and different activities that are not derived from gene fusions, multiple RNA splicing, or the proteolytic activity of promiscuous enzymes. Different proteinous constituents of ribosomes have been shown to have important moonlighting extra-ribosomal functions. In this review, we introduce the impact of key moonlight ribosomal proteins and dependent signal transduction in the initiation and progression of various cancers. As a future perspective, the potential role of these moonlight ribosomal proteins in the diagnosis, prognosis, and development of novel strategies to improve the efficacy of therapies for human cancers has been suggested.
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Affiliation(s)
- Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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40
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Fan S, Liang Z, Gao Z, Pan Z, Han S, Liu X, Zhao C, Yang W, Pan Z, Feng W. Identification of the key genes and pathways in prostate cancer. Oncol Lett 2018; 16:6663-6669. [PMID: 30405806 PMCID: PMC6202544 DOI: 10.3892/ol.2018.9491] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/17/2018] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is one of the most common malignancies in men globally. The aim of the present study was to identify the key genes and pathways involved in the occurrence of PCa. Gene expression profile (GSE55945) was downloaded from Gene Expression Omnibus, and the differentially expressed genes (DEGs) were identified. Subsequently, Gene ontology analysis, KEGG pathway analysis and protein-protein interaction (PPI) analysis of DEGs were performed. Finally, the identified key genes were confirmed by immunohistochemistry. The GO analysis results showed that the DEGs were mainly participated in cell cycle, cell division, cell development and cell junction. The KEGG pathway analysis showed that the DEGs were mainly enriched in proteoglycans in cancer, endocytosis, focal adhesion and hippo signaling pathway. The PPI analysis results showed that RPS21, FOXO1, BIRC5, POLR2H, RPL22L1 and NPM1 were the key genes involved in the occurrence of PCa, and the Module analysis indicated that the occurrence of PCa was associated with cell cycle, oocyte meiosis and ribosome biogenesis. IHC result showed that the expression of RPS21, BIRC5, POLR2H, RPL22L1 and NPM1 were significantly upregulated in PCa, while the expression of FOXO1 was significantly downregulated in PCa, matching with the bioinformatics analysis. Taken together, several key genes and pathways were identified involved in PCa, which might provide the potential biomarker for prognosis, diagnosis and drug targets.
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Affiliation(s)
- Shutong Fan
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zumu Liang
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhiqin Gao
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhiwei Pan
- Department of Internal Medicine, Laizhou Development Zone Hospital, Yantai, Shandong 261400, P.R. China
| | - Shaojie Han
- Animal Epidemic Prevention and Epidemic Control Center, Changle County Bureau of Animal Health and Production, Weifang, Shandong 262400, P.R. China
| | - Xiaoying Liu
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Chunling Zhao
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Weiwei Yang
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhifang Pan
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Weiguo Feng
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
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41
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Abstract
The rates of ribosome production by a nucleolus and of protein biosynthesis by ribosomes are tightly correlated with the rate of cell growth and proliferation. All these processes must be matched and appropriately regulated to provide optimal cell functioning. Deregulation of certain factors, including oncogenes, controlling these processes, especially ribosome biosynthesis, can lead to cell transformation. Cancer cells are characterized by intense ribosome biosynthesis which is advantageous for their growth and proliferation. On the other hand, this feature can be engaged as an anticancer strategy. Numerous nucleolar factors such as nucleolar and ribosomal proteins as well as different RNAs, in addition to their role in ribosome biosynthesis, have other functions, including those associated with cancer biology. Some of them can contribute to cell transformation and cancer development. Others, under stress evoked by different factors which often hamper function of nucleoli and thus induce nucleolar/ribosomal stress, can participate in combating cancer cells. In this sense, intentional application of therapeutic agents affecting ribosome biosynthesis can cause either release of these molecules from nucleoli or their de novo biosynthesis to mediate the activation of pathways leading to elimination of harmful cells. This review underlines the role of a nucleolus not only as a ribosome constituting apparatus but also as a hub of both positive and negative control of cancer development. The article is mainly based on original papers concerning mechanisms in which the nucleolus is implicated directly or indirectly in processes associated with neoplasia.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
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42
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Cao K, Arthurs C, Atta-Ul A, Millar M, Beltran M, Neuhaus J, Horn LC, Henrique R, Ahmed A, Thrasivoulou C. Quantitative Analysis of Seven New Prostate Cancer Biomarkers and the Potential Future of the 'Biomarker Laboratory'. Diagnostics (Basel) 2018; 8:diagnostics8030049. [PMID: 30060509 PMCID: PMC6163663 DOI: 10.3390/diagnostics8030049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/11/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
Prostate cancer is the third highest cause of male mortality in the developed world, with the burden of the disease increasing dramatically with demographic change. There are significant limitations to the current diagnostic regimens and no established effective screening modality. To this end, research has discovered hundreds of potential ‘biomarkers’ that may one day be of use in screening, diagnosis or prognostication. However, the barriers to bringing biomarkers to clinical evaluation and eventually into clinical usage have yet to be realised. This is an operational challenge that requires some new thinking and development of paradigms to increase the efficiency of the laboratory process and add ‘value’ to the clinician. Value comes in various forms, whether it be a process that is seamlessly integrated into the hospital laboratory environment or one that can provide additional ‘information’ for the clinical pathologist in terms of risk profiling. We describe, herein, an efficient and tissue-conserving pipeline that uses Tissue Microarrays in a semi-automated process that could, one day, be integrated into the hospital laboratory domain, using seven putative prostate cancer biomarkers for illustration.
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Affiliation(s)
- Kevin Cao
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London WC2R 2LS, UK.
| | - Callum Arthurs
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London WC2R 2LS, UK.
| | - Ali Atta-Ul
- Prostate Cancer Research Centre, University College London, London WC1E 6BT, UK.
| | - Michael Millar
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH8 9YL, UK.
| | - Mariana Beltran
- Aquila BioMedical, Nine, Edinburgh BioQuarter, 9 Little France Road, Edinburgh EH16 4UX, UK.
| | - Jochen Neuhaus
- Head of Urology Research Laboratories, University of Leipzig, Department of Urology, Research Laboratory, Liebigstr. 19, Building C, 04103 Leipzig, Germany.
| | - Lars-Christian Horn
- Division of Gynecologic, Breast & Perinatal Pathology, University Hospital Leipzig, Liebigstasse 24 D, 04103 Leipzig, Germany.
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Abel Salazar Institute of Biomedical Sciences, University of Porto, 4099-002 Porto, Portugal.
| | - Aamir Ahmed
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London WC2R 2LS, UK.
- Prostate Cancer Research Centre, University College London, London WC1E 6BT, UK.
| | - Christopher Thrasivoulou
- Research Department of Cell and Developmental Biology, The Centre for Cell and Molecular Dynamics, Rockefeller Building, University College London, London WC1E 6BT, UK.
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43
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Flentje A, Kober KM, Carrico AW, Neilands TB, Flowers E, Heck NC, Aouizerat BE. Minority stress and leukocyte gene expression in sexual minority men living with treated HIV infection. Brain Behav Immun 2018; 70:335-345. [PMID: 29548994 PMCID: PMC5953835 DOI: 10.1016/j.bbi.2018.03.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/20/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022] Open
Abstract
Sexual minority (i.e., non-heterosexual) individuals experience poorer mental and physical health, accounted for in part by the additional burden of sexual minority stress occurring from being situated in a culture favoring heteronormativity. Informed by previous research, the purpose of this study was to identify the relationship between sexual minority stress and leukocyte gene expression related to inflammation, cancer, immune function, and cardiovascular function. Sexual minority men living with HIV who were on anti-retroviral medication, had viral load < 200 copies/mL, and had biologically confirmed, recent methamphetamine use completed minority stress measures and submitted blood samples for RNA sequencing on leukocytes. Differential gene expression and pathway analyses were conducted comparing those with clinically elevated minority stress (n = 18) and those who did not meet the clinical cutoff (n = 20), covarying reactive urine toxicology results for very recent stimulant use. In total, 90 differentially expressed genes and 138 gene set pathways evidencing 2-directional perturbation were observed at false discovery rate (FDR) < 0.10. Of these, 41 of the differentially expressed genes and 35 of the 2-directionally perturbed pathways were identified as functionally related to hypothesized mechanisms of inflammation, cancer, immune function, and cardiovascular function. The neuroactive-ligand receptor pathway (implicated in cancer development) was identified using signaling pathway impact analysis. Our results suggest several potential biological pathways for future work investigating the relationship between sexual minority stress and health.
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Affiliation(s)
- Annesa Flentje
- Community Health Systems, School of Nursing, University of California, San Francisco, United States.
| | - Kord M Kober
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, United States; Institute for Computational Health Sciences, University of California, San Francisco, United States
| | | | - Torsten B Neilands
- Center for AIDS Prevention Studies, Department of Medicine, University of California, San Francisco, United States
| | - Elena Flowers
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, United States; Institute for Human Genetics, University of California, San Francisco, United States
| | - Nicholas C Heck
- Department of Psychology, Marquette University, United States
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, United States
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