Biology subjects

Loew, D.

Publications and source records attributed to Loew, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Cell-specific isolation and functional analysis of primary cardiomyocyte-derived large extracellular vesicles from infarcted mouse hearts

Extracellular vesicles (EVs) are membrane-bound particles secreted by all cells and serve as critical mediators of intercellular communication in both physiological and pathological contexts. However, elucidating the precise functions of endogenous EVs remains challenged by a fundamental technical bottleneck: current isolation methodologies depend on shared physical properties or generic surface markers, preventing the selective enrichment of cell-type-specific EVs within complex tissues. Consequently, EVs recovered from biofluids or tissue extracts represent heterogeneous populations, confounding the direct attribution of biochemical signatures and biological activities to distinct cellular origins. Here, we describe a versatile genetic-labeling and affinity-based purification strategy that enables the selective isolation of cell-specific primary EV. Using cardiomyocyte-derived EV (CM-EVs) as a proof-of-concept, we crossed Myh6-Cre mice with the ROSA26-mTmG reporter line to restrict membrane-targeted GFP expression to cardiomyocytes. Following myocardial infarction, cardiac EV were recovered and GFP-positive CM-EVs were selectively purified by anti-GFP nanobody-based magnetic pulldown. This approach yields highly enriched, functional cardiomyocyte-derived extracellular vesicles (CM-EVs). To accommodate diverse analytical needs, we established two distinct elution workflows: (i) a denaturing protocol optimized for downstream proteomics and immunoblotting, and (ii) a gentle, non-denaturing protocol that preserves vesicle integrity and biological activity for downstream in vitro and in vivo functional assays. Using this method, we characterized CM-EVs size distribution and proteomic signature, and demonstrated their capacity to transfer functional cargo to target cells in vitro. Because the purification approach relies solely on targeting a genetically restricted membrane tag rather than assumed surface markers, it is immediately adaptable to virtually any cell type for which a validated Cre driver exists. This method removes a long-standing bottleneck in EV research and provides a broadly applicable platform for deciphering the biochemical composition and in-vivo functions of cell-type-specific primary EV in physiological and pathological settings.

cell biology↗

bioRxiv2026

Functional analysis of novel microneme proteins from Plasmodium vivax blood stages identifies vaccine candidates

Host cell invasion by malaria parasites requires specific molecular interactions with host receptors. Plasmodium vivax merozoite invasion of reticulocytes is mediated by P. vivax Duffy binding protein (PvDBP) and its homolog, P. vivax erythrocyte binding protein (PvEBP). Here, we identify and characterize two novel P. vivax merozoite proteins, PvMP45 and PvMP36, which co- localize with PvDBP and PvEBP in the micronemes and bind reticulocyte receptors. PvMP45 and PvMP36 share high sequence identity with their P. knowlesi homologs, PkMP45 and PkMP36, which form a complex with other invasion related proteins. Field studies reveal that naturally acquired antibodies against PvMP36, PvEBP and PvDBP are associated with protection against clinical P. vivax malaria. We demonstrate that naturally acquired antibodies to PvEBP bind Fcy receptors and likely mediate protection by enabling opsonic phagocytosis. In addition, we show that combining antibodies against PvDBP and PvMP36 results in an additive invasion inhibitory effect against P. vivax blood stages. These results suggest that combining PvDBP, PvEBP and PvMP36 in a multivalent blood stage vaccine could elicit diverse immune mechanisms against P. vivax to achieve high efficacy. ImportanceAll the clinical symptoms of malaria are attributed to the blood stage of malaria parasites during which merozoites invade and multiply within red blood cells. A clear understanding of the host- parasite interactions that enable invasion can open paths for development of novel methods to block parasite growth and prevent malaria. Here, we identify and characterize two novel invasion related proteins from P. vivax merozoites that form an invasion complex and bind host RBC receptors. We demonstrate that antibodies targeting these proteins can block RBC invasion by P. vivax and naturally acquired antibodies that develop following P. vivax infection against one of these proteins are associated with protection against P. vivax malaria. These studies not only expand our understanding of the molecular mechanisms that enable host cell invasion by P. vivax but open new avenues for development of vaccines to protect against P. vivax malaria.

microbiology↗

bioRxiv2026

Nuclear acetyl-CoA production by acetyl-CoA synthetase enables dynamic histone acetylation and gene expression in Plasmodium falciparum

A complex transcriptional cascade drives the two-day intraerythrocytic developmental cycle of the most virulent human malaria parasite, Plasmodium falciparum, in the human host. Genes are rapidly activated at specific times, then silenced as quickly. Transcriptional activity correlates with histone acetylation, which is modulated by acetyltransferases that use acetyl-CoA and deacetylases that produce acetate. Acetyl-CoA synthetase (ACAS) uses acetate to produce acetyl-CoA and has been implicated in histone acetylation, providing an interesting link between parasite metabolism and transcription. Here, we show that ACAS becomes enriched in the nucleus at a time during the life cycle when the parasite undergoes rapid growth and increased levels of transcription. We use mass spectrometry to show that ACAS inhibition results in a rapid and global depletion of histone acetylation, which leads to a general decrease in chromatin accessibility at gene promoters. These widespread alterations in chromatin composition disrupted the transcriptional cascade, resulting in cell cycle arrest. Our study provides evidence that ACAS plays an important nuclear role in the histone acetylation cycle and insight into the dynamic nature and essentiality of histone acetylation in the parasites complex transcriptional program driving infection of the human host.

molecular biology↗

bioRxiv2026

Dynamic phosphoproteomics and proteomics uncover Leishmania donovani-driven ferritin hijacking, contributing to the control of iron homeostasis and iron-related oxidative stress

Leishmania donovani, the causative agent of visceral leishmaniasis, survives within the parasitophorous vacuole (PV) of mammalian macrophages by extensively rewiring host cellular pathways. Although transcriptional and proteomic changes in infected macrophages have been characterized, the impact on the host phosphoproteome, a pivotal, reversible regulator of signalling, remains largely unexplored. To address this gap, we combined time-resolved quantitative phosphoproteomics and proteomics to map the dynamic response of murine macrophages to L. donovani infection. Early after infection, the parasite rapidly attenuates the macrophage signaling cascades normally triggered by phagocytosis. Between 24 h and 48 h post-infection we observed a progressive de-phosphorylation of proteins involved in innate immunity, apoptosis and other stress-responsive pathways, consistent with a partial shutdown of multiple host kinases. From 24 h onward, a global decline in protein abundance was also detected, most notably within lysosomal network. Strikingly, only five host proteins were consistently up-regulated, suggesting their importance for parasite survival. Ferritin light chain (Ftl1) displayed the largest increase. Immunofluorescence and transmission-electron microscopy revealed that Ftl1 accumulates within the parasitophorous vacuole, colocalizes with the ferritin receptor Ncoa4, and yet fails to undergo degradation, indicating that Leishmania co-opts ferritin as its own intracellular iron-storage compartment. Ferritin is not confined to the PV; it is also internalized by the parasite. Within L. donovani, ferritin accumulates not only in the cytoplasm but also in the nucleus, where it may function both as an iron-storage depot and as an iron buffer that protects the parasite from oxidative damage. Finally, we demonstrate that Leishmania donovani pre-conditions its host macrophage for the iron-rich environments of the liver and spleen by driving the assembly of ferritin particles enriched in ferritin-light chain. This contrasts with L. amazonensis, which, residing in the iron-poor skin, induces ferritin predominated by ferritin-heavy chain (Fth1). Knock-down of Ftl1 did not decrease parasite survival because macrophages compensated for its loss by up-regulating Hspb1, which encodes a protein that limits lipid peroxidation by inhibiting the Fenton reaction. Although this response protects the host cell, it also diminishes iron import, imposing a metabolic cost on Leishmania. Hspb1 represents only one example; additional, as yet unidentified, compensatory pathways are likely activated by the parasite to mitigate the loss of ferritin-light chain. Collectively, our data uncover a previously unknown strategy whereby L. donovani hijacks host ferritin trafficking to create a protected iron reservoir, thereby preventing ferroptosis. This mechanism sets Leishmania, a eukaryotic intracellular parasite, apart from the canonical iron-acquisition tactics employed by bacteria and fungi.

microbiology↗

bioRxiv2025

CD133 shapes extracellular vesicle cargo and angiogenic function in basal-like triple-negative breast cancer

Extracellular vesicles (EVs) are central mediators of tumor-stroma communication, yet the mechanisms governing their biogenesis and functional cargo remain poorly understood. Here, we identify CD133 (Prominin-1), selectively expressed in basal-like triple-negative breast cancer (BL-TNBC) cells, as a key regulator of EV production and cargo composition. CD133 localizes to plasma membrane protrusions and lipid rafts, maintaining membrane architecture, promoting EV release, and shaping selective protein loading, including the pro-angiogenic factor CD105. Functionally, CD133 EVs potently induce endothelial tubulogenesis in a CD105-dependent manner, independently of EV uptake or endothelial proliferation. In vivo, these EVs preferentially accumulate in the lung and liver, highlighting organ-specific communication. Mechanistically, CD133 maintains lipid raft integrity, facilitating CD105 selective incorporation into vesicles, thereby establishing a spatially coordinated CD133-CD105 axis. Together, our findings define a subtype-specific EV population whose identity and angiogenic activity are dictated by membrane organization. By linking protrusion architecture to vesicle-mediated signaling, this study highlights CD133-enriched EVs as potential biomarkers and therapeutic targets in aggressive BL-TNBC.

cell biology↗

bioRxiv2025

Characterization of the dual functions of Leishmania CK1.2 in both the parasite and the macrophage using integrated proteomics and spatial mapping

Leishmania CK1.2 (L-CK1.2) is a serine/threonine protein kinase essential for the survival of the protozoan parasite Leishmania, the causative agent of Leishmaniasis. This study investigates the dynamic localization pattern of L-CK1.2 and the broad spectrum of its interacting partners within the parasite. Using proteomic analysis and confocal microscopy, we identified 230 L-CK1.2-associated proteins across the parasite life stages, promastigotes (in the insect vector), and amastigotes, (in the phagolysosomes of host macrophages). This analysis revealed the ubiquitous presence of L-CK1.2 in various cellular structures, including the cytoskeleton, basal body, and flagellum. Using an in vitro system, sixty-four host L-CK1.2-associated proteins, involved in critical host biological processes such as immune response, apoptosis, and purine biosynthesis, were shown to interact with L-CK1.2. These processes are known to be regulated by Leishmania during infection. The study highlights the dual function of L-CK1.2, in the parasite (cis) and within the host cell (trans), positioning this kinase as a key player in host-pathogen interactions. This work provides a comprehensive map of L-CK1.2 interactions and suggest its potential importance in regulating intracellular Leishmania survival, providing potential therapeutic targets for Leishmaniasis. Furthermore, given the evolutionary conservation of CK1.2 across other parasitic organisms, our findings may have broader implications for understanding and managing parasitic infections.

microbiology↗

bioRxiv2025

Rewiring of chromatin regulation underlies the evolution of brown algal multicellularity

Chromatin structure plays a central role in regulating transcription, genome stability, and epigenetic inheritance in eukaryotes. Much of our understanding of chromatin architecture and histone post-translational modifications (hPTMs) comes from a narrow set of animal and plant models, but emerging data from non-model lineages are challenging canonical views of how chromatin functions across the tree of life. Brown algae are complex multicellular eukaryotes that provide a unique perspective on chromatin evolution given their independent origin of complex multicellularity. Here, we compile the chromatin toolkit of brown algae and show that canonical silencing systems involving DNA cytosine methylation and PRC2-mediated H3K27 methylation were lost early in their evolution. By generating hPTM profiles from diverse brown algal clades, we resolve the nature and regulatory roles of chromatin states in this lineage and show how H3K79 methylation emerged and diversified as a repressive system. We further uncover sex-specific reconfigurations in species with varying degrees of sexual dimorphism and reconstruct the ancestral regulatory landscape that likely preceded the emergence of brown algae. Together, our findings illuminate the dynamic evolution of chromatin regulation in a distinct multicellular lineage and challenge assumptions about the universality of chromatin-based mechanisms across eukaryotes.

evolutionary biology↗

bioRxiv2025

Interactions of the LINE-1 encoded ORF1p with proteins and chromatin converge on a role in neuronal physiology

Retrotransposons are emerging as novel regulators of embryonic and brain development. We recently demonstrated that the LINE-1-encoded protein ORF1p is abundantly expressed in adult mouse and human neurons, although its function remains unclear. Here, we characterize the ORF1p interactome in differentiated mouse and human neurons using mass spectrometry and identify novel partners implicated in gene regulation and neuron-specific processes. ORF1p localizes not only to neuronal nuclei, where it associates with chromatin under steady-state conditions, but also to neurites, supporting a role in neuronal physiology. To further explore its nuclear functions, we sorted human post-mortem neurons with high or low nuclear ORF1p levels and performed ORF1p knockdown in cultured human neurons, followed by chromatin accessibility assays. Both approaches revealed consistent patterns of differential chromatin accessibility dependent on ORF1p. Loss of ORF1p also led to the downregulation of long, neuron-specific genes and altered neurite morphology. Together, these findings point to a physiological role of ORF1p in post-mitotic neurons, mediated through converging interactions with proteins and chromatin.

neuroscience↗

bioRxiv2025

Selective mRNA translation determines adaptative mutability of melanoma cells to anti-BRAF/MEK combination therapy

During their inevitable evolution towards acquired resistance to anti-cancer targeted therapies, cancer cells adopt distinct gene expression profiles that allow them to transiently adapt to and tolerate the treatment. Similar to bacterial cells that transiently tolerate antibiotics, cancer cells surviving therapy can increase their mutation rate, enhancing the likelihood of acquiring resistance-conferring mutations and evolving into resistant cells. This adaptive mutability has been linked to transcriptional reprogramming of DNA damage repair mechanisms and effective therapeutic strategies to target such mechanisms are currently lacking. Here we show that translational control mediates the adaptive mutability of melanoma drug-tolerant cells by regulating the translation of the error-prone non-homologous end joining (NHEJ) component 53BP1. The specific inhibition of 5UTR-driven 53BP1 mRNA translation was sufficient to impair NHEJ and mutability. We found that the eIF4A RNA helicase, a key component of the eIF4F translation complex, regulates 53BP1 mRNA translation. Consequently, targeting the eIF4A with two small molecule inhibitors significantly delays the acquisition of resistance to combination of BRAF and MEK inhibitors (BRAFi/MEKi) in BRAFV600-mutant melanoma xenograft models and cell lines by reducing the mutability of drug-tolerant cells. Our results demonstrate that a standard-of-care therapy for melanoma, by engaging non-genetic adaptation driven at the translational level, contributes to the evolution of drug-tolerant melanoma cells toward acquired resistance.

cancer biology↗

bioRxiv2025

Architecture and Function of Holocentric CENP-A-Independent Kinetochores

Kinetochores are essential macromolecular complexes that anchor chromosomes to the mitotic spindle to ensure faithful cell division1. Despite their critical role, the structural organization of kinetochores assembled on centromeres with vastly distinct architectures across diverse species remains poorly understood2,3. To address this question, we determined the cryo-EM structures of the inner kinetochore (CCAN) from the silkmoth Bombyx mori, an insect that lacks the canonical centromere-specifying histone variant CENP-A and exhibits chromosome-wide centromeric activity (holocentric). Our analysis reveals that B. mori CCAN assembles via atypical histone-fold protein dimerization into a self-contained, head-to-head dimer that topologically entraps and loops DNA, creating a point-centromere-like architecture. This structure also incorporates four previously uncharacterized Centromeric Subunit proteins that are evolutionarily repurposed from the outer kinetochore Dam1/DASH complex. Our work establishes this self-contained CCAN dimer as a key structural unit that forms the basis of a holocentric organization and suggests that large-scale centromere architectures can emerge from the modular arrangement of such discrete kinetochore units.

cell biology↗

bioRxiv2025

CARM1-mediated methylation controls interactions of ALIX with key partners important for cytokinesis

CARM1 is an arginine methyltransferase with a well-established role in regulating gene expression, but its cytoplasmic functions remain largely uncharacterized. Here, we identified ALIX, a protein acting with the ESCRT-III machinery in numerous membrane remodeling events, as a main cytoplasmic partner and a relevant substrate of CARM1. We demonstrate that CARM1 methylates arginine residues within the proline-rich motif of ALIX. At the molecular level, ALIX methylation impairs SH3-dependent association with CD2AP, CIN85, and endophilin-A2 that are required for cytokinesis. Using a mutant of ALIX that is unable to bind these proteins, we further show that these interactions are essential for ALIX functions during cytokinesis. Altogether, this work highlights the significance of arginine methylation as a regulatory post-translational modification important for the final step of cell division, by modulating interactions between proline-rich domains and their SH3-containing partners.

cell biology↗

bioRxiv2025

A Catalytically Inactive Protein Kinase C alpha Mutation Drives Chordoid Glioma by Pathway Rewiring

Abstract SummaryChordoid glioma (ChG) is a rare, low-grade brain tumor characterized by a novel recurrent point mutation, D463H, in the kinase domain of protein kinase C alpha (PKC). The mutation is invariably an Asp to His substitution, suggesting it endows a unique function beyond catalytic inactivation associated with other cancer-associated PKC mutations. Here we use in vitro and in cellulo activity assays to show that PKCD463H is catalytically inactive, functions as a dominant-negative mutant to suppress endogenous PKC and uniquely rewires the cellular interactome. Specifically, phosphoproteomic, proximity labeling, and co-immunoprecipitation mass-spectrometry data from cells overexpressing PKCD463H identify altered phosphorylation of substrates and binding to multiple proteins involved in cell-cell junctions compared to WT enzyme. Lastly, single nuclei RNAseq reveals that ChG derives from specialized tanycytes. Our data suggest that this disease-defining, fully penetrant mutation promotes neomorphic non-catalytic scaffolding to impair cell junction function.

molecular biology↗

bioRxiv2025

A metabolism-chromatin axis promotes ribosome heterogeneity in the human malaria parasite

The transmission of the most virulent human malaria parasite, Plasmodium falciparum, relies on its survival in the contrasting environments of the human host and mosquito vector. One of the most fascinating adaptations to this lifestyle is the specific silencing of individual rDNA genes in the human host that are de-repressed following host-to-vector transmission. In this study, we defined the epigenetic signatures of rRNA transcription and found that rDNA silencing relies on aerobic glycolysis, the sole energy-generating pathway in the human host. We show that disruption of NAD+ regeneration during lactate fermentation promotes rDNA de-repression and identify the sirtuin histone deacetylase Sir2a as the mediator between fluctuating NAD+ levels and a functional transcriptional outcome. Hence, rDNA activation appears to be coupled to the metabolic state of the parasite as it transitions from aerobic glycolysis to mitochondrial respiration during host-to-vector transmission.

microbiology↗

bioRxiv2025

Identification of a shared persistence program in triple-negative breast cancer across treatments and patients

Acquisition of resistance to anti-cancer therapies is a multistep process, which initiates with the survival of drug persister cells. Understanding the mechanisms driving the emergence of persister cells remains challenging, primarily because of their limited accessibility in patients. Here, using mouse models to isolate persister cells from patient tumors, we determine the identity features of persister cells from eight patients with triple-negative breast cancer (TNBC). Combining over 80 transcriptome studies, we reveal hallmarks of the persister state across patient models and treatment modalities: high expression of basal keratins together with activation of a stress response and inflammation pathways. Patient-derived persister cells are transcriptionally plastic and return to a common treatment-naive like state upon relapse, regardless of the treatment they have been exposed to. Leveraging gene regulatory networks, we identify AP-1, NFKB and IRF/STAT as the key drivers of this hallmark persister state. As a proof of concept, we show that FOSL1 - an AP-1 member - is sufficient to drive cells to the persister state by binding enhancers and reprogramming the transcriptome of cancer cells. On the contrary, cancer cells without FOSL1 have a decreased ability to reach the persister state. By defining hallmarks of drug persistence to multiple therapies of the standard of care, our study provides a resource to design novel combination therapeutic strategies to limit resistance.

cancer biology↗

bioRxiv2025

Glutamate methylation, a novel histone mark in diatoms: Mass spectrometry identification and structural characterization

Post-translational modifications of histones (PTMs) play a crucial role in regulating chromatin function. These modifications are integral to numerous biological processes, including transcription, DNA repair, replication, and chromatin remodeling. While several PTMs have been identified, enhancing our understanding of their roles in these processes, there is still much to discover given the potential for virtually any histone residue to be modified. In this study, we report the discovery of a novel PTM in the model diatom Phaeodactylum tricornutum, glutamate methylation identified by mass spectrometry at multiple positions on histone H4 and at position 96 on histone H2B. This modification was also detected in other model organisms, including Drosophila melanogaster, Caenorhabditis elegans, and humans, but not in Arabidopsis. Structural bioinformatics analyses, including molecular dynamics simulations, revealed that methylation of glutamate residues on histones induces displacement of these residues, exposing them to solvent and disrupting interactions with neighboring residues in associated histones. This disruption may interfere with histone complexes promoting histone eviction or facilitating interactions with regulatory proteins or complexes, which may compromise the overall nucleosome stability.

biochemistry↗

bioRxiv2025

Harnessing hydrodynamics for high-yield production of extracellular vesicles from stem cells spheroids with specific cargo profiling

This study presents a novel method and device for the hydrodynamic production of extracellular vesicles (EVs) derived from biomimetic multicellular 3D spheroids, enabling high-throughput particle release that is 10 to 20 times higher than in non-stimulated conditions. The device facilitates the formation of spheroids from human mesenchymal stem cells (hMSCs), offering an all-in-one approach for both spheroid generation and EV release. Production times are reduced to just a few hours, with yield further increased by alternating periods of high hydrodynamic flow and spheroid recovery in a sequential production approach. Using this system, we explored the impact of hydrodynamic and starvation conditions on the protein cargo of EVs, identifying distinct protein markers through proteomics. Specifically, hydrodynamic stimulation enriched EVs in plasma membrane-derived and mitochondrial proteins, revealing divergent biogenesis pathways. Importantly, the produced EVs exhibited therapeutic properties, with demonstrated effects in wound healing, angiogenesis, and anti-inflammatory responses, some showing enhanced efficacy under hydrodynamic stimulation.

bioengineering↗

bioRxiv2024

A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities

Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratories poses challenges for data comparability and reproducibility. In response, we conducted a harmonization study within proteomics laboratories of the Core for Life alliance with the aim to establish a common quality control framework, which facilitates comprehensive quality assessment and identification of potential sources of performance drift. Through collaborative efforts, we developed a consensus quality control standard for longitudinal assessment and we adopted a common processing software. We generated a 4-year longitudinal dataset from multiple instruments and laboratories, which enabled us to assess intra- and inter-laboratory variability, to identify causes of performance drift, and to establish community reference values for several quality control parameters. Our study enhances data comparability and reliability and fosters a culture of collaboration and continuous improvement within the proteomics community to ensure the integrity of proteomics data.

biochemistry↗

bioRxiv2023

Steady-state neuron-predominant LINE-1 encoded ORF1p protein and LINE-1 RNA increase with aging in the mouse and human brain

Recent studies have established a reciprocal causal link between aging and the activation of transposable elements, characterized in particular by a de-repression of LINE-1 retrotransposons. These LINE-1 elements represent 21% of the human genome, but only a minority of these sequences retain the coding potential essential for their mobility. LINE-1 encoded proteins can induce cell toxicity implicated in aging and neurodegenerative diseases. However, our knowledge of the expression and localization of LINE-1-encoded proteins in the central nervous system is limited. Using a novel approach combining atlas-based brain mapping with deep-learning algorithms on large-scale pyramidal brain images, we unveil a heterogeneous, neuron-predominant and widespread ORF1p expression throughout the murine brain at steady-state. In aged mice, ORF1p expression increases significantly which is corroborated in human post-mortem dopaminergic neurons by an increase in young LINE-1 elements including those with open reading frames. Mass spectrometry analysis of endogenous mouse ORF1p revealed novel, neuron-specific protein interactors. These findings contribute to a comprehensive description of the dynamics of LINE-1 and ORF1p expression in the brain at steady-state and in aging and provide insights on ORF1p protein interactions in the brain.

neuroscience↗