Biochemistry, Genetics and Molecular Biology, Cellular and Molecular Neuroscience
9
Scopus Publications
Scopus Publications
Free D-aspartate modulates the expression of proteins linked to schizophrenia and autism spectrum disorder during early postnatal life Francesco Errico, Rosita Russo, Federica Carrillo, Tommaso Nuzzo, Raffaella di Vito, Enza Canonico, Paolo Vincenzo Pedone, Ferdinando Di Cunto, Teresa Esposito, Alessandro Usiello, Angela Chambery Cellular and Molecular Life Sciences, 2026 D-aspartate is an endogenous agonist of NMDA and mGlu5 receptors, with a distinctive spatiotemporal expression profile that peaks in the prenatal and early postnatal brain. This suggests a critical role for D-aspartate metabolism in modulating neurodevelopmental processes linked to glutamatergic neurotransmission. However, the precise mechanisms through which D-aspartate exerts its effects remain unclear. To elucidate the molecular pathways orchestrated by early D-aspartate signalling, we employed a knock-in mouse model characterized by constitutive D-aspartate depletion due to the prenatal expression of its degradative enzyme, D-aspartate oxidase. Using an advanced quantitative proteomic approach based on Tandem Mass Tag isobaric labelling and nano-liquid chromatography coupled with high-resolution tandem mass spectrometry, we investigated the proteomic variations induced by D-aspartate depletion during postnatal brain development, comparing Ddo knock-in mice with their wild-type littermates. Our findings reveal that D-aspartate modulates the neonatal expression of proteins involved in glutamatergic neurotransmission, nervous system development, and cytoskeleton organization. Moreover, proteomic analysis identified a subset of D-aspartate-regulated proteins mapping molecular pathways associated with autism spectrum disorder and schizophrenia. These findings offer new perspectives on the complex protein networks influenced by D-aspartate metabolism in the developing brain and highlight its potential impact on cerebral function in health and psychiatric disorders.
Multiomics approach identifies dysregulated lipidomic and proteomic networks in Parkinson’s disease patients mutated in TMEM175 Federica Carrillo, Marco Ghirimoldi, Giorgio Fortunato, Nicole Piera Palomba, Laura Ianiro, Veronica De Giorgis, Shahzaib Khoso, Tiziana Giloni, Sara Pietracupa, Nicola Modugno, Elettra Barberis, Marcello Manfredi, Teresa Esposito Npj Parkinson S Disease, 2025 Parkinson's disease (PD) represents one of the most frequent neurodegenerative disorders for which clinically useful biomarkers remain to be identified and validated. Here, we adopted an untargeted omics approach to disclose lipidomic, metabolomic and proteomic alterations in plasma and in dermal fibroblasts of PD patients carrying mutations in TMEM175 gene. We revealed a wide dysregulation of lysosome, autophagy, and mitochondrial pathways in these patients, supporting a role of this channel in regulating these cellular processes. The most significant altered lipid classes were Fatty acyls, Glycerophospholipids and Phosphosphingolipids. The plasma level of Phosphatidylcholines (PC) and Phosphatidylinositol (PI) 34:1 significantly correlated with an earlier age at onset of the disease in TMEM175 patients (p = 0.008; p = 0.006). In plasma we also observed altered amino acids metabolic pathways in PD patients. We highlighted that increased level of L-glutamate strongly correlated (p < 0.001) with the severity of motor and non-motor symptoms in PD_TMEM175 patients. In dermal fibroblasts, we disclosed alterations of proteins involved in lipids biosynthesis (PAG15, PP4P1, GALC, FYV1, PIGO, PGPS1, PLPP1), in the insulin pathway (IGF2R), in mitochondrial metabolism (ACD10, ACD11, ACADS) and autophagy (RAB7L). Interestingly, we quantified 43 lysosomal or lysosomal-related proteins, which were differentially modulated between TMEM175 patients and controls. Integrative correlation analysis of proteome and lipidome of PD_TMEM175 cellular models identified a strong positive correlation of 13 proteins involved in biosynthetic processes with PC and Ceramides. Altogether, these data provide novel insights into the molecular and metabolic alterations underlying TMEM175 mutations and may be relevant for PD prediction, diagnosis and treatment.
Preclinical and clinical study on type 3 metabotropic glutamate receptors in Parkinson’s disease Luisa Di Menna, Marika Alborghetti, Maria Ilenia De Bartolo, Marina Borro, Giovanna Gentile, Manuela Zinni, Matteo Bologna, Carolina Cutrona, Giovanna D’Errico, Tiziana Imbriglio, Domenico Bucci, Sara Merlo, Roxana Paula Ginerete, Rosamaria Orlando, Federica Carrillo, Giorgio Fortunato, Milena Cannella, Maria Angela Sortino, Julien Pansiot, Olivier Baud, Ferdinando Nicoletti, Valeria Bruno, Maurizio Simmaco, Francesco Ernesto Pontieri, Edoardo Bianchini, Domiziana Rinaldi, Amalia de Curtis, Giovanni De Gaetano, Licia Iacoviello, Teresa Esposito, Alfredo Berardelli, Giuseppe Battaglia Npj Parkinson S Disease, 2025 Metabotropic glutamate (mGlu) receptors are candidate drug targets for therapeutic intervention in Parkinson’s disease (PD). Here we focused on mGlu3, a receptor subtype involved in synaptic regulation and neuroinflammation. mGlu3 −/− mice showed an enhanced nigro-striatal damage and microglial activation in response to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Expression of genes encoding anti-inflammatory proteins and neuroprotective factors was reduced in the striatum of MPTP-treated mGlu3 −/− mice. We also examined polymorphic variants of GRM3 (the mGlu3 receptor encoding gene) in 723 PD patients and 826 healthy controls. Two GRM3 haplotypes were associated with PD, and gene variants correlated with motor and non-motor signs. Interestingly, PD patients carrying each of the two haplotypes showed an impaired cortical plasticity in the paired associated stimulation paradigm of magnetic transcranial stimulation. These findings suggest that mGlu3 receptors are neuroprotective in mouse models of parkinsonism and shape mechanisms of cortical plasticity in PD.
Deep brain stimulation rescues the homeostasis disruption of circulating D- and L-amino acids level in men with Parkinson's disease Tommaso Nuzzo, Federica Carrillo, Marcello Serra, Claudia Gentile, Anna Di Maio, Alessandra Pizzella, Sara Pietracupa, Nicola Modugno, Francesco Errico, Teresa Esposito, Alessandro Usiello Neurobiology of Disease, 2025 Recent evidence indicates a marked downregulation of circulating D- and L-amino acids involved in regulating glutamatergic NMDAR function in Parkinson's disease (PD) patients compared with matched controls. However, the extent to which disease progression and antiparkinsonian therapies contribute to this dysregulation remains unclear. To address these issues, in the present study we measured by High Performance Liquid Chromatography the concentrations of glutamatergic system-related D- and L-amino acids and their precursors in the plasma of male and female healthy controls (HC) and PD patients across three distinct clinical stages and treatment conditions: (1) early stage L-DOPA naïve patients treated with MAO-B inhibitors; (2) mid-stage patients treated with L-DOPA; and (3) advanced stage patients receiving Deep Brain Stimulation in the subthalamic nucleus (STN-DBS) plus L-DOPA. Our results reveal notable reduction of circulating neuroactive D- and L-amino acids exclusively in male PD patients, while female patients exhibit a similar directional trend. In male patients, this dysregulation manifests early, with L-DOPA-naïve individuals showing decreased plasma levels of L-glutamate and L-aspartate. In mid-stage L-DOPA-treated PD patients, amino acid reductions extend to L-alanine, L-serine, L-glutamine, L-asparagine, and L-threonine. Remarkably, in advanced PD patients, with a median disease duration of ∼ 23 years, STN-DBS normalizes the blood concentrations of these amino acids to those observed in HC. In conclusion, our study highlights the potential of circulating D- and L-amino acid dysregulation as an early biomarker of PD and demonstrates that, in contrast to L-DOPA therapy, the STN-DBS confers systemic metabolic benefits even at advanced stages of the disease.
ANKK1, ANKRD50, GRK5, PACSIN1 and VPS8 are novel candidate genes associated with late onset Parkinson's disease: Definition of a novel predictive protocol based on polygenic model of inheritance Federica Carrillo, Nicole Piera Palomba, Sara Pietracupa, Laura Ianiro, Giorgio Fortunato, Margherita Degasperi, Tiziana Giloni, Maria Ilenia De Bartolo, Luigi Pavone, Teresa Nutile, Nicola Modugno, Danilo Licastro, Teresa Esposito Neurobiology of Disease, 2025 Parkinson's disease (PD) represents one of the most frequent neurodegenerative disorders for which genetic diagnosis is still challenging due to the high genetic heterogeneity associated with the disease and to the difficulty in interpreting test results. We have recently reported the identification of rare new gene variants in PD patients that support polygenic contribution to the disease. Here we report the identification of novel candidate PD genes and an exploratory protocol for predictive analysis of PD risk. The study includes the whole exome data of 22 PD families, 300 unrelated familiar PD, 504 unrelated sporadic PD and 664 healthy subjects. Family-based approach identified rare and disrupting variants in 44 candidate PD genes co-inherited by affected relatives. The analysis of the entire cohort discovered a significant excess of rare and deleterious variants in PD patients compared to controls in 7 genes out of the 44 identified in the families. Five of these, known as ANKK1, ANKRD50, GRK5, PACSIN1 and VPS8, were novel candidate PD genes, expressed in human dopaminergic neurons, and involved in signal transduction pathways and in endocytic recycling. In these genes, we identified both rare probably damaging variants, altering protein structure and dynamics, as well as frequent variants associated with PD risk. Moreover, we demonstrated that the co-inheritance of multiple rare variants (≥ 2) in a panel of 37 PD genes selected in this study, may predict disease risk in about 26 % of patients, both familial and sporadic cases, with high specificity (> 92 %; p ≤0.00001). Furthermore, patients carrying multiple rare variants showed higher risk of manifesting dyskinesia induced by levodopa treatment (p = 0.004), severe cognitive impairment (p = 0.009) and an earlier age at onset of the disease (p = 0.01). Despite the still exploratory nature of the study, these data provide novel insights into the genetic of PD and may be relevant for its prediction, diagnosis and treatment.
Multiomics approach discloses lipids and metabolites profiles associated to Parkinson's disease stages and applied therapies Federica Carrillo, Nicole Piera Palomba, Marco Ghirimoldi, Camilla Didò, Giorgio Fortunato, Shahzaib Khoso, Tiziana Giloni, Marco Santilli, Tommaso Bocci, Alberto Priori, Sara Pietracupa, Nicola Modugno, Elettra Barberis, Marcello Manfredi, Paola Signorelli, Teresa Esposito Neurobiology of Disease, 2024 Profiling circulating lipids and metabolites in Parkinson's disease (PD) patients could be useful not only to highlight new pathways affected in PD condition but also to identify sensitive and effective biomarkers for early disease detection and potentially effective therapeutic interventions. In this study we adopted an untargeted omics approach in three groups of patients (No L-Dopa, L-Dopa and DBS) to disclose whether long-term levodopa treatment with or without deep brain stimulation (DBS) could reflect a characteristic lipidomic and metabolomic signature at circulating level. Our findings disclosed a wide up regulation of the majority of differentially regulated lipid species that increase with disease progression and severity. We found a relevant modulation of triacylglycerols and acyl-carnitines, together with an altered profile in adiponectin and leptin, that can differentiate the DBS treated group from the others PD patients. We found a highly significant increase of exosyl ceramides (Hex2Cer) and sphingoid bases (SPB) in PD patients mainly in DBS group ( p < 0.0001), which also resulted in a highly accurate diagnostic performance. At metabolomic level, we found a wide dysregulation of pathways involved in the biosynthesis and metabolism of several amino acids. The most interesting finding was the identification of a specific modulation of L-glutamic acid in the three groups of patients. L-glutamate levels increased slightly in No L-Dopa and highly in L-Dopa patients while decreased in DBS, suggesting that DBS therapy might have a beneficial effect on the glutamatergic cascade. All together, these data provide novel insights into the molecular and metabolic alterations underlying PD therapy and might be relevant for PD prediction, diagnosis and treatment. • Hex2Cer and SPB correlated with PD severity and are effective biomarkers for PD • Dysregulation of amino acids metabolism is associated with different treatments • DBS therapy might have a beneficial effect on the glutamatergic cascade • Isoleucine and Valine correlated with severity of motor and non-motor symptoms • Data integration highlighted dysregulation of Glutathione and Tyrosine pathways
Common and Rare Variants in TMEM175 Gene Concur to the Pathogenesis of Parkinson’s Disease in Italian Patients Nicole Piera Palomba, Giorgio Fortunato, Giuseppe Pepe, Nicola Modugno, Sara Pietracupa, Immacolata Damiano, Giada Mascio, Federica Carrillo, Luca Giovanni Di Giovannantonio, Laura Ianiro, Katiuscia Martinello, Viola Volpato, Vincenzo Desiato, Riccardo Acri, Marianna Storto, Ferdinando Nicoletti, Caleb Webber, Antonio Simeone, Sergio Fucile, Vittorio Maglione, Teresa Esposito Molecular Neurobiology, 2023 Parkinson’s disease (PD) represents the most common neurodegenerative movement disorder. We recently identified 16 novel genes associated with PD. In this study, we focused the attention on the common and rare variants identified in the lysosomal K+ channel TMEM175. The study includes a detailed clinical and genetic analysis of 400 cases and 300 controls. Molecular studies were performed on patient-derived fibroblasts. The functional properties of the mutant channels were assessed by patch-clamp technique and co-immunoprecipitation. We have found that TMEM175 was highly expressed in dopaminergic neurons of the substantia nigra pars compacta and in microglia of the cerebral cortex of the human brain. Four common variants were associated with PD, including two novel variants rs2290402 (c.-10C > T) and rs80114247 (c.T1022C, p.M341T), located in the Kozak consensus sequence and TM3II domain, respectively. We also disclosed 13 novel highly penetrant detrimental mutations in the TMEM175 gene associated with PD. At least nine of these mutations (p.R35C, p. R183X, p.A270T, p.P308L, p.S348L, p. L405V, p.R414W, p.P427fs, p.R481W) may be sufficient to cause the disease, and the presence of mutations of other genes correlated with an earlier disease onset. In vitro functional analysis of the ion channel encoded by the mutated TMEM175 gene revealed a loss of the K+ conductance and a reduced channel affinity for Akt. Moreover, we observed an impaired autophagic/lysosomal proteolytic flux and an increase expression of unfolded protein response markers in patient-derived fibroblasts. These data suggest that mutations in TMEM175 gene may contribute to the pathophysiology of PD.
NCOA4 links iron bioavailability to DNA metabolism Giorgia Federico, Federica Carrillo, Francesca Dapporto, Mario Chiariello, Massimo Santoro, Roberto Bellelli, Francesca Carlomagno Cell Reports, 2022 Iron is essential for deoxyribonucleotides production and for enzymes containing an Fe-S cluster involved in DNA replication and repair. How iron bioavailability and DNA metabolism are coordinated remains poorly understood. NCOA4 protein mediates autophagic degradation of ferritin to maintain iron homeostasis and inhibits DNA replication origin activation via hindrance of the MCM2-7 DNA helicase. Here, we show that iron deficiency inhibits DNA replication, parallel to nuclear NCOA4 stabilization. In iron-depleted cells, NCOA4 knockdown leads to unscheduled DNA synthesis, with replication stress, genome instability, and cell death. In mice, NCOA4 genetic inactivation causes defective intestinal regeneration upon dextran sulfate sodium-mediated injury, with DNA damage, defective cell proliferation, and cell death; in intestinal organoids, this is fostered by iron depletion. In summary, we describe a NCOA4-dependent mechanism that coordinates iron bioavailability and DNA replication. This function prevents replication stress, maintains genome integrity, and sustains high rates of cell proliferation during tissue regeneration.
NCOA4-mediated ferritinophagy in macrophages is crucial to sustain erythropoiesis in mice Antonella Nai, Maria Rosa Lidonnici, Giorgia Federico, Mariateresa Pettinato, Violante Olivari, Federica Carrillo, Simonetta Geninatti Crich, Giuliana Ferrari, Clara Camaschella, Laura Silvestri, Francesca Carlomagno Haematologica, 2021 The Nuclear Receptor Coactivator 4 (NCOA4) promotes ferritin degradation and Ncoa4-ko mice in C57BL/6 background show microcytosis and mild anemia, aggravated by iron deficiency. To understand tissue specific contribution of NCOA4-mediated ferritinophagy we explored the effect of Ncoa4 genetic ablation in the iron-rich strain Sv129/J. Increased body iron content protects mice from anemia and, in basal conditions, Sv129/J Ncoa4-ko mice show only microcytosis; nevertheless, when fed a low-iron diet they develop a more severe anemia compared to wild-type animals. Reciprocal bone marrow (BM) transplantation from wild-type donors into Ncoa4-ko and from Ncoa4-ko into wild-type mice revealed that microcytosis and susceptibility to iron deficiency anemia depend on BM-derived cells. Erythropoiesis reconstitution with RBC count and hemoglobin normalization occurred at the same rate in transplanted animals independently of the genotype. Importantly, NCOA4 loss did not affect terminal erythropoiesis in iron deficiency, both in total and specific BM Ncoa4-ko animals compared to controls. On the contrary, upon a low iron diet, spleen from wild-type animals with Ncoa4-ko BM displayed marked iron retention compared to (wild-type BM) controls, indicating defective macrophage iron release in the former. Thus, EPO administration failed to mobilize iron from stores in Ncoa4-ko animals. Furthermore, Ncoa4 inactivation in thalassemic mice did not worsen the hematological phenotype. Overall our data reveal a major role for NCOA4-mediated ferritinophagy in macrophages to favor iron release for erythropoiesis, especially in iron deficiency.
