Biology subjects

Zacco, E.

Publications and source records attributed to Zacco, E..

11 recordsLinked to original sources

bioRxiv2026

Rethinking Syndecan-1 as a Marker of Trauma-Induced Endothelial Injury

Syndecan-1 (SDC1), a transmembrane proteoglycan and component of the glycocalyx, is widely considered the key circulating biomarker of endothelial dysfunction in trauma and critical illness. However, the tissue distribution of SDC1 and the cellular origin of plasma SDC1 in health and disease are incompletely understood. This series of experiments integrates immunostaining, spatial transcriptomics (GeoMx Digital Spatial Profiler (DSP) and Xenium), and single-cell atlases to map SDC1, as well as the other three members of the syndecan family, syndecan-2 (SDC2), syndecan-3 (SDC3), and syndecan-4 (SDC4), across mouse and human tissues, including the lung, gastrointestinal tract, and brain. Across modalities, SDC1 primarily localizes to epithelial compartments, as demonstrated by colocalization with epithelial markers and enrichment in epithelial cell types in the lung and gut. Spatial profiling further identifies SDC1 and SDC4 enrichment in airway epithelial niches, SDC3 in endothelial-rich regions, and SDC2 distributed more broadly across compartments. Mouse and human single-cell atlases confirm epithelial predominance of SDC1. These findings define the cellular and spatial landscape of syndecan expression in healthy tissues and support SDC1 as an epithelial-enriched proteoglycan. These results also challenge the specificity of circulating SDC1 as a biomarker of endotheliopathy and raise the possibility that epithelial injury contributes substantially to circulating SDC1 after trauma and critical illness.

cell biology↗

bioRxiv2025

The RNA-binding activity of SACSIN HEPN domain is connected to ARSACS

Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay (ARSACS) is a neurodegenerative disorder caused by mutations in the SACS gene, though the molecular function of its protein product, SACSIN, remains elusive. Therapeutic strategies for ARSACS are limited, mostly due to the exceptionally large size of SACSIN ([~]520 kDa), which precludes conventional gene therapy and standard molecular delivery methods. Over 200 pathogenic variants, including missense and nonsense mutations, have been identified. Regardless of variant type, patients uniformly exhibit cerebellar ataxia and spasticity. Among them, patients carrying missense mutations within the SACSIN higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain, suggesting that the alteration of the functional role of SACSIN HEPN domain could be linked to the manifestation of ARSACS symptoms. Here, we provide the first direct evidence that SACSIN HEPN domain binds RNA, corroborating the hypothesis that SACSIN functions as an RNA-binding protein. In silico predictions through the catRAPID algorithm as well as AlphaFold 3 revealed the propensity of SACSIN HEPN domain to specifically interact with RNAs. These interactions were validated both in vitro and in cell studies, confirming that SACSIN HEPN domain binds to RNA transcripts. Overall, our study unveils an unknown molecular function of SACSIN that, if altered, can contribute to the development of ARSACS disease. Therefore, paving the way for innovative therapeutic approaches for ARSACS patients.

molecular biology↗

bioRxiv2025

RNA interactions drive structural and functional diversification of alpha-synuclein fibrils

Nucleic acids, particularly RNA, exert multiple roles on protein aggregation, yet their mechanistic involvement remains poorly understood. Building on prior work demonstrating RNA-driven acceleration of protein aggregation, we now demonstrate that RNA binding markedly reshapes the structural and functional properties of alpha-synuclein (aS) fibrils, a protein implicated in Parkinsons disease (PD). Although monomeric aS exhibits negligible RNA-binding properties, aggregation markedly increases its RNA-binding capacity. Our kinetic analyses reveal that RNA incorporation during initial stages of aggregation alters fibril elongation dynamics and modulates surface-mediated secondary nucleation in a seed concentration-dependent manner. Spectroscopic and microscopic characterization (FTIR, micro-FTIR) demonstrate that RNA promotes the formation of structurally distinct, more compact aS fibrils with heterogeneous morphology. Exploiting the recently discovered catalytic hydrolase activity of aS fibrils, we show that direct RNA binding inhibits enzymatic function, consistent with RNA-induced conformational remodeling that limits the exposure of critical residues. Additionally, RNA binding to fibril surfaces impairs proteolytic degradation by proteinase K, suggesting RNA stabilizes fibrils against clearance mechanisms. Moreover, RNA sequencing of fibril-bound nucleic acids uncovers a preference towards uridine-rich motifs that computational docking locates within hydrophilic cavities of disease-associated fibril structures. Collectively, we identify RNA as an active co-factor that remodels structure, propagation kinetics, stability, and function of aS fibrils. We offer a mechanistic link between RNA interaction and amyloid polymorphism relevant to synucleinopathies and, in broader contexts, to amyloid-associated diseases. Significance statementOur work represents the first systematic evidence that RNA directly interacts with protein fibrils and modulates key functional properties such as aggregation kinetics, proteolytic resistance and catalytic activity. We demonstrate that RNA co-aggregates with alpha-synuclein inducing structural conformations that depend on RNA for efficient assembly. Given the resemblance of these RNA-associated fibrils to those found in multiple system atrophy, our findings suggest that the final fibril structures in the patient brain are influenced by multiple cofactors and may differ substantially from recombinant fibrils formed in vitro, even when seeded with patient-derived material.

biochemistry↗

bioRxiv2025

Computationally Designed RNA Aptamers Enable Selective Detection of FUS Pathology in ALS

FUS is an RNA/DNA-binding protein whose mislocalization and aggregation are defining pathological features of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Detecting pathological FUS assemblies remains challenging, as antibody-based approaches are frequently limited by epitope masking, conformational heterogeneity, and cross-reactivity with physiological FUS pools. Here we apply rationally designed RNA aptamers to selectively recognize FUS across soluble and aggregated states. The aptamers bind solvent-exposed RNA-binding regions of FUS with low-nanomolar affinity and adopt stable hairpin conformations that support high specificity. In cultured cells expressing the ALS-associated p.P525L FUS mutation, the aptamers detect cytoplasmic and nuclear FUS assemblies that are frequently missed by commercial antibodies and show reduced recognition of FUS-containing protein complexes. Using super-resolution imaging, the aptamers enable visualization of early FUS aggregation intermediates that are inaccessible to conventional amyloid dyes. In post-mortem brain tissue from individuals with FUS-ALS, aptamer staining selectively labels pathological FUS while sparing normal nuclear FUS, revealing prominent nuclear and nucleolar pathology that is poorly resolved by antibody-based methods. Together, these findings establish RNA aptamers as sensitive and selective probes for pathological FUS and uncover previously underappreciated features of FUS aggregation in ALS. This work highlights the value of nucleic-acid-based recognition tools for interrogating protein misfolding and neurodegenerative disease pathology.

biochemistry↗

bioRxiv2025

Computationally-designed aptamers targeting RAD51-BRCA2 interaction inhibit RAD51 nuclear recruitment

The interaction between RAD51 and BRCA2 plays a key role in homologous recombination (HR), a critical DNA repair mechanism essential for the survival of cancer cells. Disrupting this interaction increases the sensitivity of cancer cells to chemotherapeutic agents. Here, we employed in silico methods to design a novel class of aptamers--customized single-stranded oligonucleotides--specifically engineered to bind RAD51. These aptamers were developed with the aim of selectively modulating RAD51s nuclear recruitment and its role in DNA repair processes. The leading candidate displays high affinity for RAD51, competing with BRCA2 for the same interaction site in vitro, as confirmed through biolayer interferometry (BLI) and fluorescence lifetime imaging microscopy (FLIM). We tested the efficacy of the leading aptamer in pancreatic cancer cells and observed that it significantly impedes RAD51 nuclear localization, reduces homologous recombination (HR) efficiency, and increases DNA damage. Critically, our aptamer potentiates the cytotoxicity of the PARP inhibitor olaparib, exploiting synthetic lethality (SL) to induce cancer cell death. Our study showcases an aptamer-based approach for selectively targeting protein interactions within DNA repair pathways, introducing a promising avenue for SL-based treatments applicable to a wide range of cancers.

biochemistry↗

bioRxiv2024

The role of RNA in the nanoscale organization of alpha-synuclein phase separation

The cellular accumulation of alpha-synuclein (aS) aggregates is a hallmark of several neurodegenerative diseases. Recent studies suggest that the aberrant transition of monomeric aS into solid-like aggregates may occur through an intermediate liquid-like state, where the protein partitions between dense and dilute phases. Although aS is not typically recognized as an RNA-binding protein, it can bind RNA under aggregation conditions, but its impact on aS liquid-like phases remains unexplored. Employing a combination of fluorescence spectroscopy techniques, we investigated aS dynamics in both phases in the presence of RNA. Our analysis revealed the formation of nanoclusters involved in initiating phase separation and uncovered heterogeneity within the dense phase, discovering that aS molecules exist in two distinct mobility states. Additionally, we demonstrated that RNA induces morphological changes and promotes the liquid-to-solid transition of aS dense phase. These findings underscore the active role of RNA in modulating aS phase transitions.

biophysics↗

bioRxiv2024

Amygdala TDP-43 pathology is associated with behavioural dysfunction and ferritin accumulation in amyotrophic lateral sclerosis.

BackgroundCognitive and behavioural symptoms associated with amyotrophic lateral sclerosis and frontotemporal spectrum disorders (ALSFTSD) are thought to be driven, at least in part, by the pathological accumulation of TDP-43. MethodsHere we examine post-mortem tissue from six brain regions associated with cognitive and behavioural symptoms in a cohort of 30 people with sporadic ALS (sALS), a proportion of which underwent standardized neuropsychological behavioural assessment as part of the Edinburgh Cognitive ALS Screen (ECAS). ResultsOverall, the behavioural screen performed as part of the ECAS predicted accumulation of pathological phosphorylated TDP-43 (pTDP-43) with 100% specificity and 86% sensitivity in behaviour-associated brain regions. Notably, of these regions, pathology in the amygdala was the most predictive correlate of behavioural dysfunction in sALS. In the amygdala of sALS patients, we show variation in morphology, cell type predominance, and severity of pTDP-43 pathology. Further, we demonstrate that the presence and severity of intra-neuronal pTDP-43 pathology, but not astroglial pathology, or phosphorylated Tau pathology, is associated with behavioural dysfunction. Cases were also evaluated using a TDP-43 aptamer (TDP-43APT), which revealed that pathology was not only associated with behavioural symptoms, but also with ferritin levels, a measure of brain iron. ConclusionsIntra-neuronal pTDP-43 and cytoplasmic TDP-43APT pathology in the amygdala is associated with behavioural symptoms in sALS. TDP-43APT staining intensity is also associated with increased ferritin, regardless of behavioural phenotype, suggesting that ferritin increases may occur upstream of clinical manifestation, in line with early TDP-43APT pathology, representing a potential region-specific imaging biomarker of early disease in ALS. Key MessagesO_ST_ABSWhat is already known on this topicC_ST_ABSThe amygdala is a key brain region in regulating behavior and emotional cognition and has been shown recently, through imaging studies, to be affected in ALS and FTD patients. What this study addsHere we examine the underlying pathology driving the association between the amygdala and behavioural symptoms in sporadic ALS demonstrating that region specific TDP-43 pathology and brain iron accumulation could represent potential early biomarkers of dysfunction. How this study might affect research, practice, or policyThe correlation between early TDP-43 pathology (detected by RNA aptamer) and increased ferritin (brain iron accumulation) occurring upstream of clinical manifestation represents a potential, region-specific (amygdala), early imaging biomarker in ALS. This means that people at risk could be identified early and stratified for clinical trials prior to substantial neuronal cell loss and symptom onset.

neuroscience↗

bioRxiv2023

RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS

TDP-43 is an aggregation-prone protein which accumulates in the hallmark pathological inclusions of amyotrophic lateral sclerosis (ALS). However, analysis of deeply-phenotyped human post-mortem samples has shown that TDP-43 aggregation, revealed by standard antibody methods, correlates poorly with symptom manifestation. Recent identification of cryptic-splicing events, such as the detection of Stathmin-2 (STMN-2) cryptic exons, are providing evidence implicating TDP-43 loss-of-function as a potential driving pathomechanism, but the temporal nature of TDP-43 loss and its relation to the disease process and clinical phenotype is not known. To address these outstanding questions, we used a novel RNA aptamer, TDP-43APT, to detect TDP-43 aggregation and used single molecule in situ hybridization to sensitively reveal TDP-43 loss-of-function and applied these in a deeply-phenotyped human post-mortem tissue cohort. We demonstrate that TDP-43APT identifies pathological TDP-43, detecting aggregation events that cannot be detected by classical antibody stains. We show that nuclear TDP-43 pathology is an early event, occurring prior to cytoplasmic aggregation and is associated with loss-of-function measured by coincident STMN-2 cryptic splicing pathology. Crucially, we show that these pathological features of TDP-43 loss-of-function precede the clinical inflection point and are not required for region specific clinical manifestation. Furthermore, we demonstrate that gain-of-function in the form of extensive cytoplasmic aggregation, but not loss-of-function, is the primary molecular correlate of clinical manifestation. Taken together, our findings demonstrate implications for early diagnostics as the presence of STMN-2 cryptic exons and early TDP-43 aggregation events could be detected prior to symptom onset, holding promise for early intervention in ALS. Short AbstractRecent identification of cryptic-splicing events such as the detection of Stathmin-2 (STMN-2) cryptic exons, are providing evidence implicating TDP-43 loss-of-function as a potential driving pathomechanism in amyotrophic lateral sclerosis (ALS). However, the temporal nature of TDP-43 loss and its relation to clinical phenotype is not known. Here, we used a novel RNA aptamer to detect TDP-43 aggregation and used single molecule ISH to sensitively reveal TDP-43 loss-of-function, applying these methods in a deeply-phenotyped human post-mortem tissue cohort. We show that nuclear TDP-43 pathology is an early event, that coincides with STMN-2 cryptic splicing. Crucially, we show that these pathological features of TDP-43 loss-of-function precede the clinical inflection point and are not required for region specific clinical manifestation. Furthermore, we demonstrate that gain-of-function, but not loss-of-function, is the primary molecular correlate of clinical manifestation. Taken together, our findings demonstrate implications for early diagnostics and intervention prior to symptom onset in ALS. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/563701v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1e49c3forg.highwire.dtl.DTLVardef@1ce05b0org.highwire.dtl.DTLVardef@d77205org.highwire.dtl.DTLVardef@7ed2cd_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Content-enriched fluorescence lifetime fluctuation spectroscopy to study bio-molecular condensate formation

Quantitative fluorescence microscopy is experiencing an important revolution thanks to single-photon array detectors. These detectors provide users with so far inaccessible specimen information: The distribution of the specimens fluorescence emission at single-photon level and high spatiotemporal sampling. In laser-scanning microscopy, this photon-resolved measurement has enabled robust fluorescence lifetime imaging at sub-diffraction spatial resolution, thus opening new perspectives for structural and functional imaging. Despite these significant advances in imaging, studying the time evolution of biological processes remains a considerable challenge. Here we present a com-prehensive framework of live-cell spectroscopy methodologies - compatible with imaging - to investigate bio-molecular processes at various spatiotemporal scales. We use photon-resolved spatial and temporal measurements granted by a single-photon array detector to boost the information content of a unified fluorescence fluctuation spectroscopy and fluorescence lifetime experiment. To demonstrate the potential of this approach, we investigate the phase transition of liquid-like condensates during oxidative stress inside living cells. These condensates are generally found in several cellular processes and exhibit substantial variations in molecular composition, size, and kinetics, posing a significant challenge for quantifying their underlying molecular dynamics. This study demonstrates how the pro-posed approach reveals the mutual dynamics of different RNA-binding proteins involved in the stress granules formation - inaccessible to imaging alone. We observe condensate formation by performing time-lapse super-resolved imaging of the cellular macro-environment while simultaneously monitoring the molecular mobility, the sub-diffraction environment organization, interactions, and nano-environment properties through fluorescence lifetime fluctuation spectroscopy. We are confident that our framework offers a versatile toolkit for investigating a broad range of bio-molecular processes - not limited to liquid-liquid phase transition - and we anticipate their widespread application in future life-science research.

biophysics↗

bioRxiv2022

A Theoretical Model reveals RNA sequestration in Alpha Synuclein Aggregates

Nucleic acids can act as potent modulators of protein aggregation, and RNA is able to either hinder or facilitate protein assembly depending on the molecular context. Here we used a computational approach to characterize the physico-chemical properties of regions involved in amyloid aggregation. In different experimental datasets we observed that, while the core is hydrophobic and highly ordered, external regions, more disordered, display a distinct tendency to interact with nucleic acids. To validate our predictions, we performed aggregation assays with -synuclein (aS140), a non-nucleic acid binding amyloidogenic protein, and a mutant truncated at the acidic C-terminus (aS103) that is predicted to sequester RNA. For both aS140 and aS103 we observed acceleration of the aggregation upon RNA addition with a significantly stronger effect for aS103. Due to the favorable electrostatics, we observed enhanced nucleic-acid sequestration ability for aS103 that entrapped a larger amount of RNA. Overall, our research suggests that RNA sequestration is a rather common phenomenon linked to protein aggregation and constitutes a gain-of-function mechanism to be further investigated. STATEMENT OF SIGNIFICANCEOur study indicates that aggregation confers RNA-binding ability to non-RNA-binding proteins such as alpha synuclein. The sequestration of RNA upon protein aggregation might alter RNA homeostasis and impact multiple biochemical cascades.

biochemistry↗

bioRxiv2022

Discovering host protein interactions specific for SARS-CoV-2 RNA genome

SARS-CoV-2, a positive single-stranded RNA virus, interacts with host cell proteins throughout its life cycle. These interactions are necessary for the host to recognize and hinder the replication of SARS-CoV-2. For the virus, to translate, transcribe and replicate its genetic material. However, many details of these interactions are still missing. We focused on the proteins binding to the highly structured 5 and 3 end regions of SARS-CoV-2 RNA that were predicted by the catRAPID algorithm to attract numerous proteins, exploiting RNA-Protein Interaction Detection coupled with Mass Spectrometry (RaPID-MS) technology. The validated interactors, which agreed with our predictions, include pseudouridine synthase PUS7 that binds to both ends of the viral RNA. Nanopore direct-RNA sequencing confirmed that the RNA virus is heavily modified, and PUS7 consensus regions were found in both SARS-CoV-2 RNA end regions. Notably, a modified site was detected in the viral Transcription Regulatory Sequence - Leader (TRS-L) and can influence the viral RNA structure and interaction propensity. Overall, our data map host protein interactions within SARS-CoV-2 UTR regions, pinpointing to a potential role of pseudouridine synthases and post-transcriptional modifications in the viral life cycle. These findings contribute to understanding virus-host dynamics and may guide the development of targeted therapies.

molecular biology↗