Biology subjects

Malaspina, A.

Publications and source records attributed to Malaspina, A..

10 recordsLinked to original sources

bioRxiv2026

The resolvin D and E biogenesis pathway regulatessenescence and ageing

Ageing is considered as a process were molecular, cellular and tissular function is impaired. One classic cellular phenotype that increases during ageing is cellular senescence. Upon senescence, the cells stop proliferating and release a variety of cytokines, chemokines and extracellular vesicles. However, the implication of biomolecules derived from lipids such as resolvins are not well characterised in senescence and ageing. Here, we find that the resolvin E and D biosynthesis pathway is activated as observed by an increase in their corresponding receptors and enzymes implicated. Furthermore, knockdown of the resolvins E and D receptors impairs the induction of senescence. This pathway is conserved not only during senescence but also in fibroblasts derived from aged human individuals, aged mice and during other inflammatory responses. A metabolomics analyses shows an increase in different precursors of resolvins in senescence. In accordance with prior data, we find that small extracellular vesicles (sEV) isolated from young human donors ameliorate inflammation and the biogenesis of resolvins both in different cell models and in aged mice. In summary, here we present data showing that the resolvins biogenesis pathway is induced in ageing and cellular senescence.

cell biology↗

bioRxiv2025

TDP-43 pathology induces CD8+ T cell activation through cryptic epitope recognition

Aggregation and nuclear depletion of the RNA binding protein TDP-43 are the crucial pathological features of amyotrophic lateral sclerosis (ALS) and inclusion body myositis (IBM), two degenerative diseases of the CNS and muscle. The loss of TDP-43 nuclear function results in the aberrant inclusion of cryptic exons in mRNA transcripts, leading to the expression of de novo proteins. Clonally expanded and highly differentiated CD8+ T cells have been observed in individuals with TDP-43 proteinopathies and therapeutics modulating the T cell response have recently been found to extend survival. However, the target antigens mediating T cell activation have remained elusive. Here, we investigate whether the de novo proteins induced by aberrant cryptic splicing due to TDP-43 nuclear loss can act as neo-antigens. We detect the HDGFL2 cryptic peptide and multiple other TDP-43 cryptic exons in IBM skeletal muscle, where their presence correlates with enrichment of T cells and class I antigen presentation pathways. Furthermore, we identify epitopes deriving from HDGFL2 and IGLON5 cryptic peptides which are recognized by clonally expanded and functionally differentiated populations of CD8+ T cells in ALS and IBM Patients. Finally, we demonstrate that T cells engineered to express the identified TCRs can bind and activate in response to the cryptic peptide derived epitopes (cryptic epitopes) and are able to kill TDP-43 deficient astrocytes. This work identifies for the first time specific T cell antigens in ALS and IBM, directly linking adaptive immune response to TDP-43 pathology.

immunology↗

bioRxiv2024

Glutathione Oxidation in Cerebrospinal Fluid as a Biomarker of Oxidative Stress in Amyotrophic Lateral Sclerosis

BackgroundOxidative stress is a key feature of several neurodegenerative diseases, including Amyotrophic Lateral Sclerosis (ALS). Identification of reliable biomarkers of oxidative stress would be beneficial for drug-target engagement studies. MethodsWe performed unbiased quantitative mass spectrometry (MS)-based analysis to measure changes in protein abundance and oxidation in cerebrospinal fluid (CSF) from a cohort of ALS patients and healthy controls at two time points (approximately four months apart) to capture disease progression. In addition, we developed a sensitive and targeted quantitative MS method to measure glutathione oxidation state in the same sets of CSF samples. ResultsProteomic analysis of CSF revealed statistically significant changes in the abundance of several proteins, including CHIT1, CHI3L1, CHI3L2 and COL18A1 in ALS patients compared to healthy controls at both time points. Several sites of protein oxidation were significantly altered in ALS compared to healthy controls, and total levels of reversible protein oxidation were elevated in ALS patients. Given that glutathione oxidation could be a useful biomarker of oxidative stress, we also measured glutathione and its oxidation state in CSF in the same cohorts of samples. Total GSH (tGSH), GSSG levels and the GSSG/GSH ratio were significantly higher in the ALS than in the healthy control group for both time points. For the first visit, fold changes of tGSH, GSSG, and GSSG/GSH ratio in ALS compared to HC were 1.33 (p = 0.0215), 1.54 (p = 0.0041) and 1.80 (p = 0.0454), respectively. For the second visit, these values were 1.50 (p = 0.0143), 2.00 (p = 0.0018) and 2.14 (p = 0.0120), respectively. Furthermore, we found positive correlations between disease duration until the first visit and total glutathione (tGSH), GSSG and GSSG/GSH ratio. Finally, there was a strong positive correlation between the total intensity of reversibly oxidised proteins and the ratio of GSSG/GSH in ALS patients at both visits. ConclusionWe propose that measuring levels of glutathione oxidation in CSF could act as a stratification biomarker to select ALS patients for antioxidant therapy and an approach to monitor the treatment response to therapeutic agents targeting oxidative stress.

neuroscience↗

bioRxiv2023

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD

Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to ALS and FTD, leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. However, the possibility of de novo protein synthesis from cryptic exon transcripts has not been explored. Here, we show that mRNA transcripts harboring cryptic exons generate de novo proteins both in TDP-43 deficient cellular models and in disease. Using coordinated transcriptomic and proteomic studies of TDP-43 depleted iPSC-derived neurons, we identified numerous peptides that mapped to cryptic exons. Cryptic exons identified in iPSC models were highly predictive of cryptic exons expressed in brains of patients with TDP-43 proteinopathy, including cryptic transcripts that generated de novo proteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that these de novo peptides were present in CSF from patients with ALS. The demonstration of cryptic exon translation suggests new mechanisms for ALS pathophysiology downstream of TDP-43 dysfunction and may provide a strategy for novel biomarker development. One Sentence SummaryLoss of TDP-43 function results in the expression of de novo proteins from mis-spliced mRNA transcripts.

neuroscience↗

bioRxiv2020

Analysis of circulating protein aggregates reveals pathological hallmarks of amyotrophic lateral sclerosis

Blood-based biomarkers can be informative of brain disorders where protein aggregation play a major role. The proteome of plasma and circulating protein aggregates (CPA) reflect the inflammatory and metabolic state of the organism and can be predictive of system-level and/or organ-specific pathologies. CPA are enriched with heavy chain neurofilaments (NfH), key axonal constituents involved in brain aggregates formation and biomarkers of the fatal neurodegenerative disorder amyotrophic lateral sclerosis (ALS). Here we show that CPA and brain protein aggregates (BPA) from ALS differ in protein composition and appear as a combination of electron-dense large globular and small filamentous formations on transmission electron microscopy. CPA are highly enriched with proteins involved in the proteasome and energy metabolism. Compared to the human proteome, proteins within aggregates show distinct and tissue-dependent chemical features of aggregation propensity. The use of a TMTcalibrator proteomics workflow with ALS brain as calibrant reveals 4973 brain-derived low-abundance proteins in CPA, including the products of translation of 24 ALS risk genes. 285 of these (5.7%) are regulated in ALS CPA including FUS (p<0.05). CPA from both ALS and healthy controls affect cell viability when testing endothelial and PC12 neuronal cell lines, while CPA from ALS exert a more toxic effect at lower concentrations. The analysis of resistance to protease enzymes hydrolysis indicates an ALS-specific digestion pattern for NfH using enterokinase. This study reveals how peripheral protein aggregates are significantly enriched with brain proteins which are highly representative of ALS pathology and a potential alternative source of biomarkers and therapeutic targets for this incurable disorder. Significance StatementMolecular mechanism of neurodegeneration like protein aggregation are important brain-specific alterations which need to be addressed therapeutically. Recently described fluid biomarkers of neurodegenerative disorders provide means for stratification and monitoring of disease progression. Here we show that circulating protein aggregates are easily accessible in blood and reproduce important features of brain pathology for an incurable disorder like amyotrophic lateral sclerosis. They represent a source of biomarkers and of novel therapeutics for ALS.

neuroscience↗

bioRxiv2020

Immune reactivity to neurofilaments and dipeptide repeats in ALS progression

ObjectiveTo test antibody response and formation of immune-complexes to neurofilaments and dipeptide-repeats, the translational products of the mutated C9orf72 gene, as potential biomarkers for clinical stratification of amyotrophic lateral sclerosis (ALS). MethodsUsing neurofilament protein isoforms plasma expression as reference, antibodies and immune-complexes against neurofilament-light, medium and heavy chain and poly-(GP)-GR dipeptide-repeats were tested in blood from 105 fast and slow progressing ALS patients, 26 C9orf72 mutation carriers (C9+ve) ALS patients and 77 healthy controls (HC) using single-molecule and immune-capture assays. Longitudinal antibody/immune-complex responses were measured in serial blood samples from 37 (including 11 C9+ve) patients. ResultsAntibodies and immune-complex reactivity was higher in ALS patients than HC, particularly in C9+ve ALS patients, and modestly correlated with total neurofilament protein isoforms (r:0.24 p=0.002; r:0.18 p=0.02 respectively). Neurofilament-light immune-complexes and neurofilament-heavy antibodies had the best diagnostic performances distinguishing ALS subtypes from HC (AUC=0.68 p<0.01; AUC=0.68 p<0.001 respectively). Neurofilament-light immune-complexes (AUC=0.69 p<0.01) and poly-(GP) dipeptide-repeats antibodies (AUC=0.71 p<0.001) separated C9+ve from C9-ve patients. Multivariate mortality hazard ratio and Kaplan-Meier analyses showed low neurofilament-heavy antibody levels associated with increased survival. Longitudinal analysis identified raising levels of antibodies against neurofilaments in fast progressing ALS and of neurofilament-light immune-complexes in C9+ve patients. InterpretationC9+ve and fast progressing ALS patients have a distinct neurofilament and dipeptide-repeat immuno-phenotype, with increasing levels of blood neurofilament-light immune-complexes and neurofilament antibodies with disease progression. The study of the expression of these biomarkers in the natural history of ALS may shed light on disease initiation and progression and provide novel pharmacodynamic biomarkers in emerging C9orf72 gene silencing therapies.

neuroscience↗

bioRxiv2019

Enzymatic degradation of RNA causes widespread protein aggregation in cell and tissue lysates

Most proteins in cell and tissue lysates are soluble. Here, we show that many of these proteins, including several that are implicated in neurodegenerative diseases, are maintained in a soluble and functional state by association with endogenous RNA, as degradation of RNA invariably leads to protein aggregation. We identify the importance of nucleic acid structure, with single-stranded pyrimidine-rich bulges or loops surrounded by double-stranded regions being particularly efficient in this role, revealing an apparent one-to-one protein-nucleic acid stoichiometry. The relationship of these findings to pathological protein aggregation is suggested by our discovery that protein aggregates isolated from brain tissue from Amyotrophic Lateral Sclerosis patients can be rendered soluble after refolding by both RNA and synthetic oligonucleotides. Together, these findings open new avenues for understanding the mechanism behind protein aggregation and shed light on how certain proteins remain soluble.

molecular biology↗

bioRxiv2019

Circulating miR-181 is a prognostic biomarker for amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a relentless neurodegenerative syndrome of the human motor neuron system, for which no effective treatment exists. Variability in the rate of disease progression limits the efficacy of ALS clinical trials, suggesting that developing of better biomarkers for prognosis will facilitate therapeutic progress. Here, we applied unbiased next-generation sequencing to investigate the potential of plasma cell-free microRNAs as biomarkers of ALS prognosis, in 252 patients with detailed clinical-phenotyping. First, we identified miRNAs, whose plasma levels remain stable over the course of disease in a longitudinal cohort of 22 patients. Next, we demonstrated that high levels of miR-181, a miRNA enriched in neurons of the brain and spinal cord, predicts a >2 fold risk of death in discovery cohort (126 patients) and an independent replication cohort (additional 122 patients). miR-181 performance is comparable with the established neurofilament light chain (NfL) biomarker and when combined together, miR-181+NfL establish a novel RNA-protein biomarker pair with superior prediction capacity of ALS prognosis. Therefore, plasma miR-181 predicts ALS disease course, and a novel miRNA-protein biomarker approach, based on miR-181+NfL, boosts precision of patient stratification and may greatly enhance the power of clinical trials. One Sentence Summaryplasma miR-181 levels indicate high mortality risk in ALS patients.

neuroscience↗

bioRxiv2019

Plasma pNfH differentiate SBMA from ALS

Background and aimSpinal bulbar muscular atrophy (SBMA) is a progressive adult-onset X-linked neuromuscular disease. Although traditionally considered a motor neuron disorder, recent advances have highlighted a primary myopathic component. We evaluated levels of phosphorylated neurofilament heavy chain (pNfH), a known biomarker for neurodegeneration, in SBMA. Materials and methodsWe collected plasma and serum from 46 SBMA, 50 ALS and 50 healthy control cases, alongside with plasma from a mouse model of SBMA (AR100) and littermate controls. We measured pNfH plasma levels using Single molecule array (Simoa), we assessed functional scales and we gathered demographic data. We analysed data using Mann-Whitney U test, Kruskal-Wallis test and Cox regression analysis. ResultsPlasma pNfH levels were significantly increased in ALS, but, intriguingly, there was no change in SBMA. These results were also confirmed in SBMA mice. The ROC curve highlighted that pNfH levels can effectively distinguish between ALS and SBMA (AUC 0.95). ConclusionsUnexpectedly, levels of pNfH are normal in SBMA, whilst they are increased in ALS, and suggest pNfH could serve as a biomarker to differentiate the two diseases. Further, this finding is in agreement with recent evidence showing that primary muscle damage is a crucial feature in SBMA.

neuroscience↗

bioRxiv2018

Skeletal muscle MRI differentiates SBMA and ALS and correlates with disease severity

ObjectiveTo investigate the use of muscle MRI for the differential diagnosis and as a disease progression biomarker for two major forms of motor neuron disorders, spinal bulbar muscular atrophy (SBMA) and amyotrophic lateral sclerosis (ALS).\n\nMethodsWe applied quantitative 3-point Dixon and semi-quantitative T1-weighted and STIR imaging to bulbar and lower limb muscles and performed clinical and functional assessments in ALS (n=21) and SBMA (n=21) patients, alongside healthy controls (n=16). Acquired images were analyzed for the presence of fat infiltration or edema as well as specific patterns of muscle involvement. Quantitative MRI measurements were correlated with clinical parameters of disease severity in ALS and SBMA.\n\nResultsQuantitative imaging revealed significant fat infiltration in bulbar (p<0.001) and limb muscles in SBMA compared to controls (thigh: p<0.001; calf: p=0.001), identifying a characteristic pattern of muscle involvement. In ALS, semi-quantitative STIR imaging detected marked hyperintensities in lower limb muscles, distinguishing ALS from SBMA and controls. Lastly, MRI measurements correlated significantly with clinical scales of disease severity in both ALS and SBMA.\n\nConclusionsOur findings show that muscle MRI differentiates between SBMA and ALS and correlates with disease severity, supporting its use as a diagnostic tool and biomarker for disease progression. This highlights the clinical utility of muscle MRI in motor neuron disorders and contributes to establish objective outcome measures, which is crucial for the development of new drugs.

neuroscience↗