Biology subjects

Kim, R. Q.

Publications and source records attributed to Kim, R. Q..

4 recordsLinked to original sources

bioRxiv2025

Enhanced recognition of topoisomerase 1 upon DNA binding by a subset of anti-topoisomerase 1 autoantibodies in systemic sclerosis

ObjectivesSystemic sclerosis (SSc) is a deleterious disease. Its clinical management is complicated by strong interpatient heterogeneity. Progressive organ fibrosis is linked to autoantibodies against topoisomerase 1 (TOP1). Here, we hypothesized that the molecular interaction between anti-TOP1 autoantibodies (ATAs) and TOP1 could be a relevant determinant of SSc pathogenesis. DNA binding by TOP1 might affect its interaction with ATAs. Therefore, we studied the effect of DNA binding by TOP1 on ATA recognition. MethodsATA monoclonal antibodies (ATA mAbs) were generated from patient-derived TOP1-reactive B cells. Reactivity of ATA mAbs and antibodies in patient plasma towards TOP1 and TOP1-DNA cleavage complexes (TOP1cc) was determined by ELISA and mass photometry. Immunostimulatory properties of ATA mAbs in complex with TOP1/TOP1cc were assessed by stimulation of monocytic THP-1 cells. ResultsDNA binding by TOP1 differentially affected the recognition of TOP1 by ATA mAbs. A subset of mAbs showed enhanced binding to TOP1cc, whereas others recognized TOP1 and TOP1cc to a similar extent. ATAs with enhanced TOP1cc recognition were observed in plasma of ATA+ SSc patients and correlated with ATA levels and interstitial lung disease. These TOP1cc-enhanced ATAs variably affected the enzymatic function of TOP1 and circulated predominantly as IgG1 and IgM. The interaction of TOP1cc-enhanced ATA mAbs with TOP1cc strongly increased IL-8 production by THP-1 cells. ConclusionsThe differential recognition of TOP1 upon DNA binding by ATAs demonstrates heterogeneity in the ATA B cell response, possibly impacting on disease-relevant processes in severe SSc.

immunology↗

bioRxiv2024

USP24 is an ISG15 cross-reactive deubiquitinasethat mediates IFN-I production by de-ISGylatingthe RNA helicase MOV10

The interferon-stimulated gene 15 (ISG15) is a ubiquitin-like modifier induced by type I Interferon (IFN-I) and plays a crucial role in the innate immune response against viral infections. ISG15 is conjugated to target proteins by an enzymatic cascade through a process called ISGylation. While ubiquitin-specific protease 18 (USP18) is a well-defined deISGylase counteracting ISG15 conjugation, ISG15 cross-reactive deubiquitylating enzymes (DUBs) have also been reported. Our study reports USP24 as a novel ISG15 cross-reactive DUB identified through activity-based protein profiling (ABPP). We demonstrate that recombinant USP24 processed pro-ISG15 and ISG15-linked synthetic substrates in vitro. Moreover, the depletion of USP24 significantly increased the accumulation of ISG15 conjugates upon IFN-{beta} stimulation. An extensive proteomic analysis of the USP24-dependent ISGylome, integrating total proteome, GG-peptidome, and ISG15 interactome data, identified the helicase Moloney leukemia virus 10 (MOV10) as a specific target of USP24 for deISGylation. Further validation in cells revealed that ISGylated MOV10 enhances IFN-{beta} production/secretion, whereas USP24 deISGylates MOV10 to negatively regulate the innate immune response. This study showcases USP24s novel roles in modulating ISGylation and modulation of the IFN-I-dependent immune responses, with potential therapeutic implications in infectious diseases, cancer, autoimmunity, and neuroinflammation.

biochemistry↗

bioRxiv2024

Development of covalent probes to capture Legionella pneumophila effector enzymes

Upon infection of host cells, Legionella pneumophila releases a multitude of effector enzymes into the cells cytoplasm that hijack a plethora of cellular activities, including the hosts ubiquitination pathways. Effectors belonging to the SidE-family are involved in non-canonical serine phosphoribosyl ubiquitination of host substrate proteins contributing to the formation of a Legionella-containing vacuole that is crucial in the onset of Legionnaires disease. This dynamic process is reversed by effectors called Dups that hydrolyse the phosphodiester in the phosphoribosyl ubiquitinated protein. We installed reactive warheads on chemically prepared ribosylated ubiquitin to generate a set of probes targeting these Legionella enzymes. In vitro tests on recombinant DupA revealed that a vinyl sulfonate warhead was most efficient in covalent complex formation. Mutagenesis and x-ray crystallography approaches were used to identify the site of covalent crosslinking to be an allosteric cysteine residue. The subsequent application of this probe highlights the potential to selectively enrich the Dup enzymes from Legionella-infected cell lysates.

cell biology↗

bioRxiv2021

Malaria parasite evades mosquito immunity by glutaminyl cyclase mediated protein modification

Glutaminyl cyclase (QC) modifies N-terminal glutamine or glutamic acid residues of target proteins into cyclic pyroglutamic acid (pGlu). Here, we report the biochemical and functional analysis of Plasmodium QC. We show that Plasmodium sporozoites of QC-null mutants are recognized by the mosquito immune system and melanized when they reach the hemocoel. Sporozoite numbers in salivary glands are also reduced in mosquitoes infected with QC-null or QC catalytically-dead mutants. This phenotype can be rescued by genetic complementation or by disrupting mosquito hemocytes or melanization immune responses. Mutation of a single QC-target glutamine of the major sporozoite surface protein (CSP) also results in immune recognition of sporozoites. These findings reveal QC-mediated post-translational modification of surface proteins as a major mechanism of mosquito immune evasion by Plasmodium sporozoites.

microbiology↗