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  • 1. Erttmann, Saskia F.
    et al.
    Gekara, Nelson O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Umeå University, Sweden.
    Hydrogen peroxide release by bacteria suppresses inflammasome-dependent innate immunity2019Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, artikel-id 3493Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Hydrogen peroxide (H2O2) has a major function in host-microbial interactions. Although most studies have focused on the endogenous H2O2 produced by immune cells to kill microbes, bacteria can also produce H2O2. How microbial H2O2 influences the dynamics of host-microbial interactions is unclear. Here we show that H2O2 released by Streptococcus pneumoniae inhibits inflammasomes, key components of the innate immune system, contributing to the pathogen colonization of the host. We also show that the oral commensal H2O2-producing bacteria Streptococcus oralis can block inflammasome activation. This study uncovers an unexpected role of H2O2 in immune suppression and demonstrates how, through this mechanism, bacteria might restrain the immune system to co-exist with the host.

  • 2. Jiang, Hui
    et al.
    Panda, Swarupa
    Gekara, Nelson O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Umeå University, Sweden.
    Comet and micronucleus assays for analyzing DNA damage and genome integrity2019Ingår i: DNA Sensors and Inflammasomes / [ed] Jungsan Sohn, Elsevier, 2019, Vol. 625, s. 299-307Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Detection of DNA damage in cells is fundamental for the study of DNA repair and genome-instability associated processes including carcinogenesis. Many studies often rely on cytotoxicity assays to estimate genotoxicity. However, measurements of cytotoxicity, a delayed outcome requiring high threshold genotoxicity to induce, does not provide information about the subtle, early genotoxic effects relevant for mechanistic understanding of DNA repair processes. Here describe how to combine two simple procedures for monitoring the presence of DNA damage in individual eukaryotic cells using: (1) the Comet assay for measuring initial DNA breaks and (2) the Micronucleus assay for detecting delayed outcome DNA breaks in dividing cells. We discuss the principles, experimental design considerations and troubleshooting tips for optimizing these methods. They require standard molecular biology instruments and a fluorescent microscope.

  • 3. Jiang, Hui
    et al.
    Xue, Xiaoyu
    Panda, Swarupa
    Kawale, Ajinkya
    Hooy, Richard M.
    Liang, Fengshan
    Sohn, Jungsan
    Sung, Patrick
    Gekara, Nelson O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Umeå University, Sweden.
    Chromatin-bound cGAS is an inhibitor of DNA repair and hence accelerates genome destabilization and cell death2019Ingår i: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 38, nr 21, artikel-id e102718Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    DNA repair via homologous recombination (HR) is indispensable for genome integrity and cell survival but if unrestrained can result in undesired chromosomal rearrangements. The regulatory mechanisms of HR are not fully understood. Cyclic GMP-AMP synthase (cGAS) is best known as a cytosolic innate immune sensor critical for the outcome of infections, inflammatory diseases, and cancer. Here, we report that cGAS is primarily a chromatin-bound protein that inhibits DNA repair by HR, thereby accelerating genome destabilization, micronucleus generation, and cell death under conditions of genomic stress. This function is independent of the canonical STING-dependent innate immune activation and is physiologically relevant for irradiation-induced depletion of bone marrow cells in mice. Mechanistically, we demonstrate that inhibition of HR repair by cGAS is linked to its ability to self-oligomerize, causing compaction of bound template dsDNA into a higher-ordered state less amenable to strand invasion by RAD51-coated ssDNA filaments. This previously unknown role of cGAS has implications for understanding its involvement in genome instability-associated disorders including cancer.

  • 4. Panda, Swarupa
    et al.
    Jiang, Hui
    Gekara, Nelson O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Umeå University, Sweden.
    TUBE and UbiCRest assays for elucidating polyubiquitin modifications in protein complexes2019Ingår i: DNA Sensors and Inflammasomes / [ed] Jungsan Sohn, Elsevier, 2019, Vol. 625, s. 339-350Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Ubiquitination is a reversible posttranslational modification that regulates nearly all cellular processes. The ubiquitin polypeptide is conjugated via its C-terminus to amine groups of lysine residues on target protein. Additionally, ubiquitins moieties can be conjugated in tandem to the initial ubiquitin via any of its internal lysine residues or N terminal methionine residue, resulting in the formation of polyubiquitin chains with distinct biophysical properties and biological functions. Elucidating the types of polyubiquitin chains present in proteins is essential for understanding their function and mechanism of regulation. Traditionally, ubiqutin modifications have been elucidated by exogenously co-expressing proteins of interest with epitope-tagged ubiquitins mutated in specific lysine residues. However, this strategy is prone experimental artifacts. In this protocol, we describe how to elucidate endogenous ubiquitin modifications. This procedure combines TUBE (Tandem Ubiquitin Binding Entity)-based isolation of ubiquitin conjugates, digestion with linkage specific deubiquitinases and immunoblotting. This procedure is very robust can be applied to profile types and architectural organization polyubiquitin chains present on the any proteins of interest and has been instrumental in elucidating ubiquitin modifications in NOD2 signaling in our recent study (Panda & Gekara, 2018).

  • 5. Swacha, Patrycja
    et al.
    Gekara, Nelson O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Umeå University, Sweden.
    Erttmann, Saskia F.
    Biochemical and microscopic analysis of inflammasome complex formation2019Ingår i: DNA Sensors and Inflammasomes / [ed] Jungsan Sohn, Elsevier, 2019, Vol. 625, s. 287-298Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Inflammasomes are multiprotein signaling platforms responsible for the maturation of pro-IL-113 and pro-IL-18 as well as the induction of an inflammatory cell death termed pyroptosis. Most inflammasomes consist of an upstream sensor, in most cases an adaptor protein (ASC) and inflammatory caspases such as caspase-1. Upon activation, sensor proteins oligomerize with adaptor proteins, forming large complexes called specks. These complexes can be stabilized and detected by Western blotting or fluorescence microscopy providing a direct evidence of inflammasome activation. Here we describe protocols for two complementary methods for detecting inflammasome complexes: (1) biochemical isolation and detection of ASC oligomers by Western blot analysis and (2) microscopic visualization of active caspase-1-ASC complexes. These protocols have successfully been applied in our recent study to unveil new regulatory mechanisms for different inflammasomes including the DNA sensor AIM2 (Erttmann et al., 2016).

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