Project description:Individual variant or wild type gene expression after constitutive transduction in immortalized lung ephithelial cells (BEAS-2B). The hypothesis is that variant gene expression is associated with radiation resistance or sensitivity. The results provide transcriptomic information on genes variants that conferred radiation resistance or sensitivity.
Project description:Introduction: Breast radiotherapy is currently â??one size fits allâ?? regardless of breast cancer subtype (eg. luminal, basal). However, recent clinical data suggests that radiation response may vary significantly among subtypes. Therefore, current practice leads to over- or under-treatment of women whose tumors are more or less radiation responsive. We hypothesized that this clinical variability may be due, in part, to differences in cellular radiation response. Methods: We exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines. Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model. A candidate radiation response biomarkers with biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays. Induction in human breast tumors was confirmed in 32 patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis. Quantification of protein was performed in a blinded manner and included positive and negative controls. The objective of our study was to identify genomic determinants of radiation sensitivity using clinical samples as well as breast tumor cell lines. In order to identify differences in the radiation response gene expression profiles of specific breast cancer subtypes, we exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines. Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model. Candidate radiation response biomarker with a biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays. Induction of the genes of interest were further evaluated and confirmed in human breast tumors in 32 breast cancer patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis assays.
Project description:Adipose tissue gene expression was profiled from perigonadal adipose tissue of mice whose body mass and insulin sensitivity varied as a function of diet, gender, monogenic mutations and insulin sensitizing therapies. Mice were 22-24 weeks of age and sacrificed between 2-3 hours into the light portion of a 12/12 dark-light cycle. The goal was to identify transcripts whose adipose tissue expression is correlated with adiposity, insulin sensitivity and other measures of metabolic function. Keywords: population
Project description:Gene expression analysis of peripheral blood leukocytes (PB MNCs) to develop expression profiles that accurately reflect prior radiation exposure. Keywords: Comparative, exposure dosage, C57BI6 Murine Irradiation Studies We have made use of gene expression analysis of peripheral blood mononuclear cells (PB MNCs) to develop expression profiles that accurately reflect prior radiation exposure. Importantly, we demonstrate that expression profiles can be developed that not only predict radiation exposure in mice but also distinguish the level of radiation exposure, ranging from 50 cGy to 1000 cGy. Likewise, a molecular signature of radiation response developed solely from irradiated human patient samples can predict and distinguish irradiated human PB samples from non-irradiated samples with an accuracy of 90%, sensitivity of 85% and specificity of 94%. We further demonstrate that a radiation profile developed in the mouse can correctly distinguish PB samples from irradiated and non-irradiated human patients with an accuracy of 77%, sensitivity of 82% and specificity of 75%. Taken together, these data demonstrate that molecular profiles can be generated which are highly predictive of different levels of radiation exposure in mice and humans. Mouse Dataset only
Project description:Intra-tumor heterogeneity is a hallmark of glioblastoma multiforme, and thought to negatively affect treatment efficacy. Here we establish libraries of glioma-initiating cell (GIC) clones from patient samples and find extensive molecular and phenotypic variability between clones, including a wide range of responses to radiation and drugs. This widespread variability was observed as a continuum of multitherapy resistance phenotypes linked to a proneural-to-mesenchymal shift in the transcriptome.
Project description:Adipose tissue gene expression was profiled from perigonadal adipose tissue of mice whose body mass and insulin sensitivity varied as a function of diet, gender, monogenic mutations and insulin sensitizing therapies. Mice were 22-24 weeks of age and sacrificed between 2-3 hours into the light portion of a 12/12 dark-light cycle. The goal was to identify transcripts whose adipose tissue expression is correlated with adiposity, insulin sensitivity and other measures of metabolic function. Experiment Overall Design: Mice on the C57BL/6J strain were housed in groups of 3-5 and fed ad libitum. 2-4 days prior to collection of adipose tissue fasting blood glucose and serum insulin concentrations were measured. Mice were sacrificed 2-3 hours into the light cycle. RNA was extracted from perigonadal adipose tissue and used to generate labed cRNA for hybridization to Affymetrix Mu74Av2 microarrays.
Project description:Radiation is the frontline treatment for malignant gliomas. Intra-tumoral heterogeneity has been proposed to grant cancer cells a superior trajectory and survival advantage to avoid therapeutic interventions including radiation. However, direct evidence to support the hypothesis via the transcriptome dynamics of glioma during radiation therapy is limited. The current study aim to measure the functional subpopulation dynamics before and after radiation treatment that assist the radiation resistance at single cell resolution. We investigate the single cell transcriptome and biological pathways of primary glioma mouse model and post-radiation early/late time point. Specifically, we used the RCAS mouse model for gliomas, which overexpress PDGFRA as the model. Using single cell transcriptome, for the first time, we confirmed the proneural classification of PDGFRA RCAS glioma mouse model and its heterogeneity. We found that recurrent dominant subpopulations are featured with elevated proliferation rate and hypoxia. In addition, we identified a subpopulation of radiation resistant cells in at early time points with elevated stemness. Lastly, the subpopulations composition undergoes large changes at late time point when the tumor recurred. Single cell transcriptome profiling of radiation treated mouse glioma mouse model identified tumor cell subpopulations dynamics. It provides novel insights into the molecular phenotype and biological functions of radiation resistant tumor cell population.