Distal Tumors Elicit Distinctive Gene Expression Changes in Mouse Brain, Different from Those Induced by Arthritis

Background: Tumor progression is characterized by high mutation rates, each mutation potentially generating an “alarm” signal. The brain is the main integrator of signals arising in the periphery from changes in homeostasis. We hypothesized that tumors growing at a distant site might be a stimulus strong enough to be molecularly sensed and integrated by the brain. Results: Transcriptome analysis of the mouse hypothalamus, midbrain, and pre-fontal cortex at different time points following administration at a distant site of mammary, lung and colon cancer cells evidenced cancer-type and brain-region specific changes in gene expression. On the contrary, no significant gene expression changes were detected in the liver. The hypothalamus was the region with the largest number of differentially expressed genes. On the array and off the array analysis of hypothalamic samples using real time PCR confirmed changes in genes associated with synaptic activity and sickness response, respectively. Gene clustering allowed the discrimination between each cancer model and between the cancer models and arthritis. Conclusions: The present data provides evidence of changes in gene expression in the brain during progression of distal tumors and arthritis highlighting a potential link between distal pathological processes and the brain.Fil: Alvarez, Mariano J.. Gentron Research Unit; ArgentinaFil: Salibe, Mariano C.. Gentron Research Unit; ArgentinaFil: Stolovitzky, Gustavo. Ibm Research. Thomas J. Watson Research Center; Estados UnidosFil: Rubinstein, Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Pitossi, Fernando Juan. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Podhajcer, Osvaldo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentin

Model based analysis of real-time PCR data from DNA binding dye protocols

BACKGROUND: Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation. Despite the kinetic information generated by real-time PCR, most popular analysis methods assume constant amplification efficiency among samples, introducing strong biases when amplification efficiencies are not the same. RESULTS: We present here a new mathematical model based on the classic exponential description of the PCR, but modeling amplification efficiency as a sigmoidal function of the product yield. The model was validated with experimental results and used for the development of a new method for real-time PCR data analysis. This model based method for real-time PCR data analysis showed the best accuracy and precision compared with previous methods when used for quantification of in-silico generated and experimental real-time PCR results. Moreover, the method is suitable for the analyses of samples with similar or dissimilar amplification efficiency. CONCLUSION: The presented method showed the best accuracy and precision. Moreover, it does not depend on calibration curves, making it ideal for fully automated high-throughput applications