Biology subjects

Filippini, F.

Publications and source records attributed to Filippini, F..

7 recordsLinked to original sources

bioRxiv2026

Peroxisome dynamics during HSV-1 life cycle in human neurons

HSV-1 is increasingly implicated in Alzheimers disease, yet the mechanisms by which it reshapes neuronal metabolism remain incompletely understood. Here, we demonstrate that HSV-1 co-opts peroxisomal biogenesis and lipid metabolic pathways to promote its replication across human neuronal models. In SH-SY5Y cells, infection triggers a marked expansion of the peroxisomal compartment and alters organelle morphology through upregulation of PGC-1 and PEX13/14/19. Pharmacological stimulation of peroxisome proliferation enhances viral production, whereas inhibition of PEX3-PEX19-dependent biogenesis almost completely suppresses infection. Lipidomic profiling reveals a selective increase in peroxisome-derived plasmalogens and sphingolipids, supporting a role for peroxisomes as a metabolic hub for viral envelopment. This remodeling is recapitulated in hiPSC-derived neurons and human brain organoids, where it is strictly dependent on productive replication and re-emerges upon viral reactivation, but not during latency. Collectively, these findings identify peroxisomes as essential replication-permissive organelles exploited by HSV-1 and suggest that recurrent virus-driven peroxisomal and ether-lipid reprogramming may contribute to neuronal vulnerability in neurodegenerative disease.

microbiology↗

bioRxiv2026

Unconventional Small Molecule MNP-021 Protects Neuronal and Glial Function from Diabetes-Associated Glucotoxicity and Neuroinflammation

BackgroundDiabetes-associated neurodegeneration is amplified by methylglyoxal (MGO)-driven dicarbonyl stress linking hyperglycemia to neuronal insulin resistance and maladaptive neuroinflammation. We tested the neuroprotective activity of MNP-021, a non-electrophilic TRPA1 modulator, in neurons and glial cells in vitro. MethodsSH-SY5Y neurons were pretreated with MNP-021 and challenged with MGO, then profiled by high-content imaging, RNA-seq, Seahorse OCR/ECAR, glycolytic stress assays and AKT/ERK/CREB immunoblotting {+/-} insulin. In parallel, HMC3 glial cells were treated with MNP-021, exposed to LPS/TNF- or A{beta}(25-35) and tested for viability and inflammatory markers by ELISA and qRT-PCR. ResultsMGO increased nucleus-to-cytoplasm area ratio by 49% and dysregulated glucose handling, increasing 2-NBDG uptake by [~]25%, with GLUT1/GLUT4 membrane redistribution; MNP-021 normalized morphology, uptake, and transporter localization without cytotoxicity up to 10 {micro}M. RNA-seq identified 754 MGO-deregulated genes, including ISR/metabolic nodes (GCK, SESN2, PHGDH/PSAT1, PCK2); MNP-021 buffered stress-induced transcription with limited baseline effects, remodeled mitochondrial redox readouts consistent with controlled ROS signaling, while improving mitochondrial content/architecture and blunting stress-evoked compensatory glycolysis. MNP-021 restored pro-survival signaling (pAKT/pERK and nuclear pCREB), including insulin responsiveness during MGO exposure. MNP-021 reduced IL-6/TNF- release while increasing IL-10 and ARG1 ([~]1.9-fold vs LPS/TNF-) in HMC3 glial cells, shifting them toward a pro-resolving IL-10/ARG1 program with reduced A{beta}(25-35)-evoked cytokine release with GLP-1 remaining very low ([≤]10 pg/mL) and not significantly increased in this system. ConclusionsMNP-021 coordinates transcriptomic restraint, transporter-level glucose handling, mitochondrial resilience, and pro-survival/pro-resolving signaling across neuron-microglia compartments, supporting TRPA1-tuned small-molecule modulation as a candidate strategy against dicarbonyl-linked neuro-metabolic stress.

physiology↗

bioRxiv2025

The phytolongin AtPhyl2.1 is involved in cell plate formation and root development

SNAREs are critical elements of the membrane trafficking machinery with a wide variety of functionality across this family of proteins. Phytolongins are a recently identified subfamily of longins which possess the typical longin domain but lack a SNARE motif. Phytolongins have an ubiquitous tissue expression in Arabidopsis and are distributed throughout the secretory pathway. We focused on Phytolongin 2.1 (PHYL2.1) which localizes to the endoplasmic reticulum, and observed a strong root growth phenotype in the loss-of-function Atphyl2.1-1 mutant. We demonstrate that whilst cell elongation efficiency was not affected in the mutant, cell division was significantly reduced. The resulting decrease in root length in the Atphyl2.1-1 mutant is explained by a smaller number of cells which then elongate to enable root growth. Root apical meristem architecture of Atphyl2.1-1 and another mutant Atphyl2.1-2 was disturbed and distances from the root quiescent center to the transition zone and the first areas of mis-organized cells were affected in both mutants. Investigation of the SNARE AtKNOLLE revealed significant perturbation of Atphyl2.1-1 cell plate formation in the mis-organised areas. Our results provide a first characterization of the phytolongin AtPHYL2.1 which appears involved in root cell plate formation, root cell division and therefore root development. HighlightThe phytolongin AtPHYL2.1 significantly affects the efficiency of cell plate formation and root development in Arabidopsis thaliana.

plant biology↗

bioRxiv2025

LRP10 promotes trafficking of progranulin and prosaposin to lysosomes

Mutations in LRP10, a low-density lipoprotein receptor family member, cause familial Parkinsons disease and dementia with Lewy bodies. However, its direct cellular functions remain largely undefined. Using a multidisciplinary approach, our new data shows that LRP10 is required for the efficient trafficking of progranulin and prosaposin to lysosomes. Loss of LRP10 resulted in aberrant Golgi accumulations of progranulin and prosaposin and their reduced abundance in lysosomes. Disease-linked LRP10 missense mutations failed to support this lysosomal trafficking. Moreover, LRP10 KO mice developed striking microgliosis marked by enlarged and hyper-ramified microglia, accompanied by progranulin accumulation in the Golgi. Our results define LRP10 as a positive regulator of progranulin and prosaposin lysosomal protein trafficking and microglia homeostasis and thus shed new light on how its dysfunction may drive neurodegeneration in Parkinsons Disease and dementia with Lewy bodies.

cell biology↗

bioRxiv2024

NERVE 2.0: boosting the New Enhanced Reverse Vaccinology Environment via artificial intelligence and a user-friendly web interface

BackgroundVaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. However, the problem-solving potential of most, if not all, RV programs is still largely unexploited by experimental vaccinologists that impaired by somehow difficult interfaces, requiring bioinformatic skills. ResultsWe report here on the development and release of NERVE 2.0 (available at: https://nerve-bio.org) which keeps the original integrative and modular approach of NERVE, while showing higher predictive performance than its previous version and other web-RV programs (Vaxign and Vaxijen). We renewed some of its modules and added innovative ones, such as Loop Razor, to recover fragments of promising vaccine candidates or epitopepredict for the epitope prediction binding affinities and population coverage. Along with two newly built AI (Artificial Intelligence)-based models: ESPAAN and Virulent. To improve user-friendliness, NERVE was shifted to a tutored, web-based interface, with a noSQL-database to consent the user to submit, obtain and retrieve analysis results at any moment. ConclusionsWith its redesigned and updated environment, NERVE 2.0 allows customisable and refinable bacterial protein vaccine analyses to all different kinds of users.

bioinformatics↗

bioRxiv2024

Snapshots of Pseudomonas aeruginosa SOS response activation complex reveal structural prerequisites for LexA engagement and cleavage

Antimicrobial resistance represents a major threat to human health and Pseudomonas aeruginosa stands out among the pathogens responsible for this emergency. The SOS response to DNA damage plays a pivotal role in bacterial evolution, driving the development of resistance mechanisms and influencing the adaptability of bacterial populations to challenging environments, particularly in the context of antibiotic exposure. Recombinase A (RecA) and the transcriptional repressor LexA are the key players that orchestrate this process, determining either the silencing or the active transcription of the genes under their control. By integrating state-of-the-art structural approaches with binding and functional assays in vitro, we elucidated the molecular events governing the SOS response activation in P. aeruginosa, focusing on the RecA-LexA interaction. Our findings identify the conserved determinants and strength of the interactions that let RecA trigger the autocleavage and inactivation of the LexA repressor. These results provide the groundwork for designing novel antimicrobial strategies and for exploring the potential translation of Escherichia coli-derived approaches, to address the health-threatening implications of bacterial infections. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/585941v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@2fe1e4org.highwire.dtl.DTLVardef@19741e1org.highwire.dtl.DTLVardef@1664ddborg.highwire.dtl.DTLVardef@18195cb_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2021

Doxycycline inhibition of a pseudotyped virus transduction does not translate to inhibition of SARS-CoV-2 infectivity

The pandemic caused by the SARS-CoV-2 has created the need of compounds able to interfere with the biological processes exploited by the virus. Doxycycline, with its pleiotropic effects, including anti-viral activity, has been proposed as a therapeutic candidate for COVID-19 and about twenty clinical trials have started since the beginning of the pandemic. To gain information on the activity of doxycycline against SARS-CoV-2 infection and clarify some of the conflicting clinical data published, we designed in vitro binding tests and infection studies with a pseudotyped virus expressing the spike protein, as well as a clinically isolated SARS-CoV-2 strain. Doxycycline inhibited the transduction of the pseudotyped virus in Vero E6 and HEK-293 T cells stably expressing human receptor angiotensin-converting enzyme 2 but did not affect the entry and replication of SARS-CoV-2. Although this conclusion is apparently disappointing, it is paradigmatic of an experimental approach aimed at developing an integrated multidisciplinary platform. To avoid wasting precious time and resources we believe very stringent experimental criteria are needed in the preclinical phase, including infectious studies with SARS-CoV-2 in the platform before moving on to [failed] clinical trials. Author SummaryThe pandemic caused by the SARS-CoV-2 virus has created a completely unusual situation in rapidly searching for compounds able to interfere with the biological processes exploited by the virus. This new scenario has substantially changed the timing of drug development which has also resulted in the generation of controversial results, proving that the transition from computational screening to the clinical application requires great caution and careful studies. It is therefore necessary to establish new paradigms for evaluating the efficacy of a potential active molecule. We set up a preclinical platform aimed at identifying molecules active against SARS-CoV-2 infection developing a multidisciplinary approach based on very stringent experimental criteria, comprising in-silico studies, in vitro binding tests and infection studies with pseudovirus expressing the spike protein as well as clinically isolated SARS-CoV-2 strains. We focused our attention on doxycycline which has been suggested as potential therapeutic candidate for treating COVID-19 and is currently employed in about twenty clinical trials. Doxycycline resulted effective in inhibiting the transduction of pseudovirus but it did not affect the entry and replication of SARS-CoV-2. The results obtained underline the need to define more stringent and controlled pharmacological approaches before wasting precious time and resources with clinical trials.

pharmacology and toxicology↗