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Roumeliotou A, Strati A, Chamchougia F, Xagara A, Tserpeli V, Smilkou S, Lagopodi E, Christopoulou A, Kontopodis E, Drositis I, Androulakis N, Georgoulias V, Koinis F, Kotsakis A, Lianidou E, Kallergi G. Comprehensive Analysis of CXCR4, JUNB, and PD-L1 Expression in Circulating Tumor Cells (CTCs) from Prostate Cancer Patients. Cells 2024; 13:782. [PMID: 38727318 PMCID: PMC11083423 DOI: 10.3390/cells13090782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
CXCR4, JUNB and PD-L1 are implicated in cancer progression and metastasis. The current study investigated these biomarkers in CTCs isolated from metastatic prostate cancer (mPCa) patients at the RNA and protein levels. CTCs were isolated from 48 mPCa patients using the Ficoll density gradient and ISET system (17 out of 48). The (CK/PD-L1/CD45) and (CK/CXCR4/JUNB) phenotypes were identified using two triple immunofluorescence stainings followed by VyCAP platform analysis. Molecular analysis was conducted with an EpCAM-dependent method for 25/48 patients. CK-8, CK-18, CK-19, JUNB, CXCR4, PD-L1, and B2M (reference gene) were analyzed with RT-qPCR. The (CK+/PD-L1+/CD45-) and the (CK+/CXCR4+/JUNB+) were the most frequent phenotypes (61.1% and 62.5%, respectively). Furthermore, the (CK+/CXCR4+/JUNB-) phenotype was correlated with poorer progression-free survival [(PFS), HR: 2.5, p = 0.049], while the (CK+/PD-L1+/CD45-) phenotype was linked to decreased overall survival [(OS), HR: 262.7, p = 0.007]. Molecular analysis revealed that 76.0% of the samples were positive for CK-8,18, and 19, while 28.0% were positive for JUNB, 44.0% for CXCR4, and 48.0% for PD-L1. Conclusively, CXCR4, JUNB, and PD-L1 were highly expressed in CTCs from mPCa patients. The CXCR4 protein expression was associated with poorer PFS, while PD-L1 was correlated with decreased OS, providing new biomarkers with potential clinical relevance.
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Affiliation(s)
- Argyro Roumeliotou
- Laboratory of Biochemistry/Metastatic Signaling, Department of Biology, University of Patras, 26504 Patras, Greece; (A.R.); (F.C.)
| | - Areti Strati
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.S.); (V.T.); (S.S.); (E.L.); (E.L.)
| | - Foteini Chamchougia
- Laboratory of Biochemistry/Metastatic Signaling, Department of Biology, University of Patras, 26504 Patras, Greece; (A.R.); (F.C.)
| | - Anastasia Xagara
- Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece; (A.X.); (F.K.); (A.K.)
- Hellenic Oncology Research Group, 11526 Athens, Greece;
| | - Victoria Tserpeli
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.S.); (V.T.); (S.S.); (E.L.); (E.L.)
| | - Stavroula Smilkou
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.S.); (V.T.); (S.S.); (E.L.); (E.L.)
| | - Elina Lagopodi
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.S.); (V.T.); (S.S.); (E.L.); (E.L.)
| | | | - Emmanouil Kontopodis
- Department of Oncology, Venizeleion General Hospital of Heraklion, 71409 Heraklion, Greece; (E.K.); (I.D.); (N.A.)
| | - Ioannis Drositis
- Department of Oncology, Venizeleion General Hospital of Heraklion, 71409 Heraklion, Greece; (E.K.); (I.D.); (N.A.)
| | - Nikolaos Androulakis
- Department of Oncology, Venizeleion General Hospital of Heraklion, 71409 Heraklion, Greece; (E.K.); (I.D.); (N.A.)
| | - Vassilis Georgoulias
- Hellenic Oncology Research Group, 11526 Athens, Greece;
- First Department of Medical Oncology, Metropolitan General Hospital, 15562 Athens, Greece
| | - Filippos Koinis
- Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece; (A.X.); (F.K.); (A.K.)
- Hellenic Oncology Research Group, 11526 Athens, Greece;
| | - Athanasios Kotsakis
- Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece; (A.X.); (F.K.); (A.K.)
- Hellenic Oncology Research Group, 11526 Athens, Greece;
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.S.); (V.T.); (S.S.); (E.L.); (E.L.)
| | - Galatea Kallergi
- Laboratory of Biochemistry/Metastatic Signaling, Department of Biology, University of Patras, 26504 Patras, Greece; (A.R.); (F.C.)
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2
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Silva KCS, Tambwe N, Mahfouz DH, Wium M, Cacciatore S, Paccez JD, Zerbini LF. Transcription Factors in Prostate Cancer: Insights for Disease Development and Diagnostic and Therapeutic Approaches. Genes (Basel) 2024; 15:450. [PMID: 38674385 PMCID: PMC11050257 DOI: 10.3390/genes15040450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
Transcription factors (TFs) are proteins essential for the regulation of gene expression, and they regulate the genes involved in different cellular processes, such as proliferation, differentiation, survival, and apoptosis. Although their expression is essential in normal physiological conditions, abnormal regulation of TFs plays critical role in several diseases, including cancer. In prostate cancer, the most common malignancy in men, TFs are known to play crucial roles in the initiation, progression, and resistance to therapy of the disease. Understanding the interplay between these TFs and their downstream targets provides insights into the molecular basis of prostate cancer pathogenesis. In this review, we discuss the involvement of key TFs, including the E26 Transformation-Specific (ETS) Family (ERG and SPDEF), NF-κB, Activating Protein-1 (AP-1), MYC, and androgen receptor (AR), in prostate cancer while focusing on the molecular mechanisms involved in prostate cancer development. We also discuss emerging diagnostic strategies, early detection, and risk stratification using TFs. Furthermore, we explore the development of therapeutic interventions targeting TF pathways, including the use of small molecule inhibitors, gene therapies, and immunotherapies, aimed at disrupting oncogenic TF signaling and improving patient outcomes. Understanding the complex regulation of TFs in prostate cancer provides valuable insights into disease biology, which ultimately may lead to advancing precision approaches for patients.
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Affiliation(s)
- Karla C. S. Silva
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (K.C.S.S.); (N.T.); (D.H.M.); (M.W.); (S.C.); (J.D.P.)
| | - Nadine Tambwe
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (K.C.S.S.); (N.T.); (D.H.M.); (M.W.); (S.C.); (J.D.P.)
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Dalia H. Mahfouz
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (K.C.S.S.); (N.T.); (D.H.M.); (M.W.); (S.C.); (J.D.P.)
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (K.C.S.S.); (N.T.); (D.H.M.); (M.W.); (S.C.); (J.D.P.)
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Stefano Cacciatore
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (K.C.S.S.); (N.T.); (D.H.M.); (M.W.); (S.C.); (J.D.P.)
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Juliano D. Paccez
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (K.C.S.S.); (N.T.); (D.H.M.); (M.W.); (S.C.); (J.D.P.)
| | - Luiz F. Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (K.C.S.S.); (N.T.); (D.H.M.); (M.W.); (S.C.); (J.D.P.)
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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Ren FJ, Cai XY, Yao Y, Fang GY. JunB: a paradigm for Jun family in immune response and cancer. Front Cell Infect Microbiol 2023; 13:1222265. [PMID: 37731821 PMCID: PMC10507257 DOI: 10.3389/fcimb.2023.1222265] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Jun B proto-oncogene (JunB) is a crucial member of dimeric activator protein-1 (AP-1) complex, which plays a significant role in various physiological processes, such as placental formation, cardiovascular development, myelopoiesis, angiogenesis, endochondral ossification and epidermis tissue homeostasis. Additionally, it has been reported that JunB has great regulatory functions in innate and adaptive immune responses by regulating the differentiation and cytokine secretion of immune cells including T cells, dendritic cells and macrophages, while also facilitating the effector of neutrophils and natural killer cells. Furthermore, a growing body of studies have shown that JunB is involved in tumorigenesis through regulating cell proliferation, differentiation, senescence and metastasis, particularly affecting the tumor microenvironment through transcriptional promotion or suppression of oncogenes in tumor cells or immune cells. This review summarizes the physiological function of JunB, its immune regulatory function, and its contribution to tumorigenesis, especially focusing on its regulatory mechanisms within tumor-associated immune processes.
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Affiliation(s)
- Fu-jia Ren
- Department of Pharmacy, Hangzhou Women’s Hospital, Hangzhou, Zhejiang, China
| | - Xiao-yu Cai
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yao Yao
- Department of Pharmacy, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guo-ying Fang
- Department of Pharmacy, Hangzhou Women’s Hospital, Hangzhou, Zhejiang, China
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4
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Lu F, Hu F, Qiu B, Zou H, Xu J. Identification of novel biomarkers in septic cardiomyopathy via integrated bioinformatics analysis and experimental validation. Front Genet 2022; 13:929293. [PMID: 35957694 PMCID: PMC9358039 DOI: 10.3389/fgene.2022.929293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022] Open
Abstract
Purpose: Septic cardiomyopathy (SCM) is an important world public health problem with high morbidity and mortality. It is necessary to identify SCM biomarkers at the genetic level to identify new therapeutic targets and strategies. Method: DEGs in SCM were identified by comprehensive bioinformatics analysis of microarray datasets (GSE53007 and GSE79962) downloaded from the GEO database. Subsequently, bioinformatics analysis was used to conduct an in-depth exploration of DEGs, including GO and KEGG pathway enrichment analysis, PPI network construction, and key gene identification. The top ten Hub genes were identified, and then the SCM model was constructed by treating HL-1 cells and AC16 cells with LPS, and these top ten Hub genes were examined using qPCR. Result: STAT3, SOCS3, CCL2, IL1R2, JUNB, S100A9, OSMR, ZFP36, and HAMP were significantly elevated in the established SCM cells model. Conclusion: After bioinformatics analysis and experimental verification, it was demonstrated that STAT3, SOCS3, CCL2, IL1R2, JUNB, S100A9, OSMR, ZFP36, and HAMP might play important roles in SCM.
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Affiliation(s)
- Feng Lu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Feng Hu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Baiquan Qiu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongpeng Zou
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianjun Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Jianjun Xu,
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5
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Riedel M, Cai H, Stoltze IC, Vendelbo MH, Wagner EF, Bakiri L, Thomsen MK. Targeting AP-1 transcription factors by CRISPR in the prostate. Oncotarget 2021; 12:1956-1961. [PMID: 34548912 PMCID: PMC8448511 DOI: 10.18632/oncotarget.27997] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer is the second most diagnosed cancer in men. It is a slow progressing cancer, but when the disease reaches an advanced stage, treatment options are limited. Sequencing analyses of cancer samples have identified genes that can potentially drive disease progression. We implemented the CRISPR/Cas9 technology to simultaneously manipulate multiple genes in the murine prostate and thus to functionally test putative cancer driver genes in vivo. The activating protein-1 (AP-1) transcription factor is associated with many different cancer types, with the proto-oncogenes JUN and FOS being the two most intensely studied subunits. We analyzed expression of FOS and JUNB in human prostate cancer datasets and observed decreased expression in advanced stages. By applying CRISPR/Cas9 technology, the role of these two transcription factors in prostate cancer progression was functionally tested. Our data revealed that loss of either JunB or Fos in the context of Pten loss drives prostate cancer progression to invasive disease. Furthermore, loss of Fos increases Jun expression, and CRISPR inactivation of Jun in this context decreases cell proliferation. Overall, these in vivo studies reveal that JunB and Fos exhibit a tumor suppressor function by repressing invasive disease, whereas Jun is oncogenic and increases cell proliferation. This demonstrates that AP-1 factors are implicated in prostate cancer progression at different stages and display a dual function as tumor suppressor and as an oncogene in cancer progression.
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Affiliation(s)
- Maria Riedel
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Huiqiang Cai
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Iben C Stoltze
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Mikkel H Vendelbo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Nuclear Medicine & PET Centre, Aarhus University Hospital, Aarhus, Denmark
| | - Erwin F Wagner
- Laboratory Genes and Disease, Department of Dermatology, Medical University of Vienna (MUV), Vienna, Austria.,Laboratory Genes and Disease, Department of Laboratory Medicine, Medical University of Vienna (MUV), Vienna, Austria
| | - Latifa Bakiri
- Laboratory Genes and Disease, Department of Laboratory Medicine, Medical University of Vienna (MUV), Vienna, Austria
| | - Martin K Thomsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark
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6
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In vivo CRISPR inactivation of Fos promotes prostate cancer progression by altering the associated AP-1 subunit Jun. Oncogene 2021; 40:2437-2447. [PMID: 33674748 PMCID: PMC7610543 DOI: 10.1038/s41388-021-01724-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/22/2022]
Abstract
Prostate cancer is a major global health concern with limited treatment options for advanced disease. Its heterogeneity challenges the identification of crucial driver genes implicated in disease progression. Activating protein-1 (AP-1) transcription factor is associated with cancer since the first identification of its subunits, the proto-oncogenes JUN and FOS. Whereas both JUN and FOS, have been implicated in prostate cancer, this study provides the first functional evidence that FOS acts as a tumor suppressor during prostate cancer progression and invasion. Data mining revealed decreased FOS expression in prostate cancer and a further downregulation in metastatic disease, consistent with FOS expression in cell lines derived from different prostate cancer stages. FOS deficiency in prostate cancer cell lines increases cell proliferation and induces oncogenic pathway alterations. Importantly, in vivo CRISPR/Cas9-mediated Fos and Pten double mutation in murine prostate epithelium results in increased proliferation and invasiveness compared to the abrogation of Pten alone. Interestingly, enhanced Jun expression is observed in the murine prostatic intraepithelial neoplasia lacking Fos. CRISPR/Cas9-mediated knockout of Jun combined with Fos and Pten deficiency diminishes the increased proliferation rate in vivo, but not the ability to form invasive disease. Overall, we demonstrate that loss of Fos promotes disease progression from clinical latent prostate cancer to advanced disease through accelerated proliferation and invasiveness, partly through Jun.
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Chen W, Wang X, Wei G, Huang Y, Shi Y, Li D, Qiu S, Zhou B, Cao J, Chen M, Qin P, Jin W, Ni T. Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts. Front Genet 2020; 11:867. [PMID: 32849838 PMCID: PMC7431633 DOI: 10.3389/fgene.2020.00867] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022] Open
Abstract
Replicative senescence is a hallmark of aging, which also contributes to individual aging. Mouse embryonic fibroblasts (MEFs) provide a convenient replicative senescence model. However, the heterogeneity of single MEFs during cellular senescence has remained unclear. Here, we conducted single-cell RNA sequencing on senescent MEFs. Principal component analysis showed obvious heterogeneity among these MEFs such that they could be divided into six subpopulations. Three types of gene expression analysis revealed distinct expression features of these six subpopulations. Trajectory analysis revealed three distinct lineages during MEF senescence. In the main lineage, some senescence-associated secretory phenotypes were upregulated in a subset of cells from senescent clusters, which could not be distinguished in a previous bulk study. In the other two lineages, a possibility of escape from cell cycle arrest and coupling between translation-related genes and ATP synthesis-related genes were also discovered. Additionally, we found co-expression of transcription factor HOXD8 coding gene and its potential target genes in the main lineage. Overexpression of Hoxd8 led to senescence-associated phenotypes, suggesting HOXD8 is a new regulator of MEF senescence. Together, our single-cell sequencing on senescent MEFs largely expanded the knowledge of a basic cell model for aging research.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xuefei Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yin Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yufang Shi
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- The First Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, Suzhou, China
| | - Dan Li
- Field Application Department, Fluidigm (Shanghai) Instrument Technology Co., Ltd., Shanghai, China
| | - Shengnu Qiu
- Division of Biosciences, Faculty of Life Sciences, University College London, London, United Kingdom
| | - Bin Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Junhong Cao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Meng Chen
- Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengfei Qin
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
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Guan H, Peng R, Fang F, Mao L, Chen Z, Yang S, Dai C, Wu H, Wang C, Feng N, Xu B, Chen M. Tumor-associated macrophages promote prostate cancer progression via exosome-mediated miR-95 transfer. J Cell Physiol 2020; 235:9729-9742. [PMID: 32406953 DOI: 10.1002/jcp.29784] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/25/2020] [Accepted: 05/02/2020] [Indexed: 12/24/2022]
Abstract
Tumor-associated macrophages (TAMs) are vital constituents in mediating cell-to-cell communication within the tumor microenvironment. However, the molecular mechanisms underlying the interplay between TAMs and tumor cells that guide cell fate are largely undetermined. Extracellular vesicles, also known as exosomes, which are derived from TAMs, are the components exerting regulatory effects. Thus, understanding the underlying mechanism of "onco-vesicles" is of crucial importance for prostate cancer (PCa) therapy. In this study, we analyzed micro RNA sequences in exosomes released by THP-1 and M2 macrophages and found a significant increase in miR-95 levels in TAM-derived exosomes, demonstrating the direct uptake of miR-95 by recipient PCa cells. In vitro and in vivo loss-of-function assays suggested that miR-95 could function as a tumor promoter by directly binding to its downstream target gene, JunB, to promote PCa cell proliferation, invasion, and epithelial-mesenchymal transition. The clinical data analyses further revealed that higher miR-95 expression results in worse clinicopathological features. Collectively, our results demonstrated that TAM-mediated PCa progression is partially attributed to the aberrant expression of miR-95 in TAM-derived exosomes, and the miR-95/JunB axis provides the groundwork for research on TAMs to further develop more-personalized therapeutic approaches for patients with PCa.
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Affiliation(s)
- Han Guan
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Rui Peng
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Fang Fang
- Department of Immunology, School of Laboratory Medicine, Anhui Provincial Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Likai Mao
- Department of Urology, Second Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Zhijun Chen
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Shuai Yang
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Changyuan Dai
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Hongliang Wu
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Chengyong Wang
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No.2 Hospital of Nanjing Medical University, Wuxi, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
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Merckx G, Tay H, Lo Monaco M, van Zandvoort M, De Spiegelaere W, Lambrichts I, Bronckaers A. Chorioallantoic Membrane Assay as Model for Angiogenesis in Tissue Engineering: Focus on Stem Cells. TISSUE ENGINEERING PART B-REVIEWS 2020; 26:519-539. [PMID: 32220219 DOI: 10.1089/ten.teb.2020.0048] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tissue engineering aims to structurally and functionally regenerate damaged tissues, which requires the formation of new blood vessels that supply oxygen and nutrients by the process of angiogenesis. Stem cells are a promising tool in regenerative medicine due to their combined differentiation and paracrine angiogenic capacities. The study of their proangiogenic properties and associated potential for tissue regeneration requires complex in vivo models comprising all steps of the angiogenic process. The highly vascularized extraembryonic chorioallantoic membrane (CAM) of fertilized chicken eggs offers a simple, easy accessible, and cheap angiogenic screening tool compared to other animal models. Although the CAM assay was initially primarily performed for evaluation of tumor growth and metastasis, stem cell studies using this model are increasing. In this review, a detailed summary of angiogenic observations of different mesenchymal, cardiac, and endothelial stem cell types and derivatives in the CAM model is presented. Moreover, we focus on the variation in experimental setup, including the benefits and limitations of in ovo and ex ovo protocols, diverse biological and synthetic scaffolds, imaging techniques, and outcome measures of neovascularization. Finally, advantages and disadvantages of the CAM assay as a model for angiogenesis in tissue engineering in comparison with alternative in vivo animal models are described. Impact statement The chorioallantoic membrane (CAM) assay is an easy and cheap screening tool for the angiogenic properties of stem cells and their associated potential in the tissue engineering field. This review offers an overview of all published angiogenic studies of stem cells using this model, with emphasis on the variation in used experimental timeline, culture protocol (in ovo vs. ex ovo), stem cell type (derivatives), scaffolds, and outcome measures of vascularization. The purpose of this overview is to aid tissue engineering researchers to determine the ideal CAM experimental setup based on their specific study goals.
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Affiliation(s)
- Greet Merckx
- Faculty of Medicine and Life Sciences, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Hanna Tay
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Melissa Lo Monaco
- Faculty of Medicine and Life Sciences, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium.,Department of Veterinary Medicine, Faculty of Sciences, Integrated Veterinary Research Unit-Namur Research Institute for Life Science (IVRU-NARILIS), University of Namur, Namur, Belgium
| | - Marc van Zandvoort
- Department of Genetics and Cell Biology, School for Cardiovascular Diseases CARIM and School for Oncology and Development GROW, Maastricht University, Maastricht, the Netherlands
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ivo Lambrichts
- Faculty of Medicine and Life Sciences, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Annelies Bronckaers
- Faculty of Medicine and Life Sciences, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
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Zhang X, Koga N, Suzuki H, Kato M. Promotion of cellular senescence by THG-1/TSC22D4 knockout through activation of JUNB. Biochem Biophys Res Commun 2020; 522:897-902. [DOI: 10.1016/j.bbrc.2019.11.145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
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11
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Pei H, Guo Z, Wang Z, Dai Y, Zheng L, Zhu L, Zhang J, Hu W, Nie J, Mao W, Jia X, Li B, Hei TK, Zhou G. RAC2 promotes abnormal proliferation of quiescent cells by enhanced JUNB expression via the MAL-SRF pathway. Cell Cycle 2018; 17:1115-1123. [PMID: 29895215 PMCID: PMC6110603 DOI: 10.1080/15384101.2018.1480217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/11/2018] [Indexed: 12/28/2022] Open
Abstract
Radiation-induced lung injury (RILI) occurs most often in radiotherapy of lung cancer, esophageal cancer, and other thoracic cancers. The occurrence of RILI is a complex process that includes a variety of cellular and molecular interactions, which ultimately result in carcinogenesis. However, the underlying mechanism is unknown. Here we show that Ras-related C3 botulinum toxin substrate 2 (RAC2) and transcription factor jun-B (JUNB) were upregulated in non-small cell carcinoma (NSCLC) tissues and were associated with poor prognoses for NSCLC patients. Ionizing radiation also caused increased expression of RAC2 in quiescent stage cells, and the reentry of quiescent cells into a new cell cycle. The activity of the serum response factor (SRF) was activated by RAC2 and other Rho family genes (RhoA, ROCK, and LIM kinase). Consequently, JUNB acted as an oncogene and induced abnormal proliferation of quiescent cells. Together, the results showed that RAC2 can be used as a target gene for radiation protection. A better understanding of the RAC2 and JUNB mechanisms in the molecular etiology of lung cancer will be helpful in reducing cancer risks and side effects during treatment of this disorder. Our study therefore provides a new perspective on the involvement of RAC2 and JUNB as oncogenes in the tumorigenesis of NSCLC.
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Affiliation(s)
- Hailong Pei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Ziyang Guo
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
| | - Ziyang Wang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
| | - Yingchu Dai
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Lijun Zheng
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Lin Zhu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Jian Zhang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Jing Nie
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Weidong Mao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
- Radiotherapy Department, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xianghong Jia
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Bingyan Li
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Medical College of Soochow University, Suzhou, China
| | - Tom K. Hei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Center for Radiological Research, College of Physician and Surgeons, Columbia University, NY, New York, USA
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
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12
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Raghunath A, Sundarraj K, Nagarajan R, Arfuso F, Bian J, Kumar AP, Sethi G, Perumal E. Antioxidant response elements: Discovery, classes, regulation and potential applications. Redox Biol 2018; 17:297-314. [PMID: 29775961 PMCID: PMC6007815 DOI: 10.1016/j.redox.2018.05.002] [Citation(s) in RCA: 284] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/25/2018] [Accepted: 05/05/2018] [Indexed: 12/20/2022] Open
Abstract
Exposure to antioxidants and xenobiotics triggers the expression of a myriad of genes encoding antioxidant proteins, detoxifying enzymes, and xenobiotic transporters to offer protection against oxidative stress. This articulated universal mechanism is regulated through the cis-acting elements in an array of Nrf2 target genes called antioxidant response elements (AREs), which play a critical role in redox homeostasis. Though the Keap1/Nrf2/ARE system involves many players, AREs hold the key in transcriptional regulation of cytoprotective genes. ARE-mediated reporter constructs have been widely used, including xenobiotics profiling and Nrf2 activator screening. The complexity of AREs is brought by the presence of other regulatory elements within the AREs. The diversity in the ARE sequences not only bring regulatory selectivity of diverse transcription factors, but also confer functional complexity in the Keap1/Nrf2/ARE pathway. The different transcription factors either homodimerize or heterodimerize to bind the AREs. Depending on the nature of partners, they may activate or suppress the transcription. Attention is required for deeper mechanistic understanding of ARE-mediated gene regulation. The computational methods of identification and analysis of AREs are still in their infancy. Investigations are required to know whether epigenetics mechanism plays a role in the regulation of genes mediated through AREs. The polymorphisms in the AREs leading to oxidative stress related diseases are warranted. A thorough understanding of AREs will pave the way for the development of therapeutic agents against cancer, neurodegenerative, cardiovascular, metabolic and other diseases with oxidative stress.
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Affiliation(s)
- Azhwar Raghunath
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, Tamilnadu, India
| | - Kiruthika Sundarraj
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, Tamilnadu, India
| | - Raju Nagarajan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6009, Australia
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600 Singapore, Singapore
| | - Alan P Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600 Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Medical Science Cluster, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600 Singapore, Singapore.
| | - Ekambaram Perumal
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, Tamilnadu, India.
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13
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Sadeghi M, Ranjbar B, Ganjalikhany MR, M. Khan F, Schmitz U, Wolkenhauer O, Gupta SK. MicroRNA and Transcription Factor Gene Regulatory Network Analysis Reveals Key Regulatory Elements Associated with Prostate Cancer Progression. PLoS One 2016; 11:e0168760. [PMID: 28005952 PMCID: PMC5179129 DOI: 10.1371/journal.pone.0168760] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
Abstract
Technological and methodological advances in multi-omics data generation and integration approaches help elucidate genetic features of complex biological traits and diseases such as prostate cancer. Due to its heterogeneity, the identification of key functional components involved in the regulation and progression of prostate cancer is a methodological challenge. In this study, we identified key regulatory interactions responsible for primary to metastasis transitions in prostate cancer using network inference approaches by integrating patient derived transcriptomic and miRomics data into gene/miRNA/transcription factor regulatory networks. One such network was derived for each of the clinical states of prostate cancer based on differentially expressed and significantly correlated gene, miRNA and TF pairs from the patient data. We identified key elements of each network using a network analysis approach and validated our results using patient survival analysis. We observed that HOXD10, BCL2 and PGR are the most important factors affected in primary prostate samples, whereas, in the metastatic state, STAT3, JUN and JUNB are playing a central role. Benefiting integrative networks our analysis suggests that some of these molecules were targeted by several overexpressed miRNAs which may have a major effect on the dysregulation of these molecules. For example, in the metastatic tumors five miRNAs (miR-671-5p, miR-665, miR-663, miR-512-3p and miR-371-5p) are mainly responsible for the dysregulation of STAT3 and hence can provide an opportunity for early detection of metastasis and development of alternative therapeutic approaches. Our findings deliver new details on key functional components in prostate cancer progression and provide opportunities for the development of alternative therapeutic approaches.
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Affiliation(s)
- Mehdi Sadeghi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Faiz M. Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, Australia
- Sydney Medical School, University of Sydney, Camperdown, Australia
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Shailendra K. Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Department of Bioinformatics, CSIR-Indian Institute of Toxicology Research, Lucknow, India
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14
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Millena AC, Vo BT, Khan SA. JunD Is Required for Proliferation of Prostate Cancer Cells and Plays a Role in Transforming Growth Factor-β (TGF-β)-induced Inhibition of Cell Proliferation. J Biol Chem 2016; 291:17964-76. [PMID: 27358408 DOI: 10.1074/jbc.m116.714899] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Indexed: 12/16/2022] Open
Abstract
TGF-β inhibits proliferation of prostate epithelial cells. However, prostate cancer cells in advanced stages become resistant to inhibitory effects of TGF-β. The intracellular signaling mechanisms involved in differential effects of TGF-β during different stages are largely unknown. Using cell line models, we have shown that TGF-β inhibits proliferation in normal (RWPE-1) and prostate cancer (DU145) cells but does not have any effect on proliferation of prostate cancer (PC3) cells. We have investigated the role of Jun family proteins (c-Jun, JunB, and JunD) in TGF-β effects on cell proliferation. Jun family members were expressed at different levels and responded differentially to TGF-β treatment. TGF-β effects on JunD protein levels, but not mRNA levels, correlated with its effects on cell proliferation. TGF-β induced significant reduction in JunD protein in RWPE-1 and DU145 cells but not in PC3 cells. Selective knockdown of JunD expression using siRNA in DU145 and PC3 cells resulted in significant reduction in cell proliferation, and forced overexpression of JunD increased the proliferation rate. On the other hand, knockdown of c-Jun or JunB had little, if any, effect on cell proliferation; overexpression of c-Jun and JunB decreased the proliferation rate in DU145 cells. Further studies showed that down-regulation of JunD in response to TGF-β treatment is mediated via the proteasomal degradation pathway. In conclusion, we show that specific Jun family members exert differential effects on proliferation in prostate cancer cells in response to TGF-β, and inhibition of cell proliferation by TGF-β requires degradation of JunD protein.
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Affiliation(s)
- Ana Cecilia Millena
- From the Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, Georgia 30314
| | - BaoHan T Vo
- From the Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, Georgia 30314
| | - Shafiq A Khan
- From the Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, Georgia 30314
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15
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Birner P, Egger G, Merkel O, Kenner L. JunB and PTEN in prostate cancer: 'loss is nothing else than change'. Cell Death Differ 2015; 22:522-3. [PMID: 25747853 DOI: 10.1038/cdd.2014.232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- P Birner
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - G Egger
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - O Merkel
- 1] Department of Pathology, Medical University of Vienna, Vienna, Austria [2] Unit of Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L Kenner
- 1] Department of Pathology, Medical University of Vienna, Vienna, Austria [2] Unit of Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, Vienna, Austria [3] Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
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16
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Abdelmohsen K, Gorospe M. Noncoding RNA control of cellular senescence. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:615-29. [PMID: 26331977 DOI: 10.1002/wrna.1297] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022]
Abstract
Senescent cells accumulate in normal tissues with advancing age and arise by long-term culture of primary cells. Senescence develops following exposure to a range of stress-causing agents and broadly influences the physiology and pathology of tissues, organs, and systems in the body. While many proteins are known to control senescence, numerous noncoding (nc)RNAs are also found to promote or repress the senescent phenotype. Here, we review the regulatory ncRNAs (primarily microRNAs and lncRNAs) identified to-date as key modulators of senescence. We highlight the major senescent pathways (p53/p21 and pRB/p16), as well as the senescence-associated secretory phenotype (SASP) and other senescence-associated events governed by ncRNAs, and discuss the importance of understanding comprehensively the ncRNAs implicated in cell senescence.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
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17
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ProSim: A Method for Prioritizing Disease Genes Based on Protein Proximity and Disease Similarity. BIOMED RESEARCH INTERNATIONAL 2015; 2015:213750. [PMID: 26339594 PMCID: PMC4538409 DOI: 10.1155/2015/213750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/16/2015] [Indexed: 01/19/2023]
Abstract
Predicting disease genes for a particular genetic disease is very challenging in bioinformatics. Based on current research studies, this challenge can be tackled via network-based approaches. Furthermore, it has been highlighted that it is necessary to consider disease similarity along with the protein's proximity to disease genes in a protein-protein interaction (PPI) network in order to improve the accuracy of disease gene prioritization. In this study we propose a new algorithm called proximity disease similarity algorithm (ProSim), which takes both of the aforementioned properties into consideration, to prioritize disease genes. To illustrate the proposed algorithm, we have conducted six case studies, namely, prostate cancer, Alzheimer's disease, diabetes mellitus type 2, breast cancer, colorectal cancer, and lung cancer. We employed leave-one-out cross validation, mean enrichment, tenfold cross validation, and ROC curves to evaluate our proposed method and other existing methods. The results show that our proposed method outperforms existing methods such as PRINCE, RWR, and DADA.
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18
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c-Abl-mediated tyrosine phosphorylation of JunB is required for Adriamycin-induced expression of p21. Biochem J 2015. [PMID: 26217035 DOI: 10.1042/bj20150372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The non-receptor-type tyrosine kinase c-Abl functions as a cytoplasmic signal transducer upon activation of cell-surface receptors. c-Abl is also involved in DDR (DNA-damage response), which is initiated in the nucleus, whereas its molecular functions in DDR are not fully understood. In the present study, we found that c-Abl phosphorylates JunB, a member of the AP-1 (activator protein 1) transcription factor family. Because JunB was suggested to be involved in DDR, we analysed the role of c-Abl-mediated phosphorylation of JunB in DDR. We first analysed phosphorylation sites of JunB and found that c-Abl majorly phosphorylates JunB at Tyr(173), Tyr(182) and Tyr(188). Because c-Abl promotes expression of the cyclin-dependent kinase inhibitor p21 upon stimulation with the DNA-damaging agent Adriamycin (doxorubicin), we analysed the involvement of JunB in Adriamycin-induced p21 expression. We found that JunB suppresses p21 induction through inhibition of its promoter activity. The phosphomimetic JunB, which was generated by glutamic acid substitutions at the phosphorylation sites, failed to repress p21 induction. Recruitment of JunB to the p21 promoter was promoted by Adriamycin stimulation and was further enhanced by co-treatment with the c-Abl inhibitor imatinib. The phosphomimetic glutamic acid substitutions in JunB or Adriamycin treatment impaired the JunB-c-Fos transcription factor complex formation. Taken together, these results suggest that, although JunB represses p21 promoter activity, c-Abl phosphorylates JunB and conversely inhibits its suppressive role on p21 promoter activity upon Adriamycin stimulation. Therefore JunB is likely to be a key target of c-Abl in expression of p21 in Adriamycin-induced DDR.
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19
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Grammatikakis I, Panda AC, Abdelmohsen K, Gorospe M. Long noncoding RNAs(lncRNAs) and the molecular hallmarks of aging. Aging (Albany NY) 2015; 6:992-1009. [PMID: 25543668 PMCID: PMC4298369 DOI: 10.18632/aging.100710] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During aging, progressive deleterious changes increase the risk of disease and death. Prominent molecular hallmarks of aging are genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, cellular senescence, stem cell exhaustion, and altered intercellular communication. Long noncoding RNAs (lncRNAs) play important roles in a wide range of biological processes, including age-related diseases like cancer, cardiovascular pathologies, and neurodegenerative disorders. Evidence is emerging that lncRNAs influence the molecular processes that underlie age-associated phenotypes. Here, we review our current understanding of lncRNAs that control the development of aging traits.
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Affiliation(s)
- Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
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20
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Pollock CB, McDonough S, Wang VS, Lee H, Ringer L, Li X, Prandi C, Lee RJ, Feldman AS, Koltai H, Kapulnik Y, Rodriguez OC, Schlegel R, Albanese C, Yarden RI. Strigolactone analogues induce apoptosis through activation of p38 and the stress response pathway in cancer cell lines and in conditionally reprogrammed primary prostate cancer cells. Oncotarget 2015; 5:1683-98. [PMID: 24742967 PMCID: PMC4039240 DOI: 10.18632/oncotarget.1849] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Strigolactones are a novel class of plant hormones produced in roots and regulate shoot and root development. We have previously shown that synthetic strigolactone analogues potently inhibit growth of breast cancer cells and breast cancer stem cells. Here we show that strigolactone analogues inhibit the growth and survival of an array of cancer-derived cell lines representing solid and non-solid cancer cells including: prostate, colon, lung, melanoma, osteosarcoma and leukemic cell lines, while normal cells were minimally affected. Treatment of cancer cells with strigolactone analogues was hallmarked by activation of the stress-related MAPKs: p38 and JNK and induction of stress-related genes; cell cycle arrest and apoptosis evident by increased percentages of cells in the sub-G1 fraction and Annexin V staining. In addition, we tested the response of patient-matched conditionally reprogrammed primary prostate normal and cancer cells. The tumor cells exhibited significantly higher sensitivity to the two most potent SL analogues with increased apoptosis confirmed by PARP1 cleavage compared to their normal counterpart cells. Thus, Strigolactone analogues are promising candidates for anticancer therapy by their ability to specifically induce cell cycle arrest, cellular stress and apoptosis in tumor cells with minimal effects on growth and survival of normal cells.
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Affiliation(s)
- Claire B Pollock
- Department of Human Science, Georgetown University Medical Center, NW Washington DC
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21
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Thomsen MK, Bakiri L, Hasenfuss SC, Wu H, Morente M, Wagner EF. Loss of JUNB/AP-1 promotes invasive prostate cancer. Cell Death Differ 2014; 22:574-82. [PMID: 25526087 DOI: 10.1038/cdd.2014.213] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is a frequent cause of male death in the Western world. Relatively few genetic alterations have been identified, likely owing to disease heterogeneity. Here, we show that the transcription factor JUNB/AP-1 limits prostate cancer progression. JUNB expression is increased in low-grade prostate cancer compared with normal human prostate, but downregulated in high-grade samples and further decreased in all metastatic samples. To model the hypothesis that this downregulation is functionally significant, we genetically inactivated Junb in the prostate epithelium of mice. When combined with Pten (phosphatase and tensin homologue) loss, double-mutant mice were prone to invasive cancer development. Importantly, invasive tumours also developed when Junb and Pten were inactivated in a small cell population of the adult anterior prostate by topical Cre recombinase delivery. The resulting tumours displayed strong histological similarity with human prostate cancer. Loss of JunB expression led to increased proliferation and decreased senescence, likely owing to decreased p16(Ink4a) and p21(CIP1) in epithelial cells. Furthermore, the tumour stroma was altered with increased osteopontin and S100 calcium-binding protein A8/9 expression, which correlated with poor prognoses in patients. These data demonstrate that JUNB/AP-1 cooperates with PTEN signalling as barriers to invasive prostate cancer, whose concomitant genetic or epigenetic suppression induce malignant progression.
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Affiliation(s)
- M K Thomsen
- Genes, Development and Disease Group, F-BBVA Cancer Cell Biology Programme, National Cancer Research Centre (CNIO), Madrid, Spain
| | - L Bakiri
- Genes, Development and Disease Group, F-BBVA Cancer Cell Biology Programme, National Cancer Research Centre (CNIO), Madrid, Spain
| | - S C Hasenfuss
- Genes, Development and Disease Group, F-BBVA Cancer Cell Biology Programme, National Cancer Research Centre (CNIO), Madrid, Spain
| | - H Wu
- Genes, Development and Disease Group, F-BBVA Cancer Cell Biology Programme, National Cancer Research Centre (CNIO), Madrid, Spain
| | - M Morente
- Biobank, National Cancer Research Centre (CNIO), Madrid, Spain
| | - E F Wagner
- Genes, Development and Disease Group, F-BBVA Cancer Cell Biology Programme, National Cancer Research Centre (CNIO), Madrid, Spain
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22
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Shimada K, Anai S, Fujii T, Tanaka N, Fujimoto K, Konishi N. Syndecan-1 (CD138) contributes to prostate cancer progression by stabilizing tumour-initiating cells. J Pathol 2013; 231:495-504. [DOI: 10.1002/path.4271] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Keiji Shimada
- Department of Pathology; Nara Medical University School of Medicine; Japan
| | - Satoshi Anai
- Department of Urology; Nara Medical University School of Medicine; Japan
| | - Tomomi Fujii
- Department of Pathology; Nara Medical University School of Medicine; Japan
| | - Nobumichi Tanaka
- Department of Urology; Nara Medical University School of Medicine; Japan
| | - Kiyohide Fujimoto
- Department of Urology; Nara Medical University School of Medicine; Japan
| | - Noboru Konishi
- Department of Pathology; Nara Medical University School of Medicine; Japan
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23
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Chen JL, Hsu A, Yang X, Li J, Lee Y, Parinandi G, Li H, Lussier YA. Curation-free biomodules mechanisms in prostate cancer predict recurrent disease. BMC Med Genomics 2013; 6 Suppl 2:S4. [PMID: 23819917 PMCID: PMC3654873 DOI: 10.1186/1755-8794-6-s2-s4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Motivation Gene expression-based prostate cancer gene signatures of poor prognosis are hampered by lack of gene feature reproducibility and a lack of understandability of their function. Molecular pathway-level mechanisms are intrinsically more stable and more robust than an individual gene. The Functional Analysis of Individual Microarray Expression (FAIME) we developed allows distinctive sample-level pathway measurements with utility for correlation with continuous phenotypes (e.g. survival). Further, we and others have previously demonstrated that pathway-level classifiers can be as accurate as gene-level classifiers using curated genesets that may implicitly comprise ascertainment biases (e.g. KEGG, GO). Here, we hypothesized that transformation of individual prostate cancer patient gene expression to pathway-level mechanisms derived from automated high throughput analyses of genomic datasets may also permit personalized pathway analysis and improve prognosis of recurrent disease. Results Via FAIME, three independent prostate gene expression arrays with both normal and tumor samples were transformed into two distinct types of molecular pathway mechanisms: (i) the curated Gene Ontology (GO) and (ii) dynamic expression activity networks of cancer (Cancer Modules). FAIME-derived mechanisms for tumorigenesis were then identified and compared. Curated GO and computationally generated "Cancer Module" mechanisms overlap significantly and are enriched for known oncogenic deregulations and highlight potential areas of investigation. We further show in two independent datasets that these pathway-level tumorigenesis mechanisms can identify men who are more likely to develop recurrent prostate cancer (log-rank_p = 0.019). Conclusion Curation-free biomodules classification derived from congruent gene expression activation breaks from the paradigm of recapitulating the known curated pathway mechanism universe.
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Affiliation(s)
- James L Chen
- Center for Biomed Informatics and Department of Medicine, The University of Chicago, Chicago, IL, USA
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24
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Shimada K, Fujii T, Tsujikawa K, Anai S, Fujimoto K, Konishi N. ALKBH3 Contributes to Survival and Angiogenesis of Human Urothelial Carcinoma Cells through NADPH Oxidase and Tweak/Fn14/VEGF Signals. Clin Cancer Res 2012; 18:5247-55. [DOI: 10.1158/1078-0432.ccr-12-0955] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Giles N, Pavey S, Pinder A, Gabrielli B. Multiple melanoma susceptibility factors function in an ultraviolet radiation response pathway in skin. Br J Dermatol 2011; 166:362-71. [DOI: 10.1111/j.1365-2133.2011.10635.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Chen JH, He HC, Jiang FN, Militar J, Ran PY, Qin GQ, Cai C, Chen XB, Zhao J, Mo ZY, Chen YR, Zhu JG, Liu X, Zhong WD. Analysis of the specific pathways and networks of prostate cancer for gene expression profiles in the Chinese population. Med Oncol 2011; 29:1972-84. [PMID: 22038724 DOI: 10.1007/s12032-011-0088-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 10/07/2011] [Indexed: 01/04/2023]
Abstract
The global physiological function of specifically expressed genes of prostate cancer in Chinese patients is unclear. This study aims to determine the genome-wide expression of genes related to prostate cancer in the Chinese population. Genes that were differentially expressed in prostate cancer were identified using DNA microarray technology. Expressions were validated by using real-time PCR. The identified genes were analyzed using the ingenuity pathway analysis (IPA) to investigate the gene ontology, functional pathway and network. A total of 1,444 genes (Fold time ≥ 1.5; P ≤ 0.05) were differentially expressed in prostate primary tumor tissue compared with benign tissue. IPA revealed a unique landscape where inductions of certain pathways were involved in Cell Cycle Regulation and proliferation. Network analysis not only confirmed that protein interactions lead to the deregulation of DNA Replication, Recombination and Repair, Cellular Compromise and Cell Cycle, Genetic Disorders and Connective Tissue Disorders, but it was also observed that many of the genes regulated by Myc contributed to the modulation of lipid Metabolism and Nucleic Acid Metabolism. Both pathway and network analysis exhibited some remarkable characteristics of prostate cancer for Chinese patients, which showed profound differences from that of other non-Chinese populations. These differences may provide new insights into the molecular cascade of prostate cancer that occurs in Chinese patients.
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Affiliation(s)
- Jia-hong Chen
- Department of Urology, Guangzhou First Municipal People's Hospital, Affiliated Guangzhou Medical College, 510180 Guangzhou, China
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Liu W, Iiizumi-Gairani M, Okuda H, Kobayashi A, Watabe M, Pai SK, Pandey PR, Xing F, Fukuda K, Modur V, Hirota S, Suzuki K, Chiba T, Endo M, Sugai T, Watabe K. KAI1 gene is engaged in NDRG1 gene-mediated metastasis suppression through the ATF3-NFkappaB complex in human prostate cancer. J Biol Chem 2011; 286:18949-59. [PMID: 21454613 PMCID: PMC3099710 DOI: 10.1074/jbc.m111.232637] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
NDRG1 and KAI1 belong to metastasis suppressor genes, which impede the dissemination of tumor cells from primary tumors to distant organs. Previously, we identified the metastasis promoting transcription factor, ATF3, as a downstream target of NDRG1. Further analysis revealed that the KAI1 promoter contained a consensus binding motif of ATF3, suggesting a possibility that NDRG1 suppresses metastasis through inhibition of ATF3 expression followed by activation of the KAI1 gene. In this report, we found that ectopic expression of NDRG1 was able to augment endogenous KAI1 gene expression in prostate cancer cell lines, whereas silencing NDRG1 was accompanied with significant decrease in KAI1 expression in vitro and in vivo. In addition, our results of ChIP analysis indicate that ATF3 indeed bound to the promoter of the KAI1 gene. Importantly, our promoter-based analysis revealed that ATF3 modulated KAI1 transcription through cooperation with other endogenous transcription factor as co-activator (ATF3-JunB) or co-repressor (ATF3-NFκB). Moreover, loss of KAI1 expression significantly abrogated NDRG1-mediated metastatic suppression in vitro as well as in a spontaneous metastasis animal model, indicating that KA11 is a functional downstream target of the NDRG1 pathway. Our result of immunohistochemical analysis showed that loss of NDRG1 and KAI1 occurs in parallel as prostate cancer progresses. We also found that a combined expression status of these two genes serves as a strong independent prognostic marker to predict metastasis-free survival of prostate cancer patients. Taken together, our result revealed a novel regulatory network of two metastasis suppressor genes, NDRG1 and KAI1, which together concerted metastasis-suppressive activities through an intrinsic transcriptional cascade.
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Affiliation(s)
- Wen Liu
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Megumi Iiizumi-Gairani
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Hiroshi Okuda
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Aya Kobayashi
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Misako Watabe
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Sudha K. Pai
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Puspa R. Pandey
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Fei Xing
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Koji Fukuda
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | - Vishnu Modur
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
| | | | | | | | | | - Tamotsu Sugai
- Diagnostic Pathology, Iwate Medical School, Morioka, Iwate 0208505, Japan
| | - Kounosuke Watabe
- From the Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois 62794-9626 and
- To whom correspondence should be addressed. Tel.: 217-545-3969; Fax: 217-545-3227; E-mail:
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Sharma S, Shin JS, Grimshaw M, Clarke RA, Lee CS. The senescence pathway in prostatic carcinogenesis. Pathology 2010; 42:507-11. [DOI: 10.3109/00313025.2010.508791] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Berretta R, Moscato P. Cancer biomarker discovery: the entropic hallmark. PLoS One 2010; 5:e12262. [PMID: 20805891 PMCID: PMC2923618 DOI: 10.1371/journal.pone.0012262] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 06/26/2010] [Indexed: 12/29/2022] Open
Abstract
Background It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases.
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Affiliation(s)
- Regina Berretta
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Pablo Moscato
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
- Australian Research Council Centre of Excellence in Bioinformatics, Callaghan, New South Wales, Australia
- * E-mail:
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Neighborhood rough set reduction-based gene selection and prioritization for gene expression profile analysis and molecular cancer classification. J Biomed Biotechnol 2010; 2010:726413. [PMID: 20625410 PMCID: PMC2896865 DOI: 10.1155/2010/726413] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 04/07/2010] [Indexed: 12/25/2022] Open
Abstract
Selection of reliable cancer biomarkers is crucial for gene expression profile-based precise diagnosis of cancer type and successful treatment. However, current studies are confronted with overfitting and dimensionality curse in tumor classification and false positives in the identification of cancer biomarkers. Here, we developed a novel gene-ranking method based on neighborhood rough set reduction for molecular cancer classification based on gene expression profile. Comparison with other methods such as PAM, ClaNC, Kruskal-Wallis rank sum test, and Relief-F, our method shows that only few top-ranked genes could achieve higher tumor classification accuracy. Moreover, although the selected genes are not typical of known oncogenes, they are found to play a crucial role in the occurrence of tumor through searching the scientific literature and analyzing protein interaction partners, which may be used as candidate cancer biomarkers.
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Abstract
Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK) family members function in a cell context-specific and cell type-specific manner to integrate signals that affect proliferation, differentiation, survival and migration. Consistent with the importance of these events in tumorigenesis, JNK and p38 MAPK signalling is associated with cancers in humans and mice. Studies in mouse models have been essential to better understand how these MAPKs control cancer development, and these models are expected to provide new strategies for the design of improved therapeutic approaches. In this Review we highlight the recent progress made in defining the functions of the JNK and p38 MAPK pathways in different cancers.
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Abstract
Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK) family members function in a cell context-specific and cell type-specific manner to integrate signals that affect proliferation, differentiation, survival and migration. Consistent with the importance of these events in tumorigenesis, JNK and p38 MAPK signalling is associated with cancers in humans and mice. Studies in mouse models have been essential to better understand how these MAPKs control cancer development, and these models are expected to provide new strategies for the design of improved therapeutic approaches. In this Review we highlight the recent progress made in defining the functions of the JNK and p38 MAPK pathways in different cancers.
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Affiliation(s)
- Erwin F Wagner
- Centro Nacional de Investigaciones Oncológicas, C/Melchor Fernández Almagro 3, Madrid 28029, Spain.
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Nakamura M, Shimada K, Konishi N. The role of HRK gene in human cancer. Oncogene 2009; 27 Suppl 1:S105-13. [DOI: 10.1038/onc.2009.48] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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