Biology subjects

Berges, J.

Publications and source records attributed to Berges, J..

3 recordsLinked to original sources

bioRxiv2024

The integration of network biology and pharmacophore modeling suggests repurposing Clindamycin as an inhibitor of pyroptosis via Caspase-1 blockage in tumor-associated macrophages

BackgroundUveal melanoma (UM) is a highly malignant intraocular tumor with a poor prognosis and response to therapy, including immune checkpoint inhibitors (ICIs), after the onset of liver metastasis. The metastatic microenvironment contains high levels of tumor-associated macrophages (TAMs) that correlate positively with a worse patient prognosis. We hypothesized that one could increase the efficacy of ICIs in UM metastases by immunomodulating UM-associated macrophages. MethodsTo identify potential targets for the immunomodulation, we created a network-based representation of the biology of TAMs and employed (bulk and single-cell) differential gene expression analysis to obtain a regulatory core of UM macrophages-associated genes. We utilized selected targets for pharmacophore-based virtual screening against a library of FDA-approved chemical compounds, followed by refined flexible docking analysis. Finally, we ranked the interactions and selected one novel drug-target combination for in vitro validation. ResultsBased on the generated TAM-specific interaction network (3863 nodes, 9073 edges), we derived a UM macrophages-associated regulatory core (74 nodes, 286 edges). From the regulatory core genes, we selected eight potential targets for pharmacophore-based virtual screening (YBX1, GSTP1, NLRP3, ISG15, MYC, PTGS2, NFKB1, CASP1). Of 266 drug-target interactions screened, we identified the interaction between the antibiotic Clindamycin and Caspase-1 as a priority for experimental validation. Our in vitro validation experiments showed that Clindamycin specifically interferes with activated Caspase-1 and inhibits the secretion of IL-1{beta}, IL-18, and lactate dehydrogenase (LDH) in macrophages after stimulation. Our results suggest that repurposed Clindamycin could reduce pyroptosis in TAMs, a pro-inflammatory form of programmed immune cell death favouring tumor progression. ConclusionWe were able to predict a novel Clindamycin-Caspase-1 interaction that effectively blocks Caspase-1-mediated inflammasome activity and pyroptosis in vitro in macrophages. This interaction is a promising clinical immunomodulator of the tumor microenvironment for improving ICI responsivenss. This work demonstrates the power of combining network-based transcriptomic analysis with pharmacophore-guided screening for de novo drug-target repurposing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/576201v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@310a9aorg.highwire.dtl.DTLVardef@1af0dcaorg.highwire.dtl.DTLVardef@1b272aborg.highwire.dtl.DTLVardef@86572b_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2021

Transient accumulation and bidirectional movement of KIF13B in primary cilia

Primary cilia are microtubule-based sensory organelles whose assembly and function rely on the conserved bidirectional intraflagellar transport (IFT) system, which is powered by anterograde kinesin-2 and retrograde cytoplasmic dynein 2 motors. Nematodes additionally employ a cell type-specific kinesin-3 motor, KLP-6, which moves within cilia independently of IFT and regulates ciliary content and function. Here we provide evidence that a KLP-6 homolog, KIF13B, undergoes bursts of bidirectional movement within primary cilia of cultured immortalized human retinal pigment epithelial (hTERT-RPE1) cells. Anterograde and retrograde intraciliary velocities of KIF13B were similar to those of IFT (IFT172-eGFP), but intraciliary movement of KIF13B required its own motor domain and appeared to be cell-type specific. Our work provides the first demonstration of motor-driven, intraciliary movement by a vertebrate kinesin other than kinesin-2 motors.

biophysics↗

bioRxiv2020

Histone H4K20 methylation synchronizes cytoskeletal dynamics with cell cycle phases during epidermal differentiation

Histone tails are subject to various post-translational modifications, which play a fundamental role in altering chromatin accessibility. Although they are thought to regulate progression through development, the impact of the most abundant histone modification in vertebrates, i.e., histone H4 lysine 20 dimethylation (H4K20m2), has remained largely elusive. H4K20m2 arises from sequential methylation of new, unmodified histone H4 proteins, incorporated into chromatin during DNA replication, by the mono-methylating enzyme PR-SET7/KMT5A during G2/M phases, followed by conversion to the dimethylated state by SUV4-20H1 enzymes in the following G1/G0 phase. To address its function, we have blocked the deposition of this mark by depleting Xenopus embryos of SUV4-20H1/H2 methyltransferases, which convert H4K20 monomethylated to di- and tri-methylated states, respectively In the frog larval epidermis this results in a severe loss of cilia in multiciliated cells (MCC), a key component of all mucociliary epithelia. MCC precursor cells are correctly specified and amplify centrioles, but ultimately fail in ciliogenesis due to perturbation of cytoplasmic processes. Genome wide transcriptome profiling reveals that SUV4-20H1/H2 depleted ectodermal Animal Cap explants preferentially down-regulate the expression of several hundred cytoskeleton and cilium related genes as a consequence of persistent H4K20 monomethyl marks on postmitotic chromatin. Further analysis demonstrated that knockdown of SUV4-20H1 alone is sufficient to generate the MCC phenotype and that overexpression of the H4K20m1-specific histone demethylase PHF8 rescues the ciliogenic defect in significant, although partial, manner. Taken together, this indicates that the conversion of H4K20m1 to H4K20m2 by SUV4-20H1 is critical to synchronize cytoskeletal dynamics in concert with the cell cycle.

developmental biology↗