Biology subjects

Grillari, J.

Publications and source records attributed to Grillari, J..

17 recordsLinked to original sources

bioRxiv2026

Acetylation-dependent remodeling of the secretory pathway shapes the senescence-associated secretome

Cellular senescence is characterized by stable cell cycle arrest and the senescence-associated secretory phenotype (SASP), which drives tissue remodeling and inflammation. Underlying SASP with its increased secretion of cytokines and other secreted proteins is a massive reorganization of the secretory pathway. While transcriptional regulation of senescence has been extensively studied, the contribution of post-translational modifications (PTM) to secretory pathway regulation remains poorly understood. Here, we combined quantitative proteomics with multi-layered PTM profiling of phosphorylation, ubiquitination and acetylation to investigate how intracellular trafficking and secretion are regulated in senescence. Using doxorubicin-induced senescence as the primary model, we identified extensive proteome remodeling, with pronounced changes in ER-Golgi-associated pathways and secretory machinery. Acetylation emerged as the most prominently regulated PTM, particularly affecting proteins involved in vesicle trafficking and ER proteostasis. Comparable proteome and PTM remodeling were also observed in replicative senescence, indicating that these changes are not restricted to a single senescence model. Functional analyses revealed activation signatures of the acetyltransferases p300/CBP, linking global acetylation changes to enzymatic activity. Pharmacological inhibition of p300/CBP using A485 selectively modulated senescence-associated features without reversing growth arrest, consistent with a senomorphic-like effect during senescence establishment. Secretome profiling further demonstrated changes in the composition of secreted factors, consistent with modulation of the senescence-associated secretory phenotype. Together, these findings indicate that acetylation-dependent regulation of the secretory pathway shapes the senescence-associated secretome, revealing a mechanistic link between post-translational regulation, intracellular trafficking, and extracellular signaling in senescence.

Cell Biology↗

bioRxiv2025

Native extracellular vesicles display surface bound RNAs that are co-delivered to cells

Extracellular vesicles (EVs) can transport functional RNA between cells and therefore hold great potential for diagnostics and RNA-based therapeutics. Classically, RNA is believed to be encapsulated in the EV lumen. However, it has recently been demonstrated that cells present RNA on their surface. This RNA was found to be glycosylated, and although glycosylated tRNA was also found in EVs, its exact location remained elusive. Here, we demonstrate the presence of RNA on the surface of mesenchymal stem cell (MSC) derived EVs. By combining single-vesicle measurements with direct and selective visualization of RNA, we introduce surface RNA (surfRNA) as a new inherent component of EVs. RNA sequencing supports the surface localization of this RNA and further identifies tRNA fragments as primary constituent of surfRNA. Importantly, surfRNA is co-delivered to target cells together with EVs, suggesting a yet unrecognized uptake route of extracellular RNA. A deeper understanding of the surface-associated RNA may have significant implications for EV biogenesis, targeting, and downstream functional effects. We further envision that these findings are transferable to other nanoparticles and will thereby advance the field of therapeutic RNA delivery.

molecular biology↗

bioRxiv2025

Mitochondrial Respiratory Chain Function is crucial for Muscle Toxicity in Facioscapulohumeral Muscular Dystrophy

Facioscapulohumeral muscular dystrophy (FSHD) is driven by DUX4-induced toxicity, yet the pathomechanisms remain unclear. Here, we identify persistent transcriptional suppression of the mitochondrial respiratory chain and metabolic rewiring in FSHD muscle biopsies and myotubes. Using DUX4-inducible human myogenic cells, we show that DUX4 target gene activation is accompanied by mitochondrial function impairment and Caspase 9-mediated apoptosis. Reverse electron transfer (RET) at complex I is the dominant oxidative stress generating mechanism in FSHD muscle cells. RET-driven mitochondrial reactive oxygen species (mitoROS) are the trigger for oxidative stress and apoptosis, which is a unique feature of FSHD mitochondria. Pharmacological inhibition of RET suppresses mitoROS, reduces Caspase 9 activation, and rescues abnormal myogenesis in FSHD cell lines. Importantly, DUX4 is non-toxic in oxidative phosphorylation-deficient human myogenic cells. Our findings identify the mitochondrial respiratory chain as a key mediator of DUX4 toxicity and highlight RET inhibition as a potential therapeutic approach for FSHD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/690559v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@254927org.highwire.dtl.DTLVardef@1e5c67forg.highwire.dtl.DTLVardef@4ace42org.highwire.dtl.DTLVardef@12b710e_HPS_FORMAT_FIGEXP M_FIG (Created with BioRender.com) C_FIG

biochemistry↗

bioRxiv2024

Immortalization of mesenchymal stromal cells by hTERT does not affect the functional properties of secreted extracellular vesicles

Mesenchymal stromal cell-derived extracellular vesicles (MSC-EVs) have emerged as promising and safe therapeutic agents, however, donor heterogeneities, limited replicative life span and changes in the cellular phenotype throughout in vitro cultivation remain major hurdles for scalable EV production. For these reasons, this study aims to investigate the use of hTERT immortalized ( telomerized) MSCs as a potential source for efficient, standardized, reliable MSC-EVs production by comparing parental primary to their telomerized MSC counterparts. We observed that hTERT expression does not affect cell morphology or cellular doubling time, while ensuring unlimited, stable in vitro propagation. In addition, telomerized WJ-MSCs maintained the canonical expression profile of surface markers and the tri-lineage differentiation potential of their primary counterparts. In terms of EV characteristics, the immortalization by hTERT expression did not affect size, number, cargo composition or biological activity regarding anti-inflammatory, anti-fibrotic and wound healing properties in vitro. In summary, the use of hTERT to immortalize MSCs leads to the creation of cell lines that continuously produce MSC-EVs without altering any key functionalities of the cells or resulting EVs. This suggests that telomerization of human cells from single donors is a promising strategy for generating cell factories that can produce EVs in standardized conditions and at scale and with standardization.

cell biology↗

bioRxiv2024

Connectivity Map and perturbation-based sensitivity analysis identifies MEK inhibitors as senolytics in human lung fibroblasts

Recently, the elimination of the disease-associated accumulation of senescent cells using senolytics has been shown to exert health benefits in animal studies. However, due to the heterogeneity of cell senescence and its unrecognized master regulators, drug development faces a complexity that must be handled. Bioinformatic elucidation of genes and pathways involved in senolysis and prediction of senolytic activity of compounds can cut costs and facilitate faster achievements in the field. In the present investigation, after obtaining the consensus gene signature of senescent fibroblasts of lung origin and deriving its anti-apoptotic module, we utilized Connectivity Map (CMap) alongside small molecule and genetic perturbation sensitivity data in cancer cell lines to identify drugs and genetic interventions that might induce apoptosis or sensitize senescent cells to apoptosis. Through bioinformatic evaluations, we speculate that activation of early stages of autophagy which contributes to the formation of autophagosomes, concurrent with the activation of waste protein concealment system by the mean of p62 and chaperoning system alongside an increase in JUNB gene expression can secure the survival of the senescent cells even when homeostasis of different cellular processes is disrupted. Moreover, our bioinformatic evaluation proposed selumetinib, a MEK inhibitor, as a senolytic against senescent lung fibroblasts. The senolytic activity of a variety of MEK inhibitors in senescent lung fibroblasts was confirmed using human lung fibroblasts in vitro.

pharmacology and toxicology↗

bioRxiv2024

Snorkel-tag Based Affinity Chromatography for Recombinant Extracellular Vesicle Purification

Extracellular vesicles (EVs) are lipid nanoparticles and play an important role in cell-cell communications, making them potential therapeutic agents and allowing to engineer for targeted drug delivery. The expanding applications of EVs in next generation medicine are still limited by existing tools for scaling standardized EV production, single EV tracing and analytics, and thus provide only a snapshot of tissue-specific EV cargo information. Here, we present CD81, an EV surface marker protein, genetically fused to series of tags with additional transmembrane domain to be displayed on the EV surface, which we term Snorkel-tag. This system enables to affinity purify EVs from complex matrices in a non-destructive form. In future applications, this strategy will allow generating transgenic animals to enable tracing and analyzing EVs, and their cargo in physiological and pathophysiological set-ups, and facilitate the development of EV based diagnostic tools in murine models which can be translated to humans.

bioengineering↗

bioRxiv2024

Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden

In the last decade cellular senescence, a hallmark of aging, has come into focus for pharmacologically targeting aging processes. Senolytics are one of these interventive strategies that have advanced into clinical trials, creating an unmet need for minimally invasive biomarkers of senescent cell load to identify patients at need for senotherapy. We created a landscape of miRNA and mRNA expression in five human cell types induced to senescence in-vitro and provide proof-of-principle evidence that miRNA expression can track senescence burden dynamically in-vivo using transgenic p21high senescent cell clearance in HFD fed mice. Finally, we profiled miRNA expression in seven different tissues, total plasma, and plasma derived EVs of young and 25 months old mice. In a systematic analysis, we identified 22 candidate senomiRs with potential to serve as circulating biomarkers of senescence not only in rodents, but also in upcoming human clinical senolytic trials.

molecular biology↗

bioRxiv2022

The p-rpS6-zone delineates wounding response and the healing process

It is unknown what the spatial boundaries of tissue response to wounding are. Here we show that in mammals the ribosomal protein S6 (rpS6) is phosphorylated in response to skin injury forming a zone of activation surrounding the region of the initial insult. This p-rpS6-zone forms within minutes after wounding and is present until healing is complete. The zone encapsulates markers of the healing process, including proliferation, senescence, and angiogenesis in wounded skin. A mouse model unable to phosphorylate rpS6 shows an initial acceleration of wound closure, but results in disrupted healing. Finally, the p-rpS6-zone accurately reports on the status of dermal vasculature and the effectiveness of healing. In summary, the zone divides an otherwise homogenous tissue into regions with distinct properties.

physiology↗

bioRxiv2022

Development of a multi-sensor integrated midbrain organoid-on-a-chip platform for studying Parkinson's disease

Due to its ability to recapitulate key pathological processes in vitro, midbrain organoid technology has significantly advanced the modeling of Parkinsons disease over the last few years. However, some limitations such as insufficient tissue differentiation and maturation, deficient nutrient supply, and low analytical accessibility persist, altogether restricting the technology from reaching its full potential. To overcome these drawbacks, we have developed a multi-sensor integrated organ-on-a-chip platform capable of monitoring the electrophysiological, respiratory, and dopaminergic activity of human midbrain organoids. Our study showed that microfluidic cultivation resulted in a marked reduction in necrotic core formation, improved tissue differentiation as well as the recapitulation of key pathological hallmarks. Non-invasive monitoring employing an orthogonal sensing strategy revealed a clear time dependency in the onset of Parkinsons disease-related phenotypes, reflecting the complex progression of the neurodegenerative disorder. Furthermore, drug-mediated rescue effects were observed after treatment with the repurposed compound 2-hydroxypropyl {beta}-cyclodextrin, highlighting the platforms potential in the context of drug screening applications as well as personalized medicine.

bioengineering↗

bioRxiv2021

Interplay between mitochondria and reactive oxygen and nitrogen species in metabolic adaptation to hypoxia in facioscapulohumeral muscular dystrophy: potential therapeutic targets.

Facioscapulohumeral muscular dystrophy (FSHD) is characterised by descending skeletal muscle weakness and wasting. FSHD is caused by mis-expression of the transcription factor DUX4, which is linked to oxidative stress, a condition especially detrimental to skeletal muscle with its high metabolic activity and energy demands. Oxidative damage characterises FSHD and recent work suggests metabolic dysfunction and perturbed hypoxia signalling as novel pathomechanisms. However, redox biology of FSHD remains poorly understood, and integrating the complex dynamics of DUX4-induced metabolic changes is lacking. Here we pinpoint the kinetic involvement of altered mitochondrial RONS metabolism and impaired mitochondrial function in aetiology of oxidative stress in FSHD. Transcriptomic analysis in FSHD muscle biopsies reveals strong enrichment for pathways involved in mitochondrial complex I assembly, nitrogen metabolism, oxidative stress response and hypoxia signalling. We found elevated ROS levels correlate with increases in steady-state mitochondrial membrane potential in FSHD myogenic cells. DUX4 triggers mitochondrial membrane polarisation prior to oxidative stress generation and apoptosis through mitochondrial ROS, and affects NO{middle dot} bioavailability via mitochondrial peroxidation. We identify complex I as the primary target for DUX4-induced mitochondrial dysfunction, with strong correlation between complex I-linked respiration and cellular oxygenation/hypoxia signalling activity in environmental hypoxia. Thus, FSHD myogenesis is uniquely susceptible to hypoxia-induced oxidative stress as a consequence of metabolic mis-adaptation. Importantly, mitochondria-targeted antioxidants rescue FSHD pathology more effectively than conventional antioxidants, highlighting the central involvement of disturbed mitochondrial RONS metabolism. This work provides a pathomechanistic model by which DUX4-induced changes in oxidative metabolism impair muscle function in FSHD, amplified when metabolic adaptation to varying O2 tension is required. HighlightsO_LITranscriptomics data from FSHD muscle indicates enrichment for disturbed mitochondrial pathways C_LIO_LIDisturbed RONS metabolism correlates with mitochondrial membrane polarisation and myotube hypotrophy C_LIO_LIDUX4-induced changes in mitochondrial function precede oxidative stress through mitoROS and affect hypoxia signalling via complex I C_LIO_LIFSHD is sensitive to environmental hypoxia, which increases ROS levels in FSHD myotubes C_LIO_LIHypotrophy in hypoxic FSHD myotubes is efficiently rescued with mitochondria-targeted antioxidants C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/459509v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@16ae1a8org.highwire.dtl.DTLVardef@517caorg.highwire.dtl.DTLVardef@5d0734org.highwire.dtl.DTLVardef@183ef50_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2020

Comprehensive label-free characterization of extracellular vesicles and their surface proteins

Interest in mesenchymal stem cell derived extracellular vesicles (MSC-EVs) as therapeutic agents has dramatically increased over the last decade. Preclinical studies show that MSC-EVs have anti-apoptotic and neuroprotective effects, boost wound healing, and improve the integration of allogeneic grafts through immunomodulation. Current approaches to the characterization and quality control of EV-based therapeutics include particle tracking techniques, Western blotting, and advanced cytometry, but standardized methods are lacking. In this study, we established and verified quartz crystal microbalance (QCM) as highly sensitive label-free immunosensing technique for characterizing clinically approved umbilical cord MSC-EVs enriched by tangential flow filtration and ultracentrifugation. Using QCM in conjunction with common characterization methods, we were able to specifically detect EVs via EV (CD9, CD63, CD81) and MSC (CD44, CD49e, CD73) markers and gauge their prevalence. Additionally, we characterized the topography and elasticity of these EVs by atomic force microscopy (AFM), enabling us to distinguish between EVs and non-vesicular particles (NVPs) in a therapeutic formulation. This measurement modality makes it possible to identify EV sub-fractions, discriminate between EVs and NVPs, and to characterize EV surface proteins, all with minimal sample preparation and using label-free measurement devices with low barriers of entry for labs looking to widen their spectrum of characterization techniques. Our combination of QCM with impedance measurement (QCM-I) and AFM measurements provides a robust multi-marker approach to the characterization of clinically approved EV formulations and opens the door to improved quality control.

molecular biology↗

bioRxiv2020

Cellular senescence and quiescence are associated with altered ribosomal RNA methylation and processing

The 2-O-methylation (2-O-Me) of ribosomal RNA (rRNA) shows plasticity potentially associated with specific cell phenotypes. We used RiboMeth-seq profiling to reveal 2-O-Me patterns specific to stress induced premature senescent (SIPS), quiescent and proliferating human dermal fibroblasts. The altered methylation levels in SIPS and quiescence partially correlated with the expression of specific snoRNAs but not fibrillarin. Senescence and quiescence were accompanied by a trend towards preferred usage of one of the two alternative ribosome biogenesis pathways.

molecular biology↗

bioRxiv2020

MiR-146a controls age related bone loss

Bone loss is one of the consequences of aging, leading to diseases such as osteoporosis and increased susceptibility to fragility fractures and therefore considerable morbidity and mortality in humans. Here we identify microRNA 146a as an essential epigenetic switch controlling bone loss with age. Mice deficient in miR-146a show regular development of their skeleton. However, while WT mice start to lose bone with age, animals deficient in miR-146a continue to accrue bone throughout their life span. Increased bone mass is due to increased generation and activity of osteoblasts in miR-146a deficient mice as a result of sustained activation of bone anabolic Wnt signaling during aging. Deregulation of the miR-146a target genes Wnt1 and Wnt5a parallel bone accrual and osteoblast generation, which is accompanied by reduced development of bone marrow adiposity. Furthermore, miR-146a deficient mice are protected from ovariectomy induced bone loss. In humans, levels of miR-146a are increased in patients suffering fragility fractures in comparison to those who do not. These data identify miR-146a as a crucial epigenetic temporal regulator which essentially controls bone homeostasis during aging by regulating bone anabolic Wnt signaling. Therefore, miR-146a might be a powerful therapeutic target to prevent age related bone dysfunction such as the development of bone marrow adiposity and osteoporosis.

molecular biology↗

bioRxiv2020

The ribosomal RNA m5C methyltransferase NSUN-1 modulates healthspan and oogenesis in Caenorhabditis elegans

Our knowledge about the repertoire of ribosomal RNA modifications and the enzymes responsible for installing them is constantly expanding. Previously, we reported that NSUN-5 is responsible for depositing m5C at position C2381 on the 26S rRNA in Caenorhabditis elegans. Here, we show that NSUN-1 is writing the second known 26S rRNA m5C at position C2982. Depletion of nsun-1 or nsun-5 improved locomotion at midlife and resistance against heat stress, however, only soma-specific knockdown of nsun-1 extended lifespan. Moreover, soma-specific knockdown of nsun-1 reduced body size and impaired fecundity, suggesting non-cell-autonomous effects. While ribosome biogenesis and global protein synthesis were unaffected by nsun-1 depletion, translation of specific mRNAs was remodelled leading to reduced production of collagens, loss of structural integrity of the cuticle and impaired barrier function. We conclude that loss of a single enzyme required for rRNA methylation has profound and highly specific effects on organismal physiology.

cell biology↗

bioRxiv2019

SVF-derived extracellular vesicles carry characteristic miRNAs in lipedema

Lipedema is a chronic, progressive disease of adipose tissue with lack of consistent diagnostic criteria. The aim of this study was a thorough comparative characterization of extracellular microRNAs from the stromal vascular fraction (SVF) of healthy and lipedema adipose tissue. For this, we analyzed 187 extracellular microRNAs in concentrated conditioned media (cCM) and specifically in small extracellular vesicles (sEVs) enriched thereof by size exclusion chromatography. No significant difference in median particle size and concentration was observed between sEV fractions in healthy and lipedema. We found the majority of miRNAs located predominantly in cCM compared to sEV enriched fraction. Surprisingly, hierarchical clustering of the most variant miRNAs showed that only sEV miRNA profiles - but not cCM miRNAs - were impacted by lipedema. Seven sEV miRNAs (miR-16-5p, miR-29a-3p, miR-24-3p, miR-454-p, miR-144-5p, miR-130a-3p, let-7c-5p) were differently regulated in lipedema and healthy, whereas only one cCM miRNA (miR-188-5p) was significantly downregulated in lipedema. Comparing SVF from healthy and lipedema patients, we identified sEVs as the lipedema relevant miRNA fraction. This study contributes to identify the potential role of SVF secreted miRNAs in lipedema.

molecular biology↗

bioRxiv2019

Structural fuzziness of the RNA-organizing protein SERF1a determines a toxic gain-of-interaction

Members of the MOAG/SERF protein family have been attributed a neuropathologic significance because of their ability to enhance the proteotoxic polymerization of amyloidogenic proteins such as alpha-Synuclein (aSyn). However, the cellular function remains unknown. Here, we identify SERF1a as an RNA-organizing protein i) with no structural homology to canonical RNA-binding proteins, ii) with an RNA-chaperoning activity which favours the incorporation of RNA into nucleoli and liquid-like artificial RNA-organelles, and iii) with a high degree of conformational disorder in the RNA-bound state. We demonstrate that this type of structural fuzziness determines an undifferentiated interaction of SERF1a with aSyn and RNA. Both molecules bind to one identical, positively charged site of SERF1a by an analogous electrostatic binding mode, with similar binding affinities, and without any observable disorder-to-order transition. The absence of primary or secondary structure discriminants results in SERF1a being unable to distinguish between nucleic acid and amyloidogenic protein, leading the pro-amyloid aSyn:SERF1a interaction to prevail under conditions of cellular stress. We suggest that structural fuzziness of SERF1a accounts for an adverse gain-of-interaction which favours toxic binding to aSyn at the expense of non-toxic RNA binding, therefore promoting a functionally distorted and pathogenic process. Our results provide a direct link between structural disorder, amyloid aggregation and the malfunctioning of RNA-associated cellular processes, three hallmarks of neurodegenerative diseases.

biochemistry↗

bioRxiv2019

MicroRNA levels in bone and blood change during bisphosphonate and teriparatide therapy in an animal model of postmenopausal osteoporosis

MicroRNAs control the activity of a variety of genes that are pivotal to bone metabolism. Therefore, the clinical utility of miRNAs as biomarkers and drug targets for bone diseases certainly merits further investigation. This study describes the use of an animal model of postmenopausal osteoporosis to generate a comprehensive dataset on miRNA regulation in bone tissue and peripheral blood during bone loss and specifically anti-resorptive and osteo-anabolic treatment.\n\nForty-two Sprague-Dawley rats were randomized to SHAM surgery (n=10) or ovariectomy (OVX, n=32). Eight weeks after surgery, OVX animals were further randomized to anti-resorptive treatment with zoledronate (n=11), osteo-anabolic treatment with teriparatide (n=11), or vehicle treatment (n=10). After 12 weeks of treatment, bone and serum samples were used for microRNA analysis using next-generation sequencing (NGS), mRNA levels using RT-qPCR, and bone microarchitecture analysis using nanoCT.\n\nOvariectomy resulted in loss of trabecular bone, which was fully rescued using osteo-anabolic treatment, and partially rescued using anti-resorptive treatment. NGS revealed that both, anti-resorptive and anabolic treatment had a significant impact on miRNA levels in bone tissue and serum: out of 426 detected miRNAs, 46 miRNAs were regulated by teriparatide treatment an d 10 by zoledronate treatment (p-adj. < 0.1). Interestingly, teriparatide and zoledronate treatment were able to revert miRNA changes in tissue and serum of untreated OVX animals, such as the up-regulation of miR-203a-3p, a known osteo-inhibitory miRNA. We confirmed previously established mechanisms of miR-203a by analyzing its direct target Dlx5 in femoral head.\n\nOur data reveal a significant effect of ovariectomy-induced bone loss, as well as the two major types of anti-osteoporotic treatment on miRNA transcription in femoral head tissue. These changes are associated with altered activity of target genes relevant to bone formation, such as Dlx5. The observed effects of bone loss and treatment response on miRNA levels in bone are also reflected in the peripheral blood, suggesting the possibility of minimally-invasive monitoring of bone-derived miRNAs using liquid biopsies.\n\nHighlightsO_LImicroRNA expression in bone tissue is altered by osteo-anabolic and anti-resorptive therapy in OVX rats.\nC_LIO_LImicroRNA changes in untreated OVX rats are reverted by anti-osteoporotic therapy.\nC_LIO_LImiR-203a is up-regulated during bone loss and down-regulated following therapy.\nC_LIO_LIBone tissue and serum levels of miR-203a are highly correlated.\nC_LI

molecular biology↗