Project description:Precision mass spectrometry, animal models and organ-on-a-chip (OOC) systems have emerged as promising experimental strategies to study the molecular mechanisms governing human biology and disease, including the molecular basis of cardiovascular disorders like fibrosis where access to patient samples is limiting and subject to confounding variables. Nevertheless, no systematic comparisons have ever been reported, precluding an objective assessment of cross-platform consistency, performance and bias. Here, we apply and evaluate an integrative mass spectrometry-based platform that allows for quantitative global phospho/proteomic surveys of normal and afflicted tissue from human, mouse and OOC-derived specimens. The applicability and utility of this approach was tested in the context of cardiac fibrosis through comprehensive analyses of fibrotic cardiomyocyte samples from Biowire OOC specimens, and cardiac tissue explants from hypertrophic patients and a mouse genetic model, and show that clinically meaningful biological inferences can be generated by leveraging commonalities and unique attributes generated across each platform.
Project description:Pre-clinical models that effectively recapitulate human disease are critical for expanding our knowledge of cancer biology and drug resistance mechanisms. For haematological malignancies, the non-obese diabetic/severe combined immunodeficient (NOD/SCID) mouse is one of the most successful models to study paediatric acute lymphoblastic leukaemia (ALL). However, for this model to be effective for studying engraftment and therapy responses at the whole genome level, careful molecular characterisation is essential.Here, we sought to validate species-specific gene expression profiling in the high engraftment continuous ALL NOD/SCID xenograft. Using the human Affymetrix whole transcript platform we analysed transcriptional profiles from engrafted tissues without prior cell separation of mouse cells and found it to return highly reproducible profiles in xenografts from individual mice. The model was further tested with experimental mixtures of human and mouse cells, demonstrating that the presence of mouse cells does not significantly skew expression profiles when xenografts contain 90% or more human cells. In addition, we present a novel in silico and experimental masking approach to identify probes and transcript clusters susceptible to cross-species hybridisation.We demonstrate species-specific transcriptional profiles can be obtained from xenografts when high levels of engraftment are achieved or with the application of transcript cluster masks. Importantly, this masking approach can be applied and adapted to other xenograft models where human tissue infiltration is lower. This model provides a powerful platform for identifying genes and pathways associated with ALL disease progression and response to therapy in vivo.
Project description:Expression data from Alzheimer's disease (AD) model mouse and AD model mouse overexpressing human mitochondrial transcriptional factor A (hTFAM)
Project description:Microarray technology has had a profound impact on gene expression research. Some studies have questioned whether similar expression results are obtained when the same RNA samples are analyzed on different platforms. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and analysis issues. We demonstrate the consistency of results within a platform across test sites as well as the high level of cross-platform concordance in terms of genes identified as differentially expressed. The MAQC study provides a rich resource that will help build consensus on the use of microarrays in research, clinical and regulatory settings. Manuscripts related to the MAQC project have been published in Nature Biotechnology, 24(9), September, 2006. More information about the MAQC project can be found at http://edkb.fda.gov/MAQC/. Keywords: Cross-platform comparison