Cancer Biology

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    Protocols in Current Issue
    Enhanced-ice-COLD-PCR for the Sensitive Detection of Rare DNA Methylation Patterns in Liquid Biopsies
    Authors:  Florence Mauger and Jörg Tost, date: 12/05/2019, view: 80, Q&A: 0
    In the context of precision medicine, the identification of novel biomarkers for the diagnosis of disease, prognosis, predicting treatment outcome and monitoring of treatment success is of great importance. The analysis of methylated ...
    An Optimized Method to Isolate Human Fibroblasts from Tissue for Ex Vivo Analysis
    Despite their involvement in many physiological and pathological processes, fibroblasts remain a poorly-characterized cell type. Analysis of primary fibroblasts while maintaining their in vivo phenotype is challenging: standard methods for ...
    DNase I Chromatin Accessibility Analysis
    Authors:  Brook S. Nepon-Sixt and Mark G. Alexandrow, date: 12/05/2019, view: 89, Q&A: 0
    Chromatin consists of compacted DNA in complex with proteins and contributes to the organization of DNA and its stability. Furthermore, chromatin plays key roles in regulating cellular processes such as DNA replication, transcription, DNA repair, ...
    Enhanced-ice-COLD-PCR for the Sensitive Detection of Rare DNA Methylation Patterns in Liquid Biopsies
    Authors:  Florence Mauger and Jörg Tost, date: 12/05/2019, view: 80, Q&A: 0
    [Abstract] In the context of precision medicine, the identification of novel biomarkers for the diagnosis of disease, prognosis, predicting treatment outcome and monitoring of treatment success is of great importance. The analysis of methylated circulating-cell free DNA provides great promise to complement or replace genetic markers for these applications, ...
    An Optimized Method to Isolate Human Fibroblasts from Tissue for Ex Vivo Analysis
    [Abstract] Despite their involvement in many physiological and pathological processes, fibroblasts remain a poorly-characterized cell type. Analysis of primary fibroblasts while maintaining their in vivo phenotype is challenging: standard methods for fibroblast isolation require cell culture in vitro, which is known to alter phenotypes. ...
    DNase I Chromatin Accessibility Analysis
    Authors:  Brook S. Nepon-Sixt and Mark G. Alexandrow, date: 12/05/2019, view: 89, Q&A: 0
    [Abstract] Chromatin consists of compacted DNA in complex with proteins and contributes to the organization of DNA and its stability. Furthermore, chromatin plays key roles in regulating cellular processes such as DNA replication, transcription, DNA repair, and mitosis. Chromatin assumes more compact (inaccessible) or decondensed (accessible) conformations ...
    Labeling and Isolation of Fluorouracil Tagged RNA by Cytosine Deaminase Expression
    Authors:  Harihar Basnet and Joan Massague, date: 11/20/2019, view: 276, Q&A: 0
    [Abstract] Tissues are comprised of different cell types whose interactions elicit distinct gene expression patterns that regulate tissue formation, regeneration, homeostasis and repair. Analysis of these gene expression patterns require methods that can capture as closely as possible the transcriptomes of cells of interest in their tissue microenvironment. ...
    Isolation and Quantification of Metabolite Levels in Murine Tumor Interstitial Fluid by LC/MS
    Authors:  Mark R Sullivan, Caroline A Lewis and Alexander Muir, date: 11/20/2019, view: 688, Q&A: 0
    [Abstract] Cancer is a disease characterized by altered metabolism, and there has been renewed interest in understanding the metabolism of tumors. Even though nutrient availability is a critical determinant of tumor metabolism, there has been little systematic study of the nutrients directly available to cancer cells in the tumor microenvironment. Previous ...
    Imaging VIPER-labeled Cellular Proteins by Correlative Light and Electron Microscopy
    [Abstract] Advances in fluorescence microscopy (FM), electron microscopy (EM), and correlative light and EM (CLEM) offer unprecedented opportunities for studying diverse proteins and nanostructures involved in fundamental cell biology. It is now possible to visualize and quantify the spatial organization of cellular proteins and other macromolecules by FM, ...
    Implementing VIPER for Imaging Cellular Proteins by Fluorescence Microscopy
    Authors:  Julia K. Doh, Caroline A. Enns and Kimberly E. Beatty, date: 11/05/2019, view: 270, Q&A: 0
    [Abstract] Genetically-encoded tags are useful tools for multicolor and multi-scale cellular imaging. Versatile Interacting Peptide (VIP) tags, such as VIPER, are new genetically-encoded tags that can be used in various imaging applications. VIP tags consist of a coiled-coil heterodimer, with one peptide serving as the genetic tag and the other (“probe ...
    Generation of CoilR Probe Peptides for VIPER-labeling of Cellular Proteins
    Authors:  Julia K. Doh, Savannah J. Tobin and Kimberly E. Beatty, date: 11/05/2019, view: 303, Q&A: 0
    [Abstract] Versatile Interacting Peptide (VIP) tags are a new class of genetically-encoded tag designed for imaging cellular proteins by fluorescence and electron microscopy. In 2018, we reported the VIPER tag (Doh et al., 2018), which contains two elements: a genetically-encoded peptide tag (i.e., CoilE) and a probe peptide (i.e., ...
    F-actin Bundle Sedimentation Assay
    Authors:  Shan-Shan Lin, Mei-Chun Chuang and Ya-Wen Liu, date: 11/05/2019, view: 288, Q&A: 0
    [Abstract] Understanding the molecular mechanism governing the higher-order regulation of actin dynamics requires chemically-defined and quantitative assays. Recently, the membrane remodeling large GTPase, dynamin, has been identified as a new actin cross-linking molecule. Dynamin regulates actin cytoskeleton through binding to, self-assembling around, and ...
    Measuring Small-molecule Inhibition of Protein Interactions in Live Cells Using FLIM-FRET
    Authors:  James M. Pemberton, Qian Liu and David W. Andrews, date: 10/20/2019, view: 1754, Q&A: 0
    [Abstract] This protocol was designed to quantitatively measure small-molecule displacement of proteins in live mammalian cells using fluorescence lifetime imaging microscopy–Förster resonance energy transfer (FLIM-FRET). Tumour cell survival is often dependent on anti-apoptotic proteins, which bind to and inhibit pro-apoptotic proteins, thus preventing ...



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