Biology subjects

Moro, F.

Publications and source records attributed to Moro, F..

6 recordsLinked to original sources

bioRxiv2025

Brain infiltrating T cells mediate microglial dysregulation and neuronal loss following SAH

The contribution of T cells to neuroinflammation after aneurysmal subarachnoid hemorrhage (SAH) remains poorly understood. Using a murine pre-chiasmatic injection model of SAH we demonstrate that T cell infiltration into the brain modulates microglial activation and promotes neuronal death. Targeted transcriptomic profiling revealed a sustained neuroimmune response at 7 days post injury (dpi) characterized by a major involvement of T cells and microglia activation. Immunohistochemistry confirmed focal CD3+ T cell infiltration, predominantly CD4+, in the brain at the site of blood injection (BI), choroid plexus and meninges in SAH mice at 3- and 7-dpi. This temporal pattern was also observed in the CSF of a human SAH cohort. T cell presence spatially correlated with regions of microglial reactivity and neuronal loss. Notably, CD3-knockout mice exhibited reduced microglial activation and preserved neuronal viability. These findings identify T cells as key amplifiers of post-SAH neuroinflammation and neuronal damage. Targeting T cell-microglia crosstalk may represent a novel therapeutic avenue for SAH. Summary statementThis study shows that brain T-cell infiltration after subarachnoid hemorrhage drives microglial activation and neuronal loss in mice, with similar patterns observed in patients. Data indicate T cells as key mediators of post-injury neuroinflammation with therapeutic implications.

neuroscience↗

bioRxiv2025

DNAJC12 stabilizes activated phenylalanine hydroxylase and reduces the concentration of L-Phe needed for activation

Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin (BH4)-dependent enzyme that converts L-phenylalanine (L-Phe) to L-tyrosine. PAH dysfunction leads to the accumulation of L-Phe in the blood (hyperphenylalaninemia; HPA), which may reach neurotoxic levels, resulting in phenylketonuria (PKU). PKU is associated with pathogenic variants in PAH, most causing misfolding and instability, leading to decreased levels of PAH protein and activity. Recently, variants in the class C J-domain protein DNAJC12 have also been associated with HPA in patients, demonstrating the importance of protein homeostasis regulation for proper PAH function. DNAJC12 and PAH have previously been reported to interact, but the molecular and structural mechanisms behind complex formation have remained unclear. In this work, we show that DNAJC12 binds to PAH, but presents higher affinity for its L-Phe activated form, which resembles the conformation of unliganded tyrosine hydroxylase, a structurally and functionally-related enzyme that also binds to DNAJC12. At saturation, four monomers of DNAJC12 bind and stabilize the PAH tetramer, protecting it from aggregation and lowering the L-Phe concentration necessary for substrate-induced activation, without affecting the interaction of the enzyme with its cofactor BH4. Importantly, DNAJC12 also stabilizes and delays the aggregation of the PKU-associated variant PAH-p.R261Q. Furthermore, L-Phe activated wild-type or variant PAH is required to stimulate Hsc70 ATPase activity. SIGNIFICANCE STATEMENTDeficiencies in the cochaperone DNAJC12 have recently been linked to hyperphenylalaninemia, dystonia and intellectual disabilities as DNAJC12 regulates the proteostasis of the aromatic amino acid hydroxylases, including phenylalanine hydroxylase (PAH). This study explores the mechanisms of the PAH:DNAJC12 interaction and examines the functional effects of their complex formation on PAH activity and stability. These findings enhance our understanding on the pathogenic mechanisms behind DNAJC12 variants and provide insights that could guide the development of drugs targeting this protein-protein interaction.

biophysics↗

bioRxiv2025

MINN: A METABOLIC-INFORMED NEURAL NETWORK FOR INTEGRATING OMICS DATA INTO GENOME-SCALE METABOLIC MODELING

The understanding of cellular behavior relies on the integration of metabolism and its regulation. Multi-omics data provide a detailed snapshot of the molecular processes underpinning cellular functions and their regulation, describing the current state of the cell. While Machine Learning (ML) models can uncover complex patterns and relationships within these data, they require large datasets for training and often lack interpretability. On the other hand, mathematical models, such as Genome-Scale Metabolic Models (GEMs), offer a structured framework for analyzing the organization and dynamics of specific cellular mechanisms. At the same time, they dont allow for seamless integration of omics information. Recently, a new framework to embed GEMs in a neural network has been introduced: these hybrid models combine the strengths of mechanistic and data-driven approaches, offering a promising platform for integrating different data sources with mechanistic knowledge. In this study, we present a Metabolic-Informed Neural Network (MINN) that utilizes multi-omics data to predict metabolic fluxes in Escherichia coli, under different growth rates and gene knockouts. We test its performances against pure ML and parsimonious Flux Balance Analysis (pFBA), demonstrating its efficacy in improving prediction performances. We also highlight how conflicts can emerge between the data-driven and the mechanistic objectives, and we propose different solutions to mitigate them. Finally, we illustrate a strategy to couple the MINN with pFBA, enhancing the interpretability of the solution.

systems biology↗

bioRxiv2024

High-dimensional proteomic analysis for pathophysiological classification of Traumatic Brain Injury

Pathophysiology and outcomes after Traumatic Brain Injury (TBI) are complex and highly heterogenous. Current classifications are uninformative about pathophysiology, which limits prognostication and treatment. Fluid-based biomarkers can identify pathways and proteins relevant to TBI pathophysiology. Proteomic approaches are well suited to exploring complex mechanisms of disease, as they enable sensitive assessment of an expansive range of proteins. We used novel high-dimensional, multiplex proteomic assays to study changes in plasma protein expression in acute moderate-severe TBI. We analysed samples from 88 participants in the longitudinal BIO-AX-TBI cohort (n=38 TBI within 10 days of injury, n=22 non-TBI trauma, n=28 non-injured controls) on two platforms: Alamar NULISA CNS Diseases and OLINK(R) Target 96 Inflammation. Participants also had data available from Simoa(R) (neurofilament light, GFAP, total tau, UCHL1) and Millipore (S100B). The Alamar panel assesses 120 proteins, most of which have not been investigated before in TBI, as well as proteins, such as GFAP, which differentiate TBI from non-injured and non-TBI trauma controls. A subset (n=29 TBI, n=24 non-injured controls) also had subacute 3T MRI measures of lesion volume and white matter injury (fractional anisotropy, scanned 10 days to 6 weeks after injury). Differential Expression analysis identified 16 proteins with TBI-specific significantly different plasma expression. These were neuronal markers (calbindin2, UCHL1, visinin-like protein1), astroglial markers (S100B, GFAP), tau and other neurodegenerative disease proteins (total tau, pTau231, PSEN1, amyloid beta42, 14-3-3{gamma}), inflammatory cytokines (IL16, CCL2, ficolin2), cell signalling (SFRP1), cell metabolism (MDH1) and autophagy related (sequestome1) proteins. Acute plasma levels of UCHL1, PSEN1, total tau and pTau231 correlated with subacute lesion volume, while sequestome1 was correlated with whole white matter skeleton fractional anisotropy and CCL2 was inversely correlated with corpus callosum FA. Neuronal, astroglial, tau and neurodegenerative proteins correlated with each other, and IL16, MDH1 and sequestome1. Clustering (k means) by acute protein expression identified 3 TBI subgroups which had differential injury patterns, but did not differ in age or outcome. Proteins that overlapped on two platforms had excellent (r>0.8) correlations between values. We identified TBI-specific changes in acute plasma levels of proteins involved in amyloid processing, inflammatory and cellular processes such as autophagy. These changes were related to patterns of injury, thus demonstrating that processes previously only studied in animal models are also relevant in human TBI pathophysiology. Our study highlights the potential of proteomic analysis to improve the classification and understanding of TBI pathophysiology, with implications for prognostication and treatment development.

neuroscience↗

bioRxiv2023

Translating from mice to humans: using preclinical blood-based biomarkers for the prognosis and treatment of traumatic brain injury

Rodent models are important research tools for studying the pathophysiology of traumatic brain injury (TBI) and developing potential new therapeutic interventions for this devastating neurological disorder. However, the failure rate for the translation of drugs from animal testing to human treatments for TBI is 100%, perhaps due, in part, to distinct timescales of pathophysiological processes in rodents versus humans that impedes translational advancements. Incorporating clinically relevant biomarkers in preclinical studies may provide an opportunity to calibrate preclinical models to human TBI biomechanics and pathophysiology. To support this important translational goal, we conducted a systematic literature review of preclinical TBI studies in rodents measuring blood levels of clinically used NfL, t-Tau, p-Tau, UCH-L1, or GFAP, published in PubMed/MEDLINE up to June 13th, 2023. We focused on blood biomarker temporal trajectories and their predictive and pharmacodynamic value and discuss our findings in the context of the latest clinical TBI biomarker data. Out of 369 original studies identified through the literature search, 71 met the inclusion criteria, with a median quality score on the CAMARADES checklist of 5 (interquartile range 4-7). NfL was measured in 17 preclinical studies, GFAP in 41, t-Tau in 17, p-Tau in 7, and UCH-L1 in 19 preclinical studies. Data in rodent models show that all blood biomarkers exhibited injury severity-dependent elevations, with GFAP and UCH-L1 peaking within hours after TBI, NfL peaking within days after TBI and remaining elevated up to 6 months post-injury, whereas t-Tau and p-Tau levels were gradually increased many weeks after TBI. Blood NfL levels emerges as a prognostic indicator of white matter loss after TBI, while both NfL and GFAP hold promise for pharmacodynamic studies of neuroprotective treatments. Therefore, blood-based preclinical biomarker trajectories could serve as important anchor points that may advance translational research in the TBI field. However, further investigation into biomarker levels in the subacute and chronic phases will be needed to more clearly define pathophysiological mechanisms and identify new therapeutic targets for TBI.

neuroscience↗

bioRxiv2023

The structural architecture of an α-synuclein toxic oligomer

Oligomeric species populated during -synuclein aggregation are considered key drivers of neurodegeneration in Parkinsons disease. However, the development of oligomer-targeting therapeutics is constrained by our limited knowledge of their structure and the molecular determinants driving their conversion to fibrils. PSM3 is a nanomolar peptide binder of -synuclein oligomers that inhibits aggregation by blocking oligomer to fibril conversion. Here, we investigate the binding of PSM3 to -synuclein oligomers to discover the mechanistic basis of this protective activity. We find that PSM3 selectively targets an -synuclein N-terminal motif (residues 36-61) that populates a distinct conformation in the monomeric and oligomeric states. This -synuclein region plays a pivotal role in oligomer to fibril conversion, as its absence renders the central NAC domain insufficient to prompt this structural transition. The hereditary mutation G51D, associated with early-onset Parkinsons disease, causes a conformational fluctuation in this region, leading to delayed oligomer to fibril conversion and an accumulation of oligomers that are resistant to remodeling by molecular chaperones. Overall, our findings unveil a new targetable region in -synuclein oligomers, advance our comprehension of oligomer to amyloid fibril conversion and reveal a new facet of -synuclein pathogenic mutations.

biophysics↗