RESUMEN
PURPOSE: Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples. PATIENTS AND METHODS: A gene signature was developed from a balanced set of 73 patients with recurrent disease (high risk) and 142 patients with no recurrence (low risk) within 5 years of surgery. RESULTS: The 634-probe set signature identified high-risk patients with a hazard ratio (HR) of 2.62 (P < .001) during cross validation of the training set. In an independent validation set of 144 samples, the signature identified high-risk patients with an HR of 2.53 (P < .001) for recurrence and an HR of 2.21 (P = .0084) for cancer-related death. Additionally, the signature was shown to perform independently from known prognostic factors (P < .001). CONCLUSION: This gene signature represents a novel prognostic biomarker for patients with stage II colon cancer that can be applied to FFPE tumor samples.
Asunto(s)
Neoplasias del Colon/patología , Recurrencia Local de Neoplasia/patología , Adhesión en Parafina/métodos , Anciano , Neoplasias del Colon/genética , Femenino , Formaldehído , Perfilación de la Expresión Génica , Humanos , Masculino , Persona de Mediana Edad , Recurrencia Local de Neoplasia/genética , Estadificación de Neoplasias , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Adhesión en Parafina/normas , Pronóstico , Estudios Retrospectivos , Factores de Riesgo , Fijación del TejidoRESUMEN
Genes that are essential for viability represent potential targets for the development of anti-infective agents. However, relatively few have been determined in the filamentous fungal pathogen Aspergillus fumigatus. A novel solution employing parasexual genetics coupled with transposon mutagenesis using the Fusarium oxysporum transposon impala had previously enabled the identification of 20 essential genes from A. fumigatus; however, further use of this system required a better understanding of the mode of action of the transposon itself. Examination of a range of conditions indicated that impala is activated by prolonged exposure to low temperatures. This newly identified property was then harnessed to identify 96 loci that are critical for viability in A. fumigatus, including genes required for RNA metabolism, organelle organization, protein transport, ribosome biogenesis, and transcription, as well as a number of noncoding RNAs. A number of these genes represent potential targets for much-needed novel antifungal drugs.
Asunto(s)
Aspergillus fumigatus/citología , Aspergillus fumigatus/genética , Frío , Elementos Transponibles de ADN/genética , Genes Fúngicos/genética , Viabilidad Microbiana/genética , Aspergillus fumigatus/crecimiento & desarrollo , Aspergillus nidulans/genética , Diploidia , Fusarium/genética , Expresión Génica/genética , Haploidia , Cinética , Mutagénesis Insercional/genética , Regiones Promotoras Genéticas/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Transformación Genética , Transposasas/genéticaRESUMEN
In recent years the filamentous fungus Aspergillus fumigatus has become a significant cause of infection in man and as such has become the focus of much study. It is thought to be the leading mould pathogen in leukaemia and transplant patients and is responsible for mortality in a large number of individuals with immunological disorders. In an attempt to develop molecular mutagenesis tools for assessment of this organism, the genome of A. fumigatus was analysed to identify possible functional transposable elements. An apparently intact Fot1/Pogo type transposon with 65% identity to the active Tan1 element of Aspergillus niger was identified and designated Aft1. Aft1 is a 1.9kb element present in multiple (>20) highly conserved copies. It encodes a 332 amino acid transposase which contains all the functional motifs required for transposition. In addition, the transposase was expressed in cultures grown at 37 degrees C in all three strains assessed and excision analysis suggests Aft1 may be active and of use in transposon tagging experiments. Southern hybridisation patterns indicate that Aft1 is widely distributed amongst clinical isolates of A. fumigatus with considerable variation in genomic localisation. A comprehensive analysis of the genomic localisation of Aft1 in the sequenced strain AF293 show that one insertion is 30 bases upstream of a predicted gene encoding a G-protein coupled receptor. Expression analysis indicates that this gene has been inactivated by the insertion.
Asunto(s)
Aspergillus fumigatus/genética , Elementos Transponibles de ADN/genética , Genoma Fúngico , Secuencia de Aminoácidos , Aspergilosis/microbiología , Humanos , Datos de Secuencia Molecular , Sistemas de Lectura Abierta/genética , Receptores CCR10/genética , Alineación de SecuenciaRESUMEN
An annexin, anxC3.1, was isolated and characterised from the industrially important filamentous fungus Aspergillus niger. anxC3.1 is a single copy gene encoding a 506 amino acid predicted protein which contains four annexin repeats. Disruption of the anxC3.1 gene did not lead to any visible changes in phenotype, nor in the levels of secreted protein, nor specifically in glucoamylase production, suggesting no major role in secretion. anxC3.1 expression was found to be unaltered under a variety of conditions such as increased secretion, altered nitrogen source, heat shock, and decreased Ca2+ levels, indicating that anxC3.1 is constitutively expressed. This is the first reported functional characterisation of a fungal annexin.