Cancer Biology

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    Protocols in Current Issue
    OxiDIP-Seq for Genome-wide Mapping of Damaged DNA Containing 8-Oxo-2'-Deoxyguanosine
    Authors:  Francesca Gorini, Giovanni Scala, Susanna Ambrosio, Barbara Majello and Stefano Amente, date: 11/05/2022, view: 549, Q&A: 0
    [Abstract]

    8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) is considered to be a premutagenic DNA lesion generated by 2'-deoxyguanosine (dG) oxidation due to reactive oxygen species (ROS). In recent years, the 8-oxodG distribution in human, mouse, and yeast genomes has been underlined using various next-generation sequencing (NGS)–based strategies.

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    An Unbiased CRISPR-Cas9 Screening Method for the Identification of Positive and Negative Regulatory Proteins of Cell Adhesion
    [Abstract]

    Mature B-cell lymphomas are highly dependent upon the protective lymphoid organ microenvironment for their growth and survival. Targeting integrin-mediated homing and retention of the malignant B cells in the lymphoid organs, using the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib, is a highly efficacious FDA-approved therapy for

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    Analysis of the Ubiquitination and Phosphorylation of Vangl Proteins
    Authors:  Di Feng, Ziwei He and Bo Gao, date: 10/20/2022, view: 799, Q&A: 0
    [Abstract]

    The core planar cell polarity (PCP) protein Vang/Vangl, including Vangl1 and Vangl2 in vertebrates, is indispensable during development. Our previous studies showed that the activity of Vangl is tightly controlled by two important posttranslational modifications, ubiquitination and phosphorylation. Vangl is ubiquitinated through an endoplasmic

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    Gastrulation Screening to Identify Anti-metastasis Drugs in Zebrafish Embryos
    Authors:  Joji Nakayama, Hideki Makinoshima and Zhiyuan Gong, date: 10/05/2022, view: 602, Q&A: 0
    [Abstract]

    Few models exist that allow for rapid and effective screening of anti-metastasis drugs. Here, we present a drug screening protocol utilizing gastrulation of zebrafish embryos for identification of anti-metastasis drugs. Based on the evidence that metastasis proceeds through utilizing the molecular mechanisms of gastrulation, we hypothesized that

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    Enhanced Ribonucleoprotein Immunoprecipitation (RIP) Technique for the Identification of mRNA Species in Ribonucleoprotein Complexes
    Authors:  Saja A. Fakhraldeen, Scott M. Berry, David J. Beebe and Caroline M. Alexander, date: 10/05/2022, view: 634, Q&A: 0
    [Abstract]

    RNA binding proteins (RBPs) are critical regulators of cellular phenotypes, and dysregulated RBP expression is implicated in various diseases including cancer. A single RBP can bind to and regulate the expression of many RNA molecules via a variety of mechanisms, including translational suppression, prevention of RNA degradation, and alteration in

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    Detection of Alternative End-Joining in HNSC Cell Lines Using DNA Double-Strand Break Reporter Assays
    Authors:  Nan Zuo, Lin Ma, Weitao Hu, Yongqiang Deng, Lanlan Wei and Qi Liu, date: 09/05/2022, view: 1013, Q&A: 0
    [Abstract]

    The main cellular pathways to repair DNA double-strand breaks (DSBs) and protect the integrity of the genome are homologous recombination (HR), non-homologous end-joining (NHEJ), and alternative end-joining (Alt-EJ). Polymerase theta-regulated Alt-EJ is an error-prone DSB repair pathway characterized by microhomology usage. Considering its

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    Microscopic Detection of DNA Synthesis in Early Mitosis at Repetitive lacO Sequences in Human Cells
    Authors:  Kazumasa Yoshida, Riko Ishimoto and Masatoshi Fujita, date: 09/05/2022, view: 862, Q&A: 0
    [Abstract]

    In the human cell cycle, complete replication of DNA is a fundamental process for the maintenance of genome integrity. Replication stress interfering with the progression of replication forks causes difficult-to-replicate regions to remain under-replicated until the onset of mitosis. In early mitosis, a homology-directed repair DNA synthesis,

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    In-Cell Western Protocol for Semi-High-Throughput Screening of Single Clones
    Authors:  Arpita S. Pal, Alejandra M. Agredo and Andrea L. Kasinski, date: 08/20/2022, view: 1462, Q&A: 0
    [Abstract]

    The in-cell western (ICW) is an immunocytochemical technique that has been used to screen for effects of siRNAs, drugs, and small molecule inhibitors. The reduced time and number of cells required to follow this protocol illustrates its semi-high-throughput nature. Performing a successful ICW protocol requires fixing and permeabilizing adherent

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    A Fast and Reliable Method to Generate Pure, Single Cell-derived Clones of Mammalian Cells
    Authors:  Zhe Han, Bindhu K. Madhavan, Serap Kaymak, Peter Nawroth and Varun Kumar, date: 08/20/2022, view: 1336, Q&A: 0
    [Abstract]

    Stable cell cloning is an essential aspect of biological research. All advanced genome editing tools rely heavily on stable, pure, single cell-derived clones of genetically engineered cells. For years, researchers have depended on single-cell dilutions seeded in 96- or 192-well plates, followed by microscopic exclusion of the wells seeded with

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    CRISPR/Cas9-mediated Gene Knockout Followed by Negative Selection Leads to a Complete TCR Depletion in orthoCAR19 T Cells
    [Abstract]

    Genome-editing technologies, especially CRISPR (clustered regularly interspaced short palindrome repeats)/Cas9 (CRISPR-associated protein 9), endows researchers the ability to make efficient, simple, and precise genomic DNA changes in many eukaryotic cell types. CRISPR/Cas9-mediated efficient gene knockout holds huge potential to improve the

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