Cancer Biology

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    Protocols in Current Issue
    A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples

    The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically

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    A Flow Cytometry-Based Method for Analyzing DNA End Resection in G0- and G1-Phase Mammalian Cells
    Authors:  Bo-Ruei Chen, Jessica K. Tyler and Barry P. Sleckman, date: 05/20/2022, view: 28, Q&A: 0

    DNA double strand breaks (DSBs) constantly arise in cells during normal cellular processes or upon exposure to genotoxic agents, and are repaired mostly by homologous recombination (HR) and non-homologous end joining (NHEJ). One key determinant of

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    A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples
    [Abstract]

    The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide

    ...
    A Flow Cytometry-Based Method for Analyzing DNA End Resection in G0- and G1-Phase Mammalian Cells
    Authors:  Bo-Ruei Chen, Jessica K. Tyler and Barry P. Sleckman, date: 05/20/2022, view: 28, Q&A: 0
    [Abstract]

    DNA double strand breaks (DSBs) constantly arise in cells during normal cellular processes or upon exposure to genotoxic agents, and are repaired mostly by homologous recombination (HR) and non-homologous end joining (NHEJ). One key determinant of DNA DSB repair pathway choice is the processing of broken DNA ends to generate single strand DNA

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    Measurement of Cell Intrinsic TGF-β Activation Mediated by the Integrin αvβ8
    Authors:  Robert Ian Seed and Stephen Lloyd Nishimura, date: 04/20/2022, view: 1081, Q&A: 0
    [Abstract]

    Transforming growth factor beta (TGF-β) is a multi-functional cytokine that plays a significant role in multiple diseases, including fibrosis and tumor progression. Whilst the biologic effects of TGF-β are well characterized, it is unclear how TGF-β signaling is regulated to impart specific responses within certain cell types. One

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    Low-viscosity Matrix Suspension Culture for Human Colorectal Epithelial Organoids and Tumoroids
    [Abstract]

    Three-dimensional culture of human normal colorectal epithelium and cancer tissue as organoids and tumoroids has transformed the study of diseases of the large intestine. A widely used strategy for generating patient-derived colorectal organoids and tumoroids involves embedding cells in domes of extracellular matrix (ECM). Despite its success,

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    Conditional Human BRD4 Knock-In Transgenic Mouse Genotyping and Protein Isoform Detection
    Authors:  Michael Paul Lewis, Shwu-Yuan Wu and Cheng-Ming Chiang, date: 04/05/2022, view: 425, Q&A: 0
    [Abstract]

    Bromodomain-containing protein 4 (BRD4) is an acetyl-lysine reader protein and transcriptional regulator implicated in chromatin dynamics and cancer development. Several BRD4 isoforms have been detected in humans with the long isoform (BRD4-L, aa 1-1,362) playing a tumor-suppressive role and a major short isoform (BRD4-S, aa 1-722) having

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    Image-based Quantification of Macropinocytosis Using Dextran Uptake into Cultured Cells
    Authors:  Anh H. Le and Laura M. Machesky, date: 04/05/2022, view: 519, Q&A: 0
    [Abstract]

    Macropinocytosis is an evolutionarily conserved process, which is characterized by the formation of membrane ruffles and the uptake of extracellular fluid. We recently demonstrated a role for CYFIP-related Rac1 Interactor (CYRI) proteins in macropinocytosis. High-molecular weight dextran (70kDa or higher) has generally been used as a marker for

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    Single-cell Damagenome Profiling by Linear Copying and Splitting based Whole Genome Amplification (LCS-WGA)
    Authors:  Yichi Niu, Qiangyuan Zhu and Chenghang Zong, date: 03/20/2022, view: 491, Q&A: 0
    [Abstract]

    Spontaneous DNA damage frequently occurs on the human genome, and it could alter gene expression by inducing mutagenesis or epigenetic changes. Therefore, it is highly desired to profile DNA damage distribution on the human genome and identify the genes that are prone to DNA damage. Here, we present a novel single-cell whole-genome amplification

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    3D-Structured Illumination Microscopy of Centrosomes in Human Cell Lines
    [Abstract]

    The centrosome is the main microtubule-organizing center of animal cells, and is composed of two barrel-shaped microtubule-based centrioles embedded in protein dense pericentriolar material. Compositional and architectural re-organization of the centrosome drives its duplication, and enables its microtubule-organizing activity and capability to

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    Three-dimensional Models of the Nasopharynx for the Study of Epstein-Barr Virus Infection
    [Abstract]

    The ubiquitous and cancer-associated Epstein-Barr virus (EBV) is associated with nearly all cases of nasopharyngeal carcinoma (NPC). Nasopharyngeal tissue is comprised of both pseudostratified and stratified epithelium, which are modeled in three-dimensional (3-D) cell culture. The cellular origin of EBV-associated NPC is as yet unknown, but both

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    Small Molecule Screening of Primary Human Acute Myeloid Leukemia Using Co-culture and Multiplexed FACS Analysis
    Authors:  Aurelie Baudet, Simon Hultmark, Fredrik Ek and Mattias Magnusson, date: 03/20/2022, view: 450, Q&A: 0
    [Abstract]

    Ex vivo culture of primary acute myeloid leukemia (AML) cells is notoriously difficult due to spontaneous differentiation and cell death, which hinders mechanistic and translational studies. To overcome this bottleneck, we have implemented a co-culture system, where the OP9-M2 stromal cells support the growth, but most notably limit the

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