Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 32
Filtrar
Mais filtros

Base de dados
Tipo de documento
Intervalo de ano de publicação
1.
Genes Chromosomes Cancer ; 52(2): 126-39, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23011637

RESUMO

Histone lysine methylation plays a fundamental role in chromatin organization. Although a set of histone methyltransferases have been identified and biochemically characterized, the pathological roles of their dysfunction in human cancers are still not well understood. In this study, we demonstrate important roles of WHSC1L1 in human carcinogenesis. Expression levels of WHSC1L1 transcript were significantly elevated in various human cancers including bladder carcinoma. Immunohistochemical analysis of bladder, lung, and liver cancers confirmed overexpression of WHSC1L1. WHSC1L1-specific small interfering RNAs significantly knocked down its expression and resulted in suppression of proliferation of bladder and lung cancer cell lines. WHSC1L1 knockdown induced cell cycle arrest at the G(2)/M phase followed by multinucleation of cancer cells. Expression profile analysis using Affymetrix GeneChip(®) showed that WHSC1L1 affected the expression of a number of genes including CCNG1 and NEK7, which are known to play crucial roles in the cell cycle progression at mitosis. As WHSC1L1 expression is significantly low in various normal tissues including vital organs, WHSC1L1 could be a good candidate molecule for development of novel treatment for various types of cancer.


Assuntos
Regulação Neoplásica da Expressão Gênica , Histona-Lisina N-Metiltransferase/genética , Neoplasias/genética , Proteínas Nucleares/genética , Ciclo Celular/genética , Linhagem Celular Tumoral , Proliferação de Células , Ciclina G1/genética , Ciclina G1/metabolismo , Feminino , Citometria de Fluxo , Perfilação da Expressão Gênica , Células HEK293 , Células HeLa , Células Hep G2 , Histona-Lisina N-Metiltransferase/metabolismo , Humanos , Imuno-Histoquímica , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patologia , Masculino , Quinases Relacionadas a NIMA , Neoplasias/metabolismo , Neoplasias/patologia , Proteínas Nucleares/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , Interferência de RNA , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/metabolismo , Neoplasias da Bexiga Urinária/patologia
2.
BMC Bioinformatics ; 14: 141, 2013 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-23621955

RESUMO

BACKGROUND: Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. RESULTS: We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. CONCLUSIONS: CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its original purpose, the software can be used to visualize any dataset where entity occupancy is compared between different classes. AVAILABILITY: CPG software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox.com/u/6701906/Web/Sites/Labsite/CPG.html.


Assuntos
Gráficos por Computador , Genômica/métodos , Software , Algoritmos , Subunidades Proteicas/genética
3.
Nature ; 447(7148): 1087-93, 2007 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-17529967

RESUMO

Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r2 > 0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P < 10(-7)). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P < 0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.


Assuntos
Neoplasias da Mama/genética , Predisposição Genética para Doença/genética , Genoma Humano/genética , Alelos , Proteínas Reguladoras de Apoptose , Sudeste Asiático , Austrália , Estudos de Casos e Controles , Europa (Continente)/etnologia , Feminino , Genótipo , Proteínas de Grupo de Alta Mobilidade , Humanos , MAP Quinase Quinase Quinase 1/genética , Proteínas dos Microfilamentos/genética , América do Norte , Razão de Chances , Polimorfismo de Nucleotídeo Único/genética , Receptor Tipo 2 de Fator de Crescimento de Fibroblastos/genética , Receptores de Progesterona/genética , Transativadores
4.
Int J Cancer ; 131(3): E179-89, 2012 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-22020899

RESUMO

A number of histone demethylases have been identified and biochemically characterized, yet their biological functions largely remain uncharacterized, particularly in the context of human diseases such as cancer. In this study, we describe important roles for the histone demethylase KDM3A, also known as JMJD1A, in human carcinogenesis. Expression levels of KDM3A were significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (p < 0.0001), when assessed by real-time PCR. We confirmed that some other cancers including lung cancer also overexpressed KDM3A, using cDNA microarray analysis. Treatment of cancer cell lines with small interfering RNA targeting KDM3A significantly knocked down its expression and resulted in the suppression of proliferation. Importantly, we found that KDM3A activates transcription of the HOXA1 gene through demethylating histone H3 at lysine 9 di-methylation by binding to its promoter region. Indeed, expression levels of KDM3A and HOXA1 in several types of cancer cell lines and bladder cancer samples were statistically correlated. We observed the down-regulation of HOXA1 as well as CCND1 after treatment with KDM3A siRNA, indicating G(1) arrest of cancer cells. Together, our results suggest that elevated expression of KDM3A plays a critical role in the growth of cancer cells, and further studies may reveal a cancer therapeutic potential in KDM3A inhibition.


Assuntos
Proteínas de Homeodomínio/genética , Histona Desmetilases com o Domínio Jumonji/metabolismo , Neoplasias Pulmonares/metabolismo , Fatores de Transcrição/genética , Neoplasias da Bexiga Urinária/metabolismo , Linhagem Celular Tumoral , Proliferação de Células , Ciclina D1/biossíntese , Pontos de Checagem da Fase G1 do Ciclo Celular , Regulação Neoplásica da Expressão Gênica , Histonas/metabolismo , Humanos , Histona Desmetilases com o Domínio Jumonji/genética , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Metilação , Análise de Sequência com Séries de Oligonucleotídeos , Interferência de RNA , RNA Interferente Pequeno , Transcrição Gênica , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/patologia
5.
Hum Mol Genet ; 19(12): 2507-15, 2010 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-20332101

RESUMO

Recent genome-wide association studies have identified a breast cancer susceptibility locus on 16q12 with an unknown biological basis. We used a set of single nucleotide polymorphism (SNP) markers to generate a fine-scale map and narrowed the region of association to a 133 kb DNA segment containing the largely uncharacterized hypothetical gene LOC643714, a short intergenic region and the 5' end of TOX3. Re-sequencing this segment in European subjects identified 293 common polymorphisms, including a set of 26 highly correlated candidate causal variants. By evaluation of these SNPs in five breast cancer case-control studies involving more than 23 000 subjects from populations of European and Southeast Asian ancestry, all but 14 variants could be excluded at odds of <1:100. Most of the remaining variants lie in the intergenic region, which exhibits evolutionary conservation and open chromatin conformation, consistent with a regulatory function. African-American case-control studies exhibit a different pattern of association suggestive of an additional causative variant.


Assuntos
Neoplasias da Mama/genética , Cromossomos Humanos Par 16/genética , Predisposição Genética para Doença , Mapeamento Cromossômico , Feminino , Marcadores Genéticos , Estudo de Associação Genômica Ampla , Humanos , Polimorfismo de Nucleotídeo Único
6.
Mol Cancer ; 10: 65, 2011 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-21619671

RESUMO

BACKGROUND: The research emphasis in anti-cancer drug discovery has always been to search for a drug with the greatest antitumor potential but fewest side effects. This can only be achieved if the drug used is against a specific target located in the tumor cells. In this study, we evaluated Minichromosome Maintenance Protein 7 (MCM7) as a novel therapeutic target in cancer. RESULTS: Immunohistochemical analysis showed that MCM7 was positively stained in 196 of 331 non-small cell lung cancer (NSCLC), 21 of 29 bladder tumor and 25 of 70 liver tumor cases whereas no significant staining was observed in various normal tissues. We also found an elevated expression of MCM7 to be associated with poor prognosis for patients with NSCLC (P = 0.0055). qRT-PCR revealed a higher expression of MCM7 in clinical bladder cancer tissues than in corresponding non-neoplastic tissues (P < 0.0001), and we confirmed that a wide range of cancers also overexpressed MCM7 by cDNA microarray analysis. Suppression of MCM7 using specific siRNAs inhibited incorporation of BrdU in lung and bladder cancer cells overexpressing MCM7, and suppressed the growth of those cells more efficiently than that of normal cell strains expressing lower levels of MCM7. CONCLUSIONS: Since MCM7 expression was generally low in a number of normal tissues we examined, MCM7 has the characteristics of an ideal candidate for molecular targeted cancer therapy in various tumors and also as a good prognostic biomarker for NSCLC patients.


Assuntos
Biomarcadores Tumorais , Carcinoma Pulmonar de Células não Pequenas/fisiopatologia , Proteínas de Ciclo Celular/metabolismo , Proteínas de Ligação a DNA/metabolismo , Regulação Neoplásica da Expressão Gênica , Neoplasias Pulmonares/fisiopatologia , Neoplasias/fisiopatologia , Proteínas Nucleares/metabolismo , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Carcinoma Pulmonar de Células não Pequenas/diagnóstico , Proteínas de Ciclo Celular/genética , Linhagem Celular Tumoral , Proliferação de Células , Proteínas de Ligação a DNA/genética , Perfilação da Expressão Gênica , Inativação Gênica , Células HCT116 , Células HEK293 , Células HeLa , Células Hep G2 , Humanos , Neoplasias Pulmonares/diagnóstico , Componente 7 do Complexo de Manutenção de Minicromossomo , Proteínas Nucleares/genética , Prognóstico , Ligação Proteica , Proteína-Arginina N-Metiltransferases/metabolismo , RNA Interferente Pequeno/metabolismo
7.
Int J Cancer ; 128(3): 574-86, 2011 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-20333681

RESUMO

A number of histone demethylases have been identified and biochemically characterized, but the pathological roles of their dysfunction in human disease like cancer have not been well understood. Here, we demonstrate important roles of lysine-specific demethylase 1 (LSD1) in human carcinogenesis. Expression levels of LSD1 are significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (p < 0.0001). cDNA microarray analysis also revealed its transactivation in lung and colorectal carcinomas. LSD1-specific small interfering RNAs significantly knocked down its expression and resulted in suppression of proliferation of various bladder and lung cancer cell lines. Concordantly, introduction of exogenous LSD1 expression promoted cell cycle progression of human embryonic kidney fibroblast cells. Expression profile analysis showed that LSD1 could affect the expression of genes involved in various chromatin-modifying pathways such as chromatin remodeling at centromere, centromeric heterochromatin formation and chromatin assembly, indicating its essential roles in carcinogenesis through chromatin modification.


Assuntos
Cromatina/fisiologia , Regulação Neoplásica da Expressão Gênica , Histona Desmetilases/genética , Neoplasias/genética , Neoplasias da Bexiga Urinária/genética , Ciclo Celular , Divisão Celular , Linhagem Celular Tumoral , Cromatina/genética , DNA Complementar/genética , DNA de Neoplasias/genética , Perfilação da Expressão Gênica , Regulação Enzimológica da Expressão Gênica , Humanos , Imuno-Histoquímica , Neoplasias/enzimologia , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase , Bexiga Urinária/citologia , Bexiga Urinária/fisiologia , Neoplasias da Bexiga Urinária/patologia
8.
Int J Cancer ; 128(3): 562-73, 2011 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-20473859

RESUMO

Protein arginine methylation is a novel post-translational modification regulating a diversity of cellular processes, including histone functions, but the roles of protein arginine methyltransferases (PRMTs) in human cancer are not well investigated. To address this issue, we first examined expression levels of genes belonging to the PRMT family and found significantly higher expression of PRMT1 and PRMT6, both of which are Type I PRMTs, in cancer cells of various tissues than in non-neoplastic cells. Abrogation of the expression of these genes with specific siRNAs significantly suppressed growth of bladder and lung cancer cells. Expression profile analysis using the cells transfected with the siRNAs indicated that PRMT1 and PRMT6 interplay in multiple pathways, supporting regulatory roles in the cell cycle, RNA processing and also DNA replication that are fundamentally important for cancer cell proliferation. Furthermore, we demonstrated that serum asymmetric dimethylarginine (ADMA) levels of a number of cancer cases are significantly higher than those of nontumor control cases. In summary, our results suggest that dysregulation of PRMT1 and PRMT6 can be involved in human carcinogenesis and that these Type I arginine methyltransferases are good therapeutic targets for various types of cancer.


Assuntos
Regulação Neoplásica da Expressão Gênica , Neoplasias Pulmonares/genética , Neoplasias/genética , Proteínas Nucleares/genética , Proteína-Arginina N-Metiltransferases/genética , Proteínas Repressoras/genética , Neoplasias da Bexiga Urinária/genética , Antracenos , Arginina/análogos & derivados , Arginina/sangue , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Divisão Celular , Linhagem Celular Tumoral , Replicação do DNA , Ensaio de Imunoadsorção Enzimática , Perfilação da Expressão Gênica , Humanos , Neoplasias Pulmonares/patologia , Análise de Sequência com Séries de Oligonucleotídeos , Propano/análogos & derivados , Propano/sangue , RNA Interferente Pequeno/genética , Neoplasias da Bexiga Urinária/patologia
9.
Cancer Sci ; 102(7): 1298-305, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21539681

RESUMO

The emphasis in anticancer drug discovery has always been on finding a drug with great antitumor potential but few side-effects. This can be achieved if the drug is specific for a molecular site found only in tumor cells. Here, we find the enhancer of zeste homolog 2 (EZH2) to be highly overexpressed in lung and other cancers, and show that EZH2 is integral to proliferation in cancer cells. Quantitative real-time PCR analysis revealed higher expression of EZH2 in clinical bladder cancer tissues than in corresponding non-neoplastic tissues (P < 0.0001), and we confirmed that a wide range of cancers also overexpress EZH2, using cDNA microarray analysis. Immunohistochemical analysis showed positive staining for EZH2 in 14 of 29 cases of bladder cancer, 135 of 292 cases of non-small-cell lung cancer (NSCLC), and 214 of 245 cases of colorectal cancer, whereas no significant staining was observed in various normal tissues. We found elevated expression of EZH2 to be associated with poor prognosis for patients with NSCLC (P = 0.0239). In lung and bladder cancer cells overexpressing EZH2, suppression of EZH2 using specific siRNAs inhibited incorporation of BrdU and resulted in significant suppression of cell growth, even though no significant effect was observed in the normal cell strain CCD-18Co, which has undetectable EZH2. Because EZH2 expression was scarcely detectable in all normal tissues we examined, EZH2 shows promise as a tumor-specific therapeutic target. Furthermore, as elevated levels of EZH2 are associated with poor prognosis of patients with NSCLC, its overexpression in resected specimens could prove a useful molecular marker, indicating the necessity for a more extensive follow-up in some lung cancer patients after surgical treatment.


Assuntos
Biomarcadores Tumorais/fisiologia , Proteínas de Ligação a DNA/fisiologia , Neoplasias/tratamento farmacológico , Fatores de Transcrição/fisiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/antagonistas & inibidores , Biomarcadores Tumorais/genética , Proliferação de Células , Neoplasias Colorretais/metabolismo , Proteínas de Ligação a DNA/antagonistas & inibidores , Proteínas de Ligação a DNA/genética , Proteína Potenciadora do Homólogo 2 de Zeste , Feminino , Humanos , Neoplasias Pulmonares/metabolismo , Masculino , Pessoa de Meia-Idade , Neoplasias/metabolismo , Neoplasias/mortalidade , Complexo Repressor Polycomb 2 , Prognóstico , Modelos de Riscos Proporcionais , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/genética , Neoplasias da Bexiga Urinária/metabolismo
10.
J Appl Lab Med ; 6(3): 668-678, 2021 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-33928391

RESUMO

BACKGROUND: Aldosterone and renin are pivotal hormones in the regulation of salt and water homeostasis and blood pressure. Measurement of renin and aldosterone in serum/plasma is essential for the investigation of primary hyperaldosteronism (PA) and monitoring of glucocorticoid replacement therapy. METHODS: We report 2 LC-MS/MS methods developed to measure aldosterone and plasma renin activity (PRA). PRA was determined by endogenous enzymatic generation of angiotensin I using 150 µL of sample. Generated angiotensin I was purified by solid phase extraction prior to chromatographic separation and mass spectrometry. Aldosterone measurement required 300 µL of sample extracted with MTBE prior to LC-MS/MS analysis. RESULTS: The PRA method was linear (1.2-193 nmol/L), sensitive (LLOQ = 1.2 nmol/L), precise (CV = 4.1%), and specific (no cross reactivity for a number of structurally similar steroids). Dilutional linearity and recovery (84%) were acceptable. Accuracy was confirmed by comparison against our current RIA method. The aldosterone method had equally acceptable performance characteristics. Reference ranges in 110 healthy normotensive subjects were: PRA 0.2-3.7 nmol/L/h and aldosterone 50-950 pmol/L. Consecutive patients (n = 62) with adrenal incidentalomas shown to have no functional adrenal disease; their post overnight 1 mg dexamethasone test values were: PRA 0.2-2.6 nmol/L/h and aldosterone 55-480 pmol/L. Serum aldosterone values after 2 liter saline suppression were-normal subjects (n = 17): 78-238 pmol/L and confirmed primary hyperaldosteronism (n = 25): 131-1080 pmol/L. CONCLUSIONS: We have developed robust assays for PRA and aldosterone with appropriate clinical evaluation. These assays are now in routine practice in the UK.


Assuntos
Neoplasias das Glândulas Suprarrenais , Aldosterona , Cromatografia Líquida , Humanos , Renina , Espectrometria de Massas em Tandem
11.
Mol Cancer ; 9: 59, 2010 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-20226085

RESUMO

BACKGROUND: Although an increasing number of histone demethylases have been identified and biochemically characterized, their biological functions largely remain uncharacterized, particularly in the context of human diseases such as cancer. We investigated the role of KDM5B, a JmjC histone demethylase, in human carcinogenesis. Quantitative RT-PCR and microarray analyses were used to examine the expression profiles of histone demethylases in clinical tissue samples. We also examined the functional effects of KDM5B on the growth of cancer cell lines treated with small interfering RNAs (siRNAs). Downstream genes and signal cascades induced by KDM5B expression were identified from Affymetrix Gene Chip experiments, and validated by real-time PCR and reporter assays. Cell cycle-dependent characteristics of KDM5B were identified by immunofluorescence and FACS. RESULTS: Quantitative RT-PCR analysis confirmed that expression levels of KDM5B are significantly higher in human bladder cancer tissues than in their corresponding non-neoplastic bladder tissues (P < 0.0001). The expression profile analysis of clinical tissues also revealed up-regulation of KDM5B in various kinds of malignancies. Transfection of KDM5B-specific siRNA into various bladder and lung cancer cell lines significantly suppressed the proliferation of cancer cells and increased the number of cells in sub-G1 phase. Microarray expression analysis indicated that E2F1 and E2F2 are downstream genes in the KDM5B pathway. CONCLUSIONS: Inhibition of KDM5B may affect apoptosis and reduce growth of cancer cells. Further studies will explore the pan-cancer therapeutic potential of KDM5B inhibition.


Assuntos
Fator de Transcrição E2F1/metabolismo , Fator de Transcrição E2F2/metabolismo , Histona Desmetilases com o Domínio Jumonji/metabolismo , Proteínas Nucleares/metabolismo , Lesões Pré-Cancerosas/enzimologia , Lesões Pré-Cancerosas/patologia , Proteínas Repressoras/metabolismo , Proteína do Retinoblastoma/metabolismo , Linhagem Celular Tumoral , Proliferação de Células , Fator de Transcrição E2F1/genética , Fator de Transcrição E2F2/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Histona Desmetilases com o Domínio Jumonji/genética , Masculino , Proteínas Nucleares/genética , Análise de Sequência com Séries de Oligonucleotídeos , Lesões Pré-Cancerosas/genética , Proteínas Repressoras/genética , Reprodutibilidade dos Testes , Transdução de Sinais , Análise Serial de Tecidos , Regulação para Cima/genética
12.
BMC Bioinformatics ; 10: 180, 2009 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-19523221

RESUMO

BACKGROUND: In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once. IMPLEMENTATION: We created Seq4SNPs, a web-based, walk-away software that can process one to several hundred SNPs given rs numbers as input. It outputs a file of fully annotated sequences formatted for one of three proprietary design softwares: TaqMan's Primer-By-Design FileBuilder, Sequenom's iPLEX or SNPstream's Autoprimer, as well as unannotated fasta sequences. We found genotyping assays to be inhibited by repetitive sequences or the presence of additional variations flanking the SNP under test, and in multiplexes, repetitive sequence flanking one SNP adversely affects multiple assays. Assay design software programs avoid such regions if the input sequences are appropriately annotated, so we used Seq4SNPs to provide suitably annotated input sequences, and improved our genotyping success rate. Adjacent SNPs can also be avoided, by annotating sequences used as input for primer design. CONCLUSION: The accuracy of annotation by Seq4SNPs is significantly better than manual annotation (P < 1e-5).Using Seq4SNPs to incorporate all annotation for additional SNPs and repetitive elements into sequences, for genotyping assay designer software, minimizes assay failure at the design stage, reducing the cost of genotyping. Seq4SNPs provides a rapid route for replacement of poor test SNP sequences. We routinely use this software for assay sequence preparation. Seq4SNPs is available as a service at (http://moya.srl.cam.ac.uk/oncology/bio/s4shome.html) and (http://moya.srl.cam.ac.uk/cgi-bin/oncology/srl/ncbi/seq4snp1.pl), currently for human SNPs, but easily extended to include any species in dbSNP.


Assuntos
Biologia Computacional/métodos , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA/métodos , Software , Sequência de Bases , Bases de Dados Genéticas , Genótipo
13.
Asian J Androl ; 11(1): 49-55, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19050691

RESUMO

There is evidence that a substantial part of genetic predisposition to prostate cancer (PCa) may be due to lower penetrance genes which are found by genome-wide association studies. We have recently conducted such a study and seven new regions of the genome linked to PCa risk have been identified. Three of these loci contain candidate susceptibility genes: MSMB, LMTK2 and KLK2/3. The MSMB and KLK2/3 genes may be useful for PCa screening, and the LMTK2 gene might provide a potential therapeutic target. Together with results from other groups, there are now 23 germline genetic variants which have been reported. These results have the potential to be developed into a genetic test. However, we consider that marketing of tests to the public is premature, as PCa risk can not be evaluated fully at this stage and the appropriate screening protocols need to be developed. Follow-up validation studies, as well as studies to explore the psychological implications of genetic profile testing, will be vital prior to roll out into healthcare.


Assuntos
Predisposição Genética para Doença/genética , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/genética , Testes Genéticos , Humanos , Calicreínas/genética , Masculino , Proteínas de Membrana/genética , Proteínas Secretadas pela Próstata/genética , Proteínas Serina-Treonina Quinases/genética , Fatores de Risco
14.
Clin Chem ; 54(8): 1290-7, 2008 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-18556330

RESUMO

BACKGROUND: The recent interest of clinical laboratories in developing serum testosterone assays based on isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) stems from the lack of accuracy of direct immunoassays. In this study, we assessed the accuracy and state of standardization (traceability) of 4 published ID-LC-MS/MS procedures in a method comparison with an ID-gas chromatography (GC)-MS reference measurement procedure listed in the database of the Joint Committee for Traceability in Laboratory Medicine. METHODS: The study used 58 specimens from different patient categories. Each specimen was measured in triplicate (ID-LC-MS/MS) and quadruplicate (ID-GC-MS) in independent runs. RESULTS: The testosterone concentrations by ID-GC-MS were 0.2-4.4 nmol/L (women), 0.2-2.0 nmol/L (hypogonadal man), and 10.1-31.3 nmol/L (normogonadal men). For ID-GC-MS, the CV was nearly constant, with a median of 1.0%; for ID-LC-MS/MS, it was concentration-dependent, with a median of up to 8%. Weighted Deming regression gave mean slopes, intercepts, and correlation coefficients of 0.90-1.11, -0.055-0.013 nmol/L, and 0.993-0.997, respectively. The % difference plot showed between 7% and 26% of the results outside a total error limit of 14%, with median deviations from ID-GC-MS between -9.6 and 0.4%. CONCLUSIONS: This study demonstrated fairly good accuracy and standardization of the tested ID-LC-MS/MS procedures. Performance differences between procedures were evident in some instances, due to improper calibration and between-run calibration control. This emphasizes the need for thorough validation, including traceability, of new ID-LC-MS/MS procedures.


Assuntos
Cromatografia Líquida/métodos , Espectrometria de Massas em Tandem/métodos , Testosterona/sangue , Adolescente , Adulto , Calibragem , Isótopos de Carbono , Feminino , Humanos , Hipogonadismo/sangue , Técnicas de Diluição do Indicador , Masculino , Pessoa de Meia-Idade , Padrões de Referência , Análise de Regressão , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Manejo de Espécimes
15.
Steroids ; 110: 62-69, 2016 06.
Artigo em Inglês | MEDLINE | ID: mdl-27091764

RESUMO

INTRODUCTION: Associations of endogenous sex hormone levels and all as well as estrogen-receptor (ER)-positive breast cancers are well described. However, studies investigating their association with ER-negative tumours are limited and none use accurate assays such as mass spectrometry. METHODS: Within the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS), a nested case-control study was undertaken of postmenopausal-women who developed ER-negative (n=92) or ER-positive (n=205) breast cancer after sample donation and 297 (1:1) age-matched controls. Androgens (testosterone and androstenedione) were measured using mass spectrometry and estradiol by extraction radioimmunoassay (RIA). Bioavailable estradiol and testosterone were calculated using the total hormone level and the sex hormone-binding globulin concentration. Subjects were classified according to the quartile range among controls. Logistic regression was used to estimate odds-ratio (OR) and 95% confidence-intervals (CI) of the associations between two factors and breast cancer risk. A separate analysis was done by stratifying the women based on whether they provided their samples less than or more than 2years before diagnosis. RESULTS: Estradiol and free estradiol were significantly higher prior to diagnosis of ER-negative breast cancer compared with controls while androgens and SHBG did not show any difference. Estradiol, free estradiol, free testosterone and SHBG were significantly higher before ER-positive breast cancer diagnosis compared with controls. Women had a twofold increased ER-negative breast cancer risk if estradiol and free estradiol were in the top quartile but not androgens (testosterone and androstenedione) or SHBG. These associations remained significant only when samples closer (median 1.1y before) to diagnosis were analyzed rather than farther from diagnosis (median 2.9y before). Women had a 2.34 (95% CI: 1.21-4.61, p=0.001), 2.21 (95% CI: 1.14-4.38, p=0.001), 2 (95% CI: 1.05-3.89, p=0.005) fold increased ER-positive breast cancer risk if estradiol, free estradiol and free testosterone respectively were in the top quartile. These associations remained significant regardless of whether the samples were collected less than or more than 2years prior to diagnosis. CONCLUSION: In postmenopausal women increased estrogens but not androgens are associated with ER-negative breast cancer. Previously reported associations of estradiol and free testosterone with ER-positive breast cancer are confirmed. The use of mass spectrometry and sensitive RIA add validity to these findings.


Assuntos
Neoplasias da Mama/sangue , Neoplasias da Mama/diagnóstico , Espectrometria de Massas/métodos , Radioimunoensaio/métodos , Receptores de Estrogênio/metabolismo , Estudos de Casos e Controles , Detecção Precoce de Câncer , Estradiol/sangue , Feminino , Humanos , Razão de Chances , Globulina de Ligação a Hormônio Sexual/metabolismo , Testosterona/sangue
17.
Methods Mol Biol ; 1065: 45-74, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23996357

RESUMO

Mass spectrometry methods have the potential to measure different hormones during the same analysis and have improved specificity and a wide analytical range compared with many immunoassay methods. Increasingly in clinical laboratories liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays are replacing immunoassays for the routine measurement of testosterone, 17-hydroxyprogesterone, and other steroid hormones. Reference LC-MS/MS methods for steroid, thyroid, and peptide hormones are being used for assessment of the performance and calibration of commercial immunoassays. In this chapter, the general principles of tandem mass spectrometry and examples of hormone assays are described.


Assuntos
Hormônios/metabolismo , Espectrometria de Massas em Tandem/métodos , Hormônios/química , Humanos , Espectrometria de Massas em Tandem/normas
18.
Methods Mol Biol ; 1065: 211-26, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23996366

RESUMO

A number of androgens are measured for clinical purposes. Most laboratories will run a testosterone assay but the requirement for other androgens may be too small for a laboratory to set up their own assay. In these cases samples would be sent to a specialized laboratory. In the routine laboratory testosterone is analyzed on automated systems but these lack the sensitivity to accurately measure the hormone in children and normal women. Many laboratories analyzed such samples by radioimmunoassay, but tandem mass spectrometry is now replacing these assays. This chapter provides simple methods for measuring the androgens in serum and saliva by radioimmunoassay and tandem mass spectrometry.


Assuntos
Androgênios/metabolismo , Cromatografia Líquida , Radioimunoensaio , Espectrometria de Massas em Tandem , Androgênios/sangue , Cromatografia Líquida/métodos , Cabelo/química , Cabelo/metabolismo , Humanos , Saliva/química , Saliva/metabolismo , Espectrometria de Massas em Tandem/métodos , Testosterona/sangue , Testosterona/metabolismo
19.
Database (Oxford) ; 2012: bas024, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22554788

RESUMO

Much of the data within Model Organism Databases (MODs) comes from manual curation of the primary research literature. Given limited funding and an increasing density of published material, a significant challenge facing all MODs is how to efficiently and effectively prioritize the most relevant research papers for detailed curation. Here, we report recent improvements to the triaging process used by FlyBase. We describe an automated method to directly e-mail corresponding authors of new papers, requesting that they list the genes studied and indicate ('flag') the types of data described in the paper using an online tool. Based on the author-assigned flags, papers are then prioritized for detailed curation and channelled to appropriate curator teams for full data extraction. The overall response rate has been 44% and the flagging of data types by authors is sufficiently accurate for effective prioritization of papers. In summary, we have established a sustainable community curation program, with the result that FlyBase curators now spend less time triaging and can devote more effort to the specialized task of detailed data extraction. Database URL: http://flybase.org/


Assuntos
Sistemas de Gerenciamento de Base de Dados , Bases de Dados Factuais , Correio Eletrônico , Anotação de Sequência Molecular/métodos , Mineração de Dados , Humanos , Publicações Periódicas como Assunto
20.
Nat Commun ; 3: 1072, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22990868

RESUMO

Although heat-shock protein 70 (HSP70), an evolutionarily highly conserved molecular chaperone, is known to be post-translationally modified in various ways such as phosphorylation, ubiquitination and glycosylation, physiological significance of lysine methylation has never been elucidated. Here we identify dimethylation of HSP70 at Lys-561 by SETD1A. Enhanced HSP70 methylation was detected in various types of human cancer by immunohistochemical analysis, although the methylation was barely detectable in corresponding non-neoplastic tissues. Interestingly, methylated HSP70 predominantly localizes to the nucleus of cancer cells, whereas most of the HSP70 protein locates to the cytoplasm. Nuclear HSP70 directly interacts with Aurora kinase B (AURKB) in a methylation-dependent manner and promotes AURKB activity in vitro and in vivo. We also find that methylated HSP70 has a growth-promoting effect in cancer cells. Our findings demonstrate a crucial role of HSP70 methylation in human carcinogenesis.


Assuntos
Proteínas de Choque Térmico HSP70/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Animais , Aurora Quinase B , Aurora Quinases , Western Blotting , Células COS , Linhagem Celular Tumoral , Proliferação de Células , Chlorocebus aethiops , Humanos , Imuno-Histoquímica , Imunoprecipitação , Lisina , Metilação , Ligação Proteica , Análise Serial de Tecidos
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA