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Pecoraro M, Catanzaro G, Conte F, Besharat ZM, Messina E, Laschena L, Trocchianesi S, Splendiani E, Sciarra A, Catalano C, Paci P, Ferretti E, Panebianco V. Prospective Validation Study of a Novel Integrated Pathway Based on Clinical Features, Magnetic Resonance Imaging Biomarkers, and MicroRNAs for Early Detection of Prostate Cancer. Eur Urol Oncol 2024; 7:73-82. [PMID: 37270379 DOI: 10.1016/j.euo.2023.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/03/2023] [Accepted: 05/19/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is the most diagnosed cancer in men, with an increasing need to integrate noninvasive imaging and circulating microRNAs beyond prostate-specific antigen for screening and early detection. OBJECTIVE To validate magnetic resonance imaging (MRI) biomarkers and circulating microRNAs as triage tests for patients directed to prostate biopsy, and to test different diagnostic pathways to compare their performance on patients' outcome, in terms of unnecessary biopsy avoidance. DESIGN, SETTING, AND PARTICIPANTS A prospective single-center cohort study, enrolling patients with PCa suspicion who underwent MRI, MRI-directed fusion biopsy (MRDB), and circulating microRNAs, was conducted. A network-based analysis was used to identify MRI biomarkers and microRNA drivers of clinically significant PCa. INTERVENTION MRI, MRDB, and blood sampling. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The decision curve analysis was exploited to assess the performance of the proposed diagnostic pathways and to quantify their benefit in terms of biopsy avoidance. RESULTS AND LIMITATIONS Overall, 261 men were enrolled and underwent MRDB for PCa detection. A total of 178 patients represented the entire cohort: 55 (30.9%) were negative for PCa, 39 (21.9%) had grade group (GG) 1 PCa, and 84 (47.2%) had GG >1 PCa. The proposed integrated pathway, including clinical data, MRI biomarkers, and microRNAs, provided the best net benefit with a biopsy avoidance rate of about 20% at a low disease probability. The main limitation is the monocentric design in a referral center. CONCLUSIONS The integrated pathway represents a validated model that sees MRI biomarkers and microRNAs as a prebiopsy triage of patients at a risk for clinically significant PCa. The proposed pathway showed the highest net benefit in terms of unnecessary biopsy avoidance. PATIENT SUMMARY The proposed integrated pathway for early detection of prostate cancer (PCa) allows accurate patient allocation to biopsy and patients' stratification into risk group categories, reducing overdiagnosis and overtreatment of clinically insignificant PCa.
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Affiliation(s)
- Martina Pecoraro
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Giuseppina Catanzaro
- Department of Experimental Medicine, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Emanuele Messina
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Ludovica Laschena
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Sofia Trocchianesi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Elena Splendiani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Sciarra
- Department of Maternal Infant and Urologic Sciences, Sapienza University of Rome, Rome, Italy
| | - Carlo Catalano
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Valeria Panebianco
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, Rome, Italy.
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Vernocchi P, Marangelo C, Guerrera S, Del Chierico F, Guarrasi V, Gardini S, Conte F, Paci P, Ianiro G, Gasbarrini A, Vicari S, Putignani L. Gut microbiota functional profiling in autism spectrum disorders: bacterial VOCs and related metabolic pathways acting as disease biomarkers and predictors. Front Microbiol 2023; 14:1287350. [PMID: 38192296 PMCID: PMC10773764 DOI: 10.3389/fmicb.2023.1287350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/14/2023] [Indexed: 01/10/2024] Open
Abstract
Background Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder. Major interplays between the gastrointestinal (GI) tract and the central nervous system (CNS) seem to be driven by gut microbiota (GM). Herein, we provide a GM functional characterization, based on GM metabolomics, mapping of bacterial biochemical pathways, and anamnestic, clinical, and nutritional patient metadata. Methods Fecal samples collected from children with ASD and neurotypical children were analyzed by gas-chromatography mass spectrometry coupled with solid phase microextraction (GC-MS/SPME) to determine volatile organic compounds (VOCs) associated with the metataxonomic approach by 16S rRNA gene sequencing. Multivariate and univariate statistical analyses assessed differential VOC profiles and relationships with ASD anamnestic and clinical features for biomarker discovery. Multiple web-based and machine learning (ML) models identified metabolic predictors of disease and network analyses correlated GM ecological and metabolic patterns. Results The GM core volatilome for all ASD patients was characterized by a high concentration of 1-pentanol, 1-butanol, phenyl ethyl alcohol; benzeneacetaldehyde, octadecanal, tetradecanal; methyl isobutyl ketone, 2-hexanone, acetone; acetic, propanoic, 3-methyl-butanoic and 2-methyl-propanoic acids; indole and skatole; and o-cymene. Patients were stratified based on age, GI symptoms, and ASD severity symptoms. Disease risk prediction allowed us to associate butanoic acid with subjects older than 5 years, indole with the absence of GI symptoms and low disease severity, propanoic acid with the ASD risk group, and p-cymene with ASD symptoms, all based on the predictive CBCL-EXT scale. The HistGradientBoostingClassifier model classified ASD patients vs. CTRLs by an accuracy of 89%, based on methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, ethanol, butanoic acid, octadecane, acetic acid, skatole, and tetradecanal features. LogisticRegression models corroborated methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, skatole, and acetic acid as ASD predictors. Conclusion Our results will aid the development of advanced clinical decision support systems (CDSSs), assisted by ML models, for advanced ASD-personalized medicine, based on omics data integrated into electronic health/medical records. Furthermore, new ASD screening strategies based on GM-related predictors could be used to improve ASD risk assessment by uncovering novel ASD onset and risk predictors.
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Affiliation(s)
- Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Silvia Guerrera
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | | | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Gianluca Ianiro
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Vicari
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Life Sciences and Public Health Department, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Catanzaro G, Conte F, Trocchianesi S, Splendiani E, Bimonte VM, Mocini E, Filardi T, Po A, Besharat ZM, Gentile MC, Paci P, Morano S, Migliaccio S, Ferretti E. Network analysis identifies circulating miR-155 as predictive biomarker of type 2 diabetes mellitus development in obese patients: a pilot study. Sci Rep 2023; 13:19496. [PMID: 37945677 PMCID: PMC10636008 DOI: 10.1038/s41598-023-46516-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
Obesity is the main risk factor for many non-communicable diseases. In clinical practice, unspecific markers are used for the determination of metabolic alterations and inflammation, without allowing the characterization of subjects at higher risk of complications. Circulating microRNAs represent an attractive approach for early screening to identify subjects affected by obesity more at risk of developing connected pathologies. The aim of this study was the identification of circulating free and extracellular vesicles (EVs)-embedded microRNAs able to identify obese patients at higher risk of type 2 diabetes (DM2). The expression data of circulating microRNAs derived from obese patients (OB), with DM2 (OBDM) and healthy donors were combined with clinical data, through network-based methodology implemented by weighted gene co-expression network analysis. The six circulating microRNAs overexpressed in OBDM patients were evaluated in a second group of patients, confirming the overexpression of miR-155-5p in OBDM patients. Interestingly, the combination of miR-155-5p with serum levels of IL-8, Leptin and RAGE was useful to identify OB patients most at risk of developing DM2. These results suggest that miR-155-5p is a potential circulating biomarker for DM2 and that the combination of this microRNA with other inflammatory markers in OB patients can predict the risk of developing DM2.
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Affiliation(s)
- Giuseppina Catanzaro
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), 00185, Rome, Italy
| | - Sofia Trocchianesi
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Elena Splendiani
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Viviana Maria Bimonte
- Department of Movement, Human and Health Sciences, University of Foro Italico, 00135, Rome, Italy
| | - Edoardo Mocini
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Tiziana Filardi
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Agnese Po
- Department of Molecular Medicine, Sapienza University, 00161, Rome, Italy
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Maria Cristina Gentile
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University, 00161, Rome, Italy
| | - Susanna Morano
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy
| | - Silvia Migliaccio
- Department of Movement, Human and Health Sciences, University of Foro Italico, 00135, Rome, Italy.
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161, Rome, Italy.
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Taglino F, Cumbo F, Antognoli G, Arisi I, D'Onofrio M, Perazzoni F, Voyat R, Fiscon G, Conte F, Canevelli M, Bruno G, Mecocci P, Bertolazzi P. An ontology-based approach for modelling and querying Alzheimer's disease data. BMC Med Inform Decis Mak 2023; 23:153. [PMID: 37553569 PMCID: PMC10408169 DOI: 10.1186/s12911-023-02211-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/15/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The recent advances in biotechnology and computer science have led to an ever-increasing availability of public biomedical data distributed in large databases worldwide. However, these data collections are far from being "standardized" so to be harmonized or even integrated, making it impossible to fully exploit the latest machine learning technologies for the analysis of data themselves. Hence, facing this huge flow of biomedical data is a challenging task for researchers and clinicians due to their complexity and high heterogeneity. This is the case of neurodegenerative diseases and the Alzheimer's Disease (AD) in whose context specialized data collections such as the one by the Alzheimer's Disease Neuroimaging Initiative (ADNI) are maintained. METHODS Ontologies are controlled vocabularies that allow the semantics of data and their relationships in a given domain to be represented. They are often exploited to aid knowledge and data management in healthcare research. Computational Ontologies are the result of the combination of data management systems and traditional ontologies. Our approach is i) to define a computational ontology representing a logic-based formal conceptual model of the ADNI data collection and ii) to provide a means for populating the ontology with the actual data in the Alzheimer Disease Neuroimaging Initiative (ADNI). These two components make it possible to semantically query the ADNI database in order to support data extraction in a more intuitive manner. RESULTS We developed: i) a detailed computational ontology for clinical multimodal datasets from the ADNI repository in order to simplify the access to these data; ii) a means for populating this ontology with the actual ADNI data. Such computational ontology immediately makes it possible to facilitate complex queries to the ADNI files, obtaining new diagnostic knowledge about Alzheimer's disease. CONCLUSIONS The proposed ontology will improve the access to the ADNI dataset, allowing queries to extract multivariate datasets to perform multidimensional and longitudinal statistical analyses. Moreover, the proposed ontology can be a candidate for supporting the design and implementation of new information systems for the collection and management of AD data and metadata, and for being a reference point for harmonizing or integrating data residing in different sources.
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Affiliation(s)
- Francesco Taglino
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy.
| | - Fabio Cumbo
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, 44195, Cleveland, Ohio, USA
| | - Giulia Antognoli
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
| | - Ivan Arisi
- European Brain Research Institute (EBRI) "Rita Levi-Montalcini", Viale Regina Elena 295, 00161, Rome, Italy
| | - Mara D'Onofrio
- European Brain Research Institute (EBRI) "Rita Levi-Montalcini", Viale Regina Elena 295, 00161, Rome, Italy
| | - Federico Perazzoni
- Department of Engineering, Uninettuno International University, Corso Vittorio Emanuele II 39, 00186, Rome, Italy
| | - Roger Voyat
- Department of Engineering, University of Roma Tre, Via della Vasca Navale 79/81, 00146, Rome, Italy
| | - Giulia Fiscon
- Department of Computer, Control, and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Via Ariosto 25, 00185, Rome, Italy
| | - Federica Conte
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
| | - Marco Canevelli
- Department of Human Neuroscience, Sapienza University of Rome, Via Ariosto 25, 00185, Rome, Italy
| | - Giuseppe Bruno
- Department of Human Neuroscience, Sapienza University of Rome, Via Ariosto 25, 00185, Rome, Italy
| | - Patrizia Mecocci
- Department of Medicine and Surgery, University of Perugia, Piazzale Gambuli 1, 06129, Perugia, Italy
- Division of Clinical Geriatrics, NVS Department, Karolinska Institutet, Nobels väg 5, Solna, 17177, Stockholm, Sweden
| | - Paola Bertolazzi
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
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Conte F, Noga MJ, van Scherpenzeel M, Veizaj R, Scharn R, Sam JE, Palumbo C, van den Brandt FCA, Freund C, Soares E, Zhou H, Lefeber DJ. Isotopic Tracing of Nucleotide Sugar Metabolism in Human Pluripotent Stem Cells. Cells 2023; 12:1765. [PMID: 37443799 PMCID: PMC10340731 DOI: 10.3390/cells12131765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/14/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Metabolism not only produces energy necessary for the cell but is also a key regulator of several cellular functions, including pluripotency and self-renewal. Nucleotide sugars (NSs) are activated sugars that link glucose metabolism with cellular functions via protein N-glycosylation and O-GlcNAcylation. Thus, understanding how different metabolic pathways converge in the synthesis of NSs is critical to explore new opportunities for metabolic interference and modulation of stem cell functions. Tracer-based metabolomics is suited for this challenge, however chemically-defined, customizable media for stem cell culture in which nutrients can be replaced with isotopically labeled analogs are scarcely available. Here, we established a customizable flux-conditioned E8 (FC-E8) medium that enables stem cell culture with stable isotopes for metabolic tracing, and a dedicated liquid chromatography mass-spectrometry (LC-MS/MS) method targeting metabolic pathways converging in NS biosynthesis. By 13C6-glucose feeding, we successfully traced the time-course of carbon incorporation into NSs directly via glucose, and indirectly via other pathways, such as glycolysis and pentose phosphate pathways, in induced pluripotent stem cells (hiPSCs) and embryonic stem cells. Then, we applied these tools to investigate the NS biosynthesis in hiPSC lines from a patient affected by deficiency of phosphoglucomutase 1 (PGM1), an enzyme regulating the synthesis of the two most abundant NSs, UDP-glucose and UDP-galactose.
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Affiliation(s)
- Federica Conte
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marek J. Noga
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | - Raisa Veizaj
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rik Scharn
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Juda-El Sam
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chiara Palumbo
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | | | - Eduardo Soares
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam Neuroscience, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Huiqing Zhou
- Department of Neurology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam Neuroscience, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Dirk J. Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- GlycoMScan B.V., 5349 AB Oss, The Netherlands
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Conte F, Rinaldi L, Gerosa T, Mondini S, Costantini G, Girelli L. Cognitive Reserve Potential: Capturing Cognitive Resilience Capability in Adolescence. Assessment 2023:10731911231183363. [PMID: 37394752 DOI: 10.1177/10731911231183363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cognitive reserve (CR) represents the adaptive response of the cognitive system responsible for preserving normal functioning in the face of brain damage. Experiential factors such as education, occupation, and leisure activities influence the development of CR. Theoretically, such factors build up from childhood and across adulthood. Thus, appropriate tools to define and measure CR as early as adolescence are essential to understand its developmental processes. To this aim, we introduce the construct of "Cognitive Reserve Potential" (CRP) and its corresponding index of experiential factors tailored to youth. We investigated prototypical youth exposures potentially associated with the lifelong development of CR (e.g., sport practice, musical experiences, cultural activities, and relationships with peers and family). Principal component analysis and confirmatory factor analysis identified and replicated the CRP factor structure on two independent samples of Italian students: N = 585 (295 F) and N = 351 (201 F), ages 11 to 20. CRP was associated mainly with family socio-cultural status (i.e., socioeconomic status [SES], Home Possessions, and Books at Home). Results confirmed the strength of the factorial model and warranted the proposal of the CRP-questionnaire as an innovative tool for understanding CR evolutionary dynamics.
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Affiliation(s)
| | - Luca Rinaldi
- University of Pavia, Italy
- IRCCS Mondino Foundation, Pavia, Italy
| | | | | | | | - Luisa Girelli
- University of Milano-Bicocca, Italy
- Milan Center for Neuroscience, Milano, Italy
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Castiglioni M, Caldiroli CL, Procaccia R, Conte F, Neimeyer RA, Zamin C, Paladino A, Negri A. The Up-Side of the COVID-19 Pandemic: Are Core Belief Violation and Meaning Making Associated with Post-Traumatic Growth? Int J Environ Res Public Health 2023; 20:5991. [PMID: 37297595 PMCID: PMC10252371 DOI: 10.3390/ijerph20115991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
The negative impact of the COVID-19 pandemic on mental health has been extensively documented, while its possible positive impact on the individual, defined as Post-Traumatic Growth (PTG), has been much less investigated. The present study examines the association between PTG and socio-demographic aspects, pre-pandemic psychological adjustment, stressors directly linked to COVID-19 and four psychological factors theoretically implicated in the change processes (core belief violation, meaning-making, vulnerability and mortality perception). During the second wave of the pandemic 680 medical patients completed an online survey on direct and indirect COVID-19 stressors, health and demographic information, post-traumatic growth, core belief violation, meaning-making capacity, feelings of vulnerability and perceptions of personal mortality. Violation of core beliefs, feelings of vulnerability and mortality, and pre-pandemic mental illness positively correlated with post-traumatic growth. Moreover, the diagnosis of COVID-19, stronger violation of core beliefs, greater meaning-making ability, and lower pre-existing mental illness predicted greater PTG. Finally, a moderating effect of meaning-making ability was found. The clinical implications were discussed.
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Affiliation(s)
- Marco Castiglioni
- Department of Human Sciences “R. Massa”, University of Milano Bicocca, 20126 Milano, Italy;
| | | | | | - Federica Conte
- Department of Psychology, University of Milano Bicocca, 20126 Milano, Italy;
| | | | - Claudia Zamin
- Italian Society of Relationship Psychoanalysis, 20135 Milano, Italy
| | - Anna Paladino
- Department of Human and Social Sciences, University of Bergamo, 24129 Bergamo, Italy (A.N.)
| | - Attà Negri
- Department of Human and Social Sciences, University of Bergamo, 24129 Bergamo, Italy (A.N.)
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Conte F, Sam JE, Lefeber DJ, Passier R. Metabolic Cardiomyopathies and Cardiac Defects in Inherited Disorders of Carbohydrate Metabolism: A Systematic Review. Int J Mol Sci 2023; 24:ijms24108632. [PMID: 37239976 DOI: 10.3390/ijms24108632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Heart failure (HF) is a progressive chronic disease that remains a primary cause of death worldwide, affecting over 64 million patients. HF can be caused by cardiomyopathies and congenital cardiac defects with monogenic etiology. The number of genes and monogenic disorders linked to development of cardiac defects is constantly growing and includes inherited metabolic disorders (IMDs). Several IMDs affecting various metabolic pathways have been reported presenting cardiomyopathies and cardiac defects. Considering the pivotal role of sugar metabolism in cardiac tissue, including energy production, nucleic acid synthesis and glycosylation, it is not surprising that an increasing number of IMDs linked to carbohydrate metabolism are described with cardiac manifestations. In this systematic review, we offer a comprehensive overview of IMDs linked to carbohydrate metabolism presenting that present with cardiomyopathies, arrhythmogenic disorders and/or structural cardiac defects. We identified 58 IMDs presenting with cardiac complications: 3 defects of sugar/sugar-linked transporters (GLUT3, GLUT10, THTR1); 2 disorders of the pentose phosphate pathway (G6PDH, TALDO); 9 diseases of glycogen metabolism (GAA, GBE1, GDE, GYG1, GYS1, LAMP2, RBCK1, PRKAG2, G6PT1); 29 congenital disorders of glycosylation (ALG3, ALG6, ALG9, ALG12, ATP6V1A, ATP6V1E1, B3GALTL, B3GAT3, COG1, COG7, DOLK, DPM3, FKRP, FKTN, GMPPB, MPDU1, NPL, PGM1, PIGA, PIGL, PIGN, PIGO, PIGT, PIGV, PMM2, POMT1, POMT2, SRD5A3, XYLT2); 15 carbohydrate-linked lysosomal storage diseases (CTSA, GBA1, GLA, GLB1, HEXB, IDUA, IDS, SGSH, NAGLU, HGSNAT, GNS, GALNS, ARSB, GUSB, ARSK). With this systematic review we aim to raise awareness about the cardiac presentations in carbohydrate-linked IMDs and draw attention to carbohydrate-linked pathogenic mechanisms that may underlie cardiac complications.
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Affiliation(s)
- Federica Conte
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Applied Stem Cell Technologies, TechMed Centre, University of Twente, 7522 NH Enschede, The Netherlands
| | - Juda-El Sam
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Robert Passier
- Department of Applied Stem Cell Technologies, TechMed Centre, University of Twente, 7522 NH Enschede, The Netherlands
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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9
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Conte F, Ashikov A, Mijdam R, van de Ven EGP, van Scherpenzeel M, Veizaj R, Mahalleh-Yousefi SP, Post MA, Huijben K, Panneman DM, Rodenburg RJT, Voermans NC, Garanto A, Koopman WJH, Wessels HJCT, Noga MJ, Lefeber DJ. In Vitro Skeletal Muscle Model of PGM1 Deficiency Reveals Altered Energy Homeostasis. Int J Mol Sci 2023; 24:ijms24098247. [PMID: 37175952 PMCID: PMC10179458 DOI: 10.3390/ijms24098247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/03/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Phosphoglucomutase 1 (PGM1) is a key enzyme for the regulation of energy metabolism from glycogen and glycolysis, as it catalyzes the interconversion of glucose 1-phosphate and glucose 6-phosphate. PGM1 deficiency is an autosomal recessive disorder characterized by a highly heterogenous clinical spectrum, including hypoglycemia, cleft palate, liver dysfunction, growth delay, exercise intolerance, and dilated cardiomyopathy. Abnormal protein glycosylation has been observed in this disease. Oral supplementation with D-galactose efficiently restores protein glycosylation by replenishing the lacking pool of UDP-galactose, and rescues some symptoms, such as hypoglycemia, hepatopathy, and growth delay. However, D-galactose effects on skeletal muscle and heart symptoms remain unclear. In this study, we established an in vitro muscle model for PGM1 deficiency to investigate the role of PGM1 and the effect of D-galactose on nucleotide sugars and energy metabolism. Genome-editing of C2C12 myoblasts via CRISPR/Cas9 resulted in Pgm1 (mouse homologue of human PGM1, according to updated nomenclature) knockout clones, which showed impaired maturation to myotubes. No difference was found for steady-state levels of nucleotide sugars, while dynamic flux analysis based on 13C6-galactose suggested a block in the use of galactose for energy production in knockout myoblasts. Subsequent analyses revealed a lower basal respiration and mitochondrial ATP production capacity in the knockout myoblasts and myotubes, which were not restored by D-galactose. In conclusion, an in vitro mouse muscle cell model has been established to study the muscle-specific metabolic mechanisms in PGM1 deficiency, which suggested that galactose was unable to restore the reduced energy production capacity.
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Affiliation(s)
- Federica Conte
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Angel Ashikov
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rachel Mijdam
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Eline G P van de Ven
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | - Raisa Veizaj
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Seyed P Mahalleh-Yousefi
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Merel A Post
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Karin Huijben
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Daan M Panneman
- Radboud Center for Mitochondrial Medicine (RCMM), Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Richard J T Rodenburg
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Werner J H Koopman
- Radboud Center for Mitochondrial Medicine (RCMM), Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marek J Noga
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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10
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Locati F, Milesi A, Conte F, Campbell C, Fonagy P, Ensink K, Parolin L. Adolescence in lockdown: The protective role of mentalizing and epistemic trust. J Clin Psychol 2023; 79:969-984. [PMID: 36256870 PMCID: PMC9874639 DOI: 10.1002/jclp.23453] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Mentalizing is the ability to interpret one's own and others' behavior as driven by intentional mental states. Epistemic trust (openness to interpersonally transmitted information) has been associated with mentalizing. Balanced mentalizing abilities allow people to cope with external and internal stressors. Studies show that social isolation imposed by the COVID-19 pandemic was highly stressful for most people, especially for adolescents. Here we examine whether mentalizing and epistemic trust were protective factors in relation to emotional distress during the lockdown. METHOD A total of 131 nonclinical adolescents, aged between 12 and 18 years, were evaluated during the lockdown using the Reflective Functioning Questionnaire for Youth, Inventory of Parent and Peer Attachment, Perceived Stress Scale, and Difficulties in Emotion Regulation Scale. RESULTS Results from network analysis showed that epistemic trust and mentalizing were negatively associated with perceived stress and emotion dysregulation. Epistemic trust in fathers was associated with level of perceived stress, and epistemic trust in mothers with emotion dysregulation. CONCLUSION These findings suggest that epistemic trust and the capacity to mentalize were low in adolescents during lockdown, and this was associated with high levels of stress. However, robust levels of epistemic trust and mentalizing may have acted as protective factors that buffered individuals from the risk of emotional dysregulation during the lockdown.
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Affiliation(s)
| | - Alberto Milesi
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
| | - Federica Conte
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
| | - Chloe Campbell
- Psychoanalysis Unit, University College London and Anna Freud National Centre for Children and Families, London, UK
| | - Peter Fonagy
- Psychoanalysis Unit, University College London and Anna Freud National Centre for Children and Families, London, UK
| | - Karin Ensink
- Faculté des sciences sociales, Université Laval, Québec, Canada
| | - Laura Parolin
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
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11
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Baranyi G, Conte F, Deary IJ, Shortt N, Thompson CW, Cox SR, Pearce J. Neighbourhood deprivation across eight decades and late-life cognitive function in the Lothian Birth Cohort 1936: a life-course study. Age Ageing 2023; 52:7136746. [PMID: 37097769 PMCID: PMC10128164 DOI: 10.1093/ageing/afad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/21/2022] [Indexed: 04/26/2023] Open
Abstract
INTRODUCTION although neighbourhood may predict late-life cognitive function, studies mostly rely on measurements at a single time point, with few investigations applying a life-course approach. Furthermore, it is unclear whether the associations between neighbourhood and cognitive test scores relate to specific cognitive domains or general ability. This study explored how neighbourhood deprivation across eight decades contributed to late-life cognitive function. METHODS data were drawn from the Lothian Birth Cohort 1936 (n = 1,091) with cognitive function measured through 10 tests at ages 70, 73, 76, 79 and 82. Participants' residential history was gathered with 'lifegrid' questionnaires and linked to neighbourhood deprivation in childhood, young adulthood and mid-to-late adulthood. Associations were tested with latent growth curve models for levels and slopes of general (g) and domain-specific abilities (visuospatial ability, memory and processing speed), and life-course associations were explored with path analysis. RESULTS higher mid-to-late adulthood neighbourhood deprivation was associated with lower age 70 levels (β = -0.113, 95% confidence intervals [CI]: -0.205, -0.021) and faster decline of g over 12 years (β = -0.160, 95%CI: -0.290, -0.031). Initially apparent findings with domain-specific cognitive functions (e.g. processing speed) were due to their shared variance with g. Path analyses suggested that childhood neighbourhood disadvantage is indirectly linked to late-life cognitive function through lower education and selective residential mobility. CONCLUSIONS to our knowledge, we provide the most comprehensive assessment of the life-course neighbourhood deprivation and cognitive ageing relationship. Living in advantaged areas in mid-to-late adulthood may directly contribute to better cognitive function and slower decline, whereas an advantaged childhood neighbourhood likely affects functioning through cognitive reserves.
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Affiliation(s)
- Gergő Baranyi
- Centre for Research on Environment, Society and Health, Institute of Geography, School of GeoSciences, The University of Edinburgh, Edinburgh, UK
| | - Federica Conte
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Niamh Shortt
- Centre for Research on Environment, Society and Health, Institute of Geography, School of GeoSciences, The University of Edinburgh, Edinburgh, UK
| | - Catharine Ward Thompson
- OPENspace Research Centre, Edinburgh College of Art, The University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Jamie Pearce
- Centre for Research on Environment, Society and Health, Institute of Geography, School of GeoSciences, The University of Edinburgh, Edinburgh, UK
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12
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Montalbano M, Piccolo P, Lionetti R, Visco-Comandini U, Agrati C, Grassi G, Meschi S, Matusali G, Conte F, Angelone F, Ettorre GM, Guglielmo N, Maggi F, Francalancia M, Mereu T, Puro V, Girardi E, D'Offizi G. Third dose of SARS-CoV2 mRNA vaccination produces robust persistent cellular and humoral immune responses in liver transplant recipients. Liver Int 2023; 43:1120-1125. [PMID: 36929682 DOI: 10.1111/liv.15557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/18/2023]
Abstract
Weaker responses have been described after two doses of anti-SARS-CoV2 vaccination in liver transplant recipients. At the Italian National Institute for Infectious Diseases, 122 liver transplant recipients (84% males, median age 64 years) were tested for humoral and cell-mediated immune response after a third doses of anti-SARS-CoV2 mRNA vaccines. Humoral response was measured by quantifying anti-receptor binding domain and neutralizing antibodies; cell-mediated response was measured by quantifying IFN-γ after stimulation of T cells with SARS-CoV-2-specific peptides. Humoral and cellular responses improved significantly compared to the second vaccine dose; 86.4% of previous non-responders to the first 2 vaccine doses (N=22) became responders. Mycophenolate mofetil-containing regimens were not associated with lower response rates to a third vaccine; shorter time since transplantation (<6 years) was associated with lower humoral and cellular responses to third vaccine. Protective antibodies against Omicron variant were detected in 60% of patients 12 weeks after third vaccine dose.
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Affiliation(s)
- Marzia Montalbano
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Paola Piccolo
- Internal Medicine, Fatebenefratelli Hospital Isola Tiberina Gemelli Isola, Rome, Italy
| | - Raffaella Lionetti
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | - Chiara Agrati
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
- Department of Pediatric Hematology and Oncology, IRCCS Bambino Gesù Hospital, Rome, Italy
| | - Germana Grassi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Silvia Meschi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Giulia Matusali
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", Rome, Italy
| | - Federica Angelone
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Giuseppe Maria Ettorre
- Division of General Surgery and Liver Transplantation, San Camillo Hospital, Rome, Italy
| | - Nicola Guglielmo
- Division of General Surgery and Liver Transplantation, San Camillo Hospital, Rome, Italy
| | - Fabrizio Maggi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | - Tiziana Mereu
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Vincenzo Puro
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Enrico Girardi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Gianpiero D'Offizi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
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13
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Nava Lauson CB, Tiberti S, Corsetto PA, Conte F, Tyagi P, Machwirth M, Ebert S, Loffreda A, Scheller L, Sheta D, Mokhtari Z, Peters T, Raman AT, Greco F, Rizzo AM, Beilhack A, Signore G, Tumino N, Vacca P, McDonnell LA, Raimondi A, Greenberg PD, Huppa JB, Cardaci S, Caruana I, Rodighiero S, Nezi L, Manzo T. Linoleic acid potentiates CD8 + T cell metabolic fitness and antitumor immunity. Cell Metab 2023; 35:633-650.e9. [PMID: 36898381 DOI: 10.1016/j.cmet.2023.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/19/2022] [Accepted: 02/15/2023] [Indexed: 03/11/2023]
Abstract
The metabolic state represents a major hurdle for an effective adoptive T cell therapy (ACT). Indeed, specific lipids can harm CD8+ T cell (CTL) mitochondrial integrity, leading to defective antitumor responses. However, the extent to which lipids can affect the CTL functions and fate remains unexplored. Here, we show that linoleic acid (LA) is a major positive regulator of CTL activity by improving metabolic fitness, preventing exhaustion, and stimulating a memory-like phenotype with superior effector functions. We report that LA treatment enhances the formation of ER-mitochondria contacts (MERC), which in turn promotes calcium (Ca2+) signaling, mitochondrial energetics, and CTL effector functions. As a direct consequence, the antitumor potency of LA-instructed CD8 T cells is superior in vitro and in vivo. We thus propose LA treatment as an ACT potentiator in tumor therapy.
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Affiliation(s)
- Carina B Nava Lauson
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Milano, Italy
| | - Silvia Tiberti
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Milano, Italy
| | - Paola A Corsetto
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti," National Research Council, Rome, Italy
| | - Punit Tyagi
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Milano, Italy
| | - Markus Machwirth
- Department of Paediatric Haematology, Oncology and Stem Cell Transplantation, University Hospital of Würzburg, Würzburg, Germany
| | - Stefan Ebert
- Department of Paediatric Haematology, Oncology and Stem Cell Transplantation, University Hospital of Würzburg, Würzburg, Germany
| | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, San Raffaele Vita-Salute University, Milano, Italy
| | - Lukas Scheller
- Interdisciplinary Center for Clinical Research (IZKF), Experimental Stem Cell Transplantation Laboratory, Würzburg University Hospital, Würzburg, Germany
| | - Dalia Sheta
- Interdisciplinary Center for Clinical Research (IZKF), Experimental Stem Cell Transplantation Laboratory, Würzburg University Hospital, Würzburg, Germany
| | - Zeinab Mokhtari
- Interdisciplinary Center for Clinical Research (IZKF), Experimental Stem Cell Transplantation Laboratory, Würzburg University Hospital, Würzburg, Germany
| | - Timo Peters
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Ayush T Raman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francesco Greco
- Fondazione Pisana per la Scienza, ONLUS, San Giuliano Terme, Italy; Institute of Life Sciences, Sant' Anna School of Advanced Studies, Pisa, Italy
| | - Angela M Rizzo
- Department of Paediatric Haematology, Oncology and Stem Cell Transplantation, University Hospital of Würzburg, Würzburg, Germany
| | - Andreas Beilhack
- Interdisciplinary Center for Clinical Research (IZKF), Experimental Stem Cell Transplantation Laboratory, Würzburg University Hospital, Würzburg, Germany
| | - Giovanni Signore
- Fondazione Pisana per la Scienza, ONLUS, San Giuliano Terme, Italy
| | - Nicola Tumino
- Immunology Research Area, Innate Lymphoid Cells Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Paola Vacca
- Immunology Research Area, Innate Lymphoid Cells Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza, ONLUS, San Giuliano Terme, Italy
| | - Andrea Raimondi
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, San Raffaele Vita-Salute University, Milano, Italy
| | - Philip D Greenberg
- Clinical Research Division and Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Johannes B Huppa
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Simone Cardaci
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ignazio Caruana
- Department of Paediatric Haematology, Oncology and Stem Cell Transplantation, University Hospital of Würzburg, Würzburg, Germany
| | - Simona Rodighiero
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Milano, Italy
| | - Luigi Nezi
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Milano, Italy
| | - Teresa Manzo
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Milano, Italy.
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14
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Corley J, Conte F, Harris SE, Taylor AM, Redmond P, Russ TC, Deary IJ, Cox SR. Predictors of longitudinal cognitive ageing from age 70 to 82 including APOE e4 status, early-life and lifestyle factors: the Lothian Birth Cohort 1936. Mol Psychiatry 2023; 28:1256-1271. [PMID: 36481934 PMCID: PMC10005946 DOI: 10.1038/s41380-022-01900-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
Discovering why some people's cognitive abilities decline more than others is a key challenge for cognitive ageing research. The most effective strategy may be to address multiple risk factors from across the life-course simultaneously in relation to robust longitudinal cognitive data. We conducted a 12-year follow-up of 1091 (at age 70) men and women from the longitudinal Lothian Birth Cohort 1936 study. Comprehensive repeated cognitive measures of visuospatial ability, processing speed, memory, verbal ability, and a general cognitive factor were collected over five assessments (age 70, 73, 76, 79, and 82 years) and analysed using multivariate latent growth curve modelling. Fifteen life-course variables were used to predict variation in cognitive ability levels at age 70 and cognitive slopes from age 70 to 82. Only APOE e4 carrier status was found to be reliably informative of general- and domain-specific cognitive decline, despite there being many life-course correlates of cognitive level at age 70. APOE e4 carriers had significantly steeper slopes across all three fluid cognitive domains compared with non-carriers, especially for memory (β = -0.234, p < 0.001) and general cognitive function (β = -0.246, p < 0.001), denoting a widening gap in cognitive functioning with increasing age. Our findings suggest that when many other candidate predictors of cognitive ageing slope are entered en masse, their unique contributions account for relatively small proportions of variance, beyond variation in APOE e4 status. We conclude that APOE e4 status is important for identifying those at greater risk for accelerated cognitive ageing, even among ostensibly healthy individuals.
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Affiliation(s)
- Janie Corley
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK.
| | - Federica Conte
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Adele M Taylor
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tom C Russ
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
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15
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De Rosa O, Malloggi S, Cellini N, Conte F, Giganti F, Ficca G. The role of immediate recall performance in delayed false memory production after sleep and wake. Sleep Med 2022. [DOI: 10.1016/j.sleep.2022.05.406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Malloggi S, Conte F, De Rosa O, Cellini N, Di Iorio I, Ficca G, Giganti F. False recalls, but not false recognitions, at the DRM paradigm are increased in subjects reporting insomnia symptoms: An online study. Sleep Med 2022; 100:347-353. [PMID: 36191402 DOI: 10.1016/j.sleep.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND In insomnia, poor sleep is accompanied by several cognitive impairments affecting prefrontal functioning that could affect source-monitoring processes and contribute to false memories production. By using a modified version of the Deese-Roediger-McDermott paradigm (DRM), we previously found that individuals suffering from insomnia produced more false memories than good sleepers adopting a free-recall task, especially for sleep-related stimuli. However, whether poor sleep affects false memory production in a task-dependent manner (i.e., free recall or recognition) remains unclear. METHODS Through an online research method, we adopted the classical DRM paradigm to investigate the production of false recalls and false recognitions in 32 subjects referring insomnia symptoms (IN group) and 37 good sleepers (GS group), addressing also executive functioning and source monitoring ability in both groups. RESULTS Compared to the GS group, the IN group produced more false memories (p = .002) and intrusions (p = .004) at the free recall task and showed a lower working memory index (p = .008). No between-groups differences emerged at the recognition task. Correlational analysis revealed significant associations between DRM performance, executive functioning and source monitoring (SM) variables. Moreover, false recalls were predicted by being in the presence of insomnia symptoms (p = .012) and intrusions by the number of correct responses to the Stroop task (p = .051) and SM task (p = .015), as well as by the presence of insomnia symptoms (p = .003). CONCLUSIONS Our data show that the presence of insomnia symptoms can influence false memories production. Furthermore, the evidence that free recall is more affected than recognition suggests that poor sleep mainly affects performance at more cognitively demanding tasks. Finally, correlational and regression analyses support the hypothesis of a link between false memories production and both the presence of insomnia symptoms and executive functioning impairments.
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Affiliation(s)
- S Malloggi
- Department of NEUROFARBA, University of Florence, Via di San Salvi 12, 50135, Florence, Italy.
| | - F Conte
- Department of Psychology, University of Campania L. Vanvitelli, Viale Ellittico 31, 81100, Caserta, Italy.
| | - O De Rosa
- Department of Psychology, University of Campania L. Vanvitelli, Viale Ellittico 31, 81100, Caserta, Italy.
| | - N Cellini
- Department of General Psychology, University of Padova, Via Venezia, 8, 35131, Padova, Italy.
| | - I Di Iorio
- Department of NEUROFARBA, University of Florence, Via di San Salvi 12, 50135, Florence, Italy.
| | - G Ficca
- Department of Psychology, University of Campania L. Vanvitelli, Viale Ellittico 31, 81100, Caserta, Italy.
| | - F Giganti
- Department of NEUROFARBA, University of Florence, Via di San Salvi 12, 50135, Florence, Italy.
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Pepe J, Rossi M, Battafarano G, Vernocchi P, Conte F, Marzano V, Mariani E, Mortera SL, Cipriani C, Rana I, Buonuomo PS, Bartuli A, De Martino V, Pelle S, Pascucci L, Toniolo RM, Putignani L, Minisola S, Del Fattore A. Characterization of Extracellular Vesicles in Osteoporotic Patients Compared to Osteopenic and Healthy Controls. J Bone Miner Res 2022; 37:2186-2200. [PMID: 36053959 PMCID: PMC10086946 DOI: 10.1002/jbmr.4688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 11/06/2022]
Abstract
Extracellular vesicles (EVs) are mediators of a range of pathological conditions. However, their role in bone loss disease has not been well understood. In this study we characterized plasma EVs of 54 osteoporotic (OP) postmenopausal women compared to 48 osteopenic (OPN) and 44 healthy controls (CN), and we investigated their effects on osteoclasts and osteoblasts. We found no differences between the three groups in terms of anthropometric measurements and biochemical evaluation of serum calcium, phosphate, creatinine, PTH, 25-hydroxy vitamin D and bone biomarkers, except for an increase of CTX level in OP group. FACS analysis revealed that OP patients presented a significantly increased number of EVs and RANKL+ EVs compared with both CN and OPN subjects. Total EVs are negatively associated with the lumbar spine T-score and femoral neck T-score. Only in the OPN patients we observed a positive association between the total number of EVs and RANKL+ EVs with the serum RANKL. In vitro studies revealed that OP EVs supported osteoclastogenesis of healthy donor peripheral blood mononuclear cells at the same level observed following RANKL and M-CSF treatment, reduced the ability of mesenchymal stem cells to differentiate into osteoblasts, while inducing an increase of OSTERIX and RANKL expression in mature osteoblasts. The analysis of miRNome revealed that miR-1246 and miR-1224-5p were the most upregulated and downregulated in OP EVs; the modulated EV-miRNAs in OP and OPN compared to CN are related to osteoclast differentiation, interleukin-13 production and regulation of canonical WNT pathway. A proteomic comparison between OPN and CN EVs evidenced a decrease in fibrinogen, vitronectin, and clusterin and an increase in coagulation factors and apolipoprotein, which was also upregulated in OP EVs. Interestingly, an increase in RANKL+ EVs and exosomal miR-1246 was also observed in samples from patients affected by Gorham-Stout disease, suggesting that EVs could be good candidate as bone loss disease biomarkers. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Jessica Pepe
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Michela Rossi
- Bone Physiopathology Research Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giulia Battafarano
- Bone Physiopathology Research Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Conte
- Institute for System Analysis and Computer Science "A.Ruberti", National Research Council (CNR), Rome, Italy
| | - Valeria Marzano
- Unit of Human Microbiome, Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Eda Mariani
- Research Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Unit of Human Microbiome, Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristiana Cipriani
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Ippolita Rana
- Rare Diseases and Medical Genetic Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Paola Sabrina Buonuomo
- Rare Diseases and Medical Genetic Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Bartuli
- Rare Diseases and Medical Genetic Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Viviana De Martino
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Simone Pelle
- "Polo Sanitario San Feliciano - Villa Aurora" Clinic, Rome, Italy
| | - Luisa Pascucci
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Renato Maria Toniolo
- Department of Orthopaedics and Traumatology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Salvatore Minisola
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Andrea Del Fattore
- Bone Physiopathology Research Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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18
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Conte F, Paci P. Alzheimer's disease: insights from a network medicine perspective. Sci Rep 2022; 12:16846. [PMID: 36207441 PMCID: PMC9546925 DOI: 10.1038/s41598-022-20404-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disease that currently lacks available effective therapy. Thus, identifying novel molecular biomarkers for diagnosis and treatment of AD is urgently demanded. In this study, we exploited tools and concepts of the emerging research area of Network Medicine to unveil a novel putative disease gene signature associated with AD. We proposed a new pipeline, which combines the strengths of two consolidated algorithms of the Network Medicine: DIseAse MOdule Detection (DIAMOnD), designed to predict new disease-associated genes within the human interactome network; and SWItch Miner (SWIM), designed to predict important (switch) genes within the co-expression network. Our integrated computational analysis allowed us to enlarge the set of the known disease genes associated to AD with additional 14 genes that may be proposed as new potential diagnostic biomarkers and therapeutic targets for AD phenotype.
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Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy. .,Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy.
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19
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Vernocchi P, Ristori MV, Guerrera S, Guarrasi V, Conte F, Russo A, Lupi E, Albitar-Nehme S, Gardini S, Paci P, Ianiro G, Vicari S, Gasbarrini A, Putignani L. Gut Microbiota Ecology and Inferred Functions in Children With ASD Compared to Neurotypical Subjects. Front Microbiol 2022; 13:871086. [PMID: 35756062 PMCID: PMC9218677 DOI: 10.3389/fmicb.2022.871086] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/19/2022] [Indexed: 12/28/2022] Open
Abstract
Autism spectrum disorders (ASDs) is a multifactorial neurodevelopmental disorder. The communication between the gastrointestinal (GI) tract and the central nervous system seems driven by gut microbiota (GM). Herein, we provide GM profiling, considering GI functional symptoms, neurological impairment, and dietary habits. Forty-one and 35 fecal samples collected from ASD and neurotypical children (CTRLs), respectively, (age range, 3–15 years) were analyzed by 16S targeted-metagenomics (the V3–V4 region) and inflammation and permeability markers (i.e., sIgA, zonulin lysozyme), and then correlated with subjects’ metadata. Our ASD cohort was characterized as follows: 30/41 (73%) with GI functional symptoms; 24/41 (58%) picky eaters (PEs), with one or more dietary needs, including 10/41 (24%) with food selectivity (FS); 36/41 (88%) presenting high and medium autism severity symptoms (HMASSs). Among the cohort with GI symptoms, 28/30 (93%) showed HMASSs, 17/30 (57%) were picky eaters and only 8/30 (27%) with food selectivity. The remaining 11/41 (27%) ASDs without GI symptoms that were characterized by HMASS for 8/11 (72%) and 7/11 (63%) were picky eaters. GM ecology was investigated for the overall ASD cohort versus CTRLs; ASDs with GI and without GI, respectively, versus CTRLs; ASD with GI versus ASD without GI; ASDs with HMASS versus low ASSs; PEs versus no-PEs; and FS versus absence of FS. In particular, the GM of ASDs, compared to CTRLs, was characterized by the increase of Proteobacteria, Bacteroidetes, Rikenellaceae, Pasteurellaceae, Klebsiella, Bacteroides, Roseburia, Lactobacillus, Prevotella, Sutterella, Staphylococcus, and Haemophilus. Moreover, Sutterella, Roseburia and Fusobacterium were associated to ASD with GI symptoms compared to CTRLs. Interestingly, ASD with GI symptoms showed higher value of zonulin and lower levels of lysozyme, which were also characterized by differentially expressed predicted functional pathways. Multiple machine learning models classified correctly 80% overall ASDs, compared with CTRLs, based on Bacteroides, Lactobacillus, Prevotella, Staphylococcus, Sutterella, and Haemophilus features. In conclusion, in our patient cohort, regardless of the evaluation of many factors potentially modulating the GM profile, the major phenotypic determinant affecting the GM was represented by GI hallmarks and patients’ age.
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Affiliation(s)
- Pamela Vernocchi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Maria Vittoria Ristori
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Silvia Guerrera
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | | | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti," National Research Council, Rome, Italy
| | - Alessandra Russo
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Elisabetta Lupi
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Sami Albitar-Nehme
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | | | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Gianluca Ianiro
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" Scientific Institute for Research, Hospitalization and Healthcare, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Vicari
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Antonio Gasbarrini
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" Scientific Institute for Research, Hospitalization and Healthcare, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
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20
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Conte F, Papa F, Paci P, Farina L. StaRTrEK:in silico estimation of RNA half-lives from genome-wide time-course experiments without transcriptional inhibition. BMC Bioinformatics 2022; 23:190. [PMID: 35596139 PMCID: PMC9123730 DOI: 10.1186/s12859-022-04730-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Background Gene expression is the result of the balance between transcription and degradation. Recent experimental findings have shown fine and specific regulation of RNA degradation and the presence of various molecular machinery purposely devoted to this task, such as RNA binding proteins, non-coding RNAs, etc. A biological process can be studied by measuring time-courses of RNA abundance in response of internal and/or external stimuli, using recent technologies, such as the microarrays or the Next Generation Sequencing devices. Unfortunately, the picture provided by looking only at the transcriptome abundance may not gain insight into its dynamic regulation. By contrast, independent simultaneous measurement of RNA expression and half-lives could provide such valuable additional insight. A computational approach to the estimation of RNAs half-lives from RNA expression time profiles data, can be a low-cost alternative to its experimental measurement which may be also affected by various artifacts. Results Here we present a computational methodology, called StaRTrEK (STAbility Rates ThRough Expression Kinetics), able to estimate half-life values basing only on genome-wide gene expression time series without transcriptional inhibition. The StaRTrEK algorithm makes use of a simple first order kinetic model and of a \documentclass[12pt]{minimal}
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\begin{document}$$l_1$$\end{document}l1-norm regularized least square optimization approach to find its parameter values. Estimates provided by StaRTrEK are validated using simulated data and three independent experimental datasets of two short (6 samples) and one long (48 samples) time-courses. Conclusions We believe that our algorithm can be used as a fast valuable computational complement to time-course experimental gene expression studies by adding a relevant kinetic property, i.e. the RNA half-life, with a strong biological interpretation, thus providing a dynamic picture of what is going in a cell during the biological process under study. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04730-x.
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Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Federico Papa
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.,SysBio Centre for Systems Biology, Milan, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy.
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21
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Paci P, Fiscon G, Conte F, Wang RS, Handy DE, Farina L, Loscalzo J. Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects. NPJ Syst Biol Appl 2022; 8:12. [PMID: 35443763 PMCID: PMC9021283 DOI: 10.1038/s41540-022-00221-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/19/2022] [Indexed: 12/28/2022] Open
Abstract
Despite advances in modern medicine that led to improvements in cardiovascular outcomes, cardiovascular disease (CVD) remains the leading cause of mortality and morbidity globally. Thus, there is an urgent need for new approaches to improve CVD drug treatments. As the development time and cost of drug discovery to clinical application are excessive, alternate strategies for drug development are warranted. Among these are included computational approaches based on omics data for drug repositioning, which have attracted increasing attention. In this work, we developed an adjusted similarity measure implemented by the algorithm SAveRUNNER to reposition drugs for cardiovascular diseases while, at the same time, considering the side effects of drug candidates. We analyzed nine cardiovascular disorders and two side effects. We formulated both disease disorders and side effects as network modules in the human interactome, and considered those drug candidates that are proximal to disease modules but far from side-effects modules as ideal. Our method provides a list of drug candidates for cardiovascular diseases that are unlikely to produce common, adverse side-effects. This approach incorporating side effects is applicable to other diseases, as well.
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Affiliation(s)
- Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy. .,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Giulia Fiscon
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rui-Sheng Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Diane E Handy
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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22
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Spinato G, Fabbris C, Costantini G, Conte F, Scotton PG, Cinetto F, De Siati R, Matarazzo A, Citterio M, Contro G, De Filippis C, Agostini C, Emanuelli E, Boscolo-Rizzo P, Frezza D. The Effect of Isotonic Saline Nasal Lavages in Improving Symptoms in SARS-CoV-2 Infection: A Case-Control Study. Front Neurol 2021; 12:794471. [PMID: 34938268 PMCID: PMC8687114 DOI: 10.3389/fneur.2021.794471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mainly colonizes nasopharynx. In upper airways acute infections, e.g., the common cold, saline nasal irrigations have a significant efficacy in reducing symptoms. The present study aimed to test the efficacy of nasal lavages in upper airways symptoms of Coronavirus Disease 2019 (COVID-19). Methods: A series of consecutive adult subjects who tested positive for SARS-CoV-2 from December 2020 to February 2021 performed daily nasal lavages with saline solution (Lavonase®—Purling, Lugo di Romagna, Italy) for 12 days, starting on the day after the SARS-CoV-2 positive swab. A control group included a historical series of patients who were infected in February-March 2020 and who did not perform lavages. An ad hoc questionnaire regarding symptoms was administered to each subjects at base-line and 10 days after diagnosis (i.e., on the same day of the control swab) in both cases and controls. Results: A total of 140 subjects were enrolled. 68 participants in the treatment group and 72 in the control group were included. 90% of respondents declared the lavages were simple to use and 70% declared they were satisfied. Symptoms of blocked nose, runny nose, or sneezing decreased by an average of 24.7% after the treatment. Blocked nose and sneezing increased in the same period of time in the control group. Ears and eyes symptoms, anosmia/ageusia symptoms, and infection duration (10.53 days in the treatment group and 10.48 days in the control group) didn't vary significantly among the two groups. Conclusion: Nasal lavages resulted to significantly decrease nasal symptoms in newly diagnosed SARS-CoV-2 patients. These devices proved to be well-tolerated and easy to be used. Further studies on a larger number of subjects are needed in order to possibly confirm these preliminary results.
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Affiliation(s)
- Giacomo Spinato
- Department of Neurosciences, University of Padua, Padua, Italy
| | | | - Giulio Costantini
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
| | - Federica Conte
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
| | | | | | | | | | - Marco Citterio
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Giacomo Contro
- Department of Neurosciences, University of Padua, Padua, Italy
| | | | - Carlo Agostini
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Enzo Emanuelli
- Department of Otolaryngology, Ospedale di Treviso, Treviso, Italy
| | | | - Daniele Frezza
- Department of Otolaryngology, Ospedale di Treviso, Treviso, Italy
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23
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Malloggi S, Conte F, Albinni B, Gronchi G, Ficca G, Giganti F. Sleep and psychological characteristics in habitual self-awakeners and forced awakeners. Chronobiol Int 2021; 39:547-556. [PMID: 34872434 DOI: 10.1080/07420528.2021.2003375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Previous studies described the modifications of physiological and behavioural variables associated with self-awakening, while only few studies assessed subjective sleep quality and psychological characteristics in habitual self-awakeners. Here we investigated self-reported sleep habits and features, as well as psychological variables of habitual self-awakeners and forced-awakeners, with special regard to subjective sleep quality, personality characteristics, anxiety and depression symptoms. In our sample, the prevalence of habitual self-awakeners was 15.1%. Compared to forced-awakeners, habitual self-awakeners showed more regular sleep/wake schedules and were more frequently morning types. Moreover, habitual self-awakeners referred to be more satisfied about their sleep, to wake up more easily in the morning, to need less time to get out of bed and to feel more refreshed upon awakening than forced-awakeners. We also observed an association between the habit of self-awakening and the "ability" to set the awakening to an unusual time. Concerning psychological features, habitual self-awakeners showed higher scores in Conscientiousness and Openness and lower scores in Extraversion compared to forced-awakeners, whereas no differences between groups emerged for anxiety and depression levels. In conclusion, our findings point to an association between the habit of self-awakening and good subjective sleep quality. In this perspective, future research should objectively test in detail the effects of the self-awakening habit on sleep structure and organization, taking into account also microstructural sleep features.
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Affiliation(s)
- S Malloggi
- Department of NEUROFARBA, University of Florence, Florence, Italy
| | - F Conte
- Department of Psychology, University of Campania L. Vanvitelli, Caserta, Italy
| | - B Albinni
- Department of Psychology, University of Campania L. Vanvitelli, Caserta, Italy
| | - G Gronchi
- Department of NEUROFARBA, University of Florence, Florence, Italy
| | - G Ficca
- Department of Psychology, University of Campania L. Vanvitelli, Caserta, Italy
| | - F Giganti
- Department of NEUROFARBA, University of Florence, Florence, Italy
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24
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Spinato G, Fabbris C, Conte F, Menegaldo A, Franz L, Gaudioso P, Cinetto F, Agostini C, Costantini G, Boscolo‐Rizzo P. COVID-Q: Validation of the first COVID-19 questionnaire based on patient-rated symptom gravity. Int J Clin Pract 2021; 75:e14829. [PMID: 34510668 PMCID: PMC8646717 DOI: 10.1111/ijcp.14829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/11/2021] [Accepted: 09/03/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES The aim of the present study was to develop and validate the CoronaVirus-Disease-2019 (COVID-19) Questionnaire (COVID-Q), a novel symptom questionnaire specific for COVID-19 patients, to provide a comprehensive evaluation that may be helpful for physicians, and evaluate the questionnaire's performance in identifying subjects at higher risk of testing positive. MATERIALS AND METHODS Consecutive non-hospitalised adults who underwent nasopharyngeal-throat swab for severe-acute-respiratory-syndrome-coronavirus-2 (SARS-CoV-2) detection at Treviso Hospital in March 2020, were enrolled. Subjects were divided into positive (cases) and negative (controls). All subjects answered the COVID-Q. Patients not able to answer COVID-Q because of clinical conditions were excluded. Parallel Analysis and Principal Component Analysis identified items measuring the same dimension. The Item Response Theory (IRT)-based analyses evaluated the functioning of item categories, the presence of clusters of local dependence among items, item fit within the model and model fit to the data. RESULTS Answers obtained from 230 cases (113 males; mean age 55 years, range 20-99) and 230 controls (61 males; mean age 46 years, range 21-89) were analysed. Six components were extracted with parallel analysis: asthenia, influenza-like symptoms, ear and nose symptoms, breathing issues, throat symptoms, and anosmia/ageusia. The final IRT models retained 27 items as significant for symptom assessment. The total questionnaire's score was significantly associated with positivity to the molecular test: subjects with multiple symptoms were more likely to be affected (P < .001). Older age, male gender presence of breathing issues and anosmia/ageusia were significantly related to positivity (P < .001). Comorbidities had not a significant association with the COVID-19 diagnosis. CONCLUSION COVID-Q could be validated since the evaluated aspects were overall significantly related to infection. The application of the questionnaire to clinical practice may help to identify subjects who are likely to be affected by COVID-19 and address them to a nasopharyngeal swab in order to achieve an early diagnosis.
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Affiliation(s)
- Giacomo Spinato
- Department of NeurosciencesSection of Otolaryngology and Regional Centre for Head and Neck CancerUniversity of PadovaTrevisoItaly
- Department of Surgery, Oncology and GastroenterologySection of Oncology and ImmunologyUniversity of PadovaPadovaItaly
| | - Cristoforo Fabbris
- Department of NeurosciencesSection of Otolaryngology and Regional Centre for Head and Neck CancerUniversity of PadovaTrevisoItaly
| | - Federica Conte
- Department of PsychologyUniversity of Milano BicoccaMilanItaly
| | - Anna Menegaldo
- Department of NeurosciencesSection of Otolaryngology and Regional Centre for Head and Neck CancerUniversity of PadovaTrevisoItaly
| | - Leonardo Franz
- Department of NeurosciencesSection of Otolaryngology and Regional Centre for Head and Neck CancerUniversity of PadovaTrevisoItaly
| | - Piergiorgio Gaudioso
- Department of NeurosciencesSection of Otolaryngology and Regional Centre for Head and Neck CancerUniversity of PadovaTrevisoItaly
| | - Francesco Cinetto
- Department of MedicineClinical Immunology and HematologyUniversity of PadovaTrevisoItaly
| | - Carlo Agostini
- Department of MedicineClinical Immunology and HematologyUniversity of PadovaTrevisoItaly
| | | | - Paolo Boscolo‐Rizzo
- Section of OtorhinolaryngologyAzienda Sanitaria Universitaria Integrata di TriesteTriesteItaly
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25
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Scherpenzeel M, Conte F, Büll C, Ashikov A, Hermans E, Willems A, Tol W, Kragt E, Noga M, Moret EE, Heise T, Langereis JD, Rossing E, Zimmermann M, Rubio-Gozalbo ME, de Jonge MI, Adema GJ, Zamboni N, Boltje T, Lefeber DJ. Dynamic tracing of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs. Glycobiology 2021; 32:239-250. [PMID: 34939087 PMCID: PMC8966471 DOI: 10.1093/glycob/cwab106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 11/14/2022] Open
Abstract
Synthetic sugar analogs are widely applied in metabolic oligosaccharide engineering (MOE) and as novel drugs to interfere with glycoconjugate biosynthesis. However, mechanistic insights on their exact cellular metabolism over time are mostly lacking. We combined ion-pair ultrahigh performance liquid chromatography–triple quadrupole mass spectrometry mass spectrometry using tributyl- and triethylamine buffers for sensitive analysis of sugar metabolites in cells and organisms and identified low abundant nucleotide sugars, such as UDP-arabinose in human cell lines and CMP-sialic acid (CMP-NeuNAc) in Drosophila. Furthermore, MOE revealed that propargyloxycarbonyl (Poc)-labeled ManNPoc was metabolized to both CMP-NeuNPoc and UDP-GlcNPoc. Finally, time-course analysis of the effect of antitumor compound 3Fax-NeuNAc by incubation of B16-F10 melanoma cells with N-acetyl-D-[UL-13C6]glucosamine revealed full depletion of endogenous ManNAc 6-phosphate and CMP-NeuNAc within 24 h. Thus, dynamic tracing of sugar metabolic pathways provides a general approach to reveal time-dependent insights into the metabolism of synthetic sugars, which is important for the rational design of analogs with optimized effects.
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Affiliation(s)
- Monique Scherpenzeel
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,GlycoMScan B.V., Kloosterstraat 9, RE0329, 5349 AB Oss, The Netherlands
| | - Federica Conte
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Christian Büll
- Department of Radiation Oncology, Radiotherapy & OncoImmunology Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, Nijmegen, The Netherlands
| | - Angel Ashikov
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Esther Hermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Anke Willems
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Walinka Tol
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Else Kragt
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Marek Noga
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Ed E Moret
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Torben Heise
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Jeroen D Langereis
- Radboud Center for Infectious Diseases, Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Emiel Rossing
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, The Netherlands
| | | | - M Estela Rubio-Gozalbo
- Department of Clinical Genetics, department of Pediatrics, Maastricht University Medical Centre, Universiteitssingel 50, P.O. Box 616, box 16, 6200 MD, Maastricht, The Netherlands
| | - Marien I de Jonge
- Radboud Center for Infectious Diseases, Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Gosse J Adema
- Department of Radiation Oncology, Radiotherapy & OncoImmunology Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, Nijmegen, The Netherlands
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Thomas Boltje
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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26
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Panebianco V, Paci P, Pecoraro M, Conte F, Carnicelli G, Besharat ZM, Catanzaro G, Splendiani E, Sciarra A, Farina L, Catalano C, Ferretti E. Network Analysis Integrating microRNA Expression Profiling with MRI Biomarkers and Clinical Data for Prostate Cancer Early Detection: A Proof of Concept Study. Biomedicines 2021; 9:1470. [PMID: 34680592 PMCID: PMC8533640 DOI: 10.3390/biomedicines9101470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
The MRI of the prostate is the gold standard for the detection of clinically significant prostate cancer (csPCa). Nonetheless, MRI still misses around 11% of clinically significant disease. The aim was to comprehensively integrate tissue and circulating microRNA profiling, MRI biomarkers and clinical data to implement PCa early detection. In this prospective cohort study, 76 biopsy naïve patients underwent MRI and MRI directed biopsy. A sentinel sample of 15 patients was selected for a pilot molecular analysis. Weighted gene coexpression network analysis was applied to identify the microRNAs drivers of csPCa. MicroRNA-target gene interaction maps were constructed, and enrichment analysis performed. The ANOVA on ranks test and ROC analysis were performed for statistics. Disease status was associated with the underexpression of the miRNA profiled; a correlation was found with ADC (r = -0.51, p = 0.02) and normalized ADC values (r = -0.64, p = 0.002). The overexpression of miRNAs from plasma was associated with csPCa (r = 0.72; p = 0.02), and with PI-RADS assessment score (r = 0.73; p = 0.02); a linear correlation was found with biomarkers of diffusion and perfusion. Among the 800 profiled microRNA, eleven were identified as correlating with PCa, among which miR-548a-3p, miR-138-5p and miR-520d-3p were confirmed using the RT-qPCR approach on an additional cohort of ten subjects. ROC analysis showed an accuracy of >90%. Provided an additional validation set of the identified miRNAs on a larger cohort, we propose a diagnostic paradigm shift that sees molecular data and MRI biomarkers as the prebiopsy triage of patients at risk for PCa. This approach will allow for accurate patient allocation to biopsy, and for stratification into risk group categories, reducing overdiagnosis and overtreatment.
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Affiliation(s)
- Valeria Panebianco
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy; (M.P.); (G.C.); (C.C.)
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University, 00161 Rome, Italy; (P.P.); (L.F.)
| | - Martina Pecoraro
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy; (M.P.); (G.C.); (C.C.)
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, 00185 Rome, Italy;
| | - Giorgia Carnicelli
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy; (M.P.); (G.C.); (C.C.)
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy; (Z.M.B.); (G.C.); (E.F.)
| | - Giuseppina Catanzaro
- Department of Experimental Medicine, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy; (Z.M.B.); (G.C.); (E.F.)
| | - Elena Splendiani
- Department of Molecular Medicine, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy;
| | - Alessandro Sciarra
- Department of Maternal-Infant and Urological Sciences, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy;
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University, 00161 Rome, Italy; (P.P.); (L.F.)
| | - Carlo Catalano
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy; (M.P.); (G.C.); (C.C.)
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University, Policlinico Umberto I, 00161 Rome, Italy; (Z.M.B.); (G.C.); (E.F.)
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27
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Sibilio P, Bini S, Fiscon G, Sponziello M, Conte F, Pecce V, Durante C, Paci P, Falcone R, Norata GD, Farina L, Verrienti A. In silico drug repurposing in COVID-19: A network-based analysis. Biomed Pharmacother 2021; 142:111954. [PMID: 34358753 PMCID: PMC8316014 DOI: 10.1016/j.biopha.2021.111954] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 12/27/2022] Open
Abstract
The SARS-CoV-2 pandemic is a worldwide public health emergency. Despite the beginning of a vaccination campaign, the search for new drugs to appropriately treat COVID-19 patients remains a priority. Drug repurposing represents a faster and cheaper method than de novo drug discovery. In this study, we examined three different network-based approaches to identify potentially repurposable drugs to treat COVID-19. We analyzed transcriptomic data from whole blood cells of patients with COVID-19 and 21 other related conditions, as compared with those of healthy subjects. In addition to conventionally used drugs (e.g., anticoagulants, antihistaminics, anti-TNFα antibodies, corticosteroids), unconventional candidate compounds, such as SCN5A inhibitors and drugs active in the central nervous system, were identified. Clinical judgment and validation through clinical trials are always mandatory before use of the identified drugs in a clinical setting.
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Affiliation(s)
- Pasquale Sibilio
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy; Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Simone Bini
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy; Fondazione per la Medicina Personalizzata, Via Goffredo Mameli, 3/1, Genova, Italy
| | - Marialuisa Sponziello
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Valeria Pecce
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Cosimo Durante
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy; Department of Computer, Control, and Management Engineering, Sapienza University of Rome, Rome, Italy.
| | - Rosa Falcone
- Phase 1 Unit-Clinical Trial Center Gemelli University Hospital, Rome, Italy
| | - Giuseppe Danilo Norata
- Department of Excellence in Pharmacological and Biomolecular Sciences, University of Milan and Center for the Study of Atherosclerosis, SISA Bassini Hospital, Milan, Italy
| | - Lorenzo Farina
- Department of Computer, Control, and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Antonella Verrienti
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
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28
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Fiscon G, Conte F, Amadio S, Volonté C, Paci P. Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. Neurotherapeutics 2021; 18:1678-1691. [PMID: 33987813 PMCID: PMC8609089 DOI: 10.1007/s13311-021-01064-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
The continuous adherence to the conventional "one target, one drug" paradigm has failed so far to provide effective therapeutic solutions for heterogeneous and multifactorial diseases as amyotrophic lateral sclerosis (ALS), a rare progressive and chronic, debilitating neurological disease for which no cure is available. The present study is aimed at finding innovative solutions and paradigms for therapy in ALS pathogenesis, by exploiting new insights from Network Medicine and drug repurposing strategies. To identify new drug-ALS disease associations, we exploited SAveRUNNER, a recently developed network-based algorithm for drug repurposing, which quantifies the proximity of disease-associated genes to drug targets in the human interactome. We prioritized 403 SAveRUNNER-predicted drugs according to decreasing values of network similarity with ALS. Among catecholamine, dopamine, serotonin, histamine, and GABA receptor modulators, as well as angiotensin-converting enzymes, cyclooxygenase isozymes, and serotonin transporter inhibitors, we found some interesting no customary ALS drugs, including amoxapine, clomipramine, mianserin, and modafinil. Furthermore, we strengthened the SAveRUNNER predictions by a gene set enrichment analysis that confirmed modafinil as a drug with the highest score among the 121 identified drugs with a score > 0. Our results contribute to gathering further proofs of innovative solutions for therapy in ALS pathogenesis.
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science “A. Ruberti”, National Research Council (IASI–CNR), Via Dei Taurini 19, 00185 Rome, Italy
- Fondazione per la Medicina Personalizzata, Via Goffredo Mameli, Genova, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “A. Ruberti”, National Research Council (IASI–CNR), Via Dei Taurini 19, 00185 Rome, Italy
| | - Susanna Amadio
- IRCCS Santa Lucia Foundation, Preclinical Neuroscience, Via Del Fosso di Fiorano 65, 00143 Rome, Italy
| | - Cinzia Volonté
- Institute for Systems Analysis and Computer Science “A. Ruberti”, National Research Council (IASI–CNR), Via Dei Taurini 19, 00185 Rome, Italy
- IRCCS Santa Lucia Foundation, Preclinical Neuroscience, Via Del Fosso di Fiorano 65, 00143 Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science “A. Ruberti”, National Research Council (IASI–CNR), Via Dei Taurini 19, 00185 Rome, Italy
- Department of Computer, Control, and Management Engineering Antonio Ruberti (DIAG), Sapienza University, Rome, Italy
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29
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Fiscon G, Pegoraro S, Conte F, Manfioletti G, Paci P. Gene network analysis using SWIM reveals interplay between the transcription factor-encoding genes HMGA1, FOXM1, and MYBL2 in triple-negative breast cancer. FEBS Lett 2021; 595:1569-1586. [PMID: 33835503 DOI: 10.1002/1873-3468.14085] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 12/23/2022]
Abstract
Among breast cancer subtypes, triple-negative breast cancer (TNBC) is the most aggressive with the worst prognosis and the highest rates of metastatic disease. To identify TNBC gene signatures, we applied the network-based methodology implemented by the SWIM software to gene expression data of TNBC patients in The Cancer Genome Atlas (TCGA) database. SWIM enables to predict key (switch) genes within the co-expression network, whose perturbations in expression pattern and abundance may contribute to the (patho)biological phenotype. Here, SWIM analysis revealed an interesting interplay between the genes encoding the transcription factors HMGA1, FOXM1, and MYBL2, suggesting a potential cooperation among these three switch genes in TNBC development. The correlative nature of this interplay in TNBC was assessed by in vitro experiments, demonstrating how they may actually modulate the expression of each other.
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.,Fondazione per la Medicina Personalizzata, Genova, Italy
| | | | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | | | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.,Department of Computer, Control and Management Engineering, Sapienza University of Rome, Italy
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30
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Conte F, van Buuringen N, Voermans NC, Lefeber DJ. Galactose in human metabolism, glycosylation and congenital metabolic diseases: Time for a closer look. Biochim Biophys Acta Gen Subj 2021; 1865:129898. [PMID: 33878388 DOI: 10.1016/j.bbagen.2021.129898] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Galactose is an essential carbohydrate for cellular metabolism, as it contributes to energy production and storage in several human tissues while also being a precursor for glycosylation. Galactosylated glycoconjugates, such as glycoproteins, keratan sulfate-containing proteoglycans and glycolipids, exert a plethora of biological functions, including structural support, cellular adhesion, intracellular signaling and many more. The biological relevance of galactose is further entailed by the number of pathogenic conditions consequent to defects in galactosylation and galactose homeostasis. The growing number of rare congenital disorders involving galactose along with its recent therapeutical applications are drawing increasing attention to galactose metabolism. In this review, we aim to draw a comprehensive overview of the biological functions of galactose in human cells, including its metabolism and its role in glycosylation, and to provide a systematic description of all known congenital metabolic disorders resulting from alterations of its homeostasis.
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Affiliation(s)
- Federica Conte
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Nicole van Buuringen
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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31
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Fiscon G, Conte F, Farina L, Paci P. SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19. PLoS Comput Biol 2021; 17:e1008686. [PMID: 33544720 PMCID: PMC7891752 DOI: 10.1371/journal.pcbi.1008686] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/18/2021] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
The novelty of new human coronavirus COVID-19/SARS-CoV-2 and the lack of effective drugs and vaccines gave rise to a wide variety of strategies employed to fight this worldwide pandemic. Many of these strategies rely on the repositioning of existing drugs that could shorten the time and reduce the cost compared to de novo drug discovery. In this study, we presented a new network-based algorithm for drug repositioning, called SAveRUNNER (Searching off-lAbel dRUg aNd NEtwoRk), which predicts drug-disease associations by quantifying the interplay between the drug targets and the disease-specific proteins in the human interactome via a novel network-based similarity measure that prioritizes associations between drugs and diseases locating in the same network neighborhoods. Specifically, we applied SAveRUNNER on a panel of 14 selected diseases with a consolidated knowledge about their disease-causing genes and that have been found to be related to COVID-19 for genetic similarity (i.e., SARS), comorbidity (e.g., cardiovascular diseases), or for their association to drugs tentatively repurposed to treat COVID-19 (e.g., malaria, HIV, rheumatoid arthritis). Focusing specifically on SARS subnetwork, we identified 282 repurposable drugs, including some the most rumored off-label drugs for COVID-19 treatments (e.g., chloroquine, hydroxychloroquine, tocilizumab, heparin), as well as a new combination therapy of 5 drugs (hydroxychloroquine, chloroquine, lopinavir, ritonavir, remdesivir), actually used in clinical practice. Furthermore, to maximize the efficiency of putative downstream validation experiments, we prioritized 24 potential anti-SARS-CoV repurposable drugs based on their network-based similarity values. These top-ranked drugs include ACE-inhibitors, monoclonal antibodies (e.g., anti-IFNγ, anti-TNFα, anti-IL12, anti-IL1β, anti-IL6), and thrombin inhibitors. Finally, our findings were in-silico validated by performing a gene set enrichment analysis, which confirmed that most of the network-predicted repurposable drugs may have a potential treatment effect against human coronavirus infections.
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
- Fondazione per la Medicina Personalizzata, Genova, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
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32
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Paci P, Fiscon G, Conte F, Wang RS, Farina L, Loscalzo J. Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery. NPJ Syst Biol Appl 2021; 7:3. [PMID: 33479222 PMCID: PMC7819998 DOI: 10.1038/s41540-020-00168-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/19/2020] [Indexed: 01/29/2023] Open
Abstract
In this study, we integrate the outcomes of co-expression network analysis with the human interactome network to predict novel putative disease genes and modules. We first apply the SWItch Miner (SWIM) methodology, which predicts important (switch) genes within the co-expression network that regulate disease state transitions, then map them to the human protein-protein interaction network (PPI, or interactome) to predict novel disease-disease relationships (i.e., a SWIM-informed diseasome). Although the relevance of switch genes to an observed phenotype has been recently assessed, their performance at the system or network level constitutes a new, potentially fascinating territory yet to be explored. Quantifying the interplay between switch genes and human diseases in the interactome network, we found that switch genes associated with specific disorders are closer to each other than to other nodes in the network, and tend to form localized connected subnetworks. These subnetworks overlap between similar diseases and are situated in different neighborhoods for pathologically distinct phenotypes, consistent with the well-known topological proximity property of disease genes. These findings allow us to demonstrate how SWIM-based correlation network analysis can serve as a useful tool for efficient screening of potentially new disease gene associations. When integrated with an interactome-based network analysis, it not only identifies novel candidate disease genes, but also may offer testable hypotheses by which to elucidate the molecular underpinnings of human disease and reveal commonalities between seemingly unrelated diseases.
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Affiliation(s)
- Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- Fondazione per la Medicina Personalizzata, Via Goffredo Mameli, 3/1 Genova, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rui-Sheng Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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33
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Conte F, Fiscon G, Sibilio P, Licursi V, Paci P. An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer. Methods Mol Biol 2021; 2324:149-164. [PMID: 34165714 DOI: 10.1007/978-1-0716-1503-4_10] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pools of RNA molecules can act as competing endogenous RNAs (ceRNAs) and indirectly alter their expression levels by competitively binding shared microRNAs. This ceRNA cross talk yields an additional posttranscriptional regulatory layer, which plays key roles in both physiological and pathological processes. MicroRNAs can act as decoys by binding multiple RNAs, as well as RNAs can act as ceRNAs by competing for binding multiple microRNAs, leading to many cross talk interactions that could favor significant large-scale effects in spite of the weakness of single interactions. Identifying and studying these extended ceRNA interaction networks could provide a global view of the fine-tuning gene regulation in a wide range of biological processes and tumor progressions. In this chapter, we review current progress of predicting ceRNA cross talk, by summarizing the most up-to-date databases, which collect computationally predicted and/or experimentally validated miRNA-target and ceRNA-ceRNA interactions, as well as the widespread computational methods for discovering and modeling possible evidences of ceRNA-ceRNA interaction networks. These methods can be grouped in two categories: statistics-based methods exploit multivariate analysis to build ceRNA networks, by considering the miRNA expression levels when evaluating miRNA sponging relationships; mathematical methods build deterministic or stochastic models to analyze and predict the behavior of ceRNA cross talk.
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Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy.,Fondazione per la Medicina Personalizzata (FMP), Genova, Italy
| | - Pasquale Sibilio
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy.,Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Biology and Biotechnology Department Charles Darwin (BBCD), Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy. .,Department of Computer, Control, and Management Engineering Antonio Ruberti (DIAG), Sapienza University of Rome, Rome, Italy.
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Vernocchi P, Gili T, Conte F, Del Chierico F, Conta G, Miccheli A, Botticelli A, Paci P, Caldarelli G, Nuti M, Marchetti P, Putignani L. Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer. Int J Mol Sci 2020; 21:ijms21228730. [PMID: 33227982 PMCID: PMC7699235 DOI: 10.3390/ijms21228730] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role in disease progression through immune response, inflammation and metabolism modulation. This study focused on the use of network analysis and weighted gene co-expression network analysis (WGCNA) to identify the biological interaction between the gut ecosystem and its metabolites that could impact the immunotherapy response in non-small cell lung cancer (NSCLC) patients undergoing second-line treatment with anti-PD1. Metabolomic data were merged with operational taxonomic units (OTUs) from 16S RNA-targeted metagenomics and classified by chemometric models. The traits considered for the analyses were: (i) condition: disease or control (CTRLs), and (ii) treatment: responder (R) or non-responder (NR). Network analysis indicated that indole and its derivatives, aldehydes and alcohols could play a signaling role in GM functionality. WGCNA generated, instead, strong correlations between short-chain fatty acids (SCFAs) and a healthy GM. Furthermore, commensal bacteria such as Akkermansia muciniphila, Rikenellaceae, Bacteroides, Peptostreptococcaceae, Mogibacteriaceae and Clostridiaceae were found to be more abundant in CTRLs than in NSCLC patients. Our preliminary study demonstrates that the discovery of microbiota-linked biomarkers could provide an indication on the road towards personalized management of NSCLC patients.
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MESH Headings
- Akkermansia/classification
- Akkermansia/genetics
- Akkermansia/isolation & purification
- Alcohols/metabolism
- Aldehydes/metabolism
- Antineoplastic Agents, Immunological/therapeutic use
- Bacteroides/classification
- Bacteroides/genetics
- Bacteroides/isolation & purification
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/microbiology
- Clostridiaceae/classification
- Clostridiaceae/genetics
- Clostridiaceae/isolation & purification
- Databases, Genetic
- Disease Progression
- Drug Monitoring/methods
- Fatty Acids, Volatile/metabolism
- Gastrointestinal Microbiome/genetics
- Gastrointestinal Microbiome/immunology
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Immunotherapy/methods
- Indoles/metabolism
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/microbiology
- Metabolome/genetics
- Metabolome/immunology
- Metagenomics/methods
- Peptostreptococcus/classification
- Peptostreptococcus/genetics
- Peptostreptococcus/isolation & purification
- Precision Medicine/methods
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/immunology
- RNA, Ribosomal, 16S/genetics
- Signal Transduction
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Affiliation(s)
- Pamela Vernocchi
- Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (P.V.); (F.D.C.)
| | - Tommaso Gili
- IMT School for Advanced Studies Lucca, Networks Unit, 55100 Lucca, Italy;
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy;
| | - Federica Del Chierico
- Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (P.V.); (F.D.C.)
| | - Giorgia Conta
- Department of Chemistry, NMR-Based Metabolomics Laboratory Sapienza, University of Rome, 00185 Rome, Italy;
| | - Alfredo Miccheli
- Department of Environmental Biology and NMR-Based Metabolomics Laboratory, Sapienza University of Rome, 00185 Rome, Italy;
| | - Andrea Botticelli
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (A.B.); (P.M.)
- AOU Policlinico Umberto I, 00161 Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy;
| | - Guido Caldarelli
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari, University of Venice, 30172 Venice, Italy;
- European Centre for Living Technologies, 30172 Venice, Italy
- Institute of Complex Systems (CNR), Department of Physics, University of Rome “Sapienza”, 00185 Rome, Italy
| | - Marianna Nuti
- Department of Experimental Medicine, University Sapienza of Rome, 00185 Rome, Italy;
| | - Paolo Marchetti
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (A.B.); (P.M.)
- AOU Policlinico Umberto I, 00161 Rome, Italy
- AOU Sant’ Andrea Hospital, 00189 Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Correspondence: ; Tel.: +39-066-859-2598 (ext. 8433)
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35
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Gaglio D, Bonanomi M, Valtorta S, Bharat R, Ripamonti M, Conte F, Fiscon G, Righi N, Napodano E, Papa F, Raccagni I, Parker SJ, Cifola I, Camboni T, Paci P, Colangelo AM, Vanoni M, Metallo CM, Moresco RM, Alberghina L. Disruption of redox homeostasis for combinatorial drug efficacy in K-Ras tumors as revealed by metabolic connectivity profiling. Cancer Metab 2020; 8:22. [PMID: 33005401 PMCID: PMC7523077 DOI: 10.1186/s40170-020-00227-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/06/2020] [Indexed: 12/14/2022] Open
Abstract
Abstract Background Rewiring of metabolism induced by oncogenic K-Ras in cancer cells involves both glucose and glutamine utilization sustaining enhanced, unrestricted growth. The development of effective anti-cancer treatments targeting metabolism may be facilitated by the identification and rational combinatorial targeting of metabolic pathways. Methods We performed mass spectrometric metabolomics analysis in vitro and in vivo experiments to evaluate the efficacy of drugs and identify metabolic connectivity. Results We show that K-Ras-mutant lung and colon cancer cells exhibit a distinct metabolic rewiring, the latter being more dependent on respiration. Combined treatment with the glutaminase inhibitor CB-839 and the PI3K/aldolase inhibitor NVP-BKM120 more consistently reduces cell growth of tumor xenografts. Maximal growth inhibition correlates with the disruption of redox homeostasis, involving loss of reduced glutathione regeneration, redox cofactors, and a decreased connectivity among metabolites primarily involved in nucleic acid metabolism. Conclusions Our findings open the way to develop metabolic connectivity profiling as a tool for a selective strategy of combined drug repositioning in precision oncology.
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Affiliation(s)
- Daniela Gaglio
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, MI Italy.,ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy
| | - Marcella Bonanomi
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Silvia Valtorta
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, MI Italy.,ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Medicine and Surgery and Tecnomed Foundation, University of Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Rohit Bharat
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marilena Ripamonti
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, MI Italy.,ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy
| | - Federica Conte
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Giulia Fiscon
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Nicole Righi
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Elisabetta Napodano
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, MI Italy.,ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy
| | - Federico Papa
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Isabella Raccagni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, MI Italy.,ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Nuclear Medicine Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Seth J Parker
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA.,Moores Cancer Center, University of California, San Diego, La Jolla, CA USA
| | - Ingrid Cifola
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate, Milan, Italy
| | - Tania Camboni
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate, Milan, Italy
| | - Paola Paci
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.,Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Anna Maria Colangelo
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Vanoni
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA.,Moores Cancer Center, University of California, San Diego, La Jolla, CA USA
| | - Rosa Maria Moresco
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, MI Italy.,ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Medicine and Surgery and Tecnomed Foundation, University of Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Lilia Alberghina
- ISBE. IT/Centre of Systems Biology, Piazza della Scienza 4, 20126 Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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36
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Grimaldi AM, Conte F, Pane K, Fiscon G, Mirabelli P, Baselice S, Giannatiempo R, Messina F, Franzese M, Salvatore M, Paci P, Incoronato M. The New Paradigm of Network Medicine to Analyze Breast Cancer Phenotypes. Int J Mol Sci 2020; 21:E6690. [PMID: 32932728 PMCID: PMC7555916 DOI: 10.3390/ijms21186690] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is a heterogeneous and complex disease as witnessed by the existence of different subtypes and clinical characteristics that poses significant challenges in disease management. The complexity of this tumor may rely on the highly interconnected nature of the various biological processes as stated by the new paradigm of Network Medicine. We explored The Cancer Genome Atlas (TCGA)-BRCA data set, by applying the network-based algorithm named SWItch Miner, and mapping the findings on the human interactome to capture the molecular interconnections associated with the disease modules. To characterize BC phenotypes, we constructed protein-protein interaction modules based on "hub genes", called switch genes, both common and specific to the four tumor subtypes. Transcriptomic profiles of patients were stratified according to both clinical (immunohistochemistry) and genetic (PAM50) classifications. 266 and 372 switch genes were identified from immunohistochemistry and PAM50 classifications, respectively. Moreover, the identified switch genes were functionally characterized to select an interconnected pathway of disease genes. By intersecting the common switch genes of the two classifications, we selected a unique signature of 28 disease genes that were BC subtype-independent and classification subtype-independent. Data were validated both in vitro (10 BC cell lines) and ex vivo (66 BC tissues) experiments. Results showed that four of these hub proteins (AURKA, CDC45, ESPL1, and RAD54L) were over-expressed in all tumor subtypes. Moreover, the inhibition of one of the identified switch genes (AURKA) similarly affected all BC subtypes. In conclusion, using a network-based approach, we identified a common BC disease module which might reflect its pathological signature, suggesting a new vision to face with the disease heterogeneity.
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Affiliation(s)
- Anna Maria Grimaldi
- IRCCS SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.M.G.); (K.P.); (P.M.); (S.B.); (M.F.); (M.S.)
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy; (F.C.); (G.F.)
| | - Katia Pane
- IRCCS SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.M.G.); (K.P.); (P.M.); (S.B.); (M.F.); (M.S.)
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy; (F.C.); (G.F.)
| | - Peppino Mirabelli
- IRCCS SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.M.G.); (K.P.); (P.M.); (S.B.); (M.F.); (M.S.)
| | - Simona Baselice
- IRCCS SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.M.G.); (K.P.); (P.M.); (S.B.); (M.F.); (M.S.)
| | - Rosa Giannatiempo
- Ospedale Evangelico Betania, Via Argine 604, 80147 Naples, Italy; (R.G.); (F.M.)
| | - Francesco Messina
- Ospedale Evangelico Betania, Via Argine 604, 80147 Naples, Italy; (R.G.); (F.M.)
| | - Monica Franzese
- IRCCS SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.M.G.); (K.P.); (P.M.); (S.B.); (M.F.); (M.S.)
| | - Marco Salvatore
- IRCCS SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.M.G.); (K.P.); (P.M.); (S.B.); (M.F.); (M.S.)
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy
| | - Mariarosaria Incoronato
- IRCCS SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.M.G.); (K.P.); (P.M.); (S.B.); (M.F.); (M.S.)
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37
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Conte F, Morava E, Bakar NA, Wortmann SB, Poerink AJ, Grunewald S, Crushell E, Al-Gazali L, de Vries MC, Mørkrid L, Hertecant J, Brocke Holmefjord KS, Kronn D, Feigenbaum A, Fingerhut R, Wong SY, van Scherpenzeel M, Voermans NC, Lefeber DJ. Phosphoglucomutase-1 deficiency: Early presentation, metabolic management and detection in neonatal blood spots. Mol Genet Metab 2020; 131:135-146. [PMID: 33342467 DOI: 10.1016/j.ymgme.2020.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/19/2020] [Accepted: 08/16/2020] [Indexed: 02/07/2023]
Abstract
Phosphoglucomutase 1 deficiency is a congenital disorder of glycosylation (CDG) with multiorgan involvement affecting carbohydrate metabolism, N-glycosylation and energy production. The metabolic management consists of dietary D-galactose supplementation that ameliorates hypoglycemia, hepatic dysfunction, endocrine anomalies and growth delay. Previous studies suggest that D-galactose administration in juvenile patients leads to more significant and long-lasting effects, stressing the urge of neonatal diagnosis (0-6 months of age). Here, we detail the early clinical presentation of PGM1-CDG in eleven infantile patients, and applied the modified Beutler test for screening of PGM1-CDG in neonatal dried blood spots (DBSs). All eleven infants presented episodic hypoglycemia and elevated transaminases, along with cleft palate and growth delay (10/11), muscle involvement (8/11), neurologic involvement (5/11), cardiac defects (2/11). Standard dietary measures for suspected lactose intolerance in four patients prior to diagnosis led to worsening of hypoglycemia, hepatic failure and recurrent diarrhea, which resolved upon D-galactose supplementation. To investigate possible differences in early vs. late clinical presentation, we performed the first systematic literature review for PGM1-CDG, which highlighted respiratory and gastrointestinal symptoms as significantly more diagnosed in neonatal age. The modified Butler-test successfully identified PGM1-CDG in DBSs from seven patients, including for the first time Guthrie cards from newborn screening, confirming the possibility of future inclusion of PGM1-CDG in neonatal screening programs. In conclusion, severe infantile morbidity of PGM1-CDG due to delayed diagnosis could be prevented by raising awareness on its early presentation and by inclusion in newborn screening programs, enabling early treatments and galactose-based metabolic management.
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Affiliation(s)
- Federica Conte
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Eva Morava
- Center of Individualized Medicine, Department of Clinical Genomics, Mayo Clinic, Rochester, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA.
| | - Nurulamin Abu Bakar
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Saskia B Wortmann
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany; Department of Pediatrics, Salzburger Landeskliniken (SALK) und Paracelsus Medical University (PMU), Salzburg, Austria.
| | - Anne Jonge Poerink
- Department of Pediatrics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; Department of Pediatrics, Medisch Centrum Twente, Enschede, the Netherlands.
| | - Stephanie Grunewald
- Great Ormond Street Hospital Foundation Trust, UCL Institute of Child Health, London, Great Britain, UK.
| | - Ellen Crushell
- National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Crumlin Hospitals, Dublin, Ireland.
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine & Health Sciences, UAE University, Al-Ain, United Arab Emirates.
| | - Maaike C de Vries
- Department of Pediatrics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands.
| | - Lars Mørkrid
- Institute of Clinical Medicine, University of Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital-Rikshospitalet, Norway.
| | - Jozef Hertecant
- Genetics and Metabolics Service, Tawam Hospital, Al Ain, United Arab Emirates.
| | - Katja S Brocke Holmefjord
- Department. of Pediatric Habilitation/Department of Pediatric Neurology, Stavanger University Hospital, Stavanger, Norway.
| | - David Kronn
- Medical Genetic, Inherited Metabolic Diseases and Lysosomal Storage Disorders Center, Boston Children Hospital, MA, USA.
| | - Annette Feigenbaum
- Department of Pediatrics, University of California San Diego and Rady Children's Hospital, San Diego, CA, USA.
| | - Ralph Fingerhut
- Swiss Newborn Screening Laboratory, Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland.
| | - Sunnie Y Wong
- Hayard Genetics Center, Tulane University School of Medicine, New Orleans, LA, United States of America.
| | - Monique van Scherpenzeel
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; GlycoMScan B.V, Oss, the Netherlands.
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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38
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Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J. Molecular networks in Network Medicine: Development and applications. Wiley Interdiscip Rev Syst Biol Med 2020; 12:e1489. [PMID: 32307915 DOI: 10.1002/wsbm.1489] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/29/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
Network Medicine applies network science approaches to investigate disease pathogenesis. Many different analytical methods have been used to infer relevant molecular networks, including protein-protein interaction networks, correlation-based networks, gene regulatory networks, and Bayesian networks. Network Medicine applies these integrated approaches to Omics Big Data (including genetics, epigenetics, transcriptomics, metabolomics, and proteomics) using computational biology tools and, thereby, has the potential to provide improvements in the diagnosis, prognosis, and treatment of complex diseases. We discuss briefly the types of molecular data that are used in molecular network analyses, survey the analytical methods for inferring molecular networks, and review efforts to validate and visualize molecular networks. Successful applications of molecular network analysis have been reported in pulmonary arterial hypertension, coronary heart disease, diabetes mellitus, chronic lung diseases, and drug development. Important knowledge gaps in Network Medicine include incompleteness of the molecular interactome, challenges in identifying key genes within genetic association regions, and limited applications to human diseases. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Translational, Genomic, and Systems Medicine > Translational Medicine Analytical and Computational Methods > Analytical Methods Analytical and Computational Methods > Computational Methods.
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Affiliation(s)
- Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Harald H H W Schmidt
- Department of Pharmacology and Personalized Medicine, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, The Netherlands
| | - Eleni Anastasiadou
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Marco Angelini
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Lina Badimon
- Cardiovascular Program-ICCC, IR-Hospital de la Santa Creu i Sant Pau, CiberCV, IIB-Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Jean-Luc Balligand
- Pole of Pharmacology and Therapeutics (FATH), Institute for Clinical and Experimental Research (IREC), UCLouvain, Brussels, Belgium
| | - Giuditta Benincasa
- Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovambattista Capasso
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy.,BIOGEM, Ariano Irpino, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Antonella Di Costanzo
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Laurent Gatto
- de Duve Institute, Brussels, Belgium.,Institute for Experimental and Clinical Research (IREC), UCLouvain, Brussels, Belgium
| | - Michele Gentili
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Joseph Loscalzo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Claudio Napoli
- Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Manuela Petti
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - John Quackenbush
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Paolo Tieri
- CNR National Research Council of Italy, IAC Institute for Applied Computing, Rome, Italy
| | - Davide Viggiano
- BIOGEM, Ariano Irpino, Italy.,Department of Medicine and Health Sciences, University of Molise, Campobasso, Italy
| | - Gemma Vilahur
- Cardiovascular Program-ICCC, IR-Hospital de la Santa Creu i Sant Pau, CiberCV, IIB-Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Kimberly Glass
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jan Baumbach
- Department of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Maximus-von-Imhof-Forum 3, Freising, Germany.,Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
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Paci P, Fiscon G, Conte F, Licursi V, Morrow J, Hersh C, Cho M, Castaldi P, Glass K, Silverman EK, Farina L. Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. Sci Rep 2020; 10:3361. [PMID: 32099002 PMCID: PMC7042269 DOI: 10.1038/s41598-020-60228-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/23/2020] [Indexed: 12/17/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called "switch genes" - for the disease. Genes contributing to common biological processes or defining given cell types are usually co-regulated and co-expressed, forming expression network modules. Consistently, we found that the COPD correlation network built by SWIM consists of three well-characterized modules: one populated by switch genes, all up-regulated in COPD cases and related to the regulation of immune response, inflammatory response, and hypoxia (like TIMP1, HIF1A, SYK, LY96, BLNK and PRDX4); one populated by well-recognized immune signature genes, all up-regulated in COPD cases; one where the GWAS genes AGER and CAVIN1 are the most representative module genes, both down-regulated in COPD cases. Interestingly, 70% of AGER negative interactors are switch genes including PRDX4, whose activation strongly correlates with the activation of known COPD GWAS interactors SERPINE2, CD79A, and POUF2AF1. These results suggest that SWIM analysis can identify key network modules related to complex diseases like COPD.
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Affiliation(s)
- Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
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Licursi V, Conte F, Fiscon G, Paci P. MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis. BMC Bioinformatics 2019; 20:545. [PMID: 31684860 PMCID: PMC6829817 DOI: 10.1186/s12859-019-3105-x] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis. RESULTS We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis. The statistics is used to assess the significance of an over-representation of miRNA-target interactions and then MIENTURNET filters based on the statistical significance associated with each miRNA-target interaction. In addition, the holistic approach of the network theory is used to infer possible evidences of miRNA regulation by capturing emergent properties of the miRNA-target regulatory network that would be not evident through a pairwise analysis of the individual components. CONCLUSION MIENTURNET offers the possibility to consistently perform both statistical and network-based analyses by using only a single tool leading to a more effective prioritization of the miRNA-target interactions. This has the potential to avoid researchers without computational and informatics skills to navigate multiple websites and thus to independently investigate miRNA activity in every cellular process of interest in an easy and at the same time exhaustive way thanks to the intuitive web interface. The web application along with a well-documented and comprehensive user guide are freely available at http://userver.bio.uniroma1.it/apps/mienturnet/ without any login requirement.
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Affiliation(s)
- Valerio Licursi
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, Rome, 00185, Italy.,Department of Biology and Biotechnology "Charles Darwin", "Sapienza" University of Rome, Via dei Sardi 70, Rome, 00185, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, Rome, 00185, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, Rome, 00185, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, Rome, 00185, Italy.
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Bezhenar R, Maderich V, Schirone A, Conte F, Martazinova V. Transport and fate of 137Cs in the Mediterranean and Black Seas system during 1945-2020 period: A modelling study. J Environ Radioact 2019; 208-209:106023. [PMID: 31352265 DOI: 10.1016/j.jenvrad.2019.106023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/25/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
The compartment model POSEIDON-R with an embedded dynamic food web model was used to assess 137Cs distributions in the Mediterranean and Black Seas during 1945-2020 due to the weapon testing and accident at the Chernobyl nuclear power plant. Three maximums of contamination of surface waters can be identified from 1950 in the Mediterranean Sea system. Two of them (in 1959 and 1963) were caused by atmospheric deposition due to the nuclear weapon testing. Third maximum in 1986 was related with the Chernobyl accident. Maximum of inventory of 137Cs in the Mediterranean Sea (11461 TBq) was achieved in 1968, whereas secondary maximum caused by Chernobyl accident in 1986 was almost the same (11460 TBq). The corresponding maximum in the Black Sea (3703 TBq) was reached in 1986. It is approximately two times larger than nuclear weapon tests maximum. The results of simulations conducted with generic parameters agreed well with measurements of 137Cs concentrations in the water, bottom sediments, and in marine organisms. The inventory in the Mediterranean Sea is most sensitive to the global deposition, whereas water exchange with Atlantic Ocean and the Black Sea plays minor role. The cumulative individual dose for the period 1945-2020 from consumption of marine products contaminated by 137Cs was in the range 41-130 μSv in the Mediterranean Sea and 213-274 μSv in the Black Sea. The dose increased up to 40% due to Chernobyl accident in the Mediterranean countries and 66-103% in the Black Sea countries comparatively with dose from the global deposition. A useful application of the modelling for monitoring purposes was selection of representative regions in the Mediterranean Sea (5 regions) and in the Black Sea (4 regions) using "etalon" method for classification.
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Affiliation(s)
- R Bezhenar
- Institute of Mathematical Machine and System Problems, Kyiv, Ukraine
| | - V Maderich
- Institute of Mathematical Machine and System Problems, Kyiv, Ukraine.
| | - A Schirone
- ENEA Marine Research Centre "S. Teresa", La Spezia, Italy
| | - F Conte
- ENEA Marine Research Centre "S. Teresa", La Spezia, Italy
| | - V Martazinova
- Ukrainian Hydrometeorological Institute, Kyiv, Ukraine
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Conte F, Fiscon G, Licursi V, Bizzarri D, D'Antò T, Farina L, Paci P. A paradigm shift in medicine: A comprehensive review of network-based approaches. Biochim Biophys Acta Gene Regul Mech 2019; 1863:194416. [PMID: 31382052 DOI: 10.1016/j.bbagrm.2019.194416] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 02/01/2023]
Abstract
Network medicine is a rapidly evolving new field of medical research, which combines principles and approaches of systems biology and network science, holding the promise to uncovering the causes and to revolutionize the diagnosis and treatments of human diseases. This new paradigm reflects the fact that human diseases are not caused by single molecular defects, but driven by complex interactions among a variety of molecular mediators. The complexity of these interactions embraces different types of information: from the cellular-molecular level of protein-protein interactions to correlational studies of gene expression and regulation, to metabolic and disease pathways up to drug-disease relationships. The analysis of these complex networks can reveal new disease genes and/or disease pathways and identify possible targets for new drug development, as well as new uses for existing drugs. In this review, we offer a comprehensive overview of network types and algorithms used in the framework of network medicine. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Valerio Licursi
- Biology and Biotechnology Department "Charles Darwin" (BBCD), Sapienza University of Rome, Rome, Italy
| | - Daniele Bizzarri
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | - Tommaso D'Antò
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
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Conte F, Panebianco A. Potential Hazards Associated with Raw Donkey Milk Consumption: A Review. Int J Food Sci 2019; 2019:5782974. [PMID: 31275956 PMCID: PMC6582899 DOI: 10.1155/2019/5782974] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/20/2019] [Accepted: 04/02/2019] [Indexed: 12/02/2022]
Abstract
Donkey milk can be used as a substitute for infants and children who suffer from cow milk proteins intolerance and multiple food hypersensitivity. Up to date, this is one of the main reasons why donkey milk has become a substantial area for reasearch, with an increase over the the last fifteen years. In donkey milk chain, risk analysis should be the object of particular attention because children are the main consumers of this food. In fact, this process is one of the main tool to achieve a high level of protection of human health and life; thus, the most important safety hazards should be monitored in order to attain this goal. This review focuses on the main hazards possibly present in raw donkey milk, including bacteria, fungal toxins, parasites, and chemical pollutants. Literature data have been considered, including some information that is not provided in the international literature. In the authors' opinion, the current scientific knowledge should be improved, with the aim of allowing a suitable risk assessment along the whole donkey milk chain. However, in the meantime, the competent authorithies must carry out more stringent official controls, with particular attention given to the level of primary production. The issue of a traceability system in donkey milk chain should be considered of paramount importance.
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Affiliation(s)
- F. Conte
- Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy
| | - A. Panebianco
- Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy
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Falcone R, Conte F, Fiscon G, Pecce V, Sponziello M, Durante C, Farina L, Filetti S, Paci P, Verrienti A. BRAF V600E-mutant cancers display a variety of networks by SWIM analysis: prediction of vemurafenib clinical response. Endocrine 2019; 64:406-413. [PMID: 30850937 DOI: 10.1007/s12020-019-01890-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Several studies have shown that different tumour types sharing a driver gene mutation do not respond uniformly to the same targeted agent. Our aim was to use an unbiased network-based approach to investigate this fundamental issue using BRAFV600E mutant tumours and the BRAF inhibitor vemurafenib. METHODS We applied SWIM, a software able to identify putative regulatory (switch) genes involved in drastic changes to the cell phenotype, to gene expression profiles of different BRAFV600E mutant cancers and their normal counterparts in order to identify the switch genes that could potentially explain the heterogeneity of these tumours' responses to vemurafenib. RESULTS We identified lung adenocarcinoma as the tumour with the highest number of switch genes (298) compared to its normal counterpart. By looking for switch genes encoding for kinases with homology sequences similar to known vemurafenib targets, we found that thyroid cancer and lung adenocarcinoma have a similar number of putative targetable switch gene kinases (5 and 6, respectively) whereas colorectal cancer has just one. CONCLUSIONS We are persuaded that our network analysis may aid in the comprehension of molecular mechanisms underlying the different responses to vemurafenib in BRAFV600E mutant tumours.
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Affiliation(s)
- Rosa Falcone
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- ACT Operations Research, Research & Development, Roma, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- ACT Operations Research, Research & Development, Roma, Italy
| | - Valeria Pecce
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Marialuisa Sponziello
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Cosimo Durante
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Sebastiano Filetti
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Antonella Verrienti
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
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Abstract
In the last decade noncoding RNAs (ncRNAs) have been extensively studied in several biological processes and human diseases including cancer. microRNAs (miRNAs) are the best-known class of ncRNAs. miRNAs are small ncRNAs of around 20-22 nucleotides (nt) and are crucial posttranscriptional regulators of protein coding genes. Recently, new classes of ncRNAs, longer than miRNAs have been discovered. Those include intergenic noncoding RNAs (lincRNAs) and circular RNAs (circRNAs). These novel types of ncRNAs opened a very exciting field in biology, leading researchers to discover new relationships between miRNAs and long noncoding RNAs (lncRNAs), which act together to control protein coding gene expression. One of these new discoveries led to the formulation of the "competing endogenous RNA (ceRNA) hypothesis." This hypothesis suggests that an lncRNA acts as a sponge for miRNAs reducing their expression and causing the upregulation of miRNA targets. In this chapter we first discuss some recent discoveries in this field showing the mutual regulation of miRNAs, lncRNAs, and protein-coding genes in cancer. We then discuss the general approaches for the study of ceRNAs and present in more detail a recent computational approach to explore the ability of lncRNAs to act as ceRNAs in human breast cancer that has been shown to be, among the others, the most precise and promising.
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Affiliation(s)
- Francesco Russo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Milena Rizzo
- Institute of Clinical Physiology, National Research Council (CNR), Pisa, Italy.,Istituto Toscano Tumori (ITT), Firenze, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, Italy
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) involved in several biological processes and diseases. MiRNAs regulate gene expression at the posttranscriptional level, mostly downregulating their targets by binding specific regions of transcripts through imperfect sequence complementarity. Prediction of miRNA-binding sites is challenging, and target prediction algorithms are usually based on sequence complementarity. In the last years, it has been shown that by adding miRNA and protein coding gene expression, we are able to build tissue-, cell line-, or disease-specific networks improving our understanding of complex biological scenarios. In this chapter, we present an application of a recently published software named SWIM, that allows to identify key genes in a network of interactions by defining appropriate "roles" of genes according to their local/global positioning in the overall network. Furthermore, we show how the SWIM software can be used to build miRNA-disease networks, by applying the approach to tumor data obtained from The Cancer Genome Atlas (TCGA).
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy
- SysBio Centre for Systems Biology, Milan, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy
- SysBio Centre for Systems Biology, Milan, Italy
| | - Lorenzo Farina
- Department of Computer, Control, and Management Engineering Antonio Ruberti, Sapienza University of Rome, Rome, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics, National Research Council, Pisa, Italy
| | - Francesco Russo
- Faculty of Health and Medical Sciences¸ Novo Nordisk Foundation Center for Protein Research, Translational Disease Systems Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Paola Paci
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy.
- SysBio Centre for Systems Biology, Milan, Italy.
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Fiscon G, Conte F, Paci P. SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines. BMC Bioinformatics 2018; 19:436. [PMID: 30497369 PMCID: PMC6266956 DOI: 10.1186/s12859-018-2421-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND It is well-known that glioblastoma contains self-renewing, stem-like subpopulation with the ability to sustain tumor growth. These cells - called cancer stem-like cells - share certain phenotypic characteristics with untransformed stem cells and are resistant to many conventional cancer therapies, which might explain the limitations in curing human malignancies. Thus, the identification of genes controlling the differentiation of these stem-like cells is becoming a successful therapeutic strategy, owing to the promise of novel targets for treating malignancies. METHODS Recently, we developed SWIM, a software able to unveil a small pool of genes - called switch genes - critically associated with drastic changes in cell phenotype. Here, we applied SWIM to the expression profiling of glioblastoma stem-like cells and conventional glioma cell lines, in order to identify switch genes related to stem-like phenotype. RESULTS SWIM identifies 171 switch genes that are all down-regulated in glioblastoma stem-like cells. This list encompasses genes like CAV1, COL5A1, COL6A3, FLNB, HMMR, ITGA3, ITGA5, MET, SDC1, THBS1, and VEGFC, involved in "ECM-receptor interaction" and "focal adhesion" pathways. The inhibition of switch genes highly correlates with the activation of genes related to neural development and differentiation, such as the 4-core OLIG2, POU3F2, SALL2, SOX2, whose induction has been shown to be sufficient to reprogram differentiated glioblastoma into stem-like cells. Among switch genes, the transcription factor FOSL1 appears as the brightest star since: it is down-regulated in stem-like cells; it highly negatively correlates with the 4-core genes that are all up-regulated in stem-like cells; the promoter regions of the 4-core genes harbor a consensus binding motif for FOSL1. CONCLUSIONS We suggest that the inhibition of switch genes in stem-like cells could induce the deregulation of cell communication pathways, contributing to neoplastic progression and tumor invasiveness. Conversely, their activation could restore the physiological equilibrium between cell adhesion and migration, hampering the progression of cancer. Moreover, we posit FOSL1 as promising candidate to orchestrate the differentiation of cancer stem-like cells by repressing the 4-core genes' expression, which severely halts cancer growth and might affect the therapeutic outcome. We suggest FOSL1 as novel putative therapeutic and prognostic biomarker, worthy of further investigation.
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy
- SysBio Centre for Systems Biology, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy
- SysBio Centre for Systems Biology, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy
- SysBio Centre for Systems Biology, Rome, Italy
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48
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Falcone R, Paci P, Verrienti A, Fiscon G, Sponziello M, Conte F, Pecce V, Rosignolo F, Grani G, Lamartina L, Ramundo V, Durante C, Farina L, Filetti S. Prediction of response to vemurafenib in BRAF V600E mutant cancers based on a network approach. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy303.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fiscon G, Conte F, Farina L, Paci P. Network-Based Approaches to Explore Complex Biological Systems towards Network Medicine. Genes (Basel) 2018; 9:genes9090437. [PMID: 30200360 PMCID: PMC6162385 DOI: 10.3390/genes9090437] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/25/2018] [Accepted: 08/30/2018] [Indexed: 12/14/2022] Open
Abstract
Network medicine relies on different types of networks: from the molecular level of protein–protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topological properties of protein–protein interaction (PPI) networks, we discuss the widespread DIAMOnD (disease module detection) algorithm. Starting from the assumption that PPI networks can be viewed as maps where diseases can be identified with localized perturbation within a specific neighborhood (i.e., disease modules), DIAMOnD performs a systematic analysis of the human PPI network to uncover new disease-associated genes by exploiting the connectivity significance instead of connection density. The past few years have witnessed the increasing interest in understanding the molecular mechanism of post-transcriptional regulation with a special emphasis on non-coding RNAs since they are emerging as key regulators of many cellular processes in both physiological and pathological states. Recent findings show that coding genes are not the only targets that microRNAs interact with. In fact, there is a pool of different RNAs—including long non-coding RNAs (lncRNAs) —competing with each other to attract microRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs). The framework of regulatory networks provides a powerful tool to gather new insights into ceRNA regulatory mechanisms. Here, we describe a data-driven model recently developed to explore the lncRNA-associated ceRNA activity in breast invasive carcinoma. On the other hand, a very promising example of the co-expression network is the one implemented by the software SWIM (switch miner), which combines topological properties of correlation networks with gene expression data in order to identify a small pool of genes—called switch genes—critically associated with drastic changes in cell phenotype. Here, we describe SWIM tool along with its applications to cancer research and compare its predictions with DIAMOnD disease genes.
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, via dei Taurini 19, 00185 Rome, Italy.
- SysBio Centre of Systems Biology, Piazza della Scienza, 3, 20126 Milan, Italy.
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, via dei Taurini 19, 00185 Rome, Italy.
- SysBio Centre of Systems Biology, Piazza della Scienza, 3, 20126 Milan, Italy.
| | - Lorenzo Farina
- Department of Computer, Control, and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Viale Ariosto 25, 00185 Rome, Italy.
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, via dei Taurini 19, 00185 Rome, Italy.
- SysBio Centre of Systems Biology, Piazza della Scienza, 3, 20126 Milan, Italy.
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50
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Bescos R, Boden MJ, Jackson ML, Trewin AJ, Marin EC, Levinger I, Garnham A, Hiam DS, Falcao-Tebas F, Conte F, Owens J, Kennaway DJ, McConell GK. Four days of simulated shift work reduces insulin sensitivity in humans. Acta Physiol (Oxf) 2018; 223:e13039. [PMID: 29356345 DOI: 10.1111/apha.13039] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 01/30/2023]
Abstract
AIM The aim of this study was to investigate the effects of 4 consecutive simulated night shifts on glucose homeostasis, mitochondrial function and central and peripheral rhythmicities compared with a simulated day shift schedule. METHODS Seventeen healthy adults (8M:9F) matched for sleep, physical activity and dietary/fat intake participated in this study (night shift work n = 9; day shift work n = 8). Glucose tolerance and insulin sensitivity before and after 4 nights of shift work were measured by an intravenous glucose tolerance test and a hyperinsulinaemic euglycaemic clamp respectively. Muscles biopsies were obtained to determine insulin signalling and mitochondrial function. Central and peripheral rhythmicities were assessed by measuring salivary melatonin and expression of circadian genes from hair samples respectively. RESULTS Fasting plasma glucose increased (4.4 ± 0.1 vs. 4.6 ± 0.1 mmol L-1 ; P = .001) and insulin sensitivity decreased (25 ± 7%, P < .05) following the night shift, with no changes following the day shift. Night shift work had no effect on skeletal muscle protein expression (PGC1α, UCP3, TFAM and mitochondria Complex II-V) or insulin-stimulated pAkt Ser473, pTBC1D4Ser318 and pTBC1D4Thr642. Importantly, the metabolic changes after simulated night shifts occurred despite no changes in the timing of melatonin rhythmicity or hair follicle cell clock gene expression across the wake period (Per3, Per1, Nr1d1 and Nr1d2). CONCLUSION Only 4 days of simulated night shift work in healthy adults is sufficient to reduce insulin sensitivity which would be expected to increase the risk of T2D.
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Affiliation(s)
- R. Bescos
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
- Institute of Health & Community; Faculty of Health & Human Sciences; University of Plymouth; Plymouth UK
| | - M. J. Boden
- Robinson Research Institute and Adelaide School of Medicine; University of Adelaide; Adelaide SA Australia
- Syneos Health; Hindmarsh SA Australia
| | - M. L. Jackson
- College of Arts; Victoria University; Melbourne Vic. Australia
- School of Health and Biomedical Sciences; RMIT University; Bundoora Vic. Australia
| | - A. J. Trewin
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
- Department of Anesthesiology; University of Rochester Medical Center; Rochester NY USA
| | - E. C. Marin
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
- Department of Medicine (Austin Health); Austin Hospital; The University of Melbourne; Melbourne Victoria Australia
| | - I. Levinger
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
- Australian Institute for Musculoskeletal Science (AIMSS); Western Health; Melbourne Australia
| | - A. Garnham
- School of Exercise and Nutrition Sciences; Deakin University; Melbourne Vic. Australia
| | - D. S. Hiam
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
| | - F. Falcao-Tebas
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
| | - F. Conte
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
| | - J. A. Owens
- Robinson Research Institute and Adelaide School of Medicine; University of Adelaide; Adelaide SA Australia
| | - D. J. Kennaway
- Robinson Research Institute and Adelaide School of Medicine; University of Adelaide; Adelaide SA Australia
| | - G. K. McConell
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
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