Chemical-vapor-deposition-based polymer substrates for spatially resolved analysis of protein binding by imaging ellipsometry.

Biomolecular interactions between proteins and synthetic surfaces impact diverse biomedical fields. Simple, quantitative, label-free technologies for the analysis of protein adsorption and binding of biomolecules are thus needed. Here, we report the use of a novel type of substrate, poly-p-xylylene coatings prepared by chemical vapor deposition (CVD) polymerization, for surface plasmon resonance enhanced ellipsometry (SPREE) studies and assess the reactive coatings as spatially resolved biomolecular sensing arrays. Prior to use in binding studies, reactive coatings were fully characterized by Fourier transform infrared spectroscopy, electrochemical impedance spectroscopy, and ellipsometry. As a result, the chemical structure, thickness, and homogeneous coverage of the substrate surface were confirmed for a series of CVD-coated samples. Subsequent SPREE imaging and fluorescence microscopy indicated that the synthetic substrates supported detectable binding of a cascade of biomolecules. Moreover, analysis revealed a useful thickness range for CVD films in the assessment of protein and/or antigen-antibody binding via SPREE imaging. With a variety of functionalized end groups available for biomolecule immobilization and ease of patterning, CVD thin films are useful substrates for spatially resolved, quantitative binding arrays.

Integrative epigenetic taxonomy of primary prostate cancer.

The Androgen Receptor (AR) is the key-driving transcription factor in prostate cancer, tightly controlled by epigenetic regulation. To date, most epigenetic profiling has been performed in cell lines or limited tissue samples. Here, to comprehensively study the epigenetic landscape, we perform RNA-seq with ChIP-seq for AR and histone modification marks (H3K27ac, H3K4me3, H3K27me3) in 100 primary prostate carcinomas. Integrative molecular subtyping of the five data streams revealed three major subtypes of which two were clearly TMPRSS2-ERG dictated. Importantly, we identify a third subtype with low chromatin binding and activity of AR, but with high activity of FGF and WNT signaling. While positive for neuroendocrine-hallmark genes, these tumors were copy number-neutral with low mutational burden, significantly depleted for genes characteristic of poor-outcome associated luminal B-subtype. We present a unique resource on transcriptional and epigenetic control in prostate cancer, revealing tight control of gene regulation differentially dictated by AR over three subtypes.