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Pina M, Fernandes R, Fonseca D, Oliveira C, Rodrigues A. A Case Report of Mesothelioma Response to Endocrine Therapy in Synchronous Breast Cancer and Pleural Epithelioid Mesothelioma: A Double Exemestane Effect. Cureus 2022; 14:e31579. [DOI: 10.7759/cureus.31579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 11/17/2022] Open
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Nuvoli B, Antoniani B, Libener R, Maconi A, Sacconi A, Carosi M, Galati R. Identification of novel COX-2 / CYP19A1 axis involved in the mesothelioma pathogenesis opens new therapeutic opportunities. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:257. [PMID: 34404424 PMCID: PMC8369782 DOI: 10.1186/s13046-021-02050-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/23/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Based on previous studies highlighting that the induction of cyclooxygenase-2 (COX-2) and high prostaglandin E2 (PGE2) levels contribute to the pathogenesis of malignant pleural mesothelioma (MPM), and that aromatase (CYP19A1), an enzyme that plays a key role in estrogen biosynthesis, along with estradiol (E2) were expressed in MPM, this study aimed to investigate the possible interplay between COX-2 and CYP19A1 in the pathogenesis of mesothelioma, as well as the underlying mechanism. METHODS The interaction between COX-2 and CYP19A1 was first investigated on different MPM lines upon PGE2, and COX-2 inhibitor (rofecoxib) treatment by western blot, RT-PCR. The key regulatory pathways involved in the COX-2 and CYP19A1 axis were further studied in MPM cells, after rofecoxib and exemestane (CYP19A1 inhibitor) treatment in monotherapy and in combination, by cell cycle distribution, western blot, and combination index analysis. To explore the role of COX-2/CYP19A1 axis in 3D preclinical models of MPM cells, we analyzed the effect of combination of COX-2 and CYP19A1 inhibitors in mesosphere formation. Immunohistochemical analysis of MPM mesosphere and specimens was utilized to evaluate the involvement of COX-2 on the CYP19A1 activity and the relationship between E2 and COX-2. RESULTS PGE2 or rofecoxib treatment caused in MPM cells an increased or decreased, respectively, CYP19A1 expression at mRNA and protein levels. The effect of rofecoxib and exemestane combination in MPM cell proliferation was synergistic. Activation of caspase-3 and cleavage of PARP confirmed an apoptotic death for MPM cell lines. Increased expression levels of p53, p21, and p27, downregulation of cyclin D1 and inhibition of Akt activation (pAKT) were also found. The antagonistic effect of rofecoxib and exemestane combination found only in one cell line, was reverted by pretreatment with MK2206, a pAKT inhibitor, indicating pAKT as an actionable mediator in the COX-2-CYP19A1 axis. Reduction of size and sphere-forming efficiency in MPM spheres after treatment with both inhibitor and a decrease in COX-2 and E2 staining was found. Moreover, immunohistochemical analysis of 46 MPM samples showed a significant positive correlation between COX-2 and E2. CONCLUSIONS Collectively, the results highlighted a novel COX-2/CYP19A1 axis in the pathogenesis of MPM that can be pharmacologically targeted, consequently opening up new therapeutic options.
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Affiliation(s)
- Barbara Nuvoli
- grid.417520.50000 0004 1760 5276Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Barbara Antoniani
- grid.417520.50000 0004 1760 5276Anatomy Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Roberta Libener
- Department of Integrated Activities Research and Innovation, SS Antonio and Biagio General Hospital, Alessandria, Italy
| | - Antonio Maconi
- Department of Integrated Activities Research and Innovation, SS Antonio and Biagio General Hospital, Alessandria, Italy
| | - Andrea Sacconi
- grid.417520.50000 0004 1760 5276Clinical Trial Center, Biostatistics and Bioinformatics Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Mariantonia Carosi
- grid.417520.50000 0004 1760 5276Anatomy Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Rossella Galati
- grid.417520.50000 0004 1760 5276Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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Jänicke P, Lennicke C, Meister A, Seliger B, Wessjohann LA, Kaluđerović GN. Fluorescent spherical mesoporous silica nanoparticles loaded with emodin: Synthesis, cellular uptake and anticancer activity. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 119:111619. [PMID: 33321661 DOI: 10.1016/j.msec.2020.111619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/24/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
The natural product emodin (EO) exhibits anti-inflammatory, antiangiogenesis and antineoplastic properties in vitro and in vivo. Due to its biological properties as well as its fluorescence, EO can be useful in pharmacology and pharmacokinetics. To enhance its selectivity to cancer cells, EO was loaded into non-fluorescent and novel fluorescent spherical mesoporous nanoparticles bearing N-methyl isatoic anhydride (SNM~M) or lissamine rhodamine B sulfonyl moieties (SNM~L). The propylamine functionalized mesoporous silica nanomaterial (SNM) were characterized by powder X-ray diffraction (XRD), nitrogen gas sorption, scanning electron microscopy (SEM), transmission electron microscopy (TEM), fluorescence spectroscopy, thermogravimetric analysis (TGA) and UV spectroscopy. The cytotoxicity of EO-loaded nanoparticles was tested against the human colon carcinoma cell line HT-29. Non-loaded SNM did not affect cell proliferation, whereas those loaded with EO were at least as efficient as EO alone. It could be shown by fluorescence microscopy that the uptake of silica nanomaterial by the tumor cells occurred within 2 h and the release of EO occurred within 48 h of treatment. Flow cytometry and Western blot analysis showed that SNM containing EO induced apoptosis in HT-29 cells.
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Affiliation(s)
- Paul Jänicke
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D 06120 Halle (Saale), Germany
| | - Claudia Lennicke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, D 06112 Halle (Saale), Germany
| | - Annette Meister
- Institute for Chemistry - Physical and Theoretical Chemistry, Martin Luther University Halle-Wittenberg, D 06099 Halle (Saale), Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, D 06112 Halle (Saale), Germany
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D 06120 Halle (Saale), Germany
| | - Goran N Kaluđerović
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D 06120 Halle (Saale), Germany; Department of Engineering and Natural Sciences, University of Applied Sciences Merseburg, Eberhard-Leibnitz-Straße 2, 06217 Merseburg, Germany.
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Ma GL, Qiao ZL, He D, Wang J, Kong YY, Xin XY, Wen FQ, Bao SJ, Ma ZR, Wang FS, Xie J, Hu YH. Establishment of a low-tumorigenic MDCK cell line and study of differential molecular networks. Biologicals 2020; 68:112-121. [PMID: 32928630 DOI: 10.1016/j.biologicals.2020.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza is an acute respiratory infection caused by the influenza virus, and vaccination against influenza is considered the best way to prevent the onset and spread. MDCK (Madin-Darby canine kidney) cells are typically used to isolate the influenza virus, however, their high tumorigenicity is the main controversy in the production of influenza vaccines. Here, MDCK-C09 and MDCK-C35 monoclonal cell lines were established, which were proven to be low in tumorigenicity. RNA-seq of MDCK-C09, MDCK-C35, and MDCK-W73 cells was performed to investigate the putative tumorigenicity mechanisms. Tumor-related molecular interaction analysis of the differentially expressed genes indicates that hub genes, such as CUL3 and EGFR, may play essential roles in tumorigenicity differences between MDCK-C (MDCK-C09 and MDCK-C35) and MDCK-W (MDCK-W73) cells. Moreover, the analysis of cell proliferation regulation-associated molecular interaction shows that downregulated JUN and MYC, for instance, mediate increased proliferation of these cells. The present study provides a new low-tumorigenic MDCK cell line and describes the potential molecular mechanism for the low tumorigenicity and high proliferation rate.
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Affiliation(s)
- Gui-Lan Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China; Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Zi-Lin Qiao
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Dan He
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Yan-Yan Kong
- Huashan Hospital Affiliated to Fudan University, Shanghai, China.
| | - Xiao-Yong Xin
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
| | - Feng-Qin Wen
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
| | - Shi-Jun Bao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
| | - Zhong-Ren Ma
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Fu-Shuai Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Jiang Xie
- School of Computer Engineering and Science, Shanghai University, Shanghai, China.
| | - Yong-Hao Hu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
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Nuvoli B, Sacconi A, Cortese G, Germoni S, Murer B, Galati R. Reduction of estradiol in human malignant pleural mesothelioma tissues may prevent tumour growth, as implied by in in-vivo and in-vitro models. Oncotarget 2018; 7:47116-47126. [PMID: 27323398 PMCID: PMC5216928 DOI: 10.18632/oncotarget.9964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/17/2016] [Indexed: 12/21/2022] Open
Abstract
This study aimed to investigate intratumoural estradiol and estrogen-receptors (ERα, ERβ and GPR30) in malignant pleural mesothelioma (MPM) to understand their function. Here, we report that immunohistochemistry of estradiol showed cytoplasmatic staining in 95% of fifty-seven human MPM samples with a trend toward a negative correlation between estradiol levels and the median post-diagnosis survival time. ERβ was only focally positive in 5.3% of cases, GPR30 and ERα were negative in our cases of MPM. GPR30 was detected mainly in glycosylated form in MPM cells. Moreover, G15, a GPR30 antagonist, induced MPM cell death. Altogether, these data suggest that MPM cells produce E2 interact with glycosylated forms of GPR30, and this facilitates tumour growth. Estradiol was found in MPM cells and plasma from mice mesothelioma xenografts. Concurrent reduction in tumour mass and plasmatic estradiol levels were observed in the mice treated with exemestane, suggesting that the reduction of E2 levels inhibit MPM growth. Thus, it appears that agents reducing estradiol levels could be useful to MPM therapy.
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Affiliation(s)
- Barbara Nuvoli
- Preclinical Models and New Therapeutic Agent Unit, Regina Elena National Cancer Institute, Rome, Italy
| | - Andrea Sacconi
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Sabrina Germoni
- SAFU Unit, Regina Elena National Cancer Institute, Rome, Italy
| | - Bruno Murer
- Department of Anatomic Pathology, Mestre Hospital, Venezia, Italy
| | - Rossella Galati
- Preclinical Models and New Therapeutic Agent Unit, Regina Elena National Cancer Institute, Rome, Italy
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Nuvoli B, Camera E, Mastrofrancesco A, Briganti S, Galati R. Modulation of reactive oxygen species via ERK and STAT3 dependent signalling are involved in the response of mesothelioma cells to exemestane. Free Radic Biol Med 2018; 115:266-277. [PMID: 29229551 DOI: 10.1016/j.freeradbiomed.2017.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 11/23/2017] [Accepted: 12/06/2017] [Indexed: 12/20/2022]
Abstract
Pleural mesothelioma is a deadly form of cancer. The prognosis is extremely poor due to the limited treatment modalities. Uptake of asbestos fibres, the leading cause of mesothelioma, lead to the accumulation of reactive-oxygen-species (ROS). Interestingly, increasing ROS production by using ROS-generating drugs may offer a strategy to selectively trigger cell death. Exemestane, an aromatase inhibitor, has previously shown anti-tumor properties in mesothelioma preclinical models suggesting a role of G protein-coupled receptor 30 (GPR30) in the drug response. As exemestane, in addition to blocking estrogen biosynthesis, generates ROS that are able to arrest the growth of breast cancer, we explored the role of ROS, antioxidant defense system, and ROS-induced signalling pathways in mesothelioma cells during exemestane response. Here we report that exemestane treatment reduced cell proliferation with an increase in ROS production and reduction of cyclic adenosine monophosphate (cAMP) levels in MSTO-H211, Ist-Mes1, Ist-Mes2 and MPP89 exemestane-sensitive mesothelioma cell lines, but not in NCI-H2452 exemestane-insensitive mesothelioma cells. Exemestane induced a significant antioxidant response in NCI-H2452 cells, as highlighted by an increase in γ-glutamylcysteine levels, catalase (Cat), superoxide-dismutase and (SOD) and glutathione-peroxidase (GSH-Px) activity and nuclear factor E2-related factor 2 (Nrf2) activation, responsible for drug insensitivity. Conversely, exemestane elevated ROS levels along with increased ERK phosphorylation and a reduction of p-STA3 in exemestane-sensitive mesothelioma cells. ROS generation was the crucial event of exemestane action because ROS inhibitor N-acetyl-L-cysteine (NAC) abrogated p-ERK and p-STAT3 modulation and cellular death. Exemestane also modulates ERK and STAT3 signalling via GPR30. Results indicate an essential role of ROS in the antiproliferative action of exemestane in mesothelioma cells. It is likely that the additional oxidative insults induced by exemestane results in the lethal effects of mesothelioma cells by increasing ROS production. As such, manipulating ROS levels with exemestane seems to be a feasible strategy to selectively kill mesothelioma cells with less toxicity to normal cells by regulating ERK and STAT3 activity.
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Affiliation(s)
- Barbara Nuvoli
- Preclinical Models and New Therapeutic Agent Unit, Translational Research Functional Departmental Area, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Emanuela Camera
- Laboratory of Skin Physiopathology and Integrated Centre for Metabolomics San Gallicano Dermatologic Institute (IRCCS), Rome 00144, Italy
| | - Arianna Mastrofrancesco
- Laboratory of Skin Physiopathology and Integrated Centre for Metabolomics San Gallicano Dermatologic Institute (IRCCS), Rome 00144, Italy
| | - Stefania Briganti
- Laboratory of Skin Physiopathology and Integrated Centre for Metabolomics San Gallicano Dermatologic Institute (IRCCS), Rome 00144, Italy
| | - Rossella Galati
- Preclinical Models and New Therapeutic Agent Unit, Translational Research Functional Departmental Area, Regina Elena National Cancer Institute, Rome 00144, Italy.
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Cortes-Dericks L, Schmid RA. CD44 and its ligand hyaluronan as potential biomarkers in malignant pleural mesothelioma: evidence and perspectives. Respir Res 2017; 18:58. [PMID: 28403901 PMCID: PMC5389171 DOI: 10.1186/s12931-017-0546-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/06/2017] [Indexed: 12/11/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and highly drug resistant tumor arising from the mesothelial surfaces of the lung pleura. The standard method to confirm MPM is the tedious, time-consuming cytological examination of cancer biopsy. Biomarkers that are detectable in pleural effusion or patient serum are reasonable options to provide a faster and noninvasive diagnostic approach. As yet, the current biomarkers for MPM lack specificity and sensitivity to discriminate this neoplasm from other lung tumors. CD44, a multifunctional surface receptor has been implicated in tumor progression in different cancers including MPM. The interaction of CD44 with its ligand, hyaluronan (HA) has demonstrated an important role in modulating cell proliferation and invasiveness in MPM. In particular, the high expression levels of these molecules have shown diagnostic relevance in MPM. This review will summarize the biology and diagnostic implication of CD44 and HA as well as the interaction of both molecules in MPM that will demonstrate their potential as biomarkers. Augmentation of the current markers in MPM may lead to an earlier diagnosis and management of this disease.
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Affiliation(s)
- Lourdes Cortes-Dericks
- Department of Clinical Research, Division of General Thoracic Surgery, University Hospital Berne, Berne, Switzerland.
| | - Ralph Alexander Schmid
- Department of Clinical Research, Division of General Thoracic Surgery, University Hospital Berne, Berne, Switzerland
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Sobral AF, Amaral C, Correia-da-Silva G, Teixeira N. Unravelling exemestane: From biology to clinical prospects. J Steroid Biochem Mol Biol 2016; 163:1-11. [PMID: 26992705 DOI: 10.1016/j.jsbmb.2016.03.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/29/2016] [Accepted: 03/13/2016] [Indexed: 11/28/2022]
Abstract
Aromatase inhibitors (AIs) are anti-tumor agents used in clinic to treat hormone-dependent breast cancer. AIs block estrogens biosynthesis by inhibiting the enzyme aromatase, preventing tumor progression. Exemestane, a third-generation steroidal AI, belongs to this class of drugs and is currently used in clinic to treat postmenopausal women, due to its high efficacy and good tolerability. Here, its pharmacological and biological aspects as well as its clinical applications and comparison to other endocrine therapeutic agents, are reviewed. It is also focused the benefits and risks of exemestane, drawbacks to be overcome and aspects to be explored.
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Affiliation(s)
- Ana Filipa Sobral
- Faculty of Science and Technology, University of Coimbra, Calçada Martim de Freitas 3000-456 Coimbra, Portugal; UCIBIO-REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal
| | - Cristina Amaral
- UCIBIO-REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
| | - Georgina Correia-da-Silva
- UCIBIO-REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal
| | - Natércia Teixeira
- UCIBIO-REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
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Benedetti S, Nuvoli B, Catalani S, Galati R. Reactive oxygen species a double-edged sword for mesothelioma. Oncotarget 2016; 6:16848-65. [PMID: 26078352 PMCID: PMC4627278 DOI: 10.18632/oncotarget.4253] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
It is well known that oxidative stress can lead to chronic inflammation which, in turn, could mediate most chronic diseases including cancer. Oxidants have been implicated in the activity of crocidolite and amosite, the most powerful types of asbestos associated to the occurrence of mesothelioma. Currently rates of mesothelioma are rising and estimates indicate that the incidence of mesothelioma will peak within the next 10-15 years in the western world, while in Japan the peak is predicted not to occur until 40 years from now. Although the use of asbestos has been banned in many countries around the world, production of and the potentially hazardous exposure to asbestos is still present with locally high incidences of mesothelioma. Today a new man-made material, carbon nanotubes, has arisen as a concern; carbon nanotubes may display 'asbestos-like' pathogenicity with mesothelioma induction potential. Carbon nanotubes resulted in the greatest reactive oxygen species generation. How oxidative stress activates inflammatory pathways leading to the transformation of a normal cell to a tumor cell, to tumor cell survival, proliferation, invasion, angiogenesis, chemoresistance, and radioresistance, is the aim of this review.
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Affiliation(s)
- Serena Benedetti
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Barbara Nuvoli
- Molecular Medicine Area, Regina Elena National Cancer Institute, Rome, Italy
| | - Simona Catalani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Rossella Galati
- Molecular Medicine Area, Regina Elena National Cancer Institute, Rome, Italy
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A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping. BMC Bioinformatics 2016; 17:211. [PMID: 27170106 PMCID: PMC4864913 DOI: 10.1186/s12859-016-1066-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/29/2016] [Indexed: 01/14/2023] Open
Abstract
Background Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research in connectivity mapping mainly focused on two of the key components in the framework, namely, the reference gene expression profiles and the connectivity mapping algorithms. The other key component in this framework, the query gene signature, has been left to users to construct without much consensus on how this should be done, albeit it has been an issue most relevant to end users. As a key input to the connectivity mapping process, gene signature is crucially important in returning biologically meaningful and relevant results. This paper intends to formulate a standardized procedure for constructing high quality gene signatures from a user’s perspective. Results We describe a two-stage process for making quality gene signatures using gene expression data as initial inputs. First, a differential gene expression analysis comparing two distinct biological states; only the genes that have passed stringent statistical criteria are considered in the second stage of the process, which involves ranking genes based on statistical as well as biological significance. We introduce a “gene signature progression” method as a standard procedure in connectivity mapping. Starting from the highest ranked gene, we progressively determine the minimum length of the gene signature that allows connections to the reference profiles (drugs) being established with a preset target false discovery rate. We use a lung cancer dataset and a breast cancer dataset as two case studies to demonstrate how this standardized procedure works, and we show that highly relevant and interesting biological connections are returned. Of particular note is gefitinib, identified as among the candidate therapeutics in our lung cancer case study. Our gene signature was based on gene expression data from Taiwan female non-smoker lung cancer patients, while there is evidence from independent studies that gefitinib is highly effective in treating women, non-smoker or former light smoker, advanced non-small cell lung cancer patients of Asian origin. Conclusions In summary, we introduced a gene signature progression method into connectivity mapping, which enables a standardized procedure for constructing high quality gene signatures. This progression method is particularly useful when the number of differentially expressed genes identified is large, and when there is a need to prioritize them to be included in the query signature. The results from two case studies demonstrate that the approach we have developed is capable of obtaining pertinent candidate drugs with high precision. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1066-x) contains supplementary material, which is available to authorized users.
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