Biology subjects

Zimmermann, P.

Publications and source records attributed to Zimmermann, P..

14 recordsLinked to original sources

bioRxiv2026

ADAM10 tailors extracellular vesicles for content transfer rather than signaling by contact

Etxtracellular vesicles (EVs) support cell-to-cell communication, both in physiological and pathological contexts and emerge as new biomarkers and potential therapeutics. Yet, despite EVs holding huge promises, our understanding of core mechanisms governing EV signaling remains significantly underdeveloped. Our previous work indicated that syndecans and their cytosolic adaptor syntenin control the biogenesis of a major subset of small EVs (sEVs). Here we show that syndecans control the accumulation of ADAM10 into sEVs. ADAM10 promotes the formation of sEVs enriched in cleaved receptors (reducing sEV corona), supports the sorting of proteins with intracellular functions, and tailors sEVs for the delivery of their internal content, e.g. syntenin, into the cytosol of recipient cells. Conversely, inhibition of ADAM10 favors the production of sEVs bearing full-length, signaling-competent receptors/ligands and enhances contact-dependent signaling. These findings uncover a protease-regulated switch that tailors sEV composition and signaling modality, providing important new mechanistic insights into the core molecular pathways supporting EV-mediated communication.

cell biology↗

bioRxiv2026

Measuring capture, internalization and cytosolic delivery of extracellular vesicle-embedded syntenin

Extracellular vesicles (EVs) mediate cell-to-cell communication and are considered potential drug delivery vehicles. Nevertheless, whether EV-embedded cargo can be efficiently delivered into the cytosol of recipient cells remains debated. Here, we investigated the fate of syntenin, a well-established internal cargo of small EVs (sEVs). Using quantitative assays, we show that [~]85% of internalized sEV-embedded syntenin can be delivered to the cytosol of recipient cells within short periods of time. Yet, even at low dose, we find that the internalization of sEVs carrying syntenin is rather inefficient ([~]0.03% of the administered dose). Moreover, we observe that the capture of sEVs by recipient cells is non-saturable over time and largely more efficient than their internalization. Finally, we identify the N-terminal domain of syntenin and the phosphorylation state of a Src-targeted tyrosine residue in this domain, as key determinants for its incorporation into sEVs that support cytosolic delivery. These findings challenge, current views in the field by indicating that sEV internalization may be a marginal process (on the contrary to capture) and that cytosolic delivery can be highly efficient. Moreover, our study identifies molecular determinants governing cytosolic delivery of sEV-embedded syntenin.

cell biology↗

bioRxiv2026

A syndecan-based genetic approach to coat the surface of small extracellular vesicles with Nanobodies

Small extracellular vesicles (sEVs) are promising vehicles for targeted therapeutic delivery, but strategies for their surface functionalization remain limited. Here, we present a reliable and simple genetic approach that enables customized modification of sEV surfaces and supports enhanced sEV uptake by recipient cells. This strategy is based on the fusion of targeting moieties to the C-terminal fragment of syndecan-1 (SDC1-CTF), a peptide naturally enriched in sEVs. Combining various analytical approaches including single-vesicle analysis, we establish that this strategy enables decoration of up to 20% of secreted sEVs with nanobodies (Nbs). In quantitative bioluminescence assays, using concentrated conditioned media, we demonstrate that sEV-coating with anti-EGFR Nb supports enhanced sEV uptake by EGFR-expressing cells. This new strategy thus offers a robust and modular solution for endowing sEV surfaces with defined targeting properties to support further sEV-based therapeutic applications.

cell biology↗

bioRxiv2025

Syntenin orchestrates matrix degradation by controlling MT1-MMP secretion in small extracellular vesicles and invadopodia formation

Extracellular matrix (ECM) remodelling is essential for tumour progression. The metalloproteinase MT1-MMP promotes cell invasion by degrading ECM components. MT1-MMP accumulates at invadopodia, actin-rich structures mediating ECM degradation, and is also present on the surface of small extracellular vesicles (sEV), key players in cell-to-cell communication. The role of sEV-associated MT1-MMP in ECM degradation and the mechanisms supporting MT1-MMP loading into sEV are unknown. We previously established that the syntenin PDZ protein, in association with the syndecan (SDC), is essential for sEV from endosomal origin biogenesis. In the present study, we demonstrate that syntenin contributes to ECM degradation via invadopodia in MDA-MB-231 triple negative breast cancer (TNBC) cells, whereas SDC limit it. Moreover, we identify that syntenin colocalizes with MT1-MMP in late endosomes and directly interacts with MT1-MMP. Furthermore, we decipher that both syntenin and SDC are essential for the specific loading of MT1-MMP into sEV. Additionally, we show that sEV-mediated ECM degradation depends on MT1-MMP activity and syntenin. Our findings show how syntenin-SDC-MT1-MMP complexes orchestrate ECM degradation and pave the way for innovative rational approaches to control TNBC invasion.

cancer biology↗

bioRxiv2025

The gut microbiota and sleep in infants: a focus on diurnal rhythmicity patterns

Emerging evidence supports a bidirectional relationship between the gut microbiome and sleep, partly mediated by the microbiota-gut-brain axis. Circadian rhythms appear to influence early developmental processes and may play a role in shaping this relationship. While infancy is a critical window for both gut microbiota establishment and the maturation of sleep regulation, the role of gut bacteria in modulating infant sleep remains poorly understood. In this longitudinal study, we performed continuous within-subject sampling (monitoring across 48 hours) in 20 infants at 2, 4, and 6 months of age to examine associations between the establishment of gut microbiota and sleep patterns. We hypothesized that microbial diversity and sleep rhythmicity would be linked across both short (diurnal) and long (monthly) time scales. Gut microbiota profiles were characterized using 16S rRNA gene sequencing; gut melatonin concentrations were measured; and sleep metrics were quantified through wearable actimetry, parent-reported 24-hour sleep diaries, and the Brief Infant Sleep Questionnaire (BISQ). Parents additionally completed the Baby Care Questionnaire (BCQ), assessing parenting style, and the Ages and Stages Questionnaire (ASQ), evaluating infant behavioral development. In some infants, alpha diversity followed diurnal rhythmic patterns. Although bacterial rhythmicity was not significantly associated with sleep rhythmicity, as quantified with the Circadian Function Index, infants with higher alpha diversity had more robust sleep rhythmicity ({beta}Faith PD= 0.0721, SE = 0.0337). Infant age emerged as the strongest predictor of both gut microbiota diversity (observed features: {beta}age = 0.101, SE = 0.0172) and gut melatonin concentrations ({beta}age = 0.638, SE = 0.162). For the same age, gut microbiota temporal volatility - an indicator for bacterial community instability - was not associated with sleep patterns. This study demonstrates promising short- and long-term links between gut microbiota diversity and sleep-wake rhythm maturation in infancy. Further research is needed to elucidate the mechanistic role of the gut microbiome in sleep development.

microbiology↗

bioRxiv2024

From womb to crib: How fetal activity patterns in utero reveal postnatal sleep behavior

ImportanceThe human circadian system, a critical biological mechanism governing the sleep-wake cycle, begins to oscillate before birth. Distinct fetal behavioral states have been described using short-duration ultrasound recordings, but the alignment of fetal activity with day and night cycles (i.e., diurnal rhythms) remains poorly understood due to the lack of long-term monitoring. Accordingly, a substantial knowledge gap exists concerning the evolution of fetal diurnal rhythms into infant sleep-wake cycles. ObjectiveTo investigate the development of fetal diurnal rhythms and their evolution into postnatal infant sleep, as well as the role of maternal factors and melatonin in shaping early circadian entrainment. MethodsIn this cohort study, conducted in 2022 and 2023, we collected over 20 000 hours of wearable acceleration and temperature data from 32 fetuses and their mothers during continuous 5-day monitoring in the third trimester of pregnancy. The cohort was subsequently followed longitudinally from the prenatal period through 6 months postpartum, with infant sleep outcomes assessed at three key time points (first postnatal weeks, 3 months, and 6 months) using sleep diaries and questionnaires. The first postnatal assessment additionally included breast milk and infant stool sample collection. ResultsMulti-level modelling revealed early diurnal rhythms in fetuses that align with maternal activity and circadian rhythms. Random Forest analyses identified fetal day/night sleep duration ratio - a simplified proxy for fetal circadian entrainment - as the strongest predictor of postnatal infant sleep, with fetuses preferring nighttime sleep maintaining this preference postnatally. Maternal sleep regularity (i.e., consistent sleep patterns characterized by low day-to-day variability in sleep timing) during pregnancy also predicted infant sleep, associating with a stronger preference for nighttime sleep in infants. Conclusions and relevanceThese findings highlight the potential influence of intrauterine and maternal factors on the evolution of circadian entrainment. Our study contributes to a broader understanding of the earliest emergence of circadian rhythms, supporting future research on their long-term health impacts. Maternal sleep regularity stands out as the earliest modifiable target for interventions, offering an actionable pathway to promote infant circadian entrainment, with potential long-term benefits for family dynamics and well-being.

developmental biology↗

bioRxiv2024

Domestic freezer storage: a solution for preserving stool microbiota integrity for at-home collection

The gut microbiome is crucial for host health. Early childhood is a critical period for the development of a healthy gut microbiome, but it is particularly sensitive to external influences. Recent research has focused on using advanced techniques like shotgun metagenome sequencing to identify key microbial signatures and disruptions linked to disease. For accurate microbiome analysis, samples need to be collected and stored under specific conditions to preserve microbial integrity and composition, with -80{degrees}C storage considered the gold standard for stabilization. This study investigates the effect of domestic freezer storage on the microbial composition of stool samples from 20 children under 4 years with the use of shotgun metagenomic sequencing. Fresh stool samples were aliquoted into sterile tubes, with one aliquot stored at 4{degrees}C and analyzed within 24 hours, while others were frozen in domestic freezers (below -18{degrees}C) and analyzed after 1 week, 2 months, and 6 months. Assessments of contig assembly quality, microbial diversity, and antimicrobial resistance genes revealed no significant degradation or variation in microbial composition. ImportanceMost previous studies on sample storage have used amplicon sequencing, which limits relevance to metagenome sequencing, in which contig quality and functional gene detection are additional concerns. Moreover, the effects of domestic freezer storage for at-home stool collection on microbiome profiles, contig quality, and antimicrobial resistance gene profiles have not been tested previously. Our findings suggest that stool samples stored in domestic freezers for up to six months maintain the integrity of metagenomic data. These findings indicate that domestic freezer storage does not compromise the integrity or reproducibility of metagenomic data, offering a reliable and accessible alternative for temporary sample storage. This approach enhances the feasibility of large-scale at-home stool collection and citizen science projects, even those focused on the more easily perturbed early life microbiome. This advancement enables more inclusive research into the gut microbiome, enhancing our understanding of its role in human health.

microbiology↗

bioRxiv2024

Newborn reactions to maternal prenatal stress alter umbilical cord blood tRNA fragments targeting cholinergic transcripts

Maternal perceived prenatal stress (PPS) is a known risk factor for diverse developmental impairments in newborns, but the underlying molecular processes are incompletely understood. Here, we report that maternal PPS altered the birth profiles of blood transfer RNA fragments (tRFs), 16-50nt long non-random cleavage products of tRNAs, in a sex-dependent manner. Importantly, comparing stressed versus control maternal and umbilical cord blood serum presented alterations that were not limited to individual tRFs, but rather reflected selective changes in particular tRF families grouped by their mitochondrial or nuclear genome origin, parental tRNA coded amino acid, and cleavage type. tRF families that show stress- and sex-specific effects, revealed shared length and expression patterns which were strongest in the female newborns. Several of these tRFs carry complementary motifs to specific cholinergic mRNAs, suggesting possible translational regulation similar to microRNAs. Compatible with the cholinergic regulation of stress reactions, those "CholinotRFs" achieved an AUC of 95% when classifying female newborns according to maternal PPS. Moreover, we found altered catalytic activity of serum acetylcholinesterase, which was particularly elevated in male newborns, marking a second sex-specific effect. Our findings demonstrate an association of tRF families patterns with newborns sex-specific stress response to PPS and may lead to better diagnosis and therapeutic tools for these and other stressors.

molecular biology↗

bioRxiv2023

Downregulation of stromal syntenin sustains AML development

The crosstalk between cancer and stromal cells plays a critical role in tumor progression. Syntenin is a small scaffold protein involved in the regulation of intercellular communication that is emerging as a target for cancer therapy. Here, we show that certain aggressive forms of acute myeloid leukemia (AML) reduce the expression of syntenin in bone marrow stromal cells (BMSC), stromal syntenin deficiency, in turn, generating a pro-tumoral microenvironment. From serial transplantations in mice and co-culture experiments, we conclude that syntenin-deficient BMSC stimulate AML aggressiveness by promoting AML cell survival and protein synthesis. This pro-tumoral activity is supported by increased expression of endoglin, a classical marker of BMSC, which in trans stimulates AML translational activity. In short, our study reveals a vicious signaling loop potentially at the heart of AML-stroma crosstalk and unsuspected tumor-suppressive effects of syntenin that need to be considered during systemic targeting of syntenin in cancer therapy.

cancer biology↗

bioRxiv2021

Interactome and structural basis for targeting the human T-cell leukemia virus Tax oncoprotein

Human T-cell leukemia virus type-1 (HTLV-1) is the causative agent of adult T-cell leukemia (ATL). Although ATL is a well-characterized T-cell neoplasm, linked to intermittent expression of the viral Tax-1 protein, there is currently no strategy to target Tax-1 functions using small molecules. Here, we report a comprehensive interaction map between Tax-1 and human PDZ domain-containing proteins (hPDZome). We show that Tax-1 interacts with more than one-third of hPDZome components, including proteins involved in cell cycle, cell-cell junctions, cytoskeleton organization, and membrane complex assembly. Using nuclear magnetic resonance (NMR) spectroscopy, we have determined the structural basis of the interaction between the C-terminal PDZ binding motif (PBM) of Tax-1, and the PDZ domains of syntenin-1, an evolutionary conserved hub that controls exosome trafficking. Finally, we have used confocal imaging, molecular modelling, NMR and mammalian cell-based assays to demonstrate that the Tax-1/syntenin-1 interaction is amenable to small-molecule inhibition. Altogether, our study highlights the biological significance of Tax-PDZ interactome and its interplay with exosome formation. It shows a direct link between extracellular vesicles and HTLV-1 transmission, providing a novel framework for the design of targeted therapies for HTLV-1-induced diseases.

biochemistry↗

bioRxiv2021

A syntenin-deficient microenvironment educates AML for aggressiveness

In acute myeloid leukemia (AML), the stromal microenvironment plays a prominent role in promoting tumor cell survival and progression. Although widely explored, the crosstalk between leukemic and stromal cells remains poorly understood. Syntenin, a multi-domain PDZ protein, controls both the trafficking and signaling of key molecules involved in intercellular communication. Therefore, we aimed to clarify the role of environmental syntenin in the progression of AML. By in vivo approaches in syngeneic mice, we demonstrate that a syntenin-deficient environment reprograms AML blasts to survive independently of the stroma. Up-regulation of EEF1A2 in the blasts controls this gain of cell survival. Furthermore, using ex vivo co-culture systems, we show that syntenin-deficient bone marrow stromal cells (BMSC) enhance the survival of different types of AML cells, including patient samples, and suffice to educate syngeneic AML, recapitulating micro-environmental effects observed in vivo. We establish that syntenin-deficiency causes an increase of eIF5A and autophagy-related factors in BMSC, and provide evidence that the inhibition of autophagy prevents syntenin-deficient BMSC to stimulate AML survival. Altogether, these findings indicate that host-syntenin in the BM microenvironment acts as a repressor of AML aggressiveness. Key points- A syntenin-deficient host reprograms AML blasts, enhancing total protein synthesis and cell survival pathways - Autophagy in the syntenin-deficient microenvironment is responsible for the gain of AML cell survival

cancer biology↗

bioRxiv2020

PLD2-phosphatidic acid recruit ESCRT-I to late endosomes for exosome biogenesis.

It is important to understand the biogenesis of exosomes, extracellular vesicles of endosomal origin controlling cell-to-cell communication. We previously reported that Phospholipase D2 (PLD2) supports late endosome (LE) budding and the biogenesis of syntenin-dependent exosomes. Here, we reveal that PLD2 has a broader generic effect on exosome production. Combining gain- and loss-of-function experiments, proteomics, microscopy and lipid-binding studies with reconstituted liposomes mimicking LE, we show that: (i) PLD2 activity controls the recruitment of MVB12B to LE and the exosomal secretion of ESCRT-I; (ii) loss-of-MVB12B phenocopies loss-of-PLD2, similarly affecting LE budding, the number of exosomes released and exosome loading with cargo; (iii) MVB12B MABP domain directly interacts with phosphatidic acid, the product of PLD2. We therefore propose that PLD2 and phosphatidic acid support ESCRT-I recruitment to LE for the formation of exosomes. This work highlights a major unsuspected piece of the molecular framework supporting LE and exosome biogenesis.

cell biology↗

bioRxiv2020

The human PDZome 2.0: characterization of a new resource to test for PDZ interactions by Yeast Two-Hybrid

PSD95-disc large-zonula occludens (PDZ) domains are globular modules of 80-90 amino acids that co-evolved with multicellularity. They commonly bind to carboxy-terminal sequences of a plethora of membrane-associated proteins and influence their trafficking and signaling. We previously built a PDZ resource (PDZome) allowing to unveil human PDZ interactions by Yeast two-hybrid. Yet, this resource is partial according to the current knowledge on the human PDZ proteome. Here we built the PDZome 2.0 library for Yeast two-hybrid, based in a PDZ library manually curated from online resources. The PDZome2.0 contains 305 individual clones (266 PDZ domains in isolation and 39 tandems), for which all boundaries have been designed based on available PDZ structures. Using as bait the E6 oncoprotein from HPV16, a known promiscuous PDZ interactor, we show that PDZome 2.0 outperforms the previous resource.

molecular biology↗

bioRxiv2020

The Flemmingsome reveals an ESCRT-to-membrane coupling required for completion of cytokinesis

Cytokinesis requires the constriction of ESCRT-III filaments on the side of the midbody, where abscission occurs. After ESCRT recruitment at the midbody, it is not known how the ESCRT-III machinery localizes to the abscission site. To reveal novel actors involved in abscission, we obtained the proteome of intact, post-abscission midbodies (Flemmingsome) and identified 489 proteins enriched in this organelle. Among those proteins, we further characterized a plasma membrane-to-ESCRT module composed of the transmembrane proteoglycan syndecan-4, ALIX and syntenin, a protein that bridges ESCRT-III/ALIX to syndecans. The three proteins were highly recruited first at the midbody then at the abscission site, and their depletion delayed abscission. Mechanistically, direct interactions between ALIX, syntenin and syndecan-4 were essential for proper enrichment of the ESCRT-III machinery at the abscission site, but not at the midbody. We propose that the ESCRT-III machinery must be physically coupled to a membrane protein at the cytokinetic abscission site for efficient scission, revealing novel common requirements in cytokinesis, exosome formation and HIV budding.

cell biology↗