Biology subjects

Soenmez, A.

Publications and source records attributed to Soenmez, A..

7 recordsLinked to original sources

bioRxiv2026

Villin-SNAP25 interaction regulates insulin secretion downstream of ICA512 signaling

Pancreatic islet {beta}-cells step-up insulin production and secretion in response to the elevation of blood glucose levels. ICA512/PTPRN is a transmembrane cargo of the insulin secretory granules (SGs). Upon SG exocytosis, its Ca2+/calpain mediated cleavage at the plasma membrane generates an ICA512-cleaved cytosolic fragment (ICA512-CCF) which as a decoy phosphatase prolongs phospho-STAT5/3 activities, thereby enhancing the transcription of mRNAs for SG cargoes, including insulin and its own, to replenish SG stores. In addition, ICA512 positively regulates the expression of F-actin modifier villin. Villin, in turn, modulates the size of actin cages surrounding cortical SGs, hence regulating SG mobility and exocytosis. Here we show that villin controls the number of SG docking sites for exocytosis by directly interacting at low glucose with the t-SNARE SNAP-25, thus restricting in this condition SG access to fusion sites and insulin release. Replacement of ICA512-CCF N-terminal ubiquitin-acceptor lysine 609 (K609) with valine (V) stabilized ICA512-CCF in insulinoma cells and homozygous ICA512K609V mice and enhanced the levels of phospho-STAT5/3 and villin. In ICA512K609V female mice these molecular traits correlated with reduced body weight, improved insulin sensitivity, reduced basal insulin secretion and onset time for glucose stimulated insulin secretion. Taken together, these data demonstrates that SG exocytosis induced ICA512 retrograde signaling acts in concert with the novel SNARE complex regulator villin to plastically adapt {beta}-cell actin cytoskeleton and access to SG docking sites for optimal control of insulin secretion in response to variations in extracellular glucose levels. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/699220v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@37d835org.highwire.dtl.DTLVardef@5389f1org.highwire.dtl.DTLVardef@855d98org.highwire.dtl.DTLVardef@1c3c639_HPS_FORMAT_FIGEXP M_FIG Graphical abstract Model of ICA512 and STAT3/5-dependent regulation of -cell function. At basal conditions, villin limits secretory granule (SG) docking by interacting with SNAP-25, restricting insulin release (1). Increased metabolic load triggers hyperglycemia-induced ICA512 processing and growth factor-mediated STAT3/5 phosphorylation (2-4), enhancing ISG mRNAs, granule biogenesis, and villin expression (5,6). Villin modulates SNARE protein availability, controlling SG docking and secretion. Together, ICA512 retrograde signaling and villin-mediated SNARE regulation dynamically remodel the -cell actin cytoskeleton, adjusting SG docking site access to ensure appropriate insulin secretion in response to fluctuating glucose levels. C_FIG

cell biology↗

bioRxiv2025

Zα domain-dependent ZBP1 condensate formation induces an amyloidal necroptotic signalling complex

ZBP1 restricts viral replication by inducing host cell death. ZBP1 recognises Z-RNA or Z-DNA, left-handed double-stranded RNA or DNA structures that accumulate after virus infection. How the interaction between Z-RNA/DNA and ZBP1 governs its activation and how this mediates downstream signalling remains unclear. Using herpes simplex virus 1 (HSV-1) as an activator of human ZBP1 we find that binding of the N-terminal Z domains of ZBP1 to Z-RNA induces ZBP1 condensate formation. This then mediates oligomerisation of the RIP homotypic interaction motifs (RHIMs) of ZBP1 establishing an amyloidal signalling complex with RIPK1 and RIPK3 that induces necroptotic cell death. We find that the kinase activity of RIPK1 is essential for RIPK1 and RIPK3 oligomerisation downstream of human ZBP1. Finally, the HSV-1-encoded RHIM-containing protein ICP6, does not interfere with Z domain-mediated ZBP1 condensate formation, but instead prevents downstream RIPK1 and RIPK3 oligomerisation thereby inhibiting necroptosis and promoting viral growth. Together, this shows that ZBP1 condensate formation restricts HSV-1 infection by promoting host cell necroptosis.

immunology↗

bioRxiv2025

GGA2-depletion in beta cells by Enteroviruses causes Golgi acidification, premature activation of cathepsins and alters the MHC class I immunopeptidome

Enteroviruses (EVs), such as Coxsackievirus B5 (CVB5), are linked to pancreatic beta cell autoimmunity in type 1 diabetes (T1D). CVB5 infection of beta cells blocks their cap-dependent translation but spares cap-independent translation of insulin secretory granule (SG) cargoes, including major T1D autoantigens. Despite this, insulin SG stores are depleted. We show that CVB5 protease 2A rapidly depletes Golgi-associated sorting factor GGA2 in beta cells due to its short half-life. Immunostaining of pancreas sections from recent-onset T1D donors confirmed reduced GGA2 in beta cells expressing EV capsid protein VP1. Both GGA2 depletion and CVB5 2A expression impair SG biogenesis at the TGN without affecting MHC class I trafficking. They also disrupt the sorting of vacuolar ATPase and cathepsins, leading to TGN acidification and premature lysosomal hydrolase activation, which typically generate peptides presented in HLA-II alleles. Notably, the unique immunopeptidome of EV-infected, GGA2-depleted ECN90 beta-like cells is mainly presented via HLA-B alleles with an average isoelectric point (pI) of [~]5, compared to a pI of [~]7 of the prevailing HLA-I A allele immunopeptidome of non-infected cells. We propose that delayed sorting at the acidified TGN promotes cathepsin-mediated processing of in-transit secretory proteins, including SG cargoes, thereby generating novel peptides that may replace HLA class I antigens due to the acidic environment. This novel cross-presentation mechanism could have implications for T1D pathogenesis and antigen presentation in general.

cell biology↗

bioRxiv2023

Detecting Material State Changes in the Nucleolus by Label-free Digital Holographic Microscopy

Ribosome biogenesis is initiated in the nucleolus, a multiphase biomolecular condensate formed by liquid-liquid phase separation. The nucleolus is a powerful disease biomarker and stress biosensor whose morphology reflects its function. Here we have used digital holographic microscopy (DHM), a label-free quantitative phase contrast microscopy technique, to detect nucleoli in adherent and suspension cells. Subtle nucleolar alterations induced by drug treatment or by depletion of ribosomal proteins were efficiently detected by DHM. We trained convolutional neural networks to detect and quantify nucleoli automatically on DHM images of cultured human cells (HeLa). Holograms containing cell optical thickness information allowed us to define a novel nucleolar index which we used to distinguish nucleoli whose material state had been optogenetically modulated. We conclude that DHM is a powerful tool for quantitatively characterizing nucleoli, including material state, without any staining.

cell biology↗

bioRxiv2021

Nucleolar stress controls mutant Huntingtin toxicity and monitors Huntington disease progression

Transcriptional and cellular stress surveillance deficits are hallmarks of Huntingtons disease (HD), a fatal autosomal dominant neurodegenerative disorder, caused by a pathological expansion of CAG repeats in the Huntingtin (HTT) gene. The nucleolus, a dynamic nuclear biomolecular condensate and the site of ribosomal RNA (rRNA) transcription, is implicated in the cellular stress response and in protein quality control. While the exact pathomechanisms of HD remain unclear, the impact of nucleolar dysfunction on HD pathophysiology in vivo is elusive. Here we identified aberrant maturation of rRNA and decreased translational rate in association with human mutant Huntingtin (mHTT) expression. Genetic disruption of nucleolar integrity in vulnerable striatal neurons of the R6/2 HD mouse model decreases mHTT disperse state in the nucleus, exacerbating the motor deficits. The protein nucleophosmin 1 (NPM1), important for nucleolar integrity and rRNA maturation, loses its nucleolar localization. NPM1 de-localization occurs in the striatum and in the skeletal muscle of the progressive zQ175 knock-in HD mouse model, mimicking the phenotype of HD patients in skeletal muscle biopsies. Taken together, we showed that nucleolar integrity regulates the formation of mHTT inclusions in vivo, and identified NPM1 as a novel, readily detectable peripheral histopathological marker of HD progression.

neuroscience↗

bioRxiv2017

FLIM-based pH measurements reveal incretin-induced rejuvenation of aged insulin secretory granules.

Insulin is stored in dense-core secretory granules (SGs) and is released from beta cells in two distinct phases upon glucose stimulation. Newly synthesized insulin SGs are secreted preferentially, but the underlying mechanism of this phenomenon remains elusive. The relationship of SG age with their intraluminal pH is of particular interest: proinsulin conversion by prohormone convertases follows the acidification of immature SGs by the vacuolar proton-translocating ATPase (v-ATPase). v-ATPases may also participate in the formation of the fusion pore for SG exocytosis, with intraluminal alkalinization inhibiting membrane fusion. Previous studies examined the luminal pH of SGs on a population level only. Here we measured the pH-dependent lifetime changes of eCFP fused to the ICA512-RESP18 homology domain to assess for the first time the luminal pH of individual age-defined SGs in insulinoma INS-1 cells by fluorescence-lifetime imaging microscopy. We show that 2-4-hour-old young SGs have a pH of ~5.5, while 26-28-hour-old SGs have a pH of ~6.2. Remarkably, the GLP-1 receptor agonist Exendin-4 prompted the re-acidification of old SGs in a glutamate-dependent fashion, while it did not affect the pH of young SGs. This study demonstrates that insulin SGs change their pH over time - a change that is reversible by insulin secretagogues. Hence, it provides novel insight into the mechanisms accounting for aging and exocytosis of SGs and suggests that their rejuvenation may be exploited to enhance insulin secretion in diabetes.

cell biology↗

bioRxiv2017

DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation

Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array \"waves\", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.

genomics↗