Biology subjects

Kallabis, S.

Publications and source records attributed to Kallabis, S..

7 recordsLinked to original sources

bioRxiv2026

NLRP3 activators disrupt the endocytic AP2 complex and plasma membrane signaling

Organellar perturbations are linked to NLRP3 inflammasome activation, however, it remains unclear whether unrelated agonists converge on a common upstream pathway. Here, we traced intracellular organelle and protein movements by differential ultracentrifugation combined with mass spectrometry-based proteomics. We show that NLRP3 activators uniformly disrupt the endocytic Adaptor Protein 2 (AP2) complex, whereas other subcellular rearrangements are stimulus-specific. We discovered Dynasore as a K-efflux-independent NLRP3 activator that engages this signaling node irrespective of endocytosis inhibition. Pharmacological and genetic perturbation of AP2 renders cells unresponsive to extracellular cues, blunting GPCR signaling, cAMP production, and chemotaxis, thereby enforcing a frozen signaling state that propagates NLRP3 inflammasome activation. Collectively, our study reveals a common surveillance checkpoint linking impaired plasma membrane signaling to the execution of inflammation and cell death. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/707400v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@178eb1dorg.highwire.dtl.DTLVardef@193cb02org.highwire.dtl.DTLVardef@1f50080org.highwire.dtl.DTLVardef@1f3e3e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

miR-196a-5p and miR-342-3p mediate skeletal muscle and thermogenic adipose tissue crosstalk through extracellular vesicles

Small extracellular vesicles (small EVs) are nanovesicles found in tissues and body fluids that contain regulatory molecules including microRNAs, termed exomiRs. Research in murine models has demonstrated that exercise can trigger the release of small EVs into the circulation. The aim of this study was to study exomiR release in humans pre and post exercise and to characterise the function of these microRNAs especially in relation to thermogenic fat. We found that exercise increased the release of exomiR-196a-5p in endurance athletes, a microRNA that induces UCP1 expression and browning of white adipocytes. We observed that myotubes specifically release miR-196a-5p within small EVs after in vitro exercise-mimicking conditions such as electrical pulse stimulation and cAMP treatment. Likewise, the expression at basal levels of the exercise-induced exomiR-342-3p negatively correlated with BMI and age. EV proteomics revealed a positive correlation between FABP4+ and miR-342-3p, suggesting an adipocyte cell origin. Overexpression of miR-342-3p increased Myogenin levels during skeletal muscle cell differentiation, indicating a positive role in muscle differentiation. Our results suggest that oxidative extreme metabolic capacities in endurance athletes contribute to the enhanced release of circulatory exomiRs after exercise mediating bi-directional crosstalk between skeletal muscle and thermogenic adipose tissue. Graphical abstractO_LISerum-EVs from endurance athletes increase UCP1 expression in white adipocytes. C_LIO_LImiR-196a and miR-342-3p are increased in serum-EVs from endurance athletes. C_LIO_LIMuscle cells release EVs enriched in miR-196a after electrical pulse stimulation. C_LIO_LImiR-196a and miR-342-3p have browning and myogenic potential, respectively. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/656129v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1bd9b25org.highwire.dtl.DTLVardef@114a549org.highwire.dtl.DTLVardef@6f863borg.highwire.dtl.DTLVardef@1d5c528_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Cytohesin-2 is essential for the survival of mice and regulates Golgi volume and function

Proteins of the cytohesin family are known for their guanine-nucleotide exchange factor function for ARF-GTPases, mainly for ARF1 and ARF6. While Arf1 and Arf6 deficiency results in embryonic lethality, in vivo functions of cytohesins are rarely described and mostly inconspicuous. We analyzed the role of cytohesin-2 in vivo and in vitro and found that cytohesin-2 full knockout mice die within one day after birth. Mass spectrometry-based organellar proteomics in wildtype and CRISPR-Cas9-generated cytohesin-2-/- C2 myoblasts revealed a markedly altered Golgi compartment. Golgi volumes were reduced in different cytohesin-2-/- cell lines compared to wildtype cells as revealed by immunofluorescence. Reduced Golgi volumes were rescued by introducing cytohesin-2. Finally, we observed that typical functions of the Golgi apparatus were disrupted in cytohesin-2-deficient cells. Cytohesin2-/- C2 myoblasts exhibited significant changes in the galactose / N-acetyl-galactosamine glycosylation on the cell surface compared to wildtype cells when stained with peanut agglutinin. Further, protein secretion was overall reduced in neonatal cytohesin-2-/- mice compared to wildtype as determined by mass spectrometry-based proteomics. This study describes the essential role of cytohesin-2 in neonatal development and a novel function of the protein in Golgi regulation.

cell biology↗

bioRxiv2024

From Planning Stage To FAIR Data: A Practical Metadatasheet For Biomedical Scientists

Datasets consist of measurement data and metadata. Metadata provides context, essential for understanding and (re-)using data. Various metadata standards exist for different methods, systems and contexts. However, relevant information resides at differing stages across the data-lifecycle. Often, this information is defined and standardized only at publication stage, which can lead to data loss and workload increase. In this study, we developed Metadatasheet, a metadata standard based on interviews with members of two biomedical consortia and systematic screening of data repositories. It aligns with the data-lifecycle allowing synchronous metadata recording within Microsoft Excel, a widespread data recording software. Additionally, we provide an implementation, the Metadata Workbook, that offers user-friendly features like automation, dynamic adaption, metadata integrity checks, and export options for various metadata standards. By design and due to its extensive documentation, the proposed metadata standard simplifies recording and structuring of metadata for biomedical scientists, promoting practicality and convenience in data management. This framework can accelerate scientific progress by enhancing collaboration and knowledge transfer throughout the intermediate steps of data creation.

bioinformatics↗

bioRxiv2024

ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway

Complexes of ERLIN1 and ERLIN2 form large ring-like cup-shaped structures on the endoplasmic reticulum (ER) membrane and serve as platforms to bind cholesterol and E3-ubiquitin ligases, potentially defining functional nanodomains. Here, we show that ERLIN scaffolds mediate the interaction between the full-length isoform of TMUB1 and RNF170. We identify a luminal N-terminal conserved region in TMUB1 and RNF170 required for this interaction. Three-dimensional modelling shows that this conserved motif binds the SPFH domain of two adjacent ERLIN subunits at different interfaces. Protein variants that preclude these interactions have been previously linked to hereditary spastic paraplegia (HSP). By using omics approaches in combination with phenotypic characterisation of cells lacking both ERLINs, we demonstrate a role for ERLIN scaffolds in maintaining cholesterol levels in the ER by favouring transport to the Golgi over esterification, thereby regulating Golgi morphology and the secretory pathway.

cell biology↗

bioRxiv2021

Mitochondrial membrane proteins and VPS35 orchestrate selective removal of mtDNA

Integrity of mitochondrial DNA (mtDNA), encoding several subunits of the respiratory chain, is essential to maintain mitochondrial fitness. Mitochondria, as a central hub for metabolism, are affected in a wide variety of human diseases but also during normal ageing, where mtDNA integrity is compromised. Mitochondrial quality control mechanisms work at different levels, and mitophagy and its variants are critical to remove dysfunctional mitochondria together with mtDNA to maintain cellular homeostasis. Understanding the mechanisms governing a selective turnover of mutation-bearing mtDNA without affecting the entire mitochondrial pool is fundamental to design therapeutic strategies against mtDNA diseases and ageing. Here we show that mtDNA depletion after expressing a dominant negative version of the mitochondrial helicase Twinkle, or by chemical means, is due to an exacerbated mtDNA turnover. Targeting of nucleoids is controlled by Twinkle which, together with the mitochondrial transmembrane proteins ATAD3 and SAMM50, orchestrate mitochondrial membrane remodeling to form extrusions. mtDNA removal depends on autophagy and requires the vesicular trafficking protein VPS35 which binds to Twinkle-enriched mitochondrial subcompartments upon mtDNA damage. Stimulation of autophagy by rapamycin selectively removes mtDNA deletions which accumulated during muscle regeneration in vivo, but without affecting mtDNA copy number. With these results we unveil a new complex mechanism specifically targeting and removing mutant mtDNA which occurs outside the mitochondrial network. We reveal the molecular targets involved in a process with multiple potential benefits against human mtDNA related diseases, either inherited, acquired or due to normal ageing.

cell biology↗

bioRxiv2019

CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex

The exon junction complex (EJC) is an essential constituent and regulator of spliced messenger ribonucleoprotein particles (mRNPs) in metazoans. As a core component of the EJC, CASC3 was described to be pivotal for EJC-dependent nuclear and cytoplasmic processes. However, recent evidence suggests that CASC3 functions differently from other EJC core proteins. Here, we have established human CASC3 knockout cell lines to elucidate the cellular role of CASC3. In the knockout cells, overall EJC composition and EJC-dependent splicing are unchanged. A transcriptome-wide analysis reveals that hundreds of mRNA isoforms targeted by nonsense-mediated decay (NMD) are upregulated. Mechanistically, recruiting CASC3 to reporter mRNAs by direct tethering or via binding to the EJC stimulates mRNA decay and endonucleolytic cleavage at the termination codon. Building on existing EJC-NMD models, we propose that CASC3 equips the EJC with the ability to communicate with the NMD machinery in the cytoplasm. Collectively, our results characterize CASC3 as a peripheral EJC protein that tailors the transcriptome by promoting the degradation of EJC-dependent NMD substrates.

molecular biology↗