RESUMO
Clinically relevant biomarkers are useful to determine cancer patients' prognosis and treatments. To discover new putative biomarkers, we performed in silico analysis of a 325-gene panel previously associated with breast epithelial cell biology and clinical outcomes. Sixteen public datasets of microarray samples representing 8 cancer types and a total of 3,663 patients' samples were used for the analyses. Feature selection was used to identify the best subsets of the 325 genes for each classification, and linear discriminant analysis was used to quantify the accuracy of the classifications. A subset of 102 of the 325 genes were found to be housekeeping (HK) genes, and the classifications were repeated using only the 102 HK subset. The 325-gene panel and 102 HK subset were able to distinguish colon, gastric, lung, ovarian, pancreatic, and prostate tumors and leukemia from normal adjacent tissue, and classify disease subtypes of breast and lung cancers and leukemia with 70% or higher accuracy. HK genes have been overlooked as potential biomarkers due to their relative stability. This study describes a set of HK genes as putative biomarkers applicable to multiple cancer types worth following in subsequent validation studies.
Assuntos
Neoplasias da Mama , Perfilação da Expressão Gênica , Biomarcadores Tumorais/genética , Neoplasias da Mama/genética , Regulação Neoplásica da Expressão Gênica , Genes Essenciais , Humanos , Masculino , Análise de Sequência com Séries de Oligonucleotídeos , FenótipoRESUMO
Clinically relevant biomarkers are useful to determine cancer patients' prognosis and treatments. To discover new putative biomarkers, we performed in silico analysis of a 325-gene panel previously associated with breast epithelial cell biology and clinical outcomes. Sixteen public datasets of microarray samples representing 8 cancer types and a total of 3,663 patients' samples were used for the analyses. Feature selection was used to identify the best subsets of the 325 genes for each classification, and linear discriminant analysis was used to quantify the accuracy of the classifications. A subset of 102 of the 325 genes were found to be housekeeping (HK) genes, and the classifications were repeated using only the 102 HK subset. The 325-gene panel and 102 HK subset were able to distinguish colon, gastric, lung, ovarian, pancreatic, and prostate tumors and leukemia from normal adjacent tissue, and classify disease subtypes of breast and lung cancers and leukemia with 70% or higher accuracy. HK genes have been overlooked as potential biomarkers due to their relative stability. This study describes a set of HK genes as putative biomarkers applicable to multiple cancer types worth following in subsequent validation studies.
Assuntos
Humanos , Masculino , Neoplasias da Mama/genética , Perfilação da Expressão Gênica , Fenótipo , Biomarcadores Tumorais/genética , Regulação Neoplásica da Expressão Gênica , Análise de Sequência com Séries de Oligonucleotídeos , Genes EssenciaisRESUMO
We investigated the presence of free mRNA in the plasma of patients with chronic myeloid leukemia (CML), through RT-PCR analysis of G3PDH, a metabolism gene. We also analysed the presence of mRNA for HLM, a human oxysterol-binding protein homologue recently described as a potential marker for blood dissemination of solid tumors. Our results showed the presence of metabolism G3PDH mRNA in the plasma of 5/11 (45%) CML patients studied but HLM mRNA was not detected in any of the plasma studied. HLM mRNA was detected in the leukocytes of 4/5 (80%) CML patients. This work reports for the first time free mRNA in the plasma of CML patients. Our results also suggest that the detection of HLM could be a potential molecular marker for the follow-up in hematological malignancies.
Assuntos
Gliceraldeído-3-Fosfato Desidrogenases/genética , Leucemia Mielogênica Crônica BCR-ABL Positiva/genética , RNA Mensageiro/análise , RNA Neoplásico/genética , Receptores de Esteroides/genética , Primers do DNA/química , Eletroforese em Gel de Poliacrilamida , Gliceraldeído-3-Fosfato Desidrogenases/metabolismo , Humanos , Leucemia Mielogênica Crônica BCR-ABL Positiva/sangue , Leucócitos/metabolismo , RNA Mensageiro/sangue , RNA Neoplásico/sangue , Receptores de Esteroides/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
We have previously shown the inhibition of Mayaro virus multiplication in Aedes albopictus-infected cells maintained at a supraoptimal temperature for growth (37 degrees C) and a stimulation of virus production in response to high serum concentrations in the incubation medium. In the present study, we addressed the question of how the effect of continuous heat stress and high serum concentration soon after infection interfere with virus macromolecule synthesis. Cells maintained at 28 degrees C in the presence of 2% serum synthesized a viral genomic RNA of 12 kb and a subgenomic RNA of 5.2 kb 6 h postinfection. Analysis of the protein profile showed the presence of the viral nucleocapsid protein of 34 kDa (P34). However, if infected cells were maintained at 37 degrees C, a smear starting immediately below the 5.2-kb RNA was noticed and the viral P34 was not detected by SDS-PAGE. Addition of 10% serum to the growth medium of infected cells maintained at 37 degrees C results in a viral RNA profile and protein synthesis similar to those observed in cultures kept at 28 degrees C, i.e., the smear was not observed and the P34 protein was detected. The results suggest that the inhibition of virus multiplication by temperature may be related to the inhibition of viral nonstructural protein synthesis early during infection. The presence of high serum levels in the incubation medium protects macromolecule synthesis against heat stress.
Assuntos
Aedes/virologia , Alphavirus/fisiologia , RNA Viral/biossíntese , Temperatura , Proteínas não Estruturais Virais/fisiologia , Alphavirus/crescimento & desenvolvimento , Animais , Sangue , Células Cultivadas , Meios de Cultura , Genoma Viral , Replicação ViralRESUMO
We have previously shown the inhibition of Mayaro virus multiplication in Aedes albopictus-infected cells maintained at a supraoptimal temperature for growth (37§C) and a stimulation of virus production in response to high serum concentrations in the incubation medium. In the present study, we addressed the question of how the effect of continuous heat stress and high serum concentration soon after infection interfere with virus macromolecule synthesis. Cells maintained at 28§C in the presence of 2 percent serum synthesized a viral genomic RNA of 12 kb and a subgenomic RNA of 5.2 kb 6 h post-infection. Analysis of the protein profile showed the presence of the viral nucleocapsid protein of 34 kDa (P34). However, if infected cells were maintained at 37§C, a smear starting immediately below the 5.2-kb RNA was noticed and the viral P34 was not detected by SDS-PAGE. Addition of 10 percent serum to the growth medium of infected cells maintained at 37§C results in a viral RNA profile and proteins synthesis similar to those observed in cultures kept at 28§C, i.e., the smear was not observed and the P34 protein was detected. The results suggest that the inhibition of virus multiplication by temperature may be related to the inhibition of viral nonstructural protein synthesis early during infection. The presence of high serum levels in the incubation medium protects macromolecule synthesis against heat stress
Assuntos
Animais , Aedes/virologia , Alphavirus/fisiologia , Sangue/metabolismo , Proteínas não Estruturais Virais/fisiologia , RNA Viral/biossíntese , Temperatura , Alphavirus/crescimento & desenvolvimento , Genoma Viral , Replicação ViralRESUMO
Three major Mayaro virus proteins of 62, 50 and 34 kDa were detected in Aedes albopictus cells after 48 h postinfection at 28 degrees C. When the infected cells were shifted from 28 to 37 degrees C for 90 min (heat shock conditions), the synthesis of two major heat shock proteins (HSP) 82 and 70 kDa was induced concomitantly with strong inhibition of virus and normal protein synthesis. Total cellular RNA was isolated from mock and infected cells incubated at 28 degrees C or under heat shock. Northern blot analysis with HSP genomic probes from Drosophila sp showed that (1) the probe for HSP 82 hybridized with an RNA of 2.6 kb present only in heat-shocked cells, (2) the HSP 70 probe hybridized with RNA species of 2.5 kb, present only in RNA from heat-shocked cells. These results showed that Mayaro virus was not able to alter the reprogrammation of gene expression induced by heat shock in A. albopictus cells.