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Farnoosh G, Saeedi-Boroujeni A, Jalali A, Keikhaei B, Mahmoudian-Sani MR. Polymorphisms in genes involved in breast cancer among Iranian patients. Per Med 2021; 18:153-169. [PMID: 33565318 DOI: 10.2217/pme-2020-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review gives a summary of the important genetic polymorphisms in breast cancer with a focus on people in Iran. Several single nucleotide polymorphisms were considered as breast cancer susceptibility polymorphisms within genes (STK15, ERRs, ESR1, p53, SEP15, AURKA, SHBG, SRC, FAS, VEGF, XRCC1, GST, NFκB1, XPC, XRCC3, sirtuin-3, NKG2D). Cytosine-adenine repeat (IGF-I), rs3877899, G-2548A, GGC (eRF3a/GSPT1), IVS2nt-124A/G have shown an increased risk of breast cancers and a decreased risk has been observed in 4G/5G (PAI-1), rs6505162, tri-nucleotide (GCG TGFBR1). We observed that the signaling pathways and antioxidant related genes are the main molecular processes associated with breast cancer progression. Further studies on types of polymorphisms in breast cancer could validate the prognostic value of biomarkers.
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Affiliation(s)
- Gholamreza Farnoosh
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Saeedi-Boroujeni
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Immunology Today, Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Akram Jalali
- Department of Molecular Medicine & Genetics, School of Medicine Hamadan University of Medical Sciences
| | - Bijan Keikhaei
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad-Reza Mahmoudian-Sani
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Silveira DA, Ribeiro FM, Simão ÉM, Mattos VLD, Góes EG. Expression of genes and pathways associated with the B7-CD28 superfamily in response to irradiation of blood cells using 137Cs. Int J Radiat Biol 2020; 97:149-155. [PMID: 33253600 DOI: 10.1080/09553002.2021.1857454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE DNA damage is one of the main consequences of exposure to ionizing irradiation (IR). Recent studies indicate that IR can modulate the expression of immune system-related genes. However, the effects of IR on the expression of genes and pathways of the B7-CD28 superfamily remain poorly defined. The aim of this study was to evaluate the modulation of genes and pathways related to the B7-CD28 superfamily in response to IR. MATERIALS AND METHODS In this study, we used transcriptome data available from the Gene Expression Omnibus (GEO) database to investigate the modulation of the response of genes and pathways of samples of human peripheral blood irradiated with doses of 150, 300, and 600 cGy. The data were obtained at 6 and 24 h after irradiation. The relationship between genes and pathways was established through the Reactome database. The behavior of these pathways was analyzed using mathematical methods based on relative activity and diversity. Analysis of variance (ANOVA) followed by multiple comparisons tests (Bonferroni and Tamhanes) was used to identify differentially expressed genes. Data on transcriptomes were analyzed through ViaComplex V.1.0 and IBM SPSS Statistics 22. RESULTS For the pathways investigated in this study, we observed that the effects produced by these doses significantly modified the behavior of five pathways associated with the immune system. Also, the dose of 300 cGy might trigger signaling for the activation of T cells through the negative regulation (p < .05) of the co-inhibitory PDCD1LG2 gene. Positive regulation caused by 300 cGy (p < .05) of the CD80 receptor was observed by us, which might be related to a stimulatory signal. According to our findings, this dose induced the production of cytokines and genes that are associated with the activation and differentiation of T cells. CONCLUSIONS Our findings indicate that the irradiation modulated the organization of the biological system, suggesting that 300 cGy is more efficient in activating the immune system.
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Affiliation(s)
- Daner A Silveira
- Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, Brazil
| | - Fernanda M Ribeiro
- Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, Brazil
| | - Éder M Simão
- Nanoscience Graduate Program, Franciscan University, Santa Maria, Brazil
| | - Viviane L D Mattos
- Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, Brazil
| | - Evamberto G Góes
- Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, Brazil
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Hu Y, Zhong W, Chen M, Zhang Q. Identifying crucial genes for prognosis in septic patients: Gene integration study based on PRISMA guidelines. Medicine (Baltimore) 2019; 98:e16807. [PMID: 31415393 PMCID: PMC6831352 DOI: 10.1097/md.0000000000016807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Sepsis is a serious clinical condition with a poor prognosis, despite improvements in diagnosis and treatment.Therefore, novel biomarkers are necessary that can help with estimating prognosis and improving clinical outcomes of patients with sepsis. METHODS The gene expression profiles GSE54514 and GSE63042 were downloaded from the GEO database. DEGs were screened by t test after logarithmization of raw data; then, the common DEGs between the 2 gene expression profiles were identified by up-regulation and down-regulation intersection. The DEGs were analyzed using bioinformatics, and a protein-protein interaction (PPI) survival network was constructed using STRING. Survival curves were constructed to explore the relationship between core genes and the prognosis of sepsis patients based on GSE54514 data. RESULTS A total of 688 common DEGs were identified between survivors and non-survivors of sepsis, and 96 genes were involved in survival networks. The crucial genes Signal transducer and activator of transcription 5A (STAT5A), CCAAT/enhancer-binding protein beta (CEBPB), Myc proto-oncogene protein (MYC), and REL-associated protein (RELA) were identified and showed increased expression in sepsis survivors. These crucial genes had a positive correlation with patients' survival time according to the survival analysis. CONCLUSIONS Our findings indicate that the genes STAT5A, CEBPB, MYC, and RELA may be important in predicting the prognosis of sepsis patients.
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Affiliation(s)
| | | | | | - Qian Zhang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Lu Zhou, Si Chuan, China
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The R implementation of the CRAN package PATHChange, a tool to study genetic pathway alterations in transcriptomic data. Comput Biol Med 2016; 78:76-80. [DOI: 10.1016/j.compbiomed.2016.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 01/22/2023]
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Bioinformatics approach to evaluate differential gene expression of M1/M2 macrophage phenotypes and antioxidant genes in atherosclerosis. Cell Biochem Biophys 2015; 70:831-9. [PMID: 24771407 DOI: 10.1007/s12013-014-9987-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Atherosclerosis is a pro-inflammatory process intrinsically related to systemic redox impairments. Macrophages play a major role on disease development. The specific involvement of classically activated, M1 (pro-inflammatory), or the alternatively activated, M2 (anti-inflammatory), on plaque formation and disease progression are still not established. Thus, based on meta-data analysis of public micro-array datasets, we compared differential gene expression levels of the human antioxidant genes (HAG) and M1/M2 genes between early and advanced human atherosclerotic plaques, and among peripheric macrophages (with or without foam cells induction by oxidized low density lipoprotein, oxLDL) from healthy and atherosclerotic subjects. Two independent datasets, GSE28829 and GSE9874, were selected from gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) repository. Functional interactions were obtained with STRING (http://string-db.org/) and Medusa (http://coot.embl.de/medusa/). Statistical analysis was performed with ViaComplex(®) (http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex/) and gene score enrichment analysis (http://www.broadinstitute.org/gsea/index.jsp). Bootstrap analysis demonstrated that the activity (expression) of HAG and M1 gene sets were significantly increased in advance compared to early atherosclerotic plaque. Increased expressions of HAG, M1, and M2 gene sets were found in peripheric macrophages from atherosclerotic subjects compared to peripheric macrophages from healthy subjects, while only M1 gene set was increased in foam cells from atherosclerotic subjects compared to foam cells from healthy subjects. However, M1 gene set was decreased in foam cells from healthy subjects compared to peripheric macrophages from healthy subjects, while no differences were found in foam cells from atherosclerotic subjects compared to peripheric macrophages from atherosclerotic subjects. Our data suggest that, different to cancer, in atherosclerosis there is no M1 or M2 polarization of macrophages. Actually, M1 and M2 phenotype are equally induced, what is an important aspect to better understand the disease progression, and can help to develop new therapeutic approaches.
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da Motta LL, De Bastiani MA, Stapenhorst F, Klamt F. Oxidative stress associates with aggressiveness in lung large-cell carcinoma. Tumour Biol 2015; 36:4681-8. [PMID: 25638031 DOI: 10.1007/s13277-015-3116-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/14/2015] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress is involved in many cancer-related processes; however, current therapeutics are unable to benefit from this approach. The lungs have a very exquisite redox environment that may contribute to the frequent and deadly nature of lung cancer. Very few studies specifically address lung large-cell carcinoma (LCC), even though this is one of the major subtypes. Using bioinformatic (in silico) tools, we demonstrated that a more aggressive lung LCC cell line (HOP-92) has an overall increase activity of the human antioxidant gene (HAG) network (P = 0.0046) when compared to the less aggressive cell line H-460. Gene set enrichment analysis (GSEA) showed that the expression of metallothioneins (MT), glutathione peroxidase 1 (GPx-1), and catalase (CAT) are responsible for this difference in gene signature. This was validated in vitro, where HOP-92 showed a pro-oxidative imbalance, presenting higher antioxidant enzymes (superoxide dismutase (SOD), CAT, and GPx) activities, lower reduced sulfhydryl groups and antioxidant potential, and higher lipoperoxidation and reactive species production. Also, HAG network is upregulated in lung LCC patients with worst outcome. Finally, the prognostic value of genes enriched in the most aggressive cell line was assessed in this cohort. Isoforms of metallothioneins are associated with bad prognosis, while the thioredoxin-interacting protein (TXNIP) is associated with good prognosis. Thus, redox metabolism can be an important aspect in lung LCC aggressiveness and a possible therapeutic target.
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Affiliation(s)
- Leonardo Lisboa da Motta
- Laboratory of Cellular Biochemistry, Department of Biochemistry, ICBS/UFRGS, 2600 Ramiro Barcelos St - lab. 24, 90035-003, Porto Alegre, RS, Brazil,
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Sisto M, Lisi S, D'Amore M, De Lucro R, Carati D, Castellana D, La Pesa V, Zuccarello V, Lofrumento DD. Saponins from Tribulus terrestris L. protect human keratinocytes from UVB-induced damage. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 117:193-201. [PMID: 23142932 DOI: 10.1016/j.jphotobiol.2012.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/21/2012] [Accepted: 10/06/2012] [Indexed: 12/24/2022]
Abstract
Chronic exposure to solar UVB radiation damages skin, increasing the risk to develop cancer. Hence the identification of compounds with a photoprotective efficacy is essential. This study examined the role of saponins derived from Tribulus terrestris L. (TT) on the modulation of apoptosis in normal human keratinocytes (NHEK) exposed to physiological doses of UVB and to evaluate their antitumoral properties. In NHEK, TT saponins attenuate UVB-induced programmed cell death through inhibition of intrinsic apoptotic pathway. In squamous cell carcinomas (SCC) TT saponins do not make the malignant keratinocytes more resistant to UVB and determine an enhanced apoptotic response. The photoprotective effect of TT saponins is tightly correlated to the enhancement of NER genes expression and the block of UVB-mediated NF-κB activation. Collectively, our study shows experimental evidence that TT has a preventive efficacy against UVB-induced carcinogenesis and the molecular knowledge on the mechanisms through which TT saponins regulate cell death suggests great potential for TT to be developed into a new medicine for cancer patients.
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Affiliation(s)
- Margherita Sisto
- Department of Basic Medical Sciences, Section of Human Anatomy and Histology, University of Bari, Bari, Italy.
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Zeidán-Chuliá F, Rybarczyk-Filho JL, Gursoy M, Könönen E, Uitto VJ, Gursoy OV, Cakmakci L, Moreira JCF, Gursoy UK. Bioinformatical and in vitro approaches to essential oil-induced matrix metalloproteinase inhibition. PHARMACEUTICAL BIOLOGY 2012; 50:675-686. [PMID: 22571397 DOI: 10.3109/13880209.2012.677847] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
CONTEXT Essential oils carry diverse antimicrobial and anti-enzymatic properties. OBJECTIVE Matrix metalloproteinase (MMP) inhibition characteristics of Salvia fruticosa Miller (Labiatae), Myrtus communis Linnaeus (Myrtaceae), Juniperus communis Linnaeus (Cupressaceae), and Lavandula stoechas Linnaeus (Labiatae) essential oils were evaluated. MATERIALS AND METHODS Chemical compositions of the essential oils were analyzed by gas chromatography-mass spectrometry (GC-MS). Bioinformatical database analysis was performed by STRING 9.0 and STITCH 2.0 databases, and ViaComplex software. Antibacterial activity of essential oils against periodontopathogens was tested by the disc diffusion assay and the agar dilution method. Cellular proliferation and cytotoxicity were determined by commercial kits. MMP-2 and MMP-9 activities were measured by zymography. RESULTS Bioinformatical database analyses, under a score of 0.4 (medium) and a prior correction of 0.0, gave rise to a model of protein (MMPs and tissue inhibitors of metalloproteinases) vs. chemical (essential oil components) interaction network; where MMPs and essential oil components interconnected through interaction with hydroxyl radicals, molecular oxygen, and hydrogen peroxide. Components from L. stoechas potentially displayed a higher grade of interaction with MMP-2 and -9. Although antibacterial and growth inhibitory effects of essential oils on the tested periodontopathogens were limited, all of them inhibited MMP-2 in vitro at concentrations of 1 and 5 µL/mL. Moreover, same concentrations of M. communis and L. stoechas also inhibited MMP-9. MMP-inhibiting concentrations of essential oils were not cytotoxic against keratinocytes. DISCUSSION AND CONCLUSION We propose essential oils of being useful therapeutic agents as MMP inhibitors through a mechanism possibly based on their antioxidant potential.
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Affiliation(s)
- Fares Zeidán-Chuliá
- Department of Biochemistry, Center of Oxidative Stress Research, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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Abbasi R, Efferth T, Kuhmann C, Opatz T, Hao X, Popanda O, Schmezer P. The endoperoxide ascaridol shows strong differential cytotoxicity in nucleotide excision repair-deficient cells. Toxicol Appl Pharmacol 2012; 259:302-10. [PMID: 22280988 DOI: 10.1016/j.taap.2012.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 12/19/2011] [Accepted: 01/09/2012] [Indexed: 12/17/2022]
Abstract
Targeting synthetic lethality in DNA repair pathways has become a promising anti-cancer strategy. However little is known about such interactions with regard to the nucleotide excision repair (NER) pathway. Therefore, cell lines with a defect in the NER genes ERCC6 or XPC and their normal counterparts were screened with 53 chemically defined phytochemicals isolated from plants used in traditional Chinese medicine for differential cytotoxic effects. The screening revealed 12 drugs that killed NER-deficient cells more efficiently than proficient cells. Five drugs were further analyzed for IC(50) values, effects on cell cycle distribution, and induction of DNA damage. Ascaridol was the most effective compound with a difference of >1000-fold in resistance between normal and NER-deficient cells (IC(50) values for cells with deficiency in ERCC6: 0.15μM, XPC: 0.18μM, and normal cells: >180μM). NER-deficiency combined with ascaridol treatment led to G2/M-phase arrest, an increased percentage of subG1 cells, and a substantially higher DNA damage induction. These results were confirmed in a second set of NER-deficient and -proficient cell lines with isogenic background. Finally, ascaridol was characterized for its ability to generate oxidative DNA damage. The drug led to a dose-dependent increase in intracellular levels of reactive oxygen species at cytotoxic concentrations, but only NER-deficient cells showed a strongly induced amount of 8-oxodG sites. In summary, ascaridol is a cytotoxic and DNA-damaging compound which generates intracellular reactive oxidative intermediates and which selectively affects NER-deficient cells. This could provide a new therapeutic option to treat cancer cells with mutations in NER genes.
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Affiliation(s)
- Rashda Abbasi
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Simão ÉM, Sinigaglia M, Bugs CA, Castro MAA, Librelotto GR, Alves R, Mombach JCM. Induced genome maintenance pathways in pre-cancer tissues describe an anti-cancer barrier in tumor development. MOLECULAR BIOSYSTEMS 2012; 8:3003-9. [DOI: 10.1039/c2mb25242b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Nucleotide excision repair deficiency is intrinsic in sporadic stage I breast cancer. Proc Natl Acad Sci U S A 2010; 107:21725-30. [PMID: 21118987 DOI: 10.1073/pnas.0914772107] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The molecular etiology of breast cancer has proven to be remarkably complex. Most individual oncogenes are disregulated in only approximately 30% of breast tumors, indicating that either very few molecular alterations are common to the majority of breast cancers, or that they have not yet been identified. In striking contrast, we now show that 19 of 19 stage I breast tumors tested with the functional unscheduled DNA synthesis assay exhibited a significant deficiency of DNA nucleotide excision repair (NER) capacity relative to normal epithelial tissue from disease-free controls (n = 23). Loss of DNA repair capacity, including the complex, damage-comprehensive NER pathway, results in genomic instability, a hallmark of carcinogenesis. By microarray analysis, mRNA expression levels for 20 canonical NER genes were reduced in representative tumor samples versus normal. Significant reductions were observed in 19 of these genes analyzed by the more sensitive method of RNase protection. These results were confirmed at the protein level for five NER gene products. Taken together, these data suggest that NER deficiency may play an important role in the etiology of sporadic breast cancer, and that early-stage breast cancer may be intrinsically susceptible to genotoxic chemotherapeutic agents, such as cis-platinum, whose damage is remediated by NER. In addition, reduced NER capacity, or reduced expression of NER genes, could provide a basis for the development of biomarkers for the identification of tumorigenic breast epithelium.
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Castro MAA, Dal-Pizzol F, Zdanov S, Soares M, Müller CB, Lopes FM, Zanotto-Filho A, da Cruz Fernandes M, Moreira JCF, Shacter E, Klamt F. CFL1 expression levels as a prognostic and drug resistance marker in nonsmall cell lung cancer. Cancer 2010; 116:3645-55. [PMID: 20564088 DOI: 10.1002/cncr.25125] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Nonsmall cell lung cancer (NSCLC) is the major determinant of overall cancer mortality worldwide. Despite progress in molecular research, current treatments offer limited benefits. Because NSCLC generates early metastasis, and this behavior requires great cell motility, herein the authors assessed the potential value of CFL1 gene (main member of the invasion/metastasis pathway) as a prognostic and predictive NSCLC biomarker. METHODS Metadata analysis of tumor tissue microarray was applied to examine expression of CFL1 in archival lung cancer samples from 111 patients, and its clinicopathologic significance was investigated. The robustness of the finding was validated using another independent data set. Finally, the authors assayed in vitro the role of CFL1 levels in tumor invasiveness and drug resistance using 6 human NSCLC cell lines with different basal degrees of CFL1 gene expression. RESULTS CFL1 levels in biopsies discriminate between good and bad prognosis at early tumor stages (IA, IB, and IIA/B), where high CFL1 levels are correlated with lower overall survival rate (P<.0001). Biomarker performance was further analyzed by immunohistochemistry, hazard ratio (P<.001), and receiver-operating characteristic curve (area=0.787; P<.001). High CFL1 mRNA levels and protein content are positively correlated with cellular invasiveness (determined by Matrigel Invasion Chamber System) and resistance (2-fold increase in drug 50% growth inhibition dose) against a list of 22 alkylating agents. Hierarchical clustering analysis of the CFL1 gene network had the same robustness for stratified NSCLC patients. CONCLUSIONS This study indicates that the CFL1 gene and its functional gene network can be used as prognostic biomarkers for NSCLC and could also guide chemotherapeutic interventions.
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Noise-driven heterogeneity in the rate of genetic-variant generation as a basis for evolvability. Genetics 2010; 185:395-404. [PMID: 20606014 DOI: 10.1534/genetics.110.118190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Molecular biologists have long searched for molecular mechanisms responsible for tuning the rate of genetic-variant generation (RGVG) in fluctuating environments. In spite of several bacterial examples, no regulated variation in the RGVG has been identified in eukaryotic systems. Based notably on the example of industrial and pathogenic yeasts, this article proposes a nonregulated molecular evolutionary mechanism for the appearance of the transient increase of the RGVG in eukaryotic cell populations facing challenging environments. The stochastic nature of gene expression allows a model in which the RGVG in the population can be rapidly tuned as a result of a simple Darwinian process acting on noise-driven heterogeneity in the RGVG from cell to cell. The high flexibility conferred through this model could resolve paradoxical situations, especially concerning the mutator phenotype in cancer cells.
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Guirouilh-Barbat J, Antony S, Pommier Y. Zalypsis (PM00104) is a potent inducer of gamma-H2AX foci and reveals the importance of the C ring of trabectedin for transcription-coupled repair inhibition. Mol Cancer Ther 2009; 8:2007-14. [PMID: 19584237 DOI: 10.1158/1535-7163.mct-09-0336] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Zalypsis (PM00104) is a novel tetrahydroisoquinoline alkaloid related to trabectedin [ecteinascidin 743 (Et743)]. Et743 and PM00104 have similar A and B rings but differ in their C rings. The present study shows that Et743 and PM00104 differ in at least two ways: in their DNA binding properties and nucleotide excision repair (NER) dependency for cellular targeting. DNase I footprinting shows that the two drugs bind DNA differentially. We also found that, in contrast to Et743, the antiproliferative activity of PM00104 does not depend on transcription-coupled NER. Accordingly, PM00104 induces gamma-H2AX foci with the same efficiency in NER-deficient or NER-proficient cells. Moreover, the formation of gamma-H2AX foci is replication dependent for PM00104, whereas it is both transcription and replication dependent in the case of Et743. These findings show the importance of the C ring structure of tetrahydroisoquinoline ecteinascidin derivatives for NER targeting. Finally, PM00104 exerts antiproliferative activity at nanomolar concentrations and induces gamma-H2AX response in two Ewing's sarcoma cell lines, suggesting that gamma-H2AX could serve as a pharmacodynamic biomarker for the clinical development of PM00104.
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Affiliation(s)
- Josée Guirouilh-Barbat
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
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Castro MAA, Filho JLR, Dalmolin RJS, Sinigaglia M, Moreira JCF, Mombach JCM, de Almeida RMC. ViaComplex: software for landscape analysis of gene expression networks in genomic context. ACTA ACUST UNITED AC 2009; 25:1468-9. [PMID: 19369498 DOI: 10.1093/bioinformatics/btp246] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
UNLABELLED ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859-1867, 2007; Nucleic Acids Res., 36, 6269-6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article we analyzed this model by projecting functional information from several experiments onto the gene network topology. In order to systematize the methods developed in these articles, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm. AVAILABILITY (http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex).
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Affiliation(s)
- Mauro A A Castro
- Unidade de Bioinformática, Departamento de Bioquímica, Instituto de Física, Núcleo de Bioinformática, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Castro MAA, Dalmolin RJS, Moreira JCF, Mombach JCM, de Almeida RMC. Evolutionary origins of human apoptosis and genome-stability gene networks. Nucleic Acids Res 2008; 36:6269-83. [PMID: 18832373 PMCID: PMC2577361 DOI: 10.1093/nar/gkn636] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and genome-maintenance mechanisms have been extensively documented and include transactivation-independent and -dependent functions, in which the tumor-suppressor protein p53 works as a 'molecular node' in the DNA-damage response. Although apoptosis and genome stability have been identified as ancient pathways in eukaryote phylogeny, the biological evolution underlying the emergence of an integrated system remains largely unknown. Here, using computational methods, we reconstruct the evolutionary scenario that linked apoptosis with genome stability pathways in a functional human gene/protein association network. We found that the entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2. Also, several critical nodes that entangle apoptosis and genome stability are cancer genes (e.g. ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6 and TP53), although their orthologs have arisen in different points of evolution. Our results demonstrate how genome stability and apoptosis were co-opted during evolution recruiting genes that merge both systems. We also provide several examples to exploit this evolutionary platform, where we have judiciously extended information on gene essentiality inferred from model organisms to human.
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Affiliation(s)
- Mauro A A Castro
- Bioinformatics Unit, Department of Biochemistry, Federal University of Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003, Brazil.
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