Biology subjects

Iraci, N.

Publications and source records attributed to Iraci, N..

4 recordsLinked to original sources

bioRxiv2025

SPROUTS_DB: an implemented database of contaminants for extracellular vesicle proteomics studies

BackgroundCurrent proteomics techniques allow rapid identification and quantification of proteins within any given biological source. In particular, nanoUHPLC/High-Resolution nanoESI-MS/MS enables the characterization of proteins in complex biological samples due to its high sensitivity, accuracy, and scalability. However, LC-MS/MS proteomics might still be susceptible to laboratory and sample-associated contaminants, which can significantly compromise the quality and reliability of data. Therefore, an accurate identification and annotation of such contaminants is crucial for the development of robust proteomics databases and spectral-libraries related search engines. This approach is of special interest in the field of secretome and extracellular vesicles (EVs), membrane-enclosed nanostructures that contain a variety of proteins crucial for cell-to-cell communication and translational applications. ResultsWhen working in ex vivo/in vitro settings, proteins from fetal bovine serum (FBS), commonly employed in standard cell culture media, may interfere with the proteome analysis. To address this issue, we conceived and designed SPROUTS_DB, Serum Protein Repository Of Unwanted Target(ed) Sequences DataBase, a dedicated resource to catalog serum-derived contaminants. Starting from media supplemented with EV-depleted FBS, we simulated cell growth conditions - in the absence of cells - followed by ultracentrifugation. LC-MS/MS analysis of these samples resulted in the identification of a novel set of 1,288 contaminant proteins, which has been deposited in the ProteomeXchange repository (identifier PXD044137). SPROUTS_DB contains primarily soluble proteins, mainly related to the Gene Ontology categories Extracellular Region and Extracellular Space, in line with the nature of the starting sample. In contrast, only a small fraction of the contaminants is classified as membrane-associated proteins, supporting the limited vesicle contamination in the complete medium, due to the use of EV-depleted FBS. Of note, we demonstrated that SPROUTS_DB outperforms existing contaminants databases, ensuring that only peptide spectra relevant to the examined sample are retained and identified as true positive data. ConclusionsConsidering that even proteins from phylogenetically distant organisms share extensive stretches of sequences, SPROUTS_DB is designed to discern contaminants from real sample proteins of interest, minimizing false positive identifications. To the best of our knowledge, SPROUTS_DB is the most updated database of contaminants useful for proteomics investigations of cellular secretomes and EV-containing samples.

cell biology↗

bioRxiv2025

Varicose-projection astrocytes: a reactive phenotype associated with neuropathology

Glial cells are fundamental for the pathophysiology of all neurological disorders. Astrocytes, the primary home-ostatic cells of the central nervous system (CNS), exhibit species-specific characteristics, with human astrocytes specifically displaying unique structural and functional features. It is thus essential to investigate human-specific astrocytic responses to neuropathology using human-relevant models. Varicose projection (VP) astrocytes, traditionally considered specific to humans and apes, were suggested to reflect pathological burden, albeit direct evidence linking them to neurological diseases has been lacking. Here, we demonstrate for the first time that VP astrocytes are present in mice and tigers (Panthera tigris) and we provide evidence from four distinct human-based models that VP astrocytes are not a distinct physiological astrocyte subtype but rather a novel class of reactive astrocytes associated with neuropathology. Using human induced pluripotent stem cell (hiPSC)-derived astrocytes, mixed neural cultures, and cortical organoids, we showed that VP astrocytes are induced by pro-inflammatory cytokines interleukin-1{beta} (IL-1{beta}) and tumor necrosis factor- (TNF-) or LPS. Notably, cytokine withdrawal reverses the VP phenotype of astrocytes, indicating that it is a transient, inflammation-dependent state. We characterized the distinctive components of varicosities, including markers for extracellular vesicles, mitochondria, Golgi and endoplasmic reticulum components, suggesting roles in cellular stress responses and metabolic dysregulation. We further validated the pathological relevance of VP astrocytes by documenting their significant enrichment in postmortem brain samples from patients with several neurodegenerative diseases including as Alzheimers disease, Parkinsons disease, and multiple sclerosis, as well as in surgical resections from patients with epilepsy due to hippocampal sclerosis or brain tumors, including previously unreported subcortical regions such as basal ganglia. Additionally, we identified a higher number of VP astrocytes also in mouse astrocytes upon treatment with pro-inflammatory cytokines, suggesting that formation of VP astrocytes is an evolutionarily conserved astrocytic response to neuroinflammation. Our findings point to VP astrocytes as a novel reactive astrocyte subtype closely linked to neuropathology, highlighting their potential as biomarkers and therapeutic targets in neurological diseases. This study lays the groundwork for future investigations into the mechanisms driving VP astrocyte formation and their broader implications in neuropathology.

neuroscience↗

bioRxiv2021

Small Extracellular Vesicles Secreted by Region-specific Astrocytes Ameliorate the Mitochondrial Function in a Cellular Model of Parkinson's Disease

Extracellular vesicles (EVs) are emerging as powerful players in cell-to-cell communication both in health and diseased brain. In Parkinsons disease (PD) - characterized by selective dopaminergic (DAergic) neuron death in ventral midbrain (VMB) and degeneration of DAergic terminals in striatum (STR) - astrocytes (AS) exert dual harmful/protective functions. When activated by chemokine CCL3, AS promote a robust DAergic neuroprotection both in cellular and pre-clinical models of PD, with mechanisms not fully elucidated. Here we used a combination of techniques to characterize AS-EVs derived from VMB and STR, and investigated their potential to exert neuroprotection. First, we show that: (i) AS of both regions secrete small EVs of ~100 nm; (ii) VMB-AS release more EVs per cell than STR-AS under basal conditions; and (iii) only VMB-AS respond to CCL3 by producing more EVs, suggesting differential AS-EV secretion rate according to PD brain region. Next, addressing AS-EV potential against oxidative stress and mitochondrial toxicity, we found that AS-EVs, especially CCL3-AS-EVs, fully counteract H2O2-induced caspase-3 activation. Furthermore, using high resolution respirometry, we demonstrated that AS-EVs rescue the neuronal mitochondrial complex I function impaired by MPP+, with VMB-AS-EVs fully restoring ATP production in MPP+-injured neurons, highlighting a regional diversity of AS-EVs with neuroprotective implications for PD.

neuroscience↗

bioRxiv2020

Neural stem cells traffic functional mitochondria via extracellular vesicles to correct mitochondrial dysfunction in target cells

Neural stem cell (NSC) transplantation induces recovery in animal models of central nervous system (CNS) diseases. Although the replacement of lost endogenous cells was originally proposed as the primary healing mechanism of NSC grafts, it is now clear that transplanted NSCs operate via multiple mechanisms, including the horizontal exchange of therapeutic cargoes to host cells via extracellular vesicles (EVs). EVs are membrane particles trafficking nucleic acids, proteins, metabolites and metabolic enzymes, lipids and entire organelles. However, the function and the contribution of these cargoes to the broad therapeutic effects of NSCs is yet to be fully understood. Mitochondrial dysfunction is an established feature of several inflammatory and degenerative CNS disorders, most of which are potentially treatable with exogenous stem cell therapeutics. Herein we investigated the hypothesis that NSCs release and traffic functional mitochondria via EVs to restore mitochondrial function in target cells. Untargeted proteomics revealed a significant enrichment of mitochondrial proteins spontaneously released by NSCs in EVs. Morphological and functional analyses confirmed the presence of ultrastructurally intact mitochondria within EVs (Mito-EVs) with conserved membrane potential and respiration. We found that the transfer of Mito-EVs to mtDNA-deficient L929 Rho0 cells rescued mitochondrial function and increased Rho0 cell survival. Furthermore, the incorporation of Mito-EVs into inflammatory professional phagocytes restored normal mitochondrial dynamics and cellular metabolism and reduced the expression of pro-inflammatory markers in target cells. When transplanted in an animal model of multiple sclerosis, exogenous NSCs actively transferred mitochondria to mononuclear phagocytes and induced a significant amelioration of clinical deficits. Our data provide the first evidence that NSCs deliver functional mitochondria to target cells via Mito-EVs, paving the way for the development of novel (a)cellular approaches aimed at restoring mitochondrial dysfunction not only in multiple sclerosis, but also in degenerative neurological diseases.

neuroscience↗