Biology subjects

Falcon-Perez, J. M.

Publications and source records attributed to Falcon-Perez, J. M..

7 recordsLinked to original sources

bioRxiv2026

A single Omicron mutation reshapes ORF3a-driven host-cell remodelling

SARS-CoV-2 ORF3a remodels host membranes, but the structural basis and metabolic consequences of this process remain unclear. Here, we combine complementary imaging approaches to define ORF3a function at nanometric scale, identifying underlying mechanisms, and determining how Omicron variant rewire this activity. ORF3a from the ancestral Wuhan strain disrupts Golgi cisternae, drives the formation of ORF3a dense vesicles, remodels mitochondrial architecture, and promotes lipid droplet expansion. Multi-omics analyses further reveal selective triacylglycerol accumulation linked to DGAT1 upregulation, which we validate pharmacologically through DGAT1 inhibition. In contrast, Omicron ORF3a variant, despite carrying only the Thr223Ile substitution within the {beta}7-{beta}8 loop at the bottom of the cytosolic domain, induced a dramatic phenotypic shift: ORF3a localizes to multivesicular bodies, preserves Golgi architecture, and fails to induce lipid accumulation. All together, these results identify ORF3a as a regulator of membrane organization and lipid homeostasis, showing how minimal sequence variation rewires host-cell remodelling. Graphical TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/742305v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@135032borg.highwire.dtl.DTLVardef@1633d4borg.highwire.dtl.DTLVardef@4d4115org.highwire.dtl.DTLVardef@1ebdf65_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

A Meta-Analysis of 515 Human Proteomes Defines the Core Composition and Contaminants of Plasma Extracellular Vesicles isolates

Plasma extracellular vesicles (EVs) are promising liquid biopsy biomarkers, yet their proteomic profiling remains confounded by co-isolated lipoproteins and soluble complexes. Here, we resolve this heterogeneity through a meta-analysis of 515 human plasma EV proteomes. We demonstrate that the reproducible core proteome is dominated by soluble host-response modules rather than unique vesicular markers. Deconvolution analysis resolved the isolate into distinct biological sources, distinguishing the hepatic secretome and immune complexes from vesicular signals. Crucially, canonical tetraspanins (CD9, ADAM10) clustered with platelet and erythrocyte proteins, indicating that the bulk tetraspanin signal derives from hematopoietic ectosome shedding. In contrast, ESCRT machinery (TSG101, ALIX) formed a distinct, lower-abundance cluster, physically separating endosomal biogenesis from membrane shedding. We provide a modular atlas that mathematically distinguishes the functional matrix of coisolates from vesicular cargo, establishing a new framework for interpreting biological origin in plasma EV proteomics.

systems biology↗

bioRxiv2025

From Lab to Industry: Awareness of the translational potential of Extracellular Vesicles by the ISEV Translation, Regulation and Advocacy Committee (ISEV-TRA).

Extracellular vesicles (EVs) are critical mediators of cellular communication, with significant potential for disease diagnosis, therapeutics, and other industrial applications. However, translating EV-based innovations into real-world products faces substantial challenges, particularly concerning regulatory frameworks and scientific gaps. To address these issues, the International Society for Extracellular Vesicles (ISEV) established the Translation, Regulation, and Advocacy Committee (ISEV-TRA) to create an environment that facilitates the translation of EV research into practical societal applications. This reporet presents the results of the first survey conducted by the ISEV-TRA, assessing the degree to which EVs have been translated into society applications, awareness of EV potential, and the current use of EVs across various industry sectors. Respondents included individuals from Academia, Industry, and dual affiliation (Academia-Industry), provided an initial perspective on EV research and its translational status. The survey highlights the growing interest in EV-based products, suggesting that there is an important wave of efforts to develop these products. Several spin-outs created by academic researchers are focusing on EV-based products, a key trend in the field, while large companies are showing increasing interest in EV-based technologies. The expectations and suggestions for the newly established ISEV-TRA underscore the need for a unified approach to accelerate the translation of EV-based technologies into practical applications. The ISEV-TRA is well-positioned to play a key role by providing essential resources, organizing workshops, and promoting interdisciplinary collaboration, ultimately driving the commercialization of EV-based innovations.

scientific communication and education↗

bioRxiv2025

Metabolic and transcriptional adaptations to phagocytosis in microglia sustain their functionality and regenerative properties

Phagocytosis of apoptotic cells, or efferocytosis, is a tightly regulated process that ensures tissue homeostasis and prevents mounting inflammatory responses. In the brain parenchyma, it is executed by microglia, which are encumbered by large numbers of apoptotic debris generated during development, in adult neurogenic niches, aging, and brain diseases. Emerging evidence suggest that phagocytosis is not limited to garbage disposal, but triggers adaptations in the phagocytes that may have a functional impact. To test it we developed an in vivo model of superphagocytosis induced by low cranial irradiation (LCI, 2Gy) that specifically induced apoptosis in the neurogenic niche of the adult hippocampus, synchronizing microglia in a phagocytic state within 6h and leading to full clearance by 24h. Single cell RNA sequencing and metabolomics revealed an unexpected oxidative stress in post-phagocytic microglia, accompanied by catabolic shutdown, mitochondrial remodeling, increased expression of galectin 3, and production of polyamines that led to cell death and compensatory proliferation. To test whether these changes impaired subsequent microglial phagocytosis, we used a glioblastoma model treated with sequential irradiation to induce tumor cell apoptosis. The phagocytosis efficiency of tumor-associated microglia/macrophages was comparable in the first and second apoptotic challenge, suggesting that the metabolic remodeling induced by phagocytosis was adaptive and destined to sustain their functionality. Finally, we assessed the functional impact of post-phagocytosis adaptations using galectin 3 deficient mice under LCI. We found that the recovery of the neurogenic niche after LCI strongly depended on galectin 3, demonstrating the regenerative capacity of post-phagocytic microglia. Overall, our data unveils the complexity of post-phagocytosis adaptations in microglia, underscoring their unexplored therapeutic potential in brain disorders.

neuroscience↗

bioRxiv2025

Vesicular Rps6 released by astrocytes regulate local translation and enhance synaptic markers in neurons

In neurons, like in any other cell, their function often relies on the fine tuning of their protein levels, which is achieved by the balance between protein synthesis and turnover. Defects in protein homeostasis frequently leads to neuronal dysfunction and neurological disorders. Given their extreme morphological complexity and high compartmentalization, neurons highly depend on the asymmetrical distribution of their proteome. The common belief is that proteins that sustain axonal, dendritic and synaptic functions are synthesized in the soma and then transported to distal neuronal compartments. However, there is a complementary mechanism by which the mRNAs, and not the proteins, are transported to distal subneuronal domains, and once they reach their destination they are locally translated. Although once considered heretical, local translation (or local protein synthesis) is now widely accepted by the scientific community. Nonetheless there is one question that remains largely unexplored in the field and that is whether local translation in dendrites, axons and synapses is fully regulated by the neuron itself or if non-neuronal cells (e.g. glia) can modulate this mechanism in a non-cell-autonomous manner. Here we show that astroglia regulates local protein synthesis and enhances synaptic markers by releasing extracellular vesicles (EVs) containing ribosomal protein Rps6. To our knowledge this is the first report that directly demonstrates glial control of local translation in neurons through EV-mediated glia-to-neuron communication.

neuroscience↗

bioRxiv2024

Secreted spermidine synthase reveals a paracrine role for PGC1a-induced growth suppression in prostate cancer

Prostate cancer is the fifth cause of death by cancer worldwide, second in incidence in the male population. The definition of the molecular basis of its development and the oncogenic signals driving lethality continue to be important objectives in prostate cancer research. Prior work from others and us has demonstrated that loss of PGC1 expression results in a metabolic, signaling and transcriptional reprogramming that supports the development of metastatic disease. However, we do not fully understand the spectrum of tumor suppressive effects regulated by this co-regulator. Here we show that PGC1 governs non-cell autonomous paracrine tumor suppression in prostate cancer. A systematic analysis of the transcriptional landscapes associated to PGC1 loss of expression revealed that PGC1 alters the expression of genes encoding for secreted proteins. Cell secretome studies corroborated that PGC1-dependent ERR regulation in prostate cancer cells suppresses the growth of tumor cells exposed to their conditioned media. The integration of in vitro and in vivo secretomics data and genetic perturbation assays revealed spermidine synthase as a transcriptional target of PGC1 and mediator of a paracrine metabolic growth suppressive effect. Moreover, the activity of the regulatory axis PGC1-ERR-SRM was reflected in patients and had prognostic value. Altogether, this work provides unprecedented evidence of the non-cell autonomous tumor suppression role of PGC1, which broadens the view of this co-regulator as a multifactorial tumor suppressor in prostate cancer.

cancer biology↗

bioRxiv2024

Beyond Basic Characterization and Omics: Immunomodulatory Roles of Platelet-Derived Extracellular Vesicles Unveiled by Functional Testing

Renowned for their role in hemostasis and thrombosis, platelets are also increasingly recognized for their contribution in innate immunity, immunothrombosis and inflammatory diseases. Platelets express a wide range of receptors, which allows them to reach a variety of activation endpoints and grants them immunomodulatory functions. Activated platelets release extracellular vesicles (PEVs), whose formation and molecular cargo has been shown to depend on receptor-mediated activation and environmental cues. This study compares the immunomodulatory profiles of PEVs generated via activation of platelets by different receptors, glycoprotein VI, C-type lectin-like receptor 2, and combining all thrombin-collagen receptors. Functional assays in vivo in zebrafish and in vitro in human macrophages respectively highlighted distinct homing and secretory responses triggered by the PEVs. In contrast, omics analyses of protein and miRNA cargo combined with physicochemical particle characterization found only subtle differences between the PEV types, which were insufficient to explain their different functional immunomodulatory profiles. Constitutively released PEVs, formed in the absence of an exogenous activator, displayed a disparate activation profile from the receptor induced PEVs. Our findings underscore that PEVs are tunable through receptor-mediated activation. To truly comprehend their role(s) in mediating platelet functions among immune cells, conducting functional assays is imperative. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/570750v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@75a9dborg.highwire.dtl.DTLVardef@e2787corg.highwire.dtl.DTLVardef@543525org.highwire.dtl.DTLVardef@6d1362_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗